Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways

被引：106

作者：

Chun, Hye-Jung E. ^{[1
]}

Lim, Emilia L. ^{[1
]}

Heravi-Moussavi, Alireza ^{[1
]}

Saberi, Saeed ^{[2
]}

Mungall, Karen L. ^{[1
]}

Bilenky, Mikhail ^{[1
]}

Carles, Annaick ^{[2
]}

Tse, Kane ^{[1
]}

Shlafman, Inna ^{[1
]}

Zhu, Kelsey ^{[1
]}

Qian, Jenny Q. ^{[1
]}

Palmquist, Diana L. ^{[1
]}

He, An ^{[1
]}

Long, William ^{[1
]}

Goya, Rodrigo ^{[1
]}

Ng, Michelle ^{[1
]}

LeBlanc, Veronique G. ^{[1
]}

Pleasance, Erin ^{[1
]}

Thiessen, Nina ^{[1
]}

Wong, Tina ^{[1
]}

Chuah, Eric ^{[1
]}

Zhao, Yong-Jun ^{[1
]}

Schein, Jacquie E.

Gerhard, Daniela S. ^{[3
]}

Taylor, Michael D. ^{[4
]}

Mungall, Andrew J. ^{[1
]}

Moore, Richard A. ^{[1
]}

Ma, Yussanne ^{[1
]}

Jones, Steven J. M. ^{[1
,5
,8
]}

Perlman, Elizabeth J. ^{[6
,7
]}

Hirst, Martin ^{[1
,2
]}

Marra, Marco A. ^{[1
,8
]}

机构：

[1] British Columbia Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 1L3, Canada

[2] Univ British Columbia, Dept Microbiol & Immunol, Vancouver, BC V6T 1Z4, Canada

[3] NCI, Off Canc Genom, NIH, Bethesda, MD 20892 USA

[4] Hosp Sick Children, Arthur & Sonia Labatt Brain Tumour Res Ctr, Toronto, ON M5G IX8, Canada

[5] Simon Fraser Univ, Dept Mol Biol & Biochem, Burnaby, BC V5A 1S6, Canada

[6] Northwestern Univ, Feinberg Sch Med, Lurie Childrens Hosp, Dept Pathol & Lab Med, Chicago, IL 60611 USA

[7] Northwestern Univ, Robert H Lurie Canc Ctr, Chicago, IL 60611 USA

[8] Univ British Columbia, Dept Med Genet, Vancouver, BC V6H 3N1, Canada

来源：

CANCER CELL | 2016年 / 29卷 / 03期

关键词：

LONG-TERM SURVIVAL; ATYPICAL TERATOID/RHABDOID TUMORS; MICRORNA EXPRESSION PROFILES; PROMOTER CPG METHYLATION; SUPPRESSOR SNF5 LEADS; NATIONAL-WILMS-TUMOR; LARGE GENE LISTS; EPIGENETIC INACTIVATION; INTEGRATIVE ANALYSIS; CELL-CYCLE;

D O I：

10.1016/j.ccell.2016.02.009

中图分类号：

R73 [肿瘤学];

学科分类号：

100214 ;

摘要：

Malignant rhabdoid tumors (MRTs) are rare lethal tumors of childhood that most commonly occur in the kidney and brain. MRTs are driven by SMARCB1 loss, but the molecular consequences of SMARCB1 loss in extra-cranial tumors have not been comprehensively described and genomic resources for analyses of extra-cranial MRT are limited. To provide such data, we used whole-genome sequencing, whole-genome bisulfite sequencing, whole transcriptome (RNA-seq) and microRNA sequencing (miRNA-seq), and histone modification profiling to characterize extra-cranial MRTs. Our analyses revealed gene expression and methylation subgroups and focused on dysregulated pathways, including those involved in neural crest development.

引用

页码：394 / 406

页数：13

共 88 条

[41] Human MicroRNA targets [J].

John, B ;

Enright, AJ ;

Aravin, A ;

Tuschl, T ;

Sander, C ;

Marks, DS .

PLOS BIOLOGY, 2004, 2 (11) :1862-1879

[42] Reversible Disruption of mSWI/SNF (BAF) Complexes by the SS18-SSX Oncogenic Fusion in Synovial Sarcoma [J].

Kadoch, Cigall ;

Crabtree, Gerald R. .

CELL, 2013, 153 (01) :71-85

[43] Trastuzumab activates allogeneic or autologous antibody-dependent cellular cytotoxicity against malignant rhabdoid tumor cells and interleukin-2 augments the cytotoxicity [J].

Katsumi, Yoshiki ;

Kuwahara, Yasumichi ;

Tamura, Shinichi ;

Kikuchi, Ken ;

Otabe, Osamu ;

Tsuchiya, Kunihiko ;

Iehara, Tomoko ;

Kuroda, Hiroshi ;

Hosoi, Hajime ;

Sugimoto, Tohru .

CLINICAL CANCER RESEARCH, 2008, 14 (04) :1192-1199

[44] SWI/SNF mediates polycomb eviction and epigenetic reprogramming of the INK4b-ARF-INK4a locus [J].

Kia, Sima Kheradmand ;

Gorski, Marcin M. ;

Giannakopoulos, Stavros ;

Verrijzer, C. Peter .

MOLECULAR AND CELLULAR BIOLOGY, 2008, 28 (10) :3457-3464

[45] Integrative analysis of 111 reference human epigenomes [J].

Kundaje, Anshul ;

Meuleman, Wouter ;

Ernst, Jason ;

Bilenky, Misha ;

Yen, Angela ;

Heravi-Moussavi, Alireza ;

Kheradpour, Pouya ;

Zhang, Zhizhuo ;

Wang, Jianrong ;

Ziller, Michael J. ;

Amin, Viren ;

Whitaker, John W. ;

Schultz, Matthew D. ;

Ward, Lucas D. ;

Sarkar, Abhishek ;

Quon, Gerald ;

Sandstrom, Richard S. ;

Eaton, Matthew L. ;

Wu, Yi-Chieh ;

Pfenning, Andreas R. ;

Wang, Xinchen ;

Claussnitzer, Melina ;

Liu, Yaping ;

Coarfa, Cristian ;

Harris, R. Alan ;

Shoresh, Noam ;

Epstein, Charles B. ;

Gjoneska, Elizabeta ;

Leung, Danny ;

Xie, Wei ;

Hawkins, R. David ;

Lister, Ryan ;

Hong, Chibo ;

Gascard, Philippe ;

Mungall, Andrew J. ;

Moore, Richard ;

Chuah, Eric ;

Tam, Angela ;

Canfield, Theresa K. ;

Hansen, R. Scott ;

Kaul, Rajinder ;

Sabo, Peter J. ;

Bansal, Mukul S. ;

Carles, Annaick ;

Dixon, Jesse R. ;

Farh, Kai-How ;

Feizi, Soheil ;

Karlic, Rosa ;

Kim, Ah-Ram ;

Kulkarni, Ashwinikumar .

NATURE, 2015, 518 (7539) :317-330

[46] STAT3 is required for FIM-dependent dendritic cell differentiation [J].

Laouar, Y ;

Welte, T ;

Fu, XY ;

Flavell, RA .

IMMUNITY, 2003, 19 (06) :903-912

[47] Mutational heterogeneity in cancer and the search for new cancer-associated genes [J].

Lawrence, Michael S. ;

Stojanov, Petar ;

Polak, Paz ;

Kryukov, Gregory V. ;

Cibulskis, Kristian ;

Sivachenko, Andrey ;

Carter, Scott L. ;

Stewart, Chip ;

Mermel, Craig H. ;

Roberts, Steven A. ;

Kiezun, Adam ;

Hammerman, Peter S. ;

McKenna, Aaron ;

Drier, Yotam ;

Zou, Lihua ;

Ramos, Alex H. ;

Pugh, Trevor J. ;

Stransky, Nicolas ;

Helman, Elena ;

Kim, Jaegil ;

Sougnez, Carrie ;

Ambrogio, Lauren ;

Nickerson, Elizabeth ;

Shefler, Erica ;

Cortes, Maria L. ;

Auclair, Daniel ;

Saksena, Gordon ;

Voet, Douglas ;

Noble, Michael ;

DiCara, Daniel ;

Lin, Pei ;

Lichtenstein, Lee ;

Heiman, David I. ;

Fennell, Timothy ;

Imielinski, Marcin ;

Hernandez, Bryan ;

Hodis, Eran ;

Baca, Sylvan ;

Dulak, Austin M. ;

Lohr, Jens ;

Landau, Dan-Avi ;

Wu, Catherine J. ;

Melendez-Zajgla, Jorge ;

Hidalgo-Miranda, Alfredo ;

Koren, Amnon ;

McCarroll, Steven A. ;

Mora, Jaume ;

Lee, Ryan S. ;

Crompton, Brian ;

Onofrio, Robert .

NATURE, 2013, 499 (7457) :214-218

[48] A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers [J].

Lee, Ryan S. ;

Stewart, Chip ;

Carter, Scott L. ;

Ambrogio, Lauren ;

Cibulskis, Kristian ;

Sougnez, Carrie ;

Lawrence, Michael S. ;

Auclair, Daniel ;

Mora, Jaume ;

Golub, Todd R. ;

Biegel, Jaclyn A. ;

Getz, Gad ;

Roberts, Charles W. M. .

JOURNAL OF CLINICAL INVESTIGATION, 2012, 122 (08) :2983-2988

[49] Chromatin modification and epigenetic reprogramming in mammalian development [J].

Li, E .

NATURE REVIEWS GENETICS, 2002, 3 (09) :662-673

[50] Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients [J].

Lim, Emilia L. ;

Trinh, Diane L. ;

Scott, David W. ;

Chu, Andy ;

Krzywinski, Martin ;

Zhao, Yongjun ;

Robertson, A. Gordon ;

Mungall, Andrew J. ;

Schein, Jacqueline ;

Boyle, Merrill ;

Mottok, Anja ;

Ennishi, Daisuke ;

Johnson, Nathalie A. ;

Steidl, Christian ;

Connors, Joseph M. ;

Morin, Ryan D. ;

Gascoyne, Randy D. ;

Marra, Marco A. .

GENOME BIOLOGY, 2015, 16

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