Literature DB >> 23622249

Punctuated evolution of prostate cancer genomes.

Sylvan C Baca1, Davide Prandi, Michael S Lawrence, Juan Miguel Mosquera, Alessandro Romanel, Yotam Drier, Kyung Park, Naoki Kitabayashi, Theresa Y MacDonald, Mahmoud Ghandi, Eliezer Van Allen, Gregory V Kryukov, Andrea Sboner, Jean-Philippe Theurillat, T David Soong, Elizabeth Nickerson, Daniel Auclair, Ashutosh Tewari, Himisha Beltran, Robert C Onofrio, Gunther Boysen, Candace Guiducci, Christopher E Barbieri, Kristian Cibulskis, Andrey Sivachenko, Scott L Carter, Gordon Saksena, Douglas Voet, Alex H Ramos, Wendy Winckler, Michelle Cipicchio, Kristin Ardlie, Philip W Kantoff, Michael F Berger, Stacey B Gabriel, Todd R Golub, Matthew Meyerson, Eric S Lander, Olivier Elemento, Gad Getz, Francesca Demichelis, Mark A Rubin, Levi A Garraway.   

Abstract

The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of genome-wide alterations has not been profiled extensively in this disease. We sequenced the genomes of 57 prostate tumors and matched normal tissues to characterize somatic alterations and to study how they accumulate during oncogenesis and progression. By modeling the genesis of genomic rearrangements, we identified abundant DNA translocations and deletions that arise in a highly interdependent manner. This phenomenon, which we term "chromoplexy," frequently accounts for the dysregulation of prostate cancer genes and appears to disrupt multiple cancer genes coordinately. Our modeling suggests that chromoplexy may induce considerable genomic derangement over relatively few events in prostate cancer and other neoplasms, supporting a model of punctuated cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we charted a path of oncogenic events along which chromoplexy may drive prostate carcinogenesis.
Copyright © 2013 Elsevier Inc. All rights reserved.

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Year:  2013        PMID: 23622249      PMCID: PMC3690918          DOI: 10.1016/j.cell.2013.03.021

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  35 in total

1.  SMAD4-dependent barrier constrains prostate cancer growth and metastatic progression.

Authors:  Zhihu Ding; Chang-Jiun Wu; Gerald C Chu; Yonghong Xiao; Dennis Ho; Jingfang Zhang; Samuel R Perry; Emma S Labrot; Xiaoqiu Wu; Rosina Lis; Yujin Hoshida; David Hiller; Baoli Hu; Shan Jiang; Hongwu Zheng; Alexander H Stegh; Kenneth L Scott; Sabina Signoretti; Nabeel Bardeesy; Y Alan Wang; David E Hill; Todd R Golub; Meir J Stampfer; Wing H Wong; Massimo Loda; Lorelei Mucci; Lynda Chin; Ronald A DePinho
Journal:  Nature       Date:  2011-02-02       Impact factor: 49.962

2.  Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations.

Authors:  Tobias Rausch; David T W Jones; Marc Zapatka; Adrian M Stütz; Thomas Zichner; Joachim Weischenfeldt; Natalie Jäger; Marc Remke; David Shih; Paul A Northcott; Elke Pfaff; Jelena Tica; Qi Wang; Luca Massimi; Hendrik Witt; Sebastian Bender; Sabrina Pleier; Huriye Cin; Cynthia Hawkins; Christian Beck; Andreas von Deimling; Volkmar Hans; Benedikt Brors; Roland Eils; Wolfram Scheurlen; Jonathon Blake; Vladimir Benes; Andreas E Kulozik; Olaf Witt; Dianna Martin; Cindy Zhang; Rinnat Porat; Diana M Merino; Jonathan Wasserman; Nada Jabado; Adam Fontebasso; Lars Bullinger; Frank G Rücker; Konstanze Döhner; Hartmut Döhner; Jan Koster; Jan J Molenaar; Rogier Versteeg; Marcel Kool; Uri Tabori; David Malkin; Andrey Korshunov; Michael D Taylor; Peter Lichter; Stefan M Pfister; Jan O Korbel
Journal:  Cell       Date:  2012-01-20       Impact factor: 41.582

3.  The life history of 21 breast cancers.

Authors:  Serena Nik-Zainal; Peter Van Loo; David C Wedge; Ludmil B Alexandrov; Christopher D Greenman; King Wai Lau; Keiran Raine; David Jones; John Marshall; Manasa Ramakrishna; Adam Shlien; Susanna L Cooke; Jonathan Hinton; Andrew Menzies; Lucy A Stebbings; Catherine Leroy; Mingming Jia; Richard Rance; Laura J Mudie; Stephen J Gamble; Philip J Stephens; Stuart McLaren; Patrick S Tarpey; Elli Papaemmanuil; Helen R Davies; Ignacio Varela; David J McBride; Graham R Bignell; Kenric Leung; Adam P Butler; Jon W Teague; Sancha Martin; Goran Jönsson; Odette Mariani; Sandrine Boyault; Penelope Miron; Aquila Fatima; Anita Langerød; Samuel A J R Aparicio; Andrew Tutt; Anieta M Sieuwerts; Åke Borg; Gilles Thomas; Anne Vincent Salomon; Andrea L Richardson; Anne-Lise Børresen-Dale; P Andrew Futreal; Michael R Stratton; Peter J Campbell
Journal:  Cell       Date:  2012-05-17       Impact factor: 41.582

Review 4.  Molecular genetics of prostate cancer: new prospects for old challenges.

Authors:  Michael M Shen; Cory Abate-Shen
Journal:  Genes Dev       Date:  2010-09-15       Impact factor: 11.361

5.  TMPRSS2-ERG fusion, a common genomic alteration in prostate cancer activates C-MYC and abrogates prostate epithelial differentiation.

Authors:  C Sun; A Dobi; A Mohamed; H Li; R L Thangapazham; B Furusato; S Shaheduzzaman; S-H Tan; G Vaidyanathan; E Whitman; D J Hawksworth; Y Chen; M Nau; V Patel; M Vahey; J S Gutkind; T Sreenath; G Petrovics; I A Sesterhenn; D G McLeod; S Srivastava
Journal:  Oncogene       Date:  2008-06-09       Impact factor: 9.867

6.  Chd1 regulates open chromatin and pluripotency of embryonic stem cells.

Authors:  Alexandre Gaspar-Maia; Adi Alajem; Fanny Polesso; Rupa Sridharan; Mike J Mason; Amy Heidersbach; João Ramalho-Santos; Michael T McManus; Kathrin Plath; Eran Meshorer; Miguel Ramalho-Santos
Journal:  Nature       Date:  2009-07-08       Impact factor: 49.962

7.  TMPRSS2-ERG fusion prostate cancer: an early molecular event associated with invasion.

Authors:  Sven Perner; Juan-Miguel Mosquera; Francesca Demichelis; Matthias D Hofer; Pamela L Paris; Jeff Simko; Colin Collins; Tarek A Bismar; Arul M Chinnaiyan; Angelo M De Marzo; Mark A Rubin
Journal:  Am J Surg Pathol       Date:  2007-06       Impact factor: 6.394

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.  The genomic complexity of primary human prostate cancer.

Authors:  Michael F Berger; Michael S Lawrence; Francesca Demichelis; Yotam Drier; Kristian Cibulskis; Andrey Y Sivachenko; Andrea Sboner; Raquel Esgueva; Dorothee Pflueger; Carrie Sougnez; Robert Onofrio; Scott L Carter; Kyung Park; Lukas Habegger; Lauren Ambrogio; Timothy Fennell; Melissa Parkin; Gordon Saksena; Douglas Voet; Alex H Ramos; Trevor J Pugh; Jane Wilkinson; Sheila Fisher; Wendy Winckler; Scott Mahan; Kristin Ardlie; Jennifer Baldwin; Jonathan W Simons; Naoki Kitabayashi; Theresa Y MacDonald; Philip W Kantoff; Lynda Chin; Stacey B Gabriel; Mark B Gerstein; Todd R Golub; Matthew Meyerson; Ashutosh Tewari; Eric S Lander; Gad Getz; Mark A Rubin; Levi A Garraway
Journal:  Nature       Date:  2011-02-10       Impact factor: 49.962

10.  Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability.

Authors:  Yotam Drier; Michael S Lawrence; Scott L Carter; Chip Stewart; Stacey B Gabriel; Eric S Lander; Matthew Meyerson; Rameen Beroukhim; Gad Getz
Journal:  Genome Res       Date:  2012-11-02       Impact factor: 9.043

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  524 in total

Review 1.  Next-generation sequencing-based clinical sequencing: toward precision medicine in solid tumors.

Authors:  Toshifumi Wakai; Pankaj Prasoon; Yuki Hirose; Yoshifumi Shimada; Hiroshi Ichikawa; Masayuki Nagahashi
Journal:  Int J Clin Oncol       Date:  2018-12-04       Impact factor: 3.402

Review 2.  Genomic rearrangements in prostate cancer.

Authors:  Christopher E Barbieri; Mark A Rubin
Journal:  Curr Opin Urol       Date:  2015-01       Impact factor: 2.309

Review 3.  Research Needs for Understanding the Biology of Overdiagnosis in Cancer Screening.

Authors:  Sudhir Srivastava; Brian J Reid; Sharmistha Ghosh; Barnett S Kramer
Journal:  J Cell Physiol       Date:  2016-04-29       Impact factor: 6.384

4.  Insertions and Deletions Target Lineage-Defining Genes in Human Cancers.

Authors:  Marcin Imielinski; Guangwu Guo; Matthew Meyerson
Journal:  Cell       Date:  2017-01-12       Impact factor: 41.582

5.  Tumor suppressor SPOP ubiquitinates and degrades EglN2 to compromise growth of prostate cancer cells.

Authors:  Linli Zhang; Shan Peng; Xiangpeng Dai; Wenjian Gan; Xin Nie; Wenyi Wei; Guoqing Hu; Jianping Guo
Journal:  Cancer Lett       Date:  2017-01-13       Impact factor: 8.679

6.  Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations.

Authors:  Franklin W Huang; Juan Miguel Mosquera; Andrea Garofalo; Coyin Oh; Maria Baco; Ali Amin-Mansour; Bokang Rabasha; Samira Bahl; Stephanie A Mullane; Brian D Robinson; Saud Aldubayan; Francesca Khani; Beerinder Karir; Eejung Kim; Jeremy Chimene-Weiss; Matan Hofree; Alessandro Romanel; Joseph R Osborne; Jong Wook Kim; Gissou Azabdaftari; Anna Woloszynska-Read; Karen Sfanos; Angelo M De Marzo; Francesca Demichelis; Stacey Gabriel; Eliezer M Van Allen; Jill Mesirov; Pablo Tamayo; Mark A Rubin; Isaac J Powell; Levi A Garraway
Journal:  Cancer Discov       Date:  2017-05-17       Impact factor: 39.397

Review 7.  An arranged marriage for precision medicine: hypoxia and genomic assays in localized prostate cancer radiotherapy.

Authors:  R G Bristow; A Berlin; A Dal Pra
Journal:  Br J Radiol       Date:  2014-02-03       Impact factor: 3.039

8.  Stress-Induced Mutagenesis: Implications in Cancer and Drug Resistance.

Authors:  Devon M Fitzgerald; P J Hastings; Susan M Rosenberg
Journal:  Annu Rev Cancer Biol       Date:  2017-03

9.  Transgenic Expression of the Mitochondrial Chaperone TNFR-associated Protein 1 (TRAP1) Accelerates Prostate Cancer Development.

Authors:  Sofia Lisanti; David S Garlick; Kelly G Bryant; Michele Tavecchio; Gordon B Mills; Yiling Lu; Andrew V Kossenkov; Louise C Showe; Lucia R Languino; Dario C Altieri
Journal:  J Biol Chem       Date:  2016-10-17       Impact factor: 5.157

10.  Integrative annotation of variants from 1092 humans: application to cancer genomics.

Authors:  Ekta Khurana; Yao Fu; Vincenza Colonna; Xinmeng Jasmine Mu; Hyun Min Kang; Tuuli Lappalainen; Andrea Sboner; Lucas Lochovsky; Jieming Chen; Arif Harmanci; Jishnu Das; Alexej Abyzov; Suganthi Balasubramanian; Kathryn Beal; Dimple Chakravarty; Daniel Challis; Yuan Chen; Declan Clarke; Laura Clarke; Fiona Cunningham; Uday S Evani; Paul Flicek; Robert Fragoza; Erik Garrison; Richard Gibbs; Zeynep H Gümüş; Javier Herrero; Naoki Kitabayashi; Yong Kong; Kasper Lage; Vaja Liluashvili; Steven M Lipkin; Daniel G MacArthur; Gabor Marth; Donna Muzny; Tune H Pers; Graham R S Ritchie; Jeffrey A Rosenfeld; Cristina Sisu; Xiaomu Wei; Michael Wilson; Yali Xue; Fuli Yu; Emmanouil T Dermitzakis; Haiyuan Yu; Mark A Rubin; Chris Tyler-Smith; Mark Gerstein
Journal:  Science       Date:  2013-10-04       Impact factor: 47.728

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