Journal Article

Next-generation characterization of the Cancer Cell Line Encyclopedia

Taylor, Jordan E., Kryukov, Gregory V., Hu, Kevin, Jones, Michael D., Dunning, Caitlin M., Stegmeier, Frank, Paolella, Brenton R., Zamanighomi, Mahdi, Vazquez, Francisca, Bistline, Jonathan, Imielinski, Marcin, Mansour, Ali Amin, Mills, Gordon B., Ghandi, Mahmoud, Weir, Barbara A., Morrissey, Michael P., Gelfand, Ellen T., Lu, Yiling, Creech, Amanda L., Jaffe, Jacob D., Aguet, François, Huang, Franklin W., Korn, Joshua M., Barretina, Jordi, Hahn, William C., McDonald, E. Robert, Kim, Jaegil, Maruvka, Yosef E., Kauffmann, Audrey, Garraway, Levi A., Li, Haoxin, Venkatesan, Kavitha, Hess, Julian M., de Weck, Antoine, Bielski, Craig M., Lehar, Joseph, Golub, Todd R., Sellers, William R., Gokhale, Prafulla C., Tiv, Hong L., Haas, Brian J., Liu, Manway, Caponigro, Giordano, Rosen, Yanay, Andreev-Drakhlin, Alexander Y., McFarland, James M., Akbani, Rehan, Golji, Javad, Lawrence, Michael S., Weinstock, David M., Johannessen, Cory M., Lane, Andrew A., Porter, Dale A., Warren, Allison C., Jané-Valbuena, Judit, Rothberg, Michael V., Oh, Coyin, Cherniack, Andrew D., Boehm, Jesse S., Stransky, Nicolas, Hadi, Kevin, Ts

2019

Overview

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. The original Cancer Cell Line Encyclopedia (CCLE) is expanded with deeper characterization of over 1,000 cell lines, including genomic, transcriptomic, and proteomic data, and integration with drug-sensitivity and gene-dependency data.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 38/23 / 38/39 / 38/79 / 38/91 / 631/67/69 / 631/67/70 / Acceleration / Antineoplastic Agents - pharmacology / Bioinformatics / Biological markers / Biomarkers / Biomarkers, Tumor / Biotechnology / Cancer / Cancer research / Cell culture / Cell Line, Tumor / CRISPR / Deoxyribonucleic acid / DNA / DNA Methylation / Drug Resistance, Neoplasm / Encyclopedias / Ethnic Groups - genetics / Gene Editing / Gene expression / Generalized linear models / Genes / Genetic diversity / Genetic research / Genetic variance / Genomes / Genomics / Histone H3 / Histones - metabolism / Humanities and Social Sciences / Humans / Medical research / Methods / Methylation / MicroRNA / MicroRNAs / MicroRNAs - genetics / miRNA / Molecular Targeted Therapy / multidisciplinary / Mutation / Neoplasms - genetics / Neoplasms - metabolism / Neoplasms - pathology / Phenotypes / Protein Array Analysis / Protein arrays / Proteins / Ribonucleic acid / RNA / RNA Splicing / Science / Science (multidisciplinary) / Splicing / Technology application / Therapeutics / Tumor cell lines / Web portals