Immune checkpoint therapies such as PD-1 blockade have vastly improved the treatment of numerous cancers, including basal cell carcinoma (BCC). However, patients afflicted with pancreatic ductal carcinoma (PDAC), one of the deadliest malignancies, overwhelmingly exhibit negative responses to checkpoint therapy. We sought to combine data analysis and machine learning to differentiate the putative mechanisms of BCC and PDAC non-response. We discover that increased MHC-I expression in malignant cells and suppression of MHC and PD-1/PD-L expression in CD8+ T cells is associated with nonresponse to treatment. Furthermore, we leverage machine learning to predict response to PD-1 blockade on a cellular level. We confirm divergent resistance mechanisms between BCC, PDAC, and melanoma and highlight the potential for rapid and affordable testing of gene expression in BCC patients to accurately predict response to checkpoint therapies. Our findings present an optimistic outlook for the use of quantitative cross-cancer analyses in characterizing immune responses and predicting immunotherapy outcomes.