Immunopeptidomic analyses of colorectal cancers with and without microsatellite instability.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35367648", "kind": "science-record", "revision": 4, "content_hash": "sha256:24721fa2cbbd1b963a527520824551f410126772c0b2fb3d784ba62d3c9200da", "created_at": "2026-11-01T18:14:11Z", "updated_at": "2026-11-01T22:06:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Immunopeptidomic analyses of colorectal cancers with and without microsatellite instability.", "doi": "10.1016/j.mcpro.2022.100228", "pmid": "35367648", "authors": ["Jenna Cleyle", "Marie-Pierre Hardy", "Robin Minati", "Mathieu Courcelles", "Chantal Durette", "Joel Lanoix", "Jean-Philippe Laverdure", "Krystel Vincent", "Claude Perreault", "Pierre Thibault"], "journal": "Molecular & cellular proteomics : MCP", "year": 2022, "abstract": "Colorectal cancer is the second leading cause of cancer death worldwide, and the incidence of this disease is expected to increase as global socioeconomic changes occur. Immune checkpoint inhibition therapy is effective in treating a minority of colorectal cancer tumors; however, microsatellite stable tumors do not respond well to this treatment. Emerging cancer immunotherapeutic strategies aim to activate a cytotoxic T cell response against tumor-specific antigens, presented exclusively at the cell surface of cancer cells. These antigens are rare and are most effectively identified with a mass spectrometry-based approach, which allows the direct sampling and sequencing of these peptides. Although the few tumor-specific antigens identified to date are derived from coding regions of the genome, recent findings indicate that a large proportion of tumor-specific antigens originate from allegedly noncoding regions. Here, we employed a novel proteogenomic approach to identify tumor antigens in a collection of colorectal cancer-derived cell lines and biopsy samples consisting of matched tumor and normal adjacent tissue. The generation of personalized cancer databases paired with mass spectrometry analyses permitted the identification of more than 30,000 unique MHC I-associated peptides. We identified 19 tumor-specific antigens in both microsatellite stable and unstable tumors, over two-thirds of which were derived from noncoding regions. Many of these peptides were derived from source genes known to be involved in colorectal cancer progression, suggesting that antigens from these genes could have therapeutic potential in a wide range of tumors. These findings could benefit the development of T cell-based vaccines, in which T cells are primed against these antigens to target and eradicate tumors. Such a vaccine could be used in tandem with existing immune checkpoint inhibition therapies, to bridge the gap in treatment efficacy across subtypes of colorectal cancer with varying prognoses. Data are available via ProteomeXchange with identifier PXD028309.", "claims": [{"id": "claim-method", "statement": "All instances of p-values are determined using two-sample t test, except in the determination of significance for immunogenicity scores, in which case the Mann–Whitney test was used as the data did not have a normal distribution, as determined by the Shapiro test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35367648", "locator": "sections[35] \"Experimental Design and Statistical Rationale\" paragraph 2", "quote": "All instances of p-values are determined using two-sample t test, except in the determination of significance for immunogenicity scores, in which case the Mann–Whitney test was used as the data did not have a normal distribution, as determined by the Shapiro test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (84) via the PRIDE partner repository (85) with the dataset identifier PXD028309 and 10.6019/PXD028309.\nThe transcriptomic data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus (86) and are accessible through GEO Series accession number GSE195985 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE195985).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35367648", "locator": "sections[44] \"Data Availability\" paragraphs 1-3", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (84) via the PRIDE partner repository (85) with the dataset identifier PXD028309 and 10.6019/PXD028309.\nThe transcriptomic data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus (86) and are accessible through GEO Series accession number GSE195985 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE195985)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The proteogenomic analysis identified 19 tumor-specific antigens in microsatellite-stable and microsatellite-unstable colorectal cancers, with over two-thirds derived from noncoding regions.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35367648", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We identified 19 tumor-specific antigens in both microsatellite stable and unstable tumors, over two-thirds of which were derived from noncoding regions."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The proteogenomic analysis identified 19 tumor-specific antigens in microsatellite-stable and microsatellite-unstable colorectal cancers, with over two-thirds derived from noncoding regions.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:35367648"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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