Colorectal cancer cell line proteomes are representative of primary tumors and predict drug sensitivity

Jing Wang, Dmitri Mouradov, Xiaojing Wang, Robert N. Jorissen, Matthew C. Chambers, Lisa J. Zimmerman, Suhas Vasaikar, Christopher Love, Shan Li, Kym Lowes, Karl-Johan Leuchowius, Helene Jousset, Janet Weinstock, Christopher Yau, John Mariadason, Zhiao Shi, Yugan Ban, Xi Chen, Robert J. C. Coffey, Robbert J. C. SlebosAntony W. Burgess, Daniel C. Liebler, Bing Zhang, Oliver M. Sieber

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Abstract

Background and Aims

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.

Methods

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.

Results

Cell lines mirrored the proteomic aberrations of primary tumors, in particular for intrinsic programs. Tumor relationships of protein expression with DNA copy number aberrations and signatures of post-transcriptional regulation were recapitulated in cell lines. The five proteomic subtypes previously identified in tumors were represented among cell lines. Nonetheless, systematic differences between cell line and tumor proteomes were apparent, attributable to stroma, extrinsic signaling and growth conditions. Contribution of tumor stroma obscured signatures of DNA mismatch repair identified in cell lines with a hypermutation phenotype. Global proteomic data showed improved utility for predicting both known drug-target relationships and overall drug sensitivity as compared to genomic or transcriptomic measurements. Inhibition of targetable proteins associated with drug responses further identified corresponding synergistic or antagonistic drug combinations. Our data provide evidence for CRC proteomic subtype-specific drug responses.

Conclusions

Proteomes of established CRC cell line are representative of primary tumors. Proteomic data tend to exhibit improved prediction of drug sensitivity as compared to genomic and transcriptomic profiles. Our integrative proteogenomic analysis highlights the potential of proteome profiling to inform personalized cancer medicine.
Original languageEnglish
JournalGastroenterology
Early online date16 Jun 2017
DOIs
Publication statusE-pub ahead of print - 16 Jun 2017

Keywords

  • colorectal cancer
  • cell lines
  • proteomics
  • drug sensitivity

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