WES of patient derived pre-treatment metastatic melanoma on anti-PD-1 antibody treatment

Only tumours that cannot upregulate programmed death ligand 1 (PD-L1) upon interferon exposure should be considered negative for this ligand, and would be unlikely to respond to PD-1 blockade therapy. Here we show that genetic mutations in the Janus kinases (JAK) controlling signalling downstream of the interferon receptor prevent PD-L1 upregulation on melanoma cells upon interferon exposure and result in innate resistance to PD-1 blockade in patients. Among 50 human melanoma cell lines tested for response to interferon gamma by PD-L1 surface expression, three were negative. Two of them had loss of function mutations in JAK1 or JAK2, leading to lack of downstream signalling from the interferon receptor. Whole exome sequencing of biopsies from 23 patients with metastatic melanoma treated with the anti-PD1 antibody pembrolizumab revealed a homozygous JAK1 missense mutation in the biopsy of the patient with the highest mutational load among the 9 patients without a clinical response to anti-PD-1 therapy, and no interferon receptor pathway homozygous loss of function mutations in the biopsies of 14 patients with response to therapy. A cell line established from this biopsy showed lack of sustained signalling response to interferon alpha, beta or gamma leading to markedly decreased reactive PD-L1 expression. Analysis of whole exome sequencing of 16 cases of colon cancer with mismatch repair deficiency also showed a homozygous JAK1 loss of function mutation in a patient without a tumour response to PD-1 blockade. Analysis of 905 cell lines from the CCLE database demonstrated that approximately 0.7% of cell lines have loss of function JAK1/2 mutations that may predict lack of response to PD-1 blockade therapy, with the highest frequency in endometrial cancers. Therefore, we report on defined mutations in the interferon receptor signalling pathway that should result in innate resistance to immunotherapies based on PD-1 blockade.