Literature DB >> 24332044

Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma.

Bjoern Chapuy1, Michael R McKeown1, Charles Y Lin1, Stefano Monti2, Margaretha G M Roemer1, Jun Qi1, Peter B Rahl3, Heather H Sun4, Kelly T Yeda1, John G Doench5, Elaine Reichert1, Andrew L Kung6, Scott J Rodig4, Richard A Young3, Margaret A Shipp7, James E Bradner8.   

Abstract

Diffuse large B cell lymphoma (DLBCL) is a biologically heterogeneous and clinically aggressive disease. Here, we explore the role of bromodomain and extra-terminal domain (BET) proteins in DLBCL, using integrative chemical genetics and functional epigenomics. We observe highly asymmetric loading of bromodomain 4 (BRD4) at enhancers, with approximately 33% of all BRD4 localizing to enhancers at 1.6% of occupied genes. These super-enhancers prove particularly sensitive to bromodomain inhibition, explaining the selective effect of BET inhibitors on oncogenic and lineage-specific transcriptional circuits. Functional study of genes marked by super-enhancers identifies DLBCLs dependent on OCA-B and suggests a strategy for discovering unrecognized cancer dependencies. Translational studies performed on a comprehensive panel of DLBCLs establish a therapeutic rationale for evaluating BET inhibitors in this disease.
Copyright © 2013 Elsevier Inc. All rights reserved.

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Year:  2013        PMID: 24332044      PMCID: PMC4018722          DOI: 10.1016/j.ccr.2013.11.003

Source DB:  PubMed          Journal:  Cancer Cell        ISSN: 1535-6108            Impact factor:   31.743


  51 in total

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Authors:  Katia Basso; Riccardo Dalla-Favera
Journal:  Immunol Rev       Date:  2012-05       Impact factor: 12.988

2.  Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing.

Authors:  Jens G Lohr; Petar Stojanov; Michael S Lawrence; Daniel Auclair; Bjoern Chapuy; Carrie Sougnez; Peter Cruz-Gordillo; Birgit Knoechel; Yan W Asmann; Susan L Slager; Anne J Novak; Ahmet Dogan; Stephen M Ansell; Brian K Link; Lihua Zou; Joshua Gould; Gordon Saksena; Nicolas Stransky; Claudia Rangel-Escareño; Juan Carlos Fernandez-Lopez; Alfredo Hidalgo-Miranda; Jorge Melendez-Zajgla; Enrique Hernández-Lemus; Angela Schwarz-Cruz y Celis; Ivan Imaz-Rosshandler; Akinyemi I Ojesina; Joonil Jung; Chandra S Pedamallu; Eric S Lander; Thomas M Habermann; James R Cerhan; Margaret A Shipp; Gad Getz; Todd R Golub
Journal:  Proc Natl Acad Sci U S A       Date:  2012-02-17       Impact factor: 11.205

Review 3.  The genetic network controlling plasma cell differentiation.

Authors:  Stephen L Nutt; Nadine Taubenheim; Jhagvaral Hasbold; Lynn M Corcoran; Philip D Hodgkin
Journal:  Semin Immunol       Date:  2011-09-15       Impact factor: 11.130

4.  Integrative analysis reveals an outcome-associated and targetable pattern of p53 and cell cycle deregulation in diffuse large B cell lymphoma.

Authors:  Stefano Monti; Bjoern Chapuy; Kunihiko Takeyama; Scott J Rodig; Yansheng Hao; Kelly T Yeda; Haig Inguilizian; Craig Mermel; Treeve Currie; Ahmet Dogan; Jeffery L Kutok; Rameen Beroukhim; Donna Neuberg; Thomas M Habermann; Gad Getz; Andrew L Kung; Todd R Golub; Margaret A Shipp
Journal:  Cancer Cell       Date:  2012-09-11       Impact factor: 31.743

5.  BET bromodomain inhibition targets both c-Myc and IL7R in high-risk acute lymphoblastic leukemia.

Authors:  Christopher J Ott; Nadja Kopp; Liat Bird; Ronald M Paranal; Jun Qi; Teresa Bowman; Scott J Rodig; Andrew L Kung; James E Bradner; David M Weinstock
Journal:  Blood       Date:  2012-08-17       Impact factor: 22.113

6.  Metabolic signatures uncover distinct targets in molecular subsets of diffuse large B cell lymphoma.

Authors:  Pilar Caro; Amar U Kishan; Erik Norberg; Illana A Stanley; Bjoern Chapuy; Scott B Ficarro; Klaudia Polak; Daniel Tondera; John Gounarides; Hong Yin; Feng Zhou; Michael R Green; Linfeng Chen; Stefano Monti; Jarrod A Marto; Margaret A Shipp; Nika N Danial
Journal:  Cancer Cell       Date:  2012-10-16       Impact factor: 31.743

7.  SYK inhibition modulates distinct PI3K/AKT- dependent survival pathways and cholesterol biosynthesis in diffuse large B cell lymphomas.

Authors:  Linfeng Chen; Stefano Monti; Przemyslaw Juszczynski; Jing Ouyang; Bjoern Chapuy; Donna Neuberg; John G Doench; Agata M Bogusz; Thomas M Habermann; Ahmet Dogan; Thomas E Witzig; Jeffery L Kutok; Scott J Rodig; Todd Golub; Margaret A Shipp
Journal:  Cancer Cell       Date:  2013-06-10       Impact factor: 31.743

8.  Concurrent expression of MYC and BCL2 in diffuse large B-cell lymphoma treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone.

Authors:  Nathalie A Johnson; Graham W Slack; Kerry J Savage; Joseph M Connors; Susana Ben-Neriah; Sanja Rogic; David W Scott; King L Tan; Christian Steidl; Laurie H Sehn; Wing C Chan; Javeed Iqbal; Paul N Meyer; Georg Lenz; George Wright; Lisa M Rimsza; Carlo Valentino; Patrick Brunhoeber; Thomas M Grogan; Rita M Braziel; James R Cook; Raymond R Tubbs; Dennis D Weisenburger; Elias Campo; Andreas Rosenwald; German Ott; Jan Delabie; Christina Holcroft; Elaine S Jaffe; Louis M Staudt; Randy D Gascoyne
Journal:  J Clin Oncol       Date:  2012-07-30       Impact factor: 44.544

9.  Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia.

Authors:  Mark A Dawson; Rab K Prinjha; Antje Dittmann; George Giotopoulos; Marcus Bantscheff; Wai-In Chan; Samuel C Robson; Chun-wa Chung; Carsten Hopf; Mikhail M Savitski; Carola Huthmacher; Emma Gudgin; Dave Lugo; Soren Beinke; Trevor D Chapman; Emma J Roberts; Peter E Soden; Kurt R Auger; Olivier Mirguet; Konstanze Doehner; Ruud Delwel; Alan K Burnett; Phillip Jeffrey; Gerard Drewes; Kevin Lee; Brian J P Huntly; Tony Kouzarides
Journal:  Nature       Date:  2011-10-02       Impact factor: 49.962

10.  Histone recognition and large-scale structural analysis of the human bromodomain family.

Authors:  Panagis Filippakopoulos; Sarah Picaud; Maria Mangos; Tracy Keates; Jean-Philippe Lambert; Dalia Barsyte-Lovejoy; Ildiko Felletar; Rudolf Volkmer; Susanne Müller; Tony Pawson; Anne-Claude Gingras; Cheryl H Arrowsmith; Stefan Knapp
Journal:  Cell       Date:  2012-03-30       Impact factor: 41.582

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  369 in total

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Authors:  Tim Wang; Kıvanç Birsoy; Nicholas W Hughes; Kevin M Krupczak; Yorick Post; Jenny J Wei; Eric S Lander; David M Sabatini
Journal:  Science       Date:  2015-10-15       Impact factor: 47.728

Review 2.  Unravelling the genomic targets of small molecules using high-throughput sequencing.

Authors:  Raphaël Rodriguez; Kyle M Miller
Journal:  Nat Rev Genet       Date:  2014-10-14       Impact factor: 53.242

3.  Loss of TRIM33 causes resistance to BET bromodomain inhibitors through MYC- and TGF-β-dependent mechanisms.

Authors:  Xiarong Shi; Valia T Mihaylova; Leena Kuruvilla; Fang Chen; Stephen Viviano; Massimiliano Baldassarre; David Sperandio; Ruben Martinez; Peng Yue; Jamie G Bates; David G Breckenridge; Joseph Schlessinger; Benjamin E Turk; David A Calderwood
Journal:  Proc Natl Acad Sci U S A       Date:  2016-07-18       Impact factor: 11.205

4.  Superenhancer Analysis Defines Novel Epigenomic Subtypes of Non-APL AML, Including an RARα Dependency Targetable by SY-1425, a Potent and Selective RARα Agonist.

Authors:  Michael R McKeown; M Ryan Corces; Matthew L Eaton; Chris Fiore; Emily Lee; Jeremy T Lopez; Mei Wei Chen; Darren Smith; Steven M Chan; Julie L Koenig; Kathryn Austgen; Matthew G Guenther; David A Orlando; Jakob Lovén; Christian C Fritz; Ravindra Majeti
Journal:  Cancer Discov       Date:  2017-07-20       Impact factor: 39.397

5.  Trib1 promotes acute myeloid leukemia progression by modulating the transcriptional programs of Hoxa9.

Authors:  Seiko Yoshino; Takashi Yokoyama; Yoshitaka Sunami; Tomoko Takahara; Aya Nakamura; Yukari Yamazaki; Shuichi Tsutsumi; Hiroyuki Aburatani; Takuro Nakamura
Journal:  Blood       Date:  2021-01-07       Impact factor: 22.113

6.  Identification of recurrent noncoding mutations in B-cell lymphoma using capture Hi-C.

Authors:  Alex J Cornish; Phuc H Hoang; Sara E Dobbins; Philip J Law; Daniel Chubb; Giulia Orlando; Richard S Houlston
Journal:  Blood Adv       Date:  2019-01-08

7.  BET bromodomain inhibition suppresses innate inflammatory and profibrotic transcriptional networks in heart failure.

Authors:  Qiming Duan; Sarah McMahon; Priti Anand; Hirsh Shah; Sean Thomas; Hazel T Salunga; Yu Huang; Rongli Zhang; Aarathi Sahadevan; Madeleine E Lemieux; Jonathan D Brown; Deepak Srivastava; James E Bradner; Timothy A McKinsey; Saptarsi M Haldar
Journal:  Sci Transl Med       Date:  2017-05-17       Impact factor: 17.956

8.  Targeting nuclear receptor NR4A1-dependent adipocyte progenitor quiescence promotes metabolic adaptation to obesity.

Authors:  Yang Zhang; Alexander J Federation; Soomin Kim; John P O'Keefe; Mingyue Lun; Dongxi Xiang; Jonathan D Brown; Matthew L Steinhauser
Journal:  J Clin Invest       Date:  2018-10-02       Impact factor: 14.808

9.  Targeting transcriptional addictions in small cell lung cancer with a covalent CDK7 inhibitor.

Authors:  Camilla L Christensen; Nicholas Kwiatkowski; Brian J Abraham; Julian Carretero; Fatima Al-Shahrour; Tinghu Zhang; Edmond Chipumuro; Grit S Herter-Sprie; Esra A Akbay; Abigail Altabef; Jianming Zhang; Takeshi Shimamura; Marzia Capelletti; Jakob B Reibel; Jillian D Cavanaugh; Peng Gao; Yan Liu; Signe R Michaelsen; Hans S Poulsen; Amir R Aref; David A Barbie; James E Bradner; Rani E George; Nathanael S Gray; Richard A Young; Kwok-Kin Wong
Journal:  Cancer Cell       Date:  2014-12-08       Impact factor: 31.743

Review 10.  Enhancer deregulation in cancer and other diseases.

Authors:  Hans-Martin Herz
Journal:  Bioessays       Date:  2016-08-29       Impact factor: 4.345

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