Dataset Information

Integrative proteogenomic characterization of colorectal cancer cell lines and primary tumors

ABSTRACT: Solid tumors are complex organs comprising neoplastic cells and stroma, yet cancer cell lines remain widely used to study tumor biology, biomarkers and experimental therapy. Here, we performed a fully integrative analysis of global proteomic data comparing human colorectal cancer (CRC) cell lines to primary tumors and normal tissues. We found a significant, systematic difference between cell line and tumor proteomes, with a major contribution from tumor stroma proteomes. Nevertheless, cell lines overall mirrored the proteomic differences observed between tumors and normal tissues, in particular for genetic information processing and metabolic pathways, indicating that cell lines provide a system for the study of the intrinsic molecular programs in cancer cells. Intersection of cell line data with tumor data provided insights into tumor cell specific proteome alterations driven by genomic alterations. Our integration of cell line proteogenomic data with drug sensitivity data highlights the potential of proteomic data in predicting therapeutic response. We identified representative cell lines for the proteomic subtypes of primary tumors, and linked these to drug sensitivity data to identify subtype-specific drug candidates.

OTHER RELATED OMICS DATASETS IN: PXD013455PRJNA356046PRJNA356065

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Bing Zhang

PROVIDER: MSV000080374 | MassIVE | Thu Dec 01 19:06:00 GMT 2016

SECONDARY ACCESSION(S): PXD005483

REPOSITORIES: MassIVE

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Publications

Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity.

Wang Jing J Mouradov Dmitri D Wang Xiaojing X Jorissen Robert N RN Chambers Matthew C MC Zimmerman Lisa J LJ Vasaikar Suhas S Love Christopher G CG Li Shan S Lowes Kym K Leuchowius Karl-Johan KJ Jousset Helene H Weinstock Janet J Yau Christopher C Mariadason John J Shi Zhiao Z Ban Yuguang Y Chen Xi X Coffey Robert J C RJC Slebos Robbert J C RJC Burgess Antony W AW Liebler Daniel C DC Zhang Bing B Sieber Oliver M OM

Gastroenterology 20170616 4

<h4>Background and aims</h4>Proteomics holds promise for individualizing cancer treatment. We analyzed to what extent the proteomic landscape of human colorectal cancer (CRC) is maintained in established CRC cell lines and the utility of proteomics for predicting therapeutic responses.<h4>Methods</h4>Proteomic and transcriptomic analyses were performed on 44 CRC cell lines, compared against primary CRCs (n=95) and normal tissues (n=60), and integrated with genomic and drug sensitivity data.<h4>R ...[more]

PMID: 28625833

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