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 G. Love, Shan Li, Kym Lowes, Karl Johan Leuchowius, Helene Jousset, Janet Weinstock, Christopher Yau, John Mariadason, Zhiao Shi, Yuguan Ban, Xi Chen, Robert J.C. Coffey, Robbert J.C. Slebos & 4 others Antony W. Burgess, Daniel C. Liebler, Bing Zhang, Oliver M. Sieber

Research output: Contribution to journalArticle

10 Citations (Scopus)

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 5 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 with 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 with genomic and transcriptomic profiles. Our integrative proteogenomic analysis highlights the potential of proteome profiling to inform personalized cancer medicine.

Original languageEnglish (US)
Pages (from-to)1082-1095
Number of pages14
JournalGastroenterology
Volume153
Issue number4
DOIs
StatePublished - Oct 1 2017

Fingerprint

Proteome
Proteomics
Colorectal Neoplasms
Cell Line
Pharmaceutical Preparations
Neoplasms
Precision Medicine
DNA Mismatch Repair
Drug Combinations
Tumor Cell Line
Proteins
Phenotype
DNA
Growth

Keywords

  • Cell Lines
  • Colorectal Cancer
  • Drug Sensitivity
  • Proteomics

ASJC Scopus subject areas

  • Hepatology
  • Gastroenterology

Cite this

Wang, J., Mouradov, D., Wang, X., Jorissen, R. N., Chambers, M. C., Zimmerman, L. J., ... Sieber, O. M. (2017). Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity. Gastroenterology, 153(4), 1082-1095. https://doi.org/10.1053/j.gastro.2017.06.008

Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity. / Wang, Jing; Mouradov, Dmitri; Wang, Xiaojing; Jorissen, Robert N.; Chambers, Matthew C.; Zimmerman, Lisa J.; Vasaikar, Suhas; Love, Christopher G.; Li, Shan; Lowes, Kym; Leuchowius, Karl Johan; Jousset, Helene; Weinstock, Janet; Yau, Christopher; Mariadason, John; Shi, Zhiao; Ban, Yuguan; Chen, Xi; Coffey, Robert J.C.; Slebos, Robbert J.C.; Burgess, Antony W.; Liebler, Daniel C.; Zhang, Bing; Sieber, Oliver M.

In: Gastroenterology, Vol. 153, No. 4, 01.10.2017, p. 1082-1095.

Research output: Contribution to journalArticle

Wang, J, Mouradov, D, Wang, X, Jorissen, RN, Chambers, MC, Zimmerman, LJ, Vasaikar, S, Love, CG, Li, S, Lowes, K, Leuchowius, KJ, Jousset, H, Weinstock, J, Yau, C, Mariadason, J, Shi, Z, Ban, Y, Chen, X, Coffey, RJC, Slebos, RJC, Burgess, AW, Liebler, DC, Zhang, B & Sieber, OM 2017, 'Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity', Gastroenterology, vol. 153, no. 4, pp. 1082-1095. https://doi.org/10.1053/j.gastro.2017.06.008
Wang, Jing ; Mouradov, Dmitri ; Wang, Xiaojing ; Jorissen, Robert N. ; Chambers, Matthew C. ; Zimmerman, Lisa J. ; Vasaikar, Suhas ; Love, Christopher G. ; Li, Shan ; Lowes, Kym ; Leuchowius, Karl Johan ; Jousset, Helene ; Weinstock, Janet ; Yau, Christopher ; Mariadason, John ; Shi, Zhiao ; Ban, Yuguan ; Chen, Xi ; Coffey, Robert J.C. ; Slebos, Robbert J.C. ; Burgess, Antony W. ; Liebler, Daniel C. ; Zhang, Bing ; Sieber, Oliver M. / Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity. In: Gastroenterology. 2017 ; Vol. 153, No. 4. pp. 1082-1095.
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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 5 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 with 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 with genomic and transcriptomic profiles. Our integrative proteogenomic analysis highlights the potential of proteome profiling to inform personalized cancer medicine.",
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T1 - Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity

AU - Wang, Jing

AU - Mouradov, Dmitri

AU - Wang, Xiaojing

AU - Jorissen, Robert N.

AU - Chambers, Matthew C.

AU - Zimmerman, Lisa J.

AU - Vasaikar, Suhas

AU - Love, Christopher G.

AU - Li, Shan

AU - Lowes, Kym

AU - Leuchowius, Karl Johan

AU - Jousset, Helene

AU - Weinstock, Janet

AU - Yau, Christopher

AU - Mariadason, John

AU - Shi, Zhiao

AU - Ban, Yuguan

AU - Chen, Xi

AU - Coffey, Robert J.C.

AU - Slebos, Robbert J.C.

AU - Burgess, Antony W.

AU - Liebler, Daniel C.

AU - Zhang, Bing

AU - Sieber, Oliver M.

PY - 2017/10/1

Y1 - 2017/10/1

N2 - 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 5 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 with 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 with genomic and transcriptomic profiles. Our integrative proteogenomic analysis highlights the potential of proteome profiling to inform personalized cancer medicine.

AB - 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 5 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 with 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 with genomic and transcriptomic profiles. Our integrative proteogenomic analysis highlights the potential of proteome profiling to inform personalized cancer medicine.

KW - Cell Lines

KW - Colorectal Cancer

KW - Drug Sensitivity

KW - Proteomics

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