Ricognizione Bioinformatica Italiana

Forni:2013aa: A 175 million year history of T cell regulatory molecules reveals widespread selection, with adaptive evolution of disease alleles
D. Forni and R. Cagliani and U. Pozzoli and M. Colleoni and S. Riva and M. Biasin and G. Filippi and L. De Gioia and F. Gnudi and G. P. Comi and N. Bresolin and M. Clerici and M. Sironi
Immunity 38 1129-41 (2013)
http://dx.doi.org/10.1016/j.immuni.2013.04.008

T cell activation plays a central role in immune response and in the maintenance of self-tolerance. We analyzed the evolutionary history of T cell regulatory molecules. Nine genes involved in triggering T cell activation or in regulating the ensuing response evolved adaptively in mammals. Several positively selected sites overlap with positions interacting with the binding partner or with cellular components. Population genetic analysis in humans revealed a complex scenario of local (FASLG, CD40LG, HAVCR2) and worldwide (FAS, ICOSLG) adaptation and H. sapiens-to-Neandertal gene flow (gene transfer between populations). Disease variants in these genes are preferential targets of pathogen-driven selection, and a Crohn's disease risk polymorphism targeted by bacterial-driven selection modulates the expression of ICOSLG in response to a bacterial superantigen. Therefore, we used evolutionary information to generate experimentally testable hypotheses concerning the function of specific genetic variants and indicate that adaptation to infection underlies the maintenance of autoimmune risk alleles.
International-Wheat-Genome-Sequencing-Consortium-IWGSC:2014aa: A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
International Wheat Genome Sequencing Consortium (IWGSC)
Science 345 1251788 (2014)
http://dx.doi.org/10.1126/science.1251788

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
Costello:2014aa: A community effort to assess and improve drug sensitivity prediction algorithms
J. C. Costello and L. M. Heiser and E. Georgii and M. Gönen and M. P. Menden and N. J. Wang and M. Bansal and M. Ammad-Ud-Din and P. Hintsanen and S. A. Khan and J.-P. Mpindi and O. Kallioniemi and A. Honkela and T. Aittokallio and K. Wennerberg and NCI DREAM Community and J. J. Collins and D. Gallahan and D. Singer and J. Saez-Rodriguez and S. Kaski and J. W. Gray and G. Stolovitzky and NCI DREAM Community
Nat Biotechnol 32 1202-12 (2014)
http://dx.doi.org/10.1038/nbt.2877

Predicting the best treatment strategy from genomic information is a core goal of precision medicine. Here we focus on predicting drug response based on a cohort of genomic, epigenomic and proteomic profiling data sets measured in human breast cancer cell lines. Through a collaborative effort between the National Cancer Institute (NCI) and the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project, we analyzed a total of 44 drug sensitivity prediction algorithms. The top-performing approaches modeled nonlinear relationships and incorporated biological pathway information. We found that gene expression microarrays consistently provided the best predictive power of the individual profiling data sets; however, performance was increased by including multiple, independent data sets. We discuss the innovations underlying the top-performing methodology, Bayesian multitask MKL, and we provide detailed descriptions of all methods. This study establishes benchmarks for drug sensitivity prediction and identifies approaches that can be leveraged for the development of new methods.
Bicciato:2009aa: A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets
S. Bicciato and R. Spinelli and M. Zampieri and E. Mangano and F. Ferrari and L. Beltrame and I. Cifola and C. Peano and A. Solari and C. Battaglia
Nucleic Acids Res 37 5057-70 (2009)
http://dx.doi.org/10.1093/nar/gkp520

The integration of high-throughput genomic data represents an opportunity for deciphering the interplay between structural and functional organization of genomes and for discovering novel biomarkers. However, the development of integrative approaches to complement gene expression (GE) data with other types of gene information, such as copy number (CN) and chromosomal localization, still represents a computational challenge in the genomic arena. This work presents a computational procedure that directly integrates CN and GE profiles at genome-wide level. When applied to DNA/RNA paired data, this approach leads to the identification of Significant Overlaps of Differentially Expressed and Genomic Imbalanced Regions (SODEGIR). This goal is accomplished in three steps. The first step extends to CN a method for detecting regional imbalances in GE. The second part provides the integration of CN and GE data and identifies chromosomal regions with concordantly altered genomic and transcriptional status in a tumor sample. The last step elevates the single-sample analysis to an entire dataset of tumor specimens. When applied to study chromosomal aberrations in a collection of astrocytoma and renal carcinoma samples, the procedure proved to be effective in identifying discrete chromosomal regions of coordinated CN alterations and changes in transcriptional levels.
Chailyan:2012aa: A database of immunoglobulins with integrated tools: DIGIT
A. Chailyan and A. Tramontano and P. Marcatili
Nucleic Acids Res 40 D1230-4 (2012)
http://dx.doi.org/10.1093/nar/gkr806

The DIGIT (Database of ImmunoGlobulins with Integrated Tools) database (http://biocomputing.it/digit) is an integrated resource storing sequences of annotated immunoglobulin variable domains and enriched with tools for searching and analyzing them. The annotations in the database include information on the type of antigen, the respective germline sequences and on pairing information between light and heavy chains. Other annotations, such as the identification of the complementarity determining regions, assignment of their structural class and identification of mutations with respect to the germline, are computed on the fly and can also be obtained for user-submitted sequences. The system allows customized BLAST searches and automatic building of 3D models of the domains to be performed.
Agrawal:2013aa: A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues
G. K. Agrawal and A. Sarkar and P. G. Righetti and R. Pedreschi and S. Carpentier and T. Wang and B. J. Barkla and A. Kohli and B. K. Ndimba and N. V. Bykova and C. Rampitsch and L. Zolla and M. S. Rafudeen and R. Cramer and L. V. Bindschedler and N. Tsakirpaloglou and R. J. Ndimba and J. M. Farrant and J. Renaut and D. Job and S. Kikuchi and R. Rakwal
Mass Spectrom Rev 32 335-65 (2013)
http://dx.doi.org/10.1002/mas.21365

Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
Emiliani:2009aa: A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land
G. Emiliani and M. Fondi and R. Fani and S. Gribaldo
Biol Direct 4 7 (2009)
http://dx.doi.org/10.1186/1745-6150-4-7

BACKGROUND: The pioneering ancestor of land plants that conquered terrestrial habitats around 500 million years ago had to face dramatic stresses including UV radiation, desiccation, and microbial attack. This drove a number of adaptations, among which the emergence of the phenylpropanoid pathway was crucial, leading to essential compounds such as flavonoids and lignin. However, the origin of this specific land plant secondary metabolism has not been clarified. RESULTS: We have performed an extensive analysis of the taxonomic distribution and phylogeny of Phenylalanine Ammonia Lyase (PAL), which catalyses the first and essential step of the general phenylpropanoid pathway, leading from phenylalanine to p-Coumaric acid and p-Coumaroyl-CoA, the entry points of the flavonoids and lignin routes. We obtained robust evidence that the ancestor of land plants acquired a PAL via horizontal gene transfer (HGT) during symbioses with soil bacteria and fungi that are known to have established very early during the first steps of land colonization. This horizontally acquired PAL represented then the basis for further development of the phenylpropanoid pathway and plant radiation on terrestrial environments. CONCLUSION: Our results highlight a possible crucial role of HGT from soil bacteria in the path leading to land colonization by plants and their subsequent evolution. The few functional characterizations of sediment/soil bacterial PAL (production of secondary metabolites with powerful antimicrobial activity or production of pigments) suggest that the initial advantage of this horizontally acquired PAL in the ancestor of land plants might have been either defense against an already developed microbial community and/or protection against UV.
Radivojac:2013aa: A large-scale evaluation of computational protein function prediction
P. Radivojac and W. T. Clark and T. R. Oron and A. M. Schnoes and T. Wittkop and A. Sokolov and K. Graim and C. Funk and K. Verspoor and A. Ben-Hur and G. Pandey and J. M. Yunes and A. S. Talwalkar and S. Repo and M. L. Souza and D. Piovesan and R. Casadio and Z. Wang and J. Cheng and H. Fang and J. Gough and P. Koskinen and P. Törönen and J. Nokso-Koivisto and L. Holm and D. Cozzetto and D. W. A. Buchan and K. Bryson and D. T. Jones and B. Limaye and H. Inamdar and A. Datta and S. K. Manjari and R. Joshi and M. Chitale and D. Kihara and A. M. Lisewski and S. Erdin and E. Venner and O. Lichtarge and R. Rentzsch and H. Yang and A. E. Romero and P. Bhat and A. Paccanaro and T. Hamp and R. Kaßner and S. Seemayer and E. Vicedo and C. Schaefer and D. Achten and F. Auer and A. Boehm and T. Braun and M. Hecht and M. Heron and P. Hönigschmid and T. A. Hopf and S. Kaufmann and M. Kiening and D. Krompass and C. Landerer and Y. Mahlich and M. Roos and J. Björne and T. Salakoski and A. Wong and H. Shatkay and F. Gatzmann and I. Sommer and M. N. Wass and M. J. E. Sternberg and N. Škunca and F. Supek and M. Bošnjak and P. Panov and S. Džeroski and T. Šmuc and Y. A. I. Kourmpetis and A. D. J. van Dijk and C. J. F. ter Braak and Y. Zhou and Q. Gong and X. Dong and W. Tian and M. Falda and P. Fontana and E. Lavezzo and B. Di Camillo and S. Toppo and L. Lan and N. Djuric and Y. Guo and S. Vucetic and A. Bairoch and M. Linial and P. C. Babbitt and S. E. Brenner and C. Orengo and B. Rost and S. D. Mooney and I. Friedberg
Nat Methods 10 221-7 (2013)
http://dx.doi.org/10.1038/nmeth.2340

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools.
Cesana:2011aa: A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA
M. Cesana and D. Cacchiarelli and I. Legnini and T. Santini and O. Sthandier and M. Chinappi and A. Tramontano and I. Bozzoni
Cell 147 358-69 (2011)
http://dx.doi.org/10.1016/j.cell.2011.09.028

Recently, a new regulatory circuitry has been identified in which RNAs can crosstalk with each other by competing for shared microRNAs. Such competing endogenous RNAs (ceRNAs) regulate the distribution of miRNA molecules on their targets and thereby impose an additional level of post-transcriptional regulation. Here we identify a muscle-specific long noncoding RNA, linc-MD1, which governs the time of muscle differentiation by acting as a ceRNA in mouse and human myoblasts. Downregulation or overexpression of linc-MD1 correlate with retardation or anticipation of the muscle differentiation program, respectively. We show that linc-MD1 "sponges" miR-133 and miR-133 [corrected] to regulate the expression of MAML1 and MEF2C, transcription factors that activate muscle-specific gene expression. Finally, we demonstrate that linc-MD1 exerts the same control over differentiation timing in human myoblasts, and that its levels are strongly reduced in Duchenne muscle cells. We conclude that the ceRNA network plays an important role in muscle differentiation.
Vecchione:2013aa: A microRNA signature defines chemoresistance in ovarian cancer through modulation of angiogenesis
A. Vecchione and B. Belletti and F. Lovat and S. Volinia and G. Chiappetta and S. Giglio and M. Sonego and R. Cirombella and E. C. Onesti and P. Pellegrini and D. Califano and S. Pignata and S. Losito and V. Canzonieri and R. Sorio and H. Alder and D. Wernicke and A. Stoppacciaro and G. Baldassarre and C. M. Croce
Proc Natl Acad Sci U S A 110 9845-50 (2013)
http://dx.doi.org/10.1073/pnas.1305472110

Epithelial ovarian cancer is the most lethal gynecologic malignancy; it is highly aggressive and causes almost 125,000 deaths yearly. Despite advances in detection and cytotoxic therapies, a low percentage of patients with advanced stage disease survive 5 y after the initial diagnosis. The high mortality of this disease is mainly caused by resistance to the available therapies. Here, we profiled microRNA (miR) expression in serous epithelial ovarian carcinomas to assess the possibility of a miR signature associated with chemoresistance. We analyzed tumor samples from 198 patients (86 patients as a training set and 112 patients as a validation set) for human miRs. A signature of 23 miRs associated with chemoresistance was generated by array analysis in the training set. Quantitative RT-PCR in the validation set confirmed that three miRs (miR-484, -642, and -217) were able to predict chemoresistance of these tumors. Additional analysis of miR-484 revealed that the sensitive phenotype is caused by a modulation of tumor vasculature through the regulation of the VEGFB and VEGFR2 pathways. We present compelling evidence that three miRs can classify the response to chemotherapy of ovarian cancer patients in a large multicenter cohort and that one of these three miRs is involved in the control of tumor angiogenesis, indicating an option in the treatment of these patients. Our results suggest, in fact, that blockage of VEGF through the use of an anti-VEGFA antibody may not be sufficient to improve survival in ovarian cancer patients unless VEGFB signaling is also blocked.
Martello:2010aa: A MicroRNA targeting dicer for metastasis control
G. Martello and A. Rosato and F. Ferrari and A. Manfrin and M. Cordenonsi and S. Dupont and E. Enzo and V. Guzzardo and M. Rondina and T. Spruce and A. R. Parenti and M. G. Daidone and S. Bicciato and S. Piccolo
Cell 141 1195-207 (2010)
http://dx.doi.org/10.1016/j.cell.2010.05.017

Although specific microRNAs (miRNAs) can be upregulated in cancer, global miRNA downregulation is a common trait of human malignancies. The mechanisms of this phenomenon and the advantages it affords remain poorly understood. Here we identify a microRNA family, miR-103/107, that attenuates miRNA biosynthesis by targeting Dicer, a key component of the miRNA processing machinery. In human breast cancer, high levels of miR-103/107 are associated with metastasis and poor outcome. Functionally, miR-103/107 confer migratory capacities in vitro and empower metastatic dissemination of otherwise nonaggressive cells in vivo. Inhibition of miR-103/107 opposes migration and metastasis of malignant cells. At the cellular level, a key event fostered by miR-103/107 is induction of epithelial-to-mesenchymal transition (EMT), attained by downregulating miR-200 levels. These findings suggest a new pathway by which Dicer inhibition drifts epithelial cancer toward a less-differentiated, mesenchymal fate to foster metastasis.
Mattei:2014aa: A novel approach to represent and compare RNA secondary structures
E. Mattei and G. Ausiello and F. Ferrè and M. Helmer-Citterich
Nucleic Acids Res 42 6146-57 (2014)
http://dx.doi.org/10.1093/nar/gku283

Structural information is crucial in ribonucleic acid (RNA) analysis and functional annotation; nevertheless, how to include such structural data is still a debated problem. Dot-bracket notation is the most common and simple representation for RNA secondary structures but its simplicity leads also to ambiguity requiring further processing steps to dissolve. Here we present BEAR (Brand nEw Alphabet for RNA), a new context-aware structural encoding represented by a string of characters. Each character in BEAR encodes for a specific secondary structure element (loop, stem, bulge and internal loop) with specific length. Furthermore, exploiting this informative and yet simple encoding in multiple alignments of related RNAs, we captured how much structural variation is tolerated in RNA families and convert it into transition rates among secondary structure elements. This allowed us to compute a substitution matrix for secondary structure elements called MBR (Matrix of BEAR-encoded RNA secondary structures), of which we tested the ability in aligning RNA secondary structures. We propose BEAR and the MBR as powerful resources for the RNA secondary structure analysis, comparison and classification, motif finding and phylogeny.
Palmeri:2014aa: A proteome-wide Domain-centric Perspective on Protein Phosphorylation
A. Palmeri and G. Ausiello and F. Ferre and M. Helmer-Citterich and P. F. Gherardini
Mol Cell Proteomics (2014)
http://dx.doi.org/10.1074/mcp.M114.039990

Phosphorylation is a widespread post-translational modification that modulates the function of a large number of proteins. Here we show that a significant proportion of all the domains in the human proteome are significantly enriched or depleted in phosphorylation events. A substantial improvement in phosphosites prediction is achieved by leveraging this observation, which has not been tapped by existing methods. Phosphorylation sites are often not shared between multiple occurrences of the same domain in the proteome, even when the phosphoacceptor residue is conserved. This is partly due to different functional constraints acting on the same domain in different protein contexts. Moreover, by augmenting domain alignments with structural information, we were able to provide direct evidence that phosphosites in protein-protein interfaces need not be positionally conserved, likely because they can modulate interactions simply by sitting in the same general surface area.
Caputo:2012aa: A restricted spectrum of mutations in the SMAD4 tumor-suppressor gene underlies Myhre syndrome
V. Caputo and L. Cianetti and M. Niceta and C. Carta and A. Ciolfi and G. Bocchinfuso and E. Carrani and M. L. Dentici and E. Biamino and E. Belligni and L. Garavelli and L. Boccone and D. Melis and G. Andria and B. D. Gelb and L. Stella and M. Silengo and B. Dallapiccola and M. Tartaglia
Am J Hum Genet 90 161-9 (2012)
http://dx.doi.org/10.1016/j.ajhg.2011.12.011

Myhre syndrome is a developmental disorder characterized by reduced growth, generalized muscular hypertrophy, facial dysmorphism, deafness, cognitive deficits, joint stiffness, and skeletal anomalies. Here, by performing exome sequencing of a single affected individual and coupling the results to a hypothesis-driven filtering strategy, we establish that heterozygous mutations in SMAD4, which encodes for a transducer mediating transforming growth factor β and bone morphogenetic protein signaling branches, underlie this rare Mendelian trait. Two recurrent de novo SMAD4 mutations were identified in eight unrelated subjects. Both mutations were missense changes altering Ile500 within the evolutionary conserved MAD homology 2 domain, a well known mutational hot spot in malignancies. Structural analyses suggest that the substituted residues are likely to perturb the binding properties of the mutant protein to signaling partners. Although SMAD4 has been established as a tumor suppressor gene somatically mutated in pancreatic, gastrointestinal, and skin cancers, and germline loss-of-function lesions and deletions of this gene have been documented to cause disorders that predispose individuals to gastrointestinal cancer and vascular dysplasias, the present report identifies a previously unrecognized class of mutations in the gene with profound impact on development and growth.
Mueller:2009aa: A Snapshot of the Emerging Tomato Genome Sequence
L. A. Mueller and R. K. Lankhorst and S. D. Tanksley and J. J. Giovannoni and R. White and J. Vrebalov and Z. Fei and J. van Eck and R. Buels and A. A. Mills and N. Menda and I. Y. Tecle and A. Bombarely and S. Stack and S. M. Royer and S.-B. Chang and L. A. Shearer and B. D. Kim and S.-H. Jo and C.-G. Hur and D. Choi and C.-B. Li and J. Zhao and H. Jiang and Y. Geng and Y. Dai and H. Fan and J. Chen and F. Lu and J. Shi and S. Sun and J. Chen and X. Yang and C. Lu and M. Chen and Z. Cheng and C. Li and H. Ling and Y. Xue and Y. Wang and G. B. Seymour and G. J. Bishop and G. Bryan and J. Rogers and S. Sims and S. Butcher and D. Buchan and J. Abbott and H. Beasley and C. Nicholson and C. Riddle and S. Humphray and K. McLaren and S. Mathur and S. Vyas and A. U. Solanke and R. Kumar and V. Gupta and A. K. Sharma and P. Khurana and J. P. Khurana and A. Tyagi and Sarita and P. Chowdhury and S. Shridhar and D. Chattopadhyay and A. Pandit and P. Singh and A. Kumar and R. Dixit and A. Singh and S. Praveen and V. Dalal and M. Yadav and I. A. Ghazi and K. Gaikwad and T. R. Sharma and T. Mohapatra and N. K. Singh and D. Szinay and H. de Jong and S. Peters and M. van Staveren and E. Datema and M. W. E. J. Fiers and R. C. H. J. van Ham and P. Lindhout and M. Philippot and P. Frasse and F. Regad and M. Zouine and M. Bouzayen and E. Asamizu and S. Sato and H. Fukuoka and S. Tabata and D. Shibata and M. A. Botella and M. Perez-Alonso and V. Fernandez-Pedrosa and S. Osorio and A. Mico and A. Granell and Z. Zhang and J. He and S. Huang and Y. Du and D. Qu and L. Liu and D. Liu and J. Wang and Z. Ye and W. Yang and G. Wang and A. Vezzi and S. Todesco and G. Valle and G. Falcone and M. Pietrella and G. Giuliano and S. Grandillo and A. Traini and N. D'Agostino and M. L. Chiusano and M. Ercolano and A. Barone and L. Frusciante and H. Schoof and A. Joecker and R. Bruggmann and M. Spannagl and K. X. F. Mayer and R. Guigo and F. Camara and S. Rombauts and J. A. Fawcett and Y. Van de Peer and S. Knapp and D. Zamir and W. Stiekema
Plant Genome 2 78--92 (2009)
http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/WOS:000208575800010

The genome of tomato (Solanum lycopersicum L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger "International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation" initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is similar to 40,000, based on an estimate from a preliminary annotation of 11\% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato (Solanum tuberosum L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.
Metzeler:2013aa: A stem cell-like gene expression signature associates with inferior outcomes and a distinct microRNA expression profile in adults with primary cytogenetically normal acute myeloid leukemia
K. H. Metzeler and K. Maharry and J. Kohlschmidt and S. Volinia and K. Mrózek and H. Becker and D. Nicolet and S. P. Whitman and J. H. Mendler and S. Schwind and A.-K. Eisfeld and Y.-Z. Wu and B. L. Powell and T. H. Carter and M. Wetzler and J. E. Kolitz and M. R. Baer and A. J. Carroll and R. M. Stone and M. A. Caligiuri and G. Marcucci and C. D. Bloomfield
Leukemia 27 2023-31 (2013)
http://dx.doi.org/10.1038/leu.2013.181

Acute myeloid leukemia (AML) is hypothesized to be sustained by self-renewing leukemia stem cells (LSCs). Recently, gene expression signatures (GES) from functionally defined AML LSC populations were reported, and expression of a 'core enriched' (CE) GES, representing 44 genes activated in LCSs, conferred shorter survival in cytogenetically normal (CN) AML. The prognostic impact of the CE GES in the context of other molecular markers, including gene mutations and microRNA (miR) expression alterations, is unknown and its clinical utility is unclear. We studied associations of the CE GES with known molecular prognosticators, miR expression profiles, and outcomes in 364 well-characterized CN-AML patients. A high CE score (CE(high)) associated with FLT3-internal tandem duplication, WT1 and RUNX1 mutations, wild-type CEBPA and TET2, and high ERG, BAALC and miR-155 expression. CE(high) patients had a lower complete remission (CR) rate (P=0.003) and shorter disease-free (DFS, P<0.001) and overall survival (OS, P<0.001) than CE(low) patients. These associations persisted in multivariable analyses adjusting for other prognosticators (CR, P=0.02; DFS, P<0.001; and OS, P<0.001). CE(high) status was accompanied by a characteristic miR expression signature. Fifteen miRs were upregulated in both younger and older CE(high) patients, including miRs relevant for stem cell function. Our results support the clinical relevance of LSCs and improve risk stratification in AML.
Guffanti:2009aa: A transcriptional sketch of a primary human breast cancer by 454 deep sequencing
A. Guffanti and M. Iacono and P. Pelucchi and N. Kim and G. Soldà and L. J. Croft and R. J. Taft and E. Rizzi and M. Askarian-Amiri and R. J. Bonnal and M. Callari and F. Mignone and G. Pesole and G. Bertalot and L. R. Bernardi and A. Albertini and C. Lee and J. S. Mattick and I. Zucchi and G. De Bellis
BMC Genomics 10 163 (2009)
http://dx.doi.org/10.1186/1471-2164-10-163

BACKGROUND: The cancer transcriptome is difficult to explore due to the heterogeneity of quantitative and qualitative changes in gene expression linked to the disease status. An increasing number of "unconventional" transcripts, such as novel isoforms, non-coding RNAs, somatic gene fusions and deletions have been associated with the tumoral state. Massively parallel sequencing techniques provide a framework for exploring the transcriptional complexity inherent to cancer with a limited laboratory and financial effort. We developed a deep sequencing and bioinformatics analysis protocol to investigate the molecular composition of a breast cancer poly(A)+ transcriptome. This method utilizes a cDNA library normalization step to diminish the representation of highly expressed transcripts and biology-oriented bioinformatic analyses to facilitate detection of rare and novel transcripts. RESULTS: We analyzed over 132,000 Roche 454 high-confidence deep sequencing reads from a primary human lobular breast cancer tissue specimen, and detected a range of unusual transcriptional events that were subsequently validated by RT-PCR in additional eight primary human breast cancer samples. We identified and validated one deletion, two novel ncRNAs (one intergenic and one intragenic), ten previously unknown or rare transcript isoforms and a novel gene fusion specific to a single primary tissue sample. We also explored the non-protein-coding portion of the breast cancer transcriptome, identifying thousands of novel non-coding transcripts and more than three hundred reads corresponding to the non-coding RNA MALAT1, which is highly expressed in many human carcinomas. CONCLUSION: Our results demonstrate that combining 454 deep sequencing with a normalization step and careful bioinformatic analysis facilitates the discovery and quantification of rare transcripts or ncRNAs, and can be used as a qualitative tool to characterize transcriptome complexity, revealing many hitherto unknown transcripts, splice isoforms, gene fusion events and ncRNAs, even at a relatively low sequence sampling.
Cagliani:2012aa: A trans-specific polymorphism in ZC3HAV1 is maintained by long-standing balancing selection and may confer susceptibility to multiple sclerosis
R. Cagliani and F. R. Guerini and M. Fumagalli and S. Riva and C. Agliardi and D. Galimberti and U. Pozzoli and A. Goris and B. Dubois and C. Fenoglio and D. Forni and S. Sanna and I. Zara and M. Pitzalis and M. Zoledziewska and F. Cucca and F. Marini and G. P. Comi and E. Scarpini and N. Bresolin and M. Clerici and M. Sironi
Mol Biol Evol 29 1599-613 (2012)
http://dx.doi.org/10.1093/molbev/mss002

The human ZC3HAV1 gene encodes an antiviral protein. The longest splicing isoform of ZC3HAV1 contains a C-terminal PARP-like domain, which has evolved under positive selection in primates. We analyzed the evolutionary history of this same domain in humans and in Pan troglodytes. We identified two variants that segregate in both humans and chimpanzees; one of them (rs3735007) does not occur at a hypermutable site and accounts for a nonsynonymous substitution (Thr851Ile). The probability that the two trans-specific polymorphisms have occurred independently in the two lineages was estimated to be low (P = 0.0054), suggesting that at least one of them has arisen before speciation and has been maintained by selection. Population genetic analyses in humans indicated that the region surrounding the shared variants displays strong evidences of long-standing balancing selection. Selection signatures were also observed in a chimpanzee population sample. Inspection of 1000 Genomes data confirmed these findings but indicated that search for selection signatures using low-coverage whole-genome data may need masking of repetitive sequences. A case-control study of more than 1,000 individuals from mainland Italy indicated that the Thr851Ile SNP is significantly associated with susceptibility to multiple sclerosis (MS) (odds ratio [OR] = 1.47, 95% confidence intervals [CI]: 1.08-1.99, P = 0.011). This finding was confirmed in a larger sample of 4,416 Sardinians cases/controls (OR = 1.18, 95% CI: 1.037-1.344, P = 0.011), but not in a population from Belgium. We provide one of the first instances of human/chimpanzee trans-specific coding variant located outside the major histocompatibility complex region. The selective pressure is likely to be virus driven; in modern populations, this variant associates with susceptibility to MS, possibly via the interaction with environmental factors.
Rumi:2013aa: Acquired copy-neutral loss of heterozygosity of chromosome 1p as a molecular event associated with marrow fibrosis in MPL-mutated myeloproliferative neoplasms
E. Rumi and D. Pietra and P. Guglielmelli and R. Bordoni and I. Casetti and C. Milanesi and E. Sant'Antonio and V. Ferretti and A. Pancrazzi and G. Rotunno and M. Severgnini and A. Pietrelli and C. Astori and E. Fugazza and C. Pascutto and E. Boveri and F. Passamonti and G. De Bellis and A. Vannucchi and M. Cazzola and Associazione Italiana per la Ricerca sul Cancro Gruppo Italiano Malattie Mieloproliferative
Blood 121 4388-95 (2013)
http://dx.doi.org/10.1182/blood-2013-02-486050

We studied mutations of MPL exon 10 in patients with essential thrombocythemia (ET) or primary myelofibrosis (PMF), first investigating a cohort of 892 consecutive patients. MPL mutation scanning was performed on granulocyte genomic DNA by using a high-resolution melt assay, and the mutant allele burden was evaluated by using deep sequencing. Somatic mutations of MPL, all but one involving codon W515, were detected in 26/661 (4%) patients with ET, 10/187 (5%) with PMF, and 7/44 (16%) patients with post-ET myelofibrosis. Comparison of JAK2 (V617F)-mutated and MPL-mutated patients showed only minor phenotypic differences. In an extended group of 62 MPL-mutated patients, the granulocyte mutant allele burden ranged from 1% to 95% and was significantly higher in patients with PMF or post-ET myelofibrosis compared with those with ET. Patients with higher mutation burdens had evidence of acquired copy-neutral loss of heterozygosity (CN-LOH) of chromosome 1p in granulocytes, consistent with a transition from heterozygosity to homozygosity for the MPL mutation in clonal cells. A significant association was found between MPL-mutant allele burden greater than 50% and marrow fibrosis. These observations suggest that acquired CN-LOH of chromosome 1p involving the MPL location may represent a molecular mechanism of fibrotic transformation in MPL-mutated myeloproliferative neoplasms.
Cox:2012aa: Activated innate immunity and the involvement of CX3CR1-fractalkine in promoting hematuria in patients with IgA nephropathy
S. N. Cox and F. Sallustio and G. Serino and A. Loverre and F. Pesce and M. Gigante and G. Zaza and P. F. Stifanelli and N. Ancona and F. P. Schena
Kidney Int 82 548-60 (2012)
http://dx.doi.org/10.1038/ki.2012.147

A hallmark of immunoglobulin A nephropathy (IgAN) is episodes of gross hematuria coinciding with mucosal infections that can represent the disease-triggering event. Here we performed a whole genomic screen of IgAN patients during gross hematuria to clarify the link between mucosal antigens and glomerular hematuria. Modulated genes showed a clear involvement of the intracellular interferon signaling, antigen-presenting pathway, and the immunoproteasome. The mRNA and protein level of the chemokine receptor characterizing cytotoxic effector lymphocytes, CX3CR1, was upregulated. In vitro antigenic stimulation of peripheral blood mononuclear cells from IgAN patients, healthy blood donors, and other nephropathies with microscopic hematuria showed that only in IgAN patients was CX3CR1 enhanced in a dose-dependent manner. A significantly higher amount of glomerular and urinary fractalkine, the only ligand of CX3CR1, was also found in IgAN patients with recurrent episodes of gross hematuria compared with other patients with microscopic or no hematuria. This suggests a predisposition for cytotoxic cell extravasation only in patients with recurrent gross hematuria. Thus, we found a defect in antigen handling in peripheral blood mononuclear cells of IgAN patients with a specific increase of CX3CR1. This constitutive upregulation of glomerular and urinary fractalkine suggests an involvement of the CX3CR1-fractalkine axis in the exacerbation of gross hematuria.
Soriano:2009aa: Adenosine A2A receptor-antagonist/dopamine D2 receptor-agonist bivalent ligands as pharmacological tools to detect A2A-D2 receptor heteromers
A. Soriano and R. Ventura and A. Molero and R. Hoen and V. Casadó and A. Cortés and F. Fanelli and F. Albericio and C. Lluís and R. Franco and M. Royo
J Med Chem 52 5590-602 (2009)
http://dx.doi.org/10.1021/jm900298c

Adenosine A(2A) (A(2A)R) and dopamine D(2) (D(2)R) receptors mediate the antagonism between adenosinergic and dopaminergic transmission in striatopallidal GABAergic neurons and are pharmacological targets for the treatment of Parkinson's disease. Here, a family of heterobivalent ligands containing a D(2)R agonist and an A(2A)R antagonist linked through a spacer of variable size was designed and synthesized to study A(2A)R-D(2)R heteromers. Bivalent ligands with shorter linkers bound to D(2)R or A(2A)R with higher affinity than the corresponding monovalent controls in membranes from brain striatum and from cells coexpressing both receptors. In contrast, no differences in affinity of bivalent versus monovalent ligands were detected in experiments using membranes from cells expressing only one receptor. These findings indicate the existence of A(2A)R-D(2)R heteromers and of a simultaneous interaction of heterobivalent ligands with both receptors. The cooperative effect derived from the simultaneous interaction suggests the occurrence of A(2A)R-D(2)R heteromers in cotransfected cells and in brain striatum. The dopamine/adenosine bivalent action could constitute a novel concept in Parkinson's disease pharmacotherapy.
Buttari:2011aa: Advanced glycation end products of human β₂ glycoprotein I modulate the maturation and function of DCs
B. Buttari and E. Profumo and A. Capozzi and F. Facchiano and L. Saso and M. Sorice and R. Riganò
Blood 117 6152-61 (2011)
http://dx.doi.org/10.1182/blood-2010-12-325514

In chronic disorders related to endothelial cell dysfunction, plasma β₂ glycoprotein I (β₂GPI) plays a role as a target antigen of pathogenetic autoimmune responses. However, information is still lacking to clarify why β₂GPI triggers autoimmunity. It is possible that posttranslational modification of the protein, such as nonenzymatic glycosylation, leads to the formation of advanced glycation end products (AGEs). The aim of our study was to explore whether glucose-modified β₂GPI is able to interact and activate monocyte-derived immature dendritic cells (iDCs) from healthy human donors. SDS-PAGE and spectrofluorometric analyses indicated that β₂GPI incubated with glucose was sugar modified, and that this modification likely consisted of AGE formation, resulting in AGE-β₂GPI. AGE-β₂GPI caused phenotypical and functional maturation of iDCs involving the activation of p38 MAPK, ERK, and NF-κB. It also induced on DCs a significant up-regulation of RAGE, the receptor for AGEs. Evidence for RAGE involvement comes from blocking experiments with an anti-RAGE mAb, confocal analysis, and coimmunoprecipitation experiments. AGE-β₂GPI-stimulated DCs had increased allostimulatory ability and primed naive T lymphocytes toward a Th2 polarization. These findings might explain in part the interactive role of β₂GPI, AGEs, and DCs in chronic disorders related to endothelial cell dysfunction.
Martini:2013aa: Along signal paths: an empirical gene set approach exploiting pathway topology
P. Martini and G. Sales and M. S. Massa and M. Chiogna and C. Romualdi
Nucleic Acids Res 41 e19 (2013)
http://dx.doi.org/10.1093/nar/gks866

Gene set analysis using biological pathways has become a widely used statistical approach for gene expression analysis. A biological pathway can be represented through a graph where genes and their interactions are, respectively, nodes and edges of the graph. From a biological point of view only some portions of a pathway are expected to be altered; however, few methods using pathway topology have been proposed and none of them tries to identify the signal paths, within a pathway, mostly involved in the biological problem. Here, we present a novel algorithm for pathway analysis clipper, that tries to fill in this gap. clipper implements a two-step empirical approach based on the exploitation of graph decomposition into a junction tree to reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it identifies within these pathways the signal paths having the greatest association with a specific phenotype. We test our approach on simulated and two real expression datasets. Our results demonstrate the efficacy of clipper in the identification of signal transduction paths totally coherent with the biological problem.
Cabras01102010: Alterations of the Salivary Secretory Peptidome Profile in Children Affected by Type 1 Diabetes
T. Cabras and E. Pisano and A. Mastinu and G. Denotti and P. P. Pusceddu and R. Inzitari and C. Fanali and S. Nemolato and M. Castagnola and I. Messana
Molecular & Cellular Proteomics 9 2099-2108 (2010)
http://www.mcponline.org/content/9/10/2099.abstract
http://dx.doi.org/10.1074/mcp.M110.001057

The acidic soluble fraction of whole saliva of type 1 diabetic children was analyzed by reversed phase (RP)1--HPLC-ESI-MS and compared with that of sex- and age-matched control subjects. Salivary acidic proline-rich phosphoproteins (aPRP), histatins, α-defensins, salivary cystatins, statherin, proline-rich peptide P-B (P-B), beta-thymosins, S100A8 and S100A9*(S100A9* corresponds to S100A9 vairant lacking the first four amino acids), as well some naturally occurring peptides derived from salivary acidic proline-rich phosphoproteins, histatins, statherin, and P-B peptide, were detected and quantified on the basis of the extracted ion current peak area. The level of phosphorylation of salivary acidic proline-rich phosphoproteins, histatin-1 (Hst-1), statherin and S100A9* and the percentage of truncated forms of salivary acidic proline-rich phosphoproteins was also determined in the two groups. The study revealed that statherin, proline-rich peptide P-B, P-C peptide, and histatins, were significantly less concentrated in saliva of diabetic subjects than in controls, while concentration of α-defensins 1, 2 and 4 and S100A9* was higher. The low concentration of P-C peptide was paralleled by high levels of some of its fragments. On the whole, the study highlighted the severe impairment of the repertoire of peptides involved in the safeguard of the oral cavity in children who have diabetes, as well as an higher concentration of the proinflammatory mediator S100A9* with respect to healthy children.
Cox:2010aa: Altered modulation of WNT-beta-catenin and PI3K/Akt pathways in IgA nephropathy
S. N. Cox and F. Sallustio and G. Serino and P. Pontrelli and R. Verrienti and F. Pesce and D. D. Torres and N. Ancona and P. Stifanelli and G. Zaza and F. P. Schena
Kidney Int 78 396-407 (2010)
http://dx.doi.org/10.1038/ki.2010.138

Immunoglobulin A nephropathy (IgAN) is the most common form of primary glomerulonephritis worldwide. The basic defect lies within the IgA immune system and in peripheral blood leukocytes, rather than local kidney abnormalities. To define the intracellular mechanisms leading to the disease, we conducted a microarray study to identify genes and pathways differentially modulated in peripheral blood leukocytes isolated from 12 IgAN patients and 8 healthy controls. The genes whose expression discriminated between the IgAN patients and controls were primarily involved in canonical WNT-beta-catenin and PI3K/Akt pathways. We also tested peripheral blood mononuclear cells and their subpopulations isolated from an independent group of IgAN patients and healthy controls. There were low protein levels of inversin and PTEN, key regulators of WNT-beta-catenin and PI3K/Akt, in IgAN patients, suggesting hyperactivation of these pathways. Also, there were increased phospho-Akt protein levels and nuclear beta-catenin accumulation with an enhanced peripheral blood mononuclear cell proliferation rate. Subpopulation analysis uncovered a major irregularity of WNT signaling in monocytes. Hence, hyperactivation of these pathways may provide insight into mechanisms contributing to the pathogenesis of IgAN.
Mussolin:2014aa: An aberrant microRNA signature in childhood T-cell lymphoblastic lymphoma affecting CDKN1B expression, NOTCH1 and growth factor signaling pathways
L. Mussolin and A. B. Holmes and C. Romualdi and G. Sales and E. S. G. D'Amore and M. Ghisi and M. Pillon and A. Rosolen and K. Basso
Leukemia 28 1909-12 (2014)
http://dx.doi.org/10.1038/leu.2014.134
Forni:2014aa: An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection
D. Forni and R. Cagliani and C. Tresoldi and U. Pozzoli and L. De Gioia and G. Filippi and S. Riva and G. Menozzi and M. Colleoni and M. Biasin and S. Lo Caputo and F. Mazzotta and G. P. Comi and N. Bresolin and M. Clerici and M. Sironi
PLoS Genet 10 e1004189 (2014)
http://dx.doi.org/10.1371/journal.pgen.1004189

The antigenic repertoire presented by MHC molecules is generated by the antigen processing and presentation (APP) pathway. We analyzed the evolutionary history of 45 genes involved in APP at the inter- and intra-species level. Results showed that 11 genes evolved adaptively in mammals. Several positively selected sites involve positions of fundamental importance to the protein function (e.g. the TAP1 peptide-binding domains, the sugar binding interface of langerin, and the CD1D trafficking signal region). In CYBB, all selected sites cluster in two loops protruding into the endosomal lumen; analysis of missense mutations responsible for chronic granulomatous disease (CGD) showed the action of different selective forces on the very same gene region, as most CGD substitutions involve aminoacid positions that are conserved in all mammals. As for ERAP2, different computational methods indicated that positive selection has driven the recurrent appearance of protein-destabilizing variants during mammalian evolution. Application of a population-genetics phylogenetics approach showed that purifying selection represented a major force acting on some APP components (e.g. immunoproteasome subunits and chaperones) and allowed identification of positive selection events in the human lineage. We also investigated the evolutionary history of APP genes in human populations by developing a new approach that uses several different tests to identify the selection target, and that integrates low-coverage whole-genome sequencing data with Sanger sequencing. This analysis revealed that 9 APP genes underwent local adaptation in human populations. Most positive selection targets are located within noncoding regions with regulatory function in myeloid cells or act as expression quantitative trait loci. Conversely, balancing selection targeted nonsynonymous variants in TAP1 and CD207 (langerin). Finally, we suggest that selected variants in PSMB10 and CD207 contribute to human phenotypes. Thus, we used evolutionary information to generate experimentally-testable hypotheses and to provide a list of sites to prioritize in follow-up analyses.
1000-Genomes-Project-Consortium:2012aa: An integrated map of genetic variation from 1,092 human genomes
1000 Genomes Project Consortium and G. R. Abecasis and A. Auton and L. D. Brooks and M. A. DePristo and R. M. Durbin and R. E. Handsaker and H. M. Kang and G. T. Marth and G. A. McVean
Nature 491 56-65 (2012)
http://dx.doi.org/10.1038/nature11632

By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations.
Severi:2011aa: Analysis of Reptilian APOBEC1 Suggests that RNA Editing May Not Be Its Ancestral Function
F. Severi and A. Chicca and S. G. Conticello
Mol. Biol. Evol. 28 1125--1129 (2011)
http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/WOS:000287745200001

The Activation Induced Deaminase (AID)/APOBEC family of deaminases targeting nucleic acids arose at the beginning of the vertebrate radiation and further expanded in mammals. Following an analysis of the available genomic data, we report the identification of the APOBEC5, a novel group of paralogues in tetrapods. Moreover, we find bona fide homologues of Apolipoprotein B Editing Complex 1 (APOBEC1) in the genomes of anole lizard and zebra finch, thus implying its appearance prior to the divergence of the amniotes. apolipoprotein B editing complex 1 (APOBEC1), in contrast with other AID/APOBECs acting on DNA, is an RNA-editing enzyme that targets the transcript of Apolipoprotein B (ApoB), thereby causing the translation of a truncated form of the protein. 3'RACE experiments reveal a lizard APOBEC1-like molecule lacking a C-terminal region important for mammalian ApoB RNA editing. This observation pairs with the finding that lizard ApoB is not deaminated at the region corresponding to the mammalian site of editing. Similar to mammalian APOBEC1, the lizard protein is able to deaminate DNA in bacteria and shows a conserved mutational context. Although not precluding the possibility that lizard APOBEC1 acts on unknown mRNA targets, these findings suggest that its ability to target DNA predates its role in RNA editing.
Bessede:2014aa: Aryl hydrocarbon receptor control of a disease tolerance defence pathway
A. Bessede and M. Gargaro and M. T. Pallotta and D. Matino and G. Servillo and C. Brunacci and S. Bicciato and E. M. C. Mazza and A. Macchiarulo and C. Vacca and R. Iannitti and L. Tissi and C. Volpi and M. L. Belladonna and C. Orabona and R. Bianchi and T. V. Lanz and M. Platten and M. A. Della Fazia and D. Piobbico and T. Zelante and H. Funakoshi and T. Nakamura and D. Gilot and M. S. Denison and G. J. Guillemin and J. B. DuHadaway and G. C. Prendergast and R. Metz and M. Geffard and L. Boon and M. Pirro and A. Iorio and B. Veyret and L. Romani and U. Grohmann and F. Fallarino and P. Puccetti
Nature 511 184-90 (2014)
http://dx.doi.org/10.1038/nature13323

Disease tolerance is the ability of the host to reduce the effect of infection on host fitness. Analysis of disease tolerance pathways could provide new approaches for treating infections and other inflammatory diseases. Typically, an initial exposure to bacterial lipopolysaccharide (LPS) induces a state of refractoriness to further LPS challenge (endotoxin tolerance). We found that a first exposure of mice to LPS activated the ligand-operated transcription factor aryl hydrocarbon receptor (AhR) and the hepatic enzyme tryptophan 2,3-dioxygenase, which provided an activating ligand to the former, to downregulate early inflammatory gene expression. However, on LPS rechallenge, AhR engaged in long-term regulation of systemic inflammation only in the presence of indoleamine 2,3-dioxygenase 1 (IDO1). AhR-complex-associated Src kinase activity promoted IDO1 phosphorylation and signalling ability. The resulting endotoxin-tolerant state was found to protect mice against immunopathology in Gram-negative and Gram-positive infections, pointing to a role for AhR in contributing to host fitness.
Martelli:2011aa: ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing
P. L. Martelli and M. D'Antonio and P. Bonizzoni and T. Castrignanò and A. M. D'Erchia and P. D'Onorio De Meo and P. Fariselli and M. Finelli and F. Licciulli and M. Mangiulli and F. Mignone and G. Pavesi and E. Picardi and R. Rizzi and I. Rossi and A. Valletti and A. Zauli and F. Zambelli and R. Casadio and G. Pesole
Nucleic Acids Res 39 D80-5 (2011)
http://dx.doi.org/10.1093/nar/gkq1073

Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at http://www.caspur.it/ASPicDB/.
Marchini:2011aa: Association between miR-200c and the survival of patients with stage I epithelial ovarian cancer: a retrospective study of two independent tumour tissue collections
S. Marchini and D. Cavalieri and R. Fruscio and E. Calura and D. Garavaglia and I. F. Nerini and C. Mangioni and G. Cattoretti and L. Clivio and L. Beltrame and D. Katsaros and L. Scarampi and G. Menato and P. Perego and G. Chiorino and A. Buda and C. Romualdi and M. D'Incalci
Lancet Oncol. 12 273--285 (2011)
http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/WOS:000288483500026

Background International Federation of Gynecology and Obstetrics stage I epithelial ovarian cancer (EOC) has a significantly better prognosis than stage III/IV EOC, with about 80\% of patients surviving at 5 years (compared with about 20\% of those with stage III/IV EOC). However, 20\% of patients with stage I EOC relapse within 5 years. It is therefore crucial that the biological properties of stage I EOCs are further elucidated. MicroRNAs (miRNAs) have shown diagnostic and prognostic potential in stage III and IV EOCs, but the small number of patients diagnosed with stage I EOC has so far prevented an investigation of its molecular features. We profiled miRNA expression in stage I EOC tumours to assess whether there is a miRNA signature associated with overall and progression-free survival (PFS) in stage I EOC. Methods We analysed tumour samples from 144 patients (29 of whom relapsed) with stage I EOC gathered from two independent tumour tissue collections (A and B), both with a median follow-up of 9 years. 89 samples from tumour tissue collection A were stratified into a training set (51 samples, 15 of which were from patients who relapsed) for miRNA signature generation, and into a validation set (38 samples, seven of which were from patients who relapsed) for signature validation. Tumour tissue collection B (55 samples, seven of which were from patients who relapsed) was used as an independent test set. The Cox proportional hazards model and the log-rank test were used to assess the correlation of quantitative reverse transcription PCR (qRT-PCR)-validated miRNAs with overall survival and PFS. Findings A signature of 34 miRNAs associated with survival was generated by microarray analysis in the training set. In both the training set and validation set, qRT-PCR analysis confirmed that 11 miRNAs (miR-214, miR-199a-3p, miR-199a-5p, miR-145, miR-200b, miR-30a, miR-30a*, miR-30d, miR-200c, miR-20a, and miR-143) were expressed differently in relapsers compared with non-relapsers. Three of these miRNAs (miR-200c, miR-199a-3p, miR-199a-5p) were associated with PFS, overall survival, or both in multivariate analysis. qRT-PCR analysis in the test set confirmed the downregulation of miR-200c in relapsers compared with non-relapsers, but not the upregulation of miR-199a-3p and miR-199a-5p. Multivariate analysis confirmed that downregulation of miR-200c in the test set was associated with overall survival (HR 0.094, 95\% CI 0.012-0.766, p=0.0272) and PFS (0.035, 0.004-0.311; p=0.0026), independent of clinical covariates. Interpretation miR-200c has potential as a predictor of survival, and is a biomarker of relapse, in stage I EOC.
Piovesan:2011aa: BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences
D. Piovesan and P. L. Martelli and P. Fariselli and A. Zauli and I. Rossi and R. Casadio
Nucleic Acids Res 39 W197-202 (2011)
http://dx.doi.org/10.1093/nar/gkr292

We introduce BAR-PLUS (BAR(+)), a web server for functional and structural annotation of protein sequences. BAR(+) is based on a large-scale genome cross comparison and a non-hierarchical clustering procedure characterized by a metric that ensures a reliable transfer of features within clusters. In this version, the method takes advantage of a large-scale pairwise sequence comparison of 13,495,736 protein chains also including 988 complete proteomes. Available sequence annotation is derived from UniProtKB, GO, Pfam and PDB. When PDB templates are present within a cluster (with or without their SCOP classification), profile Hidden Markov Models (HMMs) are computed on the basis of sequence to structure alignment and are cluster-associated (Cluster-HMM). Therefrom, a library of 10,858 HMMs is made available for aligning even distantly related sequences for structural modelling. The server also provides pairwise query sequence-structural target alignments computed from the correspondent Cluster-HMM. BAR(+) in its present version allows three main categories of annotation: PDB [with or without SCOP (*)] and GO and/or Pfam; PDB (*) without GO and/or Pfam; GO and/or Pfam without PDB (*) and no annotation. Each category can further comprise clusters where GO and Pfam functional annotations are or are not statistically significant. BAR(+) is available at http://bar.biocomp.unibo.it/bar2.0.
Tonikian:2009aa: Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins
R. Tonikian and X. Xin and C. P. Toret and D. Gfeller and C. Landgraf and S. Panni and S. Paoluzi and L. Castagnoli and B. Currell and S. Seshagiri and H. Yu and B. Winsor and M. Vidal and M. B. Gerstein and G. D. Bader and R. Volkmer and G. Cesareni and D. G. Drubin and P. M. Kim and S. S. Sidhu and C. Boone
PLoS Biol 7 e1000218 (2009)
http://dx.doi.org/10.1371/journal.pbio.1000218

SH3 domains are peptide recognition modules that mediate the assembly of diverse biological complexes. We scanned billions of phage-displayed peptides to map the binding specificities of the SH3 domain family in the budding yeast, Saccharomyces cerevisiae. Although most of the SH3 domains fall into the canonical classes I and II, each domain utilizes distinct features of its cognate ligands to achieve binding selectivity. Furthermore, we uncovered several SH3 domains with specificity profiles that clearly deviate from the two canonical classes. In conjunction with phage display, we used yeast two-hybrid and peptide array screening to independently identify SH3 domain binding partners. The results from the three complementary techniques were integrated using a Bayesian algorithm to generate a high-confidence yeast SH3 domain interaction map. The interaction map was enriched for proteins involved in endocytosis, revealing a set of SH3-mediated interactions that underlie formation of protein complexes essential to this biological pathway. We used the SH3 domain interaction network to predict the dynamic localization of several previously uncharacterized endocytic proteins, and our analysis suggests a novel role for the SH3 domains of Lsb3p and Lsb4p as hubs that recruit and assemble several endocytic complexes.
Horner:2010aa: Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing
D. S. Horner and G. Pavesi and T. Castrignanò and P. D. De Meo and S. Liuni and M. Sammeth and E. Picardi and G. Pesole
Brief Bioinform 11 181-97 (2010)
http://dx.doi.org/10.1093/bib/bbp046

Technical advances such as the development of molecular cloning, Sanger sequencing, PCR and oligonucleotide microarrays are key to our current capacity to sequence, annotate and study complete organismal genomes. Recent years have seen the development of a variety of so-called 'next-generation' sequencing platforms, with several others anticipated to become available shortly. The previously unimaginable scale and economy of these methods, coupled with their enthusiastic uptake by the scientific community and the potential for further improvements in accuracy and read length, suggest that these technologies are destined to make a huge and ongoing impact upon genomic and post-genomic biology. However, like the analysis of microarray data and the assembly and annotation of complete genome sequences from conventional sequencing data, the management and analysis of next-generation sequencing data requires (and indeed has already driven) the development of informatics tools able to assemble, map, and interpret huge quantities of relatively or extremely short nucleotide sequence data. Here we provide a broad overview of bioinformatics approaches that have been introduced for several genomics and functional genomics applications of next-generation sequencing.
Castagnola:2011aa: Biotechnological implications of the salivary proteome
M. Castagnola and T. Cabras and A. Vitali and M. T. Sanna and I. Messana
Trends Biotechnol 29 409-18 (2011)
http://dx.doi.org/10.1016/j.tibtech.2011.04.002

Although very attractive for noninvasive specimen collection, saliva has not yet been considered a relevant bodily fluid for the diagnosis and prognosis of diseases. The functional roles of specific salivary peptides and proteins have also not yet been studied in detail. Recent proteomic analysis of human whole saliva has shown that salivary biomarkers could contribute to the detection of local and systemic diseases, provided the standardization of proper sampling procedures exists. Recently, interesting and novel functions for different families of specific secretory peptides and proteins have been demonstrated, which could be a basis for the design of peptidomimetics with relevant biotechnological applications. In this review, we focus on the most recent advances in analysing salivary proteins and their potential application in biotechnology.
Liumbruno:2010aa: Blood-related proteomics
G. Liumbruno and A. D'Alessandro and G. Grazzini and L. Zolla
J Proteomics 73 483-507 (2010)
http://dx.doi.org/10.1016/j.jprot.2009.06.010

Blood-related proteomics is an emerging field, recently gaining momentum. Indeed, a wealth of data is now available and a plethora of groups has contributed to add pieces to the jigsaw puzzle of protein complexity within plasma and blood cells. In this review article we purported to sail across the mare magnum of the actual knowledge in this research endeavour. The main strides in proteomic investigations on red blood cells, platelets, plasma and white blood cells are hereby presented in a chronological order. Moreover, a glance is given at prospective studies which promise to shift the focus of attention from the end product to its provider, the donor, in a sort of Kantian "Copernican revolution". A well-rounded portrait of the usefulness of proteomics in blood-related research is accurately given. In particular, proteomic tools could be adopted to follow the main steps of the blood-banking production processes (a comparison of collection methods, pathogen inactivation techniques, storage protocols). Thus proteomics has been recently transformed from a mere basic-research extremely-expensive toy into a dramatically-sensitive and efficient eye-lens to either delve into the depths of the molecular mechanisms of blood and blood components or to establish quality parameters in the blood-banking production chain totally anew.
Volinia:2012aa: Breast cancer signatures for invasiveness and prognosis defined by deep sequencing of microRNA
S. Volinia and M. Galasso and M. E. Sana and T. F. Wise and J. Palatini and K. Huebner and C. M. Croce
Proc Natl Acad Sci U S A 109 3024-9 (2012)
http://dx.doi.org/10.1073/pnas.1200010109

The transition from ductal carcinoma in situ to invasive ductal carcinoma is a key event in breast cancer progression that is still not well understood. To discover the microRNAs regulating this critical transition, we used 80 biopsies from invasive ductal carcinoma, 8 from ductal carcinoma in situ, and 6 from normal breast. We selected them from a recently published deep-sequencing dataset [Farazi TA, et al. (2011) Cancer Res 71:4443-4453]. The microRNA profile established for the normal breast to ductal carcinoma in situ transition was largely maintained in the in situ to invasive ductal carcinoma transition. Nevertheless, a nine-microRNA signature was identified that differentiated invasive from in situ carcinoma. Specifically, let-7d, miR-210, and -221 were down-regulated in the in situ and up-regulated in the invasive transition, thus featuring an expression reversal along the cancer progression path. Additionally, we identified microRNAs for overall survival and time to metastasis. Five noncoding genes were associated with both prognostic signatures--miR-210, -21, -106b*, -197, and let-7i, with miR-210 the only one also involved in the invasive transition. To pinpoint critical cellular functions affected in the invasive transition, we identified the protein coding genes with inversely related profiles to miR-210: BRCA1, FANCD, FANCF, PARP1, E-cadherin, and Rb1 were all activated in the in situ and down-regulated in the invasive carcinoma. Additionally, we detected differential splicing isoforms with special features, including a truncated EGFR lacking the kinase domain and overexpressed only in ductal carcinoma in situ.
Tornatore:2014aa: Cancer-selective targeting of the NF-κB survival pathway with GADD45β/MKK7 inhibitors
L. Tornatore and A. Sandomenico and D. Raimondo and C. Low and A. Rocci and C. Tralau-Stewart and D. Capece and D. D'Andrea and M. Bua and E. Boyle and M. van Duin and P. Zoppoli and A. Jaxa-Chamiec and A. K. Thotakura and J. Dyson and B. A. Walker and A. Leonardi and A. Chambery and C. Driessen and P. Sonneveld and G. Morgan and A. Palumbo and A. Tramontano and A. Rahemtulla and M. Ruvo and G. Franzoso
Cancer Cell 26 495-508 (2014)
http://dx.doi.org/10.1016/j.ccr.2014.07.027

Constitutive NF-κB signaling promotes survival in multiple myeloma (MM) and other cancers; however, current NF-κB-targeting strategies lack cancer cell specificity. Here, we identify the interaction between the NF-κB-regulated antiapoptotic factor GADD45β and the JNK kinase MKK7 as a therapeutic target in MM. Using a drug-discovery strategy, we developed DTP3, a D-tripeptide, which disrupts the GADD45β/MKK7 complex, kills MM cells effectively, and, importantly, lacks toxicity to normal cells. DTP3 has similar anticancer potency to the clinical standard, bortezomib, but more than 100-fold higher cancer cell specificity in vitro. Notably, DTP3 ablates myeloma xenografts in mice with no apparent side effects at the effective doses. Hence, cancer-selective targeting of the NF-κB pathway is possible and, at least for myeloma patients, promises a profound benefit.
Masetti:2013aa: CBFA2T3-GLIS2 fusion transcript is a novel common feature in pediatric, cytogenetically normal AML, not restricted to FAB M7 subtype
R. Masetti and M. Pigazzi and M. Togni and A. Astolfi and V. Indio and E. Manara and R. Casadio and A. Pession and G. Basso and F. Locatelli
Blood 121 3469-72 (2013)
http://dx.doi.org/10.1182/blood-2012-11-469825

Pediatric cytogenetically normal acute myeloid leukemia (CN-AML) is a heterogeneous subgroup of myeloid clonal disorders that do not harbor known mutations. To investigate the mutation spectrum of pediatric CN-AML, we performed whole-transcriptome massively parallel sequencing on blasts from 7 CN-AML pediatric patients. In 3 patients we identified a recurrent cryptic inversion of chromosome 16, encoding a CBFA2T3-GLIS2 fusion transcript. In a validation cohort of 230 pediatric CN-AML samples we identified 17 new cases. Among a total of 20 patients with CBFA2T3-GLIS2 fusion transcript out of 237 investigated (8.4%), 10 patients (50%) did not belong to the French-American-British (FAB) M7 subgroup. The 5-year event-free survival for these 20 children was worse than that for the other CN-AML patients (27.4% vs 59.6%; P = .01). These data suggest that the presence of CBFA2T3-GLIS2 fusion transcript is a novel common feature of pediatric CN-AML, not restricted to the FAB M7 subtype, predicting poorer outcome.
Romano:2009aa: Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines
P. Romano and A. Manniello and O. Aresu and M. Armento and M. Cesaro and B. Parodi
Nucleic Acids Res 37 D925-32 (2009)
http://dx.doi.org/10.1093/nar/gkn730

The Cell Line Data Base (CLDB) is a well-known reference information source on human and animal cell lines including information on more than 6000 cell lines. Main biological features are coded according to controlled vocabularies derived from international lists and taxonomies. HyperCLDB (http://bioinformatics.istge.it/hypercldb/) is a hypertext version of CLDB that improves data accessibility by also allowing information retrieval through web spiders. Access to HyperCLDB is provided through indexes of biological characteristics and navigation in the hypertext is granted by many internal links. HyperCLDB also includes links to external resources. Recently, an interest was raised for a reference nomenclature for cell lines and CLDB was seen as an authoritative system. Furthermore, to overcome the cell line misidentification problem, molecular authentication methods, such as fingerprinting, single-locus short tandem repeat (STR) profile and single nucleotide polymorphisms validation, were proposed. Since this data is distributed, a reference portal on authentication of human cell lines is needed. We present here the architecture and contents of CLDB, its recent enhancements and perspectives. We also present a new related database, the Cell Line Integrated Molecular Authentication (CLIMA) database (http://bioinformatics.istge.it/clima/), that allows to link authentication data to actual cell lines.
Cerasa:2009aa: Cerebellar atrophy in essential tremor using an automated segmentation method
A. Cerasa and D. Messina and G. Nicoletti and F. Novellino and P. Lanza and F. Condino and G. Arabia and M. Salsone and A. Quattrone
AJNR Am J Neuroradiol 30 1240-3 (2009)
http://dx.doi.org/10.3174/ajnr.A1544

BACKGROUND AND PURPOSE: Essential tremor (ET) is a slowly progressive disorder characterized by postural and kinetic tremors most commonly affecting the forearms and hands. Several lines of evidence from physiologic and neuroimaging studies point toward a major role of the cerebellum in this disease. Recently, voxel-based morphometry (VBM) has been proposed to quantify cerebellar atrophy in ET. However, VBM was not originally designed to study subcortical structures, and the complicated anatomy of the cerebellum may hamper the automatic processing of VBM. The aim of this study was to determine the efficacy and utility of using automated subcortical segmentation to identify atrophy of the cerebellum and other subcortical structures in patients with ET. MATERIALS AND METHODS: We used a recently developed automated volumetric method (FreeSurfer) to quantify subcortical atrophy in ET by comparing results obtained with this method with those provided by previous evidence. The study included T1-weighted MR images of 46 patients with ET grouped into those having arm ET (n = 27, a-ET) or head ET (n = 19, h-ET) and 28 healthy controls. RESULTS: Results revealed the expected reduction of cerebellar volume in patients with h-ET with respect to healthy controls after controlling for intracranial volume. No significant difference was detected in any other subcortical area. CONCLUSIONS: Volumetric data obtained with automated segmentation of subcortical and cerebellar structures approximate data from a previous study based on VBM. The current findings extend the literature by providing initial validation for using fully automated segmentation to derive cerebellar volumetric information from patients with ET.
Fulci:2009aa: Characterization of B- and T-lineage acute lymphoblastic leukemia by integrated analysis of MicroRNA and mRNA expression profiles
V. Fulci and T. Colombo and S. Chiaretti and M. Messina and F. Citarella and S. Tavolaro and A. Guarini and R. Foà and G. Macino
Genes Chromosomes Cancer 48 1069-82 (2009)
http://dx.doi.org/10.1002/gcc.20709

Acute lymphoblastic leukemia (ALL) is an heterogeneous disease comprising several subentities that differ for both immunophenotypic and molecular characteristics. Over the years, the biological understanding of this neoplasm has largely increased. Gene expression profiling has allowed to identify specific signatures for the different ALL subsets and permitted the identification of pathways deregulated by a given lesion. MicroRNAs (miRNAs) are small noncoding RNAs, which play a pivotal role in several cellular functions. In this study, we investigated miRNAs expression profiles in a series of adult ALL cases by microarray analysis. Unsupervised hierarchical clustering largely recapitulated ALL subgroups. Furthermore, we identified miR-148, miR-151, and miR-424 as discriminative of T-lineage versus B-lineage ALL; ANOVA highlighted a set of six miRNAs-namely miR-425-5p, miR-191, miR-146b, miR-128, miR-629, and miR-126-that can discriminate B-lineage ALL subgroups harboring specific molecular lesions. These results were confirmed and extended by quantitative-PCR on a further cohort of cases. Finally, we used Pearson correlation analysis to combine miRNA and gene expression profiles. The distribution of correlation coefficients generated by comparing the expression of every miRNA/gene pair in our data set shows enrichment of both positively and negatively correlated pairs over background distributions obtained using randomized data. Moreover, a clear enrichment for predicted miRNA:target pairs is observed at negative correlation coefficient intervals. Signal-to-noise ratio highlighted several miRNA/gene pairs with a possible role in the disease. In fact, gene set enrichment analysis of genes composing the selected miRNA/gene pairs displays over-representation of functional categories related to cancer and cell-cycle regulation.
Zenoni:2010aa: Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq
S. Zenoni and A. Ferrarini and E. Giacomelli and L. Xumerle and M. Fasoli and G. Malerba and D. Bellin and M. Pezzotti and M. Delledonne
Plant Physiol 152 1787-95 (2010)
http://dx.doi.org/10.1104/pp.109.149716

The development of massively parallel sequencing technologies enables the sequencing of total cDNA (RNA-Seq) to derive accurate measure of individual gene expression, differential splicing activity, and to discover novel regions of transcription, dramatically changing the way that the functional complexity of transcriptomes can be studied. Here we report on the first use of RNA-Seq to gain insight into the wide range of transcriptional responses that are associated with berry development in Vitis vinifera 'Corvina'. More than 59 million sequence reads, 36 to 44 bp in length, were generated from three developmental stages: post setting, véraison, and ripening. The sequence reads were aligned onto the 8.4-fold draft sequence of the Pinot Noir 40024 genome and then analyzed to measure gene expression levels, to detect alternative splicing events, and expressed single nucleotide polymorphisms. We detected 17,324 genes expressed during berry development, 6,695 of which were expressed in a stage-specific manner, suggesting differences in expression for genes in numerous functional categories and a significant transcriptional complexity. This exhaustive overview of gene expression dynamics demonstrates the utility of RNA-Seq for identifying single nucleotide polymorphisms and splice variants and for describing how plant transcriptomes change during development.
Santanam:2010aa: Chronic lymphocytic leukemia modeled in mouse by targeted miR-29 expression
U. Santanam and N. Zanesi and A. Efanov and S. Costinean and A. Palamarchuk and J. P. Hagan and S. Volinia and H. Alder and L. Rassenti and T. Kipps and C. M. Croce and Y. Pekarsky
Proc Natl Acad Sci U S A 107 12210-5 (2010)
http://dx.doi.org/10.1073/pnas.1007186107

B-cell chronic lymphocytic leukemia (B-CLL), the most common leukemia in the Western world, occurs in two forms, aggressive (showing for the most part high ZAP-70 expression and unmutated IgH V(H)) and indolent (showing low ZAP-70 expression and mutated IgH V(H)). We found that miR-29a is up-regulated in indolent human B-CLL as compared with aggressive B-CLL and normal CD19(+) B cells. To study the role of miR-29 in B-CLL, we generated Emu-miR-29 transgenic mice overexpressing miR-29 in mouse B cells. Flow cytometric analysis revealed a markedly expanded CD5(+) population in the spleen of these mice starting at 2 mo of age, with 85% (34/40) of miR-29 transgenic mice exhibiting expanded CD5(+) B-cell populations, a characteristic of B-CLL. On average, 50% of B cells in these transgenic mice were CD5 positive. At 2 y of age the mice showed significantly enlarged spleens and an increase in the CD5(+) B-cell population to approximately 100%. Of 20 Emu-miR-29 transgenic mice followed to 24-26 mo of age, 4 (20%) developed frank leukemia and died of the disease. These results suggest that dysregulation of miR-29 can contribute to the pathogenesis of indolent B-CLL.
Marcucci:2013aa: Clinical role of microRNAs in cytogenetically normal acute myeloid leukemia: miR-155 upregulation independently identifies high-risk patients
G. Marcucci and K. S. Maharry and K. H. Metzeler and S. Volinia and Y.-Z. Wu and K. Mrózek and D. Nicolet and J. Kohlschmidt and S. P. Whitman and J. H. Mendler and S. Schwind and H. Becker and A.-K. Eisfeld and A. J. Carroll and B. L. Powell and J. E. Kolitz and R. Garzon and M. A. Caligiuri and R. M. Stone and C. D. Bloomfield
J Clin Oncol 31 2086-93 (2013)
http://dx.doi.org/10.1200/JCO.2012.45.6228

PURPOSE: To evaluate the impact of miR-155 on the outcome of adults with cytogenetically normal (CN) acute myeloid leukemia (AML) in the context of other clinical and molecular prognosticators and to gain insight into the leukemogenic role of this microRNA. PATIENTS AND METHODS: We evaluated 363 patients with primary CN-AML. miR-155 levels were measured in pretreatment marrow and blood by NanoString nCounter assays that quantified the expression of the encoding gene MIR155HG. All molecular prognosticators were assessed centrally. miR-155-associated gene and microRNA expression profiles were derived using microarrays. RESULTS: Considering all patients, high miR-155 expression was associated with a lower complete remission (CR) rate (P < .001) and shorter disease-free survival (P = .001) and overall survival (OS; P < .001) after adjusting for age. In multivariable analyses, high miR-155 expression remained an independent predictor for a lower CR rate (P = .007) and shorter OS (P < .001). High miR-155 expressers had approximately 50% reduction in the odds of achieving CR and 60% increase in the risk of death compared with low miR-155 expressers. Although high miR-155 expression was not associated with a distinct microRNA expression profile, it was associated with a gene expression profile enriched for genes involved in cellular mechanisms deregulated in AML (eg, apoptosis, nuclear factor-κB activation, and inflammation), thereby supporting a pivotal and unique role of this microRNA in myeloid leukemogenesis. CONCLUSION: miR-155 expression levels are associated with clinical outcome independently of other strong clinical and molecular predictors. The availability of emerging compounds with antagonistic activity to microRNAs in the clinic provides the opportunity for future therapeutic targeting of miR-155 in AML.
Leoni:2011aa: Coding potential of the products of alternative splicing in human
G. Leoni and L. Le Pera and F. Ferrè and D. Raimondo and A. Tramontano
Genome Biol 12 R9 (2011)
http://dx.doi.org/10.1186/gb-2011-12-1-r9

BACKGROUND: Analysis of the human genome has revealed that as much as an order of magnitude more of the genomic sequence is transcribed than accounted for by the predicted and characterized genes. A number of these transcripts are alternatively spliced forms of known protein coding genes; however, it is becoming clear that many of them do not necessarily correspond to a functional protein. RESULTS: In this study we analyze alternative splicing isoforms of human gene products that are unambiguously identified by mass spectrometry and compare their properties with those of isoforms of the same genes for which no peptide was found in publicly available mass spectrometry datasets. We analyze them in detail for the presence of uninterrupted functional domains, active sites as well as the plausibility of their predicted structure. We report how well each of these strategies and their combination can correctly identify translated isoforms and derive a lower limit for their specificity, that is, their ability to correctly identify non-translated products. CONCLUSIONS: The most effective strategy for correctly identifying translated products relies on the conservation of active sites, but it can only be applied to a small fraction of isoforms, while a reasonably high coverage, sensitivity and specificity can be achieved by analyzing the presence of non-truncated functional domains. Combining the latter with an assessment of the plausibility of the modeled structure of the isoform increases both coverage and specificity with a moderate cost in terms of sensitivity.
Bellin:2009aa: Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species
D. Bellin and A. Ferrarini and A. Chimento and O. Kaiser and N. Levenkova and P. Bouffard and M. Delledonne
BMC Genomics 10 555 (2009)
http://dx.doi.org/10.1186/1471-2164-10-555

BACKGROUND: The next generation sequencing technologies provide new options to characterize the transcriptome and to develop affordable tools for functional genomics. We describe here an innovative approach for this purpose and demonstrate its potential also for non-model species. RESULTS: The method we developed is based on 454 sequencing of 3' cDNA fragments from a normalized library constructed from pooled RNAs to generate, through de novo reads assembly, a large catalog of unique transcripts in organisms for which a comprehensive collection of transcripts or the complete genome sequence, is not available. This "virtual transcriptome" provides extensive coverage depth, and can be used for the setting up of a comprehensive microarray based expression analysis. We evaluated the potential of this approach by monitoring gene expression during berry maturation in Vitis vinifera as if no other sequence information was available for this species. The microarray designed on the berries' transcriptome derived from half of a 454 run detected the expression of 19,609 genes, and proved to be more informative than one of the most comprehensive grape microarrays available to date, the GrapeArray 1.2 developed by the Italian-French Public Consortium for Grapevine Genome Characterization, which could detect the expression of 15,556 genes in the same samples. CONCLUSION: This approach provides a powerful method to rapidly build up an extensive catalog of unique transcripts that can be successfully used to develop a microarray for large scale analysis of gene expression in any species, without the need for prior sequence knowledge.
Alagna:2009aa: Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development
F. Alagna and N. D'Agostino and L. Torchia and M. Servili and R. Rao and M. Pietrella and G. Giuliano and M. L. Chiusano and L. Baldoni and G. Perrotta
BMC Genomics 10 399 (2009)
http://dx.doi.org/10.1186/1471-2164-10-399

BACKGROUND: Despite its primary economic importance, genomic information on olive tree is still lacking. 454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and to identify genes involved in expression of fruit quality traits. RESULTS: Fruits of Coratina, a widely cultivated variety characterized by a very high phenolic content, and Tendellone, an oleuropein-lacking natural variant, were used as starting material for monitoring the transcriptome. Four different cDNA libraries were sequenced, respectively at the beginning and at the end of drupe development. A total of 261,485 reads were obtained, for an output of about 58 Mb. Raw sequence data were processed using a four step pipeline procedure and data were stored in a relational database with a web interface. CONCLUSION: Massively parallel sequencing of different fruit cDNA collections has provided large scale information about the structure and putative function of gene transcripts accumulated during fruit development. Comparative transcript profiling allowed the identification of differentially expressed genes with potential relevance in regulating the fruit metabolism and phenolic content during ripening.
Rinaldi:2014aa: Comparison of the isomerization mechanisms of human melanopsin and invertebrate and vertebrate rhodopsins
S. Rinaldi and F. Melaccio and S. Gozem and F. Fanelli and M. Olivucci
Proc Natl Acad Sci U S A 111 1714-9 (2014)
http://dx.doi.org/10.1073/pnas.1309508111

Comparative modeling and ab initio multiconfigurational quantum chemistry are combined to investigate the reactivity of the human nonvisual photoreceptor melanopsin. It is found that both the thermal and photochemical isomerization of the melanopsin 11-cis retinal chromophore occur via a space-saving mechanism involving the unidirectional, counterclockwise twisting of the =C11H-C12H= moiety with respect to its Lys340-linked frame as proposed by Warshel for visual pigments [Warshel A (1976) Nature 260(5553):679-683]. A comparison with the mechanisms documented for vertebrate (bovine) and invertebrate (squid) visual photoreceptors shows that such a mechanism is not affected by the diversity of the three chromophore cavities. Despite such invariance, trajectory computations indicate that although all receptors display less than 100 fs excited state dynamics, human melanopsin decays from the excited state ∼40 fs earlier than bovine rhodopsin. Some diversity is also found in the energy barriers controlling thermal isomerization. Human melanopsin features the highest computed barrier which appears to be ∼2.5 kcal mol(-1) higher than that of bovine rhodopsin. When assuming the validity of both the reaction speed/quantum yield correlation discussed by Warshel, Mathies and coworkers [Weiss RM, Warshel A (1979) J Am Chem Soc 101:6131-6133; Schoenlein RW, Peteanu LA, Mathies RA, Shank CV (1991) Science 254(5030):412-415] and of a relationship between thermal isomerization rate and thermal activation of the photocycle, melanopsin turns out to be a highly sensitive pigment consistent with the low number of melanopsin-containing cells found in the retina and with the extraretina location of melanopsin in nonmammalian vertebrates.
Sannino:2014aa: COMT Genetic Reduction Produces Sexually Divergent Effects on Cortical Anatomy and Working Memory in Mice and Humans
S. Sannino and A. Gozzi and A. Cerasa and F. Piras and D. Scheggia and F. Managò and M. Damiano and A. Galbusera and L. C. Erickson and D. De Pietri Tonelli and A. Bifone and S. A. Tsaftaris and C. Caltagirone and D. R. Weinberger and G. Spalletta and F. Papaleo
Cereb Cortex (2014)
http://dx.doi.org/10.1093/cercor/bhu053

Genetic variations in catechol-O-methyltransferase (COMT) that modulate cortical dopamine have been associated with pleiotropic behavioral effects in humans and mice. Recent data suggest that some of these effects may vary among sexes. However, the specific brain substrates underlying COMT sexual dimorphisms remain unknown. Here, we report that genetically driven reduction in COMT enzyme activity increased cortical thickness in the prefrontal cortex (PFC) and postero-parieto-temporal cortex of male, but not female adult mice and humans. Dichotomous changes in PFC cytoarchitecture were also observed: reduced COMT increased a measure of neuronal density in males, while reducing it in female mice. Consistent with the neuroanatomical findings, COMT-dependent sex-specific morphological brain changes were paralleled by divergent effects on PFC-dependent working memory in both mice and humans. These findings emphasize a specific sex-gene interaction that can modulate brain morphological substrates with influence on behavioral outcomes in healthy subjects and, potentially, in neuropsychiatric populations.
Calabrese:2009aa: Cortical lesions in primary progressive multiple sclerosis: a 2-year longitudinal MR study
M. Calabrese and M. A. Rocca and M. Atzori and I. Mattisi and V. Bernardi and A. Favaretto and L. Barachino and C. Romualdi and L. Rinaldi and P. Perini and P. Gallo and M. Filippi
Neurology 72 1330-6 (2009)
http://dx.doi.org/10.1212/WNL.0b013e3181a0fee5

BACKGROUND: In primary progressive multiple sclerosis (PPMS), a discrepancy exists between the modest brain white matter (WM) lesion burden and the severity of neurologic disability. Double-inversion recovery (DIR) sequences have improved MRI sensitivity in the detection of cortical lesions (CLs) in patients with relapsing-onset MS. OBJECTIVE: This 2-year longitudinal study was designed to assess the frequency, extent, and rate of formation of CLs in PPMS and their relationship with T2 lesion volume (LV), gray matter (GM) atrophy, and disability. METHODS: Forty-eight patients with PPMS underwent clinical and magnetic resonance examinations at baseline and after 2 years. The number and volume of CLs, WM T2 LV, and GM fraction (GMf) were assessed at baseline and at follow-up. RESULTS: At baseline, CLs were detected in 81.2% of patients with PPMS. At least one new CL was found in 28 patients during the follow-up. In patients with PPMS, CL and T2 WM LVs increased over the follow-up. At baseline, CL number and volumes were significantly correlated with T2 WM LV, GMf, disease duration, and Expanded Disability Status Scale score, as well as with increasing GM atrophy and disability during the follow-up. A multivariate analysis showed that CL volume at baseline was an independent predictor of percentage GM volume change and disability accumulation during the subsequent 2-year period. CONCLUSIONS: Cortical lesions are a frequent finding in primary progressive multiple sclerosis. The extent of such abnormalities is associated with the extent of cortical atrophy and clinical disability, and is able to predict their changes over a medium time period.
Aghaeepour:2013aa: Critical assessment of automated flow cytometry data analysis techniques
N. Aghaeepour and G. Finak and FlowCAP Consortium and DREAM Consortium and H. Hoos and T. R. Mosmann and R. Brinkman and R. Gottardo and R. H. Scheuermann
Nat Methods 10 228-38 (2013)
http://dx.doi.org/10.1038/nmeth.2365

Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational methods for identifying cell populations in multidimensional FCM data. The Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP) challenges were established to compare the performance of these methods on two tasks: (i) mammalian cell population identification, to determine whether automated algorithms can reproduce expert manual gating and (ii) sample classification, to determine whether analysis pipelines can identify characteristics that correlate with external variables (such as clinical outcome). This analysis presents the results of the first FlowCAP challenges. Several methods performed well as compared to manual gating or external variables using statistical performance measures, which suggests that automated methods have reached a sufficient level of maturity and accuracy for reliable use in FCM data analysis.
Moult:2011aa: Critical assessment of methods of protein structure prediction (CASP)--round IX
J. Moult and K. Fidelis and A. Kryshtafovych and A. Tramontano
Proteins 79 Suppl 10 1-5 (2011)
http://dx.doi.org/10.1002/prot.23200

This article is an introduction to the special issue of the journal PROTEINS, dedicated to the ninth Critical Assessment of Structure Prediction (CASP) experiment to assess the state of the art in protein structure modeling. The article describes the conduct of the experiment, the categories of prediction included, and outlines the evaluation and assessment procedures. Methods for modeling protein structure continue to advance, although at a more modest pace than in the early CASP experiments. CASP developments of note are indications of improvement in model accuracy for some classes of target, an improved ability to choose the most accurate of a set of generated models, and evidence of improvement in accuracy for short "new fold" models. In addition, a new analysis of regions of models not derivable from the most obvious template structure has revealed better performance than expected.
Cagliani:2013aa: Crohn's disease loci are common targets of protozoa-driven selection
R. Cagliani and U. Pozzoli and D. Forni and A. Cassinotti and M. Fumagalli and M. Giani and M. Fichera and M. Lombardini and S. Ardizzone and R. Asselta and R. de Franchis and S. Riva and M. Biasin and G. P. Comi and N. Bresolin and M. Clerici and M. Sironi
Mol Biol Evol 30 1077-87 (2013)
http://dx.doi.org/10.1093/molbev/mst020

Previous studies indicated that a few risk variants for autoimmune diseases are subject to pathogen-driven selection. Nonetheless, the proportion of risk loci that has been targeted by pathogens and the type of infectious agent(s) that exerted the strongest pressure remain to be evaluated. We assessed whether different pathogens exerted a pressure on known Crohn's disease (CD) risk variants and demonstrate that these single-nucleotide polymorphisms (SNPs) are preferential targets of protozoa-driven selection (P = 0.008). In particular, 19% of SNPs associated with CD have been subject to protozoa-driven selective pressure. Analysis of P values from genome-wide association studies (GWASs) and meta-analyses indicated that protozoan-selected SNPs display significantly stronger association with CD compared with nonselected variants. This same behavior was not observed for GWASs of other autoimmune diseases. Thus, we integrated selection signatures and meta-analysis results to prioritize five genic SNPs for replication in an Italian cohort. Three SNPs were significantly associated with CD risk, and combination with meta-analysis results yielded P values < 4 × 10(-6). The bona fide risk alleles are located in ARHGEF2, an interactor of NOD2, NSF, a gene involved in autophagy, and HEBP1, encoding a possible mediator of inflammation. Pathway analysis indicated that ARHGEF2 and NSF participate in a molecular network, which also contains VAMP3 (previously associated to CD) and is centered around miR-31 (known to be disregulated in CD). Thus, we show that protozoa-driven selective pressure had a major role in shaping predisposition to CD. We next used this information for the identification of three bona fide novel susceptibility loci.
Osnato:2010aa: Cross talk between the KNOX and ethylene pathways is mediated by intron-binding transcription factors in barley
M. Osnato and M. R. Stile and Y. Wang and D. Meynard and S. Curiale and E. Guiderdoni and Y. Liu and D. S. Horner and P. B. F. Ouwerkerk and C. Pozzi and K. J. Müller and F. Salamini and L. Rossini
Plant Physiol 154 1616-32 (2010)
http://dx.doi.org/10.1104/pp.110.161984

In the barley (Hordeum vulgare) Hooded (Kap) mutant, the duplication of a 305-bp intron sequence leads to the overexpression of the Barley knox3 (Bkn3) gene, resulting in the development of an extra flower in the spikelet. We used a one-hybrid screen to identify four proteins that bind the intron-located regulatory element (Kap intron-binding proteins). Three of these, Barley Ethylene Response Factor1 (BERF1), Barley Ethylene Insensitive Like1 (BEIL1), and Barley Growth Regulating Factor1 (BGRF1), were characterized and their in vitro DNA-binding capacities verified. Given the homology of BERF1 and BEIL1 to ethylene signaling proteins, we investigated if these factors might play a dual role in intron-mediated regulation and ethylene response. In transgenic rice (Oryza sativa), constitutive expression of the corresponding genes produced phenotypic alterations consistent with perturbations in ethylene levels and variations in the expression of a key gene of ethylene biosynthesis. In barley, ethylene treatment results in partial suppression of the Kap phenotype, accompanied by up-regulation of BERF1 and BEIL1 expression, followed by down-regulation of Bkn3 mRNA levels. In rice protoplasts, BEIL1 activates the expression of a reporter gene driven by the 305-bp intron element, while BERF1 can counteract this activation. Thus, BEIL1 and BERF1, likely in association with other Kap intron-binding proteins, should mediate the fine-tuning of Bkn3 expression by ethylene. We propose a hypothesis for the cross talk between the KNOX and ethylene pathways.
Zambelli:2012aa: Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets
F. Zambelli and G. M. Prazzoli and G. Pesole and G. Pavesi
Nucleic Acids Res 40 W510-5 (2012)
http://dx.doi.org/10.1093/nar/gks483

The regulation of transcription of eukaryotic genes is a very complex process, which involves interactions between transcription factors (TFs) and DNA, as well as other epigenetic factors like histone modifications, DNA methylation, and so on, which nowadays can be studied and characterized with techniques like ChIP-Seq. Cscan is a web resource that includes a large collection of genome-wide ChIP-Seq experiments performed on TFs, histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes' loci. The input can be a cluster of co-expressed genes, or any other set of genes sharing a common regulatory profile. Users can thus single out which TFs are likely to be common regulators of the genes, and their respective correlations. Also, by examining results on promoter activation, transcription, histone modifications, polymerase binding and so on, users can investigate the effect of the TFs (activation or repression of transcription) as well as of the cell or tissue specificity of the genes' regulation and expression. The web interface is free for use, and there is no login requirement. Available at: http://www.beaconlab.it/cscan.
Haas:2013aa: De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
B. J. Haas and A. Papanicolaou and M. Yassour and M. Grabherr and P. D. Blood and J. Bowden and M. B. Couger and D. Eccles and B. Li and M. Lieber and M. D. Macmanes and M. Ott and J. Orvis and N. Pochet and F. Strozzi and N. Weeks and R. Westerman and T. William and C. N. Dewey and R. Henschel and R. D. Leduc and N. Friedman and A. Regev
Nat Protoc 8 1494-512 (2013)
http://dx.doi.org/10.1038/nprot.2013.084

De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.
Minguez:2012aa: Deciphering a global network of functionally associated post-translational modifications
P. Minguez and L. Parca and F. Diella and D. R. Mende and R. Kumar and M. Helmer-Citterich and A.-C. Gavin and V. van Noort and P. Bork
Mol Syst Biol 8 599 (2012)
http://dx.doi.org/10.1038/msb.2012.31

Various post-translational modifications (PTMs) fine-tune the functions of almost all eukaryotic proteins, and co-regulation of different types of PTMs has been shown within and between a number of proteins. Aiming at a more global view of the interplay between PTM types, we collected modifications for 13 frequent PTM types in 8 eukaryotes, compared their speed of evolution and developed a method for measuring PTM co-evolution within proteins based on the co-occurrence of sites across eukaryotes. As many sites are still to be discovered, this is a considerable underestimate, yet, assuming that most co-evolving PTMs are functionally associated, we found that PTM types are vastly interconnected, forming a global network that comprise in human alone >50,000 residues in about 6000 proteins. We predict substantial PTM type interplay in secreted and membrane-associated proteins and in the context of particular protein domains and short-linear motifs. The global network of co-evolving PTM types implies a complex and intertwined post-translational regulation landscape that is likely to regulate multiple functional states of many if not all eukaryotic proteins.
Falconi:2009aa: Deciphering the structural properties that confer stability to a DNA nanocage
M. Falconi and F. Oteri and G. Chillemi and F. F. Andersen and D. Tordrup and C. L. P. Oliveira and J. S. Pedersen and B. R. Knudsen and A. Desideri
ACS Nano 3 1813-22 (2009)
http://dx.doi.org/10.1021/nn900468y

A DNA nanocage has been recently characterized by small-angle X-ray scattering (SAXS) and cryo-transmission electron microscopy as a DNA octahedron having a central cavity larger than the apertures in the surrounding DNA lattice. Starting from the SAXS data, a DNA nanocage has been modeled and simulated by classical molecular dynamics to evaluate in silico its structural properties and stability. Global properties, principal component analysis, and DNA geometrical parameters, calculated along the entire trajectory, indicate that the cage is stable and that the B-DNA conformation, also if slightly distorted, is maintained for all the simulation time. Starting from the initial model, the nanocage scaffold undergoes a contraction of the thymidine strands, connecting the DNA double helices, suggesting that the length of the thymidine strands is a crucial aspect in the modulation of the nanocage stability. A comparison of the average structure as obtained from the simulation shows good agreement with the SAXS experimental data.
De-Grassi:2014aa: Deep sequencing of the X chromosome reveals the proliferation history of colorectal adenomas
A. De Grassi and F. Iannelli and M. Cereda and S. Volorio and V. Melocchi and A. Viel and G. Basso and L. Laghi and M. Caselle and F. D. Ciccarelli
Genome Biol 15 437 (2014)
http://dx.doi.org/10.1186/s13059-014-0437-8

BACKGROUND: Mismatch repair deficient colorectal adenomas are composed of transformed cells that descend from a common founder and progressively accumulate genomic alterations. The proliferation history of these tumors is still largely unknown. Here we present a novel approach to rebuild the proliferation trees that recapitulate the history of individual colorectal adenomas by mapping the progressive acquisition of somatic point mutations during tumor growth. RESULTS: Using our approach, we called high and low frequency mutations acquired in the X chromosome of four mismatch repair deficient colorectal adenomas deriving from male individuals. We clustered these mutations according to their frequencies and rebuilt the proliferation trees directly from the mutation clusters using a recursive algorithm. The trees of all four lesions were formed of a dominant subclone that co-existed with other genetically heterogeneous subpopulations of cells. However, despite this similar hierarchical organization, the growth dynamics varied among and within tumors, likely depending on a combination of tumor-specific genetic and environmental factors. CONCLUSIONS: Our study provides insights into the biological properties of individual mismatch repair deficient colorectal adenomas that may influence their growth and also the response to therapy. Extended to other solid tumors, our novel approach could inform on the mechanisms of cancer progression and on the best treatment choice.
Botti:2011aa: Developmental factor IRF6 exhibits tumor suppressor activity in squamous cell carcinomas
E. Botti and G. Spallone and F. Moretti and B. Marinari and V. Pinetti and S. Galanti and P. D. De Meo and F. De Nicola and F. Ganci and T. Castrignanò and G. Pesole and S. Chimenti and L. Guerrini and M. Fanciulli and G. Blandino and M. Karin and A. Costanzo
Proc Natl Acad Sci U S A 108 13710-5 (2011)
http://dx.doi.org/10.1073/pnas.1110931108

The transcription factor interferon regulatory factor 6 (IRF6) regulates craniofacial development and epidermal proliferation. We recently showed that IRF6 is a component of a regulatory feedback loop that controls the proliferative potential of epidermal cells. IRF6 is transcriptionally activated by p63 and induces its proteasome-mediated down-regulation, thereby limiting keratinocyte proliferative potential. We hypothesized that IRF6 may also be involved in skin carcinogenesis. Hence, we analyzed IRF6 expression in a large series of squamous cell carcinomas (SCCs) and found a strong down-regulation of IRF6 that correlated with tumor invasive and differentiation status. IRF6 down-regulation in SCC cell lines and primary tumors correlates with methylation on a CpG dinucleotide island located in its promoter region. To identify the molecular mechanisms regulating IRF6 potential tumor suppressive activity, we performed a genome-wide analysis by combining ChIP sequencing for IRF6 binding sites and gene expression profiling in primary human keratinocytes after siRNA-mediated IRF6 depletion. We observed dysregulation of cell cycle-related genes and genes involved in differentiation, cell adhesion, and cell-cell contact. Many of these genes were direct IRF6 targets. We also performed in vitro invasion assays showing that IRF6 down-regulation promotes invasive behavior and that reintroduction of IRF6 into SCC cells strongly inhibits cell growth. These results indicate a function for IRF6 in suppression of tumorigenesis in stratified epithelia.
Paris:2012aa: Direct regulation of microRNA biogenesis and expression by estrogen receptor beta in hormone-responsive breast cancer
O. Paris and L. Ferraro and O. M. V. Grober and M. Ravo and M. R. De Filippo and G. Giurato and G. Nassa and R. Tarallo and C. Cantarella and F. Rizzo and A. Di Benedetto and M. Mottolese and V. Benes and C. Ambrosino and E. Nola and A. Weisz
Oncogene 31 4196-206 (2012)
http://dx.doi.org/10.1038/onc.2011.583

Estrogen effects on mammary epithelial and breast cancer (BC) cells are mediated by the nuclear receptors ERα and ERβ, transcription factors that display functional antagonism with each other, with ERβ acting as oncosuppressor and interfering with the effects of ERα on cell proliferation, tumor promotion and progression. Indeed, hormone-responsive, ERα+ BC cells often lack ERβ, which when present associates with a less aggressive clinical phenotype of the disease. Recent evidences point to a significant role of microRNAs (miRNAs) in BC, where specific miRNA expression profiles associate with distinct clinical and biological phenotypes of the lesion. Considering the possibility that ERβ might influence BC cell behavior via miRNAs, we compared miRNome expression in ERβ+ vs ERβ- hormone-responsive BC cells and found a widespread effect of this ER subtype on the expression pattern of these non-coding RNAs. More importantly, the expression pattern of 67 miRNAs, including 10 regulated by ERβ in BC cells, clearly distinguishes ERβ+, node-negative, from ERβ-, metastatic, mammary tumors. Molecular dissection of miRNA biogenesis revealed multiple mechanisms for direct regulation of this process by ERβ+ in BC cell nuclei. In particular, ERβ downregulates miR-30a by binding to two specific sites proximal to the gene and thereby inhibiting pri-miR synthesis. On the other hand, the receptor promotes miR-23b, -27b and 24-1 accumulation in the cell by binding in close proximity of the corresponding gene cluster and preventing in situ the inhibitory effects of ERα on pri-miR maturation by the p68/DDX5-Drosha microprocessor complex. These results indicate that cell autonomous regulation of miRNA expression is part of the mechanism of action of ERβ in BC cells and could contribute to establishment or maintenance of a less aggressive tumor phenotype mediated by this nuclear receptor.
Parisi:2010aa: Direct targets of Klf5 transcription factor contribute to the maintenance of mouse embryonic stem cell undifferentiated state
S. Parisi and L. Cozzuto and C. Tarantino and F. Passaro and S. Ciriello and L. Aloia and D. Antonini and V. De Simone and L. Pastore and T. Russo
BMC Biol 8 128 (2010)
http://dx.doi.org/10.1186/1741-7007-8-128

BACKGROUND: A growing body of evidence has shown that Krüppel-like transcription factors play a crucial role in maintaining embryonic stem cell (ESC) pluripotency and in governing ESC fate decisions. Krüppel-like factor 5 (Klf5) appears to play a critical role in these processes, but detailed knowledge of the molecular mechanisms of this function is still not completely addressed. RESULTS: By combining genome-wide chromatin immunoprecipitation and microarray analysis, we have identified 161 putative primary targets of Klf5 in ESCs. We address three main points: (1) the relevance of the pathways governed by Klf5, demonstrating that suppression or constitutive expression of single Klf5 targets robustly affect the ESC undifferentiated phenotype; (2) the specificity of Klf5 compared to factors belonging to the same family, demonstrating that many Klf5 targets are not regulated by Klf2 and Klf4; and (3) the specificity of Klf5 function in ESCs, demonstrated by the significant differences between Klf5 targets in ESCs compared to adult cells, such as keratinocytes. CONCLUSIONS: Taken together, these results, through the definition of a detailed list of Klf5 transcriptional targets in mouse ESCs, support the important and specific functional role of Klf5 in the maintenance of the undifferentiated ESC phenotype. See: http://www.biomedcental.com/1741-7007/8/125.
Cagliani:2009aa: Diverse evolutionary histories for beta-adrenoreceptor genes in humans
R. Cagliani and M. Fumagalli and U. Pozzoli and S. Riva and G. P. Comi and F. Torri and F. Macciardi and N. Bresolin and M. Sironi
Am J Hum Genet 85 64-75 (2009)
http://dx.doi.org/10.1016/j.ajhg.2009.06.005

In humans, three genes--ADRB1, ADRB2 and ADRB3--encode beta-adrenoreceptors (ADRB); these molecules mediate the action of catecholamines in multiple tissues and play pivotal roles in cardiovascular, respiratory, metabolic, and immunological functions. Genetic variants in ADRB genes have been associated with widespread diseases and conditions, but inconsistent results have often been obtained. Here, we addressed the recent evolutionary history of ADRB genes in human populations. Although ADRB1 is neutrally evolving, most tests rejected neutral evolution for ADRB2 in European, African, and Asian population samples. Analysis of inferred haplotypes for ADRB2 revealed three major clades with a coalescence time of 1-1.5 million years, suggesting that the gene is either subjected to balancing selection or undergoing a selective sweep. Haplotype analysis also revealed ethnicity-specific differences. Additionally, we observed significant deviations from Hardy-Weinberg equilibrium (HWE) for ADRB2 genotypes in distinct European cohorts; HWE deviation depends on sex (only females are in disequilibrium), and genotypes displaying maximum and minimum relative fitness differ across population samples, suggesting a complex situation possibly involving epistasis or maternal selection. Overall, our data indicate that future association studies involving ADRB2 will benefit from taking into account ethnicity-specific haplotype distributions and sex-based effects. With respect to ADRB3, our data indicate that the gene has been subjected to a selective sweep in African populations, the Trp64 variant possibly representing the selection target. Given the previous association of the ancestral ADRB3 Arg64 allele with obesity and type 2 diabetes, dietary adaptations might represent the underlying selective force.
Turroni:2012aa: Diversity of bifidobacteria within the infant gut microbiota
F. Turroni and C. Peano and D. A. Pass and E. Foroni and M. Severgnini and M. J. Claesson and C. Kerr and J. Hourihane and D. Murray and F. Fuligni and M. Gueimonde and A. Margolles and G. De Bellis and P. W. O'Toole and D. van Sinderen and J. R. Marchesi and M. Ventura
PLoS One 7 e36957 (2012)
http://dx.doi.org/10.1371/journal.pone.0036957

BACKGROUND: The human gastrointestinal tract (GIT) represents one of the most densely populated microbial ecosystems studied to date. Although this microbial consortium has been recognized to have a crucial impact on human health, its precise composition is still subject to intense investigation. Among the GIT microbiota, bifidobacteria represent an important commensal group, being among the first microbial colonizers of the gut. However, the prevalence and diversity of members of the genus Bifidobacterium in the infant intestinal microbiota has not yet been fully characterized, while some inconsistencies exist in literature regarding the abundance of this genus. METHODS/PRINCIPAL FINDINGS: In the current report, we assessed the complexity of the infant intestinal bifidobacterial population by analysis of pyrosequencing data of PCR amplicons derived from two hypervariable regions of the 16 S rRNA gene. Eleven faecal samples were collected from healthy infants of different geographical origins (Italy, Spain or Ireland), feeding type (breast milk or formula) and mode of delivery (vaginal or caesarean delivery), while in four cases, faecal samples of corresponding mothers were also analyzed. CONCLUSIONS: In contrast to several previously published culture-independent studies, our analysis revealed a predominance of bifidobacteria in the infant gut as well as a profile of co-occurrence of bifidobacterial species in the infant's intestine.
Bardini:2010aa: DNA copy-number abnormalities do not occur in infant ALL with t(4;11)/MLL-AF4
M. Bardini and R. Spinelli and S. Bungaro and E. Mangano and L. Corral and I. Cifola and G. Fazio and M. Giordan and G. Basso and G. De Rossi and A. Biondi and C. Battaglia and G. Cazzaniga
Leukemia 24 169-76 (2010)
http://dx.doi.org/10.1038/leu.2009.203

The pathogenesis of infant acute lymphoblastic leukemia (ALL) is still not well defined. Short latency to leukemia and very high concordance rate for ALL in Mixed-Lineage Leukemia (MLL)-positive infant twins suggest that the MLL rearrangement itself could be sufficient for overt leukemia. Attempts to generate a suitable mouse model for MLL-AF4-positive ALL did not thoroughly resolve the issue of whether cooperating mutations are required to reduce latency and to generate overt leukemia in vivo. In this study, we applied single-nucleotide polymorphism array technology to perform genomic profiling of 28 infant ALL cases carrying t(4;11) to detect MLL-cooperating aberrations hidden to conventional techniques and to gain new insights into infant ALL pathogenesis. In contrast to pediatric, adolescent and adult ALL cases, the MLL rearrangement in infant ALL is associated with an exceptionally low frequency of copy-number abnormalities, thus confirming the unique nature of this disease. By contrast, additional genetic aberrations are acquired at disease relapse. Small-segmental uniparental disomy traits were frequently detected, mostly constitutional, and widely distributed throughout the genome. It can be argued that the MLL rearrangement as a first hit, rather than inducing the acquisition of additional genetic lesions, has a major role to drive and hasten the onset of leukemia.
Pichiorri:2010aa: Downregulation of p53-inducible microRNAs 192, 194, and 215 impairs the p53/MDM2 autoregulatory loop in multiple myeloma development
F. Pichiorri and S.-S. Suh and A. Rocci and L. De Luca and C. Taccioli and R. Santhanam and W. Zhou and D. M. Benson, Jr and C. Hofmainster and H. Alder and M. Garofalo and G. Di Leva and S. Volinia and H.-J. Lin and D. Perrotti and M. Kuehl and R. I. Aqeilan and A. Palumbo and C. M. Croce
Cancer Cell 18 367-81 (2010)
http://dx.doi.org/10.1016/j.ccr.2010.09.005

In multiple myeloma (MM), an incurable B cell neoplasm, mutation or deletion of p53 is rarely detected at diagnosis. Using small-molecule inhibitors of MDM2, we provide evidence that miR-192, 194, and 215, which are downregulated in a subset of newly diagnosed MMs, can be transcriptionally activated by p53 and then modulate MDM2 expression. Furthermore, ectopic re-expression of these miRNAs in MM cells increases the therapeutic action of MDM2 inhibitors in vitro and in vivo by enhancing their p53-activating effects. In addition, miR-192 and 215 target the IGF pathway, preventing enhanced migration of plasma cells into bone marrow. The results suggest that these miRNAs are positive regulators of p53 and that their downregulation plays a key role in MM development.
Garofalo:2012aa: EGFR and MET receptor tyrosine kinase-altered microRNA expression induces tumorigenesis and gefitinib resistance in lung cancers
M. Garofalo and G. Romano and G. Di Leva and G. Nuovo and Y.-J. Jeon and A. Ngankeu and J. Sun and F. Lovat and H. Alder and G. Condorelli and J. A. Engelman and M. Ono and J. K. Rho and L. Cascione and S. Volinia and K. P. Nephew and C. M. Croce
Nat Med 18 74-82 (2012)
http://dx.doi.org/10.1038/nm.2577

The involvement of the MET oncogene in de novo and acquired resistance of non-small cell lung cancers (NSCLCs) to tyrosine kinase inhibitors (TKIs) has previously been reported, but the precise mechanism by which MET overexpression contributes to TKI-resistant NSCLC remains unclear. MicroRNAs (miRNAs) negatively regulate gene expression, and their dysregulation has been implicated in tumorigenesis. To understand their role in TKI-resistant NSCLCs, we examined changes in miRNA that are mediated by tyrosine kinase receptors. Here we report that miR-30b, miR-30c, miR-221 and miR-222 are modulated by both epidermal growth factor (EGF) and MET receptors, whereas miR-103 and miR-203 are controlled only by MET. We showed that these miRNAs have important roles in gefitinib-induced apoptosis and epithelial-mesenchymal transition of NSCLC cells in vitro and in vivo by inhibiting the expression of the genes encoding BCL2-like 11 (BIM), apoptotic peptidase activating factor 1 (APAF-1), protein kinase C ɛ (PKC-ɛ) and sarcoma viral oncogene homolog (SRC). These findings suggest that modulation of specific miRNAs may provide a therapeutic approach for the treatment of NSCLCs.
Oliva:2010aa: Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity
R. Oliva and G. Calamita and J. M. Thornton and M. Pellegrini-Calace
Proc Natl Acad Sci U S A 107 4135-40 (2010)
http://dx.doi.org/10.1073/pnas.0910632107

Aquaporins are homotetrameric channel proteins, which allow the diffusion of water and small solutes across biological membranes. According to their transport function, aquaporins can be divided into "orthodox aquaporins", which allow the flux of water molecules only, and "aquaglyceroporins", which facilitate the diffusion of glycerol and other small solutes in addition to water. The contribution of individual residues in the pore to the selectivity of orthodox aquaporins and aquaglyceroporins is not yet fully understood. To gain insights into aquaporin selectivity, we focused on the sequence variation and electrostatics of their channels. The continuum Poisson-Boltzmann electrostatic potential along the channel was calculated and compared for ten three-dimensional-structures which are representatives of different aquaporin subfamilies, and a panel of functionally characterized mutants, for which high-accuracy three-dimensional-models could be derived. Interestingly, specific electrostatic profiles associated with the main selectivity to water or glycerol could be identified. In particular: (i) orthodox aquaporins showed a distinctive electrostatic potential maximum at the periplasmic side of the channel around the aromatic/Arg (ar/R) constriction site; (ii) aquaporin-0 (AQP0), a mammalian aquaporin with considerably low water permeability, had an additional deep minimum at the cytoplasmic side; (iii) aquaglyceroporins showed a rather flat potential all along the channel; and (iv) the bifunctional protozoan PfAQP had an unusual all negative profile. Evaluation of electrostatics of the mutants, along with a thorough sequence analysis of the aquaporin pore-lining residues, illuminated the contribution of specific residues to the electrostatics of the channels and possibly to their selectivity.
Gould:2010aa: ELM: the status of the 2010 eukaryotic linear motif resource
C. M. Gould and F. Diella and A. Via and P. Puntervoll and C. Gemünd and S. Chabanis-Davidson and S. Michael and A. Sayadi and J. C. Bryne and C. Chica and M. Seiler and N. E. Davey and N. Haslam and R. J. Weatheritt and A. Budd and T. Hughes and J. Pas and L. Rychlewski and G. Travé and R. Aasland and M. Helmer-Citterich and R. Linding and T. J. Gibson
Nucleic Acids Res 38 D167-80 (2010)
http://dx.doi.org/10.1093/nar/gkp1016

Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. Many thousands of linear motif instances, most notably phosphorylation sites, have now been reported. Although clearly very abundant, linear motifs are difficult to predict de novo in protein sequences due to the difficulty of obtaining robust statistical assessments. The ELM resource at http://elm.eu.org/ provides an expanding knowledge base, currently covering 146 known motifs, with annotation that includes >1300 experimentally reported instances. ELM is also an exploratory tool for suggesting new candidates of known linear motifs in proteins of interest. Information about protein domains, protein structure and native disorder, cellular and taxonomic contexts is used to reduce or deprecate false positive matches. Results are graphically displayed in a 'Bar Code' format, which also displays known instances from homologous proteins through a novel 'Instance Mapper' protocol based on PHI-BLAST. ELM server output provides links to the ELM annotation as well as to a number of remote resources. Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation.
Dinkel:2012aa: ELM--the database of eukaryotic linear motifs
H. Dinkel and S. Michael and R. J. Weatheritt and N. E. Davey and K. Van Roey and B. Altenberg and G. Toedt and B. Uyar and M. Seiler and A. Budd and L. Jödicke and M. A. Dammert and C. Schroeter and M. Hammer and T. Schmidt and P. Jehl and C. McGuigan and M. Dymecka and C. Chica and K. Luck and A. Via and A. Chatr-Aryamontri and N. Haslam and G. Grebnev and R. J. Edwards and M. O. Steinmetz and H. Meiselbach and F. Diella and T. J. Gibson
Nucleic Acids Res 40 D242-51 (2012)
http://dx.doi.org/10.1093/nar/gkr1064

Linear motifs are short, evolutionarily plastic components of regulatory proteins and provide low-affinity interaction interfaces. These compact modules play central roles in mediating every aspect of the regulatory functionality of the cell. They are particularly prominent in mediating cell signaling, controlling protein turnover and directing protein localization. Given their importance, our understanding of motifs is surprisingly limited, largely as a result of the difficulty of discovery, both experimentally and computationally. The Eukaryotic Linear Motif (ELM) resource at http://elm.eu.org provides the biological community with a comprehensive database of known experimentally validated motifs, and an exploratory tool to discover putative linear motifs in user-submitted protein sequences. The current update of the ELM database comprises 1800 annotated motif instances representing 170 distinct functional classes, including approximately 500 novel instances and 24 novel classes. Several older motif class entries have been also revisited, improving annotation and adding novel instances. Furthermore, addition of full-text search capabilities, an enhanced interface and simplified batch download has improved the overall accessibility of the ELM data. The motif discovery portion of the ELM resource has added conservation, and structural attributes have been incorporated to aid users to discriminate biologically relevant motifs from stochastically occurring non-functional instances.
Marcello:2013aa: Endocytosis of synaptic ADAM10 in neuronal plasticity and Alzheimer's disease
E. Marcello and C. Saraceno and S. Musardo and H. Vara and A. G. de la Fuente and S. Pelucchi and D. Di Marino and B. Borroni and A. Tramontano and I. Pérez-Otaño and A. Padovani and M. Giustetto and F. Gardoni and M. Di Luca
J Clin Invest 123 2523-38 (2013)
http://dx.doi.org/10.1172/JCI65401

A disintegrin and metalloproteinase 10 (ADAM10), a disintegrin and metalloproteinase that resides in the postsynaptic densities (PSDs) of excitatory synapses, has previously been shown to limit β-amyloid peptide (Aβ) formation in Alzheimer's disease (AD). ADAM10 also plays a critical role in regulating functional membrane proteins at the synapse. Using human hippocampal homogenates, we found that ADAM10 removal from the plasma membrane was mediated by clathrin-dependent endocytosis. Additionally, we identified the clathrin adaptor AP2 as an interacting partner of a previously uncharacterized atypical binding motif in the ADAM10 C-terminal domain. This domain was required for ADAM10 endocytosis and modulation of its plasma membrane levels. We found that the ADAM10/AP2 association was increased in the hippocampi of AD patients compared with healthy controls. Long-term potentiation (LTP) in hippocampal neuronal cultures induced ADAM10 endocytosis through AP2 association and decreased surface ADAM10 levels and activity. Conversely, long-term depression (LTD) promoted ADAM10 synaptic membrane insertion and stimulated its activity. ADAM10 interaction with the synapse-associated protein-97 (SAP97) was necessary for LTD-induced ADAM10 trafficking and required for LTD maintenance and LTD-induced changes in spine morphogenesis. These data identify and characterize a mechanism controlling ADAM10 localization and activity at excitatory synapses that is relevant to AD pathogenesis.
Shukla:2013aa: Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma
R. Shukla and K. R. Upton and M. Muñoz-Lopez and D. J. Gerhardt and M. E. Fisher and T. Nguyen and P. M. Brennan and J. K. Baillie and A. Collino and S. Ghisletti and S. Sinha and F. Iannelli and E. Radaelli and A. Dos Santos and D. Rapoud and C. Guettier and D. Samuel and G. Natoli and P. Carninci and F. D. Ciccarelli and J. L. Garcia-Perez and J. Faivre and G. J. Faulkner
Cell 153 101-11 (2013)
http://dx.doi.org/10.1016/j.cell.2013.02.032

LINE-1 (L1) retrotransposons are mobile genetic elements comprising ~17% of the human genome. New L1 insertions can profoundly alter gene function and cause disease, though their significance in cancer remains unclear. Here, we applied enhanced retrotransposon capture sequencing (RC-seq) to 19 hepatocellular carcinoma (HCC) genomes and elucidated two archetypal L1-mediated mechanisms enabling tumorigenesis. In the first example, 4/19 (21.1%) donors presented germline retrotransposition events in the tumor suppressor mutated in colorectal cancers (MCC). MCC expression was ablated in each case, enabling oncogenic β-catenin/Wnt signaling. In the second example, suppression of tumorigenicity 18 (ST18) was activated by a tumor-specific L1 insertion. Experimental assays confirmed that the L1 interrupted a negative feedback loop by blocking ST18 repression of its enhancer. ST18 was also frequently amplified in HCC nodules from Mdr2(-/-) mice, supporting its assignment as a candidate liver oncogene. These proof-of-principle results substantiate L1-mediated retrotransposition as an important etiological factor in HCC.
Souza-Rocha-Simonini:2010aa: Epigenetically deregulated microRNA-375 is involved in a positive feedback loop with estrogen receptor alpha in breast cancer cells
P. de Souza Rocha Simonini and A. Breiling and N. Gupta and M. Malekpour and M. Youns and R. Omranipour and F. Malekpour and S. Volinia and C. M. Croce and H. Najmabadi and S. Diederichs and O. Sahin and D. Mayer and F. Lyko and J. D. Hoheisel and Y. Riazalhosseini
Cancer Res 70 9175-84 (2010)
http://dx.doi.org/10.1158/0008-5472.CAN-10-1318

Estrogen receptor α (ERα) upregulation causes abnormal cell proliferation in about two thirds of breast cancers, yet understanding of the underlying mechanisms remains incomplete. Here, we show that high expression of the microRNA miR-375 in ERα-positive breast cell lines is a key driver of their proliferation. miR-375 overexpression was caused by loss of epigenetic marks including H3K9me2 and local DNA hypomethylation, dissociation of the transcriptional repressor CTCF from the miR-375 promoter, and interactions of ERα with regulatory regions of miR-375. Inhibiting miR-375 in ERα-positive MCF-7 cells resulted in reduced ERα activation and cell proliferation. A combination of expression profiling from tumor samples and miRNA target prediction identified RASD1 as a potential miR-375 target. Mechanistic investigations revealed that miR-375 regulates RASD1 by targeting the 3' untranslated region in RASD1 mRNA. Additionally, we found that RASD1 negatively regulates ERα expression. Our findings define a forward feedback pathway in control of ERα expression, highlighting new strategies to treat ERα-positive invasive breast tumors.
Marcucci:2014aa: Epigenetics meets genetics in acute myeloid leukemia: clinical impact of a novel seven-gene score
G. Marcucci and P. Yan and K. Maharry and D. Frankhouser and D. Nicolet and K. H. Metzeler and J. Kohlschmidt and K. Mrózek and Y.-Z. Wu and D. Bucci and J. P. Curfman and S. P. Whitman and A.-K. Eisfeld and J. H. Mendler and S. Schwind and H. Becker and C. Bär and A. J. Carroll and M. R. Baer and M. Wetzler and T. H. Carter and B. L. Powell and J. E. Kolitz and J. C. Byrd and C. Plass and R. Garzon and M. A. Caligiuri and R. M. Stone and S. Volinia and R. Bundschuh and C. D. Bloomfield
J Clin Oncol 32 548-56 (2014)
http://dx.doi.org/10.1200/JCO.2013.50.6337

PURPOSE: Molecular risk stratification of acute myeloid leukemia (AML) is largely based on genetic markers. However, epigenetic changes, including DNA methylation, deregulate gene expression and may also have prognostic impact. We evaluated the clinical relevance of integrating DNA methylation and genetic information in AML. METHODS: Next-generation sequencing analysis of methylated DNA identified differentially methylated regions (DMRs) associated with prognostic mutations in older (≥ 60 years) cytogenetically normal (CN) patients with AML (n = 134). Genes with promoter DMRs and expression levels significantly associated with outcome were used to compute a prognostic gene expression weighted summary score that was tested and validated in four independent patient sets (n = 355). RESULTS: In the training set, we identified seven genes (CD34, RHOC, SCRN1, F2RL1, FAM92A1, MIR155HG, and VWA8) with promoter DMRs and expression associated with overall survival (OS; P ≤ .001). Each gene had high DMR methylation and lower expression, which were associated with better outcome. A weighted summary expression score of the seven gene expression levels was computed. A low score was associated with a higher complete remission (CR) rate and longer disease-free survival and OS (P < .001 for all end points). This was validated in multivariable models and in two younger (< 60 years) and two older independent sets of patients with CN-AML. Considering the seven genes individually, the fewer the genes with high expression, the better the outcome. Younger and older patients with no genes or one gene with high expression had the best outcomes (CR rate, 94% and 87%, respectively; 3-year OS, 80% and 42%, respectively). CONCLUSION: A seven-gene score encompassing epigenetic and genetic prognostic information identifies novel AML subsets that are meaningful for treatment guidance.
Cicatiello:2010aa: Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs
L. Cicatiello and M. Mutarelli and O. M. V. Grober and O. Paris and L. Ferraro and M. Ravo and R. Tarallo and S. Luo and G. P. Schroth and M. Seifert and C. Zinser and M. L. Chiusano and A. Traini and M. De Bortoli and A. Weisz
Am J Pathol 176 2113-30 (2010)
http://dx.doi.org/10.2353/ajpath.2010.090837

Luminal-like breast tumor cells express estrogen receptor alpha (ERalpha), a member of the nuclear receptor family of ligand-activated transcription factors that controls their proliferation, survival, and functional status. To identify the molecular determinants of this hormone-responsive tumor phenotype, a comprehensive genome-wide analysis was performed in estrogen stimulated MCF-7 and ZR-75.1 cells by integrating time-course mRNA expression profiling with global mapping of genomic ERalpha binding sites by chromatin immunoprecipitation coupled to massively parallel sequencing, microRNA expression profiling, and in silico analysis of transcription units and receptor binding regions identified. All 1270 genes that were found to respond to 17beta-estradiol in both cell lines cluster in 33 highly concordant groups, each of which showed defined kinetics of RNA changes. This hormone-responsive gene set includes several direct targets of ERalpha and is organized in a gene regulation cascade, stemming from ligand-activated receptor and reaching a large number of downstream targets via AP-2gamma, B-cell activating transcription factor, E2F1 and 2, E74-like factor 3, GTF2IRD1, hairy and enhancer of split homologue-1, MYB, SMAD3, RARalpha, and RXRalpha transcription factors. MicroRNAs are also integral components of this gene regulation network because miR-107, miR-424, miR-570, miR-618, and miR-760 are regulated by 17beta-estradiol along with other microRNAs that can target a significant number of transcripts belonging to one or more estrogen-responsive gene clusters.
Dieci:2009aa: Eukaryotic snoRNAs: a paradigm for gene expression flexibility
G. Dieci and M. Preti and B. Montanini
Genomics 94 83-8 (2009)
http://dx.doi.org/10.1016/j.ygeno.2009.05.002

Small nucleolar RNAs (snoRNAs) are one of the most ancient and numerous families of non-protein-coding RNAs (ncRNAs). The main function of snoRNAs - to guide site-specific rRNA modification - is the same in Archaea and all eukaryotic lineages. In contrast, as revealed by recent genomic and RNomic studies, their genomic organization and expression strategies are the most varied. Seemingly snoRNA coding units have adopted, in the course of evolution, all the possible ways of being transcribed, thus providing a unique paradigm of gene expression flexibility. By focusing on representative fungal, plant and animal genomes, we review here all the documented types of snoRNA gene organization and expression, and we provide a comprehensive account of snoRNA expressional freedom by precisely estimating the frequency, in each genome, of each type of genomic organization. We finally discuss the relevance of snoRNA genomic studies for our general understanding of ncRNA family evolution and expression in eukaryotes.
Monastyrskyy:2011aa: Evaluation of disorder predictions in CASP9
B. Monastyrskyy and K. Fidelis and J. Moult and A. Tramontano and A. Kryshtafovych
Proteins 79 Suppl 10 107-18 (2011)
http://dx.doi.org/10.1002/prot.23161

Lack of stable three-dimensional structure, or intrinsic disorder, is a common phenomenon in proteins. Naturally, unstructured regions are proven to be essential for carrying function by many proteins, and therefore identification of such regions is an important issue. CASP has been assessing the state of the art in predicting disorder regions from amino acid sequence since 2002. Here, we present the results of the evaluation of the disorder predictions submitted to CASP9. The assessment is based on the evaluation measures and procedures used in previous CASPs. The balanced accuracy and the Matthews correlation coefficient were chosen as basic measures for evaluating the correctness of binary classifications. The area under the receiver operating characteristic curve was the measure of choice for evaluating probability-based predictions of disorder. The CASP9 methods are shown to perform slightly better than the CASP7 methods but not better than the methods in CASP8. It was also shown that capability of most CASP9 methods to predict disorder decreases with increasing minimum disorder segment length.
Kryshtafovych:2011aa: Evaluation of model quality predictions in CASP9
A. Kryshtafovych and K. Fidelis and A. Tramontano
Proteins 79 Suppl 10 91-106 (2011)
http://dx.doi.org/10.1002/prot.23180

CASP has been assessing the state of the art in the a priori estimation of accuracy of protein structure prediction since 2006. The inclusion of model quality assessment category in CASP contributed to a rapid development of methods in this area. In the last experiment, 46 quality assessment groups tested their approaches to estimate the accuracy of protein models as a whole and/or on a per-residue basis. We assessed the performance of these methods predominantly on the basis of the correlation between the predicted and observed quality of the models on both global and local scales. The ability of the methods to identify the models closest to the best one, to differentiate between good and bad models, and to identify well modeled regions was also analyzed. Our evaluations demonstrate that even though global quality assessment methods seem to approach perfection point (weighted average per-target Pearson's correlation coefficients are as high as 0.97 for the best groups), there is still room for improvement. First, all top-performing methods use consensus approaches to generate quality estimates, and this strategy has its own limitations. Second, the methods that are based on the analysis of individual models lag far behind clustering techniques and need a boost in performance. The methods for estimating per-residue accuracy of models are less accurate than global quality assessment methods, with an average weighted per-model correlation coefficient in the range of 0.63-0.72 for the best 10 groups.
Cozzetto:2009aa: Evaluation of template-based models in CASP8 with standard measures
D. Cozzetto and A. Kryshtafovych and K. Fidelis and J. Moult and B. Rost and A. Tramontano
Proteins 77 Suppl 9 18-28 (2009)
http://dx.doi.org/10.1002/prot.22561

The strategy for evaluating template-based models submitted to CASP has continuously evolved from CASP1 to CASP5, leading to a standard procedure that has been used in all subsequent editions. The established approach includes methods for calculating the quality of each individual model, for assigning scores based on the distribution of the results for each target and for computing the statistical significance of the differences in scores between prediction methods. These data are made available to the assessor of the template-based modeling category, who uses them as a starting point for further evaluations and analyses. This article describes the detailed workflow of the procedure, provides justifications for a number of choices that are customarily made for CASP data evaluation, and reports the results of the analysis of template-based predictions at CASP8.
Fiorani:2009aa: Evidence of the crucial role of the linker domain on the catalytic activity of human topoisomerase I by experimental and simulative characterization of the Lys681Ala mutant
P. Fiorani and C. Tesauro and G. Mancini and G. Chillemi and I. D'Annessa and G. Graziani and L. Tentori and A. Muzi and A. Desideri
Nucleic Acids Res 37 6849-58 (2009)
http://dx.doi.org/10.1093/nar/gkp669

The functional and structural-dynamical properties of the Lys681Ala mutation in the human topoisomerase IB linker domain have been investigated by catalytic assays and molecular dynamics simulation. The mutant is characterized by a comparable cleavage and a strongly reduced religation rate when compared to the wild type protein. The mutant also displays perturbed linker dynamics, as shown by analysis of the principal components of the motion, and a reduced electrostatic interaction with DNA. Inspection of the inter atomic distances in proximity of the active site shows that in the mutant the distance between the amino group of Lys532 side chain and the 5' OH of the scissile phosphate is longer than the wild type enzyme, providing an atomic explanation for the reduced religation rate of the mutant. Taken together these results indicate the existence of a long range communication between the linker domain and the active site region and points out the crucial role of the linker in the modulation of the catalytic activity.
Sironi:2014aa: Evolutionary analysis identifies an MX2 haplotype associated with natural resistance to HIV-1 infection
M. Sironi and M. Biasin and R. Cagliani and F. Gnudi and I. Saulle and S. Ibba and G. Filippi and S. Yahyaei and C. Tresoldi and S. Riva and D. Trabattoni and L. De Gioia and S. Lo Caputo and F. Mazzotta and D. Forni and C. Pontremoli and J. A. Pineda and U. Pozzoli and A. Rivero-Juarez and A. Caruz and M. Clerici
Mol Biol Evol 31 2402-14 (2014)
http://dx.doi.org/10.1093/molbev/msu193

The protein product of the myxovirus resistance 2 (MX2) gene restricts HIV-1 and simian retroviruses. We demonstrate that MX2 evolved adaptively in mammals with distinct sites representing selection targets in distinct branches; selection mainly involved residues in loop 4, previously shown to carry antiviral determinants. Modeling data indicated that positively selected sites form a continuous surface on loop 4, which folds into two antiparallel α-helices protruding from the stalk domain. A population genetics-phylogenetics approach indicated that the coding region of MX2 mainly evolved under negative selection in the human lineage. Nonetheless, population genetic analyses demonstrated that natural selection operated on MX2 during the recent history of human populations: distinct selective events drove the frequency increase of two haplotypes in the populations of Asian and European ancestry. The Asian haplotype carries a susceptibility allele for melanoma; the European haplotype is tagged by rs2074560, an intronic variant. Analyses performed on three independent European cohorts of HIV-1-exposed seronegative individuals with different geographic origin and distinct exposure route showed that the ancestral (G) allele of rs2074560 protects from HIV-1 infection with a recessive effect (combined P = 1.55 × 10(-4)). The same allele is associated with lower in vitro HIV-1 replication and increases MX2 expression levels in response to IFN-α. Data herein exploit evolutionary information to identify a novel host determinant of HIV-1 infection susceptibility.
Cagliani:2013ab: Evolutionary analysis of the contact system indicates that kininogen evolved adaptively in mammals and in human populations
R. Cagliani and D. Forni and S. Riva and U. Pozzoli and M. Colleoni and N. Bresolin and M. Clerici and M. Sironi
Mol Biol Evol 30 1397-408 (2013)
http://dx.doi.org/10.1093/molbev/mst054

Activation of the contact system leads to the cleavage of kininogen by plasma kallikrein resulting in kinin release and in the initiation of the intrinsic pathway of coagulation. Proteolysis of kininogen also generates antimicrobial peptides (AMPs) and can be induced by diverse pathogens. Thus, the contact system is regarded as a branch of innate immunity. We performed an evolutionary analysis of contact system genes by analyzing both inter- and intraspecies diversity. Results indicated that mammalian kininogen genes evolved adaptively. Positively selected sites are located in all protein domains with the exclusion of the bradykinin region and also involve AMP sequences (including the highly effective NAT26 peptide); positively selected sites also occur at alternative cleavage sites for neutrophil-released kinins. Population genetic analysis in humans indicated that a region of the kininogen gene (KNG1) has been a target of long-standing multiallelic balancing selection and that the coalescence time of the haplotype phylogeny dates back to the split between the humans and chimpanzees. No selection signature was detected in the Pan troglodytes KNG1 gene or in human genes encoding other components of the contact system. The selection targets in human KNG1 might be accounted for by variants with transcriptional regulatory activity. Results herein indicate a continuum in selective pressure acting on different timescales and targeting KNG1. This is in line with evidences suggesting a central role for kininogen in modulating of immune response and with its being a target of an extremely diverse array of pathogen species.
Magi:2013aa: EXCAVATOR: detecting copy number variants from whole-exome sequencing data
A. Magi and L. Tattini and I. Cifola and R. D'Aurizio and M. Benelli and E. Mangano and C. Battaglia and E. Bonora and A. Kurg and M. Seri and P. Magini and B. Giusti and G. Romeo and T. Pippucci and G. De Bellis and R. Abbate and G. F. Gensini
Genome Biol 14 R120 (2013)
http://dx.doi.org/10.1186/gb-2013-14-10-r120

We developed a novel software tool, EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outperforms the other methods and is therefore a valuable tool for the investigation of CNVs in largescale projects, as well as in clinical research and diagnostics. EXCAVATOR is freely available at http://sourceforge.net/projects/excavatortool/.
Perfetto:2013aa: Exploring the diversity of SPRY/B30.2-mediated interactions
L. Perfetto and P. F. Gherardini and N. E. Davey and F. Diella and M. Helmer-Citterich and G. Cesareni
Trends Biochem Sci 38 38-46 (2013)
http://dx.doi.org/10.1016/j.tibs.2012.10.001

The SPla/Ryanodine receptor (SPRY)/B30.2 domain is one of the most common folds in higher eukaryotes. The human genome encodes 103 SPRY/B30.2 domains, several of which are involved in the immune response. Approximately 45% of human SPRY/B30.2-containing proteins are E3 ligases. The role and function of the majority of SPRY/B30.2 domains are still poorly understood, however, in several cases mutations in this domain have been linked to congenital disorders. The recent characterization of SPRY/B30.2-mediated protein interactions has provided evidence for a role of this domain as an adaptor module to assemble macromolecular complexes, analogous to Src homology (SH)2, SH3, and WW domains. However, functional and structural evidence suggests that SPRY/B30.2 is a more versatile fold, allowing a wide range of binding modes.
Leoni:2011ab: Expression of c-jun is not mandatory for mouse hepatocyte proliferation induced by two nuclear receptor ligands: TCPOBOP and T3
V. P. Leoni and G. M. Ledda-Columbano and M. Pibiri and C. Saliba and A. Perra and M. A. Kowalik and O. M. V. Grober and M. Ravo and A. Weisz and J. Locker and E. Ghiso and S. Giordano and A. Columbano
J Hepatol 55 1069-78 (2011)
http://dx.doi.org/10.1016/j.jhep.2011.02.016

BACKGROUND & AIMS: Mice lacking c-jun in the liver display impaired regeneration after partial hepatectomy (PH), and were reported to be more resistant to chemically-induced hepatocellular carcinoma (HCC). We investigated the role of c-jun in normal and preneoplastic hepatocyte proliferation induced by ligands of nuclear receptors, which cause liver hyperplasia in the absence of cell loss/death. METHODS: The effect of 1,4-bis[2-(3,5-dichloropyridyloxy)]benzene (TCPOBOP) on hepatocyte proliferation was determined in c-jun conditional knockout (c-jun(Δli)) or in mouse liver where c-jun has been silenced. To study the role of c-jun in HCC development, c-jun(Δli) and WT mice were given diethylnitrosamine (DENA) followed by repeated injections of TCPOBOP. RESULTS: Hepatocyte proliferation induced by TCPOBOP was associated with a stronger proliferative response and earlier S phase entry in c-jun(Δli) mice, compared to WT animals. Moreover, silencing of c-jun in the liver of CD-1 mice caused increased hepatocyte proliferation. A stronger hepatocyte proliferative response of c-jun(Δli) mice was observed also following treatment with a ligand of thyroid hormone receptor. Finally, loss of c-jun did not inhibit the development of HCC induced by DENA and promoted by TCPOBOP. CONCLUSIONS: (i) c-jun may, under certain conditions, negatively regulate proliferation of normal hepatocytes, (ii) c-jun is not an absolute requirement for DENA/TCPOBOP-induced HCC formation, suggesting that the therapeutic potential of c-jun/JNK inhibition in liver tumors might be impaired by an increased stimulation of cell growth due to blockade of the c-jun pathway.
Striano:2011aa: Familial temporal lobe epilepsy with psychic auras associated with a novel LGI1 mutation
P. Striano and G. Busolin and L. Santulli and E. Leonardi and A. Coppola and L. Vitiello and L. Rigon and R. Michelucci and S. C. E. Tosatto and S. Striano and C. Nobile
Neurology 76 1173-6 (2011)
http://dx.doi.org/10.1212/WNL.0b013e318212ab2e

BACKGROUND: Autosomal dominant lateral temporal epilepsy (ADLTE) is characterized by focal seizures with auditory features or aphasia. Mutations in the LGI1 gene have been reported in up to 50% of ADLTE pedigrees. We report a family with temporal lobe epilepsy characterized by psychic symptoms associated with a novel LGI1 mutation. METHODS: All participants were personally interviewed and underwent neurologic examination and video-EEG recordings. LGI1 exons were sequenced by standard methods. Mutant cDNA was transfected into human embryonic kidney 293 cells; both cell lysates and media were analyzed by Western blot. In silico modeling of the Lgi1 protein EPTP domain was carried out using the structure of WD repeat protein and manually refined. RESULTS: Three affected family members were ascertained, 2 of whom had temporal epilepsy with psychic symptoms (déjà vu, fear) but no auditory or aphasic phenomena, while the third had complex partial seizures without any aura. In all patients, we found a novel LGI1 mutation, Arg407Cys, which did not hamper protein secretion in vitro. Mapping of the mutation on a 3-dimensional protein model showed that this mutation does not induce large structural rearrangements but could destabilize interactions of Lgi1 with target proteins. CONCLUSIONS: The Arg407Cys is the first mutation with no effect on Lgi1 protein secretion. The uncommon, isolated psychic symptoms associated with it suggests that ADLTE encompasses a wider range of auras of temporal origin than hitherto reported.
DAndrea:2013aa: FIDEA: a server for the functional interpretation of differential expression analysis
D. D'Andrea and L. Grassi and M. Mazzapioda and A. Tramontano
Nucleic Acids Res 41 W84-8 (2013)
http://dx.doi.org/10.1093/nar/gkt516

The results of differential expression analyses provide scientists with hundreds to thousands of differentially expressed genes that need to be interpreted in light of the biology of the specific system under study. This requires mapping the genes to functional classifications that can be, for example, the KEGG pathways or InterPro families they belong to, their GO Molecular Function, Biological Process or Cellular Component. A statistically significant overrepresentation of one or more category terms in the set of differentially expressed genes is an essential step for the interpretation of the biological significance of the results. Ideally, the analysis should be performed by scientists who are well acquainted with the biological problem, as they have a wealth of knowledge about the system and can, more easily than a bioinformatician, discover less obvious and, therefore, more interesting relationships. To allow experimentalists to explore their data in an easy and at the same time exhaustive fashion within a single tool and to test their hypothesis quickly and effortlessly, we developed FIDEA. The FIDEA server is located at http://www.biocomputing.it/fidea; it is free and open to all users, and there is no login requirement.
Mazzotta:2013aa: Fly cryptochrome and the visual system
G. Mazzotta and A. Rossi and E. Leonardi and M. Mason and C. Bertolucci and L. Caccin and B. Spolaore and A. J. M. Martin and M. Schlichting and R. Grebler and C. Helfrich-Förster and S. Mammi and R. Costa and S. C. E. Tosatto
Proc Natl Acad Sci U S A 110 6163-8 (2013)
http://dx.doi.org/10.1073/pnas.1212317110

Cryptochromes are flavoproteins, structurally and evolutionarily related to photolyases, that are involved in the development, magnetoreception, and temporal organization of a variety of organisms. Drosophila CRYPTOCHROME (dCRY) is involved in light synchronization of the master circadian clock, and its C terminus plays an important role in modulating light sensitivity and activity of the protein. The activation of dCRY by light requires a conformational change, but it has been suggested that activation could be mediated also by specific "regulators" that bind the C terminus of the protein. This C-terminal region harbors several protein-protein interaction motifs, likely relevant for signal transduction regulation. Here, we show that some functional linear motifs are evolutionarily conserved in the C terminus of cryptochromes and that class III PDZ-binding sites are selectively maintained in animals. A coimmunoprecipitation assay followed by mass spectrometry analysis revealed that dCRY interacts with Retinal Degeneration A (RDGA) and with Neither Inactivation Nor Afterpotential C (NINAC) proteins. Both proteins belong to a multiprotein complex (the Signalplex) that includes visual-signaling molecules. Using bioinformatic and molecular approaches, dCRY was found to interact with Neither Inactivation Nor Afterpotential C through Inactivation No Afterpotential D (INAD) in a light-dependent manner and that the CRY-Inactivation No Afterpotential D interaction is mediated by specific domains of the two proteins and involves the CRY C terminus. Moreover, an impairment of the visual behavior was observed in fly mutants for dCRY, indicative of a role, direct or indirect, for this photoreceptor in fly vision.
Bizzarri:2011aa: Fractal analysis in a systems biology approach to cancer
M. Bizzarri and A. Giuliani and A. Cucina and F. D'Anselmi and A. M. Soto and C. Sonnenschein
Semin. Cancer Biol. 21 175--182 (2011)
http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/WOS:000293931200005

Cancer is a highly complex disease due to the disruption of tissue architecture. Thus, tissues, and not individual cells, are the proper level of observation for the study of carcinogenesis. This paradigm shift from a reductionist approach to a systems biology approach is long overdue. Indeed, cell phenotypes are emergent modes arising through collective non-linear interactions among different cellular and microenvironmental components, generally described by "phase space diagrams", where stable states (attractors) are embedded into a landscape model. Within this framework, cell states and cell transitions are generally conceived as mainly specified by gene-regulatory networks. However, the system's dynamics is not reducible to the integrated functioning of the genome-proteome network alone; the epithelia-stroma interacting system must be taken into consideration in order to give a more comprehensive picture. Given that cell shape represents the spatial geometric configuration acquired as a result of the integrated set of cellular and environmental cues, we posit that fractal-shape parameters represent "omics" descriptors of the epithelium-stroma system. Within this framework, function appears to follow form, and not the other way around. (C) 2011 Elsevier Ltd. All rights reserved.
Calabrese:2009ab: Functional annotations improve the predictive score of human disease-related mutations in proteins
R. Calabrese and E. Capriotti and P. Fariselli and P. L. Martelli and R. Casadio
Hum Mutat 30 1237-44 (2009)
http://dx.doi.org/10.1002/humu.21047

Single nucleotide polymorphisms (SNPs) are the simplest and most frequent form of human DNA variation, also valuable as genetic markers of disease susceptibility. The most investigated SNPs are missense mutations resulting in residue substitutions in the protein. Here we propose SNPs&GO, an accurate method that, starting from a protein sequence, can predict whether a mutation is disease related or not by exploiting the protein functional annotation. The scoring efficiency of SNPs&GO is as high as 82%, with a Matthews correlation coefficient equal to 0.63 over a wide set of annotated nonsynonymous mutations in proteins, including 16,330 disease-related and 17,432 neutral polymorphisms. SNPs&GO collects in unique framework information derived from protein sequence, evolutionary information, and function as encoded in the Gene Ontology terms, and outperforms other available predictive methods.
Chiefari:2011aa: Functional variants of the HMGA1 gene and type 2 diabetes mellitus
E. Chiefari and S. Tanyolaç and F. Paonessa and C. R. Pullinger and C. Capula and S. Iiritano and T. Mazza and M. Forlin and A. Fusco and V. Durlach and A. Durlach and M. J. Malloy and J. P. Kane and S. W. Heiner and M. Filocamo and D. P. Foti and I. D. Goldfine and A. Brunetti
JAMA 305 903-12 (2011)
http://dx.doi.org/10.1001/jama.2011.207

CONTEXT: High-mobility group A1 (HMGA1) protein is a key regulator of insulin receptor (INSR) gene expression. We previously identified a functional HMGA1 gene variant in 2 insulin-resistant patients with decreased INSR expression and type 2 diabetes mellitus (DM). OBJECTIVE: To examine the association of HMGA1 gene variants with type 2 DM. DESIGN, SETTINGS, AND PARTICIPANTS: Case-control study that analyzed the HMGA1 gene in patients with type 2 DM and controls from 3 populations of white European ancestry. Italian patients with type 2 DM (n = 3278) and 2 groups of controls (n = 3328) were attending the University of Catanzaro outpatient clinics and other health care sites in Calabria, Italy, during 2003-2009; US patients with type 2 DM (n = 970) were recruited in Northern California clinics between 1994 and 2005 and controls (n = 958) were senior athletes without DM collected in 2004 and 2009; and French patients with type 2 DM (n = 354) and healthy controls (n = 50) were enrolled at the University of Reims in 1992. Genomic DNA was either directly sequenced or analyzed for specific HMGA1 mutations. Messenger RNA and protein expression for HMGA1 and INSR were measured in both peripheral lymphomonocytes and cultured Epstein-Barr virus-transformed lymphoblasts from patients with type 2 DM and controls. MAIN OUTCOME MEASURES: The frequency of HMGA1 gene variants among cases and controls. Odds ratios (ORs) for type 2 DM were estimated by logistic regression analysis. RESULTS: The most frequent functional HMGA1 variant, IVS5-13insC, was present in 7% to 8% of patients with type 2 DM in all 3 populations. The prevalence of IVS5-13insC variant was higher among patients with type 2 DM than among controls in the Italian population (7.23% vs 0.43% in one control group; OR, 15.77 [95% confidence interval {CI}, 8.57-29.03]; P < .001 and 7.23% vs 3.32% in the other control group; OR, 2.03 [95% CI, 1.51-3.43]; P < .001). In the US population, the prevalence of IVS5-13insC variant was 7.7% among patients with type 2 DM vs 4.7% among controls (OR, 1.64 [95% CI, 1.05-2.57]; P = .03). In the French population, the prevalence of IVS5-13insC variant was 7.6% among patients with type 2 DM and 0% among controls (P = .046). In the Italian population, 3 other functional variants were observed. When all 4 variants were analyzed, HMGA1 defects were present in 9.8% of Italian patients with type 2 DM and 0.6% of controls. In addition to the IVS5 C-insertion, the c.310G>T (p.E104X) variant was found in 14 patients and no controls (Bonferroni-adjusted P = .01); the c.*82G>A variant (rs2780219) was found in 46 patients and 5 controls (Bonferroni-adjusted P < .001); the c.*369del variant was found in 24 patients and no controls (Bonferroni-adjusted P < .001). In circulating monocytes and Epstein-Barr virus-transformed lymphoblasts from patients with type 2 DM and the IVS5-13insC variant, the messenger RNA levels and protein content of both HMGA1 and the INSR were decreased by 40% to 50%, and these defects were corrected by transfection with HMGA1 complementary DNA. CONCLUSIONS: Compared with healthy controls, the presence of functional HMGA1 gene variants in individuals of white European ancestry was associated with type 2 DM.
Polesani:2010aa: General and species-specific transcriptional responses to downy mildew infection in a susceptible (Vitis vinifera) and a resistant (V. riparia) grapevine species
M. Polesani and L. Bortesi and A. Ferrarini and A. Zamboni and M. Fasoli and C. Zadra and A. Lovato and M. Pezzotti and M. Delledonne and A. Polverari
BMC Genomics 11 117 (2010)
http://dx.doi.org/10.1186/1471-2164-11-117

BACKGROUND: Downy mildew is a destructive grapevine disease caused by Plasmopara viticola (Berk. and Curt.) Berl. and de Toni, which can only be controlled by intensive fungicide treatments. Natural sources of resistance from wild grapevine (Vitis) species are used in conventional breeding approaches, but the signals and effectors involved in resistance in this important crop species are not well understood. RESULTS: Early transcriptional changes associated with P. viticola infection in susceptible V. vinifera and resistant V. riparia plants were analyzed using the Combimatrix microarray platform. Transcript levels were measured 12 and 24 h post-inoculation, reflecting the time points immediately preceding the onset of resistance in V. riparia, as determined by microscopic analysis. Our data indicate that resistance in V. riparia is induced after infection, and is not based on differences in basal gene expression between the two species. The strong and rapid transcriptional reprogramming involves the induction of pathogenesis-related proteins and enzymes required for the synthesis of phenylpropanoid-derived compounds, many of which are also induced, albeit to a lesser extent, in V. vinifera. More interestingly, resistance in V. riparia also involves the specific modulation of numerous transcripts encoding components of signal transduction cascades, hypersensitive reaction markers and genes involved in jasmonate biosynthesis. The limited transcriptional modulation in V. vinifera represents a weak attempted defense response rather than the activation of compatibility-specific pathways. CONCLUSIONS: Several candidate resistance genes were identified that could be exploited in future biotechnological approaches to increase disease resistance in susceptible grapevine species. Measurements of jasmonic acid and methyl jasmonate in infected leaves suggest that this hormone may also be involved in V. riparia resistance to P. viticola.
Caizzi:2014aa: Genome-wide activity of unliganded estrogen receptor-α in breast cancer cells
L. Caizzi and G. Ferrero and S. Cutrupi and F. Cordero and C. Ballaré and V. Miano and S. Reineri and L. Ricci and O. Friard and A. Testori and D. Corà and M. Caselle and L. Di Croce and M. De Bortoli
Proc Natl Acad Sci U S A 111 4892-7 (2014)
http://dx.doi.org/10.1073/pnas.1315445111

Estrogen receptor-α (ERα) has central role in hormone-dependent breast cancer and its ligand-induced functions have been extensively characterized. However, evidence exists that ERα has functions that are independent of ligands. In the present work, we investigated the binding of ERα to chromatin in the absence of ligands and its functions on gene regulation. We demonstrated that in MCF7 breast cancer cells unliganded ERα binds to more than 4,000 chromatin sites. Unexpectedly, although almost entirely comprised in the larger group of estrogen-induced binding sites, we found that unliganded-ERα binding is specifically linked to genes with developmental functions, compared with estrogen-induced binding. Moreover, we found that siRNA-mediated down-regulation of ERα in absence of estrogen is accompanied by changes in the expression levels of hundreds of coding and noncoding RNAs. Down-regulated mRNAs showed enrichment in genes related to epithelial cell growth and development. Stable ERα down-regulation using shRNA, which caused cell growth arrest, was accompanied by increased H3K27me3 at ERα binding sites. Finally, we found that FOXA1 and AP2γ binding to several sites is decreased upon ERα silencing, suggesting that unliganded ERα participates, together with other factors, in the maintenance of the luminal-specific cistrome in breast cancer cells.
Papait:2013aa: Genome-wide analysis of histone marks identifying an epigenetic signature of promoters and enhancers underlying cardiac hypertrophy
R. Papait and P. Cattaneo and P. Kunderfranco and C. Greco and P. Carullo and A. Guffanti and V. Viganò and G. G. Stirparo and M. V. G. Latronico and G. Hasenfuss and J. Chen and G. Condorelli
Proc Natl Acad Sci U S A 110 20164-9 (2013)
http://dx.doi.org/10.1073/pnas.1315155110

Cardiac hypertrophy, initially an adaptive response of the myocardium to stress, can progress to heart failure. The epigenetic signature underlying this phenomenon is poorly understood. Here, we report on the genome-wide distribution of seven histone modifications in adult mouse cardiomyocytes subjected to a prohypertrophy stimulus in vivo. We found a set of promoters with an epigenetic pattern that distinguishes specific functional classes of genes regulated in hypertrophy and identified 9,207 candidate active enhancers whose activity was modulated. We also analyzed the transcriptional network within which these genetic elements act to orchestrate hypertrophy gene expression, finding a role for myocyte enhancer factor (MEF)2C and MEF2A in regulating enhancers. We propose that the epigenetic landscape is a key determinant of gene expression reprogramming in cardiac hypertrophy and provide a basis for understanding the role of chromatin in regulating this phenomenon.
Fumagalli:2010aa: Genome-wide identification of susceptibility alleles for viral infections through a population genetics approach
M. Fumagalli and U. Pozzoli and R. Cagliani and G. P. Comi and N. Bresolin and M. Clerici and M. Sironi
PLoS Genet 6 e1000849 (2010)
http://dx.doi.org/10.1371/journal.pgen.1000849

Viruses have exerted a constant and potent selective pressure on human genes throughout evolution. We utilized the marks left by selection on allele frequency to identify viral infection-associated allelic variants. Virus diversity (the number of different viruses in a geographic region) was used to measure virus-driven selective pressure. Results showed an excess of variants correlated with virus diversity in genes involved in immune response and in the biosynthesis of glycan structures functioning as viral receptors; a significantly higher than expected number of variants was also seen in genes encoding proteins that directly interact with viral components. Genome-wide analyses identified 441 variants significantly associated with virus-diversity; these are more frequently located within gene regions than expected, and they map to 139 human genes. Analysis of functional relationships among genes subjected to virus-driven selective pressure identified a complex network enriched in viral products-interacting proteins. The novel approach to the study of infectious disease epidemiology presented herein may represent an alternative to classic genome-wide association studies and provides a large set of candidate susceptibility variants for viral infections.
Tavenet:2009aa: Genome-wide location analysis reveals a role for Sub1 in RNA polymerase III transcription
A. Tavenet and A. Suleau and G. Dubreuil and R. Ferrari and C. Ducrot and M. Michaut and J.-C. Aude and G. Dieci and O. Lefebvre and C. Conesa and J. Acker
Proc Natl Acad Sci U S A 106 14265-70 (2009)
http://dx.doi.org/10.1073/pnas.0900162106

Human PC4 and the yeast ortholog Sub1 have multiple functions in RNA polymerase II transcription. Genome-wide mapping revealed that Sub1 is present on Pol III-transcribed genes. Sub1 was found to interact with components of the Pol III transcription system and to stimulate the initiation and reinitiation steps in a system reconstituted with all recombinant factors. Sub1 was required for optimal Pol III gene transcription in exponentially growing cells.
Koga:2009aa: Genome-wide screen of promoter methylation identifies novel markers in melanoma
Y. Koga and M. Pelizzola and E. Cheng and M. Krauthammer and M. Sznol and S. Ariyan and D. Narayan and A. M. Molinaro and R. Halaban and S. M. Weissman
Genome Res 19 1462-70 (2009)
http://dx.doi.org/10.1101/gr.091447.109

DNA methylation is an important component of epigenetic modifications, which influences the transcriptional machinery aberrant in many human diseases. In this study we present the first genome-wide integrative analysis of promoter methylation and gene expression for the identification of methylation markers in melanoma. Genome-wide promoter methylation and gene expression of eight early-passage human melanoma cell strains were compared with newborn and adult melanocytes. We used linear mixed effect models (LME) in combination with a series of filters based on the localization of promoter methylation relative to the transcription start site, overall promoter CpG content, and differential gene expression to discover DNA methylation markers. This approach identified 76 markers, of which 68 were hyper- and eight hypomethylated (LME, P < 0.05). Promoter methylation and differential gene expression of five markers (COL1A2, NPM2, HSPB6, DDIT4L, MT1G) were validated by sequencing of bisulfite-modified DNA and real-time reverse transcriptase PCR, respectively. Importantly, the incidence of promoter methylation of the validated markers increased moderately in early and significantly in advanced-stage melanomas, using early-passage cell strains and snap-frozen tissues (n = 18 and n = 24, respectively) compared with normal melanocytes and nevi (n = 11 and n = 9, respectively). Our approach allows robust identification of methylation markers that can be applied to other studies involving genome-wide promoter methylation. In conclusion, this study represents the first unbiased systematic effort to determine methylation markers in melanoma and revealed several novel genes regulated by promoter methylation that were not described in cancer cells before.
LAbbate:2014aa: Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer
A. L'Abbate and G. Macchia and P. D'Addabbo and A. Lonoce and D. Tolomeo and D. Trombetta and K. Kok and C. Bartenhagen and C. W. Whelan and O. Palumbo and M. Severgnini and I. Cifola and M. Dugas and M. Carella and G. De Bellis and M. Rocchi and L. Carbone and C. T. Storlazzi
Nucleic Acids Res 42 9131-45 (2014)
http://dx.doi.org/10.1093/nar/gku590

The mechanism for generating double minutes chromosomes (dmin) and homogeneously staining regions (hsr) in cancer is still poorly understood. Through an integrated approach combining next-generation sequencing, single nucleotide polymorphism array, fluorescent in situ hybridization and polymerase chain reaction-based techniques, we inferred the fine structure of MYC-containing dmin/hsr amplicons harboring sequences from several different chromosomes in seven tumor cell lines, and characterized an unprecedented number of hsr insertion sites. Local chromosome shattering involving a single-step catastrophic event (chromothripsis) was recently proposed to explain clustered chromosomal rearrangements and genomic amplifications in cancer. Our bioinformatics analyses based on the listed criteria to define chromothripsis led us to exclude it as the driving force underlying amplicon genesis in our samples. Instead, the finding of coexisting heterogeneous amplicons, differing in their complexity and chromosome content, in cell lines derived from the same tumor indicated the occurrence of a multi-step evolutionary process in the genesis of dmin/hsr. Our integrated approach allowed us to gather a complete view of the complex chromosome rearrangements occurring within MYC amplicons, suggesting that more than one model may be invoked to explain the origin of dmin/hsr in cancer. Finally, we identified PVT1 as a target of fusion events, confirming its role as breakpoint hotspot in MYC amplification.
Grober:2011aa: Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation
O. M. V. Grober and M. Mutarelli and G. Giurato and M. Ravo and L. Cicatiello and M. R. De Filippo and L. Ferraro and G. Nassa and M. F. Papa and O. Paris and R. Tarallo and S. Luo and G. P. Schroth and V. Benes and A. Weisz
BMC Genomics 12 36 (2011)
http://dx.doi.org/10.1186/1471-2164-12-36

BACKGROUND: Estrogen receptors alpha (ERα) and beta (ERβ) are transcription factors (TFs) that mediate estrogen signaling and define the hormone-responsive phenotype of breast cancer (BC). The two receptors can be found co-expressed and play specific, often opposite, roles, with ERβ being able to modulate the effects of ERα on gene transcription and cell proliferation. ERβ is frequently lost in BC, where its presence generally correlates with a better prognosis of the disease. The identification of the genomic targets of ERβ in hormone-responsive BC cells is thus a critical step to elucidate the roles of this receptor in estrogen signaling and tumor cell biology. RESULTS: Expression of full-length ERβ in hormone-responsive, ERα-positive MCF-7 cells resulted in a marked reduction in cell proliferation in response to estrogen and marked effects on the cell transcriptome. By ChIP-Seq we identified 9702 ERβ and 6024 ERα binding sites in estrogen-stimulated cells, comprising sites occupied by either ERβ, ERα or both ER subtypes. A search for TF binding matrices revealed that the majority of the binding sites identified comprise one or more Estrogen Response Element and the remaining show binding matrixes for other TFs known to mediate ER interaction with chromatin by tethering, including AP2, E2F and SP1. Of 921 genes differentially regulated by estrogen in ERβ+ vs ERβ- cells, 424 showed one or more ERβ site within 10 kb. These putative primary ERβ target genes control cell proliferation, death, differentiation, motility and adhesion, signal transduction and transcription, key cellular processes that might explain the biological and clinical phenotype of tumors expressing this ER subtype. ERβ binding in close proximity of several miRNA genes and in the mitochondrial genome, suggests the possible involvement of this receptor in small non-coding RNA biogenesis and mitochondrial genome functions. CONCLUSIONS: Results indicate that the vast majority of the genomic targets of ERβ can bind also ERα, suggesting that the overall action of ERβ on the genome of hormone-responsive BC cells depends mainly on the relative concentration of both ERs in the cell.
Fadista:2014aa: Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism
J. Fadista and P. Vikman and E. O. Laakso and I. G. Mollet and J. L. Esguerra and J. Taneera and P. Storm and P. Osmark and C. Ladenvall and R. B. Prasad and K. B. Hansson and F. Finotello and K. Uvebrant and J. K. Ofori and B. Di Camillo and U. Krus and C. M. Cilio and O. Hansson and L. Eliasson and A. H. Rosengren and E. Renström and C. B. Wollheim and L. Groop
Proc Natl Acad Sci U S A 111 13924-9 (2014)
http://dx.doi.org/10.1073/pnas.1402665111

Genetic variation can modulate gene expression, and thereby phenotypic variation and susceptibility to complex diseases such as type 2 diabetes (T2D). Here we harnessed the potential of DNA and RNA sequencing in human pancreatic islets from 89 deceased donors to identify genes of potential importance in the pathogenesis of T2D. We present a catalog of genetic variants regulating gene expression (eQTL) and exon use (sQTL), including many long noncoding RNAs, which are enriched in known T2D-associated loci. Of 35 eQTL genes, whose expression differed between normoglycemic and hyperglycemic individuals, siRNA of tetraspanin 33 (TSPAN33), 5'-nucleotidase, ecto (NT5E), transmembrane emp24 protein transport domain containing 6 (TMED6), and p21 protein activated kinase 7 (PAK7) in INS1 cells resulted in reduced glucose-stimulated insulin secretion. In addition, we provide a genome-wide catalog of allelic expression imbalance, which is also enriched in known T2D-associated loci. Notably, allelic imbalance in paternally expressed gene 3 (PEG3) was associated with its promoter methylation and T2D status. Finally, RNA editing events were less common in islets than previously suggested in other tissues. Taken together, this study provides new insights into the complexity of gene regulation in human pancreatic islets and better understanding of how genetic variation can influence glucose metabolism.
Sales:2013aa: Graphite Web: Web tool for gene set analysis exploiting pathway topology
G. Sales and E. Calura and P. Martini and C. Romualdi
Nucleic Acids Res 41 W89-97 (2013)
http://dx.doi.org/10.1093/nar/gkt386

Graphite web is a novel web tool for pathway analyses and network visualization for gene expression data of both microarray and RNA-seq experiments. Several pathway analyses have been proposed either in the univariate or in the global and multivariate context to tackle the complexity and the interpretation of expression results. These methods can be further divided into 'topological' and 'non-topological' methods according to their ability to gain power from pathway topology. Biological pathways are, in fact, not only gene lists but can be represented through a network where genes and connections are, respectively, nodes and edges. To this day, the most used approaches are non-topological and univariate although they miss the relationship among genes. On the contrary, topological and multivariate approaches are more powerful, but difficult to be used by researchers without bioinformatic skills. Here we present Graphite web, the first public web server for pathway analysis on gene expression data that combines topological and multivariate pathway analyses with an efficient system of interactive network visualizations for easy results interpretation. Specifically, Graphite web implements five different gene set analyses on three model organisms and two pathway databases. Graphite Web is freely available at http://graphiteweb.bio.unipd.it/.
Schnorr:2014aa: Gut microbiome of the Hadza hunter-gatherers
S. L. Schnorr and M. Candela and S. Rampelli and M. Centanni and C. Consolandi and G. Basaglia and S. Turroni and E. Biagi and C. Peano and M. Severgnini and J. Fiori and R. Gotti and G. De Bellis and D. Luiselli and P. Brigidi and A. Mabulla and F. Marlowe and A. G. Henry and A. N. Crittenden
Nat Commun 5 3654 (2014)
http://dx.doi.org/10.1038/ncomms4654

Human gut microbiota directly influences health and provides an extra means of adaptive potential to different lifestyles. To explore variation in gut microbiota and to understand how these bacteria may have co-evolved with humans, here we investigate the phylogenetic diversity and metabolite production of the gut microbiota from a community of human hunter-gatherers, the Hadza of Tanzania. We show that the Hadza have higher levels of microbial richness and biodiversity than Italian urban controls. Further comparisons with two rural farming African groups illustrate other features unique to Hadza that can be linked to a foraging lifestyle. These include absence of Bifidobacterium and differences in microbial composition between the sexes that probably reflect sexual division of labour. Furthermore, enrichment in Prevotella, Treponema and unclassified Bacteroidetes, as well as a peculiar arrangement of Clostridiales taxa, may enhance the Hadza's ability to digest and extract valuable nutrition from fibrous plant foods.
Piacentini:2009aa: Heterochromatin protein 1 (HP1a) positively regulates euchromatic gene expression through RNA transcript association and interaction with hnRNPs in Drosophila
L. Piacentini and L. Fanti and R. Negri and V. Del Vescovo and A. Fatica and F. Altieri and S. Pimpinelli
PLoS Genet 5 e1000670 (2009)
http://dx.doi.org/10.1371/journal.pgen.1000670

Heterochromatin Protein 1 (HP1a) is a well-known conserved protein involved in heterochromatin formation and gene silencing in different species including humans. A general model has been proposed for heterochromatin formation and epigenetic gene silencing in different species that implies an essential role for HP1a. According to the model, histone methyltransferase enzymes (HMTases) methylate the histone H3 at lysine 9 (H3K9me), creating selective binding sites for itself and the chromodomain of HP1a. This complex is thought to form a higher order chromatin state that represses gene activity. It has also been found that HP1a plays a role in telomere capping. Surprisingly, recent studies have shown that HP1a is present at many euchromatic sites along polytene chromosomes of Drosophila melanogaster, including the developmental and heat-shock-induced puffs, and that this protein can be removed from these sites by in vivo RNase treatment, thus suggesting an association of HP1a with the transcripts of many active genes. To test this suggestion, we performed an extensive screening by RIP-chip assay (RNA-immunoprecipitation on microarrays), and we found that HP1a is associated with transcripts of more than one hundred euchromatic genes. An expression analysis in HP1a mutants shows that HP1a is required for positive regulation of these genes. Cytogenetic and molecular assays show that HP1a also interacts with the well known proteins DDP1, HRB87F, and PEP, which belong to different classes of heterogeneous nuclear ribonucleoproteins (hnRNPs) involved in RNA processing. Surprisingly, we found that all these hnRNP proteins also bind heterochromatin and are dominant suppressors of position effect variegation. Together, our data show novel and unexpected functions for HP1a and hnRNPs proteins. All these proteins are in fact involved both in RNA transcript processing and in heterochromatin formation. This suggests that, in general, similar epigenetic mechanisms have a significant role on both RNA and heterochromatin metabolisms.
Mica:2009aa: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera
E. Mica and V. Piccolo and M. Delledonne and A. Ferrarini and M. Pezzotti and C. Casati and C. Del Fabbro and G. Valle and A. Policriti and M. Morgante and G. Pesole and M. E. Pè and D. S. Horner
BMC Genomics 10 558 (2009)
http://dx.doi.org/10.1186/1471-2164-10-558

BACKGROUND: MicroRNAs are short (approximately 21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. The recent annotation of the genome of the grapevine (Vitis vinifera L.) allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families. RESULTS: Here we use oligonucleotide arrays to provide the first indication that many of these microRNAs show differential expression patterns between tissues and during the maturation of fruit in the grapevine. Furthermore we demonstrate that whole transcriptome sequencing and deep-sequencing of small RNA fractions can be used both to identify which microRNA precursors are expressed in different tissues and to estimate genomic coordinates and patterns of splicing and alternative splicing for many primary miRNA transcripts. CONCLUSION: Our results show that many microRNAs are differentially expressed in different tissues and during fruit maturation in the grapevine. Furthermore, the demonstration that whole transcriptome sequencing can be used to identify candidate splicing events and approximate primary microRNA transcript coordinates represents a significant step towards the large-scale elucidation of mechanisms regulating the expression of microRNAs at the transcriptional and post-transcriptional levels.
Chawla:2014aa: Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs
M. Chawla and S. Abdel-Azeim and R. Oliva and L. Cavallo
Nucleic Acids Res 42 714-26 (2014)
http://dx.doi.org/10.1093/nar/gkt800

The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch.
Popovic:2014aa: Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation
R. Popovic and E. Martinez-Garcia and E. G. Giannopoulou and Q. Zhang and Q. Zhang and T. Ezponda and M. Y. Shah and Y. Zheng and C. M. Will and E. C. Small and Y. Hua and M. Bulic and Y. Jiang and M. Carrara and R. A. Calogero and W. L. Kath and N. L. Kelleher and J.-P. Wang and O. Elemento and J. D. Licht
PLoS Genet 10 e1004566 (2014)
http://dx.doi.org/10.1371/journal.pgen.1004566

Overexpression of the histone methyltransferase MMSET in t(4;14)+ multiple myeloma patients is believed to be the driving factor in the pathogenesis of this subtype of myeloma. MMSET catalyzes dimethylation of lysine 36 on histone H3 (H3K36me2), and its overexpression causes a global increase in H3K36me2, redistributing this mark in a broad, elevated level across the genome. Here, we demonstrate that an increased level of MMSET also induces a global reduction of lysine 27 trimethylation on histone H3 (H3K27me3). Despite the net decrease in H3K27 methylation, specific genomic loci exhibit enhanced recruitment of the EZH2 histone methyltransferase and become hypermethylated on this residue. These effects likely contribute to the myeloma phenotype since MMSET-overexpressing cells displayed increased sensitivity to EZH2 inhibition. Furthermore, we demonstrate that such MMSET-mediated epigenetic changes require a number of functional domains within the protein, including PHD domains that mediate MMSET recruitment to chromatin. In vivo, targeting of MMSET by an inducible shRNA reversed histone methylation changes and led to regression of established tumors in athymic mice. Together, our work elucidates previously unrecognized interplay between MMSET and EZH2 in myeloma oncogenesis and identifies domains to be considered when designing inhibitors of MMSET function.
Lister:2011aa: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
R. Lister and M. Pelizzola and Y. S. Kida and R. D. Hawkins and J. R. Nery and G. Hon and J. Antosiewicz-Bourget and R. O'Malley and R. Castanon and S. Klugman and M. Downes and R. Yu and R. Stewart and B. Ren and J. A. Thomson and R. M. Evans and J. R. Ecker
Nature 471 68-73 (2011)
http://dx.doi.org/10.1038/nature09798

Induced pluripotent stem cells (iPSCs) offer immense potential for regenerative medicine and studies of disease and development. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem (ES) cells. However, it remains unknown how complete the reestablishment of ES-cell-like DNA methylation patterns is throughout the genome. Here we report the first whole-genome profiles of DNA methylation at single-base resolution in five human iPSC lines, along with methylomes of ES cells, somatic cells, and differentiated iPSCs and ES cells. iPSCs show significant reprogramming variability, including somatic memory and aberrant reprogramming of DNA methylation. iPSCs share megabase-scale differentially methylated regions proximal to centromeres and telomeres that display incomplete reprogramming of non-CG methylation, and differences in CG methylation and histone modifications. Lastly, differentiation of iPSCs into trophoblast cells revealed that errors in reprogramming CG methylation are transmitted at a high frequency, providing an iPSC reprogramming signature that is maintained after differentiation.
Via:2014aa: How pathogens use linear motifs to perturb host cell networks
A. Via and B. Uyar and C. Brun and A. Zanzoni
Trends Biochem Sci (2014)
http://dx.doi.org/10.1016/j.tibs.2014.11.001

Molecular mimicry is one of the powerful stratagems that pathogens employ to colonise their hosts and take advantage of host cell functions to guarantee their replication and dissemination. In particular, several viruses have evolved the ability to interact with host cell components through protein short linear motifs (SLiMs) that mimic host SLiMs, thus facilitating their internalisation and the manipulation of a wide range of cellular networks. Here we present convincing evidence from the literature that motif mimicry also represents an effective, widespread hijacking strategy in prokaryotic and eukaryotic parasites. Further insights into host motif mimicry would be of great help in the elucidation of the molecular mechanisms behind host cell invasion and the development of anti-infective therapeutic strategies.
Lister:2009aa: Human DNA methylomes at base resolution show widespread epigenomic differences
R. Lister and M. Pelizzola and R. H. Dowen and R. D. Hawkins and G. Hon and J. Tonti-Filippini and J. R. Nery and L. Lee and Z. Ye and Q.-M. Ngo and L. Edsall and J. Antosiewicz-Bourget and R. Stewart and V. Ruotti and A. H. Millar and J. A. Thomson and B. Ren and J. R. Ecker
Nature 462 315-22 (2009)
http://dx.doi.org/10.1038/nature08514

DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA-protein interaction for several key regulatory factors. Widespread differences were identified in the composition and patterning of cytosine methylation between the two genomes. Nearly one-quarter of all methylation identified in embryonic stem cells was in a non-CG context, suggesting that embryonic stem cells may use different methylation mechanisms to affect gene regulation. Methylation in non-CG contexts showed enrichment in gene bodies and depletion in protein binding sites and enhancers. Non-CG methylation disappeared upon induced differentiation of the embryonic stem cells, and was restored in induced pluripotent stem cells. We identified hundreds of differentially methylated regions proximal to genes involved in pluripotency and differentiation, and widespread reduced methylation levels in fibroblasts associated with lower transcriptional activity. These reference epigenomes provide a foundation for future studies exploring this key epigenetic modification in human disease and development.
Colonna:2014aa: Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
V. Colonna and Q. Ayub and Y. Chen and L. Pagani and P. Luisi and M. Pybus and E. Garrison and Y. Xue and C. Tyler-Smith and 1000 Genomes Project Consortium and G. R. Abecasis and A. Auton and L. D. Brooks and M. A. DePristo and R. M. Durbin and R. E. Handsaker and H. M. Kang and G. T. Marth and G. A. McVean
Genome Biol 15 R88 (2014)
http://dx.doi.org/10.1186/gb-2014-15-6-r88

BACKGROUND: Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. RESULTS: We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively. CONCLUSIONS: We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.
Potenza:2011aa: Human microRNA hsa-miR-125a-5p interferes with expression of hepatitis B virus surface antigen
N. Potenza and U. Papa and N. Mosca and F. Zerbini and V. Nobile and A. Russo
Nucleic Acids Res 39 5157-63 (2011)
http://dx.doi.org/10.1093/nar/gkr067

MicroRNAs are small non-coding RNAs that modulate gene expression at post-transcriptional level, playing a crucial role in cell differentiation and development. Recently, some reports have shown that a limited number of mammalian microRNAs are also involved in anti-viral defense. In this study, the analysis of the hepatitis B virus (HBV) genome by the computer program MiRanda led to the identification of seven sites that are potential targets for human liver microRNAs. These sites were found to be clustered in a 995-bp segment within the viral polymerase ORF and the overlapping surface antigen ORF, and conserved among the most common HBV subtypes. The HBV genomic targets were then subjected to a validation test based on cultured hepatic cells (HepG2, HuH-7 and PLC/PRF/5) and luciferase reporter genes. In this test, one of the selected microRNAs, hsa-miR-125a-5p, was found to interact with the viral sequence and to suppress the reporter activity markedly. The microRNA was then shown to interfere with the viral translation, down-regulating the expression of the surface antigen. Overall, these results support the emerging concept that some mammalian microRNAs play a role in virus-host interaction. Furthermore, they provide the basis for the development of new strategies for anti-HBV intervention.
Gissi:2010aa: Hypervariability of ascidian mitochondrial gene order: exposing the myth of deuterostome organelle genome stability
C. Gissi and G. Pesole and F. Mastrototaro and F. Iannelli and V. Guida and F. Griggio
Mol Biol Evol 27 211-5 (2010)
http://dx.doi.org/10.1093/molbev/msp234

The few sequenced mitochondrial (mt) genomes of the class Ascidiacea (Chordata, Tunicata), mostly belonging to congeneric species of the Phlebobranchia order, show extraordinary gene order rearrangements. In order to assess if this hypervariability in gene order is a general feature of Ascidiacea, we report here the gene arrangement of five ascidians belonging to the Aplousobranchia and Stolidobranchia orders. Our data show that Ascidiacea are characterized by: 1) extensive gene order rearrangements both within and between the three major lineages; 2) lack of significant similarities to the gene order of other deuterostomes; and 3) an extent of rearrangements comparable with that of Mollusca (especially the Gastropoda, Bivalvia, and Scaphopoda classes), a phylum with highly rearranged mtDNAs. The only conserved feature is the location of all genes on the same strand, which suggests that selective constraints are related to the mt transcription. Finally, a higher mobility of the tRNA genes is undetectable because of saturation effect, and only the partially conserved cox2-cob gene block seems to retain some phylogenetic signals.
Zappa:2010aa: IBWS: IST Bioinformatics Web Services
A. Zappa and M. Miele and P. Romano
Nucleic Acids Res 38 W712-8 (2010)
http://dx.doi.org/10.1093/nar/gkq416

The Bioinformatics group at the National Cancer Research Institute (IST) of Genoa has been involved since many years in the development and maintenance of biomedical information systems. Among them, the Common Access to Biological Resources and Information network services offer access to more than 130,000 biological resources, like strains of micro-organisms and human and animal cell lines, included in 29 collections from some of the most known European Biological Resource Centers. An Sequence Retrieval System (SRS) implementation of the TP53 Mutation Database of the International Agency for Research on Cancer (Lyon) was made available in order to improve interoperability of this data with other molecular biology databases. 'SRS by WS (SWS)', a system for retrieving information on public SRS sites and for directly querying them, was also implemented. In order to make this information available through application programming interfaces, we implemented a suite of free web services (WS), called the 'IST Bioinformatics Web Services (IBWS)'. A support web site, including a description of the system, a list of available WS together with help pages, links to corresponding WSDLs and forms for testing services, is available at http://bioinformatics.istge.it/ibws/. WSDL definitions can also be retrieved directly at http://bioinformatics.istge.it:8080/axis/services.
Pantaleo:2010aa: Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis
V. Pantaleo and G. Szittya and S. Moxon and L. Miozzi and V. Moulton and T. Dalmay and J. Burgyan
Plant J 62 960-76 (2010)
http://dx.doi.org/10.1111/j.0960-7412.2010.04208.x

In plants, microRNAs (miRNAs) comprise one of three classes of small RNAs regulating gene expression at the post-transcriptional level. Many plant miRNAs are conserved, and play a role in development, abiotic stress responses or pathogen responses. However, some miRNAs have only been found in certain species. Here, we use deep-sequencing, computational and molecular methods to identify, profile, and describe conserved and non-conserved miRNAs in four grapevine (Vitis vinifera) tissues. A total of 24 conserved miRNA families were identified in all four tissues, and 26 known but non-conserved miRNAs were also found. In addition to known miRNAs, we also found 21 new grapevine-specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. Furthermore, 21 other plausible miRNA candidates have been described. We have found that many known and new miRNAs showed tissue-specific expression. Finally, 112 target mRNAs of known and 44 target mRNAs of new grapevine-specific miRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs.
Lionetti:2009aa: Identification of microRNA expression patterns and definition of a microRNA/mRNA regulatory network in distinct molecular groups of multiple myeloma
M. Lionetti and M. Biasiolo and L. Agnelli and K. Todoerti and L. Mosca and S. Fabris and G. Sales and G. L. Deliliers and S. Bicciato and L. Lombardi and S. Bortoluzzi and A. Neri
Blood 114 e20-6 (2009)
http://dx.doi.org/10.1182/blood-2009-08-237495

To date, little evidence of miRNA expression/deregulation in multiple myeloma has been reported. To characterize miRNA in the context of the major multiple myeloma molecular types, we generated miRNA expression profiles of highly purified malignant plasma cells from 40 primary tumors. Furthermore, transcriptional profiles, available for all patients, were used to investigate the occurrence of miRNA/predicted target mRNA pair anticorrelations, and the miRNA and genome-wide DNA data were integrated in a subset of patients to evaluate the influence of allelic imbalances on miRNA expression. Differential miRNA expression patterns were identified, which were mainly associated with the major IGH translocations; particularly, t(4;14) patients showed specific overexpression of let-7e, miR-125a-5p, and miR-99b belonging to a cluster at 19q13.33. The occurrence of other lesions (ie, 1q gain, 13q and 17p deletions, and hyperdiploidy) was slightly characterized by specific miRNA signatures. Furthermore, the occurrence of several allelic imbalances or loss of heterozygosity was found significantly associated with the altered expression of miRNAs located in the involved regions, such as let-7b at 22q13.31 or miR-140-3p at 16q22. Finally, the integrative analysis based on computational target prediction and miRNA/mRNA profiling defined a network of putative functional miRNA-target regulatory relations supported by expression data.
Gregis:2013aa: Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis
V. Gregis and F. Andrés and A. Sessa and R. F. Guerra and S. Simonini and J. L. Mateos and S. Torti and F. Zambelli and G. M. Prazzoli and K. N. Bjerkan and P. E. Grini and G. Pavesi and L. Colombo and G. Coupland and M. M. Kater
Genome Biol 14 R56 (2013)
http://dx.doi.org/10.1186/gb-2013-14-6-r56

BACKGROUND: MADS-domain transcription factors play important roles during plant development. The Arabidopsis MADS-box gene SHORT VEGETATIVE PHASE (SVP) is a key regulator of two developmental phases. It functions as a repressor of the floral transition during the vegetative phase and later it contributes to the specification of floral meristems. How these distinct activities are conferred by a single transcription factor is unclear, but interactions with other MADS domain proteins which specify binding to different genomic regions is likely one mechanism. RESULTS: To compare the genome-wide DNA binding profile of SVP during vegetative and reproductive development we performed ChIP-seq analyses. These ChIP-seq data were combined with tiling array expression analysis, induction experiments and qRT-PCR to identify biologically relevant binding sites. In addition, we compared genome-wide target genes of SVP with those published for the MADS domain transcription factors FLC and AP1, which interact with SVP during the vegetative and reproductive phases, respectively. CONCLUSIONS: Our analyses resulted in the identification of pathways that are regulated by SVP including those controlling meristem development during vegetative growth and flower development whereas floral transition pathways and hormonal signaling were regulated predominantly during the vegetative phase. Thus, SVP regulates many developmental pathways, some of which are common to both of its developmental roles whereas others are specific to only one of them.
Zamboni:2010aa: Identification of putative stage-specific grapevine berry biomarkers and omics data integration into networks
A. Zamboni and M. Di Carli and F. Guzzo and M. Stocchero and S. Zenoni and A. Ferrarini and P. Tononi and K. Toffali and A. Desiderio and K. S. Lilley and M. E. Pè and E. Benvenuto and M. Delledonne and M. Pezzotti
Plant Physiol 154 1439-59 (2010)
http://dx.doi.org/10.1104/pp.110.160275

The analysis of grapevine (Vitis vinifera) berries at the transcriptomic, proteomic, and metabolomic levels can provide great insight into the molecular events underlying berry development and postharvest drying (withering). However, the large and very different data sets produced by such investigations are difficult to integrate. Here, we report the identification of putative stage-specific biomarkers for berry development and withering and, to our knowledge, the first integrated systems-level study of these processes. Transcriptomic, proteomic, and metabolomic data were integrated using two different strategies, one hypothesis free and the other hypothesis driven. A multistep hypothesis-free approach was applied to data from four developmental stages and three withering intervals, with integration achieved using a hierarchical clustering strategy based on the multivariate bidirectional orthogonal projections to latent structures technique. This identified stage-specific functional networks of linked transcripts, proteins, and metabolites, providing important insights into the key molecular processes that determine the quality characteristics of wine. The hypothesis-driven approach was used to integrate data from three withering intervals, starting with subdata sets of transcripts, proteins, and metabolites. We identified transcripts and proteins that were modulated during withering as well as specific classes of metabolites that accumulated at the same time and used these to select subdata sets of variables. The multivariate bidirectional orthogonal projections to latent structures technique was then used to integrate the subdata sets, identifying variables representing selected molecular processes that take place specifically during berry withering. The impact of this holistic approach on our knowledge of grapevine berry development and withering is discussed.
Everitt:2012aa: IFITM3 restricts the morbidity and mortality associated with influenza
A. R. Everitt and S. Clare and T. Pertel and S. P. John and R. S. Wash and S. E. Smith and C. R. Chin and E. M. Feeley and J. S. Sims and D. J. Adams and H. M. Wise and L. Kane and D. Goulding and P. Digard and V. Anttila and J. K. Baillie and T. S. Walsh and D. A. Hume and A. Palotie and Y. Xue and V. Colonna and C. Tyler-Smith and J. Dunning and S. B. Gordon and GenISIS Investigators and MOSAIC Investigators and R. L. Smyth and P. J. Openshaw and G. Dougan and A. L. Brass and P. Kellam
Nature 484 519-23 (2012)
http://dx.doi.org/10.1038/nature10921

The 2009 H1N1 influenza pandemic showed the speed with which a novel respiratory virus can spread and the ability of a generally mild infection to induce severe morbidity and mortality in a subset of the population. Recent in vitro studies show that the interferon-inducible transmembrane (IFITM) protein family members potently restrict the replication of multiple pathogenic viruses. Both the magnitude and breadth of the IFITM proteins' in vitro effects suggest that they are critical for intrinsic resistance to such viruses, including influenza viruses. Using a knockout mouse model, we now test this hypothesis directly and find that IFITM3 is essential for defending the host against influenza A virus in vivo. Mice lacking Ifitm3 display fulminant viral pneumonia when challenged with a normally low-pathogenicity influenza virus, mirroring the destruction inflicted by the highly pathogenic 1918 'Spanish' influenza. Similar increased viral replication is seen in vitro, with protection rescued by the re-introduction of Ifitm3. To test the role of IFITM3 in human influenza virus infection, we assessed the IFITM3 alleles of individuals hospitalized with seasonal or pandemic influenza H1N1/09 viruses. We find that a statistically significant number of hospitalized subjects show enrichment for a minor IFITM3 allele (SNP rs12252-C) that alters a splice acceptor site, and functional assays show the minor CC genotype IFITM3 has reduced influenza virus restriction in vitro. Together these data reveal that the action of a single intrinsic immune effector, IFITM3, profoundly alters the course of influenza virus infection in mouse and humans.
Cieri:2013aa: IL-7 and IL-15 instruct the generation of human memory stem T cells from naive precursors
N. Cieri and B. Camisa and F. Cocchiarella and M. Forcato and G. Oliveira and E. Provasi and A. Bondanza and C. Bordignon and J. Peccatori and F. Ciceri and M. T. Lupo-Stanghellini and F. Mavilio and A. Mondino and S. Bicciato and A. Recchia and C. Bonini
Blood 121 573--584 (2013)
http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/WOS:000314866500005

Long-living memory stem T cells (T-SCM) with the ability to self-renew and the plasticity to differentiate into potent effectors could be valuable weapons in adoptive T-cell therapy against cancer. Nonetheless, procedures to specifically target this T-cell population remain elusive. Here, we show that it is possible to differentiate in vitro, expand, and gene modify in clinically compliant conditions CD8(+) T-SCM lymphocytes starting from naive precursors. Requirements for the generation of this T-cell subset, described as CD62L(+)CCR7(+)CD45RA(+)CD45R0(+)IL-7R alpha(+)CD95(+), are CD3/CD28 engagement and culture with IL-7 and IL-15. Accordingly, T-SCM accumulates early after hematopoietic stem cell transplantation. The gene expression signature and functional phenotype define this population as a distinct memory T-lymphocyte subset, intermediate between naive and central memory cells. When transplanted in immunodeficient mice, gene-modified naive-derived T-SCM prove superior to other memory lymphocytes for the ability to expand and differentiate into effectors able to mediate a potent xenogeneic GVHD. Furthermore, gene-modified T-SCM are the only T-cell subset able to expand and mediate GVHD on serial transplantation, suggesting self-renewal capacity in a clinically relevant setting. These findings provide novel insights into the origin and requirements for T-SCM generation and pave the way for their clinical rapid exploitation in adoptive cell therapy. (Blood. 2013; 121(4): 573-584)
De-Filippo:2010aa: Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
C. De Filippo and D. Cavalieri and M. Di Paola and M. Ramazzotti and J. B. Poullet and S. Massart and S. Collini and G. Pieraccini and P. Lionetti
Proc Natl Acad Sci U S A 107 14691-6 (2010)
http://dx.doi.org/10.1073/pnas.1005963107

Gut microbial composition depends on different dietary habits just as health depends on microbial metabolism, but the association of microbiota with different diets in human populations has not yet been shown. In this work, we compared the fecal microbiota of European children (EU) and that of children from a rural African village of Burkina Faso (BF), where the diet, high in fiber content, is similar to that of early human settlements at the time of the birth of agriculture. By using high-throughput 16S rDNA sequencing and biochemical analyses, we found significant differences in gut microbiota between the two groups. BF children showed a significant enrichment in Bacteroidetes and depletion in Firmicutes (P < 0.001), with a unique abundance of bacteria from the genus Prevotella and Xylanibacter, known to contain a set of bacterial genes for cellulose and xylan hydrolysis, completely lacking in the EU children. In addition, we found significantly more short-chain fatty acids (P < 0.001) in BF than in EU children. Also, Enterobacteriaceae (Shigella and Escherichia) were significantly underrepresented in BF than in EU children (P < 0.05). We hypothesize that gut microbiota coevolved with the polysaccharide-rich diet of BF individuals, allowing them to maximize energy intake from fibers while also protecting them from inflammations and noninfectious colonic diseases. This study investigates and compares human intestinal microbiota from children characterized by a modern western diet and a rural diet, indicating the importance of preserving this treasure of microbial diversity from ancient rural communities worldwide.
Sales:2010aa: Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection
G. Sales and A. Coppe and S. Bicciato and S. Bortoluzzi and C. Romualdi
Nucleic Acids Res 38 e97 (2010)
http://dx.doi.org/10.1093/nar/gkp1239

MicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome some of its limitations by carefully integrating into the analysis the paired expression profiles of miRNAs and mRNAs. In this work, we show how the choice of a proper probe annotation for microarray platforms is an essential requirement to achieve good sensitivity in the identification of miRNA-mRNA interactions. We compare the results obtained from the analysis of the same expression profiles using both gene and transcript based custom CDFs that we have developed for a number of different annotations (ENSEMBL, RefSeq, AceView). In all cases, transcript-based annotations clearly improve the effectiveness of data integration and thus provide a more reliable confirmation of computationally predicted miRNA-mRNA interactions.
Havelange:2014aa: Implications of the miR-10 family in chemotherapy response of NPM1-mutated AML
V. Havelange and P. Ranganathan and S. Geyer and D. Nicolet and X. Huang and X. Yu and S. Volinia and S. M. Kornblau and M. Andreeff and C. M. Croce and G. Marcucci and C. D. Bloomfield and R. Garzon
Blood 123 2412-5 (2014)
http://dx.doi.org/10.1182/blood-2013-10-532374

Nucleophosmin-mutated acute myeloid leukemia (NPM1mut-AML) patients have a high rate of complete remission (CR) to induction chemotherapy. However, the mechanisms responsible for such effects are unknown. Because miR-10 family members are expressed at high levels in NPM1mut-AML, we evaluated whether these microRNAs could predict chemotherapy response in AML. We found that high baseline miR-10 family expression in 54 untreated cytogenetically heterogeneous AML patients was associated with achieving CR. However, when we included NPM1 mutation status in the multivariable model, there was a significant interaction effect between miR-10a-5p expression and NPM1 mutation status. Similar results were observed when using a second cohort of 183 cytogenetically normal older (age ≥ 60 years) AML patients. Loss- and gain-of-function experiments using miR-10a-5p in cell lines and primary blasts did not demonstrate any effect in apoptosis or cell proliferation at baseline or after chemotherapy. These data support a bystander role for the miR-10 family in NPM1mut-AML.
Pichiorri:2013aa: In vivo NCL targeting affects breast cancer aggressiveness through miRNA regulation
F. Pichiorri and D. Palmieri and L. De Luca and J. Consiglio and J. You and A. Rocci and T. Talabere and C. Piovan and A. Lagana and L. Cascione and J. Guan and P. Gasparini and V. Balatti and G. Nuovo and V. Coppola and C. C. Hofmeister and G. Marcucci and J. C. Byrd and S. Volinia and C. L. Shapiro and M. A. Freitas and C. M. Croce
J Exp Med 210 951-68 (2013)
http://dx.doi.org/10.1084/jem.20120950

Numerous studies have described the altered expression and the causal role of microRNAs (miRNAs) in human cancer. However, to date, efforts to modulate miRNA levels for therapeutic purposes have been challenging to implement. Here we find that nucleolin (NCL), a major nucleolar protein, posttranscriptionally regulates the expression of a specific subset of miRNAs, including miR-21, miR-221, miR-222, and miR-103, that are causally involved in breast cancer initiation, progression, and drug resistance. We also show that NCL is commonly overexpressed in human breast tumors and that its expression correlates with that of NCL-dependent miRNAs. Finally, inhibition of NCL using guanosine-rich aptamers reduces the levels of NCL-dependent miRNAs and their target genes, thus reducing breast cancer cell aggressiveness both in vitro and in vivo. These findings illuminate a path to novel therapeutic approaches based on NCL-targeting aptamers for the modulation of miRNA expression in the treatment of breast cancer.
Pallotta:2011aa: Indoleamine 2,3-dioxygenase is a signaling protein in long-term tolerance by dendritic cells
M. T. Pallotta and C. Orabona and C. Volpi and C. Vacca and M. L. Belladonna and R. Bianchi and G. Servillo and C. Brunacci and M. Calvitti and S. Bicciato and E. M. C. Mazza and L. Boon and F. Grassi and M. C. Fioretti and F. Fallarino and P. Puccetti and U. Grohmann
Nat Immunol 12 870-8 (2011)
http://dx.doi.org/10.1038/ni.2077

Regulation of tryptophan metabolism by indoleamine 2,3-dioxygenase (IDO) in dendritic cells (DCs) is a highly versatile modulator of immunity. In inflammation, interferon-γ is the main inducer of IDO for the prevention of hyperinflammatory responses, yet IDO is also responsible for self-tolerance effects in the longer term. Here we show that treatment of mouse plasmacytoid DCs (pDCs) with transforming growth factor-β (TGF-β) conferred regulatory effects on IDO that were mechanistically separable from its enzymic activity. We found that IDO was involved in intracellular signaling events responsible for the self-amplification and maintenance of a stably regulatory phenotype in pDCs. Thus, IDO has a tonic, nonenzymic function that contributes to TGF-β-driven tolerance in noninflammatory contexts.
Chin:2009aa: Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures
M. H. Chin and M. J. Mason and W. Xie and S. Volinia and M. Singer and C. Peterson and G. Ambartsumyan and O. Aimiuwu and L. Richter and J. Zhang and I. Khvorostov and V. Ott and M. Grunstein and N. Lavon and N. Benvenisty and C. M. Croce and A. T. Clark and T. Baxter and A. D. Pyle and M. A. Teitell and M. Pelegrini and K. Plath and W. E. Lowry
Cell Stem Cell 5 111-23 (2009)
http://dx.doi.org/10.1016/j.stem.2009.06.008

Induced pluripotent stem cells (iPSCs) outwardly appear to be indistinguishable from embryonic stem cells (ESCs). A study of gene expression profiles of mouse and human ESCs and iPSCs suggests that, while iPSCs are quite similar to their embryonic counterparts, a recurrent gene expression signature appears in iPSCs regardless of their origin or the method by which they were generated. Upon extended culture, hiPSCs adopt a gene expression profile more similar to hESCs; however, they still retain a gene expression signature unique from hESCs that extends to miRNA expression. Genome-wide data suggested that the iPSC signature gene expression differences are due to differential promoter binding by the reprogramming factors. High-resolution array profiling demonstrated that there is no common specific subkaryotypic alteration that is required for reprogramming and that reprogramming does not lead to genomic instability. Together, these data suggest that iPSCs should be considered a unique subtype of pluripotent cell.
Peng:2013aa: Insulin growth factor signaling is regulated by microRNA-486, an underexpressed microRNA in lung cancer
Y. Peng and Y. Dai and C. Hitchcock and X. Yang and E. S. Kassis and L. Liu and Z. Luo and H.-L. Sun and R. Cui and H. Wei and T. Kim and T. J. Lee and Y.-J. Jeon and G. J. Nuovo and S. Volinia and Q. He and J. Yu and P. Nana-Sinkam and C. M. Croce
Proc Natl Acad Sci U S A 110 15043-8 (2013)
http://dx.doi.org/10.1073/pnas.1307107110

MicroRNAs (miRNAs) are small 19- to 24-nt noncoding RNAs that have the capacity to regulate fundamental biological processes essential for cancer initiation and progression. In cancer, miRNAs may function as oncogenes or tumor suppressors. Here, we conducted global profiling for miRNAs in a cohort of stage 1 nonsmall cell lung cancers (n = 81) and determined that miR-486 was the most down-regulated miRNA in tumors compared with adjacent uninvolved lung tissues, suggesting that miR-486 loss may be important in lung cancer development. We report that miR-486 directly targets components of insulin growth factor (IGF) signaling including insulin-like growth factor 1 (IGF1), IGF1 receptor (IGF1R), and phosphoinositide-3-kinase, regulatory subunit 1 (alpha) (PIK3R1, or p85a) and functions as a potent tumor suppressor of lung cancer both in vitro and in vivo. Our findings support the role for miR-486 loss in lung cancer and suggest a potential biological link to p53.
Palumbo:2014aa: Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development
M. C. Palumbo and S. Zenoni and M. Fasoli and M. Massonnet and L. Farina and F. Castiglione and M. Pezzotti and P. Paci
Plant Cell (2014)
http://dx.doi.org/10.1105/tpc.114.133710

We developed an approach that integrates different network-based methods to analyze the correlation network arising from large-scale gene expression data. By studying grapevine (Vitis vinifera) and tomato (Solanum lycopersicum) gene expression atlases and a grapevine berry transcriptomic data set during the transition from immature to mature growth, we identified a category named "fight-club hubs" characterized by a marked negative correlation with the expression profiles of neighboring genes in the network. A special subset named "switch genes" was identified, with the additional property of many significant negative correlations outside their own group in the network. Switch genes are involved in multiple processes and include transcription factors that may be considered master regulators of the previously reported transcriptome remodeling that marks the developmental shift from immature to mature growth. All switch genes, expressed at low levels in vegetative/green tissues, showed a significant increase in mature/woody organs, suggesting a potential regulatory role during the developmental transition. Finally, our analysis of tomato gene expression data sets showed that wild-type switch genes are downregulated in ripening-deficient mutants. The identification of known master regulators of tomato fruit maturation suggests our method is suitable for the detection of key regulators of organ development in different fleshy fruit crops.
Xiong:2012aa: Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets
Q. Xiong and N. Ancona and E. R. Hauser and S. Mukherjee and T. S. Furey
Genome Res 22 386-97 (2012)
http://dx.doi.org/10.1101/gr.124370.111

Single variant or single gene analyses generally account for only a small proportion of the phenotypic variation in complex traits. Alternatively, gene set or pathway association analyses are playing an increasingly important role in uncovering genetic architectures of complex traits through the identification of systematic genetic interactions. Two dominant paradigms for gene set analyses are association analyses based on SNP genotypes and those based on gene expression profiles. However, gene-disease association can manifest in many ways, such as alterations of gene expression, genotype, and copy number; thus, an integrative approach combining multiple forms of evidence can more accurately and comprehensively capture pathway associations. We have developed a single statistical framework, Gene Set Association Analysis (GSAA), that simultaneously measures genome-wide patterns of genetic variation and gene expression variation to identify sets of genes enriched for differential expression and/or trait-associated genetic markers. Simulation studies illustrate that joint analyses of genomic data increase the power to detect real associations when compared with gene set methods that use only one genomic data type. The analysis of two human diseases, glioblastoma and Crohn's disease, detected abnormalities in previously identified disease-associated pathways, such as pathways related to PI3K signaling, DNA damage response, and the activation of NFKB. In addition, GSAA predicted novel pathway associations, for example, differential genetic and expression characteristics in genes from the ABC transporter family in glioblastoma and from the HLA system in Crohn's disease. These demonstrate that GSAA can help uncover biological pathways underlying human diseases and complex traits.
Khurana:2013aa: Integrative annotation of variants from 1092 humans: application to cancer genomics
E. Khurana and Y. Fu and V. Colonna and X. J. Mu and H. M. Kang and T. Lappalainen and A. Sboner and L. Lochovsky and J. Chen and A. Harmanci and J. Das and A. Abyzov and S. Balasubramanian and K. Beal and D. Chakravarty and D. Challis and Y. Chen and D. Clarke and L. Clarke and F. Cunningham and U. S. Evani and P. Flicek and R. Fragoza and E. Garrison and R. Gibbs and Z. H. Gümüs and J. Herrero and N. Kitabayashi and Y. Kong and K. Lage and V. Liluashvili and S. M. Lipkin and D. G. MacArthur and G. Marth and D. Muzny and T. H. Pers and G. R. S. Ritchie and J. A. Rosenfeld and C. Sisu and X. Wei and M. Wilson and Y. Xue and F. Yu and 1000 Genomes Project Consortium and E. T. Dermitzakis and H. Yu and M. A. Rubin and C. Tyler-Smith and M. Gerstein
Science 342 1235587 (2013)
http://dx.doi.org/10.1126/science.1235587

Interpreting variants, especially noncoding ones, in the increasing number of personal genomes is challenging. We used patterns of polymorphisms in functionally annotated regions in 1092 humans to identify deleterious variants; then we experimentally validated candidates. We analyzed both coding and noncoding regions, with the former corroborating the latter. We found regions particularly sensitive to mutations ("ultrasensitive") and variants that are disruptive because of mechanistic effects on transcription-factor binding (that is, "motif-breakers"). We also found variants in regions with higher network centrality tend to be deleterious. Insertions and deletions followed a similar pattern to single-nucleotide variants, with some notable exceptions (e.g., certain deletions and enhancers). On the basis of these patterns, we developed a computational tool (FunSeq), whose application to ~90 cancer genomes reveals nearly a hundred candidate noncoding drivers.
Mosca:2010aa: Integrative genomics analyses reveal molecularly distinct subgroups of B-cell chronic lymphocytic leukemia patients with 13q14 deletion
L. Mosca and S. Fabris and M. Lionetti and K. Todoerti and L. Agnelli and F. Morabito and G. Cutrona and A. Andronache and S. Matis and F. Ferrari and M. Gentile and M. Spriano and V. Callea and G. Festini and S. Molica and G. L. Deliliers and S. Bicciato and M. Ferrarini and A. Neri
Clin Cancer Res 16 5641-53 (2010)
http://dx.doi.org/10.1158/1078-0432.CCR-10-0151

PURPOSE: Chromosome 13q14 deletion occurs in a substantial number of chronic lymphocytic leukemia (CLL) patients and it is believed to play a pathogenetic role. The exact mechanisms involved in this lesion have not yet been fully elucidated because of its heterogeneity and the imprecise knowledge of the implicated genes. This study was addressed to further contribute to the molecular definition of this lesion in CLL. EXPERIMENTAL DESIGN: We applied single-nucleotide polymorphism (SNP)-array technology and gene expression profiling data to investigate the 13q14 deletion occurring in a panel of 100 untreated, early-stage (Binet A) patients representative of the major genetics, molecular, and biological features of the disease. RESULTS: Concordantly with FISH analysis, SNP arrays identified 44 patients with del(13)(q14) including 11 cases with a biallelic deletion. The shorter monoallelic deletion was 635-kb long. The loss of the miR-15a/16-1 cluster occurred in all del(13)(q14) cases except in 2 patients with a monoallelic deletion, who retained both copies. MiR-15a/16 expression was significantly downregulated only in patients with the biallelic loss of the miRNA cluster compared to 13q normal cases. Finally, the natural grouping of SNP profiles by nonnegative matrix factorization algorithm showed that patients could be classified into 2 separate clusters, mainly characterized by short/biallelic versus wide/monoallelic 13q14 deletions. Supervised analyses of expression data showed that specific transcriptional profiles are correlated with these 2 genomic subgroups. CONCLUSIONS: Overall, our data highlight the presence of 2 distinct molecular types of 13q14 deletions, which may be of clinical relevance in CLL.
Camarca:2009aa: Intestinal T cell responses to gluten peptides are largely heterogeneous: implications for a peptide-based therapy in celiac disease
A. Camarca and R. P. Anderson and G. Mamone and O. Fierro and A. Facchiano and S. Costantini and D. Zanzi and J. Sidney and S. Auricchio and A. Sette and R. Troncone and C. Gianfrani
J Immunol 182 4158-66 (2009)
http://dx.doi.org/10.4049/jimmunol.0803181

The identification of gluten peptides eliciting intestinal T cell responses is crucial for the design of a peptide-based immunotherapy in celiac disease (CD). To date, several gluten peptides have been identified to be active in CD. In the present study, we investigated the recognition profile of gluten immunogenic peptides in adult HLA-DQ2(+) celiac patients. Polyclonal, gliadin-reactive T cell lines were generated from jejunal mucosa and assayed for both proliferation and IFN-gamma production in response to 21 peptides from wheat glutenins and alpha-, gamma-, and omega-gliadins. A magnitude analysis of the IFN-gamma responses was performed to assess the hierarchy of peptide potency. Remarkably, 12 of the 14 patients recognized a different array of peptides. All alpha-gliadin stimulatory peptides mapped the 57-89 N-terminal region, thus confirming the relevance of the known polyepitope 33-mer, although it was recognized by only 50% of the patients. By contrast, gamma-gliadin peptides were collectively recognized by the great majority (11 of 14, 78%) of CD volunteers. A 17-mer variant of 33-mer, QLQPFPQPQLPYPQPQP, containing only one copy of DQ2-alpha-I and DQ2-alpha-II epitopes, was as potent as 33-mer in stimulating intestinal T cell responses. A peptide from omega-gliadin, QPQQPFPQPQQPFPWQP, although structurally related to the alpha-gliadin 17-mer, is a distinct epitope and was active in 5 out of 14 patients. In conclusion, these results showed that there is a substantial heterogeneity in intestinal T cell responses to gluten and highlighted the relevance of gamma- and omega-gliadin peptides for CD pathogenesis. Our findings indicated that alpha-gliadin (57-73), gamma-gliadin (139-153), and omega-gliadin (102-118) are the most active gluten peptides in DQ2(+) celiac patients.
Visone:2009aa: Karyotype-specific microRNA signature in chronic lymphocytic leukemia
R. Visone and L. Z. Rassenti and A. Veronese and C. Taccioli and S. Costinean and B. D. Aguda and S. Volinia and M. Ferracin and J. Palatini and V. Balatti and H. Alder and M. Negrini and T. J. Kipps and C. M. Croce
Blood 114 3872-9 (2009)
http://dx.doi.org/10.1182/blood-2009-06-229211

Chromosomal abnormalities, immunoglobulin heavy chain variable-region (IGHV) gene mutation status, and zeta-associated protein 70 (ZAP-70) expression levels have independent prognostic relevance in chronic lymphocytic leukemia (CLL); however, their concordance is variable. Because deregulation of microRNAs has been linked to disease initiation and progression in CLL, we studied the value of the microRNAs as a signature for CLL patients with specific chromosomal abnormalities. We identified 32 microRNAs able to discriminate the 11q deletion, 17p deletion, trisomy 12, 13q deletion, and normal karyotype cytogenetic subgroups. The expression values of 9 among the 32 microRNAs (miR-151-3p, miR-34a, miR-29c, miR-29b, miR-155, miR-148a, miR-146a, miR-146b5p, and miR-640) were correlated with gene expression data from the same samples to assess their biologic impact on CLL. In this study we also found that IGHV unmutated, high expression of ZAP-70 protein, and low expression of the miR-223, miR-29c, miR-29b, and miR-181 family were strongly associated with disease progression in CLL cases harboring 17p deletion, whereas in those harboring trisomy 12 only high expression of the miR-181a, among the analyzed parameters, suggested more aggressive disease. Thus, the use of the microRNA-based classifications may yield clinically useful biomarkers of tumor behavior in CLL.
Horn:2014aa: KinomeXplorer: an integrated platform for kinome biology studies
H. Horn and E. M. Schoof and J. Kim and X. Robin and M. L. Miller and F. Diella and A. Palma and G. Cesareni and L. J. Jensen and R. Linding
Nat Methods 11 603-4 (2014)
http://dx.doi.org/10.1038/nmeth.2968
Tamminen:2012aa: Large-scale analysis of plasmid relationships through gene-sharing networks
M. Tamminen and M. Virta and R. Fani and M. Fondi
Mol Biol Evol 29 1225-40 (2012)
http://dx.doi.org/10.1093/molbev/msr292

Plasmids are vessels of genetic exchange in microbial communities. They are known to transfer between different host organisms and acquire diverse genetic elements from chromosomes and/or other plasmids. Therefore, they constitute an important element in microbial evolution by rapidly disseminating various genetic properties among different communities. A paradigmatic example of this is the dissemination of antibiotic resistance (AR) genes that has resulted in the emergence of multiresistant pathogenic bacterial strains. To globally analyze the evolutionary dynamics of plasmids, we built a large graph in which 2,343 plasmids (nodes) are connected according to the proteins shared by each other. The analysis of this gene-sharing network revealed an overall coherence between network clustering and the phylogenetic classes of the corresponding microorganisms, likely resulting from genetic barriers to horizontal gene transfer between distant phylogenetic groups. Habitat was not a crucial factor in clustering as plasmids from organisms inhabiting different environments were often found embedded in the same cluster. Analyses of network metrics revealed a statistically significant correlation between plasmid mobility and their centrality within the network, providing support to the observation that mobile plasmids are particularly important in spreading genes in microbial communities. Finally, our study reveals an extensive (and previously undescribed) sharing of AR genes between Actinobacteria and Gammaproteobacteria, suggesting that the former might represent an important reservoir of AR genes for the latter.
Picardi:2010aa: Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing
E. Picardi and D. S. Horner and M. Chiara and R. Schiavon and G. Valle and G. Pesole
Nucleic Acids Res 38 4755-67 (2010)
http://dx.doi.org/10.1093/nar/gkq202

RNA editing is a widespread post-transcriptional molecular phenomenon that can increase proteomic diversity, by modifying the sequence of completely or partially non-functional primary transcripts, through a variety of mechanistically and evolutionarily unrelated pathways. Editing by base substitution has been investigated in both animals and plants. However, conventional strategies based on directed Sanger sequencing are time-consuming and effectively preclude genome wide identification of RNA editing and assessment of partial and tissue-specific editing sites. In contrast, the high-throughput RNA-Seq approach allows the generation of a comprehensive landscape of RNA editing at the genome level. Short reads from Solexa/Illumina GA and ABI SOLiD platforms have been used to investigate the editing pattern in mitochondria of Vitis vinifera providing significant support for 401 C-to-U conversions in coding regions and an additional 44 modifications in non-coding RNAs. Moreover, 76% of all C-to-U conversions in coding genes represent partial RNA editing events and 28% of them were shown to be significantly tissue specific. Solexa/Illumina and SOLiD platforms showed different characteristics with respect to the specific issue of large-scale editing analysis, and the combined approach presented here reduces the false positive rate of discovery of editing events.
Ostuni:2013aa: Latent enhancers activated by stimulation in differentiated cells
R. Ostuni and V. Piccolo and I. Barozzi and S. Polletti and A. Termanini and S. Bonifacio and A. Curina and E. Prosperini and S. Ghisletti and G. Natoli
Cell 152 157-71 (2013)
http://dx.doi.org/10.1016/j.cell.2012.12.018

According to current models, once the cell has reached terminal differentiation, the enhancer repertoire is completely established and maintained by cooperatively acting lineage-specific transcription factors (TFs). TFs activated by extracellular stimuli operate within this predetermined repertoire, landing close to where master regulators are constitutively bound. Here, we describe latent enhancers, defined as regions of the genome that in terminally differentiated cells are unbound by TFs and lack the histone marks characteristic of enhancers but acquire these features in response to stimulation. Macrophage stimulation caused sequential binding of stimulus-activated and lineage-determining TFs to these regions, enabling deposition of enhancer marks. Once unveiled, many of these enhancers did not return to a latent state when stimulation ceased; instead, they persisted and mediated a faster and stronger response upon restimulation. We suggest that stimulus-specific expansion of the cis-regulatory repertoire provides an epigenomic memory of the exposure to environmental agents.
Nobile:2009aa: LGI1 mutations in autosomal dominant and sporadic lateral temporal epilepsy
C. Nobile and R. Michelucci and S. Andreazza and E. Pasini and S. C. E. Tosatto and P. Striano
Hum Mutat 30 530-6 (2009)
http://dx.doi.org/10.1002/humu.20925

Autosomal dominant lateral temporal epilepsy (ADLTE) or autosomal dominant partial epilepsy with auditory features (ADPEAF) is an inherited epileptic syndrome with onset in childhood/adolescence and benign evolution. The hallmark of the syndrome consists of typical auditory auras or ictal aphasia in most affected family members. ADTLE/ADPEAF is associated in about half of the families with mutations of the leucine-rich, glioma-inactivated 1 (LGI1) gene. In addition, de novo LGI1 mutations are found in about 2% of sporadic cases with idiopathic partial epilepsy with auditory features, who are clinically similar to the majority of patients with ADLTE/ADPEAF but have no family history. Twenty-five LGI1 mutations have been described in familial and sporadic lateral temporal epilepsy patients. The mutations are distributed throughout the gene and are mostly missense mutations occurring in both the N-terminal leucine rich repeat (LRR) and C-terminal EPTP (beta propeller) protein domains. We show a tridimensional model of the LRR protein region that allows missense mutations of this region to be divided into two distinct groups: structural and functional mutations. Frameshift, nonsense and splice site point mutations have also been reported that result in protein truncation or internal deletion. The various types of mutations are associated with a rather homogeneous phenotype, and no obvious genotype-phenotype correlation can be identified. Both truncating and missense mutations appear to prevent secretion of mutant proteins, suggesting a loss of function effect of mutations. The function of LGI1 is unclear. Several molecular mechanisms possibly leading to lateral temporal epilepsy are illustrated and briefly discussed.
Nakanishi:2014aa: Loss of miR-125b-1 contributes to head and neck cancer development by dysregulating TACSTD2 and MAPK pathway
H. Nakanishi and C. Taccioli and J. Palatini and C. Fernandez-Cymering and R. Cui and T. Kim and S. Volinia and C. M. Croce
Oncogene 33 702-12 (2014)
http://dx.doi.org/10.1038/onc.2013.13

MicroRNAs (miRNAs) have important roles in the initiation and progression of human cancer, but their role in head and neck cancer development and progression is not well defined. We aimed to determine whether specific miRNAs and their target mRNAs contribute to head and neck cancer pathogenesis and progression. To identify miRNAs associated with head and neck squamous cell carcinomas (HNSCCs), we analyzed HNSCC cell lines, normal head and neck tissues and normal keratinocytes by miRNA profiling; a group of differentially expressed miRNAs was identified, which includes miR-125b. Decreased expression of miR-125b is known to occur in epithelial cancers and many target mRNAs for this miR have been reported. We found decreased expression of miR-125b-1 and hypermethylation of its promoter in HNSCC compared with its non-malignant counterpart. The TACSTD2 (also known as TROP2) gene was identified and validated as a direct target of miR-125b-1. Abnormal expression of TACSTD2 cell-surface glycoprotein has been reported in most epithelial tumors, and the overexpressions of this mRNA and protein product has been considered a useful tumor marker. We report that miR-125b-1 causes mitogen-activated protein kinase pathway dysfunction through regulation of TACSTD2 expression. Thus, loss of miR-125b-1 may have a key role in the pathogenesis and progression of squamous cell carcinomas of head and neck and possibly of other tumors.
Sales:2010ab: MAGIA, a web-based tool for miRNA and Genes Integrated Analysis
G. Sales and A. Coppe and A. Bisognin and M. Biasiolo and S. Bortoluzzi and C. Romualdi
Nucleic Acids Res 38 W352-9 (2010)
http://dx.doi.org/10.1093/nar/gkq423

MAGIA (miRNA and genes integrated analysis) is a novel web tool for the integrative analysis of target predictions, miRNA and gene expression data. MAGIA is divided into two parts: the query section allows the user to retrieve and browse updated miRNA target predictions computed with a number of different algorithms (PITA, miRanda and Target Scan) and Boolean combinations thereof. The analysis section comprises a multistep procedure for (i) direct integration through different functional measures (parametric and non-parametric correlation indexes, a variational Bayesian model, mutual information and a meta-analysis approach based on P-value combination) of mRNA and miRNA expression data, (ii) construction of bipartite regulatory network of the best miRNA and mRNA putative interactions and (iii) retrieval of information available in several public databases of genes, miRNAs and diseases and via scientific literature text-mining. MAGIA is freely available for Academic users at http://gencomp.bio.unipd.it/magia.
Bisognin:2012aa: MAGIA²: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update)
A. Bisognin and G. Sales and A. Coppe and S. Bortoluzzi and C. Romualdi
Nucleic Acids Res 40 W13-21 (2012)
http://dx.doi.org/10.1093/nar/gks460

MAGIA(2) (http://gencomp.bio.unipd.it/magia2) is an update, extension and evolution of the MAGIA web tool. It is dedicated to the integrated analysis of in silico target prediction, microRNA (miRNA) and gene expression data for the reconstruction of post-transcriptional regulatory networks. miRNAs are fundamental post-transcriptional regulators of several key biological and pathological processes. As miRNAs act prevalently through target degradation, their expression profiles are expected to be inversely correlated to those of the target genes. Low specificity of target prediction algorithms makes integration approaches an interesting solution for target prediction refinement. MAGIA(2) performs this integrative approach supporting different association measures, multiple organisms and almost all target predictions algorithms. Nevertheless, miRNAs activity should be viewed as part of a more complex scenario where regulatory elements and their interactors generate a highly connected network and where gene expression profiles are the result of different levels of regulation. The updated MAGIA(2) tries to dissect this complexity by reconstructing mixed regulatory circuits involving either miRNA or transcription factor (TF) as regulators. Two types of circuits are identified: (i) a TF that regulates both a miRNA and its target and (ii) a miRNA that regulates both a TF and its target.
Al-Daghri:2012aa: Mammalian NPC1 genes may undergo positive selection and human polymorphisms associate with type 2 diabetes
N. M. Al-Daghri and R. Cagliani and D. Forni and M. S. Alokail and U. Pozzoli and K. M. Alkharfy and S. Sabico and M. Clerici and M. Sironi
BMC Med 10 140 (2012)
http://dx.doi.org/10.1186/1741-7015-10-140

BACKGROUND: The NPC1 gene encodes a protein involved in intracellular lipid trafficking; its second endosomal loop (loop 2) is a receptor for filoviruses. A polymorphism (His215Arg) in NPC1 was associated with obesity in Europeans. Adaptations to diet and pathogens represented powerful selective forces; thus, we analyzed the evolutionary history of the gene and exploited this information for the identification of variants/residues of functional importance in human disease. METHODS: We performed phylogenetic analysis, population genetic tests, and genotype-phenotype analysis in a population from Saudi Arabia. RESULTS: Maximum-likelihood ratio tests indicated the action of positive selection on loop 2 and identified three residues as selection targets; these were confirmed by an independent random effects likelihood (REL) analysis. No selection signature was detected in present-day human populations, but analysis of nonsynonymous polymorphisms showed that a variant (Ile642Met, rs1788799) in the sterol sensing domain affects a highly conserved position. This variant and the previously described His215Arg polymorphism were tested for association with obesity and type 2 diabetes (T2D) in a cohort from Saudi Arabia. Whereas no association with obesity was detected, 642Met allele was found to predispose to T2D. A significant interaction was noted with sex (P = 0.041), and stratification on the basis of gender indicated that the association is driven by men (P = 0.0021, OR = 1.5). Notably, two NPC1 haplotypes were also associated with T2D in men (rs1805081-rs1788799, His-Met: P = 0.0012, OR = 1.54; His-Ile: P = 0.0004, OR = 0.63). CONCLUSIONS: Our data indicate a sex-specific effect of NPC1 variants on T2D risk and describe putative binding sites for filoviruses entry.
Sacco:2012aa: Mapping the human phosphatome on growth pathways
F. Sacco and P. F. Gherardini and S. Paoluzi and J. Saez-Rodriguez and M. Helmer-Citterich and A. Ragnini-Wilson and L. Castagnoli and G. Cesareni
Mol Syst Biol 8 603 (2012)
http://dx.doi.org/10.1038/msb.2012.36

Large-scale siRNA screenings allow linking the function of poorly characterized genes to phenotypic readouts. According to this strategy, genes are associated with a function of interest if the alteration of their expression perturbs the phenotypic readouts. However, given the intricacy of the cell regulatory network, the mapping procedure is low resolution and the resulting models provide little mechanistic insights. We have developed a new strategy that combines multiparametric analysis of cell perturbation with logic modeling to achieve a more detailed functional mapping of human genes onto complex pathways. A literature-derived optimized model is used to infer the cell activation state following upregulation or downregulation of the model entities. By matching this signature with the experimental profile obtained in the high-throughput siRNA screening it is possible to infer the target of each protein, thus defining its 'entry point' in the network. By this novel approach, 41 phosphatases that affect key growth pathways were identified and mapped onto a human epithelial cell-specific growth model, thus providing insights into the mechanisms underlying their function.
Iannelli:2014aa: Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency
F. Iannelli and A. Collino and S. Sinha and E. Radaelli and P. Nicoli and L. D'Antiga and A. Sonzogni and J. Faivre and M. A. Buendia and E. Sturm and R. J. Thompson and A. S. Knisely and G. Natoli and S. Ghisletti and F. D. Ciccarelli
Nat Commun 5 3850 (2014)
http://dx.doi.org/10.1038/ncomms4850

Hepatocellular carcinoma (HCC) is almost invariably associated with an underlying inflammatory state, whose direct contribution to the acquisition of critical genomic changes is unclear. Here we map acquired genomic alterations in human and mouse HCCs induced by defects in hepatocyte biliary transporters, which expose hepatocytes to bile salts and cause chronic inflammation that develops into cancer. In both human and mouse cancer genomes, we find few somatic point mutations with no impairment of cancer genes, but massive gene amplification and rearrangements. This genomic landscape differs from that of virus- and alcohol-associated liver cancer. Copy-number gains preferentially occur at late stages of cancer development and frequently target the MAPK signalling pathway, and in particular direct regulators of JNK. The pharmacological inhibition of JNK retards cancer progression in the mouse. Our study demonstrates that intrahepatic cholestasis leading to hepatocyte exposure to bile acids and inflammation promotes cancer through genomic modifications that can be distinguished from those determined by other aetiological factors.
Pierleoni:2011aa: MemPype: a pipeline for the annotation of eukaryotic membrane proteins
A. Pierleoni and V. Indio and C. Savojardo and P. Fariselli and P. L. Martelli and R. Casadio
Nucleic Acids Res 39 W375-80 (2011)
http://dx.doi.org/10.1093/nar/gkr282

MemPype is a Python-based pipeline including previously published methods for the prediction of signal peptides (SPEP), glycophosphatidylinositol (GPI) anchors (PredGPI), all-alpha membrane topology (ENSEMBLE), and a recent method (MemLoci) that specifically discriminates the localization of eukaryotic membrane proteins in: 'cell membrane', 'internal membranes', 'organelle membranes'. MemLoci scores with accuracy of 70% and generalized correlation coefficient (GCC) of 0.50 on a rigorous homology-unbiased validation set and overpasses other predictors for subcellular localization. The annotation process is based both on inheritance through homology and computational methods. Each submitted protein first retrieves, when available, up to 25 similar proteins (with sequence identity ≥50% and alignment coverage ≥50% on both sequences). This helps the identification of membrane-associated proteins and detailed localization tags. Each protein is also filtered for the presence of a GPI anchor [0.8% false positive rate (FPR)]. A positive score of GPI anchor prediction labels the sequence as exposed to 'Cell surface'. Concomitantly the sequence is analysed for the presence of a signal peptide and classified with MemLoci into one of three discriminated classes. Finally the sequence is filtered for predicting its putative all-alpha protein membrane topology (FPR <1%). The web server is available at: http://mu2py.biocomp.unibo.it/mempype.
Calderone:2013aa: mentha: a resource for browsing integrated protein-interaction networks
A. Calderone and L. Castagnoli and G. Cesareni
Nat Methods 10 690-1 (2013)
http://dx.doi.org/10.1038/nmeth.2561
Bolser:2012aa: MetaBase--the wiki-database of biological databases
D. M. Bolser and P.-Y. Chibon and N. Palopoli and S. Gong and D. Jacob and V. D. Del Angel and D. Swan and S. Bassi and V. González and P. Suravajhala and S. Hwang and P. Romano and R. Edwards and B. Bishop and J. Eargle and T. Shtatland and N. J. Provart and D. Clements and D. P. Renfro and D. Bhak and J. Bhak
Nucleic Acids Res 40 D1250-4 (2012)
http://dx.doi.org/10.1093/nar/gkr1099

Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project.
Fallarino:2010aa: Metabotropic glutamate receptor-4 modulates adaptive immunity and restrains neuroinflammation
F. Fallarino and C. Volpi and F. Fazio and S. Notartomaso and C. Vacca and C. Busceti and S. Bicciato and G. Battaglia and V. Bruno and P. Puccetti and M. C. Fioretti and F. Nicoletti and U. Grohmann and R. Di Marco
Nat Med 16 897-902 (2010)
http://dx.doi.org/10.1038/nm.2183

High amounts of glutamate are found in the brains of people with multiple sclerosis, an inflammatory disease marked by progressive demyelination. Glutamate might affect neuroinflammation via effects on immune cells. Knockout mice lacking metabotropic glutamate receptor-4 (mGluR4) were markedly vulnerable to experimental autoimmune encephalomyelitis (EAE, a mouse model of multiple sclerosis) and developed responses dominated by interleukin-17-producing T helper (T(H)17) cells. In dendritic cells (DCs) from those mice, defective mGluR4 signaling-which would normally decrease intracellular cAMP formation-biased T(H) cell commitment to the T(H)17 phenotype. In wild-type mice, mGluR4 was constitutively expressed in all peripheral DCs, and this expression increased after cell activation. Treatment of wild-type mice with a selective mGluR4 enhancer increased EAE resistance via regulatory T (T(reg)) cells. The high amounts of glutamate in neuroinflammation might reflect a counterregulatory mechanism that is protective in nature and might be harnessed therapeutically for restricting immunopathology in multiple sclerosis.
Andreini:2009aa: Metalloproteomes: a bioinformatic approach
C. Andreini and I. Bertini and A. Rosato
Acc Chem Res 42 1471-9 (2009)
http://dx.doi.org/10.1021/ar900015x

Genome-wide studies are providing researchers with a potentially complete list of the molecular components present in living systems. It is now evident that several metal ions are essential to life and that metalloproteins, that is, proteins that require a metal ion to perform their physiological function, are widespread in all organisms. However, there is currently a lack of well-established experimental methods aimed at analyzing the complete set of metalloproteins encoded by an organism (the metalloproteome). This information is essential for a comprehensive understanding of the whole of the processes occurring in living systems. Predictive tools must thus be applied to define metalloproteomes. In this Account, we discuss the current progress in the development of bioinformatics methods for the prediction, based solely on protein sequences, of metalloproteins. With these methods, it is possible to scan entire proteomes for metalloproteins, such as zinc proteins or copper proteins, which are identified by the presence of specific metal-binding sites, metal-binding domains, or both. The predicted metalloproteins can be then analyzed to obtain information on their function and evolution. For example, the comparative analysis of the content and usage of different metalloproteins across living organisms can be used to obtain hints on the evolution of metalloproteomes. As case studies, we predicted the content of zinc, nonheme iron, and copper-proteins in a representative set of organisms taken from the three domains of life. The zinc proteome represents about 9% of the entire proteome in eukaryotes, but it ranges from 5% to 6% in prokaryotes, therefore indicating a substantial increase of the number of zinc proteins in higher organisms. In contrast, the number of nonheme iron proteins is relatively constant in eukaryotes and prokaryotes, and therefore their relative share diminishes in passing from archaea (about 7%), to bacteria (about 4%), to eukaryotes (about 1%). Copper proteins represent less than 1% of the proteomes in all the organisms studied. We also discuss the limits of these methods, the approaches used to overcome some of these limits to improve our predictions, and possible future developments in the field of bioinformatics-based investigation of metalloproteins. As a long-standing goal of the biological sciences, the understanding of life at the systems level, or systems biology, is experiencing a rekindling of interest; ready access to complete information on metalloproteomes is crucial to correctly represent the role of metal ions in living organisms.
Andreini:2013aa: MetalPDB: a database of metal sites in biological macromolecular structures
C. Andreini and G. Cavallaro and S. Lorenzini and A. Rosato
Nucleic Acids Res 41 D312-9 (2013)
http://dx.doi.org/10.1093/nar/gks1063

We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal-macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner.
Garzon:2009aa: MicroRNA 29b functions in acute myeloid leukemia
R. Garzon and C. E. A. Heaphy and V. Havelange and M. Fabbri and S. Volinia and T. Tsao and N. Zanesi and S. M. Kornblau and G. Marcucci and G. A. Calin and M. Andreeff and C. M. Croce
Blood 114 5331-41 (2009)
http://dx.doi.org/10.1182/blood-2009-03-211938

MicroRNAs (miRNAs) are associated with cytogenetics and molecular subtypes of acute myelogeneous leukemia (AML), but their impact on AML pathogenesis is poorly understood. We have previously shown that miR-29b expression is deregulated in primary AML blasts. In this work, we investigated the functional role of miR-29b in leukemogenesis. Restoration of miR-29b in AML cell lines and primary samples induces apoptosis and dramatically reduces tumorigenicity in a xenograft leukemia model. Transcriptome analysis after ectopic transfection of synthetic miR-29b into leukemia cells indicates that miR-29b target apoptosis, cell cycle, and proliferation pathways. A significant enrichment for apoptosis genes, including MCL-1, was found among the mRNAs inversely correlated with miR-29b expression in 45 primary AML samples. Together, the data support a tumor suppressor role for miR-29 and provide a rationale for the use of synthetic miR-29b oligonucleotides as a novel strategy to improve treatment response in AML.
Di-Leva:2010aa: MicroRNA cluster 221-222 and estrogen receptor alpha interactions in breast cancer
G. Di Leva and P. Gasparini and C. Piovan and A. Ngankeu and M. Garofalo and C. Taccioli and M. V. Iorio and M. Li and S. Volinia and H. Alder and T. Nakamura and G. Nuovo and Y. Liu and K. P. Nephew and C. M. Croce
J Natl Cancer Inst 102 706-21 (2010)
http://dx.doi.org/10.1093/jnci/djq102

BACKGROUND: Several lines of evidence have suggested that estrogen receptor alpha (ERalpha)-negative breast tumors, which are highly aggressive and nonresponsive to hormonal therapy, arise from ERalpha-positive precursors through different molecular pathways. Because microRNAs (miRNAs) modulate gene expression, we hypothesized that they may have a role in ER-negative tumor formation. METHODS: Gene expression profiles were used to highlight the global changes induced by miRNA modulation of ERalpha protein. miRNA transfection and luciferase assays enabled us to identify new targets of miRNA 206 (miR-206) and miRNA cluster 221-222 (miR-221-222). Northern blot, luciferase assays, estradiol treatment, and chromatin immunoprecipitation were performed to identify the miR-221-222 transcription unit and the mechanism implicated in its regulation. RESULTS: Different global changes in gene expression were induced by overexpression of miR-221-222 and miR-206 in ER-positive cells. miR-221 and -222 increased proliferation of ERalpha-positive cells, whereas miR-206 had an inhibitory effect (mean absorbance units [AU]: miR-206: 500 AU, 95% confidence interval [CI]) = 480 to 520; miR-221: 850 AU, 95% CI = 810 to 873; miR-222: 879 AU, 95% CI = 850 to 893; P < .05). We identified hepatocyte growth factor receptor and forkhead box O3 as new targets of miR-206 and miR-221-222, respectively. We demonstrated that ERalpha negatively modulates miR-221 and -222 through the recruitment of transcriptional corepressor partners: nuclear receptor corepressor and silencing mediator of retinoic acid and thyroid hormone receptor. CONCLUSIONS: These findings suggest that the negative regulatory loop involving miR-221-222 and ERalpha may confer proliferative advantage and migratory activity to breast cancer cells and promote the transition from ER-positive to ER-negative tumors.
Baffa:2009aa: MicroRNA expression profiling of human metastatic cancers identifies cancer gene targets
R. Baffa and M. Fassan and S. Volinia and B. O'Hara and C.-G. Liu and J. P. Palazzo and M. Gardiman and M. Rugge and L. G. Gomella and C. M. Croce and A. Rosenberg
J Pathol 219 214-21 (2009)
http://dx.doi.org/10.1002/path.2586

Small non-coding microRNAs (miRNAs) contribute to cancer development and progression, and are differentially expressed in normal tissues and cancers. However, the specific role of miRNAs in the metastatic process is still unknown. To seek a specific miRNA expression signature characterizing the metastatic phenotype of solid tumours, we performed a miRNA microarray analysis on 43 paired primary tumours (ten colon, ten bladder, 13 breast, and ten lung cancers) and one of their related metastatic lymph nodes. We identified a metastatic cancer miRNA signature comprising 15 overexpressed and 17 underexpressed miRNAs. Our results were confirmed by qRT-PCR analysis. Among the miRNAs identified, some have a well-characterized association with cancer progression, eg miR-10b, miR-21, miR-30a, miR-30e, miR-125b, miR-141, miR-200b, miR-200c, and miR-205. To further support our data, we performed an immunohistochemical analysis for three well-defined miRNA gene targets (PDCD4, DHFR, and HOXD10 genes) on a small series of paired colon, breast, and bladder cancers, and one of their metastatic lymph nodes. We found that the immunohistochemical expression of these targets significantly follows the corresponding miRNA deregulation. Our results suggest that specific miRNAs may be directly involved in cancer metastasis and that they may represent a novel diagnostic tool in the characterization of metastatic cancer gene targets.
Fassan:2009aa: MicroRNA expression profiling of male breast cancer
M. Fassan and R. Baffa and J. P. Palazzo and J. Lloyd and M. Crosariol and C.-G. Liu and S. Volinia and H. Alder and M. Rugge and C. M. Croce and A. Rosenberg
Breast Cancer Res 11 R58 (2009)
http://dx.doi.org/10.1186/bcr2348

INTRODUCTION: MicroRNAs (miRNAs) are a class of small noncoding RNAs that control gene expression by targeting mRNAs and triggering either translation repression or RNA degradation. Their aberrant expression may be involved in human diseases, including cancer. To test the hypothesis that there is a specific miRNA expression signature which characterizes male breast cancers, we performed miRNA microarray analysis in a series of male breast cancers and compared them with cases of male gynecomastia and female breast cancers. METHODS: Paraffin blocks were obtained at the Department of Pathology of Thomas Jefferson University from 28 male patients including 23 breast cancers and five cases of male gynecomastia, and from 10 female ductal breast carcinomas. The RNA harvested was hybridized to miRNA microarrays (~1,100 miRNA probes, including 326 human and 249 mouse miRNA genes, spotted in duplicate). To further support the microarray data, an immunohistochemical analysis for two specific miRNA gene targets (HOXD10 and VEGF) was performed in a small series of male breast carcinoma and gynecomastia samples. RESULTS: We identified a male breast cancer miRNA signature composed of a large portion of underexpressed miRNAs. In particular, 17 miRNAs with increased expression and 26 miRNAs with decreased expression were identified in male breast cancer compared with gynecomastia. Among these miRNAs, some had well-characterized cancer development association and some showed a deregulation in cancer specimens similar to the one previously observed in the published signatures of female breast cancer. Comparing male with female breast cancer miRNA expression signatures, 17 significantly deregulated miRNAs were observed (four overexpressed and 13 underexpressed in male breast cancers). The HOXD10 and VEGF gene immunohistochemical expression significantly follows the corresponding miRNA deregulation. CONCLUSIONS: Our results suggest that specific miRNAs may be directly involved in male breast cancer development and that they may represent a novel diagnostic tool in the characterization of specific cancer gene targets.
Rossi:2010aa: microRNA fingerprinting of CLL patients with chromosome 17p deletion identify a miR-21 score that stratifies early survival
S. Rossi and M. Shimizu and E. Barbarotto and M. S. Nicoloso and F. Dimitri and D. Sampath and M. Fabbri and S. Lerner and L. L. Barron and L. Z. Rassenti and L. Jiang and L. Xiao and J. Hu and P. Secchiero and G. Zauli and S. Volinia and M. Negrini and W. Wierda and T. J. Kipps and W. Plunkett and K. R. Coombes and L. V. Abruzzo and M. J. Keating and G. A. Calin
Blood 116 945-52 (2010)
http://dx.doi.org/10.1182/blood-2010-01-263889

Aberrant expression of microRNAs (miRNAs) has been associated with clinical outcome in patients with chronic lymphocytic leukemia (CLL). To identify a powerful and easily assessable miRNA bio-marker of prognosis and survival, we performed quantitative reverse-transcription polymerase chain reaction (qRT-PCR) profiling in 104 CLL patients with a well-defined chromosome 17p status, and we validated our findings with miRNA microarray data from an independent cohort of 80 patients. We found that miR-15a, miR-21, miR-34a, miR-155, and miR-181b were differentially expressed between CLLs with chromosome 17p deletion and CLLs with normal 17p and normal karyotype, and that miR-181b was down-regulated in therapy-refractory cases. miR-21 expression levels were significantly higher in patients with poor prognosis and predicted overall survival (OS), and miR-181b expression levels significantly predicted treatment-free survival. We developed a 21FK score (miR-21 qRT-PCR, fluorescence in situ hybridization, Karyotype) to stratify patients according to OS and found that patients with a low score had a significantly longer OS time. When we evaluated the relative power of the 21FK score with the most used prognostic factors, the score was the most significant in both CLL cohorts. We conclude that the 21FK score represents a useful tool for distinguishing between good-prognosis and poor-prognosis CLL patients.
Garzon:2009ab: MicroRNA-29b induces global DNA hypomethylation and tumor suppressor gene reexpression in acute myeloid leukemia by targeting directly DNMT3A and 3B and indirectly DNMT1
R. Garzon and S. Liu and M. Fabbri and Z. Liu and C. E. A. Heaphy and E. Callegari and S. Schwind and J. Pang and J. Yu and N. Muthusamy and V. Havelange and S. Volinia and W. Blum and L. J. Rush and D. Perrotti and M. Andreeff and C. D. Bloomfield and J. C. Byrd and K. Chan and L.-C. Wu and C. M. Croce and G. Marcucci
Blood 113 6411-8 (2009)
http://dx.doi.org/10.1182/blood-2008-07-170589

Aberrant DNA hypermethylation contributes to myeloid leukemogenesis by silencing structurally normal genes involved in hematopoiesis. MicroRNAs (miRNAs) are noncoding RNAs that regulate gene expression by targeting protein-coding mRNAs. Recently, miRNAs have been shown to play a role as both targets and effectors in gene hypermethylation and silencing in malignant cells. In the current study, we showed that enforced expression of miR-29b in acute myeloid leukemia cells resulted in marked reduction of the expression of DNA methyltransferases DNMT1, DNMT3A, and DNMT3B at both RNA and protein levels. This in turn led to decrease in global DNA methylation and reexpression of p15(INK4b) and ESR1 via promoter DNA hypomethylation. Although down-regulation of DNMT3A and DNMT3B was the result of a direct interaction of miR-29b with the 3' untranslated regions of these genes, no predicted miR-29b interaction sites were found in the DNMT1 3' untranslated regions. Further experiments revealed that miR-29b down-regulates DNMT1 indirectly by targeting Sp1, a transactivator of the DNMT1 gene. Altogether, these data provide novel functional links between miRNAs and aberrant DNA hypermethylation in acute myeloid leukemia and suggest a potentially therapeutic use of synthetic miR-29b oligonucleotides as effective hypomethylating compounds.
Meng:2013aa: MicroRNA-31 predicts the presence of lymph node metastases and survival in patients with lung adenocarcinoma
W. Meng and Z. Ye and R. Cui and J. Perry and V. Dedousi-Huebner and A. Huebner and Y. Wang and B. Li and S. Volinia and H. Nakanishi and T. Kim and S.-S. Suh and L. W. Ayers and P. Ross and C. M. Croce and A. Chakravarti and V. X. Jin and T. Lautenschlaeger
Clin Cancer Res 19 5423-33 (2013)
http://dx.doi.org/10.1158/1078-0432.CCR-13-0320

PURPOSE: We conducted genome-wide miRNA-sequencing (miRNA-seq) in primary cancer tissue from patients of lung adenocarcinoma to identify markers for the presence of lymph node metastasis. EXPERIMENTAL DESIGN: Markers for lymph node metastasis identified by sequencing were validated in a separate cohort using quantitative PCR. After additional validation in the The Cancer Genome Atlas (TCGA) dataset, functional characterization studies were conducted in vitro. RESULTS: MiR-31 was upregulated in lung adenocarcinoma tissues from patients with lymph node metastases compared with those without lymph node metastases. We confirmed miR-31 to be upregulated in lymph node-positive patients in a separate patient cohort (P = 0.009, t test), and to be expressed at higher levels in adenocarcinoma tissue than in matched normal adjacent lung tissues (P < 0.0001, paired t test). MiR-31 was then validated as a marker for lymph node metastasis in an external validation cohort of 233 lung adenocarcinoma cases of the TCGA (P = 0.031, t test). In vitro functional assays showed that miR-31 increases cell migration, invasion, and proliferation in an ERK1/2 signaling-dependent manner. Notably, miR-31 was a significant predictor of survival in a multivariate cox regression model even when controlling for cancer staging. Exploratory in silico analysis showed that low expression of miR-31 is associated with excellent survival for T2N0 patients. CONCLUSIONS: We applied miRNA-seq to study microRNomes in lung adenocarcinoma tissue samples for the first time and potentially identified a miRNA predicting the presence of lymph node metastasis and survival outcomes in patients of lung adenocarcinoma.
Parikh:2014aa: microRNA-181a has a critical role in ovarian cancer progression through the regulation of the epithelial-mesenchymal transition
A. Parikh and C. Lee and P. Joseph and S. Marchini and A. Baccarini and V. Kolev and C. Romualdi and R. Fruscio and H. Shah and F. Wang and G. Mullokandov and D. Fishman and M. D'Incalci and J. Rahaman and T. Kalir and R. W. Redline and B. D. Brown and G. Narla and A. Difeo
Nat. Commun. 5 (2014)
http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/WOS:000331079800001

Ovarian cancer is a leading cause of cancer deaths among women. Effective targets to treat advanced epithelial ovarian cancer (EOC) and biomarkers to predict treatment response are still lacking because of the complexity of pathways involved in ovarian cancer progression. Here we show that miR-181a promotes TGF-beta-mediated epithelial-to-mesenchymal transition via repression of its functional target, Smad7. miR-181a and phosphorylated Smad2 are enriched in recurrent compared with matched-primary ovarian tumours and their expression is associated with shorter time to recurrence and poor outcome in patients with EOC. Furthermore, ectopic expression of miR-181a results in increased cellular survival, migration, invasion, drug resistance and in vivo tumour burden and dissemination. In contrast, miR-181a inhibition via decoy vector suppression and Smad7 re-expression results in significant reversion of these phenotypes. Combined, our findings highlight an unappreciated role for miR-181a, Smad7, and the TGF-beta signalling pathway in high-grade serous ovarian cancer.
Buffa:2011aa: microRNA-associated progression pathways and potential therapeutic targets identified by integrated mRNA and microRNA expression profiling in breast cancer
F. M. Buffa and C. Camps and L. Winchester and C. E. Snell and H. E. Gee and H. Sheldon and M. Taylor and A. L. Harris and J. Ragoussis
Cancer Res 71 5635-45 (2011)
http://dx.doi.org/10.1158/0008-5472.CAN-11-0489

microRNA expression profiling plays an emerging role in cancer classification and identification of therapeutic strategies. In this study, we have evaluated the benefits of a joint microRNA-mRNA analysis in breast cancer. Matched mRNA and microRNA global expression profiling was conducted in a well-annotated cohort of 207 cases with complete 10-year follow-up. Penalized Cox regression including microRNA expression, mRNA expression, and clinical covariates was used to identify microRNAs associated with distant relapse-free survival (DRFS) that provide independent prognostic information, and are not simply surrogates of previously identified prognostic covariates. Penalized regression was chosen to prevent overfitting. Furthermore, microRNA-mRNA relationships were explored by global expression analysis, and exploited to validate results in several published cohorts (n = 592 with DRFS, n = 1,050 with recurrence-free survival). Four microRNAs were independently associated with DRFS in estrogen receptor (ER)-positive (3 novel and 1 known; miR-128a) and 6 in ER-negative (5 novel and 1 known; miR-210) cases. Of the latter, miR-342, -27b, and -150 were prognostic also in triple receptor-negative tumors. Coordinated expression of predicted target genes and prognostic microRNAs strengthened these results, most significantly for miR-210, -128a, and -27b, whose targets were prognostic in meta-analysis of several cohorts. In addition, miR-210 and -128a showed coordinated expression with their cognate pri-microRNAs, which were themselves prognostic in independent cohorts. Our integrated microRNA-mRNA global profiling approach has identified microRNAs independently associated with prognosis in breast cancer. Furthermore, it has validated known and predicted microRNA-target interactions, and elucidated their association with key pathways that could represent novel therapeutic targets.
Frampton:2014aa: MicroRNAs cooperatively inhibit a network of tumor suppressor genes to promote pancreatic tumor growth and progression
A. E. Frampton and L. Castellano and T. Colombo and E. Giovannetti and J. Krell and J. Jacob and L. Pellegrino and L. Roca-Alonso and N. Funel and T. M. H. Gall and A. De Giorgio and F. G. Pinho and V. Fulci and D. J. Britton and R. Ahmad and N. A. Habib and R. C. Coombes and V. Harding and T. Knösel and J. Stebbing and L. R. Jiao
Gastroenterology 146 268-77.e18 (2014)
http://dx.doi.org/10.1053/j.gastro.2013.10.010

BACKGROUND & AIMS: There has not been a broad analysis of the combined effects of altered activities of microRNAs (miRNAs) in pancreatic ductal adenocarcinoma (PDAC) cells, and it is unclear how these might affect tumor progression or patient outcomes. METHODS: We combined data from miRNA and messenger RNA (mRNA) expression profiles and bioinformatic analyses to identify an miRNA-mRNA regulatory network in PDAC cell lines (PANC-1 and MIA PaCa-2) and in PDAC samples from patients. We used this information to identify miRNAs that contribute most to tumorigenesis. RESULTS: We identified 3 miRNAs (MIR21, MIR23A, and MIR27A) that acted as cooperative repressors of a network of tumor suppressor genes that included PDCD4, BTG2, and NEDD4L. Inhibition of MIR21, MIR23A, and MIR27A had synergistic effects in reducing proliferation of PDAC cells in culture and growth of xenograft tumors in mice. The level of inhibition was greater than that of inhibition of MIR21 alone. In 91 PDAC samples from patients, high levels of a combination of MIR21, MIR23A, and MIR27A were associated with shorter survival times after surgical resection. CONCLUSIONS: In an integrated data analysis, we identified functional miRNA-mRNA interactions that contribute to growth of PDACs. These findings indicate that miRNAs act together to promote tumor progression; therapeutic strategies might require inhibition of several miRNAs.
Ceol:2010aa: MINT, the molecular interaction database: 2009 update
A. Ceol and A. Chatr Aryamontri and L. Licata and D. Peluso and L. Briganti and L. Perfetto and L. Castagnoli and G. Cesareni
Nucleic Acids Res 38 D532-9 (2010)
http://dx.doi.org/10.1093/nar/gkp983

MINT (http://mint.bio.uniroma2.it/mint) is a public repository for molecular interactions reported in peer-reviewed journals. Since its last report, MINT has grown considerably in size and evolved in scope to meet the requirements of its users. The main changes include a more precise definition of the curation policy and the development of an enhanced and user-friendly interface to facilitate the analysis of the ever-growing interaction dataset. MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium.
Licata:2012aa: MINT, the molecular interaction database: 2012 update
L. Licata and L. Briganti and D. Peluso and L. Perfetto and M. Iannuccelli and E. Galeota and F. Sacco and A. Palma and A. P. Nardozza and E. Santonico and L. Castagnoli and G. Cesareni
Nucleic Acids Res 40 D857-61 (2012)
http://dx.doi.org/10.1093/nar/gkr930

The Molecular INTeraction Database (MINT, http://mint.bio.uniroma2.it/mint/) is a public repository for protein-protein interactions (PPI) reported in peer-reviewed journals. The database grows steadily over the years and at September 2011 contains approximately 235,000 binary interactions captured from over 4750 publications. The web interface allows the users to search, visualize and download interactions data. MINT is one of the members of the International Molecular Exchange consortium (IMEx) and adopts the Molecular Interaction Ontology of the Proteomics Standard Initiative (PSI-MI) standards for curation and data exchange. MINT data are freely accessible and downloadable at http://mint.bio.uniroma2.it/mint/download.do. We report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction.
Peschiaroli:2013aa: miR-143 regulates hexokinase 2 expression in cancer cells
A. Peschiaroli and A. Giacobbe and A. Formosa and E. K. Markert and L. Bongiorno-Borbone and A. J. Levine and E. Candi and A. D'Alessandro and L. Zolla and A. Finazzi Agrò and G. Melino
Oncogene 32 797-802 (2013)
http://dx.doi.org/10.1038/onc.2012.100

Tumor cells activate pathways that facilitate and stimulate glycolysis even in the presence of adequate levels of oxygen in order to satisfy their continuous need of molecules, such as nucleotides, ATP and fatty acids, necessary to support their rapid proliferation. Accordingly, a variety of human tumors are characterized by elevated expression levels of the hexokinase 2 isoform (HK2). Although different molecular mechanisms, including genetic and epigenetic mechanisms, have been suggested to account for the altered expression of HK2 in tumors, the potential role of microRNAs (miRNAs) in the regulation of HK2 expression has not been evaluated. Here, we report that miR-143 inhibits HK2 expression via a conserved miR-143 recognition motif located in the 3'-untranslated region (3'UTR) of HK2 mRNA. We demonstrate that miR143 inhibits HK2 expression both in primary keratinocytes and in head and neck squamous cell carcinoma (HNSCC)-derived cell lines. Importantly, we found that miR-143 inversely correlates with HK2 expression in HNSCC-derived cell lines and in primary tumors. We also report that the miRNA-dependent regulation of hexokinase expression is not limited to HK2 as miR-138 targets HK1 via a specific recognition motif located in its 3'UTR. All these data unveil a new miRNA-dependent mechanism of regulation of hexokinase expression potentially important in the regulation of glucose metabolism of cancer cells.
Sandhu:2012aa: miR-155 targets histone deacetylase 4 (HDAC4) and impairs transcriptional activity of B-cell lymphoma 6 (BCL6) in the Eμ-miR-155 transgenic mouse model
S. K. Sandhu and S. Volinia and S. Costinean and M. Galasso and R. Neinast and R. Santhanam and M. R. Parthun and D. Perrotti and G. Marcucci and R. Garzon and C. M. Croce
Proc Natl Acad Sci U S A 109 20047-52 (2012)
http://dx.doi.org/10.1073/pnas.1213764109

Multiple studies have established that microRNAs (miRNAs) are involved in the initiation and progression of cancer. Notably, miR-155 is one of the most overexpressed miRNAs in several solid and hematological malignancies. Ectopic miR-155 expression in mice B cells (Eμ-miR-155 transgenic mice) has been shown to induce pre-B-cell proliferation followed by high-grade lymphoma/leukemia. Loss of miR-155 in mice resulted in impaired immunity due to defective T-cell-mediated immune response. Here we provide a mechanistic insight into miR-155-induced leukemogenesis in the Eμ-miR-155 mouse model through genome-wide transcriptome analysis of naïve B cells and target studies. We found that a key transcriptional repressor and proto-oncogene, Bcl6 is significantly down-regulated in Eμ-miR-155 mice. The reduction of Bcl6 subsequently leads to de-repression of some of the known Bcl6 targets like inhibitor of differentiation (Id2), interleukin-6 (IL6), cMyc, Cyclin D1, and Mip1α/ccl3, all of which promote cell survival and proliferation. We show that Bcl6 is indirectly regulated by miR-155 through Mxd1/Mad1 up-regulation. Interestingly, we found that miR-155 directly targets HDAC4, a corepressor partner of BCL6. Furthermore, ectopic expression of HDAC4 in human-activated B-cell-type diffuse large B-cell lymphoma (DLBCL) cells results in reduced miR-155-induced proliferation, clonogenic potential, and increased apoptosis. Meta-analysis of the diffuse large B-cell lymphoma patient microarray data showed that miR-155 expression is inversely correlated with Bcl6 and Hdac4. Hence this study provides a better understanding of how miR-155 causes disruption of the BCL6 transcriptional machinery that leads to up-regulation of the survival and proliferation genes in miR-155-induced leukemias.
Pineau:2010aa: miR-221 overexpression contributes to liver tumorigenesis
P. Pineau and S. Volinia and K. McJunkin and A. Marchio and C. Battiston and B. Terris and V. Mazzaferro and S. W. Lowe and C. M. Croce and A. Dejean
Proc Natl Acad Sci U S A 107 264-9 (2010)
http://dx.doi.org/10.1073/pnas.0907904107

MicroRNA (miRNAs) are negative regulators of gene expression and can function as tumor suppressors or oncogenes. Expression patterns of miRNAs and their role in the pathogenesis of hepatocellular carcinoma (HCC) are still poorly understood. We profiled miRNA expression in tissue samples (104 HCC, 90 adjacent cirrhotic livers, 21 normal livers) as well as in 35 HCC cell lines. A set of 12 miRNAs (including miR-21, miR-221/222, miR-34a, miR-519a, miR-93, miR-96, and let-7c) was linked to disease progression from normal liver through cirrhosis to full-blown HCC. miR-221/222, the most up-regulated miRNAs in tumor samples, are shown to target the CDK inhibitor p27 and to enhance cell growth in vitro. Conversely, these activities can be efficiently inhibited by an antagomiR specific for miR-221. In addition, we show, using a mouse model of liver cancer, that miR-221 overexpression stimulates growth of tumorigenic murine hepatic progenitor cells. Finally, we identified DNA damage-inducible transcript 4 (DDIT4), a modulator of mTOR pathway, as a bona fide target of miR-221. Taken together, these data reveal an important contribution for miR-221 in hepatocarcinogenesis and suggest a role for DDIT4 dysregulation in this process. Thus, the use of synthetic inhibitors of miR-221 may prove to be a promising approach to liver cancer treatment.
Tarantino:2010aa: miRNA 34a, 100, and 137 modulate differentiation of mouse embryonic stem cells
C. Tarantino and G. Paolella and L. Cozzuto and G. Minopoli and L. Pastore and S. Parisi and T. Russo
FASEB J 24 3255-63 (2010)
http://dx.doi.org/10.1096/fj.09-152207

MicroRNAs (miRNAs) play an important role in proper function and differentiation of mouse embryonic stem cells (ESCs). We performed a systematic comparison of miRNA expression in undifferentiated vs. differentiating ESCs. We report that 138 miRNAs are increased on the induction of differentiation. We compared the entire list of candidate mRNA targets of up-regulated miRNAs with that of mRNA down-regulated in ESCs on induction of differentiation. Among the candidate targets emerging from this analysis, we found three genes, Smarca5, Jarid1b, and Sirt1, previously demonstrated to be involved in sustaining the undifferentiated phenotype in ESCs. On this basis, we first demonstrated that Smarca5 is a direct target of miR-100, Jarid1b of miR-137, and we also confirmed previously published data demonstrating that Sirt1 is a direct target of miR-34a in a different context. The suppression of these three miRNAs by anti-miRs caused the block of ESC differentiation induced by LIF withdrawal. On the other hand, the overexpression of the three miRNAs resulted in an altered expression of differentiation markers. These results demonstrate that miR-34a, miR-100, and miR-137 are required for proper differentiation of mouse ESCs, and that they function in part by targeting Sirt1, Smarca5, and Jarid1b mRNAs.
Calura:2013aa: miRNA Landscape in Stage I Epithelial Ovarian Cancer Defines the Histotype Specificities
E. Calura and R. Fruscio and L. Paracchini and E. Bignotti and A. Ravaggi and P. Martini and G. Sales and L. Beltrame and L. Clivio and L. Ceppi and M. Di Marino and I. F. Nerini and L. Zanotti and D. Cavalieri and G. Cattoretti and P. Perego and R. Milani and D. Katsaros and G. Tognon and E. Sartori and S. Pecorelli and C. Mangioni and M. D'Incalci and C. Romualdi and S. Marchini
Clin. Cancer Res. 19 4114--4123 (2013)
http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/WOS:000322598900012

Purpose: Epithelial ovarian cancer (EOC) is one of the most lethal gynecologic diseases, with survival rate virtually unchanged for the past 30 years. EOC comprises different histotypes with molecular and clinical heterogeneity, but up till now the present gold standard platinum-based treatment has been conducted without any patient stratification. The aim of the present study is to generate microRNA (miRNA) profiles characteristic of each stage I EOC histotype, to identify subtype-specific biomarkers to improve our understanding underlying the tumor mechanisms. Experimental Design: A collection of 257 snap-frozen stage I EOC tumor biopsies was gathered together from three tumor tissue collections and stratified into independent training (n = 183) and validation sets (n = 74). Microarray and quantitative real-time PCR (qRT-PCR) were used to generate and validate the histotype-specific markers. A novel dedicated resampling inferential strategy was developed and applied to identify the highest reproducible results. mRNA and miRNA profiles were integrated to identify novel regulatory circuits. Results: Robust miRNA markers for clear cell and mucinous histotypes were found. Specifically, the clear cell histotype is characterized by a five-fold (log scale) higher expression of miR-30a and miR-30a*, whereas mucinous histotype has five-fold (log scale) higher levels of miR-192/194. Furthermore, a mucinous-specific regulatory loop involving miR-192/194 cluster and a differential regulation of E2F3 in clear cell histotype were identified. Conclusions: Our findings showed that stage I EOC histotypes have their own characteristic miRNA expression and specific regulatory circuits. (C) 2013 AACR.
Picardi:2012aa: Mitochondrial genomes gleaned from human whole-exome sequencing
E. Picardi and G. Pesole
Nat Methods 9 523-4 (2012)
http://dx.doi.org/10.1038/nmeth.2029
DOnorio-de-Meo:2012aa: MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa
P. D'Onorio de Meo and M. D'Antonio and F. Griggio and R. Lupi and M. Borsani and G. Pavesi and T. Castrignanò and G. Pesole and C. Gissi
Nucleic Acids Res 40 D1168-72 (2012)
http://dx.doi.org/10.1093/nar/gkr1144

The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa.
Potenza:2014aa: MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins
E. Potenza and T. D. Domenico and I. Walsh and S. C. E. Tosatto
Nucleic Acids Res (2014)
http://dx.doi.org/10.1093/nar/gku982

MobiDB (http://mobidb.bio.unipd.it/) is a database of intrinsically disordered and mobile proteins. Intrinsically disordered regions are key for the function of numerous proteins. Here we provide a new version of MobiDB, a centralized source aimed at providing the most complete picture on different flavors of disorder in protein structures covering all UniProt sequences (currently over 80 million). The database features three levels of annotation: manually curated, indirect and predicted. Manually curated data is extracted from the DisProt database. Indirect data is inferred from PDB structures that are considered an indication of intrinsic disorder. The 10 predictors currently included (three ESpritz flavors, two IUPred flavors, two DisEMBL flavors, GlobPlot, VSL2b and JRONN) enable MobiDB to provide disorder annotations for every protein in absence of more reliable data. The new version also features a consensus annotation and classification for long disordered regions. In order to complement the disorder annotations, MobiDB features additional annotations from external sources. Annotations from the UniProt database include post-translational modifications and linear motifs. Pfam annotations are displayed in graphical form and are link-enabled, allowing the user to visit the corresponding Pfam page for further information. Experimental protein-protein interactions from STRING are also classified for disorder content.
Gherardini:2010aa: Modular architecture of nucleotide-binding pockets
P. F. Gherardini and G. Ausiello and R. B. Russell and M. Helmer-Citterich
Nucleic Acids Res 38 3809-16 (2010)
http://dx.doi.org/10.1093/nar/gkq090

Recently, modularity has emerged as a general attribute of complex biological systems. This is probably because modular systems lend themselves readily to optimization via random mutation followed by natural selection. Although they are not traditionally considered to evolve by this process, biological ligands are also modular, being composed of recurring chemical fragments, and moreover they exhibit similarities reminiscent of mutations (e.g. the few atoms differentiating adenine and guanine). Many ligands are also promiscuous in the sense that they bind to many different protein folds. Here, we investigated whether ligand chemical modularity is reflected in an underlying modularity of binding sites across unrelated proteins. We chose nucleotides as paradigmatic ligands, because they can be described as composed of well-defined fragments (nucleobase, ribose and phosphates) and are quite abundant both in nature and in protein structure databases. We found that nucleotide-binding sites do indeed show a modular organization and are composed of fragment-specific protein structural motifs, which parallel the modular structure of their ligands. Through an analysis of the distribution of these motifs in different proteins and in different folds, we discuss the evolutionary implications of these findings and argue that the structural features we observed can arise both as a result of divergence from a common ancestor or convergent evolution.
Valeri:2010aa: Modulation of mismatch repair and genomic stability by miR-155
N. Valeri and P. Gasparini and M. Fabbri and C. Braconi and A. Veronese and F. Lovat and B. Adair and I. Vannini and F. Fanini and A. Bottoni and S. Costinean and S. K. Sandhu and G. J. Nuovo and H. Alder and R. Gafa and F. Calore and M. Ferracin and G. Lanza and S. Volinia and M. Negrini and M. A. McIlhatton and D. Amadori and R. Fishel and C. M. Croce
Proc Natl Acad Sci U S A 107 6982-7 (2010)
http://dx.doi.org/10.1073/pnas.1002472107

Inactivation of mismatch repair (MMR) is the cause of the common cancer predisposition disorder Lynch syndrome (LS), also known as hereditary nonpolyposis colorectal cancer (HNPCC), as well as 10-40% of sporadic colorectal, endometrial, ovarian, gastric, and urothelial cancers. Elevated mutation rates (mutator phenotype), including simple repeat instability [microsatellite instability (MSI)] are a signature of MMR defects. MicroRNAs (miRs) have been implicated in the control of critical cellular pathways involved in development and cancer. Here we show that overexpression of miR-155 significantly down-regulates the core MMR proteins, hMSH2, hMSH6, and hMLH1, inducing a mutator phenotype and MSI. An inverse correlation between the expression of miR-155 and the expression of MLH1 or MSH2 proteins was found in human colorectal cancer. Finally, a number of MSI tumors with unknown cause of MMR inactivation displayed miR-155 overexpression. These data provide support for miR-155 modulation of MMR as a mechanism of cancer pathogenesis.
Cordeddu:2014aa: Mutations in ZBTB20 cause Primrose syndrome
V. Cordeddu and B. Redeker and E. Stellacci and A. Jongejan and A. Fragale and T. E. J. Bradley and M. Anselmi and A. Ciolfi and S. Cecchetti and V. Muto and L. Bernardini and M. Azage and D. R. Carvalho and A. J. Espay and A. Male and A.-M. Molin and R. Posmyk and C. Battisti and A. Casertano and D. Melis and A. van Kampen and F. Baas and M. M. Mannens and G. Bocchinfuso and L. Stella and M. Tartaglia and R. C. Hennekam
Nat Genet 46 815-7 (2014)
http://dx.doi.org/10.1038/ng.3035

Primrose syndrome and 3q13.31 microdeletion syndrome are clinically related disorders characterized by tall stature, macrocephaly, intellectual disability, disturbed behavior and unusual facial features, with diabetes, deafness, progressive muscle wasting and ectopic calcifications specifically occurring in the former. We report that missense mutations in ZBTB20, residing within the 3q13.31 microdeletion syndrome critical region, underlie Primrose syndrome. This finding establishes a genetic link between these disorders and delineates the impact of ZBTB20 dysregulation on development, growth and metabolism.
Tili:2011aa: Mutator activity induced by microRNA-155 (miR-155) links inflammation and cancer
E. Tili and J.-J. Michaille and D. Wernicke and H. Alder and S. Costinean and S. Volinia and C. M. Croce
Proc Natl Acad Sci U S A 108 4908-13 (2011)
http://dx.doi.org/10.1073/pnas.1101795108

Infection-driven inflammation has been implicated in the pathogenesis of ~15-20% of human tumors. Expression of microRNA-155 (miR-155) is elevated during innate immune response and autoimmune disorders as well as in various malignancies. However, the molecular mechanisms providing miR-155 with its oncogenic properties remain unclear. We examined the effects of miR-155 overexpression and proinflammatory environment on the frequency of spontaneous hypoxanthine phosphoribosyltransferase (HPRT) mutations that can be detected based on the resistance to 6-thioguanine. Both miR-155 overexpression and inflammatory environment increased the frequency of HPRT mutations and down-regulated WEE1 (WEE1 homolog-S. pombe), a kinase that blocks cell-cycle progression. The increased frequency of HPRT mutation was only modestly attributable to defects in mismatch repair machinery. This result suggests that miR-155 enhances the mutation rate by simultaneously targeting different genes that suppress mutations and decreasing the efficiency of DNA safeguard mechanisms by targeting of cell-cycle regulators such as WEE1. By simultaneously targeting tumor suppressor genes and inducing a mutator phenotype, miR-155 may allow the selection of gene alterations required for tumor development and progression. Hence, we anticipate that the development of drugs reducing endogenous miR-155 levels might be key in the treatment of inflammation-related cancers.
Fleming:2013aa: NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors
J. D. Fleming and G. Pavesi and P. Benatti and C. Imbriano and R. Mantovani and K. Struhl
Genome Res 23 1195-209 (2013)
http://dx.doi.org/10.1101/gr.148080.112

NF-Y, a trimeric transcription factor (TF) composed of two histone-like subunits (NF-YB and NF-YC) and a sequence-specific subunit (NF-YA), binds to the CCAAT motif, a common promoter element. Genome-wide mapping reveals 5000-15,000 NF-Y binding sites depending on the cell type, with the NF-YA and NF-YB subunits binding asymmetrically with respect to the CCAAT motif. Despite being characterized as a proximal promoter TF, only 25% of NF-Y sites map to promoters. A comparable number of NF-Y sites are located at enhancers, many of which are tissue specific, and nearly half of the NF-Y sites are in select subclasses of HERV LTR repeats. Unlike most TFs, NF-Y can access its target DNA motif in inactive (nonmodified) or polycomb-repressed chromatin domains. Unexpectedly, NF-Y extensively colocalizes with FOS in all genomic contexts, and this often occurs in the absence of JUN and the AP-1 motif. NF-Y also coassociates with a select cluster of growth-controlling and oncogenic TFs, consistent with the abundance of CCAAT motifs in the promoters of genes overexpressed in cancer. Interestingly, NF-Y and several growth-controlling TFs bind in a stereo-specific manner, suggesting a mechanism for cooperative action at promoters and enhancers. Our results indicate that NF-Y is not merely a commonly used proximal promoter TF, but rather performs a more diverse set of biological functions, many of which are likely to involve coassociation with FOS.
Tramontano:2009aa: No protein is an island
A. Tramontano
Curr Opin Struct Biol 19 310-1 (2009)
http://dx.doi.org/10.1016/j.sbi.2009.05.001
Parca:2013aa: Nucleos: a web server for the identification of nucleotide-binding sites in protein structures
L. Parca and F. Ferré and G. Ausiello and M. Helmer-Citterich
Nucleic Acids Res 41 W281-5 (2013)
http://dx.doi.org/10.1093/nar/gkt390

Nucleos is a web server for the identification of nucleotide-binding sites in protein structures. Nucleos compares the structure of a query protein against a set of known template 3D binding sites representing nucleotide modules, namely the nucleobase, carbohydrate and phosphate. Structural features, clustering and conservation are used to filter and score the predictions. The predicted nucleotide modules are then joined to build whole nucleotide-binding sites, which are ranked by their score. The server takes as input either the PDB code of the query protein structure or a user-submitted structure in PDB format. The output of Nucleos is composed of ranked lists of predicted nucleotide-binding sites divided by nucleotide type (e.g. ATP-like). For each ranked prediction, Nucleos provides detailed information about the score, the template structure and the structural match for each nucleotide module composing the nucleotide-binding site. The predictions on the query structure and the template-binding sites can be viewed directly on the web through a graphical applet. In 98% of the cases, the modules composing correct predictions belong to proteins with no homology relationship between each other, meaning that the identification of brand-new nucleotide-binding sites is possible using information from non-homologous proteins. Nucleos is available at http://nucleos.bio.uniroma2.it/nucleos/.
Goparaju:2011aa: Onconase mediated NFKβ downregulation in malignant pleural mesothelioma
C. M. Goparaju and J. D. Blasberg and S. Volinia and J. Palatini and S. Ivanov and J. S. Donington and C. Croce and M. Carbone and H. Yang and H. I. Pass
Oncogene 30 2767-77 (2011)
http://dx.doi.org/10.1038/onc.2010.643

Treatment of malignant pleural mesothelioma (MPM) with Ranpirnase (Onconase) results in disruption of protein translation and cell apoptosis. We hypothesize that Onconase exerts an effect via downregulation of nuclear factor kappa B (NFKβ) by specific microRNAs (miRNAs) and that interference of this pathway could have implications for MPM resistance to chemotherapy. Three immortalized MPM cell lines (H2959, H2373 and H2591) were exposed to Onconase at 0-20 μg/ml. Cell counts were measured at 48 and 72 h. Gene expression in miRNA-enriched RNA was validated by reverse transcription-PCR (RT-PCR). The functional implications of miRNA expression were evaluated by transfecting miRNA mimics or inhibitors into MPM cell lines, and performing Matrigel invasion, cell proliferation, soft agar colony formation and scratch closure assays. Effects on NFKβ expression and downstream targets including ABC transporters, BCL-xl and IAP were assessed by RT-PCR and western blotting. Treatment with 20 μg/ml of Onconase significantly decreased cell count and invasion. Hsa-miR-17* was significantly upregulated and hsa-miR-30c was significantly downregulated by Onconase treatment in all cell lines. Forced expression of hsa-miR-17* mimic and hsa-miR-30c inhibitor each significantly decreased functional activity of Onconase in all assays. NFKB1 (p50) expression and downstream targets were also decreased with Onconase treatment, as well as with forced expression of miRNA mimic and inhibitors. Onconase treatment caused a significant decrease in cell proliferation, invasion and in expression of certain miRNAs. Recapitulation of the resultant miRNA expression pattern with hsa-miR-17* mimic and hsa-miR-30c inhibitor resulted in downregulation of NFKB1 and reduced malignant behavior in functional assays. Thus, Onconase likely exerts its antitumor effect through these miRNAs.
Kim:2011aa: p53 regulates epithelial-mesenchymal transition through microRNAs targeting ZEB1 and ZEB2
T. Kim and A. Veronese and F. Pichiorri and T. J. Lee and Y.-J. Jeon and S. Volinia and P. Pineau and A. Marchio and J. Palatini and S.-S. Suh and H. Alder and C.-G. Liu and A. Dejean and C. M. Croce
J Exp Med 208 875-83 (2011)
http://dx.doi.org/10.1084/jem.20110235

p53 suppresses tumor progression and metastasis. Epithelial-mesenchymal transition (EMT) is a key process in tumor progression and metastasis. The transcription factors ZEB1 and ZEB2 promote EMT. Here, we show that p53 suppresses EMT by repressing expression of ZEB1 and ZEB2. By profiling 92 primary hepatocellular carcinomas (HCCs) and 9 HCC cell lines, we found that p53 up-regulates microRNAs (miRNAs), including miR-200 and miR-192 family members. The miR-200 family members transactivated by p53 then repress ZEB1/2 expression. p53-regulated miR-192 family members also repress ZEB2 expression. Inhibition or overexpression of the miRNAs affects p53-regulated EMT by altering ZEB1 and ZEB2 expression. Our findings indicate that p53 can regulate EMT, and that p53-regulated miRNAs are critical mediators of p53-regulated EMT.
Fumagalli:2009aa: Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions
M. Fumagalli and U. Pozzoli and R. Cagliani and G. P. Comi and S. Riva and M. Clerici and N. Bresolin and M. Sironi
J Exp Med 206 1395-408 (2009)
http://dx.doi.org/10.1084/jem.20082779

Many human genes have adapted to the constant threat of exposure to infectious agents; according to the "hygiene hypothesis," lack of exposure to parasites in modern settings results in immune imbalances, augmenting susceptibility to the development of autoimmune and allergic conditions. Here, by estimating the number of pathogen species/genera in a specific geographic location (pathogen richness) for 52 human populations and analyzing 91 interleukin (IL)/IL receptor genes (IL genes), we show that helminths have been a major selective force on a subset of these genes. A population genetics analysis revealed that five IL genes, including IL7R and IL18RAP, have been a target of balancing selection, a selection process that maintains genetic variability within a population. Previous identification of polymorphisms in some of these loci, and their association with autoimmune conditions, prompted us to investigate the relationship between adaptation and disease. By searching for variants in IL genes identified in genome-wide association studies, we verified that six risk alleles for inflammatory bowel (IBD) or celiac disease are significantly correlated with micropathogen richness. These data support the hygiene hypothesis for IBD and provide a large set of putative targets for susceptibility to helminth infections.
Parca:2011aa: Phosfinder: a web server for the identification of phosphate-binding sites on protein structures
L. Parca and I. Mangone and P. F. Gherardini and G. Ausiello and M. Helmer-Citterich
Nucleic Acids Res 39 W278-82 (2011)
http://dx.doi.org/10.1093/nar/gkr389

Phosfinder is a web server for the identification of phosphate binding sites in protein structures. Phosfinder uses a structural comparison algorithm to scan a query structure against a set of known 3D phosphate binding motifs. Whenever a structural similarity between the query protein and a phosphate binding motif is detected, the phosphate bound by the known motif is added to the protein structure thus representing a putative phosphate binding site. Predicted binding sites are then evaluated according to (i) their position with respect to the query protein solvent-excluded surface and (ii) the conservation of the binding residues in the protein family. The server accepts as input either the PDB code of the protein to be analyzed or a user-submitted structure in PDB format. All the search parameters are user modifiable. Phosfinder outputs a list of predicted binding sites with detailed information about their structural similarity with known phosphate binding motifs, and the conservation of the residues involved. A graphical applet allows the user to visualize the predicted binding sites on the query protein structure. The results on a set of 52 apo/holo structure pairs show that the performance of our method is largely unaffected by ligand-induced conformational changes. Phosfinder is available at http://phosfinder.bio.uniroma2.it.
Parca:2011ab: Phosphate binding sites identification in protein structures
L. Parca and P. F. Gherardini and M. Helmer-Citterich and G. Ausiello
Nucleic Acids Res 39 1231-42 (2011)
http://dx.doi.org/10.1093/nar/gkq987

Nearly half of known protein structures interact with phosphate-containing ligands, such as nucleotides and other cofactors. Many methods have been developed for the identification of metal ions-binding sites and some for bigger ligands such as carbohydrates, but none is yet available for the prediction of phosphate-binding sites. Here we describe Pfinder, a method that predicts binding sites for phosphate groups, both in the form of ions or as parts of other non-peptide ligands, in proteins of known structure. Pfinder uses the Query3D local structural comparison algorithm to scan a protein structure for the presence of a number of structural motifs identified for their ability to bind the phosphate chemical group. Pfinder has been tested on a data set of 52 proteins for which both the apo and holo forms were available. We obtained at least one correct prediction in 63% of the holo structures and in 62% of the apo. The ability of Pfinder to recognize a phosphate-binding site in unbound protein structures makes it an ideal tool for functional annotation and for complementing docking and drug design methods. The Pfinder program is available at http://pdbfun.uniroma2.it/pfinder.
Zanzoni:2011aa: Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites
A. Zanzoni and D. Carbajo and F. Diella and P. F. Gherardini and A. Tramontano and M. Helmer-Citterich and A. Via
Nucleic Acids Res 39 D268-71 (2011)
http://dx.doi.org/10.1093/nar/gkq936

Phospho3D is a database of three-dimensional (3D) structures of phosphorylation sites (P-sites) derived from the Phospho.ELM database, which also collects information on the residues surrounding the P-site in space (3D zones). The database also provides the results of a large-scale structural comparison of the 3D zones versus a representative dataset of structures, thus associating to each P-site a number of structurally similar sites. The new version of Phospho3D presents an 11-fold increase in the number of 3D sites and incorporates several additional features, including new structural descriptors, the possibility of selecting non-redundant sets of 3D structures and the availability for download of non-redundant sets of structurally annotated P-sites. Moreover, it features P3Dscan, a new functionality that allows the user to submit a protein structure and scan it against the 3D zones collected in the Phospho3D database. Phospho3D version 2.0 is available at: http://www.phospho3d.org/.
Dinkel:2011aa: Phospho.ELM: a database of phosphorylation sites--update 2011
H. Dinkel and C. Chica and A. Via and C. M. Gould and L. J. Jensen and T. J. Gibson and F. Diella
Nucleic Acids Res 39 D261-7 (2011)
http://dx.doi.org/10.1093/nar/gkq1104

The Phospho.ELM resource (http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises 42,574 serine, threonine and tyrosine non-redundant phosphorylation sites. Several new features have been implemented, such as structural disorder/order and accessibility information and a conservation score. Additionally, the conservation of the phosphosites can now be visualized directly on the multiple sequence alignment used for the score calculation. Finally, special emphasis has been put on linking to external resources such as interaction networks and other databases.
Volinia:2014aa: Pluripotent Stem Cell miRNAs and Metastasis in Invasive Breast Cancer
S. Volinia and G. Nuovo and A. Drusco and S. Costinean and R. Abujarour and C. Desponts and M. Garofalo and R. Baffa and R. Aeqilan and K. Maharry and M. E. S. R. Garzon and G. Di Leva and P. Gasparini and P. Dama and J. Marchesini and M. Galasso and M. Manfrini and C. Zerbinati and F. Corrà and T. Wise and S. E. Wojcik and M. Previati and F. Pichiorri and N. Zanesi and H. Alder and J. Palatini and K. F. Huebner and C. L. Shapiro and M. Negrini and A. Vecchione and A. L. Rosenberg and C. M. Croce
J Natl Cancer Inst 106 (2014)
http://dx.doi.org/10.1093/jnci/dju324

BACKGROUND: The purpose of this study is to determine whether microRNA for pluripotent stem cells are also expressed in breast cancer and are associated with metastasis and outcome. METHODS: We studied global microRNA profiles during differentiation of human embryonic stem cells (n =26) and in breast cancer patients (n = 33) and human cell lines (n = 35). Using in situ hybridization, we then investigated MIR302 expression in 318 untreated breast cancer patients (test cohort, n = 22 and validation cohort, n = 296). In parallel, using next-generation sequencing data from breast cancer patients (n = 684), we assessed microRNA association with stem cell markers. All statistical tests were two-sided. RESULTS: In healthy tissues, the MIR302 (high)/MIR203 (low) asymmetry was exclusive for pluripotent stem cells. MIR302 was expressed in a small population of cancer cells within invasive ductal carcinoma, but not in normal breast (P < .001). Furthermore, MIR302 was expressed in the tumor cells together with stem cell markers, such as CD44 and BMI1. Conversely, MIR203 expression in 684 breast tumors negatively correlated with CD44 (Spearman correlation, Rho = -0.08, P = .04) and BMI1 (Rho = -0.11, P = .004), but positively correlated with differentiation marker CD24 (Rho = 0.15, P < .001). Primary tumors with lymph node metastasis had cancer cells showing scattered expression of MIR302 and widespread repression of MIR203. Finally, overall survival was statistically significantly shorter in patients with MIR302-positive cancer cells (P = .03). CONCLUSIONS: In healthy tissues the MIR302(high)/MIR203(low) asymmetry was characteristic of embryonic and induced pluripotency. In invasive ductal carcinoma, the MIR302/MIR203 asymmetry was associated with stem cell markers, metastasis, and shorter survival.
Cagliani:2010aa: Polymorphisms in the CPB2 gene are maintained by balancing selection and result in haplotype-preferential splicing of exon 7
R. Cagliani and M. Fumagalli and S. Riva and U. Pozzoli and M. Fracassetti and N. Bresolin and G. P. Comi and M. Sironi
Mol Biol Evol 27 1945-54 (2010)
http://dx.doi.org/10.1093/molbev/msq082

The CPB2 gene encodes thrombin-activatable fibrinolysis inhibitor (TAFI), a hepatically secreted zymogen acting as a molecular link among coagulation, fibrinolysis, and inflammation. Variants in CPB2 have been associated with several human conditions. We resequenced and analyzed the two regions carrying previously known nonsynonimous single-nucleotide polymorphisms (Ala147Thr and Ile325Thr) and variants affecting transcript stability. Our data indicate that whereas the gene portion extending from exon 9 to the 3' untranslated region fits a model of neutral evolution, variants in the region encompassing exons 6-7 have been maintained by balancing selection. Indeed, we verified that the region displays high nucleotide diversity, many intermediate frequency variants, and an excess of polymorphism compared with interspecific divergence. Consistently, haplotype analysis indicated the presence of two major haplotype clades separated by deep branches. Transcript analysis revealed that in both HepG2 cells and human liver samples, CPB2 exon 7 undergoes haplotype-preferential skipping. Therefore, we indicate that balancing selection has been maintaining functional variants that promote alternative exon 7 splicing. Although transcripts lacking exon 7 represent a minority of total CPB2 products, the effect on antifibrinolytic activity might be much greater as the intrinsic instability of TAFI is a major determinant of its antifibrinolytic potential. These data highlight the contribution of population genetics approaches to the analysis of functional genetic variation and may orient further biochemical and genetics studies on the pathophysiologic role of CPB2 gene products.
Fumagalli:2010ab: Population genetics of IFIH1: ancient population structure, local selection, and implications for susceptibility to type 1 diabetes
M. Fumagalli and R. Cagliani and S. Riva and U. Pozzoli and M. Biasin and L. Piacentini and G. P. Comi and N. Bresolin and M. Clerici and M. Sironi
Mol Biol Evol 27 2555-66 (2010)
http://dx.doi.org/10.1093/molbev/msq141

The human interferon induced with helicase C domain 1 (IFIH1) gene encodes a sensor of double-strand RNA involved in innate immunity against viruses, indicating that this gene is a likely target of virus-driven selective pressure. Notably, IFIH1 also plays a role in autoimmunity, as common and rare polymorphisms in this gene have been associated with type 1 diabetes (T1D). We analyzed the evolutionary history of IFIH1 in human populations. Results herein suggest that two major IFIH1 haplotype clades originated from ancestral population structure (or balancing selection) in the African continent and that local selective pressures have acted on the gene. Specifically, directional selection in Europe and Asia resulted in the spread of a common IFIH1 haplotype carrying a derived His460 allele. This variant changes a highly conserved arginine residue in the helicase domain, possibly conferring altered specificity in viral recognition. An alternative common haplotype has swept to high frequency in South Americans as a result of recent positive selection. Previous studies suggested that a portion of risk alleles for autoimmune diseases could have been maintained in humans as they conferred a selective advantage against infections. This is not the case for IFIH1, as population genetic differentiation and haplotype analyses indicated that the T1D susceptibility alleles behaved as neutral or nearly neutral polymorphisms. Our findings suggest that variants in IFIH1 confer different susceptibility to diverse viral infections and provide insight into the relationship between adaptation to past infection and predisposition to autoimmunity in modern populations.
Nassa:2014aa: Post-transcriptional regulation of human breast cancer cell proteome by unliganded estrogen receptor β via microRNAs
G. Nassa and R. Tarallo and G. Giurato and M. R. De Filippo and M. Ravo and F. Rizzo and C. Stellato and C. Ambrosino and M. Baumann and N. Lietzèn and T. A. Nyman and A. Weisz
Mol Cell Proteomics 13 1076-90 (2014)
http://dx.doi.org/10.1074/mcp.M113.030403

Estrogen receptor β (ERβ) is a member of the nuclear receptor family of homeostatic regulators that is frequently lost in breast cancer (BC), where its presence correlates with a better prognosis and a less aggressive clinical outcome of the disease. In contrast to ERα, its closest homolog, ERβ shows significant estrogen-independent activities, including the ability to inhibit cell cycle progression and regulate gene transcription in the absence of the ligand. Investigating the nature and extent of this constitutive activity of ERβ in BC MCF-7 and ZR-75.1 cells by means of microRNA (miRNA) sequencing, we identified 30 miRNAs differentially expressed in ERβ+ versus ERβ- cells in the absence of ligand, including up-regulated oncosuppressor miRs such miR-30a. In addition, a significant fraction of >1,600 unique proteins identified in MCF-7 cells by iTRAQ quantitative proteomics were either increased or decreased by ERβ, revealing regulation of multiple cell pathways by ligand-free receptors. Transcriptome analysis showed that for a large number of proteins regulated by ERβ, the corresponding mRNAs are unaffected, including a large number of putative targets of ERβ-regulated miRNAs, indicating a central role of miRNAs in mediating BC cell proteome regulation by ERβ. Expression of a mimic of miR-30a-5p, a direct target and downstream effector of ERβ in BC, led to the identification of several target transcripts of this miRNA, including 11 encoding proteins whose intracellular concentration was significantly affected by unliganded receptor. These results demonstrate a significant effect of ligand-free ERβ on BC cell functions via modulation of the cell proteome and suggest that miRNA regulation might represent a key event in the control of the biological and clinical phenotype of hormone-responsive BC by this nuclear receptor.
Galli:2012aa: Prdm5 regulates collagen gene transcription by association with RNA polymerase II in developing bone
G. G. Galli and K. Honnens de Lichtenberg and M. Carrara and W. Hans and M. Wuelling and B. Mentz and H. A. Multhaupt and C. K. Fog and K. T. Jensen and J. Rappsilber and A. Vortkamp and L. Coulton and H. Fuchs and V. Gailus-Durner and M. Hrabě de Angelis and R. A. Calogero and J. R. Couchman and A. H. Lund
PLoS Genet 8 e1002711 (2012)
http://dx.doi.org/10.1371/journal.pgen.1002711

PRDM family members are transcriptional regulators involved in tissue specific differentiation. PRDM5 has been reported to predominantly repress transcription, but a characterization of its molecular functions in a relevant biological context is lacking. We demonstrate here that Prdm5 is highly expressed in developing bones; and, by genome-wide mapping of Prdm5 occupancy in pre-osteoblastic cells, we uncover a novel and unique role for Prdm5 in targeting all mouse collagen genes as well as several SLRP proteoglycan genes. In particular, we show that Prdm5 controls both Collagen I transcription and fibrillogenesis by binding inside the Col1a1 gene body and maintaining RNA polymerase II occupancy. In vivo, Prdm5 loss results in delayed ossification involving a pronounced impairment in the assembly of fibrillar collagens. Collectively, our results define a novel role for Prdm5 in sustaining the transcriptional program necessary to the proper assembly of osteoblastic extracellular matrix.
Niederwieser:2014aa: Prognostic and biologic significance of DNMT3B expression in older patients with cytogenetically normal primary acute myeloid leukemia
C. Niederwieser and J. Kohlschmidt and S. Volinia and S. P. Whitman and K. H. Metzeler and A.-K. Eisfeld and K. Maharry and P. Yan and D. Frankhouser and H. Becker and S. Schwind and A. J. Carroll and D. Nicolet and J. H. Mendler and J. P. Curfman and Y.-Z. Wu and M. R. Baer and B. L. Powell and J. E. Kolitz and J. O. Moore and T. H. Carter and R. Bundschuh and R. A. Larson and R. M. Stone and K. Mrózek and G. Marcucci and C. D. Bloomfield
Leukemia (2014)
http://dx.doi.org/10.1038/leu.2014.267

DNMT3B encodes a DNA methyltransferase implicated in aberrant epigenetic changes contributing to leukemogenesis. We tested whether DNMT3B expression, measured by NanoString nCounter assay, associates with outcome, gene and microRNA expression and DNA methylation profiles in 210 older (⩾60 years) adults with primary, cytogenetically normal acute myeloid leukemia (CN-AML). Patients were dichotomized into high versus low expressers using median cut. Outcomes were assessed in the context of known CN-AML prognosticators. Gene and microRNA expression, and DNA methylation profiles were analyzed using microarrays and MethylCap-sequencing, respectively. High DNMT3B expressers had fewer complete remissions (CR; P=0.002) and shorter disease-free (DFS; P=0.02) and overall (OS; P<0.001) survival. In multivariable analyses, high DNMT3B expression remained an independent predictor of lower CR rates (P=0.04) and shorter DFS (P=0.04) and OS (P=0.001). High DNMT3B expression associated with a gene expression profile comprising 363 genes involved in differentiation, proliferation and survival pathways, but with only four differentially expressed microRNAs (miR-133b, miR-148a, miR-122, miR-409-3p) and no differential DNA methylation regions. We conclude that high DNMT3B expression independently associates with adverse outcome in older CN-AML patients. Gene expression analyses suggest that DNMT3B is involved in the modulation of several genes, although the regulatory mechanisms remain to be investigated to devise therapeutic approaches specific for these patients.Leukemia advance online publication, 7 October 2014; doi:10.1038/leu.2014.267.
Volinia:2013aa: Prognostic microRNA/mRNA signature from the integrated analysis of patients with invasive breast cancer
S. Volinia and C. M. Croce
Proc Natl Acad Sci U S A 110 7413-7 (2013)
http://dx.doi.org/10.1073/pnas.1304977110

The optimal management of breast cancer (BC) presents challenges due to the heterogeneous molecular classification of the disease. We performed survival analysis on a cohort of 466 patients with primary invasive ductal carcinoma (IDC), the most frequent type of BC, by integrating mRNA, microRNA (miRNA), and DNA methylation next-generation sequencing data from The Cancer Genome Atlas (TCGA). Expression data from eight other BC cohorts were used for validation. The prognostic value of the resulting miRNA/mRNA signature was compared with that of other prognostic BC signatures. Thirty mRNAs and seven miRNAs were associated with overall survival across different clinical and molecular subclasses of a 466-patient IDC cohort from TCGA. The prognostic RNAs included PIK3CA, one of the two most frequently mutated genes in IDC, and miRNAs such as hsa-miR-328, hsa-miR-484, and hsa-miR-874. The area under the curve of the receiver-operator characteristic for the IDC risk predictor in the TCGA cohort was 0.74 at 60 mo of overall survival (P < 0.001). Most relevant for clinical application, the integrated signature had the highest prognostic value in early stage I and II tumors (receiver-operator characteristic area under the curve = 0.77, P value < 0.001). The genes in the RNA risk predictor had an independent prognostic value compared with the clinical covariates, as shown by multivariate analysis. The integrated RNA signature was successfully validated on eight BC cohorts, comprising a total of 2,399 patients, and it had superior performance for risk stratification with respect to other RNA predictors, including the mRNAs used in MammaPrint and Oncotype DX assays.
Ezkurdia:2009aa: Progress and challenges in predicting protein-protein interaction sites
I. Ezkurdia and L. Bartoli and P. Fariselli and R. Casadio and A. Valencia and M. L. Tress
Brief Bioinform 10 233-46 (2009)
http://dx.doi.org/10.1093/bib/bbp021

The identification of protein-protein interaction sites is an essential intermediate step for mutant design and the prediction of protein networks. In recent years a significant number of methods have been developed to predict these interface residues and here we review the current status of the field. Progress in this area requires a clear view of the methodology applied, the data sets used for training and testing the systems, and the evaluation procedures. We have analysed the impact of a representative set of features and algorithms and highlighted the problems inherent in generating reliable protein data sets and in the posterior analysis of the results. Although it is clear that there have been some improvements in methods for predicting interacting sites, several major bottlenecks remain. Proteins in complexes are still under-represented in the structural databases and in particular many proteins involved in transient complexes are still to be crystallized. We provide suggestions for effective feature selection, and make it clear that community standards for testing, training and performance measures are necessary for progress in the field.
Rustighi:2014aa: Prolyl-isomerase Pin1 controls normal and cancer stem cells of the breast
A. Rustighi and A. Zannini and L. Tiberi and R. Sommaggio and S. Piazza and G. Sorrentino and S. Nuzzo and A. Tuscano and V. Eterno and F. Benvenuti and L. Santarpia and I. Aifantis and A. Rosato and S. Bicciato and A. Zambelli and G. Del Sal
EMBO Mol Med 6 99-119 (2014)
http://dx.doi.org/10.1002/emmm.201302909

Mammary epithelial stem cells are fundamental to maintain tissue integrity. Cancer stem cells (CSCs) are implicated in both treatment resistance and disease relapse, and the molecular bases of their malignant properties are still poorly understood. Here we show that both normal stem cells and CSCs of the breast are controlled by the prolyl-isomerase Pin1. Mechanistically, following interaction with Pin1, Notch1 and Notch4, key regulators of cell fate, escape from proteasomal degradation by their major ubiquitin-ligase Fbxw7α. Functionally, we show that Fbxw7α acts as an essential negative regulator of breast CSCs' expansion by restraining Notch activity, but the establishment of a Notch/Pin1 active circuitry opposes this effect, thus promoting breast CSCs self-renewal, tumor growth and metastasis in vivo. In human breast cancers, despite Fbxw7α expression, high levels of Pin1 sustain Notch signaling, which correlates with poor prognosis. Suppression of Pin1 holds promise in reverting aggressive phenotypes, through CSC exhaustion as well as recovered drug sensitivity carrying relevant implications for therapy of breast cancers.
Di-Paola:2013ab: Protein contact networks: an emerging paradigm in chemistry
L. Di Paola and M. De Ruvo and P. Paci and D. Santoni and A. Giuliani
Chem Rev 113 1598-613 (2013)
http://dx.doi.org/10.1021/cr3002356
Di-Paola:2013aa: Protein Contact Networks: An Emerging Paradigm in Chemistry
L. Di Paola and M. De Ruvo and P. Paci and D. Santoni and A. Giuliani
Chem. Rev. 113 1598--1613 (2013)
http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/WOS:000316243600007
Loewenstein:2009aa: Protein function annotation by homology-based inference
Y. Loewenstein and D. Raimondo and O. C. Redfern and J. Watson and D. Frishman and M. Linial and C. Orengo and J. Thornton and A. Tramontano
Genome Biol 10 207 (2009)
http://dx.doi.org/10.1186/gb-2009-10-2-207

With many genomes now sequenced, computational annotation methods to characterize genes and proteins from their sequence are increasingly important. The BioSapiens Network has developed tools to address all stages of this process, and here we review progress in the automated prediction of protein function based on protein sequence and structure.
Orchard:2012aa: Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
S. Orchard and S. Kerrien and S. Abbani and B. Aranda and J. Bhate and S. Bidwell and A. Bridge and L. Briganti and F. S. L. Brinkman and F. Brinkman and G. Cesareni and A. Chatr-aryamontri and E. Chautard and C. Chen and M. Dumousseau and J. Goll and R. E. W. Hancock and R. Hancock and L. I. Hannick and I. Jurisica and J. Khadake and D. J. Lynn and U. Mahadevan and L. Perfetto and A. Raghunath and S. Ricard-Blum and B. Roechert and L. Salwinski and V. Stümpflen and M. Tyers and P. Uetz and I. Xenarios and H. Hermjakob
Nat Methods 9 345-50 (2012)
http://dx.doi.org/10.1038/nmeth.1931

The International Molecular Exchange (IMEx) consortium is an international collaboration between major public interaction data providers to share literature-curation efforts and make a nonredundant set of protein interactions available in a single search interface on a common website (http://www.imexconsortium.org/). Common curation rules have been developed, and a central registry is used to manage the selection of articles to enter into the dataset. We discuss the advantages of such a service to the user, our quality-control measures and our data-distribution practices.
Cecconi:2009aa: Protein nitration during defense response in Arabidopsis thaliana
D. Cecconi and S. Orzetti and E. Vandelle and S. Rinalducci and L. Zolla and M. Delledonne
Electrophoresis 30 2460-8 (2009)
http://dx.doi.org/10.1002/elps.200800826

Nitric oxide and reactive oxygen species play a key role in the plant hypersensitive disease resistance response, and protein tyrosine nitration is emerging as an important mechanism of their co-operative interaction. Up to now, the proteins targeted by this post-translational modification in plants are still totally unknown. In this study, we analyzed for the first time proteins undergoing nitration during the hypersensitive response by analyzing via 1D- and 2D-western blot the protein extracts from Arabidopsis thaliana plants challenged with an avirulent bacterial pathogen (Pseudomonas syringae pv. Tomato). We show that the plant disease resistance response is correlated with a modulation of nitration of proteins involved in important cellular process, such as photosynthesis, glycolysis and nitrate assimilation. These findings shed new light on the signaling functions of nitric oxide and reactive oxygen species, paving the way on studies on the role of this post-translational modification in plants.
Yam:2013aa: Proteomic analysis of detergent-resistant membrane microdomains in trophozoite blood stage of the human malaria parasite Plasmodium falciparum
X. Y. Yam and C. Birago and F. Fratini and F. Di Girolamo and C. Raggi and M. Sargiacomo and A. Bachi and L. Berry and G. Fall and C. Currà and E. Pizzi and C. B. Breton and M. Ponzi
Mol Cell Proteomics 12 3948-61 (2013)
http://dx.doi.org/10.1074/mcp.M113.029272

Intracellular pathogens contribute to a significant proportion of infectious diseases worldwide. The successful strategy of evading the immune system by hiding inside host cells is common to all the microorganism classes, which exploit membrane microdomains, enriched in cholesterol and sphingolipids, to invade and colonize the host cell. These assemblies, with distinct biochemical properties, can be isolated by means of flotation in sucrose density gradient centrifugation because they are insoluble in nonionic detergents at low temperature. We analyzed the protein and lipid contents of detergent-resistant membranes from erythrocytes infected by Plasmodium falciparum, the most deadly human malaria parasite. Proteins associated with membrane microdomains of trophic parasite blood stages (trophozoites) include an abundance of chaperones, molecules involved in vesicular trafficking, and enzymes implicated in host hemoglobin degradation. About 60% of the identified proteins contain a predicted localization signal suggesting a role of membrane microdomains in protein sorting/trafficking. To validate our proteomic data, we raised antibodies against six Plasmodium proteins not characterized previously. All the selected candidates were recovered in floating low-density fractions after density gradient centrifugation. The analyzed proteins localized either to internal organelles, such as the mitochondrion and the endoplasmic reticulum, or to exported membrane structures, the parasitophorous vacuole membrane and Maurer's clefts, implicated in targeting parasite proteins to the host erythrocyte cytosol or surface. The relative abundance of cholesterol and phospholipid species varies in gradient fractions containing detergent-resistant membranes, suggesting heterogeneity in the lipid composition of the isolated microdomain population. This study is the first report showing the presence of cholesterol-rich microdomains with distinct properties and subcellular localization in trophic stages of Plasmodium falciparum.
Ferraccioli:2010aa: Proteomic approaches to Sjögren's syndrome: a clue to interpret the pathophysiology and organ involvement of the disease
G. Ferraccioli and M. De Santis and G. Peluso and R. Inzitari and C. Fanali and S. L. Bosello and F. Iavarone and M. Castagnola
Autoimmun Rev 9 622-6 (2010)
http://dx.doi.org/10.1016/j.autrev.2010.05.010

Sjögren's syndrome (SS) is a chronic, inflammatory, autoimmune disease characterized by lymphocytic infiltration of the exocrine glands leading to qualitatively altered and diminished or absent salivary and lachrymal secretion, and by marked B-cell hyperreactivity. Many efforts have been made to define a panel of salivary and lachrymal markers helpful to design diagnostic tests able to replace blood tests and tissue biopsies for the diagnosis of primary and secondary SS. Several proteomic-based studies have indicated that a number of proteins and peptides can be considered SS biomarkers, being 2-3-fold up- or down-regulated compared to normal subject or having an exclusive presence in the saliva or tears of SS patients. Unfortunately, several factors make it difficult to define a comprehensive salivary and lachrymal panel of markers of SS, as the lack of a comprehensive proteomic analysis of human tears and saliva of healthy subjects, the lack of uniform protocols to collect and treat these samples, and the high grade of posttranslational modification of the proteins in these fluids.
Zambelli:2009aa: Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes
F. Zambelli and G. Pesole and G. Pavesi
Nucleic Acids Res 37 W247-52 (2009)
http://dx.doi.org/10.1093/nar/gkp464

The first step in gene expression, transcription, is modulated by the interaction of transcription factors with their corresponding binding sites on the DNA sequence. Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are significantly over- or under-represented, providing thus hints on which transcription factors could be common regulators of the genes studied, together with the location of their candidate binding sites in the sequences. Pscan does not resort to comparisons with orthologous sequences and experimental results show that it compares favorably to other tools for the same task in terms of false positive predictions and computation time. The website is free and open to all users and there is no login requirement. Address: http://www.beaconlab.it/pscan.
Zambelli:2013aa: PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments
F. Zambelli and G. Pesole and G. Pavesi
Nucleic Acids Res 41 W535-43 (2013)
http://dx.doi.org/10.1093/nar/gkt448

Chromatin immunoprecipitation followed by sequencing with next-generation technologies (ChIP-Seq) has become the de facto standard for building genome-wide maps of regions bound by a given transcription factor (TF). The regions identified, however, have to be further analyzed to determine the actual DNA-binding sites for the TF, as well as sites for other TFs belonging to the same TF complex or in general co-operating or interacting with it in transcription regulation. PscanChIP is a web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria. PscanChIP can successfully identify not only the actual binding sites for the TF investigated by a ChIP-Seq experiment but also secondary motifs corresponding to other TFs that tend to bind the same regions, and, if present, precise positional correlations among their respective sites. The web interface is free for use, and there is no login requirement. It is available at http://www.beaconlab.it/pscan_chip_dev.
Aranda:2011aa: PSICQUIC and PSISCORE: accessing and scoring molecular interactions
B. Aranda and H. Blankenburg and S. Kerrien and F. S. L. Brinkman and A. Ceol and E. Chautard and J. M. Dana and J. De Las Rivas and M. Dumousseau and E. Galeota and A. Gaulton and J. Goll and R. E. W. Hancock and R. Isserlin and R. C. Jimenez and J. Kerssemakers and J. Khadake and D. J. Lynn and M. Michaut and G. O'Kelly and K. Ono and S. Orchard and C. Prieto and S. Razick and O. Rigina and L. Salwinski and M. Simonovic and S. Velankar and A. Winter and G. Wu and G. D. Bader and G. Cesareni and I. M. Donaldson and D. Eisenberg and G. J. Kleywegt and J. Overington and S. Ricard-Blum and M. Tyers and M. Albrecht and H. Hermjakob
Nat Methods 8 528-9 (2011)
http://dx.doi.org/10.1038/nmeth.1637
Molteni:2010aa: PTPN11 mutations in childhood acute lymphoblastic leukemia occur as a secondary event associated with high hyperdiploidy
C. G. Molteni and G. Te Kronnie and S. Bicciato and T. Villa and M. Tartaglia and G. Basso and A. Biondi and G. Cazzaniga
Leukemia 24 232-5 (2010)
http://dx.doi.org/10.1038/leu.2009.200
Benkert:2009aa: QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information
P. Benkert and T. Schwede and S. C. Tosatto
BMC Struct Biol 9 35 (2009)
http://dx.doi.org/10.1186/1472-6807-9-35

BACKGROUND: The selection of the most accurate protein model from a set of alternatives is a crucial step in protein structure prediction both in template-based and ab initio approaches. Scoring functions have been developed which can either return a quality estimate for a single model or derive a score from the information contained in the ensemble of models for a given sequence. Local structural features occurring more frequently in the ensemble have a greater probability of being correct. Within the context of the CASP experiment, these so called consensus methods have been shown to perform considerably better in selecting good candidate models, but tend to fail if the best models are far from the dominant structural cluster. In this paper we show that model selection can be improved if both approaches are combined by pre-filtering the models used during the calculation of the structural consensus. RESULTS: Our recently published QMEAN composite scoring function has been improved by including an all-atom interaction potential term. The preliminary model ranking based on the new QMEAN score is used to select a subset of reliable models against which the structural consensus score is calculated. This scoring function called QMEANclust achieves a correlation coefficient of predicted quality score and GDT_TS of 0.9 averaged over the 98 CASP7 targets and perform significantly better in selecting good models from the ensemble of server models than any other groups participating in the quality estimation category of CASP7. Both scoring functions are also benchmarked on the MOULDER test set consisting of 20 target proteins each with 300 alternatives models generated by MODELLER. QMEAN outperforms all other tested scoring functions operating on individual models, while the consensus method QMEANclust only works properly on decoy sets containing a certain fraction of near-native conformations. We also present a local version of QMEAN for the per-residue estimation of model quality (QMEANlocal) and compare it to a new local consensus-based approach. CONCLUSION: Improved model selection is obtained by using a composite scoring function operating on single models in order to enrich higher quality models which are subsequently used to calculate the structural consensus. The performance of consensus-based methods such as QMEANclust highly depends on the composition and quality of the model ensemble to be analysed. Therefore, performance estimates for consensus methods based on large meta-datasets (e.g. CASP) might overrate their applicability in more realistic modelling situations with smaller sets of models based on individual methods.
Martinez:2012aa: Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis
M. R. Martínez and A. Corradin and U. Klein and M. J. Álvarez and G. M. Toffolo and B. di Camillo and A. Califano and G. A. Stolovitzky
Proc Natl Acad Sci U S A 109 2672-7 (2012)
http://dx.doi.org/10.1073/pnas.1113019109

Mature B-cell exit from germinal centers is controlled by a transcriptional regulatory module that integrates antigen and T-cell signals and, ultimately, leads to terminal differentiation into memory B cells or plasma cells. Despite a compact structure, the module dynamics are highly complex because of the presence of several feedback loops and self-regulatory interactions, and understanding its dysregulation, frequently associated with lymphomagenesis, requires robust dynamical modeling techniques. We present a quantitative kinetic model of three key gene regulators, BCL6, IRF4, and BLIMP, and use gene expression profile data from mature human B cells to determine appropriate model parameters. The model predicts the existence of two different hysteresis cycles that direct B cells through an irreversible transition toward a differentiated cellular state. By synthetically perturbing the interactions in this network, we can elucidate known mechanisms of lymphomagenesis and suggest candidate tumorigenic alterations, indicating that the model is a valuable quantitative tool to simulate B-cell exit from the germinal center under a variety of physiological and pathological conditions.
Di-Niro:2010aa: Rapid interactome profiling by massive sequencing
R. Di Niro and A.-M. Sulic and F. Mignone and S. D'Angelo and R. Bordoni and M. Iacono and R. Marzari and T. Gaiotto and M. Lavric and A. R. M. Bradbury and L. Biancone and D. Zevin-Sonkin and G. De Bellis and C. Santoro and D. Sblattero
Nucleic Acids Res 38 e110 (2010)
http://dx.doi.org/10.1093/nar/gkq052

We have developed a high-throughput protein expression and interaction analysis platform that combines cDNA phage display library selection and massive gene sequencing using the 454 platform. A phage display library of open reading frame (ORF) fragments was created from mRNA derived from different tissues. This was used to study the interaction network of the enzyme transglutaminase 2 (TG2), a multifunctional enzyme involved in the regulation of cell growth, differentiation and apoptosis, associated with many different pathologies. After two rounds of panning with TG2 we assayed the frequency of ORFs within the selected phage population using 454 sequencing. Ranking and analysis of more than 120,000 sequences allowed us to identify several potential interactors, which were subsequently confirmed in functional assays. Within the identified clones, three had been previously described as interacting proteins (fibronectin, SMOC1 and GSTO2), while all the others were new. When compared with standard systems, such as microtiter enzyme-linked immunosorbant assay, the method described here is dramatically faster and yields far more information about the interaction under study, allowing better characterization of complex systems. For example, in the case of fibronectin, it was possible to identify the specific domains involved in the interaction.
Salwinski:2009aa: Recurated protein interaction datasets
L. Salwinski and L. Licata and A. Winter and D. Thorneycroft and J. Khadake and A. Ceol and A. C. Aryamontri and R. Oughtred and M. Livstone and L. Boucher and D. Botstein and K. Dolinski and T. Berardini and E. Huala and M. Tyers and D. Eisenberg and G. Cesareni and H. Hermjakob
Nat Methods 6 860-1 (2009)
http://dx.doi.org/10.1038/nmeth1209-860
Tsigankov:2014aa: Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends
P. Tsigankov and P. F. Gherardini and M. Helmer-Citterich and G. F. Späth and P. J. Myler and D. Zilberstein
Mol Cell Proteomics 13 1787-99 (2014)
http://dx.doi.org/10.1074/mcp.M114.037705

Leishmania are obligatory intracellular parasitic protozoa that cause a wide range of diseases in humans, cycling between extracellular promastigotes in the mid-gut of sand flies and intracellular amastigotes in the phagolysosomes of mammalian macrophages. Although many of the molecular mechanisms of development inside macrophages remain a mystery, the development of a host-free system that simulates phagolysosome conditions (37 $\,^{\circ}$C and pH 5.5) has provided new insights into these processes. The time course of promastigote-to-amastigote differentiation can be divided into four morphologically distinct phases: I, signal perception (0-5 h after exposure); II, movement cessation and aggregation (5-10 h); III, amastigote morphogenesis (10-24 h); and IV, maturation (24-120 h). Transcriptomic and proteomic analyses have indicated that differentiation is a coordinated process that results in adaptation to life inside phagolysosomes. Recent phosphoproteomic analysis revealed extensive differences in phosphorylation between promastigotes and amastigotes and identified stage-specific phosphorylation motifs. We hypothesized that the differentiation signal activates a phosphorylation pathway that initiates Leishmania transformation, and here we used isobaric tags for relative and absolute quantitation to interrogate the dynamics of changes in the phosphorylation profile during Leishmania donovani promastigote-to-amastigote differentiation. Analysis of 163 phosphopeptides (from 106 proteins) revealed six distinct kinetic profiles; with increases in phosphorylation predominated during phases I and III, whereas phases II and IV were characterized by greater dephosphorylation. Several proteins (including a protein kinase) were phosphorylated in phase I after exposure to the complete differentiation signal (i.e. signal-specific; 37 $\,^{\circ}$C and pH 5.5), but not after either of the physical parameters separately. Several other protein kinases (including regulatory subunits) and phosphatases also showed changes in phosphorylation during differentiation. This work constitutes the first genome-scale interrogation of phosphorylation dynamics in a parasitic protozoa, revealing the outline of a signaling pathway during Leishmania differentiation. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (identifier PXD000671). Data can be viewed using ProteinPilot™ software.
Ueda:2010aa: Relation between microRNA expression and progression and prognosis of gastric cancer: a microRNA expression analysis
T. Ueda and S. Volinia and H. Okumura and M. Shimizu and C. Taccioli and S. Rossi and H. Alder and C.-g. Liu and N. Oue and W. Yasui and K. Yoshida and H. Sasaki and S. Nomura and Y. Seto and M. Kaminishi and G. A. Calin and C. M. Croce
Lancet Oncol 11 136-46 (2010)
http://dx.doi.org/10.1016/S1470-2045(09)70343-2

BACKGROUND: Analyses of microRNA expression profiles have shown that many microRNAs are expressed aberrantly and correlate with tumorigenesis, progression, and prognosis of various haematological and solid tumours. We aimed to assess the relation between microRNA expression and progression and prognosis of gastric cancer. METHODS: 353 gastric samples from two independent subsets of patients from Japan were analysed by microRNA microarray. MicroRNA expression patterns were compared between non-tumour mucosa and cancer samples, graded by diffuse and intestinal histological types and by progression-related factors (eg, depth of invasion, metastasis, and stage). Disease outcome was calculated by multivariable regression analysis to establish whether microRNAs are independent prognostic factors. FINDINGS: In 160 paired samples of non-tumour mucosa and cancer, 22 microRNAs were upregulated and 13 were downregulated in gastric cancer; 292 (83%) samples were distinguished correctly by this signature. The two histological subtypes of gastric cancer showed different microRNA signatures: eight microRNAs were upregulated in diffuse-type and four in intestinal-type cancer. In the progression-related signature, miR-125b, miR-199a, and miR-100 were the most important microRNAs involved. Low expression of let-7g (hazard ratio 2.6 [95% CI 1.3-4.9]) and miR-433 (2.1 [1.1-3.9]) and high expression of miR-214 (2.4 [1.2-4.5]) were associated with unfavourable outcome in overall survival independent of clinical covariates, including depth of invasion, lymph-node metastasis, and stage. INTERPRETATION: MicroRNAs are expressed differentially in gastric cancers, and histological subtypes are characterised by specific microRNA signatures. Unique microRNAs are associated with progression and prognosis of gastric cancer. FUNDING: National Cancer Institute.
Di-Domenico:2014aa: RepeatsDB: a database of tandem repeat protein structures
T. Di Domenico and E. Potenza and I. Walsh and R. G. Parra and M. Giollo and G. Minervini and D. Piovesan and A. Ihsan and C. Ferrari and A. V. Kajava and S. C. E. Tosatto
Nucleic Acids Res 42 D352-7 (2014)
http://dx.doi.org/10.1093/nar/gkt1175

RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repeat types haven been studied over the years, but their annotation was done in a case-by-case basis, thus making large-scale analysis difficult. We developed RepeatsDB to fill this gap. Using state-of-the-art repeat detection methods and manual curation, we systematically annotated the Protein Data Bank, predicting 10,745 repeat structures. In all, 2797 structures were classified according to a recently proposed classification schema, which was expanded to accommodate new findings. In addition, detailed annotations were performed in a subset of 321 proteins. These annotations feature information on start and end positions for the repeat regions and units. RepeatsDB is an ongoing effort to systematically classify and annotate structural protein repeats in a consistent way. It provides users with the possibility to access and download high-quality datasets either interactively or programmatically through web services.
Volinia:2010aa: Reprogramming of miRNA networks in cancer and leukemia
S. Volinia and M. Galasso and S. Costinean and L. Tagliavini and G. Gamberoni and A. Drusco and J. Marchesini and N. Mascellani and M. E. Sana and R. Abu Jarour and C. Desponts and M. Teitell and R. Baffa and R. Aqeilan and M. V. Iorio and C. Taccioli and R. Garzon and G. Di Leva and M. Fabbri and M. Catozzi and M. Previati and S. Ambs and T. Palumbo and M. Garofalo and A. Veronese and A. Bottoni and P. Gasparini and C. C. Harris and R. Visone and Y. Pekarsky and A. de la Chapelle and M. Bloomston and M. Dillhoff and L. Z. Rassenti and T. J. Kipps and K. Huebner and F. Pichiorri and D. Lenze and S. Cairo and M.-A. Buendia and P. Pineau and A. Dejean and N. Zanesi and S. Rossi and G. A. Calin and C.-G. Liu and J. Palatini and M. Negrini and A. Vecchione and A. Rosenberg and C. M. Croce
Genome Res 20 589-99 (2010)
http://dx.doi.org/10.1101/gr.098046.109

We studied miRNA profiles in 4419 human samples (3312 neoplastic, 1107 nonmalignant), corresponding to 50 normal tissues and 51 cancer types. The complexity of our database enabled us to perform a detailed analysis of microRNA (miRNA) activities. We inferred genetic networks from miRNA expression in normal tissues and cancer. We also built, for the first time, specialized miRNA networks for solid tumors and leukemias. Nonmalignant tissues and cancer networks displayed a change in hubs, the most connected miRNAs. hsa-miR-103/106 were downgraded in cancer, whereas hsa-miR-30 became most prominent. Cancer networks appeared as built from disjointed subnetworks, as opposed to normal tissues. A comparison of these nets allowed us to identify key miRNA cliques in cancer. We also investigated miRNA copy number alterations in 744 cancer samples, at a resolution of 150 kb. Members of miRNA families should be similarly deleted or amplified, since they repress the same cellular targets and are thus expected to have similar impacts on oncogenesis. We correctly identified hsa-miR-17/92 family as amplified and the hsa-miR-143/145 cluster as deleted. Other miRNAs, such as hsa-miR-30 and hsa-miR-204, were found to be physically altered at the DNA copy number level as well. By combining differential expression, genetic networks, and DNA copy number alterations, we confirmed, or discovered, miRNAs with comprehensive roles in cancer. Finally, we experimentally validated the miRNA network with acute lymphocytic leukemia originated in Mir155 transgenic mice. Most of miRNAs deregulated in these transgenic mice were located close to hsa-miR-155 in the cancer network.
Ayub:2014aa: Revisiting the thrifty gene hypothesis via 65 loci associated with susceptibility to type 2 diabetes
Q. Ayub and L. Moutsianas and Y. Chen and K. Panoutsopoulou and V. Colonna and L. Pagani and I. Prokopenko and G. R. S. Ritchie and C. Tyler-Smith and M. I. McCarthy and E. Zeggini and Y. Xue
Am J Hum Genet 94 176-85 (2014)
http://dx.doi.org/10.1016/j.ajhg.2013.12.010

We have investigated the evidence for positive selection in samples of African, European, and East Asian ancestry at 65 loci associated with susceptibility to type 2 diabetes (T2D) previously identified through genome-wide association studies. Selection early in human evolutionary history is predicted to lead to ancestral risk alleles shared between populations, whereas late selection would result in population-specific signals at derived risk alleles. By using a wide variety of tests based on the site frequency spectrum, haplotype structure, and population differentiation, we found no global signal of enrichment for positive selection when we considered all T2D risk loci collectively. However, in a locus-by-locus analysis, we found nominal evidence for positive selection at 14 of the loci. Selection favored the protective and risk alleles in similar proportions, rather than the risk alleles specifically as predicted by the thrifty gene hypothesis, and may not be related to influence on diabetes. Overall, we conclude that past positive selection has not been a powerful influence driving the prevalence of T2D risk alleles.
Wang:2010aa: RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana
X.-B. Wang and Q. Wu and T. Ito and F. Cillo and W.-X. Li and X. Chen and J.-L. Yu and S.-W. Ding
Proc Natl Acad Sci U S A 107 484-9 (2010)
http://dx.doi.org/10.1073/pnas.0904086107

In diverse eukaryotic organisms, Dicer-processed, virus-derived small interfering RNAs direct antiviral immunity by RNA silencing or RNA interference. Here we show that in addition to core dicing and slicing components of RNAi, the RNAi-mediated viral immunity in Arabidopsis thaliana requires host RNA-directed RNA polymerase (RDR) 1 or RDR6 to produce viral secondary siRNAs following viral RNA replication-triggered biogenesis of primary siRNAs. We found that the two antiviral RDRs exhibited specificity in targeting the tripartite positive-strand RNA genome of cucumber mosaic virus (CMV). RDR1 preferentially amplified the 5'-terminal siRNAs of each of the three viral genomic RNAs, whereas an increased production of siRNAs targeting the 3' half of RNA3 detected in rdr1 mutant plants appeared to be RDR6-dependent. However, siRNAs derived from a single-stranded 336-nucleotide satellite RNA of CMV were not amplified by either antiviral RDR, suggesting avoidance of the potent RDR-dependent silencing as a strategy for the molecular parasite of CMV to achieve preferential replication. Our work thus identifies a distinct mechanism for the amplification of immunity effectors, which together with the requirement for the biogenesis of endogenous siRNAs, may play a role in the emergence and expansion of eukaryotic RDRs.
Cereda:2014aa: RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing
M. Cereda and U. Pozzoli and G. Rot and P. Juvan and A. Schweitzer and T. Clark and J. Ule
Genome Biol 15 R20 (2014)
http://dx.doi.org/10.1186/gb-2014-15-1-r20

RNA-binding proteins (RBPs) regulate splicing according to position-dependent principles, which can be exploited for analysis of regulatory motifs. Here we present RNAmotifs, a method that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs. We show that diverse RBPs share basic positional principles, but differ in their propensity to enhance or repress exon inclusion. We assess exons differentially spliced between brain and heart, identifying known and new regulatory motifs, and predict the expression pattern of RBPs that bind these motifs. RNAmotifs is available at https://bitbucket.org/rogrro/rna_motifs.
Lanni:2013aa: Role of CTCF protein in regulating FMR1 locus transcription
S. Lanni and M. Goracci and L. Borrelli and G. Mancano and P. Chiurazzi and U. Moscato and F. Ferrè and M. Helmer-Citterich and E. Tabolacci and G. Neri
PLoS Genet 9 e1003601 (2013)
http://dx.doi.org/10.1371/journal.pgen.1003601

Fragile X syndrome (FXS), the leading cause of inherited intellectual disability, is caused by epigenetic silencing of the FMR1 gene, through expansion and methylation of a CGG triplet repeat (methylated full mutation). An antisense transcript (FMR1-AS1), starting from both promoter and intron 2 of the FMR1 gene, was demonstrated in transcriptionally active alleles, but not in silent FXS alleles. Moreover, a DNA methylation boundary, which is lost in FXS, was recently identified upstream of the FMR1 gene. Several nuclear proteins bind to this region, like the insulator protein CTCF. Here we demonstrate for the first time that rare unmethylated full mutation (UFM) alleles present the same boundary described in wild type (WT) alleles and that CTCF binds to this region, as well as to the FMR1 gene promoter, exon 1 and intron 2 binding sites. Contrariwise, DNA methylation prevents CTCF binding to FXS alleles. Drug-induced CpGs demethylation does not restore this binding. CTCF knock-down experiments clearly established that CTCF does not act as insulator at the active FMR1 locus, despite the presence of a CGG expansion. CTCF depletion induces heterochromatinic histone configuration of the FMR1 locus and results in reduction of FMR1 transcription, which however is not accompanied by spreading of DNA methylation towards the FMR1 promoter. CTCF depletion is also associated with FMR1-AS1 mRNA reduction. Antisense RNA, like sense transcript, is upregulated in UFM and absent in FXS cells and its splicing is correlated to that of the FMR1-mRNA. We conclude that CTCF has a complex role in regulating FMR1 expression, probably through the organization of chromatin loops between sense/antisense transcriptional regulatory regions, as suggested by bioinformatics analysis.
Wang:2009aa: Role of microRNA-155 at early stages of hepatocarcinogenesis induced by choline-deficient and amino acid-defined diet in C57BL/6 mice
B. Wang and S. Majumder and G. Nuovo and H. Kutay and S. Volinia and T. Patel and T. D. Schmittgen and C. Croce and K. Ghoshal and S. T. Jacob
Hepatology 50 1152-61 (2009)
http://dx.doi.org/10.1002/hep.23100

UNLABELLED: MicroRNAs (miRs) are conserved, small (20-25 nucleotide) noncoding RNAs that negatively regulate expression of messenger RNAs (mRNAs) at the posttranscriptional level. Aberrant expression of certain microRNAs plays a causal role in tumorigenesis. Here, we report identification of hepatic microRNAs that are dysregulated at early stages of feeding C57BL/6 mice choline-deficient and amino acid-defined (CDAA) diet that is known to promote nonalcoholic steatohepatitis (NASH)-induced hepatocarcinogenesis after 84 weeks. Microarray analysis identified 30 hepatic microRNAs that are significantly (P < or = 0.01) altered in mice fed CDAA diet for 6, 18, 32, and 65 weeks compared with those fed choline-sufficient and amino acid-defined (CSAA) diet. Real-time reverse transcription polymerase chain reaction (RT-PCR) analysis demonstrated up-regulation of oncogenic miR-155, miR-221/222, and miR-21 and down-regulation of the most abundant liver-specific miR-122 at early stages of hepatocarcinogenesis. Western blot analysis showed reduced expression of hepatic phosphatase and tensin homolog (PTEN) and CCAAT/enhancer binding protein beta (C/EBPbeta), respective targets of miR-21 and miR-155, in these mice at early stages. DNA binding activity of nuclear factor kappa B (NF-kappaB) that transactivates miR-155 gene was significantly (P = 0.002) elevated in the liver nuclear extract of mice fed CDAA diet. Furthermore, the expression of miR-155, as measured by in situ hybridization and real-time RT-PCR, correlated with diet-induced histopathological changes in the liver. Ectopic expression of miR-155 promoted growth of hepatocellular carcinoma (HCC) cells, whereas its depletion inhibited cell growth. Notably, miR-155 was significantly (P = 0.0004) up-regulated in primary human HCCs with a concomitant decrease (P = 0.02) in C/EBPbeta level compared with matching liver tissues. CONCLUSION: Temporal changes in microRNA profile occur at early stages of CDAA diet-induced hepatocarcinogenesis. Reciprocal regulation of specific oncomirs and their tumor suppressor targets implicate their role in NASH-induced hepatocarcinogenesis and suggest their use in the diagnosis, prognosis, and therapy of liver cancer.
Azzolin:2012aa: Role of TAZ as mediator of Wnt signaling
L. Azzolin and F. Zanconato and S. Bresolin and M. Forcato and G. Basso and S. Bicciato and M. Cordenonsi and S. Piccolo
Cell 151 1443-56 (2012)
http://dx.doi.org/10.1016/j.cell.2012.11.027

Wnt growth factors are fundamental regulators of cell fate, but how the Wnt signal is translated into biological responses is incompletely understood. Here, we report that TAZ, a biologically potent transcriptional coactivator, serves as a downstream element of the Wnt/β-catenin cascade. This function of TAZ is independent from its well-established role as mediator of Hippo signaling. In the absence of Wnt activity, the components of the β-catenin destruction complex--APC, Axin, and GSK3--are also required to keep TAZ at low levels. TAZ degradation depends on phosphorylated β-catenin that bridges TAZ to its ubiquitin ligase β-TrCP. Upon Wnt signaling, escape of β-catenin from the destruction complex impairs TAZ degradation and leads to concomitant accumulation of β-catenin and TAZ. At the genome-wide level, a substantial portion of Wnt transcriptional responses is mediated by TAZ. TAZ activation is a general feature of Wnt signaling and is functionally relevant to mediate Wnt biological effects.
Coletta:2013aa: Role of the protein in the DNA sequence specificity of the cleavage site stabilized by the camptothecin topoisomerase IB inhibitor: a metadynamics study
A. Coletta and A. Desideri
Nucleic Acids Res 41 9977-86 (2013)
http://dx.doi.org/10.1093/nar/gkt790

Camptothecin (CPT) is a topoisomerase IB (TopIB) selective inhibitor whose derivatives are currently used in cancer therapy. TopIB cleaves DNA at any sequence, but in the presence of CPT the only stabilized protein-DNA covalent complex is the one having a thymine in position -1 with respect to the cleavage site. A metadynamics simulation of two TopIB-DNA-CPT ternary complexes differing for the presence of a thymine or a cytosine in position -1 indicates the occurrence of two different drug's unbinding pathways. The free-energy difference between the bound state and the transition state is large when a thymine is present in position -1 and is strongly reduced in presence of a cytosine, in line with the different drug stabilization properties of the two systems. Such a difference is strictly related to the changes in the hydrogen bond network between the protein, the DNA and the drug in the two systems, indicating a direct role of the protein in determining the specificity of the cleavage site sequence stabilized by the CPT. Calculations carried out in presence of one compound of the indenoisoquinoline family (NSC314622) indicate a comparable energy difference between the bound and the transition state independently of the presence of a thymine or a cytosine in position -1, in line with the experimental results.
Dupont:2011aa: Role of YAP/TAZ in mechanotransduction
S. Dupont and L. Morsut and M. Aragona and E. Enzo and S. Giulitti and M. Cordenonsi and F. Zanconato and J. Le Digabel and M. Forcato and S. Bicciato and N. Elvassore and S. Piccolo
Nature 474 179-83 (2011)
http://dx.doi.org/10.1038/nature10137

Cells perceive their microenvironment not only through soluble signals but also through physical and mechanical cues, such as extracellular matrix (ECM) stiffness or confined adhesiveness. By mechanotransduction systems, cells translate these stimuli into biochemical signals controlling multiple aspects of cell behaviour, including growth, differentiation and cancer malignant progression, but how rigidity mechanosensing is ultimately linked to activity of nuclear transcription factors remains poorly understood. Here we report the identification of the Yorkie-homologues YAP (Yes-associated protein) and TAZ (transcriptional coactivator with PDZ-binding motif, also known as WWTR1) as nuclear relays of mechanical signals exerted by ECM rigidity and cell shape. This regulation requires Rho GTPase activity and tension of the actomyosin cytoskeleton, but is independent of the Hippo/LATS cascade. Crucially, YAP/TAZ are functionally required for differentiation of mesenchymal stem cells induced by ECM stiffness and for survival of endothelial cells regulated by cell geometry; conversely, expression of activated YAP overrules physical constraints in dictating cell behaviour. These findings identify YAP/TAZ as sensors and mediators of mechanical cues instructed by the cellular microenvironment.
Merelli:2010aa: RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes
I. Merelli and A. Guffanti and M. Fabbri and A. Cocito and L. Furia and U. Grazini and R. J. Bonnal and L. Milanesi and F. McBlane
Nucleic Acids Res 38 W262-7 (2010)
http://dx.doi.org/10.1093/nar/gkq391

Recombination signal sequences (RSSs) flanking V, D and J gene segments are recognized and cut by the VDJ recombinase during development of B and T lymphocytes. All RSSs are composed of seven conserved nucleotides, followed by a spacer (containing either 12 +/- 1 or 23 +/- 1 poorly conserved nucleotides) and a conserved nonamer. Errors in V(D)J recombination, including cleavage of cryptic RSS outside the immunoglobulin and T cell receptor loci, are associated with oncogenic translocations observed in some lymphoid malignancies. We present in this paper the RSSsite web server, which is available from the address http://www.itb.cnr.it/rss. RSSsite consists of a web-accessible database, RSSdb, for the identification of pre-computed potential RSSs, and of the related search tool, DnaGrab, which allows the scoring of potential RSSs in user-supplied sequences. This latter algorithm makes use of probability models, which can be recasted to Bayesian network, taking into account correlations between groups of positions of a sequence, developed starting from specific reference sets of RSSs. In validation laboratory experiments, we selected 33 predicted cryptic RSSs (cRSSs) from 11 chromosomal regions outside the immunoglobulin and TCR loci for functional testing.
Pantaleo:2011aa: SDHA loss-of-function mutations in KIT-PDGFRA wild-type gastrointestinal stromal tumors identified by massively parallel sequencing
M. A. Pantaleo and A. Astolfi and V. Indio and R. Moore and N. Thiessen and M. C. Heinrich and C. Gnocchi and D. Santini and F. Catena and S. Formica and P. L. Martelli and R. Casadio and A. Pession and G. Biasco
J Natl Cancer Inst 103 983-7 (2011)
http://dx.doi.org/10.1093/jnci/djr130

Approximately 10%-15% of gastrointestinal stromal tumors (GISTs) in adults do not harbor any mutation in the KIT or PDGFRA genes (ie, KIT/PDGFRA wild-type GISTs). Recently, mutations in SDHB and SDHC (which encode succinate dehydrogenase subunits B and C, respectively) but not in SDHA and SDHD (which encode subunits A and D, respectively) were identified in KIT/PDGFRA wild-type GISTs. To search for novel pathogenic mutations, we sequenced the tumor transcriptome of two young adult patients who developed sporadic KIT/PDGFRA wild-type GISTs by using a massively parallel sequencing approach. The only variants identified as disease related by computational analysis were in SDHA. One patient carried the homozygous nonsense mutation p.Ser384X, the other patient was a compound heterozygote harboring a p.Arg31X nonsense mutation and a p.Arg589Trp missense mutation. The heterozygous nonsense mutations in both patients were present in germline DNA isolated from peripheral blood. Protein structure analysis indicates that all three mutations lead to functional inactivation of the protein. This is the first report, to our knowle dge, that identifies SDHA inactivation as a common oncogenic event in GISTs that lack a mutation in KIT and PDGFRA.
Sabo:2014aa: Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis
A. Sabò and T. R. Kress and M. Pelizzola and S. de Pretis and M. M. Gorski and A. Tesi and M. J. Morelli and P. Bora and M. Doni and A. Verrecchia and C. Tonelli and G. Fagà and V. Bianchi and A. Ronchi and D. Low and H. Müller and E. Guccione and S. Campaner and B. Amati
Nature 511 488-92 (2014)
http://dx.doi.org/10.1038/nature13537

The c-myc proto-oncogene product, Myc, is a transcription factor that binds thousands of genomic loci. Recent work suggested that rather than up- and downregulating selected groups of genes, Myc targets all active promoters and enhancers in the genome (a phenomenon termed 'invasion') and acts as a general amplifier of transcription. However, the available data did not readily discriminate between direct and indirect effects of Myc on RNA biogenesis. We addressed this issue with genome-wide chromatin immunoprecipitation and RNA expression profiles during B-cell lymphomagenesis in mice, in cultured B cells and fibroblasts. Consistent with long-standing observations, we detected general increases in total RNA or messenger RNA copies per cell (hereby termed 'amplification') when comparing actively proliferating cells with control quiescent cells: this was true whether cells were stimulated by mitogens (requiring endogenous Myc for a proliferative response) or by deregulated, oncogenic Myc activity. RNA amplification and promoter/enhancer invasion by Myc were separable phenomena that could occur without one another. Moreover, whether or not associated with RNA amplification, Myc drove the differential expression of distinct subsets of target genes. Hence, although having the potential to interact with all active or poised regulatory elements in the genome, Myc does not directly act as a global transcriptional amplifier. Instead, our results indicate that Myc activates and represses transcription of discrete gene sets, leading to changes in cellular state that can in turn feed back on global RNA production and turnover.
Juncker:2009aa: Sequence-based feature prediction and annotation of proteins
A. S. Juncker and L. J. Jensen and A. Pierleoni and A. Bernsel and M. L. Tress and P. Bork and G. von Heijne and A. Valencia and C. A. Ouzounis and R. Casadio and S. Brunak
Genome Biol 10 206 (2009)
http://dx.doi.org/10.1186/gb-2009-10-2-206

A recent trend in computational methods for annotation of protein function is that many prediction tools are combined in complex workflows and pipelines to facilitate the analysis of feature combinations, for example, the entire repertoire of kinase-binding motifs in the human proteome.
Montagner:2012aa: SHARP1 suppresses breast cancer metastasis by promoting degradation of hypoxia-inducible factors
M. Montagner and E. Enzo and M. Forcato and F. Zanconato and A. Parenti and E. Rampazzo and G. Basso and G. Leo and A. Rosato and S. Bicciato and M. Cordenonsi and S. Piccolo
Nature 487 380-4 (2012)
http://dx.doi.org/10.1038/nature11207

The molecular determinants of malignant cell behaviours in breast cancer remain only partially understood. Here we show that SHARP1 (also known as BHLHE41 or DEC2) is a crucial regulator of the invasive and metastatic phenotype in triple-negative breast cancer (TNBC), one of the most aggressive types of breast cancer. SHARP1 is regulated by the p63 metastasis suppressor and inhibits TNBC aggressiveness through inhibition of hypoxia-inducible factor 1α (HIF-1α) and HIF-2α (HIFs). SHARP1 opposes HIF-dependent TNBC cell migration in vitro, and invasive or metastatic behaviours in vivo. SHARP1 is required, and sufficient, to limit expression of HIF-target genes. In primary TNBC, endogenous SHARP1 levels are inversely correlated with those of HIF targets. Mechanistically, SHARP1 binds to HIFs and promotes HIF proteasomal degradation by serving as the HIF-presenting factor to the proteasome. This process is independent of pVHL (von Hippel-Lindau tumour suppressor), hypoxia and the ubiquitination machinery. SHARP1 therefore determines the intrinsic instability of HIF proteins to act in parallel to, and cooperate with, oxygen levels. This work sheds light on the mechanisms and pathways by which TNBC acquires invasiveness and metastatic propensity.
Fumagalli:2011aa: Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution
M. Fumagalli and M. Sironi and U. Pozzoli and A. Ferrer-Admetlla and A. Ferrer-Admettla and L. Pattini and R. Nielsen
PLoS Genet 7 e1002355 (2011)
http://dx.doi.org/10.1371/journal.pgen.1002355

Previous genome-wide scans of positive natural selection in humans have identified a number of non-neutrally evolving genes that play important roles in skin pigmentation, metabolism, or immune function. Recent studies have also shown that a genome-wide pattern of local adaptation can be detected by identifying correlations between patterns of allele frequencies and environmental variables. Despite these observations, the degree to which natural selection is primarily driven by adaptation to local environments, and the role of pathogens or other ecological factors as selective agents, is still under debate. To address this issue, we correlated the spatial allele frequency distribution of a large sample of SNPs from 55 distinct human populations to a set of environmental factors that describe local geographical features such as climate, diet regimes, and pathogen loads. In concordance with previous studies, we detected a significant enrichment of genic SNPs, and particularly non-synonymous SNPs associated with local adaptation. Furthermore, we show that the diversity of the local pathogenic environment is the predominant driver of local adaptation, and that climate, at least as measured here, only plays a relatively minor role. While background demography by far makes the strongest contribution in explaining the genetic variance among populations, we detected about 100 genes which show an unexpectedly strong correlation between allele frequencies and pathogenic environment, after correcting for demography. Conversely, for diet regimes and climatic conditions, no genes show a similar correlation between the environmental factor and allele frequencies. This result is validated using low-coverage sequencing data for multiple populations. Among the loci targeted by pathogen-driven selection, we found an enrichment of genes associated to autoimmune diseases, such as celiac disease, type 1 diabetes, and multiples sclerosis, which lends credence to the hypothesis that some susceptibility alleles for autoimmune diseases may be maintained in human population due to past selective processes.
Cabras:2013aa: Significant modifications of the salivary proteome potentially associated with complications of Down syndrome revealed by top-down proteomics
T. Cabras and E. Pisano and C. Montaldo and M. R. Giuca and F. Iavarone and G. Zampino and M. Castagnola and I. Messana
Mol Cell Proteomics 12 1844-52 (2013)
http://dx.doi.org/10.1074/mcp.M112.026708

People with Down syndrome, a frequent genetic disorder in humans, have increased risk of health problems associated with this condition. One clinical feature of Down syndrome is the increased prevalence and severity of periodontal disease in comparison with the general population. Because saliva plays an important role in maintaining oral health, in the present study the salivary proteome of Down syndrome subjects was investigated to explore modifications with respect to healthy subjects. Whole saliva of 36 Down syndrome subjects, divided in the age groups 10-17 yr and 18-50 yr, was analyzed by a top-down proteomic approach, based on the high performance liquid chromatography-electrospray ionization-MS analysis of the intact proteins and peptides, and the qualitative and quantitative profiles were compared with sex- and age-matched control groups. The results showed the following interesting features: 1) as opposed to controls, in Down syndrome subjects the concentration of the major salivary proteins of gland origin did not increase with age; as a consequence concentration of acidic proline rich proteins and S cystatins were found significantly reduced in older Down syndrome subjects with respect to matched controls; 2) levels of the antimicrobial α-defensins 1 and 2 and histatins 3 and 5 were significantly increased in whole saliva of older Down syndrome subjects with respect to controls; 3) S100A7, S100A8, and S100A12 levels were significantly increased in whole saliva of Down syndrome subjects in comparison with controls. The increased level of S100A7 and S100A12 may be of particular interest as a biomarker of early onset Alzheimer's disease, which is frequently associated with Down syndrome.
DAnnessa:2014aa: Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein-DNA binding site
I. D'Annessa and A. Coletta and T. Sutthibutpong and J. Mitchell and G. Chillemi and S. Harris and A. Desideri
Nucleic Acids Res 42 9304-12 (2014)
http://dx.doi.org/10.1093/nar/gku654

Human topoisomerase 1B has been simulated covalently bound to a negatively supercoiled DNA minicircle, and its behavior compared to the enzyme bound to a simple linear DNA duplex. The presence of the more realistic supercoiled substrate facilitates the formation of larger number of protein-DNA interactions when compared to a simple linear duplex fragment. The number of protein-DNA hydrogen bonds doubles in proximity to the active site, affecting all of the residues in the catalytic pentad. The clamp over the DNA, characterized by the salt bridge between Lys369 and Glu497, undergoes reduced fluctuations when bound to the supercoiled minicircle. The linker domain of the enzyme, which is implicated in the controlled relaxation of superhelical stress, also displays an increased number of contacts with the minicircle compared to linear DNA. Finally, the more complex topology of the supercoiled DNA minicircle gives rise to a secondary DNA binding site involving four residues located on subdomain III. The simulation trajectories reveal significant changes in the interactions between the enzyme and the DNA for the more complex DNA topology, which are consistent with the experimental observation that the protein has a preference for binding to supercoiled DNA.
Francia:2012aa: Site-specific DICER and DROSHA RNA products control the DNA-damage response
S. Francia and F. Michelini and A. Saxena and D. Tang and M. de Hoon and V. Anelli and M. Mione and P. Carninci and F. d'Adda di Fagagna
Nature 488 231-5 (2012)
http://dx.doi.org/10.1038/nature11179

Non-coding RNAs (ncRNAs) are involved in an increasingly recognized number of cellular events. Some ncRNAs are processed by DICER and DROSHA RNases to give rise to small double-stranded RNAs involved in RNA interference (RNAi). The DNA-damage response (DDR) is a signalling pathway that originates from a DNA lesion and arrests cell proliferation3. So far, DICER and DROSHA RNA products have not been reported to control DDR activation. Here we show, in human, mouse and zebrafish, that DICER and DROSHA, but not downstream elements of the RNAi pathway, are necessary to activate the DDR upon exogenous DNA damage and oncogene-induced genotoxic stress, as studied by DDR foci formation and by checkpoint assays. DDR foci are sensitive to RNase A treatment, and DICER- and DROSHA-dependent RNA products are required to restore DDR foci in RNase-A-treated cells. Through RNA deep sequencing and the study of DDR activation at a single inducible DNA double-strand break, we demonstrate that DDR foci formation requires site-specific DICER- and DROSHA-dependent small RNAs, named DDRNAs, which act in a MRE11--RAD50--NBS1-complex-dependent manner (MRE11 also known as MRE11A; NBS1 also known as NBN). DDRNAs, either chemically synthesized or in vitro generated by DICER cleavage, are sufficient to restore the DDR in RNase-A-treated cells, also in the absence of other cellular RNAs. Our results describe an unanticipated direct role of a novel class of ncRNAs in the control of DDR activation at sites of DNA damage.
Alachkar:2014aa: SPARC promotes leukemic cell growth and predicts acute myeloid leukemia outcome
H. Alachkar and R. Santhanam and K. Maharry and K. H. Metzeler and X. Huang and J. Kohlschmidt and J. H. Mendler and J. M. Benito and C. Hickey and P. Neviani and A. M. Dorrance and M. Anghelina and J. Khalife and S. S. Tarighat and S. Volinia and S. P. Whitman and P. Paschka and P. Hoellerbauer and Y.-Z. Wu and L. Han and B. N. Bolon and W. Blum and K. Mrózek and A. J. Carroll and D. Perrotti and M. Andreeff and M. A. Caligiuri and M. Konopleva and R. Garzon and C. D. Bloomfield and G. Marcucci
J Clin Invest 124 1512-24 (2014)
http://dx.doi.org/10.1172/JCI70921

Aberrant expression of the secreted protein, acidic, cysteine-rich (osteonectin) (SPARC) gene, which encodes a matricellular protein that participates in normal tissue remodeling, is associated with a variety of diseases including cancer, but the contribution of SPARC to malignant growth remains controversial. We previously reported that SPARC was among the most upregulated genes in cytogenetically normal acute myeloid leukemia (CN-AML) patients with gene-expression profiles predictive of unfavorable outcome, such as mutations in isocitrate dehydrogenase 2 (IDH2-R172) and overexpression of the oncogenes brain and acute leukemia, cytoplasmic (BAALC) and v-ets erythroblastosis virus E26 oncogene homolog (ERG). In contrast, SPARC was downregulated in CN-AML patients harboring mutations in nucleophosmin (NPM1) that are associated with favorable prognosis. Based on these observations, we hypothesized that SPARC expression is clinically relevant in AML. Here, we found that SPARC overexpression is associated with adverse outcome in CN-AML patients and promotes aggressive leukemia growth in murine models of AML. In leukemia cells, SPARC expression was mediated by the SP1/NF-κB transactivation complex. Furthermore, secreted SPARC activated the integrin-linked kinase/AKT (ILK/AKT) pathway, likely via integrin interaction, and subsequent β-catenin signaling, which is involved in leukemia cell self-renewal. Pharmacologic inhibition of the SP1/NF-κB complex resulted in SPARC downregulation and leukemia growth inhibition. Together, our data indicate that evaluation of SPARC expression has prognosticative value and SPARC is a potential therapeutic target for AML.
Benatti:2011aa: Specific inhibition of NF-Y subunits triggers different cell proliferation defects
P. Benatti and D. Dolfini and A. Viganò and M. Ravo and A. Weisz and C. Imbriano
Nucleic Acids Res 39 5356-68 (2011)
http://dx.doi.org/10.1093/nar/gkr128

Regulated gene expression is essential for a proper progression through the cell cycle. The transcription factor NF-Y has a fundamental function in transcriptional regulation of cell cycle genes, particularly of G2/M genes. In order to investigate common and distinct functions of NF-Y subunits in cell cycle regulation, NF-YA, NF-YB and NF-YC have been silenced by shRNAs in HCT116 cells. NF-YA loss led to a delay in S-phase progression, DNA damage and apoptosis: we showed the activation of the replication checkpoint, through the recruitment of Δp53 and of the replication proteins PCNA and Mcm7 to chromatin. Differently, NF-YB depletion impaired cells from exiting G2/M, but did not interfere with S-phase progression. Gene expression analysis of NF-YA and NF-YB inactivated cells highlighted a common set of hit genes, as well as a plethora of uncommon genes, unveiling a different effect of NF-Y subunits loss on NF-Y binding to its target genes. Chromatin extracts and ChIP analysis showed that NF-YA depletion was more effective than NF-YB in hitting NF-Y recruitment to CCAAT-promoters. Our data suggest a critical role of NF-Y expression, highlighting that the lack of the single subunits are differently perceived by the cells, which activate diverse cell cycle blocks and signaling pathways.
Verardo:2014aa: Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer
R. Verardo and S. Piazza and E. Klaric and Y. Ciani and G. Bussadori and S. Marzinotto and L. Mariuzzi and D. Cesselli and A. P. Beltrami and M. Mano and M. Itoh and H. Kawaji and T. Lassmann and P. Carninci and Y. Hayashizaki and A. R. R. Forrest and Fantom Consortium and C. A. Beltrami and C. Schneider
Stem Cells 32 2998-3011 (2014)
http://dx.doi.org/10.1002/stem.1791

Mesenchymal stem/stromal cells (MSCs) are the precursors of various cell types that compose both normal and cancer tissue microenvironments. In order to support the widely diversified parenchymal cells and tissue organization, MSCs are characterized by a large degree of heterogeneity, although available analyses of molecular and transcriptional data do not provide clear evidence. We have isolated MSCs from high-grade serous ovarian cancers (HG-SOCs) and various normal tissues (N-MSCs), demonstrated their normal genotype and analyzed their transcriptional activity with respect to the large comprehensive FANTOM5 sample dataset. Our integrative analysis conducted against the extensive panel of primary cells and tissues of the FANTOM5 project allowed us to mark the HG-SOC-MSCs CAGE-seq transcriptional heterogeneity and to identify a cell-type-specific transcriptional activity showing a significant relationship with primary mesothelial cells. Our analysis shows that MSCs isolated from different tissues are highly heterogeneous. The mesothelial-related gene signature identified in this study supports the hypothesis that HG-SOC-MSCs are bona fide representatives of the ovarian district. This finding indicates that HG-SOC-MSCs could actually derive from the coelomic mesothelium, suggesting that they might be linked to the epithelial tumor through common embryological precursors.
Giulietti:2013aa: SpliceAid-F: a database of human splicing factors and their RNA-binding sites
M. Giulietti and F. Piva and M. D'Antonio and P. D'Onorio De Meo and D. Paoletti and T. Castrignanò and A. M. D'Erchia and E. Picardi and F. Zambelli and G. Principato and G. Pavesi and G. Pesole
Nucleic Acids Res 41 D125-31 (2013)
http://dx.doi.org/10.1093/nar/gks997

A comprehensive knowledge of all the factors involved in splicing, both proteins and RNAs, and of their interaction network is crucial for reaching a better understanding of this process and its functions. A large part of relevant information is buried in the literature or collected in various different databases. By hand-curated screenings of literature and databases, we retrieved experimentally validated data on 71 human RNA-binding splicing regulatory proteins and organized them into a database called 'SpliceAid-F' (http://www.caspur.it/SpliceAidF/). For each splicing factor (SF), the database reports its functional domains, its protein and chemical interactors and its expression data. Furthermore, we collected experimentally validated RNA-SF interactions, including relevant information on the RNA-binding sites, such as the genes where these sites lie, their genomic coordinates, the splicing effects, the experimental procedures used, as well as the corresponding bibliographic references. We also collected information from experiments showing no RNA-SF binding, at least in the assayed conditions. In total, SpliceAid-F contains 4227 interactions, 2590 RNA-binding sites and 1141 'no-binding' sites, including information on cellular contexts and conditions where binding was tested. The data collected in SpliceAid-F can provide significant information to explain an observed splicing pattern as well as the effect of mutations in functional regulatory elements.
Papaleo:2012aa: Sponge-associated microbial Antarctic communities exhibiting antimicrobial activity against Burkholderia cepacia complex bacteria
M. C. Papaleo and M. Fondi and I. Maida and E. Perrin and A. Lo Giudice and L. Michaud and S. Mangano and G. Bartolucci and R. Romoli and R. Fani
Biotechnol Adv 30 272-93 (2012)
http://dx.doi.org/10.1016/j.biotechadv.2011.06.011

The aerobic heterotrophic bacterial communities isolated from three different Antarctic sponge species were analyzed for their ability to produce antimicrobial compounds active toward Cystic Fibrosis opportunistic pathogens belonging to the Burkholderia cepacia complex (Bcc). The phylogenetic analysis performed on the 16S rRNA genes affiliated the 140 bacterial strains analyzed to 15 genera. Just three of them (Psychrobacter, Pseudoalteromonas and Arthrobacter) were shared by the three sponges. The further Random Amplified Polymorphic DNA analysis allowed to demonstrate that microbial communities are highly sponge-specific and a very low degree of genus/species/strain sharing was detected. Data obtained revealed that most of these sponge-associated Antarctic bacteria and belonging to different genera were able to completely inhibit the growth of bacteria belonging to the Bcc. On the other hand, the same Antarctic strains did not have any effect on the growth of other pathogenic bacteria, strongly suggesting that the inhibition is specific for Bcc bacteria. Moreover, the antimicrobial compounds synthesized by the most active Antarctic bacteria are very likely Volatile Organic Compounds (VOCs), a finding that was confirmed by the SPME-GC-MS technique, which revealed the production of a large set of VOCs by a representative set of Antarctic bacteria. The synthesis of these VOCs appeared to be related neither to the presence of pks genes nor the presence of plasmid molecules. The whole body of data obtained in this work indicates that sponge-associated bacteria represent an untapped source for the identification of new antimicrobial compounds and are paving the way for the discovery of new drugs that can be efficiently and successfully used for the treatment of CF infections.
Kiel:2011aa: Structural and functional protein network analyses predict novel signaling functions for rhodopsin
C. Kiel and A. Vogt and A. Campagna and A. Chatr-aryamontri and M. Swiatek-de Lange and M. Beer and S. Bolz and A. F. Mack and N. Kinkl and G. Cesareni and L. Serrano and M. Ueffing
Mol Syst Biol 7 551 (2011)
http://dx.doi.org/10.1038/msb.2011.83

Orchestration of signaling, photoreceptor structural integrity, and maintenance needed for mammalian vision remain enigmatic. By integrating three proteomic data sets, literature mining, computational analyses, and structural information, we have generated a multiscale signal transduction network linked to the visual G protein-coupled receptor (GPCR) rhodopsin, the major protein component of rod outer segments. This network was complemented by domain decomposition of protein-protein interactions and then qualified for mutually exclusive or mutually compatible interactions and ternary complex formation using structural data. The resulting information not only offers a comprehensive view of signal transduction induced by this GPCR but also suggests novel signaling routes to cytoskeleton dynamics and vesicular trafficking, predicting an important level of regulation through small GTPases. Further, it demonstrates a specific disease susceptibility of the core visual pathway due to the uniqueness of its components present mainly in the eye. As a comprehensive multiscale network, it can serve as a basis to elucidate the physiological principles of photoreceptor function, identify potential disease-associated genes and proteins, and guide the development of therapies that target specific branches of the signaling pathway.
Oliveira:2010aa: Structure of nanoscale truncated octahedral DNA cages: variation of single-stranded linker regions and influence on assembly yields
C. L. P. Oliveira and S. Juul and H. L. Jørgensen and B. Knudsen and D. Tordrup and F. Oteri and M. Falconi and J. Koch and A. Desideri and J. S. Pedersen and F. F. Andersen and B. R. Knudsen
ACS Nano 4 1367-76 (2010)
http://dx.doi.org/10.1021/nn901510v

The assembly, structure, and stability of DNA nanocages with the shape of truncated octahedra have been studied. The cages are composed of 12 double-stranded B-DNA helices interrupted by single-stranded linkers of thymidines of varying length that constitute the truncated corners of the structure. The structures assemble with a high efficiency in a one-step procedure, compared to previously published structures of similar complexity. The structures of the cages were determined by small-angle X-ray scattering. With increasing linker length, there is a systematic increase of the cage size and decrease of the twist angle of the double helices with respect to the symmetry planes of the cage structure. In the present study, we demonstrate the length of the single-stranded linker regions, which impose a certain degree of flexibility to the structure, to be the important determinant for efficient assembly. The linker length can be decreased to three thymidines without affecting assembly yield or the overall structural characteristics of the DNA cages. A linker length of two thymidines represents a sharp cutoff abolishing cage assembly. This is supported by energy minimization calculations suggesting substantial hydrogen bond deformation in a cage with linkers of two thymidines.
Gomez:2014aa: Suppression of microRNA-9 by mutant EGFR signaling upregulates FOXP1 to enhance glioblastoma tumorigenicity
G. G. Gomez and S. Volinia and C. M. Croce and C. Zanca and M. Li and R. Emnett and D. H. Gutmann and C. W. Brennan and F. B. Furnari and W. K. Cavenee
Cancer Res 74 1429-39 (2014)
http://dx.doi.org/10.1158/0008-5472.CAN-13-2117

The EGF receptor (EGFR) is amplified and mutated in glioblastoma, in which its common mutation (ΔEGFR, also called EGFRvIII) has a variety of activities that promote growth and inhibit death, thereby conferring a strong tumor-enhancing effect. This range of activities suggested to us that ΔEGFR might exert its influence through pleiotropic effectors, and we hypothesized that microRNAs might serve such a function. Here, we report that ΔEGFR specifically suppresses one such microRNA, namely miR-9, through the Ras/PI3K/AKT axis that it is known to activate. Correspondingly, expression of miR-9 antagonizes the tumor growth advantage conferred by ΔEGFR. Silencing of FOXP1, a miR-9 target, inhibits ΔEGFR-dependent tumor growth and, conversely, de-repression of FOXP1, as a consequence of miR-9 inhibition, increases tumorigenicity. FOXP1 was sufficient to increase tumor growth in the absence of oncogenic ΔEGFR signaling. The significance of these findings is underscored by our finding that high FOXP1 expression predicts poor survival in a cohort of 131 patients with glioblastoma. Collectively, these data suggest a novel regulatory mechanism by which ΔEGFR suppression of miR-9 upregulates FOXP1 to increase tumorigenicity.
Chiara:2012aa: SVM²: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data
M. Chiara and G. Pesole and D. S. Horner
Nucleic Acids Res 40 e145 (2012)
http://dx.doi.org/10.1093/nar/gks606

Several bioinformatics methods have been proposed for the detection and characterization of genomic structural variation (SV) from ultra high-throughput genome resequencing data. Recent surveys show that comprehensive detection of SV events of different types between an individual resequenced genome and a reference sequence is best achieved through the combination of methods based on different principles (split mapping, reassembly, read depth, insert size, etc.). The improvement of individual predictors is thus an important objective. In this study, we propose a new method that combines deviations from expected library insert sizes and additional information from local patterns of read mapping and uses supervised learning to predict the position and nature of structural variants. We show that our approach provides greatly increased sensitivity with respect to other tools based on paired end read mapping at no cost in specificity, and it makes reliable predictions of very short insertions and deletions in repetitive and low-complexity genomic contexts that can confound tools based on split mapping of reads.
Mosca:2012aa: Systems biology of the metabolic network regulated by the Akt pathway
E. Mosca and M. Barcella and R. Alfieri and A. Bevilacqua and G. Canti and L. Milanesi
Biotechnol Adv 30 131-41 (2012)
http://dx.doi.org/10.1016/j.biotechadv.2011.08.004

Cancer has been proposed as an example of systems biology disease or network disease. Accordingly, tumor cells differ from their normal counterparts more in terms of intracellular network dynamics than single markers. Here we shall focus on a recently recognized hallmark of cancer, the deregulation of cellular energetics. The constitutive activation of the phosphatidylinositol 3-kinase (PI3K)/Akt pathway has been confirmed as an essential step toward cell transformation. We will consider how the effects of Akt activation are connected with cell metabolism; more precisely, we will review existing metabolic models and discuss the current knowledge available to construct a kinetic model of the most relevant metabolic processes regulated by the PI3K/Akt pathway. The model will enable a systems biology approach to predict the metabolic targets that may inhibit cell growth under hyper activation of Akt.
Fumagalli:2012aa: Telomeric DNA damage is irreparable and causes persistent DNA-damage-response activation
M. Fumagalli and F. Rossiello and M. Clerici and S. Barozzi and D. Cittaro and J. M. Kaplunov and G. Bucci and M. Dobreva and V. Matti and C. M. Beausejour and U. Herbig and M. P. Longhese and F. d'Adda di Fagagna
Nat Cell Biol 14 355-65 (2012)
http://dx.doi.org/10.1038/ncb2466

The DNA-damage response (DDR) arrests cell-cycle progression until damage is removed. DNA-damage-induced cellular senescence is associated with persistent DDR. The molecular bases that distinguish transient from persistent DDR are unknown. Here we show that a large fraction of exogenously induced persistent DDR markers is associated with telomeric DNA in cultured cells and mammalian tissues. In yeast, a chromosomal DNA double-strand break next to a telomeric sequence resists repair and impairs DNA ligase 4 recruitment. In mammalian cells, ectopic localization of telomeric factor TRF2 next to a double-strand break induces persistent DNA damage and DDR. Linear, but not circular, telomeric DNA or scrambled DNA induces a prolonged checkpoint in normal cells. In terminally differentiated tissues of old primates, DDR markers accumulate at telomeres that are not critically short. We propose that linear genomes are not uniformly reparable and that telomeric DNA tracts, if damaged, are irreparable and trigger persistent DDR and cellular senescence.
DellOglio:2010aa: The anti-fibrotic effect of mycophenolic acid-induced neutral endopeptidase
M. P. Dell'Oglio and G. Zaza and M. Rossini and C. Divella and P. Pontrelli and R. Verrienti and M. Rutigliano and P. Ditonno and P. Stifanelli and N. Ancona and F. P. Schena and G. Grandaliano
J Am Soc Nephrol 21 2157-68 (2010)
http://dx.doi.org/10.1681/ASN.2010020181

Mycophenolic acid (MPA) appears to have anti-fibrotic effects, but the molecular mechanisms underlying this are unknown. We prospectively studied 35 stable kidney transplant recipients maintained on cyclosporine and azathioprine. We converted 20 patients from azathioprine to enteric-coated mycophenolate sodium (EC-MPS) and continued the remaining 15 patients on azathioprine. Exploratory mRNA expression profiling, performed on five randomly selected EC-MPS patients, revealed significant upregulation of neutral endopeptidase (NEP), which is an enzyme that degrades angiotensin II. We confirmed these microarray data by measuring levels of NEP expression in all subjects; in addition, we found that NEP gene expression correlated inversely with proteinuria. In an additional 33 patients, glomerular and tubular NEP protein levels from renal graft biopsies were significantly higher among the 13 patients receiving cyclosporine + EC-MPS than among the 12 patients receiving cyclosporine + azathioprine or 8 patients receiving cyclosporine alone. Glomerular NEP expression inversely correlated with glomerulosclerosis and proteinuria, and tubular NEP expression inversely correlated with interstitial fibrosis. Incubation of human proximal tubular cells with MPA increased NEP gene expression in a dose- and time-dependent manner. Moreover, MPA reduced angiotensin II-induced expression of the profibrotic factor plasminogen activator inhibitor-1, and a specific NEP inhibitor completely reversed this effect. Taken together, our data suggest that MPA directly induces expression of neutral endopeptidase, which may reduce proteinuria and slow the progression of renal damage in kidney transplant recipients.
Meldal:2014aa: The complex portal - an encyclopaedia of macromolecular complexes
B. H. M. Meldal and O. Forner-Martinez and M. C. Costanzo and J. Dana and J. Demeter and M. Dumousseau and S. S. Dwight and A. Gaulton and L. Licata and A. N. Melidoni and S. Ricard-Blum and B. Roechert and M. S. Skyzypek and M. Tiwari and S. Velankar and E. D. Wong and H. Hermjakob and S. Orchard
Nucleic Acids Res (2014)
http://dx.doi.org/10.1093/nar/gku975

The IntAct molecular interaction database has created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/intact/complex), through which protein complexes from major model organisms are being collated and made available for search, viewing and download. It has been built in close collaboration with other bioinformatics services and populated with data from ChEMBL, MatrixDB, PDBe, Reactome and UniProtKB. Each entry contains information about the participating molecules (including small molecules and nucleic acids), their stoichiometry, topology and structural assembly. Complexes are annotated with details about their function, properties and complex-specific Gene Ontology (GO) terms. Consistent nomenclature is used throughout the resource with systematic names, recommended names and a list of synonyms all provided. The use of the Evidence Code Ontology allows us to indicate for which entries direct experimental evidence is available or if the complex has been inferred based on homology or orthology. The data are searchable using standard identifiers, such as UniProt, ChEBI and GO IDs, protein, gene and complex names or synonyms. This reference resource will be maintained and grow to encompass an increasing number of organisms. Input from groups and individuals with specific areas of expertise is welcome.
Tili:2012aa: The down-regulation of miR-125b in chronic lymphocytic leukemias leads to metabolic adaptation of cells to a transformed state
E. Tili and J.-J. Michaille and Z. Luo and S. Volinia and L. Z. Rassenti and T. J. Kipps and C. M. Croce
Blood 120 2631-8 (2012)
http://dx.doi.org/10.1182/blood-2012-03-415737

MiR-125b-1 maps at 11q24, a chromosomal region close to the epicenter of 11q23 deletions in chronic lymphocytic leukemias (CLLs). Our results establish that both aggressive and indolent CLL patients show reduced expression of miR-125b. Overexpression of miR-125b in CLL-derived cell lines resulted in the repression of many transcripts encoding enzymes implicated in cell metabolism. Metabolomics analyses showed that miR-125b overexpression modulated glucose, glutathione, lipid, and glycerolipid metabolism. Changes on the same metabolic pathways also were observed in CLLs. We furthermore analyzed the expression of some of miR-125b-target transcripts that are potentially involved in the aforementioned metabolic pathways and defined a miR-125b-dependent CLL metabolism-related transcript signature. Thus, miR-125b acts as a master regulator for the adaptation of cell metabolism to a transformed state. MiR-125b and miR-125b-dependent metabolites therefore warrant further investigation as possible novel therapeutic approaches for patients with CLL.
Leitner:2010aa: The FEBS Letters/BioCreative II.5 experiment: making biological information accessible
F. Leitner and A. Chatr-aryamontri and S. A. Mardis and A. Ceol and M. Krallinger and L. Licata and L. Hirschman and G. Cesareni and A. Valencia
Nat Biotechnol 28 897-9 (2010)
http://dx.doi.org/10.1038/nbt0910-897
Fasoli:2012aa: The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program
M. Fasoli and S. Dal Santo and S. Zenoni and G. B. Tornielli and L. Farina and A. Zamboni and A. Porceddu and L. Venturini and M. Bicego and V. Murino and A. Ferrarini and M. Delledonne and M. Pezzotti
Plant Cell 24 3489-505 (2012)
http://dx.doi.org/10.1105/tpc.112.100230

We developed a genome-wide transcriptomic atlas of grapevine (Vitis vinifera) based on 54 samples representing green and woody tissues and organs at different developmental stages as well as specialized tissues such as pollen and senescent leaves. Together, these samples expressed ∼91% of the predicted grapevine genes. Pollen and senescent leaves had unique transcriptomes reflecting their specialized functions and physiological status. However, microarray and RNA-seq analysis grouped all the other samples into two major classes based on maturity rather than organ identity, namely, the vegetative/green and mature/woody categories. This division represents a fundamental transcriptomic reprogramming during the maturation process and was highlighted by three statistical approaches identifying the transcriptional relationships among samples (correlation analysis), putative biomarkers (O2PLS-DA approach), and sets of strongly and consistently expressed genes that define groups (topics) of similar samples (biclustering analysis). Gene coexpression analysis indicated that the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of clusters of neighboring genes and global regulation based on codon preference. This global transcriptomic reprogramming during maturation has not been observed in herbaceous annual species and may be a defining characteristic of perennial woody plants.
International-Peach-Genome-Initiative:2013aa: The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
International Peach Genome Initiative and I. Verde and A. G. Abbott and S. Scalabrin and S. Jung and S. Shu and F. Marroni and T. Zhebentyayeva and M. T. Dettori and J. Grimwood and F. Cattonaro and A. Zuccolo and L. Rossini and J. Jenkins and E. Vendramin and L. A. Meisel and V. Decroocq and B. Sosinski and S. Prochnik and T. Mitros and A. Policriti and G. Cipriani and L. Dondini and S. Ficklin and D. M. Goodstein and P. Xuan and C. Del Fabbro and V. Aramini and D. Copetti and S. Gonzalez and D. S. Horner and R. Falchi and S. Lucas and E. Mica and J. Maldonado and B. Lazzari and D. Bielenberg and R. Pirona and M. Miculan and A. Barakat and R. Testolin and A. Stella and S. Tartarini and P. Tonutti and P. Arús and A. Orellana and C. Wells and D. Main and G. Vizzotto and H. Silva and F. Salamini and J. Schmutz and M. Morgante and D. S. Rokhsar
Nat Genet 45 487-94 (2013)
http://dx.doi.org/10.1038/ng.2586

Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.
Cordenonsi:2011aa: The Hippo transducer TAZ confers cancer stem cell-related traits on breast cancer cells
M. Cordenonsi and F. Zanconato and L. Azzolin and M. Forcato and A. Rosato and C. Frasson and M. Inui and M. Montagner and A. R. Parenti and A. Poletti and M. G. Daidone and S. Dupont and G. Basso and S. Bicciato and S. Piccolo
Cell 147 759-72 (2011)
http://dx.doi.org/10.1016/j.cell.2011.09.048

Cancer stem cells (CSCs) are proposed to drive tumor initiation and progression. Yet, our understanding of the cellular and molecular mechanisms that underlie CSC properties is limited. Here we show that the activity of TAZ, a transducer of the Hippo pathway, is required to sustain self-renewal and tumor-initiation capacities in breast CSCs. TAZ protein levels and activity are elevated in prospective CSCs and in poorly differentiated human tumors and have prognostic value. Gain of TAZ endows self-renewal capacity to non-CSCs. In epithelial cells, TAZ forms a complex with the cell-polarity determinant Scribble, and loss of Scribble--or induction of the epithelial-mesenchymal transition (EMT)--disrupts the inhibitory association of TAZ with the core Hippo kinases MST and LATS. This study links the CSC concept to the Hippo pathway in breast cancer and reveals a mechanistic basis of the control of Hippo kinases by cell polarity.
Tremblay:2014aa: The Hippo transducer YAP1 transforms activated satellite cells and is a potent effector of embryonal rhabdomyosarcoma formation
A. M. Tremblay and E. Missiaglia and G. G. Galli and S. Hettmer and R. Urcia and M. Carrara and R. N. Judson and K. Thway and G. Nadal and J. L. Selfe and G. Murray and R. A. Calogero and C. De Bari and P. S. Zammit and M. Delorenzi and A. J. Wagers and J. Shipley and H. Wackerhage and F. D. Camargo
Cancer Cell 26 273-87 (2014)
http://dx.doi.org/10.1016/j.ccr.2014.05.029

The role of the Hippo pathway effector YAP1 in soft tissue sarcomas is poorly defined. Here we report that YAP1 activity is elevated in human embryonal rhabdomyosarcoma (ERMS). In mice, sustained YAP1 hyperactivity in activated, but not quiescent, satellite cells induces ERMS with high penetrance and short latency. Via its transcriptional program with TEAD1, YAP1 directly regulates several major hallmarks of ERMS. YAP1-TEAD1 upregulate pro-proliferative and oncogenic genes and maintain the ERMS differentiation block by interfering with MYOD1 and MEF2 pro-differentiation activities. Normalization of YAP1 expression reduces tumor burden in human ERMS xenografts and allows YAP1-driven ERMS to differentiate in situ. Collectively, our results identify YAP1 as a potent ERMS oncogenic driver and a promising target for differentiation therapy.
Giannotta:2012aa: The KDEL receptor couples to Gαq/11 to activate Src kinases and regulate transport through the Golgi
M. Giannotta and C. Ruggiero and M. Grossi and J. Cancino and M. Capitani and T. Pulvirenti and G. M. L. Consoli and C. Geraci and F. Fanelli and A. Luini and M. Sallese
EMBO J 31 2869-81 (2012)
http://dx.doi.org/10.1038/emboj.2012.134

Membrane trafficking involves large fluxes of cargo and membrane across separate compartments. These fluxes must be regulated by control systems to maintain homoeostasis. While control systems for other key functions such as protein folding or the cell cycle are well known, the mechanisms that control secretory transport are poorly understood. We have previously described a signalling circuit operating at the Golgi complex that regulates intra-Golgi trafficking and is initiated by the KDEL receptor (KDEL-R), a protein previously known to mediate protein recycling from the Golgi to the endoplasmic reticulum (ER). Here, we investigated the KDEL-R signalling mechanism. We show that the KDEL-R is predicted to fold like a G-protein-coupled receptor (GPCR), and that it binds and activates the heterotrimeric signalling G-protein Gα(q/11) which, in turn, regulates transport through the Golgi complex. These findings reveal an unexpected GPCR-like mode of action of the KDEL-R and shed light on a core molecular control mechanism of intra-Golgi traffic.
Orchard:2014aa: The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases
S. Orchard and M. Ammari and B. Aranda and L. Breuza and L. Briganti and F. Broackes-Carter and N. H. Campbell and G. Chavali and C. Chen and N. del-Toro and M. Duesbury and M. Dumousseau and E. Galeota and U. Hinz and M. Iannuccelli and S. Jagannathan and R. Jimenez and J. Khadake and A. Lagreid and L. Licata and R. C. Lovering and B. Meldal and A. N. Melidoni and M. Milagros and D. Peluso and L. Perfetto and P. Porras and A. Raghunath and S. Ricard-Blum and B. Roechert and A. Stutz and M. Tognolli and K. van Roey and G. Cesareni and H. Hermjakob
Nucleic Acids Res 42 D358-63 (2014)
http://dx.doi.org/10.1093/nar/gkt1115

IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org).
Bomben:2012aa: The miR-17∼92 family regulates the response to Toll-like receptor 9 triggering of CLL cells with unmutated IGHV genes
R. Bomben and S. Gobessi and M. Dal Bo and S. Volinia and D. Marconi and E. Tissino and D. Benedetti and A. Zucchetto and D. Rossi and G. Gaidano and G. Del Poeta and L. Laurenti and D. G. Efremov and V. Gattei
Leukemia 26 1584-93 (2012)
http://dx.doi.org/10.1038/leu.2012.44

Chronic lymphocytic leukemia (CLL) cells from clinically aggressive cases have a greater capacity to respond to external microenvironmental stimuli, including those transduced through Toll-like-receptor-9 (TLR9). Concomitant microRNA and gene expression profiling in purified CLL cells (n=17) expressing either unmutated (UM) or mutated (M) IGHV genes selected microRNAs from the miR-17∼92 family as significantly upregulated and in part responsible for modifications in the gene expression profile of UM CLL cells stimulated with the TLR9 agonist CpG. Notably, the stable and sustained upregulation of miR-17∼92 microRNAs by CpG was preceded by a transient induction of the proto-oncogene MYC. The enforced expression of miR-17, a major member from this family, reduced the expression of the tumor suppressor genes E2F5, TP53INP1, TRIM8 and ZBTB4, and protected cells from serum-free-induced apoptosis (P ≤ 0.05). Consistently, transfection with miR-17∼92 family antagomiRs reduced Bromo-deoxy-uridine incorporation in CpG-stimulated UM CLL cells. Finally, miR-17 expression levels, evaluated in 83 CLL samples, were significantly higher in UM (P=0.03) and ZAP-70(high) (P=0.02) cases. Altogether, these data reveal a role for microRNAs of the miR-17∼92 family in regulating pro-survival and growth-promoting responses of CLL cells to TLR9 triggering. Overall, targeting of this pathway may represent a novel therapeutic option for management of aggressive CLL.
Borrelli:2010aa: The p63 target HBP1 is required for skin differentiation and stratification
S. Borrelli and E. Candi and B. Hu and D. Dolfini and M. Ravo and O. M. V. Grober and A. Weisz and G. P. Dotto and G. Melino and M. A. Viganò and R. Mantovani
Cell Death Differ 17 1896-907 (2010)
http://dx.doi.org/10.1038/cdd.2010.59

Genetic experiments established that p63 is crucial for the development and maintenance of pluristratified epithelia. In the RNA interference (RNAi) screening for targets of p63 in keratinocytes, we identified the transcription factor, High Mobility Group (HMG) box protein 1 (HBP1). HBP1 is an HMG-containing repressor transiently induced during differentiation of several cell lineages. We investigated the relationship between the two factors: using RNAi, overexpression, chromatin immunoprecipitations and transient transfections with reporter constructs, we established that HBP1 is directly repressed by p63. This was further confirmed in vivo by evaluating expression in p63 knockout mice and in transgenics expressing p63 in basal keratinocytes. Consistent with these findings, expression of HBP1 increases upon differentiation of primary keratinocytes and HaCaT cells in culture, and it is higher in the upper layers of human skin. Inactivation of HBP1 by RNAi prevents differentiation of keratinocytes and stratification of organotypic skin cultures. Finally, we analyzed the keratinocyte transcriptomes after HBP1 RNAi; in addition to repression of growth-promoting genes, unexpected activation of differentiation genes was uncovered, coexisting with repression of other genes involved in epithelial cornification. Our data indicate that suppression of HBP1 is part of the growth-promoting strategy of p63 in the lower layers of epidermis and that HBP1 temporally coordinates expression of genes involved in stratification, leading to the formation of the skin barrier.
Carducci:2012aa: The protein interaction network mediated by human SH3 domains
M. Carducci and L. Perfetto and L. Briganti and S. Paoluzi and S. Costa and J. Zerweck and M. Schutkowski and L. Castagnoli and G. Cesareni
Biotechnol Adv 30 4-15 (2012)
http://dx.doi.org/10.1016/j.biotechadv.2011.06.012

Families of conserved protein domains, specialized in mediating interactions with short linear peptide motifs, are responsible for the formation of a variety of dynamic complexes in the cell. An important subclass of these motifs are characterized by a high proline content and play a pivotal role in biological processes requiring the coordinated assembly of multi-protein complexes. This is achieved via interaction of proteins containing modules such as Src Homology-3 (SH3) or WW domains and specific proline rich patterns. Here we make available via a publicly accessible database a synopsis of our current understanding of the interaction landscape of the human SH3 protein family. This is achieved by integrating an information extraction strategy with a new experimental approach. In a first approach we have used a text mining strategy to capture a large number of manuscripts reporting interactions between SH3 domains and target peptides. Relevant information was annotated in the MINT database. In a second experimental approach we have used a variant of the WISE (Whole Interactome Scanning Experiment) strategy to probe a large number of naturally occurring and chemically-synthesized peptides arrayed at high density on a glass surface. By this method we have tested 60 human SH3 domains for their ability to bind a collection of 9192 poly-proline containing peptides immobilized on a glass chip. To evaluate the quality of the resulting interaction dataset, we retested some of the interactions on a smaller scale and performed a series of pull down experiments on native proteins. Peptide chips, pull down assays, SPOT synthesis and phage display experiments have allowed us to further characterize the specificity and promiscuity of proline-rich binding domains and to map their interaction network. Both the information captured from the literature and the interactions inferred from the peptide chip experiments were collected and stored in the PepspotDB (http://mint.bio.uniroma2.it/PepspotDB/).
Agnelli:2011aa: The reconstruction of transcriptional networks reveals critical genes with implications for clinical outcome of multiple myeloma
L. Agnelli and M. Forcato and F. Ferrari and G. Tuana and K. Todoerti and B. A. Walker and G. J. Morgan and L. Lombardi and S. Bicciato and A. Neri
Clin Cancer Res 17 7402-12 (2011)
http://dx.doi.org/10.1158/1078-0432.CCR-11-0596

PURPOSE: The combined use of microarray technologies and bioinformatics analysis has improved our understanding of biological complexity of multiple myeloma (MM). In contrast, the application of the same technology in the attempt to predict clinical outcome has been less successful with the identification of heterogeneous molecular signatures. Herein, we have reconstructed gene regulatory networks in a panel of 1,883 samples from MM patients derived from publicly available gene expression sets, to allow the identification of robust and reproducible signatures associated with poor prognosis across independent data sets. EXPERIMENTAL DESIGN: Gene regulatory networks were reconstructed by using Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) and microarray data from seven MM data sets. Critical analysis of network components was applied to identify genes playing an essential role in transcriptional networks, which are conserved between data sets. RESULTS: Network critical analysis revealed that (i) CCND1 and CCND2 were the most critical genes; (ii) CCND2, AIF1, and BLNK had the largest number of connections shared among the data sets; (iii) robust gene signatures with prognostic power were derived from the most critical transcripts and from shared primary neighbors of the most connected nodes. Specifically, a critical-gene model, comprising FAM53B, KIF21B, WHSC1, and TMPO, and a neighbor-gene model, comprising BLNK shared neighbors CSGALNACT1 and SLC7A7, predicted survival in all data sets with follow-up information. CONCLUSIONS: The reconstruction of gene regulatory networks in a large panel of MM tumors defined robust and reproducible signatures with prognostic importance, and may lead to identify novel molecular mechanisms central to MM biology.
DAlessandro:2010aa: The red blood cell proteome and interactome: an update
A. D'Alessandro and P. G. Righetti and L. Zolla
J Proteome Res 9 144-63 (2010)
http://dx.doi.org/10.1021/pr900831f

Although a preliminary portrait of the red blood cell proteome and interactome has already been provided, the recent identification of 1578 gene products from the erythrocyte cytosol asks for an updated and improved view. In this paper, we exploit data available from recent literature to compile a nonredundant list of 1989 proteins and elaborate it with pathway and network analyses. Upon network analysis, it is intuitively confirmed that red blood cells likely suffer of exacerbated oxidative stress and continuously strive against protein and cytoskeletal damage. It also emerges that erythrocyte interaction networks display a high degree of maturity. Indeed, a series of core proteins were individuated to play a central role. A catalytic ring of proteins counteracting oxidative stress was individuated as well. In parallel, pathway analysis confirmed the validity of observations about the SEC23B gene role in CDA II in a fast and unbiased way.
Saraconi:2014aa: The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas
G. Saraconi and F. Severi and C. Sala and G. Mattiuz and S. G. Conticello
Genome Biol 15 417 (2014)
http://dx.doi.org/10.1186/s13059-014-0417-z

BACKGROUND: The AID/APOBECs are deaminases that act on cytosines in a diverse set of pathways and some of them have been linked to the onset of genetic alterations in cancer. Among them, APOBEC1 is the only family member to physiologically target RNA, as the catalytic subunit in the Apolipoprotein B mRNA editing complex. APOBEC1 has been linked to cancer development in mice but its oncogenic mechanisms are not yet well understood. RESULTS: We analyze whether expression of APOBEC1 induces a mutator phenotype in vertebrate cells, likely through direct targeting of genomic DNA. We show its ability to increase the inactivation of a stably inserted reporter gene in a chicken cell line that lacks any other AID/APOBEC proteins, and to increase the number of imatinib-resistant clones in a human cellular model for chronic myeloid leukemia through induction of mutations in the BCR-ABL1 fusion gene. Moreover, we find the presence of an AID/APOBEC mutational signature in esophageal adenocarcinomas, a type of tumor where APOBEC1 is expressed, that mimics the one preferred by APOBEC1 in vitro. CONCLUSIONS: Our findings suggest that the ability of APOBEC1 to trigger genetic alterations represents a major layer in its oncogenic potential. Such APOBEC1-induced mutator phenotypes could play a role in the onset of esophageal adenocarcinomas. APOBEC1 could be involved in cancer promotion at the very early stages of carcinogenesis, as it is highly expressed in Barrett's esophagus, a condition often associated with esophageal adenocarcinoma.
Pozzoli:2010aa: The role of protozoa-driven selection in shaping human genetic variability
U. Pozzoli and M. Fumagalli and R. Cagliani and G. P. Comi and N. Bresolin and M. Clerici and M. Sironi
Trends Genet 26 95-9 (2010)
http://dx.doi.org/10.1016/j.tig.2009.12.010

Protozoa exert a strong selective pressure in humans. The selection signatures left by these pathogens can be exploited to identify genetic modulators of infection susceptibility. We show that protozoa diversity in different geographic locations is a good measure of protozoa-driven selective pressure; protozoa diversity captured selection signatures at known malaria resistance loci and identified several selected single nucleotide polymorphisms in immune and hemolytic anemia genes. A genome-wide search enabled us to identify 5180 variants mapping to 1145 genes that are subjected to protozoa-driven selective pressure. We provide a genome-wide estimate of protozoa-driven selective pressure and identify candidate susceptibility genes for protozoa-borne diseases.
Tinti:2013aa: The SH2 domain interaction landscape
M. Tinti and L. Kiemer and S. Costa and M. L. Miller and F. Sacco and J. V. Olsen and M. Carducci and S. Paoluzi and F. Langone and C. T. Workman and N. Blom and K. Machida and C. M. Thompson and M. Schutkowski and S. Brunak and M. Mann and B. J. Mayer and L. Castagnoli and G. Cesareni
Cell Rep 3 1293-305 (2013)
http://dx.doi.org/10.1016/j.celrep.2013.03.001

Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a high-density peptide chip technology that allows for probing of the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique, we have experimentally identified thousands of putative SH2-peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2-mediated probabilistic interaction network, which we make available as a community resource in the PepspotDB database. A predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the extracellular signal-regulated kinase activation loop was validated by experiments in living cells.
Dolfini:2012aa: The short isoform of NF-YA belongs to the embryonic stem cell transcription factor circuitry
D. Dolfini and M. Minuzzo and G. Pavesi and R. Mantovani
Stem Cells 30 2450-9 (2012)
http://dx.doi.org/10.1002/stem.1232

Totipotency of embryonic stem cells (ESCs) is controlled at the transcriptional level by a handful of transcription factors (TFs) that promote stemness and prevent differentiation. One of the most enriched DNA elements in promoters and enhancers of genes specifically active in ESCs is the CCAAT box, which is recognized by NF-Y, a trimer with histone-like subunits--NF-YB/NF--YC--and the sequence-specific NF-YA. We show that the levels of the short NF-YA isoform--NF-YAs--is high in mouse ESCs (mESCs) and drops after differentiation; a dominant negative mutant affects expression of important stem cells genes, directly and indirectly. Protein transfections of TAT-NF-YAs stimulate growth and compensate for withdrawal of leukemia inhibitory factor (LIF) in cell cultures. Bioinformatic analysis identifies NF-Y sites as highly enriched in genomic loci of stem TFs in ESCs. Specifically, 30%-50% of NANOG peaks have NF-Y sites and indeed NF-Y-binding is required for NANOG association to DNA. These data indicate that NF-Y belongs to the restricted circle of TFs that govern mESCs, and, specifically, that NF-YAs is the active isoform in these cells.
Castagnola:2011ab: The surprising composition of the salivary proteome of preterm human newborn
M. Castagnola and R. Inzitari and C. Fanali and F. Iavarone and A. Vitali and C. Desiderio and G. Vento and C. Tirone and C. Romagnoli and T. Cabras and B. Manconi and M. T. Sanna and R. Boi and E. Pisano and A. Olianas and M. Pellegrini and S. Nemolato and C. W. Heizmann and G. Faa and I. Messana
Mol Cell Proteomics 10 M110.003467 (2011)
http://dx.doi.org/10.1074/mcp.M110.003467

Saliva is a body fluid of a unique composition devoted to protect the mouth cavity and the digestive tract. Our high performance liquid chromatography (HPLC)-electrospray ionization-MS analysis of the acidic soluble fraction of saliva from preterm human newborn surprisingly revealed more than 40 protein masses often undetected in adult saliva. We were able to identify the following proteins: stefin A and stefin B, S100A7 (two isoforms), S100A8, S100A9 (four isoforms), S100A11, S100A12, small proline-rich protein 3 (two isoforms), lysozyme C, thymosins β(4) and β(10), antileukoproteinase, histone H1c, and α and γ globins. The average mass value reported in international data banks was often incongruent with our experimental results mostly because of post-translational modifications of the proteins, e.g. acetylation of the N-terminal residue. A quantitative label-free MS analysis showed protein levels altered in relation to the postconceptional age and suggested coordinate and hierarchical functions for these proteins during development. In summary, this study shows for the first time that analysis of these proteins in saliva of preterm newborns might represent a noninvasive way to obtain precious information of the molecular mechanisms of development of human fetal oral structures.
Preti:2010aa: The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae
M. Preti and C. Ribeyre and C. Pascali and M. C. Bosio and B. Cortelazzi and J. Rougemont and E. Guarnera and F. Naef and D. Shore and G. Dieci
Mol Cell 38 614-20 (2010)
http://dx.doi.org/10.1016/j.molcel.2010.04.016

Small nucleolar RNAs (snoRNAs) play a key role in ribosomal RNA biogenesis, yet factors controlling their expression are unknown. We found that the majority of Saccharomyces snoRNA promoters display an aRCCCTaa sequence motif at the upstream border of a TATA-containing nucleosome-free region. Genome-wide ChIP-seq analysis showed that these motifs are bound by Tbf1, a telomere-binding protein known to recognize mammalian-like T(2)AG(3) repeats at subtelomeric regions. Tbf1 has over 100 additional promoter targets, including several other genes involved in ribosome biogenesis and the TBF1 gene itself. Tbf1 is required for full snoRNA expression, yet it does not influence nucleosome positioning at snoRNA promoters. In contrast, Tbf1 contributes to nucleosome exclusion at non-snoRNA promoters, where it selectively colocalizes with the Tbf1-interacting zinc-finger proteins Vid22 and Ygr071c. Our data show that, besides the ribosomal protein gene regulator Rap1, a second telomere-binding protein also functions as a transcriptional regulator linked to yeast ribosome biogenesis.
Tomato-Genome-Consortium:2012aa: The tomato genome sequence provides insights into fleshy fruit evolution
Tomato Genome Consortium
Nature 485 635-41 (2012)
http://dx.doi.org/10.1038/nature11119

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
Rizzo:2014aa: Timed regulation of P-element-induced wimpy testis-interacting RNA expression during rat liver regeneration
F. Rizzo and A. Hashim and G. Marchese and M. Ravo and R. Tarallo and G. Nassa and G. Giurato and A. Rinaldi and A. Cordella and M. Persico and P. Sulas and A. Perra and G. M. Ledda-Columbano and A. Columbano and A. Weisz
Hepatology 60 798-806 (2014)
http://dx.doi.org/10.1002/hep.27267

UNLABELLED: Small noncoding RNAs comprise a growing family of molecules that regulate key cellular processes, including messenger RNA (mRNA) degradation, translational repression, and transcriptional gene silencing. P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) represent a class of small RNAs initially identified in the germline of a variety of species, where they contribute to maintenance of genome stability, and recently found expressed also in stem and somatic cells, where their role and responsiveness to physiopathological signals remain elusive. Here, we investigated piRNA expression in rat liver and its response to the stimuli exerted by regenerative proliferation of this organ. Quantitative polymerase chain reaction analysis identify in the liver the RNAs encoding PIWIL2/HILI, PIWIL4/HIWI2, and other components of the piRNA biogenesis pathways, suggesting that this is indeed functional. RNA sequencing before, during, and after the wave of cell proliferation that follows partial hepatectomy (PH) identified ∼1,400 mammalian germline piRNAs expressed in rat liver, including 72 showing timed changes in expression 24-48 hours post-PH, a timing that corresponds to cell transition through the S phase, returning to basal levels by 168 hours, when organ regeneration is completed and hepatocytes reach quiescence. CONCLUSION: The piRNA pathway is active in somatic cells of the liver and is subject to regulation during the pathophysiological process of organ regeneration, when these molecules are available to exert their regulatory functions on the cell genome and transcriptome, as demonstrated by the identification of several liver mRNAs representing candidate targets of these regulatory RNAs.
Zoppoli:2010aa: TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach
P. Zoppoli and S. Morganella and M. Ceccarelli
BMC Bioinformatics 11 154 (2010)
http://dx.doi.org/10.1186/1471-2105-11-154

BACKGROUND: One of main aims of Molecular Biology is the gain of knowledge about how molecular components interact each other and to understand gene function regulations. Using microarray technology, it is possible to extract measurements of thousands of genes into a single analysis step having a picture of the cell gene expression. Several methods have been developed to infer gene networks from steady-state data, much less literature is produced about time-course data, so the development of algorithms to infer gene networks from time-series measurements is a current challenge into bioinformatics research area. In order to detect dependencies between genes at different time delays, we propose an approach to infer gene regulatory networks from time-series measurements starting from a well known algorithm based on information theory. RESULTS: In this paper we show how the ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks) algorithm can be used for gene regulatory network inference in the case of time-course expression profiles. The resulting method is called TimeDelay-ARACNE. It just tries to extract dependencies between two genes at different time delays, providing a measure of these dependencies in terms of mutual information. The basic idea of the proposed algorithm is to detect time-delayed dependencies between the expression profiles by assuming as underlying probabilistic model a stationary Markov Random Field. Less informative dependencies are filtered out using an auto calculated threshold, retaining most reliable connections. TimeDelay-ARACNE can infer small local networks of time regulated gene-gene interactions detecting their versus and also discovering cyclic interactions also when only a medium-small number of measurements are available. We test the algorithm both on synthetic networks and on microarray expression profiles. Microarray measurements concern S. cerevisiae cell cycle, E. coli SOS pathways and a recently developed network for in vivo assessment of reverse engineering algorithms. Our results are compared with ARACNE itself and with the ones of two previously published algorithms: Dynamic Bayesian Networks and systems of ODEs, showing that TimeDelay-ARACNE has good accuracy, recall and F-score for the network reconstruction task. CONCLUSIONS: Here we report the adaptation of the ARACNE algorithm to infer gene regulatory networks from time-course data, so that, the resulting network is represented as a directed graph. The proposed algorithm is expected to be useful in reconstruction of small biological directed networks from time course data.
Galli:2013aa: Toll-like receptor 3 (TLR3) activation induces microRNA-dependent reexpression of functional RARβ and tumor regression
R. Galli and A. Paone and M. Fabbri and N. Zanesi and F. Calore and L. Cascione and M. Acunzo and A. Stoppacciaro and A. Tubaro and F. Lovat and P. Gasparini and P. Fadda and H. Alder and S. Volinia and A. Filippini and E. Ziparo and A. Riccioli and C. M. Croce
Proc Natl Acad Sci U S A 110 9812-7 (2013)
http://dx.doi.org/10.1073/pnas.1304610110

Toll-like receptor 3 (TLR3) is a key effector of the innate immune system against viruses. Activation of TLR3 exerts an antitumoral effect through a mechanism of action still poorly understood. Here we show that TLR3 activation by polyinosinic:polycytidylic acid induces up-regulation of microRNA-29b, -29c, -148b, and -152 in tumor-derived cell lines and primary tumors. In turn, these microRNAs induce reexpression of epigenetically silenced genes by targeting DNA methyltransferases. In DU145 and TRAMP-C1 prostate and MDA-MB-231 breast cancer cells, we demonstrated that polyinosinic:polycytidylic acid-mediated activation of TLR3 induces microRNAs targeting DNA methyltransferases, leading to demethylation and reexpression of the oncosuppressor retinoic acid receptor beta (RARβ). As a result, cancer cells become sensitive to retinoic acid and undergo apoptosis both in vitro and in vivo. This study provides evidence of an antitumoral mechanism of action upon TLR3 activation and the biological rationale for a combined TLR3 agonist/retinoic acid treatment of prostate and breast cancer.
Singh:2012aa: Transforming fusions of FGFR and TACC genes in human glioblastoma
D. Singh and J. M. Chan and P. Zoppoli and F. Niola and R. Sullivan and A. Castano and E. M. Liu and J. Reichel and P. Porrati and S. Pellegatta and K. Qiu and Z. Gao and M. Ceccarelli and R. Riccardi and D. J. Brat and A. Guha and K. Aldape and J. G. Golfinos and D. Zagzag and T. Mikkelsen and G. Finocchiaro and A. Lasorella and R. Rabadan and A. Iavarone
Science 337 1231-5 (2012)
http://dx.doi.org/10.1126/science.1220834

The brain tumor glioblastoma multiforme (GBM) is among the most lethal forms of human cancer. Here, we report that a small subset of GBMs (3.1%; 3 of 97 tumors examined) harbors oncogenic chromosomal translocations that fuse in-frame the tyrosine kinase coding domains of fibroblast growth factor receptor (FGFR) genes (FGFR1 or FGFR3) to the transforming acidic coiled-coil (TACC) coding domains of TACC1 or TACC3, respectively. The FGFR-TACC fusion protein displays oncogenic activity when introduced into astrocytes or stereotactically transduced in the mouse brain. The fusion protein, which localizes to mitotic spindle poles, has constitutive kinase activity and induces mitotic and chromosomal segregation defects and triggers aneuploidy. Inhibition of FGFR kinase corrects the aneuploidy, and oral administration of an FGFR inhibitor prolongs survival of mice harboring intracranial FGFR3-TACC3-initiated glioma. FGFR-TACC fusions could potentially identify a subset of GBM patients who would benefit from targeted FGFR kinase inhibition.
Marigo:2010aa: Tumor-induced tolerance and immune suppression depend on the C/EBPbeta transcription factor
I. Marigo and E. Bosio and S. Solito and C. Mesa and A. Fernandez and L. Dolcetti and S. Ugel and N. Sonda and S. Bicciato and E. Falisi and F. Calabrese and G. Basso and P. Zanovello and E. Cozzi and S. Mandruzzato and V. Bronte
Immunity 32 790-802 (2010)
http://dx.doi.org/10.1016/j.immuni.2010.05.010

Tumor growth is associated with a profound alteration in myelopoiesis, leading to recruitment of immunosuppressive cells known as myeloid-derived suppressor cells (MDSCs). We showed that among factors produced by various experimental tumors, the cytokines GM-CSF, G-CSF, and IL-6 allowed a rapid generation of MDSCs from precursors present in mouse and human bone marrow (BM). BM-MDSCs induced by GM-CSF+IL-6 possessed the highest tolerogenic activity, as revealed by the ability to impair the priming of CD8(+) T cells and allow long term acceptance of pancreatic islet allografts. Cytokines inducing MDSCs acted on a common molecular pathway and the immunoregulatory activity of both tumor-induced and BM-derived MDSCs was entirely dependent on the C/EBPbeta transcription factor. Adoptive transfer of tumor antigen-specific CD8(+) T lymphocytes resulted in therapy of established tumors only in mice lacking C/EBPbeta in the myeloid compartment, suggesting that C/EBPbeta is a critical regulator of the immunosuppressive environment created by growing cancers.
Sabatino:2012aa: UHRF1 coordinates peroxisome proliferator activated receptor gamma (PPARG) epigenetic silencing and mediates colorectal cancer progression
L. Sabatino and A. Fucci and M. Pancione and V. Carafa and A. Nebbioso and C. Pistore and F. Babbio and C. Votino and C. Laudanna and M. Ceccarelli and L. Altucci and I. M. Bonapace and V. Colantuoni
Oncogene 31 5061-72 (2012)
http://dx.doi.org/10.1038/onc.2012.3

Peroxisome proliferator-activated receptor gamma (PPARG) inactivation has been identified as an important step in colorectal cancer (CRC) progression, although the events involved have been partially clarified. UHRF1 is emerging as a cofactor that coordinates the epigenetic silencing of tumor suppressor genes, but its role in CRC remains elusive. Here, we report that UHRF1 negatively regulates PPARG and is associated with a higher proliferative, clonogenic and migration potential. Consistently, UHRF1 ectopic expression induces PPARG repression through its recruitment on the PPARG promoter fostering DNA methylation and histone repressive modifications. In agreement, UHRF1 knockdown elicits PPARG re-activation, accompanied by positive histone marks and DNA demethylation, corroborating its role in PPARG silencing. UHRF1 overexpression, as well as PPARG-silencing, imparts higher growth rate and phenotypic features resembling those occurring in the epithelial-mesenchymal transition. In our series of 110 sporadic CRCs, high UHRF1-expressing tumors are characterized by an undifferentiated phenotype, higher proliferation rate and poor clinical outcome only in advanced stages III-IV. In addition, the inverse relationship with PPARG found in vitro is detected in vivo and UHRF1 prognostic significance appears closely related to PPARG low expression, as remarkably validated in an independent dataset. The results demonstrate that UHRF1 regulates PPARG silencing and both genes appear to be part of a complex regulatory network. These findings suggest that the relationship between UHRF1 and PPARG may have a relevant role in CRC progression.
De-Grassi:2010aa: Ultradeep sequencing of a human ultraconserved region reveals somatic and constitutional genomic instability
A. De Grassi and C. Segala and F. Iannelli and S. Volorio and L. Bertario and P. Radice and L. Bernard and F. D. Ciccarelli
PLoS Biol 8 e1000275 (2010)
http://dx.doi.org/10.1371/journal.pbio.1000275

Early detection of cancer-associated genomic instability is crucial, particularly in tumour types in which this instability represents the essential underlying mechanism of tumourigenesis. Currently used methods require the presence of already established neoplastic cells because they only detect clonal mutations. In principle, parallel sequencing of single DNA filaments could reveal the early phases of tumour initiation by detecting low-frequency mutations, provided an adequate depth of coverage and an effective control of the experimental error. We applied ultradeep sequencing to estimate the genomic instability of individuals with hereditary non-polyposis colorectal cancer (HNPCC). To overcome the experimental error, we used an ultraconserved region (UCR) of the human genome as an internal control. By comparing the mutability outside and inside the UCR, we observed a tendency of the ultraconserved element to accumulate significantly fewer mutations than the flanking segments in both neoplastic and nonneoplastic HNPCC samples. No difference between the two regions was detectable in cells from healthy donors, indicating that all three HNPCC samples have mutation rates higher than the healthy genome. This is the first, to our knowledge, direct evidence of an intrinsic genomic instability of individuals with heterozygous mutations in mismatch repair genes, and constitutes the proof of principle for the development of a more sensitive molecular assay of genomic instability.
Costa:2010aa: Uncovering the complexity of transcriptomes with RNA-Seq
V. Costa and C. Angelini and I. De Feis and A. Ciccodicola
J Biomed Biotechnol 2010 853916 (2010)
http://dx.doi.org/10.1155/2010/853916

In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousand DNA fragments, dramatically changed the landscape of the genetics studies. RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction, CNV-Seq for large genome nucleotide variations are only some of the intriguing new applications supported by these innovative platforms. Among them RNA-Seq is perhaps the most complex NGS application. Expression levels of specific genes, differential splicing, allele-specific expression of transcripts can be accurately determined by RNA-Seq experiments to address many biological-related issues. All these attributes are not readily achievable from previously widespread hybridization-based or tag sequence-based approaches. However, the unprecedented level of sensitivity and the large amount of available data produced by NGS platforms provide clear advantages as well as new challenges and issues. This technology brings the great power to make several new biological observations and discoveries, it also requires a considerable effort in the development of new bioinformatics tools to deal with these massive data files. The paper aims to give a survey of the RNA-Seq methodology, particularly focusing on the challenges that this application presents both from a biological and a bioinformatics point of view.
Fanelli:2011aa: Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors
F. Fanelli and P. G. De Benedetti
Chem Rev 111 PR438-535 (2011)
http://dx.doi.org/10.1021/cr100437t
Frezzetti:2011aa: Upregulation of miR-21 by Ras in vivo and its role in tumor growth
D. Frezzetti and M. De Menna and P. Zoppoli and C. Guerra and A. Ferraro and A. M. Bello and P. De Luca and C. Calabrese and A. Fusco and M. Ceccarelli and M. Zollo and M. Barbacid and R. Di Lauro and G. De Vita
Oncogene 30 275-86 (2011)
http://dx.doi.org/10.1038/onc.2010.416

miR-21 is a microRNA (miRNA) frequently overexpressed in human cancers. Here we show that miR-21 is upregulated both in vitro and in vivo by oncogenic Ras, thus linking this miRNA to one of the most frequently activated oncogenes in human cancers. Ras regulation of miR-21 occurs with a delayed kinetic and requires at least two Ras downstream pathways. A screen of human thyroid cancers and non-small-cell lung cancers for the expression of miR-21 reveals that it is overexpressed mainly in anaplastic thyroid carcinomas, the most aggressive form of thyroid cancer, whereas in lung its overexpression appears to be inversely correlated with tumor progression. We also show that a LNA directed against miR-21 slows down tumor growth in mice. Consistently, a search for mRNAs downregulated by miR-21 shows an enrichment for mRNAs encoding cell cycle checkpoints regulators, suggesting an important role for miR-21 in oncogenic Ras-induced cell proliferation.
Zambelli:2014aa: Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences
F. Zambelli and G. Pesole and G. Pavesi
Curr Protoc Bioinformatics 47 2.11.1-2.11.31 (2014)
http://dx.doi.org/10.1002/0471250953.bi0211s47

One of the greatest challenges facing modern molecular biology is understanding the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of sequence motifs involved in the regulation of gene expression at transcriptional and post-transcriptional levels. In particular, transcription is modulated by the interaction of transcription factors (TFs) with their corresponding binding sites. Weeder, Pscan, and PscanChIP are software tools freely available for noncommercial users as a stand-alone or Web-based applications for the automatic discovery of conserved motifs in a set of DNA sequences likely to be bound by the same TFs. Input for the tools can be promoter sequences from co-expressed or co-regulated genes (for which Weeder and Pscan are suitable), or regions identified through genome wide ChIP-seq or similar experiments (Weeder and PscanChIP). The motifs are either found by a de novo approach (Weeder) or by using descriptors of the binding specificity of TFs (Pscan and PscanChIP). Curr. Protoc. Bioinform. 47:2.11.1-2.11.31. © 2014 by John Wiley & Sons, Inc.
Grillo:2010aa: UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
G. Grillo and A. Turi and F. Licciulli and F. Mignone and S. Liuni and S. Banfi and V. A. Gennarino and D. S. Horner and G. Pavesi and E. Picardi and G. Pesole
Nucleic Acids Res 38 D75-80 (2010)
http://dx.doi.org/10.1093/nar/gkp902

The 5' and 3' untranslated regions of eukaryotic mRNAs (UTRs) play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and message stability. UTRdb is a curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, derived from several sources of primary data. Experimentally validated functional motifs are annotated and also collated as the UTRsite database where more specific information on the functional motifs and cross-links to interacting regulatory protein are provided. In the current update, the UTR entries have been organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. All internet resources implemented for retrieval and functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs are accessible at http://utrdb.ba.itb.cnr.it/.
Calderone:2014aa: VirusMentha: a new resource for virus-host protein interactions
A. Calderone and L. Licata and G. Cesareni
Nucleic Acids Res (2014)
http://dx.doi.org/10.1093/nar/gku830

Viral infections often cause diseases by perturbing several cellular processes in the infected host. Viral proteins target host proteins and either form new complexes or modulate the formation of functional host complexes. Describing and understanding the perturbation of the host interactome following viral infection is essential for basic virology and for the development of antiviral therapies. In order to provide a general overview of such interactions, a few years ago we developed VirusMINT. We have now extended the scope and coverage of VirusMINT and established VirusMentha, a new virus-virus and virus-host interaction resource build on the detailed curation protocols of the IMEx consortium and on the integration strategies developed for mentha. VirusMentha is regularly and automatically updated every week by capturing, via the PSICQUIC protocol, interactions curated by five different databases that are part of the IMEx consortium. VirusMentha can be freely browsed at http://virusmentha.uniroma2.it/ and its complete data set is available for download.
Chatr-aryamontri:2009aa: VirusMINT: a viral protein interaction database
A. Chatr-aryamontri and A. Ceol and D. Peluso and A. Nardozza and S. Panni and F. Sacco and M. Tinti and A. Smolyar and L. Castagnoli and M. Vidal and M. E. Cusick and G. Cesareni
Nucleic Acids Res 37 D669-73 (2009)
http://dx.doi.org/10.1093/nar/gkn739

Understanding the consequences on host physiology induced by viral infection requires complete understanding of the perturbations caused by virus proteins on the cellular protein interaction network. The VirusMINT database (http://mint.bio.uniroma2.it/virusmint/) aims at collecting all protein interactions between viral and human proteins reported in the literature. VirusMINT currently stores over 5000 interactions involving more than 490 unique viral proteins from more than 110 different viral strains. The whole data set can be easily queried through the search pages and the results can be displayed with a graphical viewer. The curation effort has focused on manuscripts reporting interactions between human proteins and proteins encoded by some of the most medically relevant viruses: papilloma viruses, human immunodeficiency virus 1, Epstein-Barr virus, hepatitis B virus, hepatitis C virus, herpes viruses and Simian virus 40.
Bianchi:2013aa: webPDBinder: a server for the identification of ligand binding sites on protein structures
V. Bianchi and I. Mangone and F. Ferrè and M. Helmer-Citterich and G. Ausiello
Nucleic Acids Res 41 W308-13 (2013)
http://dx.doi.org/10.1093/nar/gkt457

The webPDBinder (http://pdbinder.bio.uniroma2.it/PDBinder) is a web server for the identification of small ligand-binding sites in a protein structure. webPDBinder searches a protein structure against a library of known binding sites and a collection of control non-binding pockets. The number of similarities identified with the residues in the two sets is then used to derive a propensity value for each residue of the query protein associated to the likelihood that the residue is part of a ligand binding site. The predicted binding residues can be further refined using conservation scores derived from the multiple alignment of the PFAM protein family. webPDBinder correctly identifies residues belonging to the binding site in 77% of the cases and is able to identify binding pockets starting from holo or apo structures with comparable performances. This is important for all the real world cases where the query protein has been crystallized without a ligand and is also difficult to obtain clear similarities with bound pockets from holo pocket libraries. The input is either a PDB code or a user-submitted structure. The output is a list of predicted binding pocket residues with propensity and conservation values both in text and graphical format.
Marabotti:2009aa: When it comes to homology, bad habits die hard
A. Marabotti and A. Facchiano
Trends Biochem Sci 34 98-9 (2009)
http://dx.doi.org/10.1016/j.tibs.2008.12.001
Fumagalli:2009ab: Widespread balancing selection and pathogen-driven selection at blood group antigen genes
M. Fumagalli and R. Cagliani and U. Pozzoli and S. Riva and G. P. Comi and G. Menozzi and N. Bresolin and M. Sironi
Genome Res 19 199-212 (2009)
http://dx.doi.org/10.1101/gr.082768.108

Historically, allelic variations in blood group antigen (BGA) genes have been regarded as possible susceptibility factors for infectious diseases. Since host-pathogen interactions are major determinants in evolution, BGAs can be thought of as selection targets. In order to verify this hypothesis, we obtained an estimate of pathogen richness for geographic locations corresponding to 52 populations distributed worldwide; after correction for multiple tests and for variables different from selective forces, significant correlations with pathogen richness were obtained for multiple variants at 11 BGA loci out of 26. In line with this finding, we demonstrate that three BGA genes, namely CD55, CD151, and SLC14A1, have been subjected to balancing selection, a process, rare outside MHC genes, which maintains variability at a locus. Moreover, we identified a gene region immediately upstream the transcription start site of FUT2 which has undergone non-neutral evolution independently from the coding region. Finally, in the case of BSG, we describe the presence of a highly divergent haplotype clade and the possible reasons for its maintenance, including frequency-dependent balancing selection, are discussed. These data indicate that BGAs have been playing a central role in the host-pathogen arms race during human evolutionary history and no other gene category shows similar levels of widespread selection, with the only exception of loci involved in antigen recognition.
Calabrese:2010aa: Widespread cortical thinning characterizes patients with MS with mild cognitive impairment
M. Calabrese and F. Rinaldi and I. Mattisi and P. Grossi and A. Favaretto and M. Atzori and V. Bernardi and L. Barachino and C. Romualdi and L. Rinaldi and P. Perini and P. Gallo
Neurology 74 321-8 (2010)
http://dx.doi.org/10.1212/WNL.0b013e3181cbcd03

BACKGROUND: Although cognitive dysfunction affects a relevant portion of patients with multiple sclerosis (MS), its pathologic substrate has not been clarified and it does not seem entirely explained by white matter changes. METHODS: A total of 100 consecutive patients with relapsing remitting MS (RRMS) and 42 normal controls (NC) were enrolled in the study. Cognitive performance was assessed by Rao's Brief Repeatable Battery of Neuropsychological Tests (BRB). Regional cortical thickness (CTh) was evaluated by Freesurfer. RESULTS: Thirty-one patients with RRMS failed 1 or 2 tests of BRB and were considered to have a mild cognitive impairment (mCI-RRMS), while 8 patients failed at least 3 tests and were classified as markedly impaired (sCI-RRMS). The mean CTh of mCI-RRMS and sCI-RRMS group was significantly lower than in NC (p < 0.001) and cognitively normal patients with RRMS (CN-RRMS) (p < 0.001). The regional analysis revealed significant cortical thinning in frontal and temporal regions (frontotemporal thinning) of CN-RRMS compared to NC, while a widespread pattern of cortical thinning was observed in mCI-RRMS and in sCI-RRMS compared to both CN-RRMS and NC. A correlation was observed between cognitive score (CS) and the mean CTh (r = -0.69, p < 0.001) and between CS and CTh of almost all the cortical areas analyzed (r value between -0.20 and -0.65, p < 0.01). A correlation was found between T2-WM-LV and mean CTh (r = -0.31, p = 0.004) or CS (r = 0.21, p = 0.031). The multivariate analysis confirmed a widespread cortical thinning as the best predictor of cognitive impairment. CONCLUSIONS: A widespread pattern of cortical thinning characterizes patients with cognitive dysfunction, suggesting such dysfunction as expression of a more aggressive and widespread cortical pathology.
Dowen:2012aa: Widespread dynamic DNA methylation in response to biotic stress
R. H. Dowen and M. Pelizzola and R. J. Schmitz and R. Lister and J. M. Dowen and J. R. Nery and J. E. Dixon and J. R. Ecker
Proc Natl Acad Sci U S A 109 E2183-91 (2012)
http://dx.doi.org/10.1073/pnas.1209329109

Regulation of gene expression by DNA methylation is crucial for defining cellular identities and coordinating organism-wide developmental programs in many organisms. In plants, modulation of DNA methylation in response to environmental conditions represents a potentially robust mechanism to regulate gene expression networks; however, examples of dynamic DNA methylation are largely limited to gene imprinting. Here we report an unexpected role for DNA methylation in regulation of the Arabidopsis thaliana immune system. Profiling the DNA methylomes of plants exposed to bacterial pathogen, avirulent bacteria, or salicylic acid (SA) hormone revealed numerous stress-induced differentially methylated regions, many of which were intimately associated with differentially expressed genes. In response to SA, transposon-associated differentially methylated regions, which were accompanied by up-regulation of 21-nt siRNAs, were often coupled to transcriptional changes of the transposon and/or the proximal gene. Thus, dynamic DNA methylation changes within repetitive sequences or transposons can regulate neighboring genes in response to SA stress.
Orioli:2011aa: Widespread occurrence of non-canonical transcription termination by human RNA polymerase III
A. Orioli and C. Pascali and J. Quartararo and K. W. Diebel and V. Praz and D. Romascano and R. Percudani and L. F. van Dyk and N. Hernandez and M. Teichmann and G. Dieci
Nucleic Acids Res 39 5499-512 (2011)
http://dx.doi.org/10.1093/nar/gkr074

Human RNA polymerase (Pol) III-transcribed genes are thought to share a simple termination signal constituted by four or more consecutive thymidine residues in the coding DNA strand, just downstream of the RNA 3'-end sequence. We found that a large set of human tRNA genes (tDNAs) do not display any T(≥4) stretch within 50 bp of 3'-flanking region. In vitro analysis of tDNAs with a distanced T(≥4) revealed the existence of non-canonical terminators resembling degenerate T(≥5) elements, which ensure significant termination but at the same time allow for the production of Pol III read-through pre-tRNAs with unusually long 3' trailers. A panel of such non-canonical signals was found to direct transcription termination of unusual Pol III-synthesized viral pre-miRNA transcripts in gammaherpesvirus 68-infected cells. Genome-wide location analysis revealed that human Pol III tends to trespass into the 3'-flanking regions of tDNAs, as expected from extensive terminator read-through. The widespread occurrence of partial termination suggests that the Pol III primary transcriptome in mammals is unexpectedly enriched in 3'-trailer sequences with the potential to contribute novel functional ncRNAs.
Calura:2014aa: Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles
E. Calura and P. Martini and G. Sales and L. Beltrame and G. Chiorino and M. D'Incalci and S. Marchini and C. Romualdi
Nucleic Acids Res 42 e96 (2014)
http://dx.doi.org/10.1093/nar/gku354

The production rate of gene expression data is nothing less than astounding. However, with the benefit of hindsight we can assert that, since we completely ignored the non-coding part of the transcriptome, we spent the last decade to study cell mechanisms having few data in our hands. In this scenario, microRNAs, which are key post-trascriptional regulators, deserve special attention. Given the state of knowledge about their biogenesis, mechanisms of action and the numerous experimentally validated target genes, miRNAs are also gradually appearing in the formal pathway representations such as KEGG and Reactome maps. However, the number of miRNAs annotated in pathway maps are very few and pathway analyses exploiting this new regulatory layer are still lacking. To fill these gaps, we present 'micrographite' a new pipeline to perform topological pathway analysis integrating gene and miRNA expression profiles. Here, micrographite is used to study and dissect the epithelial ovarian cancer gene and miRNA transcriptome defining and validating a new regulatory circuit related to ovarian cancer histotype specificity.
Seeber:2011aa: Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
M. Seeber and A. Felline and F. Raimondi and S. Muff and R. Friedman and F. Rao and A. Caflisch and F. Fanelli
J Comput Chem 32 1183-94 (2011)
http://dx.doi.org/10.1002/jcc.21688

Wordom is a versatile, user-friendly, and efficient program for manipulation and analysis of molecular structures and dynamics. The following new analysis modules have been added since the publication of the original Wordom paper in 2007: assignment of secondary structure, calculation of solvent accessible surfaces, elastic network model, motion cross correlations, protein structure network, shortest intra-molecular and inter-molecular communication paths, kinetic grouping analysis, and calculation of mincut-based free energy profiles. In addition, an interface with the Python scripting language has been built and the overall performance and user accessibility enhanced. The source code of Wordom (in the C programming language) as well as documentation for usage and further development are available as an open source package under the GNU General Purpose License from http://wordom.sf.net.
Azzolin:2014aa: YAP/TAZ incorporation in the β-catenin destruction complex orchestrates the Wnt response
L. Azzolin and T. Panciera and S. Soligo and E. Enzo and S. Bicciato and S. Dupont and S. Bresolin and C. Frasson and G. Basso and V. Guzzardo and A. Fassina and M. Cordenonsi and S. Piccolo
Cell 158 157-70 (2014)
http://dx.doi.org/10.1016/j.cell.2014.06.013

The Hippo transducers YAP/TAZ have been shown to play positive, as well as negative, roles in Wnt signaling, but the underlying mechanisms remain unclear. Here, we provide biochemical, functional, and genetic evidence that YAP and TAZ are integral components of the β-catenin destruction complex that serves as cytoplasmic sink for YAP/TAZ. In Wnt-ON cells, YAP/TAZ are physically dislodged from the destruction complex, allowing their nuclear accumulation and activation of Wnt/YAP/TAZ-dependent biological effects. YAP/TAZ are required for intestinal crypt overgrowth induced by APC deficiency and for crypt regeneration ex vivo. In Wnt-OFF cells, YAP/TAZ are essential for β-TrCP recruitment to the complex and β-catenin inactivation. In Wnt-ON cells, release of YAP/TAZ from the complex is instrumental for Wnt/β-catenin signaling. In line, the β-catenin-dependent maintenance of ES cells in an undifferentiated state is sustained by loss of YAP/TAZ. This work reveals an unprecedented signaling framework relevant for organ size control, regeneration, and tumor suppression.