Systematic identification of tumor-intrinsic resistance mechanisms and combinatorial therapy targets for immunotherapy

A number of reports have demonstrated that tumor-intrinsic mechanisms of resistance, such as the loss of genes critical for antigen presentation and inflammatory responses, along with the activation of various cellular signaling cascades, can limit the efficacy of immunotherapy. Strategies to sensitize tumor cells to immunotherapy may overcome some resistance mechanisms, but identifying therapeutic targets has remained challenging. Here, we integrate a two-cell type (2CT) whole-genome CRISPR-Cas9 screen with dynamic transcriptional profiling of the tumor/T cell interaction to comprehensively identify tumor genes that are induced to promote tumor survival. We assessed the therapeutic potential of pharmacological inhibition of these and other top CRISPR identified targets as combinatorial targets to improve the efficacy of tumor destruction by T cells. Overall design: RNA expression was measured by RNAseq on sorted Mel624 tumor and primary human NY-ESO TCR T cell samples after 0 or 6 hours of coculture. Additional experiments measured RNA expression by RNAseq when A375 tumor cells with non-targeting of BIRC2 targeting sgRNAs and Cas9 expression were treated with vehicle or 100 ng TNFa for 16 hrs