Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy

D Chowell, C Krishna, F Pierini, V Makarov, NA Rizvi… - Nature medicine, 2019 - nature.com
Nature medicine, 2019nature.com
Functional diversity of the highly polymorphic human leukocyte antigen class I (HLA-I) genes
underlies successful immunologic control of both infectious disease and cancer. The
divergent allele advantage hypothesis dictates that an HLA-I genotype with two alleles with
sequences that are more divergent enables presentation of more diverse
immunopeptidomes,–. However, the effect of sequence divergence between HLA-I alleles—
a quantifiable measure of HLA-I evolution—on the efficacy of immune checkpoint inhibitor …
Abstract
Functional diversity of the highly polymorphic human leukocyte antigen class I (HLA-I) genes underlies successful immunologic control of both infectious disease and cancer. The divergent allele advantage hypothesis dictates that an HLA-I genotype with two alleles with sequences that are more divergent enables presentation of more diverse immunopeptidomes, –. However, the effect of sequence divergence between HLA-I alleles—a quantifiable measure of HLA-I evolution—on the efficacy of immune checkpoint inhibitor (ICI) treatment for cancer remains unknown. In the present study the germline HLA-I evolutionary divergence (HED) of patients with cancer treated with ICIs was determined by quantifying the physiochemical sequence divergence between HLA-I alleles of each patient’s genotype. HED was a strong determinant of survival after treatment with ICIs. Even among patients fully heterozygous at HLA-I, patients with an HED in the upper quartile respond better to ICIs than patients with a low HED. Furthermore, HED strongly impacts the diversity of tumor, viral and self-immunopeptidomes and intratumoral T cell receptor clonality. Similar to tumor mutation burden, HED is a fundamental metric of diversity at the major histocompatibility complex–peptide complex, which dictates ICI efficacy. The data link divergent HLA allele advantage to immunotherapy efficacy and unveil how ICI response relies on the evolved efficiency of HLA-mediated immunity.
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