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Next-generation characterization of the Cancer Cell Line Encyclopedia

Author

Listed:
  • Mahmoud Ghandi

    (Broad Institute of Harvard and MIT)

  • Franklin W. Huang

    (Broad Institute of Harvard and MIT
    Dana-Farber Cancer Institute
    University of California San Francisco)

  • Judit Jané-Valbuena

    (Broad Institute of Harvard and MIT
    Dana-Farber Cancer Institute)

  • 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
    Dana-Farber Cancer Institute)

  • 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
    Massachusetts General Hospital Cancer Center
    Massachusetts General Hospital
    Harvard Medical School)

  • 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
    Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medicine)

  • 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
    National Cancer Institute)

  • 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
    Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medicine)

  • Yosef E. Maruvka

    (Broad Institute of Harvard and MIT
    Massachusetts General Hospital Cancer Center)

  • Andrew D. Cherniack

    (Broad Institute of Harvard and MIT
    Dana-Farber Cancer Institute)

  • 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
    Dana-Farber Cancer Institute)

  • Gad Getz

    (Broad Institute of Harvard and MIT
    Massachusetts General Hospital Cancer Center
    Massachusetts General Hospital
    Harvard Medical School)

  • 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
    Dana-Farber Cancer Institute
    Howard Hughes Medical Institute)

  • Levi A. Garraway

    (Broad Institute of Harvard and MIT
    Dana-Farber Cancer Institute)

  • William R. Sellers

    (Novartis Institutes for Biomedical Research
    Broad Institute of Harvard and MIT)

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.

Suggested Citation

  • 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 & , 2019. "Next-generation characterization of the Cancer Cell Line Encyclopedia," Nature, Nature, vol. 569(7757), pages 503-508, May.
    • Handle: RePEc:nat:nature:v:569:y:2019:i:7757:d:10.1038_s41586-019-1186-3
    DOI: 10.1038/s41586-019-1186-3
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