A simple approach for detecting HLA‐A*02 alleles in archival formalin‐fixed paraffin‐embedded tissue samples and an application example for studying cancer immunoediting

Abstract

33867cancer. In archival formalin-fixed paraffin-embedded (FFPE) tissue, the HLA type is difficult to analyze because of fragmentation of DNA, hindering the application of commonly used assays that rely on long DNA stretches. Addressing these difficulties, we present a refined approach for characterizing presence or absence of HLA-A*02, the most common HLA-A allele in the Caucasian population, in archival samples. We validated our genotyping strategy in a cohort of 90 samples with HLA status obtained by an NGS-based method. 90% (n = 81) of the samples could be analyzed with the approach. For all of them, the presence or absence of HLA-A*02 alleles was correctly determined with the method, demonstrating 100% sensitivity and specificity (95% CI: 91.40%-100% and 91.19%-100%). Furthermore, we provide an example of application in an independent cohort of 73 FFPE microsatellite-unstable (MSI) colorectal cancer samples. As MSI cancer cells encompass a high number of mutations in coding microsatellites, leading to the generation of highly immunogenic frameshift peptide antigens, they are ideally suited for studying relations between the mutational landscape of tumor cells and interindividual differences in the immune system, including the HLA genotype. Overall, our method can help to promote studying HLA type-dependency during the pathogenesis of a wide range of diseases, making archival and historic tissue samples accessible for identifying HLA-A*02 alleles.

Lynch syndrome cancer vaccines: A roadmap for the development of precision immunoprevention strategies

“…If HLA type in fact influences immune surveillance, the HLA genotype may influence the tumor incidence or tumor risk in LS carriers. Studies analyzing the possible effect of the individual HLA type on cancer risk in LS have been initiated ( 100 , 103 ). The findings expected from these studies will guide the future development of next-generation HLA-adapted individualized neoantigen vaccines.…”