Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines

Tiannan Guo; Augustin Luna; Vinodh N Rajapakse; Ching Chiek Koh; Zhicheng Wu; Wei Liu; Yaoting Sun; Huanhuan Gao; Michael P Menden; Chao Xu; Laurence Calzone; Loredana Martignetti; Chiara Auwerx; Marija Buljan; Amir Banaei-Esfahani; Alessandro Ori; Murat Iskar; Ludovic Gillet; Ran Bi; Jiangnan Zhang; Huanhuan Zhang; Chenhuan Yu; Qing Zhong; Sudhir Varma; Uwe Schmitt; Peng Qiu; Qiushi Zhang; Yi Zhu; Peter J Wild; Mathew J Garnett; Peer Bork; Martin Beck; Kexin Liu; Julio Saez-Rodriguez; Fathi Elloumi; William C Reinhold; Chris Sander; Yves Pommier; Ruedi Aebersold

doi:10.1016/j.isci.2019.10.059

Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines

iScience. 2019 Nov 22:21:664-680. doi: 10.1016/j.isci.2019.10.059. Epub 2019 Oct 31.

Authors

Tiannan Guo¹, Augustin Luna², Vinodh N Rajapakse³, Ching Chiek Koh⁴, Zhicheng Wu⁵, Wei Liu⁶, Yaoting Sun⁵, Huanhuan Gao⁵, Michael P Menden⁷, Chao Xu⁸, Laurence Calzone⁹, Loredana Martignetti⁹, Chiara Auwerx⁴, Marija Buljan⁴, Amir Banaei-Esfahani¹⁰, Alessandro Ori¹¹, Murat Iskar¹², Ludovic Gillet⁴, Ran Bi¹³, Jiangnan Zhang¹³, Huanhuan Zhang¹⁴, Chenhuan Yu¹⁴, Qing Zhong¹⁵, Sudhir Varma¹⁶, Uwe Schmitt¹⁷, Peng Qiu¹⁸, Qiushi Zhang⁵, Yi Zhu¹⁹, Peter J Wild²⁰, Mathew J Garnett²¹, Peer Bork²², Martin Beck²³, Kexin Liu¹³, Julio Saez-Rodriguez²⁴, Fathi Elloumi³, William C Reinhold³, Chris Sander², Yves Pommier²⁵, Ruedi Aebersold²⁶

Affiliations

¹ Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. Electronic address: guotiannan@westlake.edu.cn.
² cBio Center, Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
³ Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
⁴ Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
⁵ Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
⁶ Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China.
⁷ RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany; Bioscience, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK.
⁸ Faculty of Software, Fujian Normal University, Fuzhou, China.
⁹ Institut Curie, PSL Research University, INSERM, U900, Mines Paris Tech 75005, Paris, France.
¹⁰ Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland.
¹¹ Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany.
¹² Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
¹³ Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China.
¹⁴ Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China.
¹⁵ Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; Cancer Data Science Group, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia.
¹⁶ HiThru Analytics, Laurel, MD 20707, USA.
¹⁷ Scientific IT Services, ETH Zurich, Zurich, Switzerland.
¹⁸ Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Dr., Atlanta, GA 30332, USA.
¹⁹ Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
²⁰ Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland.
²¹ Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
²² Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
²³ Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
²⁴ RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.
²⁵ Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: yves.pommier@nih.gov.
²⁶ Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland. Electronic address: aebersold@imsb.biol.ethz.ch.

Abstract

Here we describe a proteomic data resource for the NCI-60 cell lines generated by pressure cycling technology and SWATH mass spectrometry. We developed the DIA-expert software to curate and visualize the SWATH data, leading to reproducible detection of over 3,100 SwissProt proteotypic proteins and systematic quantification of pathway activities. Stoichiometric relationships of interacting proteins for DNA replication, repair, the chromatin remodeling NuRD complex, β-catenin, RNA metabolism, and prefoldins are more evident than that at the mRNA level. The data are available in CellMiner (discover.nci.nih.gov/cellminercdb and discover.nci.nih.gov/cellminer), allowing casual users to test hypotheses and perform integrative, cross-database analyses of multi-omic drug response correlations for over 20,000 drugs. We demonstrate the value of proteome data in predicting drug response for over 240 clinically relevant chemotherapeutic and targeted therapies. In summary, we present a novel proteome resource for the NCI-60, together with relevant software tools, and demonstrate the benefit of proteome analyses.

Keywords: Biological Sciences; Cancer Systems Biology; Proteomics; Systems Biology.

Grants and funding

102696/WT_/Wellcome Trust/United Kingdom