Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types

被引：98

作者：

Yu, K. ^{[1
,2
]}

Chen, B. ^{[3
,4
]}

Aran, D. ^{[1
]}

Charalel, J. ^{[5
]}

Yau, C. ^{[6
,7
]}

Wolf, D. M. ^{[7
]}

van 't Veer, L. J. ^{[8
]}

Butte, A. J. ^{[1
,2
]}

Goldstein, T. ^{[1
]}

Sirota, M. ^{[1
,2
]}

机构：

[1] Univ Calif San Francisco, Bakar Computat Hlth Sci Inst, San Francisco, CA 94158 USA

[2] Univ Calif San Francisco, Dept Pediat, San Francisco, CA 94143 USA

[3] Michigan State Univ, Coll Human Med, Dept Pediat & Human Dev, Grand Rapids, MI 49503 USA

[4] Michigan State Univ, Coll Human Med, Dept Pharmacol & Toxicol, Grand Rapids, MI 49503 USA

[5] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[6] Buck Inst Res Aging, Novato, CA 94945 USA

[7] Univ Calif San Francisco, Dept Surg, San Francisco, CA 94143 USA

[8] Univ Calif San Francisco, Dept Lab Med, San Francisco, CA 94143 USA

来源：

NATURE COMMUNICATIONS | 2019年 / 10卷 / 1期

关键词：

INTEGRATED GENOMIC CHARACTERIZATION; CONSENSUS MOLECULAR SUBTYPES; PATHWAYS; ADENOCARCINOMA; CLASSIFICATION; HEDGEHOG;

D O I：

10.1038/s41467-019-11415-2

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Cancer cell lines are a cornerstone of cancer research but previous studies have shown that not all cell lines are equal in their ability to model primary tumors. Here we present a comprehensive pan-cancer analysis utilizing transcriptomic profiles from The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia to evaluate cell lines as models of primary tumors across 22 tumor types. We perform correlation analysis and gene set enrichment analysis to understand the differences between cell lines and primary tumors. Additionally, we classify cell lines into tumor subtypes in 9 tumor types. We present our pancreatic cancer results as a case study and find that the commonly used cell line MIA PaCa-2 is transcriptionally unrepresentative of primary pancreatic adenocarcinomas. Lastly, we propose a new cell line panel, the TCGA-110-CL, for pan-cancer studies. This study provides a resource to help researchers select more representative cell line models.

引用

页数：11

共 46 条

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Laird, Peter W. ;

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Schultz, Nikolaus ;

Shen, Ronglai ;

Weinhold, Nils ;

Keiser, David P. ;

Bowlby, Reanne ;

Sipahimalani, Payal ;

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Carter, Scott L. ;

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Onofrio, Robert C. ;

Winckler, Wendy ;

Weir, Barbara A. ;

Beroukhim, Rameen ;

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Getz, Gad .

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Ceccarelli, Michele ;

Barthel, Floris P. ;

Malta, Tathiane M. ;

Sabedot, Thais S. ;

Salama, Sofie R. ;

Murray, Bradley A. ;

Morozova, Olena ;

Newton, Yulia ;

Radenbaugh, Amie ;

Pagnotta, Stefano M. ;

Anjum, Samreen ;

Wang, Jiguang ;

Manyam, Ganiraju ;

Zoppoli, Pietro ;

Ling, Shiyun ;

Rao, Arjun A. ;

Grifford, Mia ;

Cherniack, Andrew D. ;

Zhang, Hailei ;

Poisson, Laila ;

Carlotti, Carlos Gilberto, Jr. ;

Tirapelli, Daniela Pretti da Cunha ;

Rao, Arvind ;

Mikkelsen, Tom ;

Lau, Ching C. ;

Yung, W. K. Alfred ;

Rabadan, Raul ;

Huse, Jason ;

Brat, Daniel J. ;

Lehman, Norman L. ;

Barnholtz-Sloan, Jill S. ;

Zheng, Siyuan ;

Hess, Kenneth ;

Rao, Ganesh ;

Meyerson, Matthew ;

Beroukhim, Rameen ;

Cooper, Lee ;

Akbani, Rehan ;

Wrensch, Margaret ;

Haussler, David ;

Aldape, Kenneth D. ;

Laird, Peter W. ;

Gutmann, David H. ;

Noushmehr, Houtan ;

Iavarone, Antonio ;

Verhaak, Roel G. W. .

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← 1 2 3 4 5 →

共 46 条

[1] The Molecular Taxonomy of Primary Prostate Cancer [J].

Abeshouse, Adam ;

Ahn, Jaeil ;

Akbani, Rehan ;

Ally, Adrian ;

Amin, Samirkumar ;

Andry, Christopher D. ;

Annala, Matti ;

Aprikian, Armen ;

Armenia, Joshua ;

Arora, Arshi ;

Auman, J. Todd ;

Balasundaram, Miruna ;

Balu, Saianand ;

Barbieri, Christopher E. ;

Bauer, Thomas ;

Benz, Christopher C. ;

Bergeron, Alain ;

Beroukhim, Rameen ;

Berrios, Mario ;

Bivol, Adrian ;

Bodenheimer, Tom ;

Boice, Lori ;

Bootwalla, Moiz S. ;

dos Reis, Rodolfo Borges ;

Boutros, Paul C. ;

Bowen, Jay ;

Bowlby, Reanne ;

Boyd, Jeffrey ;

Bradley, Robert K. ;

Breggia, Anne ;

Brimo, Fadi ;

Bristow, Christopher A. ;

Brooks, Denise ;

Broom, Bradley M. ;

Bryce, Alan H. ;

Bubley, Glenn ;

Burks, Eric ;

Butterfield, Yaron S. N. ;

Button, Michael ;

Canes, David ;

Carlotti, Carlos G. ;

Carlsen, Rebecca ;

Carmel, Michel ;

Carroll, Peter R. ;

Carter, Scott L. ;

Cartun, Richard ;

Carver, Brett S. ;

Chan, June M. ;

Chang, Matthew T. ;

Chen, Yu .

CELL, 2015, 163 (04) :1011-1025

[2] Integrated Genomic Characterization of Papillary Thyroid Carcinoma [J].

Agrawal, Nishant ;

Akbani, Rehan ;

Aksoy, B. Arman ;

Ally, Adrian ;

Arachchi, Harindra ;

Asa, Sylvia L. ;

Auman, J. Todd ;

Balasundaram, Miruna ;

Balu, Saianand ;

Baylin, Stephen B. ;

Behera, Madhusmita ;

Bernard, Brady ;

Beroukhim, Rameen ;

Bishop, Justin A. ;

Black, Aaron D. ;

Bodenheimer, Tom ;

Boice, Lori ;

Bootwalla, Moiz S. ;

Bowen, Jay ;

Bowlby, Reanne ;

Bristow, Christopher A. ;

Brookens, Robin ;

Brooks, Denise ;

Bryant, Robert ;

Buda, Elizabeth ;

Butterfield, Yaron S. N. ;

Carling, Tobias ;

Carlsen, Rebecca ;

Carter, Scott L. ;

Carty, Sally E. ;

Chan, Timothy A. ;

Chen, Amy Y. ;

Cherniack, Andrew D. ;

Cheung, Dorothy ;

Chin, Lynda ;

Cho, Juok ;

Chu, Andy ;

Chuah, Eric ;

Cibulskis, Kristian ;

Ciriello, Giovanni ;

Clarke, Amanda ;

Clayman, Gary L. ;

Cope, Leslie ;

Copland, John A. ;

Covington, Kyle ;

Danilova, Ludmila ;

Davidsen, Tanja ;

Demchok, John A. ;

DiCara, Daniel ;

Dhalla, Noreen .

CELL, 2014, 159 (03) :676-690

[3] Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma [J].

Aguirre, Andrew J. ;

Hruban, Ralph H. ;

Raphael, Benjamin J. .

CANCER CELL, 2017, 32 (02) :185-+

[4] Genomic Classification of Cutaneous Melanoma [J].

Akbani, Rehan ;

Akdemir, Kadir C. ;

Aksoy, B. Arman ;

Albert, Monique ;

Ally, Adrian ;

Amin, Samirkumar B. ;

Arachchi, Harindra ;

Arora, Arshi ;

Auman, J. Todd ;

Ayala, Brenda ;

Baboud, Julien ;

Balasundaram, Miruna ;

Balu, Saianand ;

Barnabas, Nandita ;

Bartlett, John ;

Bartlett, Pam ;

Bastian, Boris C. ;

Baylin, Stephen B. ;

Behera, Madhusmita ;

Belyaev, Dmitry ;

Benz, Christopher ;

Bernard, Brady ;

Beroukhim, Rameen ;

Bir, Natalie ;

Black, Aaron D. ;

Bodenheimer, Tom ;

Boice, Lori ;

Boland, Genevieve M. ;

Bono, Riccardo ;

Bootwalla, Moiz S. ;

Bosenberg, Marcus ;

Bowen, Jay ;

Bowlby, Reanne ;

Bristow, Christopher A. ;

Brockway-Lunardi, Laura ;

Brooks, Denise ;

Brzezinski, Jakub ;

Bshara, Wiam ;

Buda, Elizabeth ;

Burns, William R. ;

Butterfield, Yaron S. N. ;

Button, Michael ;

Calderone, Tiffany ;

Cappellini, Giancarlo Antonini ;

Carter, Candace ;

Carter, Scott L. ;

Cherney, Lynn ;

Cherniack, Andrew D. ;

Chevalier, Aaron ;

Chin, Lynda .

CELL, 2015, 161 (07) :1681-1696

[5] Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma [J].

Ally, Adrian ;

Balasundaram, Miruna ;

Carlsen, Rebecca ;

Chuah, Eric ;

Clarke, Amanda ;

Dhalla, Noreen ;

Holt, Robert A. ;

Jones, Steven J. M. ;

Lee, Darlene ;

Ma, Yussanne ;

Marra, Marco A. ;

Mayo, Michael ;

Moore, Richard A. ;

Mungall, Andrew J. ;

Schein, Jacqueline E. ;

Sipahimalani, Payal ;

Tam, Angela ;

Thiessen, Nina ;

Cheung, Dorothy ;

Wong, Tina ;

Brooks, Denise ;

Robertson, A. Gordon ;

Bowlby, Reanne ;

Mungall, Karen ;

Sadeghi, Sara ;

Xi, Liu ;

Covington, Kyle ;

Shinbrot, Eve ;

Wheeler, David A. ;

Gibbs, Richard A. ;

Donehower, Lawrence A. ;

Wang, Linghua ;

Bowen, Jay ;

Gastier-Foster, Julie M. ;

Gerken, Mark ;

Helsel, Carmen ;

Leraas, Kristen M. ;

Lichtenberg, Tara M. ;

Ramirez, Nilsa C. ;

Wise, Lisa ;

Zmuda, Erik ;

Gabriel, Stacey B. ;

Meyerson, Matthew ;

Cibulskis, Carrie ;

Murray, Bradley A. ;

Shih, Juliann ;

Beroukhim, Rameen ;

Cherniack, Andrew D. ;

Schumacher, Steven E. ;

Saksena, Gordon .

CELL, 2017, 169 (07) :1327-+

[6] Systematic pan-cancer analysis of tumour purity [J].

Aran, Dvir ;

Sirota, Marina ;

Butte, Atul J. .

NATURE COMMUNICATIONS, 2015, 6

[7] Comprehensive molecular characterization of gastric adenocarcinoma [J].

Bass, Adam J. ;

Thorsson, Vesteinn ;

Shmulevich, Ilya ;

Reynolds, Sheila M. ;

Miller, Michael ;

Bernard, Brady ;

Hinoue, Toshinori ;

Laird, Peter W. ;

Curtis, Christina ;

Shen, Hui ;

Weisenberger, Daniel J. ;

Schultz, Nikolaus ;

Shen, Ronglai ;

Weinhold, Nils ;

Keiser, David P. ;

Bowlby, Reanne ;

Sipahimalani, Payal ;

Cherniack, Andrew D. ;

Getz, Gad ;

Liu, Yingchun ;

Noble, Michael S. ;

Pedamallu, Chandra ;

Sougnez, Carrie ;

Taylor-Weiner, Amaro ;

Akbani, Rehan ;

Lee, Ju-Seog ;

Liu, Wenbin ;

Mills, Gordon B. ;

Yang, Da ;

Zhang, Wei ;

Pantazi, Angeliki ;

Parfenov, Michael ;

Gulley, Margaret ;

Piazuelo, M. Blanca ;

Schneider, Barbara G. ;

Kim, Jihun ;

Boussioutas, Alex ;

Sheth, Margi ;

Demchok, John A. ;

Rabkin, Charles S. ;

Willis, Joseph E. ;

Ng, Sam ;

Garman, Katherine ;

Beer, David G. ;

Pennathur, Arjun ;

Raphael, Benjamin J. ;

Wu, Hsin-Ta ;

Odze, Robert ;

Kim, Hark K. ;

Bowen, Jay .

NATURE, 2014, 513 (7517) :202-209

[8] Developmental pathways in colon cancer Crosstalk between WNT, BMP, Hedgehog and Notch [J].

Bertrand, Fred E. ;

Angus, C. William ;

Partis, William J. ;

Sigounas, George .

CELL CYCLE, 2012, 11 (23) :4344-4351

[9] Absolute quantification of somatic DNA alterations in human cancer [J].

Carter, Scott L. ;

Cibulskis, Kristian ;

Helman, Elena ;

McKenna, Aaron ;

Shen, Hui ;

Zack, Travis ;

Laird, Peter W. ;

Onofrio, Robert C. ;

Winckler, Wendy ;

Weir, Barbara A. ;

Beroukhim, Rameen ;

Pellman, David ;

Levine, Douglas A. ;

Lander, Eric S. ;

Meyerson, Matthew ;

Getz, Gad .

NATURE BIOTECHNOLOGY, 2012, 30 (05) :413-+

[10] Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma [J].

Ceccarelli, Michele ;

Barthel, Floris P. ;

Malta, Tathiane M. ;

Sabedot, Thais S. ;

Salama, Sofie R. ;

Murray, Bradley A. ;

Morozova, Olena ;

Newton, Yulia ;

Radenbaugh, Amie ;

Pagnotta, Stefano M. ;

Anjum, Samreen ;

Wang, Jiguang ;

Manyam, Ganiraju ;

Zoppoli, Pietro ;

Ling, Shiyun ;

Rao, Arjun A. ;

Grifford, Mia ;

Cherniack, Andrew D. ;

Zhang, Hailei ;

Poisson, Laila ;

Carlotti, Carlos Gilberto, Jr. ;

Tirapelli, Daniela Pretti da Cunha ;

Rao, Arvind ;

Mikkelsen, Tom ;

Lau, Ching C. ;

Yung, W. K. Alfred ;

Rabadan, Raul ;

Huse, Jason ;

Brat, Daniel J. ;

Lehman, Norman L. ;

Barnholtz-Sloan, Jill S. ;

Zheng, Siyuan ;

Hess, Kenneth ;

Rao, Ganesh ;

Meyerson, Matthew ;

Beroukhim, Rameen ;

Cooper, Lee ;

Akbani, Rehan ;

Wrensch, Margaret ;

Haussler, David ;

Aldape, Kenneth D. ;

Laird, Peter W. ;

Gutmann, David H. ;

Noushmehr, Houtan ;

Iavarone, Antonio ;

Verhaak, Roel G. W. .

CELL, 2016, 164 (03) :550-563

← 1 2 3 4 5 →