The shared frameshift mutation landscape of microsatellite-unstable cancers suggests immunoediting during tumor evolution

The immune system can recognize and attack cancer cells, especially those with a high load of mutation-induced neoantigens. Such neoantigens are abundant in DNA mismatch repair (MMR)-deficient, microsatellite-unstable (MSI) cancers. MMR deficiency leads to insertion/deletion (indel) mutations at coding microsatellites (cMS) and to neoantigen-inducing translational frameshifts. Here, we develop a tool to quantify frameshift mutations in MSI colorectal and endometrial cancer. Our results show that frameshift mutation frequency is negatively correlated to the predicted immunogenicity of the resulting peptides, suggesting counterselection of cell clones with highly immunogenic frameshift peptides. This correlation is absent in tumors with Beta-2-microglobulin mutations, and HLA-A*02:01 status is related to cMS mutation patterns. Importantly, certain outlier mutations are common in MSI cancers despite being related to frameshift peptides with functionally confirmed immunogenicity, suggesting a possible driver role during MSI tumor evolution. Neoantigens resulting from shared mutations represent promising vaccine candidates for prevention of MSI cancers.


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Life sciences study design
All studies must disclose on these points even when the disclosure is negative. Sample sizes were selected to obtain a comprehensive overview of frameshift mutation patterns in MSI colorectal and endometrial cancer (n>25). In order to detect expected differences of cMS mutation patterns depending on B2M mutation status and/or HLA-A*02:01 status among MSI colorectal cancers (expected effect size>10%) with a power of 80%, cohort sizes were selected to obtain a minimum group size for B2M-mutant tumors (expected B2M mutation frequency: 30%) of n=30 tumors and HLA-A*02:01-positive tumors (expected HLA-A*02:01 population frequency 50%) of n=30.
cMS marker/tumor combinations not producing detectable peaks above threshold in fragment length analysis were excluded from final analysis. cMS marker/tumor combinations not producing reproducible results in replication experiments were also excluded.
All analyses were replicated twice, and in quadruplicate for reference normal DNA. Only samples with successful replication were considered in the data set.
This is a non-interventional, exploratory study. Randomization Experimentators were blinded for MSI status upon pseudonymization during performing wet lab procedures. Fragment length analyses were performed and processed for all tumors in identical and automated manner. MSI status was added as annotation in the results table.