Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

Theodoros I. Roumeliotis, Steven P. Williams, Emanuel Gonçalves, Clara Alsinet, Martin Del Castillo Velasco-Herrera, Nanne Aben, Fatemeh Zamanzad Ghavidel, Magali Michaut, Michael Schubert, Stacey Price, Lodewyk Wessels, More Authors

Research output: Contribution to journalArticleScientificpeer-review

42 Citations (Scopus)
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Abstract

Assessing the impact of genomic alterations on protein networks is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labeling to characterize the proteomic landscapes of 50 colorectal cancer cell lines and to decipher the functional consequences of somatic genomic variants. The robust quantification of over 9,000 proteins and 11,000 phosphopeptides on average enabled the de novo construction of a functional protein correlation network, which ultimately exposed the collateral effects of mutations on protein complexes. CRISPR-cas9 deletion of key chromatin modifiers confirmed that the consequences of genomic alterations can propagate through protein interactions in a transcript-independent manner. Lastly, we leveraged the quantified proteome to perform unsupervised classification of the cell lines and to build predictive models of drug response in colorectal cancer. Overall, we provide a deep integrative view of the functional network and the molecular structure underlying the heterogeneity of colorectal cancer cells.

Original languageEnglish
Pages (from-to)2201-2214
Number of pages14
JournalCell Reports
Volume20
Issue number9
DOIs
Publication statusPublished - 2017

Keywords

  • cell lines
  • colorectal cancer
  • CRISPR/cas9
  • drug response
  • mutations
  • networks
  • phosphorylation
  • protein complexes
  • proteomics
  • TMT

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