Journal ArticleDOI
Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing
Julia Richter,Matthias Schlesner,Steve Hoffmann,Markus Kreuz,Ellen Leich,Birgit Burkhardt,Maciej Rosolowski,Ole Ammerpohl,Rabea Wagener,Stephan H. Bernhart,Dido Lenze,Monika Szczepanowski,Maren Paulsen,Simone Lipinski,Robert B. Russell,Sabine Adam-Klages,Gordana Apic,Alexander Claviez,Dirk Hasenclever,Volker Hovestadt,Nadine Hornig,Jan O. Korbel,Dieter Kube,David Langenberger,Chris Lawerenz,Jasmin Lisfeld,Katharina Meyer,Simone Picelli,Jordan Pischimarov,Bernhard Radlwimmer,Tobias Rausch,Marius Rohde,Markus Schilhabel,René Scholtysik,Rainer Spang,Heiko Trautmann,Thorsten Zenz,Thorsten Zenz,Thorsten Zenz,Arndt Borkhardt,Hans G. Drexler,Peter Möller,Roderick A.F. MacLeod,Christiane Pott,Stefan Schreiber,Lorenz Trümper,Markus Loeffler,Peter F. Stadler,Peter Lichter,Roland Eils,Ralf Küppers,Michael Hummel,Wolfram Klapper,Philip Rosenstiel,Andreas Rosenwald,Benedikt Brors,Reiner Siebert +56 more
TLDR
Findings suggest that cooperation between ID3 inactivation and IG-MYC translocation is a hallmark of Burkitt lymphomagenesis.Abstract:
Burkitt lymphoma is a mature aggressive B-cell lymphoma derived from germinal center B cells(1). Its cytogenetic hallmark is the Burkitt translocation t(8;14)(q24;q32) and its variants, which juxtapose the MYC oncogene with one of the three immunoglobulin loci(2). Consequently, MYC is deregulated, resulting in massive perturbation of gene expression(3). Nevertheless, MYC deregulation alone seems not to be sufficient to drive Burkitt lymphomagenesis. By whole-genome, whole-exome and transcriptome sequencing of four prototypical Burkitt lymphomas with immunoglobulin gene (IG)-MYC translocation, we identified seven recurrently mutated genes. One of these genes, ID3, mapped to a region of focal homozygous loss in Burkitt lymphoma(4). In an extended cohort, 36 of 53 molecularly defined Burkitt lymphomas (68%) carried potentially damaging mutations of ID3. These were strongly enriched at somatic hypermutation motifs. Only 6 of 47 other B-cell lymphomas with the IG-MYC translocation (13%) carried ID3 mutations. These findings suggest that cooperation between ID3 inactivation and IG-MYC translocation is a hallmark of Burkitt lymphomagenesis.read more
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The 2016 revision of the World Health Organization classification of lymphoid neoplasms
Steven H. Swerdlow,Elias Campo,Stefano Pileri,Nancy L. Harris,Harald Stein,Reiner Siebert,Ranjana H. Advani,Michele Ghielmini,Gilles Salles,Andrew D. Zelenetz,Elaine S. Jaffe +10 more
TL;DR: The revision clarifies the diagnosis and management of lesions at the very early stages of lymphomagenesis, refines the diagnostic criteria for some entities, details the expanding genetic/molecular landscape of numerous lymphoid neoplasms and their clinical correlates, and refers to investigations leading to more targeted therapeutic strategies.
Integrative Genomics Viewer
James T. Robinson,Helga Thorvaldsdottir,Wendy Winckler,Mitchell Guttman,Eric S. Lander,Eric S. Lander,Gad Getz,Jill P. Mesirov +7 more
TL;DR: The sheer volume and scope of data posed by this flood of data pose a significant challenge to the development of efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
Journal ArticleDOI
A proteome-scale map of the human interactome network
Thomas Rolland,Murat Tasan,Benoit Charloteaux,Samuel J. Pevzner,Quan Zhong,Quan Zhong,Nidhi Sahni,Song Yi,Irma Lemmens,Celia Fontanillo,Roberto Mosca,Atanas Kamburov,Susan Dina Ghiassian,Susan Dina Ghiassian,Xinping Yang,Lila Ghamsari,Dawit Balcha,Bridget E. Begg,Pascal Braun,Marc Brehme,Martin P. Broly,Anne-Ruxandra Carvunis,Dan Convery-Zupan,Roser Corominas,Jasmin Coulombe-Huntington,Jasmin Coulombe-Huntington,Elizabeth Dann,Matija Dreze,Amélie Dricot,Changyu Fan,Eric A. Franzosa,Eric A. Franzosa,Fana Gebreab,Bryan J. Gutierrez,Madeleine F. Hardy,Mike Jin,Shuli Kang,Ruth Kiros,Guan Ning Lin,Katja Luck,Andrew MacWilliams,Jörg Menche,Jörg Menche,Ryan R. Murray,Alexandre Palagi,Matthew M. Poulin,Xavier Rambout,Xavier Rambout,John Rasla,Patrick Reichert,Viviana Romero,Elien Ruyssinck,Julie M. Sahalie,Annemarie Scholz,Akash A. Shah,Amitabh Sharma,Amitabh Sharma,Yun Shen,Kerstin Spirohn,Stanley Tam,Alexander O. Tejeda,Shelly A. Trigg,Jean-Claude Twizere,Jean-Claude Twizere,Kerwin Vega,Jennifer M. Walsh,Michael E. Cusick,Yu Xia,Yu Xia,Albert-László Barabási,Albert-László Barabási,Albert-László Barabási,Lilia M. Iakoucheva,Patrick Aloy,Javier De Las Rivas,Jan Tavernier,Michael A. Calderwood,David E. Hill,Tong Hao,Frederick P. Roth,Marc Vidal +80 more
TL;DR: The map uncovers significant interconnectivity between known and candidate cancer gene products, providing unbiased evidence for an expanded functional cancer landscape, while demonstrating how high-quality interactome models will help "connect the dots" of the genomic revolution.
Journal ArticleDOI
Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy
Cigall Kadoch,Diana C. Hargreaves,Courtney Hodges,Laura Elias,Lena Ho,Jeff Ranish,Gerald R. Crabtree +6 more
TL;DR: It is demonstrated that mSWI/SNF is the most frequently mutated chromatin-regulatory complex (CRC) in human cancer, exhibiting a broad mutation pattern, similar to that of TP53, and proper functioning of polymorphic BAF complexes may constitute a major mechanism of tumor suppression.
Posted ContentDOI
Pan-cancer analysis of whole genomes
Peter J. Campbell,Peter J. Campbell,Gaddy Getz,Joshua M. Stuart,Jan O. Korbel,Lincoln Stein,Lincoln Stein +6 more
TL;DR: The integrative analysis of more than 2,600 whole cancer genomes and their matching normal tissues across 39 distinct tumour types represents the most comprehensive look at cancer whole genomes to date.
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