Functional antigen presentation is required to interpret the tumor mutation burden (TMB) test

Therapeutic response to checkpoint inhibitors requires a prior, suppressed immune response that is released by a monoclonal antibody blocking the interaction of the checkpoint receptors with their cognate ligands. The presence of this suppressed immune response can be detected by a variety of tests including tumor mutation burden (TMB), tumor infiltrating leukocytes, T-cell receptor clonality, circulating interferons and cytokines, and upregulation of the expression of the checkpoint ligands. Today, TMB has proven to be the most predictive biomarker of response to immunotherapy. TMB is a surrogate marker of immune response. The test works by sampling a small region of the cancer genome to estimate the number of mutations/Mb of the cancer exome. A high TMB score is associated with better response to immunotherapy because it carries more somatic mutations and a higher chance of presenting an immunogenic neoepitope that will lead to CD-8+ T-cell mediated destruction. Restriction or loss of antigen presentation caused by mutations and loss of heterozygosity (LOH) of the beta-2-microglobulin (B2M) and HLA Class I genes has been shown to be a common means of evading CD-8+ T-Cell destruction. Consequently, the outcome for high TMB tumors will be dependent on their ability to present antigens, so that the mutation count will not matter in cells that are unable to present antigens in their HLA Class I/B2M complex. We propose that TMB should be considered together with the ability of the tumor to present these putative neoantigens. To test this hypothesis, we used the PGDx elio™ Tissue Complete test (507 genes in 1.3 Mb) to measure TMB and antigen presentation in the same assay. We tested 212 cancer patients and showed that in FFPET samples with >20% tumor content, we could detect LOH of the MHC Class I and B2M genes with >90% accuracy compared to whole exome data from the same sample. These data confirmed our hypothesis that it was possible to measure TMB and evaluate the genes involved in antigen presentation in the same in silico analysis of a 507 gene next-generation sequencing (NGS) panel. We are currently using this combined analysis to measure TMB and somatic alterations of the antigen presentation complex in several different cancers and to test the hypothesis that adding neoantigen presentation capability to TMB scores will significantly improve prediction of response to a variety of immunotherapies. Citation Format: Gustavo C. Cerqueira, Laurel A. Keefer, Donna Nichol, Julie R. Meyer, Nicholas C. Dracopoli. Functional antigen presentation is required to interpret the tumor mutation burden (TMB) test [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3515.