A Microsatellite in the Coding Sequence of HLA-A/B Is a Mutation Hotspot in Colon Cancer With Microsatellite Instability

Recently, while attempting the cloning of tumor antigens recognized by cytotoxic T lymphocytes in human CRCs, we discovered a deleterious mutation in an HLA-A allele of a CRC cell line. The mutation consisted in a single cytosine insertion within a 7-cytosine (C7) repeat found in exon 4 of an HLA-A*0301 allele (nucleotide positions: c.621_627), causing a frameshift of the coding sequence. Since the C7 repeat targeted by the mutation was conserved across multiple HLA-A alleles (c.621_627) and mirrored by a paralogous 6-cytosine (C6) repeat in HLA-B alleles (c.621_626), and because it fulfilled the molecular definition of microsatellite and was previously reported as the target of sporadic mutations,6 we conducted a survey to understand whether it represented a mutational hotspot in CRCs with MSI. Our findings demonstrate that the C6/C7 repeats found in exon 4 of HLA-A and HLA-B represent mutational hot spots in CRCs with MSI. This observation has important clinical implications. MSI CRCs are exceptionally responsive to ICIs, but emerging evidence indicates that (1) a subset of MSI CRCs display primary resistance to ICIs1 and that (2) in malignancies treated with ICIs, a reduced HLA class Ia repertoire, due to homozygosity or loss of heterozygosity of even 1 of 3 HLA class-Ia loci (HLA-A, HLA-B, or HLA-C) associates with reduced therapeutic efficacy. We therefore expect that among MSI CRCs, those harboring deleterious HLA class Ia mutations, even of a single allele, might display resistance to ICIs. Because the mutations described in this study can be identified using conventional HLA-typing techniques, such as sequence-based typing, we advocate for clinical trials to implement such techniques to identify MSI CRCs harboring HLA-A or HLA-B mutations and test for associations with resistance to ICIs.