Effects of tumor mutation burden on the antigen presentation pathway

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Tumor mutation burden (TMB) is used to select patients to receive immune checkpoint inhibitors (ICIs) but has mixed predictive capabilities. We hypothesized that inactivation of antigen presenting genes (APGs) that result from increased TMBs would result in inherent resistance to ICIs. We observed that somatic mutations in APGs were associated with increasing TMBs across 9,418 tumors of 33 different types. In adenocarcinomas of the lung, ITGAX and CD1B were some of the most commonly mutated APGs. In 62 patients with non-small cell lung cancers treated with a PD-1 inhibitor in second or later lines of therapy, there was an association of increased TMB with mutations in APGs; however, mutations in one or more APGs were associated with improved progression-free survival. Contrary to our hypothesis, mutations in APGs were associated with improved progression-free survival with nivolumab, possibly due to the involvement of single alleles rather than complete loss.

nference, Cambridge, Massachusetts, USA Mayo Clinic, Division of Medical Oncology, Rochester, MN, USA Mayo Clinic, Division of Hematology and Oncology, Scottsdale, AZ, USA Mayo Clinic, Co-Directors of Precision Cancer Therapeutics within the Center of Individualized Medicine, USA Georges-Francois LeClerc Cancer Center, Unit of Molecular Biology, Dijon, France Genetic and Immunology Medical Institute, Dijon, France University of Burgundy Franche-Comte, France