Noncanonical Transcription and Splicing Shape the Colorectal Cancer Immunopeptidome in MSI and MSS Tumors

Sep 22, 2026

Colorectal cancer immunogenicity is shown to depend on distinct origins between microsatellite instability-high (MSI-H) and microsatellite-stable (MSS) tumors. Using HLA class I immunopeptidomics and matched RNA-seq from 26 primary CRC tumors, the study finds broadly comparable MHC-I peptide loads and tumor-specific antigen counts despite different mutational burdens. Proteogenomics identifies 266 tumor antigens with 70 aberrantly expressed tumor-specific antigens, predominantly from MSS tumors. Noncanonical transcription, intronic translation, UTR usage, and retroelement reactivation reshape the antigen landscape, supporting new vaccine and immunotherapy targets.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages20

Reading Time50 min

AccessFree to download

Research

Study rationale and approach

Antigen identification and comparative results

Noncanonical sources of antigens

Disease context and molecular pathways

Noncanonical Transcription and Splicing Shape the Colorectal Cancer Immunopeptidome in MSI and MSS Tumors Authors Mathieu Courcelles, Marie-Pierre Hardy, Chantal Durette, Joel Lanoix, Robin Minati, Jean-Philippe Laverdure, Krystel Vincent, Claude Perreault, and Pierre Thibault Correspondence [claude.perreault@umontreal.ca](claude.perreault@umontreal.ca) ; [pierre.thibault@umontreal.ca](pierre.thibault@umontreal.ca) In Brief This study reveals that colorectal cancer immunogenicity arises through distinct mechanisms: mutation-driven in microsatelliteinstable (MSI-H) tumors and transcription-and epigeneticdriven in microsatellite-stable (MSS) tumors. Despite their differing mutational burdens, MSI-H and MSS tumors display broadly comparable overall MHCI peptide loads and tumorspecific antigen counts per tumor, but they draw on qualitatively distinct antigen sources. In our cohort, most tumor-associated and noncanonical aberrantly expressed tumor-specific antigens arose from MSS tumors, reflecting extensive intron retention, aberrant splicing, and retroelement reactivation. These findings redefine the antigenic landscape of colorectal cancer and highlight new opportunities for vaccine and immunotherapy development targeting transcriptionally derived tumor antigens in both MSI-H and MSS disease. Graphical Abstract 2026, Mol Cell Proteomics 25(6), 101581 © 2026 THE AUTHORS. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology. This is an open access article under the CC BY license ([http://creativecommons.org/](http://creativecommons.org/)[ ](http://creativecommons.org/)[licenses/by/4.0/](licenses/by/4.0/)). [https://doi.org/10.1016/j.mcpro.2026.101581](https://doi.org/10.1016/j.mcpro.2026.101581) Highlights • Proteogenomics of 26 CRC tumors uncovered 266 CRC tumor antigens, including 70 aeTSAs. • MSI-H and MSS tumors showed comparable MHC-I loads and TSA counts. • MSS tumors contributed ~85% of identified TAAs/aeTSAs, reflecting diversity. • MSI-H and MSS antigen landscapes arise from distinct molecular mechanisms. RESEARCH | Noncanonical Transcription and Splicing Shape the Colorectal Cancer Immunopeptidome in MSI and MSS Tumors
Mathieu Courcelles 1 , Marie-Pierre Hardy1 , Chantal Durette1 , Joel Lanoix 1,
Robin Minati 1 ,2 , Jean-Philippe Laverdure 1 , Krystel Vincent 1 , Claude Perreault 1 ,3 ,* ,
and Pierre Thibault1 ,4 ,* | | | --- | --- | | Treatment with immune checkpoint inhibitors in colorectal cancer (CRC) has largely benefited patients with microsatellite instability–high (MSI-H) and not the larger proportion of patient with microsatellite-stable (MSS) tumors. This clinical dichotomy has fueled the view that high mutational burden is the dominant driver of tumor immunogenicity and that MSS CRC fails to respond because it is “antigen poor”. To directly test this premise and define the origins of presented tumor antigens, we integrated HLA class I immunopeptidomics and matched RNA-seq from 26 primary CRC tumors spanning MSI-Hand MSS subtypes. Using patient-specific canonical and cancer-specific proteogenomic databases, we identified 115,292 unique major histocompatibility complex (MHC) -associated peptides (MAPs) across 61 HLA alleles, with a mean of 9292 MAPs per tumor and no significant difference in MAP counts between MSI-H and MSS tumors. Intoto, we identified 266 tumor antigens, all coded by unmutated genomic sequences, comprising 70 aberrantly expressed tumor-specific antigens (aeTSAs) and 196 tumor-associated antigens (TAAs). In our cohort, MSS tumors presented more TAAs and a comparable number of aeTSAs per tumor relative to MSI-H tumors. In TCGACOAD stratified analyses (483 tumors), MSS tumors yielded more presentable aeTSAs and TAAs per patient than MSI-H tumors. Across both subtypes, aeTSAs arose predominantly from intronic translation, UTR usage, retroelement activation, and germline-like transcription, including recurrent

FAQs

What main question does the study address about MSI-H versus MSS colorectal cancer?

It tests whether MSI-H tumors are more immunogenic solely because of higher mutational burden and whether MSS tumors are truly “antigen poor,” by tracing the origins of presented tumor antigens.

How were tumor antigens identified in the research?

The study combined HLA class I immunopeptidomics with matched RNA-seq from 26 primary CRC tumors, using patient-specific canonical and cancer-specific proteogenomic databases.

What did the study find about antigen loads in MSI-H and MSS tumors?

MHC-I peptide loads and tumor-specific antigen counts were broadly comparable between MSI-H and MSS tumors, with MSS tumors contributing most of the identified tumor antigens in the cohort.

Which noncanonical mechanisms were implicated in generating aberrantly expressed tumor-specific antigens?

Aberrantly expressed tumor-specific antigens arose mainly from intronic translation, UTR usage, retroelement activation, and germline-like transcription, including recurrent sources from PIWIL1, L1TD1, and endogenous retroviral loci.

Sep 22, 2026

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