Next-generation characterization of the Cancer Cell Line Encyclopedia

Mahmoud Ghandi, Franklin W. Huang, Judit Jané-Valbuena, Gregory V. Kryukov, Christopher C. Lo, E. Robert McDonald, Jordi Barretina, Ellen T. Gelfand, Craig M. Bielski, Haoxin Li, Kevin Hu, Alexander Y. Andreev-Drakhlin, Jaegil Kim, Julian M. Hess, Brian J. Haas, François Aguet, Barbara A. Weir, Michael V. Rothberg, Brenton R. Paolella, Michael S. Lawrence, Rehan Akbani, Yiling Lu, Hong L. Tiv, Prafulla C. Gokhale, Antoine de Weck, Ali Amin Mansour, Coyin Oh, Juliann Shih, Kevin Hadi, Yanay Rosen, Jonathan Bistline, Kavitha Venkatesan, Anupama Reddy, Dmitriy Sonkin, Manway Liu, Joseph Lehar, Joshua M. Korn, Dale A. Porter, Michael D. Jones, Javad Golji, Giordano Caponigro, Jordan E. Taylor, Caitlin M. Dunning, Amanda L. Creech, Allison C. Warren, James M. McFarland, Mahdi Zamanighomi, Audrey Kauffmann, Nicolas Stransky, Marcin Imielinski, Yosef E. Maruvka, Andrew D. Cherniack, Aviad Tsherniak, Francisca Vazquez, Jacob D. Jaffe, Andrew A. Lane, David M. Weinstock, Cory M. Johannessen, Michael P. Morrissey, Frank Stegmeier, Robert Schlegel, William C. Hahn, Gad Getz, Gordon B. Mills, Jesse S. Boehm, Todd R. Golub, Levi A. Garraway and William R. Sellers ()
Additional contact information
Mahmoud Ghandi: Broad Institute of Harvard and MIT
Franklin W. Huang: Broad Institute of Harvard and MIT
Judit Jané-Valbuena: Broad Institute of Harvard and MIT
Gregory V. Kryukov: Broad Institute of Harvard and MIT
Christopher C. Lo: Broad Institute of Harvard and MIT
E. Robert McDonald: Novartis Institutes for Biomedical Research
Jordi Barretina: Novartis Institutes for Biomedical Research
Ellen T. Gelfand: Broad Institute of Harvard and MIT
Craig M. Bielski: Broad Institute of Harvard and MIT
Haoxin Li: Broad Institute of Harvard and MIT
Kevin Hu: Broad Institute of Harvard and MIT
Alexander Y. Andreev-Drakhlin: Broad Institute of Harvard and MIT
Jaegil Kim: Broad Institute of Harvard and MIT
Julian M. Hess: Broad Institute of Harvard and MIT
Brian J. Haas: Broad Institute of Harvard and MIT
François Aguet: Broad Institute of Harvard and MIT
Barbara A. Weir: Broad Institute of Harvard and MIT
Michael V. Rothberg: Broad Institute of Harvard and MIT
Brenton R. Paolella: Broad Institute of Harvard and MIT
Michael S. Lawrence: Broad Institute of Harvard and MIT
Rehan Akbani: The University of Texas MD Anderson Cancer Center
Yiling Lu: The University of Texas MD Anderson Cancer Center
Hong L. Tiv: Belfer Center for Applied Cancer Science
Prafulla C. Gokhale: Belfer Center for Applied Cancer Science
Antoine de Weck: Novartis Institutes for Biomedical Research
Ali Amin Mansour: Broad Institute of Harvard and MIT
Coyin Oh: Broad Institute of Harvard and MIT
Juliann Shih: Broad Institute of Harvard and MIT
Kevin Hadi: New York Genome Center
Yanay Rosen: Broad Institute of Harvard and MIT
Jonathan Bistline: Broad Institute of Harvard and MIT
Kavitha Venkatesan: Novartis Institutes for Biomedical Research
Anupama Reddy: Novartis Institutes for Biomedical Research
Dmitriy Sonkin: Novartis Institutes for Biomedical Research
Manway Liu: Novartis Institutes for Biomedical Research
Joseph Lehar: Novartis Institutes for Biomedical Research
Joshua M. Korn: Novartis Institutes for Biomedical Research
Dale A. Porter: Novartis Institutes for Biomedical Research
Michael D. Jones: Novartis Institutes for Biomedical Research
Javad Golji: Novartis Institutes for Biomedical Research
Giordano Caponigro: Novartis Institutes for Biomedical Research
Jordan E. Taylor: Broad Institute of Harvard and MIT
Caitlin M. Dunning: Broad Institute of Harvard and MIT
Amanda L. Creech: Broad Institute of Harvard and MIT
Allison C. Warren: Broad Institute of Harvard and MIT
James M. McFarland: Broad Institute of Harvard and MIT
Mahdi Zamanighomi: Broad Institute of Harvard and MIT
Audrey Kauffmann: Novartis Institutes for Biomedical Research
Nicolas Stransky: Broad Institute of Harvard and MIT
Marcin Imielinski: New York Genome Center
Yosef E. Maruvka: Broad Institute of Harvard and MIT
Andrew D. Cherniack: Broad Institute of Harvard and MIT
Aviad Tsherniak: Broad Institute of Harvard and MIT
Francisca Vazquez: Broad Institute of Harvard and MIT
Jacob D. Jaffe: Broad Institute of Harvard and MIT
Andrew A. Lane: Dana-Farber Cancer Institute
David M. Weinstock: Dana-Farber Cancer Institute
Cory M. Johannessen: Broad Institute of Harvard and MIT
Michael P. Morrissey: Novartis Institutes for Biomedical Research
Frank Stegmeier: Novartis Institutes for Biomedical Research
Robert Schlegel: Novartis Institutes for Biomedical Research
William C. Hahn: Broad Institute of Harvard and MIT
Gad Getz: Broad Institute of Harvard and MIT
Gordon B. Mills: The University of Texas MD Anderson Cancer Center
Jesse S. Boehm: Broad Institute of Harvard and MIT
Todd R. Golub: Broad Institute of Harvard and MIT
Levi A. Garraway: Broad Institute of Harvard and MIT
William R. Sellers: Novartis Institutes for Biomedical Research

Nature, 2019, vol. 569, issue 7757, 503-508

Abstract: Abstract Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets, and small-molecule and biological therapeutics and to identify new marker-driven cancer dependencies. To improve our understanding of the molecular features that contribute to cancer phenotypes, including drug responses, here we have expanded the characterizations of cancer cell lines to include genetic, RNA splicing, DNA methylation, histone H3 modification, microRNA expression and reverse-phase protein array data for 1,072 cell lines from individuals of various lineages and ethnicities. Integration of these data with functional characterizations such as drug-sensitivity, short hairpin RNA knockdown and CRISPR–Cas9 knockout data reveals potential targets for cancer drugs and associated biomarkers. Together, this dataset and an accompanying public data portal provide a resource for the acceleration of cancer research using model cancer cell lines.

Date: 2019
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DOI: 10.1038/s41586-019-1186-3

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