Jonchere V1,2, Marisa L1,2, Greene M1, Virouleau A1,3,4, Buhard O1, Bertrand R1, Svrcek M1,5, Cervera P1,5, Goloudina A1,6, Guillerm E1,7, Coulet F1,7, Landman S1, Ratovomanana T1, Job S2, Ayadi M2, Elarouci N2, Armenoult L2, Merabtene F1,8, Dumont S1,8, Parc Y1,9, Lefèvre JH1,9, André T1,10, Fléjou JF1,5, Guilloux A3,4, Collura A1, de Reyniès A2, Duval A1.
BACKGROUND & AIMS:
Recent studies have shown that cancers arise as a result of the positive selection of driver somatic events in tumor DNA, with negative selection playing only a minor role, if any. However, these investigations were concerned with alterations at nonrepetitive sequences and did not take into account mutations in repetitive sequences that have very high pathophysiological relevance in the tumors showing microsatellite instability (MSI) resulting from mismatch repair deficiency investigated in the present study.
We performed whole-exome sequencing of 47 MSI colorectal cancers (CRCs) and confirmed results in an independent cohort of 53 MSI CRCs. We used a probabilistic model of mutational events within microsatellites, while adapting pre-existing models to analyze nonrepetitive DNA sequences. Negatively selected coding alterations in MSI CRCs 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 true driver genes associated with the MSI-driven tumorigenic process. Several coding negatively selected MSI-related mutational events (n = 5) were shown to have deleterious effects on tumor cells. In the tumors in which deleterious MSI mutations were observed despite the negative selection, they were associated with worse survival in MSI CRC patients (hazard ratio, 3; 95% CI, 1.1-7.9; P = .03), suggesting their anticancer impact should be offset by other as yet unknown oncogenic processes that contribute to a poor prognosis.
The present results identify the positive and negative driver somatic mutations acting in MSI-driven tumorigenesis, suggesting that genomic instability in MSI CRC plays a dual role in achieving tumor cell transformation. Exome sequencing data have been deposited in the European genome-phenome archive (accession: EGAS00001002477).
CRC, colorectal cancer; Colorectal Cancer; Driver Gene Mutations; HR, hazard ratio; MLH1, MutL Homolog 1; MMR, mismatch repair; MSH, MutS Homolog; MSI, microsatellite instability; Microsatellite Instability; NR, nonrepetitive; PBS, phosphate-buffered saline; PCR, polymerase chain reaction; Positive and Negative Selection; R, repetitive; RFS, relapse-free survival; RTCA, Real-Time Cell Analyzer; Tumorigenic Process; UTR, untranslated region; WES, whole-exome sequencing; WGA, whole-genome amplification; bp, base pair; indel, insertion/deletion; mRNA, messenger RNA; shRNA, short hairpin RNA; siRNA, small interfering RNA