Abstract
Cancer immunotherapy aims to boost T cell responses against tumor cells. However, a large fraction of patients with cancer exhibit intrinsic or acquired resistance to immunotherapy. To better understand resistance mechanisms in tumor cells, we used CRISPR-Cas9 whole-genome screening to uncover tumor-specific genes that influence sensitivity to T cell killing. Among the top hits, we identified the transcription factor zinc-finger protein X-linked (Zfx). Zfx knockout tumor cells are resistant to T cell killing both in vitro and in vivo. We demonstrate that Zfx regulates expression of the apoptotic machinery, with Caspase-3 being a central element in mediating T cell killing. Mechanistically, our ChIP-Seq analyses in multiple human cancer cell lines show ZFX directly binds to the promoters of key apoptosis genes, including Caspase-3, to control their expression. Notably, ZFX expression is decreased in several human cancer tissues compared to healthy tissues. Female patients with kidney renal clear cell carcinoma (KIRC) with high ZFX expression showed longer survival compared to patients with low ZFX expression. In addition, we find that higher ZFX expression in patients with melanoma correlates with a positive response to anti-PD-1 immunotherapy. Our results demonstrate a novel resistant mechanism in tumor cells, highlighting ZFX as a potential biomarker for immunotherapy response, and suggest that targeting tumor cell intrinsic resistance genes in combination with immune therapies could benefit patients with cancer.