Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities
Open accessAbstract
We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired tumor and normal adjacent tissues produced a catalog of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers, drug targets, and cancer/testis antigens. Proteogenomic integration not only prioritized genomically inferred targets, such as copy-number drivers and mutation-derived neoantigens, but also yielded novel findings. Phosphoproteomics data associated Rb phosphorylation with increased proliferation and decreased apoptosis in colon cancer, which explains why this classical tumor suppressor is amplified in colon tumors and suggests a rationale for targeting Rb phosphorylation in colon cancer. Proteomics identified an association between decreased CD8 T cell infiltration and increased glycolysis in microsatellite instability-high (MSI-H) tumors, suggesting glycolysis as a potential target to overcome the resistance of MSI-H tumors to immune checkpoint blockade. Proteogenomics presents new avenues for biological discoveries and therapeutic development.
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CPTAC and ICPC collaborators have comprehensively characterized 13 cancer types at the proteogenomics level, with all datasets publicly accessible.
“Collectively, CPTAC and ICPC collaborators have comprehensively characterized 13 cancer types at the proteogenomics level, with all datasets publicly accessible109–117.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [112]
The flagship efforts of the Cancer Proteomics Consortium, CPTAC, have brought targeted proteomics and proteogenomics into regular use and produced major studies on ovarian, breast, and colorectal cancer.
“The flagship efforts of the Cancer Proteomics Consortium, CPTAC, have brought targeted proteomics and proteogenomics into regular use and produced major studies on ovarian ( 10 ), breast ( 11 ), and colorectal cancer ( 12 ).”
From The Human Proteoform Project: Defining the human proteome (2021) · cites this paper as [12]
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The Human Proteoform Project: Defining the human proteome
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Cancer proteogenomics: current impact and future prospects
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Self-citationA high-stringency blueprint of the human proteome
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“RB1 phosphorylation has been implicated in CRC progression, but that analysis did not stratify by KRAS alleles, a factor that our previous work shows can drive distinct downstream signaling (Poulin et al., 2019; Vasaikar et al., 2019).”
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- Authors
- Vasaikar, S., Huang, C., Wang, X., Petyuk, V. A., Savage, S. R., Wen, B., Dou, Y., Zhang, Y., Shi, Z., Arshad, O. A., Gritsenko, M. A., Zimmerman, L. J., McDermott, J. E., Clauss, T. R., Moore, R. J., Zhao, R., Monroe, M. E., Wang, Y.-T., Chambers, M. C., Slebos, R. J. C., Lau, K. S., Mo, Q., Ding, L., Ellis, M., Thiagarajan, M., Kinsinger, C. R., Rodriguez, H., Smith, R. D., Rodland, K. D., Liebler, D. C., Liu, T., Zhang, B., Pandey, A., Paulovich, A., Hoofnagle, A., Mani, D. R., Chan, D. W., Ransohoff, D. F., Fenyo, D., Tabb, D. L., Levine, D. A., Boja, E. S., Kuhn, E., White, F. M., Whiteley, G. A., Zhu, H., Zhang, H., Shih, I.-M., Bavarva, J., Whiteaker, J., Ketchum, K. A., Clauser, K. R., Ruggles, K., Elburn, K., Hannick, L., Watson, M., Oberti, M., Mesri, M., Sanders, M. E., Borucki, M., Gillette, M. A., Snyder, M., Edwards, N. J., Vatanian, N., Rudnick, P. A., McGarvey, P. B., Mertins, P., Townsend, R. R., Thangudu, R. R., Rivers, R. C., Payne, S. H., Davies, S. R., Cai, S., Stein, S. E., Carr, S. A., Skates, S. J., Madhavan, S., Hiltke, T., Chen, X., Zhao, Y., Wang, Y., & Zhang, Z.
- Affiliations
- Baylor College of Medicine (US)
- Pacific Northwest National Laboratory (US)
- Vanderbilt University Medical Center (US)
- Vanderbilt University (US)
- Washington University in St. Louis (US)
- Frederick National Laboratory for Cancer Research (US)
- National Cancer Institute (US)
- Corresponding author
- Rodland, Karin D.
- Liebler, Daniel C.
- Liu, Tao
- Zhang, Bing
- ORCID
- Vasaikar, Suhas
- Huang, Chen
- Wang, Xiaojing
- Petyuk, Vladislav A.
- Savage, Sara R.
- Wen, Bo
- Dou, Yongchao
- Zhang, Yun
- Shi, Zhiao
- Gritsenko, Marina A.
- Zimmerman, Lisa J.
- McDermott, Jason E.
- Moore, Ronald J.
- Zhao, Rui
- Monroe, Matthew E.
- Chambers, Matthew C.
- Slebos, Robbert J.C.
- Lau, Ken S.
- Mo, Qianxing
- Ding, Li
- Ellis, Matthew
- Thiagarajan, Mathangi
- Kinsinger, Christopher R.
- Rodriguez, Henry
- Smith, Richard D.
- Rodland, Karin D.
- Liebler, Daniel C.
- Liu, Tao
- Zhang, Bing
- Pandey, Akhilesh
- Paulovich, Amanda
- Hoofnagle, Andrew
- Mani, D.R.
- Chan, Daniel W.
- Ransohoff, David F.
- Tabb, David L.
- Levine, Douglas A.
- Boja, Emily S.
- Kuhn, Eric
- White, Forest M.
- Zhu, Heng
- Zhang, Hui
- Shih, Ie-Ming
- Whiteaker, Jeffrey
- Ketchum, Karen A.
- Clauser, Karl R.
- Ruggles, Kelly
- Hannick, Linda
- Watson, Mark
- Oberti, Mauricio
- Mesri, Mehdi
- Sanders, Melinda E.
- Gillette, Michael A.
- Snyder, Michael
- Edwards, Nathan J.
- Rudnick, Paul A.
- McGarvey, Peter B.
- Mertins, Philip
- Townsend, R. Reid
- Thangudu, Ratna R.
- Rivers, Robert C.
- Davies, Sherri R.
- Cai, Shuang
- Stein, Stephen E.
- Carr, Steven A.
- Skates, Steven J.
- Madhavan, Subha
- Hiltke, Tara
- Chen, Xian
- Zhao, Yingming
- Wang, Yue
- Zhang, Zhen
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2019-05
- Volume
- 177
- Issue
- 4
- Pages
- 1035-1049.e19
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC6768830
- OpenAlex
- W2940627982
- Cited by
- 799
- References
- 81
- Citations by year
- 2026: 85 · 2025: 102 · 2024: 103 · 2023: 123 · 2022: 137 · 2021: 128 · 2020: 91 · 2019: 29
- FWCI
- 39.43
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (acceptedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- Robert and Janice McNair Foundation
- National Cancer Institute
- Cancer Prevention and Research Institute of Texas
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
- Keywords
- colon cancer, proteogenomics, phosphoproteomics, tumor-associated proteins, phosphosites, biomarkers, therapeutic target, cancer-testis antigens, neoantigens, retinoblastoma protein phosphorylation, CD8+ T cell infiltration, glycolysis, microsatellite instability-high, immune checkpoint inhibitor resistance
- MeSH terms
- Proteogenomics, Colonic Neoplasms, Glycolysis, Humans, Mutation, Phosphorylation, Prospective Studies, Biomarkers, Tumor, Retinoblastoma Protein, Apoptosis, CD8-Positive T-Lymphocytes, Genomics, Proteomics, Cell Proliferation, Microsatellite Instability
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