Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines.

Biological Sciences Cancer Systems Biology Proteomics Systems Biology

Journal

iScience
ISSN: 2589-0042
Titre abrégé: iScience
Pays: United States
ID NLM: 101724038

Informations de publication

Date de publication:
22 Nov 2019
Historique:
received: 11 10 2019
revised: 21 10 2019
accepted: 28 10 2019
pubmed: 17 11 2019
medline: 17 11 2019
entrez: 17 11 2019
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1016/j.isci.2019.10.059 PMID: 31733513 PMC: PMC6889472
pubmed: 31733513
pii: S2589-0042(19)30440-7
doi: 10.1016/j.isci.2019.10.059
pmc: PMC6889472
pii:
doi:

Types de publication

Journal Article

Langues

eng

Pagination

664-680

Subventions

Organisme : Wellcome Trust
ID : 102696
Pays : United Kingdom

Informations de copyright

Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved.

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Auteurs

Tiannan Guo (T)

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.

Augustin Luna (A)

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.

Vinodh N Rajapakse (VN)

Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

Ching Chiek Koh (CC)

Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.

Zhicheng Wu (Z)

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.

Wei Liu (W)

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.

Yaoting Sun (Y)

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.

Huanhuan Gao (H)

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.

Michael P Menden (MP)

RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany; Bioscience, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK.

Chao Xu (C)

Faculty of Software, Fujian Normal University, Fuzhou, China.

Laurence Calzone (L)

Institut Curie, PSL Research University, INSERM, U900, Mines Paris Tech 75005, Paris, France.

Loredana Martignetti (L)

Institut Curie, PSL Research University, INSERM, U900, Mines Paris Tech 75005, Paris, France.

Chiara Auwerx (C)

Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.

Marija Buljan (M)

Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.

Amir Banaei-Esfahani (A)

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.

Alessandro Ori (A)

Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany.

Murat Iskar (M)

Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

Ludovic Gillet (L)

Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.

Ran Bi (R)

Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China.

Jiangnan Zhang (J)

Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China.

Huanhuan Zhang (H)

Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China.

Chenhuan Yu (C)

Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China.

Qing Zhong (Q)

Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; Cancer Data Science Group, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia.

Sudhir Varma (S)

HiThru Analytics, Laurel, MD 20707, USA.

Uwe Schmitt (U)

Scientific IT Services, ETH Zurich, Zurich, Switzerland.

Peng Qiu (P)

Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Dr., Atlanta, GA 30332, USA.

Qiushi Zhang (Q)

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.

Yi Zhu (Y)

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.

Peter J Wild (PJ)

Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland.

Mathew J Garnett (MJ)

Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

Peer Bork (P)

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.

Martin Beck (M)

Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

Kexin Liu (K)

Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China.

Julio Saez-Rodriguez (J)

RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.

Fathi Elloumi (F)

Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

William C Reinhold (WC)

Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

Chris Sander (C)

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.

Yves Pommier (Y)

Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: yves.pommier@nih.gov.

Ruedi Aebersold (R)

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.

Classifications MeSH