Recent studies have shown that cancers arise due to the positive selection of driver somatic events in tumor DNA, with negative selection playing only a minor role. However, these investigations were concerned with alterations at non-repetitive sequences and did not take into account mutations in repetitive sequences that have very high pathophysiological relevance in the tumors displaying Microsatellite Instability (MSI) due to mismatch repair deficiency investigated in the present study.
We performed whole exome sequencing of 47 MSI CRC and confirmed results in an independent cohort of 53 MSI CRC. We used probabilistic model of mutational events within microsatellites, while adapting preexisting models to analyze non-repetitive DNA sequences. Negatively selected coding alterations in MSI CRC were investigated for their functional and clinical impact in CRC cell lines and in a third cohort of 164 MSI CRC patients.
Both positive and negative selection of somatic mutations in DNA repeats was observed, leading us to identify the expected driver genes associated with the MSI-driven tumorigenic process. Several Coding negatively selected, MSI-related mutational events (n = 5) were demonstrated to have deleterious effects on tumor cells. In the tumors in which deleterious MSI mutations are observed despite the negative selection, they were associated with worse survival in MSI CRC patients (hazard ratio [HR], 3; 95% confidence interval, 1.1-7.9; p = 0.03), suggesting their anticancer impact should be offset by other as yet unknown oncogenic processes that contribute to poor prognosis.
The present results shed new light on the main driver somatic mutations acting in MSI-driven tumorigenesis, suggesting that genomic instability in MSI CRC plays a dual role in achieving tumor cell transformation.
Clinical trial identification
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This work was supported by grants from the ‘Institut National du Cancer’ (INCa, PRTK MICROSPLICOTHER, SIRIC, and HTE CoLi, to AD), the Fondation ARC (to AC) and the Canceropole Ile de France (to AC). AD group has the label ‘La Ligue Contre le Cancer’. This work is part of the Cartes d’Identité des Tumeurs (CIT) research program, funded and developed by the Ligue Nationale Contre le Cancer.
All authors have declared no conflicts of interest.