Literature DB >> 28029156

Copy number alterations unmasked as enhancer hijackers.

Rameen Beroukhim1, Xiaoyang Zhang1, Matthew Meyerson1.   

Abstract

Our understanding of how DNA copy number changes contribute to disease, including cancer, has to a large degree been focused on the changes in gene dosage that they generate and has neglected the effects of the DNA rearrangements that lead to their formation. A new study reports an innovative analytical framework for copy number alterations that are oncogenic primarily owing to the genomic rearrangements that underlie them.

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Year:  2016        PMID: 28029156     DOI: 10.1038/ng.3754

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


  15 in total

Review 1.  Enhancer function: new insights into the regulation of tissue-specific gene expression.

Authors:  Chin-Tong Ong; Victor G Corces
Journal:  Nat Rev Genet       Date:  2011-03-01       Impact factor: 53.242

2.  Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.

Authors:  Paul A Northcott; Catherine Lee; Thomas Zichner; Adrian M Stütz; Serap Erkek; Daisuke Kawauchi; David J H Shih; Volker Hovestadt; Marc Zapatka; Dominik Sturm; David T W Jones; Marcel Kool; Marc Remke; Florence M G Cavalli; Scott Zuyderduyn; Gary D Bader; Scott VandenBerg; Lourdes Adriana Esparza; Marina Ryzhova; Wei Wang; Andrea Wittmann; Sebastian Stark; Laura Sieber; Huriye Seker-Cin; Linda Linke; Fabian Kratochwil; Natalie Jäger; Ivo Buchhalter; Charles D Imbusch; Gideon Zipprich; Benjamin Raeder; Sabine Schmidt; Nicolle Diessl; Stephan Wolf; Stefan Wiemann; Benedikt Brors; Chris Lawerenz; Jürgen Eils; Hans-Jörg Warnatz; Thomas Risch; Marie-Laure Yaspo; Ursula D Weber; Cynthia C Bartholomae; Christof von Kalle; Eszter Turányi; Peter Hauser; Emma Sanden; Anna Darabi; Peter Siesjö; Jaroslav Sterba; Karel Zitterbart; David Sumerauer; Peter van Sluis; Rogier Versteeg; Richard Volckmann; Jan Koster; Martin U Schuhmann; Martin Ebinger; H Leighton Grimes; Giles W Robinson; Amar Gajjar; Martin Mynarek; Katja von Hoff; Stefan Rutkowski; Torsten Pietsch; Wolfram Scheurlen; Jörg Felsberg; Guido Reifenberger; Andreas E Kulozik; Andreas von Deimling; Olaf Witt; Roland Eils; Richard J Gilbertson; Andrey Korshunov; Michael D Taylor; Peter Lichter; Jan O Korbel; Robert J Wechsler-Reya; Stefan M Pfister
Journal:  Nature       Date:  2014-06-22       Impact factor: 49.962

3.  Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking.

Authors:  Joachim Weischenfeldt; Taronish Dubash; Alexandros P Drainas; Balca R Mardin; Yuanyuan Chen; Adrian M Stütz; Sebastian M Waszak; Graziella Bosco; Ann Rita Halvorsen; Benjamin Raeder; Theocharis Efthymiopoulos; Serap Erkek; Christine Siegl; Hermann Brenner; Odd Terje Brustugun; Sebastian M Dieter; Paul A Northcott; Iver Petersen; Stefan M Pfister; Martin Schneider; Steinar K Solberg; Erik Thunissen; Wilko Weichert; Thomas Zichner; Roman Thomas; Martin Peifer; Aslaug Helland; Claudia R Ball; Martin Jechlinger; Rocio Sotillo; Hanno Glimm; Jan O Korbel
Journal:  Nat Genet       Date:  2016-11-21       Impact factor: 38.330

Review 4.  Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control.

Authors:  Denes Hnisz; Daniel S Day; Richard A Young
Journal:  Cell       Date:  2016-11-17       Impact factor: 41.582

5.  The human c-myc oncogene: structural consequences of translocation into the IgH locus in Burkitt lymphoma.

Authors:  J Battey; C Moulding; R Taub; W Murphy; T Stewart; H Potter; G Lenoir; P Leder
Journal:  Cell       Date:  1983-10       Impact factor: 41.582

6.  Activation of proto-oncogenes by disruption of chromosome neighborhoods.

Authors:  Denes Hnisz; Abraham S Weintraub; Daniel S Day; Anne-Laure Valton; Rasmus O Bak; Charles H Li; Johanna Goldmann; Bryan R Lajoie; Zi Peng Fan; Alla A Sigova; Jessica Reddy; Diego Borges-Rivera; Tong Ihn Lee; Rudolf Jaenisch; Matthew H Porteus; Job Dekker; Richard A Young
Journal:  Science       Date:  2016-03-03       Impact factor: 47.728

7.  Comprehensive molecular characterization of human colon and rectal cancer.

Authors: 
Journal:  Nature       Date:  2012-07-18       Impact factor: 49.962

8.  Massive genomic rearrangement acquired in a single catastrophic event during cancer development.

Authors:  Philip J Stephens; Chris D Greenman; Beiyuan Fu; Fengtang Yang; Graham R Bignell; Laura J Mudie; Erin D Pleasance; King Wai Lau; David Beare; Lucy A Stebbings; Stuart McLaren; Meng-Lay Lin; David J McBride; Ignacio Varela; Serena Nik-Zainal; Catherine Leroy; Mingming Jia; Andrew Menzies; Adam P Butler; Jon W Teague; Michael A Quail; John Burton; Harold Swerdlow; Nigel P Carter; Laura A Morsberger; Christine Iacobuzio-Donahue; George A Follows; Anthony R Green; Adrienne M Flanagan; Michael R Stratton; P Andrew Futreal; Peter J Campbell
Journal:  Cell       Date:  2011-01-07       Impact factor: 41.582

9.  Pan-cancer patterns of somatic copy number alteration.

Authors:  Travis I Zack; Stephen E Schumacher; Scott L Carter; Andre D Cherniack; Gordon Saksena; Barbara Tabak; Michael S Lawrence; Cheng-Zhong Zhsng; Jeremiah Wala; Craig H Mermel; Carrie Sougnez; Stacey B Gabriel; Bryan Hernandez; Hui Shen; Peter W Laird; Gad Getz; Matthew Meyerson; Rameen Beroukhim
Journal:  Nat Genet       Date:  2013-10       Impact factor: 38.330

10.  Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers.

Authors:  Xiaoyang Zhang; Peter S Choi; Joshua M Francis; Marcin Imielinski; Hideo Watanabe; Andrew D Cherniack; Matthew Meyerson
Journal:  Nat Genet       Date:  2015-12-14       Impact factor: 38.330

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  19 in total

1.  Functional Enhancers Shape Extrachromosomal Oncogene Amplifications.

Authors:  Andrew R Morton; Nergiz Dogan-Artun; Zachary J Faber; Graham MacLeod; Cynthia F Bartels; Megan S Piazza; Kevin C Allan; Stephen C Mack; Xiuxing Wang; Ryan C Gimple; Qiulian Wu; Brian P Rubin; Shashirekha Shetty; Stephane Angers; Peter B Dirks; Richard C Sallari; Mathieu Lupien; Jeremy N Rich; Peter C Scacheri
Journal:  Cell       Date:  2019-11-21       Impact factor: 41.582

2.  Enhancer-gene rewiring in the pathogenesis of Quebec platelet disorder.

Authors:  Minggao Liang; Asim Soomro; Subia Tasneem; Luis E Abatti; Azad Alizada; Xuefei Yuan; Liis Uusküla-Reimand; Lina Antounians; Sana Akhtar Alvi; Andrew D Paterson; Georges-Étienne Rivard; Ian C Scott; Jennifer A Mitchell; Catherine P M Hayward; Michael D Wilson
Journal:  Blood       Date:  2020-12-03       Impact factor: 22.113

3.  Single-cell analysis of structural variations and complex rearrangements with tri-channel processing.

Authors:  Ashley D Sanders; Sascha Meiers; Maryam Ghareghani; David Porubsky; Hyobin Jeong; M Alexandra C C van Vliet; Tobias Rausch; Paulina Richter-Pechańska; Joachim B Kunz; Silvia Jenni; Davide Bolognini; Gabriel M C Longo; Benjamin Raeder; Venla Kinanen; Jürgen Zimmermann; Vladimir Benes; Martin Schrappe; Balca R Mardin; Andreas E Kulozik; Beat Bornhauser; Jean-Pierre Bourquin; Tobias Marschall; Jan O Korbel
Journal:  Nat Biotechnol       Date:  2019-12-23       Impact factor: 54.908

Review 4.  Enhancer dysfunction in leukemia.

Authors:  Anand S Bhagwat; Bin Lu; Christopher R Vakoc
Journal:  Blood       Date:  2018-02-09       Impact factor: 25.476

5.  Facultative CTCF sites moderate mammary super-enhancer activity and regulate juxtaposed gene in non-mammary cells.

Authors:  M Willi; K H Yoo; F Reinisch; T M Kuhns; H K Lee; C Wang; L Hennighausen
Journal:  Nat Commun       Date:  2017-07-17       Impact factor: 14.919

Review 6.  When TADs go bad: chromatin structure and nuclear organisation in human disease.

Authors:  Vera B Kaiser; Colin A Semple
Journal:  F1000Res       Date:  2017-03-24

7.  Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor.

Authors:  Xiaoyang Zhang; Peter S Choi; Joshua M Francis; Galen F Gao; Joshua D Campbell; Aruna Ramachandran; Yoichiro Mitsuishi; Gavin Ha; Juliann Shih; Francisca Vazquez; Aviad Tsherniak; Alison M Taylor; Jin Zhou; Zhong Wu; Ashton C Berger; Marios Giannakis; William C Hahn; Andrew D Cherniack; Matthew Meyerson
Journal:  Cancer Discov       Date:  2017-09-29       Impact factor: 39.397

8.  Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival.

Authors:  Riaz Gillani; Bo Kyung A Seong; Jett Crowdis; Jake R Conway; Neekesh V Dharia; Saif Alimohamed; Brian J Haas; Kyuho Han; Jihye Park; Felix Dietlein; Meng Xiao He; Alma Imamovic; Clement Ma; Michael C Bassik; Jesse S Boehm; Francisca Vazquez; Alexander Gusev; David Liu; Katherine A Janeway; James M McFarland; Kimberly Stegmaier; Eliezer M Van Allen
Journal:  Cancer Res       Date:  2021-06-07       Impact factor: 13.312

9.  Genomic copy number gains of ErbB family members predict poor clinical outcomes in glioma patients.

Authors:  Rui Liu; Yiping Qu; Lihong Chen; Jun Pu; Sharui Ma; Xiaozhi Zhang; Qi Yang; Bingyin Shi; Peng Hou; Meiju Ji
Journal:  Oncotarget       Date:  2017-09-23

10.  Effective normalization for copy number variation in Hi-C data.

Authors:  Nicolas Servant; Nelle Varoquaux; Edith Heard; Emmanuel Barillot; Jean-Philippe Vert
Journal:  BMC Bioinformatics       Date:  2018-09-06       Impact factor: 3.169

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