Cancer intrinsic protein neddylation modulates the intra-tumoral immune landscape to constrain immune checkpoint blockade therapy

Abstract

The cancer intrinsic network controlling response to immune checkpoint blockade therapy remains elusive. Using a published single-cell RNA sequencing (scRNA-seq) dataset from breast cancer patients, we found that pre-therapy mRNA expression of NEDD8, which encodes the regulatory protein essential for neddylation, in cancer cells was negatively associated with T-cell expansion upon pembrolizumab treatment. Genetic ablation of protein neddylation in murine tumors induced curative response to PD-1 or PD-L1 blockade in mice. Combined analysis of neddylation-deficient murine tumors using scRNA-seq and high-resolution spatial transcriptomics revealed distinct spatial immune co-localization and immune cell signatures. In a high-content phenotypic screen of known compounds, protein neddylation was required for the induction of phenotypic changes by lipid inhibitors and ferroptosis inducers in human breast cancer cells. In accordance, these compounds enhanced the efficacy of PD-1 blockade and protected mice from tumor rechallenge. Altogether, we delineate the unknown functions of protein neddylation on antitumor immunity and provide therapeutic options that can enhance immunotherapy.