High order chromatin architecture shapes the landscape of chromosomal alterations in cancer

被引：156

作者：

Fudenberg, Geoff ^{[2
]}

Getz, Gad ^{[1
]}

Meyerson-, Matthew ^{[1
,3
,4
,5
]}

Mirny, Leonid A. ^{[1
,6
,7
]}

机构：

[1] Broad Inst Massachusetts Inst Technol & Harvard, Cambridge, MA USA

[2] Harvard Univ, Program Biophys, Boston, MA 02115 USA

[3] Harvard Univ, Sch Med, Boston, MA USA

[4] Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02115 USA

[5] Dana Farber Canc Inst, Ctr Canc Genome Discovery, Boston, MA 02115 USA

[6] MIT, Harvard Mit Div Hlth Sci & Technol, Cambridge, MA 02139 USA

[7] MIT, Dept Phys, Cambridge, MA 02139 USA

来源：

NATURE BIOTECHNOLOGY | 2011年 / 29卷 / 12期

基金：

美国国家卫生研究院;

关键词：

SEQUENCING REVEALS; COPY-NUMBER; GENOME; REARRANGEMENTS; TRANSLOCATIONS; MECHANISMS; PROXIMITY; MUTATION; CELLS; LOCI;

D O I：

10.1038/nbt.2049

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

The accumulation of data on structural variation in cancer genomes provides an opportunity to better understand the mechanisms of genomic alterations and the forces of selection that act upon these alterations in cancer. Here we test evidence supporting the influence of two major forces, spatial chromosome structure and purifying (or negative) selection, on the landscape of somatic copy-number alterations (SCNAs) in cancer(1). Using a maximum likelihood approach, we compare SCNA maps and three-dimensional genome architecture as determined by genome-wide chromosome conformation capture (HiC) and described by the proposed fractal-globule model(2,3). This analysis suggests that the distribution of chromosomal alterations in cancer is spatially related to three-dimensional genomic architecture and that purifying selection, as well as positive selection, influences SCNAs during somatic evolution of cancer cells.

引用

页码：1109 / U75

页数：6

共 27 条

[1]

Armitage P., 2001, STAT METHODS MED RES, V4th

[2] The genomic complexity of primary human prostate cancer [J].

Berger, Michael F. ;

Lawrence, Michael S. ;

Demichelis, Francesca ;

Drier, Yotam ;

Cibulskis, Kristian ;

Sivachenko, Andrey Y. ;

Sboner, Andrea ;

Esgueva, Raquel ;

Pflueger, Dorothee ;

Sougnez, Carrie ;

Onofrio, Robert ;

Carter, Scott L. ;

Park, Kyung ;

Habegger, Lukas ;

Ambrogio, Lauren ;

Fennell, Timothy ;

Parkin, Melissa ;

Saksena, Gordon ;

Voet, Douglas ;

Ramos, Alex H. ;

Pugh, Trevor J. ;

Wilkinson, Jane ;

Fisher, Sheila ;

Winckler, Wendy ;

Mahan, Scott ;

Ardlie, Kristin ;

Baldwin, Jennifer ;

Simons, Jonathan W. ;

Kitabayashi, Naoki ;

MacDonald, Theresa Y. ;

Kantoff, Philip W. ;

Chin, Lynda ;

Gabriel, Stacey B. ;

Gerstein, Mark B. ;

Golub, Todd R. ;

Meyerson, Matthew ;

Tewari, Ashutosh ;

Lander, Eric S. ;

Getz, Gad ;

Rubin, Mark A. ;

Garraway, Levi A. .

NATURE, 2011, 470 (7333) :214-220

[3] Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma [J].

Beroukhim, Rameen ;

Getz, Gad ;

Nghiemphu, Leia ;

Barretina, Jordi ;

Hsueh, Teli ;

Linhart, David ;

Vivanco, Igor ;

Lee, Jeffrey C. ;

Huang, Julie H. ;

Alexander, Sethu ;

Du, Jinyan ;

Kau, Tweeny ;

Thomas, Roman K. ;

Shah, Kinial ;

Soto, Horacio ;

Perner, Sven ;

Prensner, John ;

Debiasi, Ralph M. ;

Demichelis, Francesca ;

Hatton, Charlie ;

Rubin, Mark A. ;

Garraway, Levi A. ;

Nelson, Stan F. ;

Liau, Linda ;

Mischel, Paul S. ;

Cloughesy, Tim F. ;

Meyerson, Matthew ;

Golub, Todd A. ;

Lander, Eric S. ;

Mellinghoff, Ingo K. ;

Sellers, William R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (50) :20007-20012

[4] The landscape of somatic copy-number alteration across human cancers [J].

Beroukhim, Rameen ;

Mermel, Craig H. ;

Porter, Dale ;

Wei, Guo ;

Raychaudhuri, Soumya ;

Donovan, Jerry ;

Barretina, Jordi ;

Boehm, Jesse S. ;

Dobson, Jennifer ;

Urashima, Mitsuyoshi ;

Mc Henry, Kevin T. ;

Pinchback, Reid M. ;

Ligon, Azra H. ;

Cho, Yoon-Jae ;

Haery, Leila ;

Greulich, Heidi ;

Reich, Michael ;

Winckler, Wendy ;

Lawrence, Michael S. ;

Weir, Barbara A. ;

Tanaka, Kumiko E. ;

Chiang, Derek Y. ;

Bass, Adam J. ;

Loo, Alice ;

Hoffman, Carter ;

Prensner, John ;

Liefeld, Ted ;

Gao, Qing ;

Yecies, Derek ;

Signoretti, Sabina ;

Maher, Elizabeth ;

Kaye, Frederic J. ;

Sasaki, Hidefumi ;

Tepper, Joel E. ;

Fletcher, Jonathan A. ;

Tabernero, Josep ;

Baselga, Jose ;

Tsao, Ming-Sound ;

Demichelis, Francesca ;

Rubin, Mark A. ;

Janne, Pasi A. ;

Daly, Mark J. ;

Nucera, Carmelo ;

Levine, Ross L. ;

Ebert, Benjamin L. ;

Gabriel, Stacey ;

Rustgi, Anil K. ;

Antonescu, Cristina R. ;

Ladanyi, Marc ;

Letai, Anthony .

NATURE, 2010, 463 (7283) :899-905

[5] Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations [J].

Branco, Miguel R. ;

Pombo, Ana .

PLOS BIOLOGY, 2006, 4 (05) :780-788

[6] Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells [J].

Chiarle, Roberto ;

Zhang, Yu ;

Frock, Richard L. ;

Lewis, Susanna M. ;

Molinie, Benoit ;

Ho, Yu-Jui ;

Myers, Darienne R. ;

Choi, Vivian W. ;

Compagno, Mara ;

Malkin, Daniel J. ;

Neuberg, Donna ;

Monti, Stefano ;

Giallourakis, Cosmas C. ;

Gostissa, Monica ;

Alt, Frederick W. .

CELL, 2011, 147 (01) :107-119

[7] Comprehensive genomic characterization defines human glioblastoma genes and core pathways [J].

Chin, L. ;

Meyerson, M. ;

Aldape, K. ;

Bigner, D. ;

Mikkelsen, T. ;

VandenBerg, S. ;

Kahn, A. ;

Penny, R. ;

Ferguson, M. L. ;

Gerhard, D. S. ;

Getz, G. ;

Brennan, C. ;

Taylor, B. S. ;

Winckler, W. ;

Park, P. ;

Ladanyi, M. ;

Hoadley, K. A. ;

Verhaak, R. G. W. ;

Hayes, D. N. ;

Spellman, Paul T. ;

Absher, D. ;

Weir, B. A. ;

Ding, L. ;

Wheeler, D. ;

Lawrence, M. S. ;

Cibulskis, K. ;

Mardis, E. ;

Zhang, Jinghui ;

Wilson, R. K. ;

Donehower, L. ;

Wheeler, D. A. ;

Purdom, E. ;

Wallis, J. ;

Laird, P. W. ;

Herman, J. G. ;

Schuebel, K. E. ;

Weisenberger, D. J. ;

Baylin, S. B. ;

Schultz, N. ;

Yao, Jun ;

Wiedemeyer, R. ;

Weinstein, J. ;

Sander, C. ;

Gibbs, R. A. ;

Gray, J. ;

Kucherlapati, R. ;

Lander, E. S. ;

Myers, R. M. ;

Perou, C. M. ;

McLendon, Roger .

NATURE, 2008, 455 (7216) :1061-1068

[8] Patterns of somatic mutation in human cancer genomes [J].

Greenman, Christopher ;

Stephens, Philip ;

Smith, Raffaella ;

Dalgliesh, Gillian L. ;

Hunter, Christopher ;

Bignell, Graham ;

Davies, Helen ;

Teague, Jon ;

Butler, Adam ;

Edkins, Sarah ;

O'Meara, Sarah ;

Vastrik, Imre ;

Schmidt, Esther E. ;

Avis, Tim ;

Barthorpe, Syd ;

Bhamra, Gurpreet ;

Buck, Gemma ;

Choudhury, Bhudipa ;

Clements, Jody ;

Cole, Jennifer ;

Dicks, Ed ;

Forbes, Simon ;

Gray, Kris ;

Halliday, Kelly ;

Harrison, Rachel ;

Hills, Katy ;

Hinton, Jon ;

Jenkinson, Andy ;

Jones, David ;

Menzies, Andy ;

Mironenko, Tatiana ;

Perry, Janet ;

Raine, Keiran ;

Richardson, Dave ;

Shepherd, Rebecca ;

Small, Alexandra ;

Tofts, Calli ;

Varian, Jennifer ;

Webb, Tony ;

West, Sofie ;

Widaa, Sara ;

Yates, Andy ;

Cahill, Daniel P. ;

Louis, David N. ;

Goldstraw, Peter ;

Nicholson, Andrew G. ;

Brasseur, Francis ;

Looijenga, Leendert ;

Weber, Barbara L. ;

Chiew, Yoke-Eng .

NATURE, 2007, 446 (7132) :153-158

[9] THE ROLE OF TOPOLOGICAL CONSTRAINTS IN THE KINETICS OF COLLAPSE OF MACROMOLECULES [J].

GROSBERG, AY ;

NECHAEV, SK ;

SHAKHNOVICH, EI .

JOURNAL DE PHYSIQUE, 1988, 49 (12) :2095-2100

[10] Cancer - Drivers and passengers [J].

Haber, Daniel A. ;

Settleman, Jeff .

NATURE, 2007, 446 (7132) :145-146

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