BRAF mutant colorectal cancers can be stratified according to the presence of microsatellite instability (MSI). BRAF mutant cancers that are MSI, confer an excellent prognosis and are well described. In contrast, microsatellite stable (MSS), BRAF mutant cancers are aggressive and correlate with a poor prognosis, however the molecular mechanisms underlying this are not well understood. Chromosomal instability (CIN) is commonly observed in BRAF wild type, MSS cancers and associates with a worse prognosis, whilst BRAF mutant, MSI cancers are diploid. We hypothesized that CIN would be frequent in BRAF mutant, MSS cancers.
Presence of CIN was investigated in 60 BRAF mutant/MSS (BRAFmut/MSS), and 90 BRAF wild type/MSS (BRAFwt/MSS) using loss of heterozygosity (LOH) analysis encompassing chromosomal regions 5q, 8p, 17p and 18q. Genome-wide SNP arrays (Illumina CytoSNP-12) were conducted on a subset of MSS cancers and compared to 30 BRAFmutant/MSI cancers.
LOH analysis demonstrated comparably high rates of CIN in the MSS subgroups (72% BRAFmut/MSS, 82% BRAFwt/MSS). In BRAFmut/MSS cancers, CIN correlated with advanced stage, lymph node involvement, distant metastases and worse survival at specific chromosomal regions. SNP arrays confirmed similarly frequent rates of CIN in both MSS cohorts, with 60% BRAFmut/MSS and 62% BRAFwt/MSS chromosomal arms affected. BRAFmut/MSI cancers had a low degree of CIN (13%). Of the regions with copy number variation, loss events were predominant over gain in both MSS cohorts (BRAFmut/MSS 533/736,72%; BRAFwt/MSS 279/389,72%). BRAFwt/MSS cancers mostly demonstrated whole chromosomal arm loss events (185/279,66%), whereas BRAFmut/MSS cancers showed primarily regional loss events (336/533,63%)(p<0.0001). BRAFmut/MSS cancers had significantly greater rates of loss at 17q, 6p and 6q compared to BRAFwt/MSS cancers (p=0.002, p=0.009, p=0.04 respectively).
This study has identified a novel form of genetic instability associated with BRAF mutant/MSS cancers primarily involving regional rather than whole arm deletions. High rates of loss were identified in regions not typically implicated in colorectal cancer, which may contain putative tumour suppressor genes associated with the aggressiveness of this cancer type.