CRISPR screens establish regulatory maps of immunosuppressive surface molecules in cancer

Abstract

Cancer cells can evade immune surveillance by triggering inhibitory checkpoint responses in tumor-associated T cells through the expression of immunosuppressive surface molecules. While therapeutic blockade of such receptors has emerged as a pillar of cancer therapy, tumor cell-intrinsic mechanisms controlling their expression remain incompletely understood. Fluorescence-activated cell sorting (FACS)-based genetic screens can be used to decipher regulatory pathways, but conventional screening approaches are biased towards regulators that are dispensable for cancer cell proliferation and survival. Here, we used a tetracycline-inducible Cas9 system enabling fully time-controllable CRISPR-based mutagenesis to gain a more comprehensive and comparative survey of regulators controlling the expression of four major immunosuppressive surface molecules, PD-L1 (CD274), CD47, CD276 and HLA-E, as well as CD151, a candidate surface target associated with tumor growth and invasion. As a prominent hit, our screens identify the membrane-trafficking factor DNAJC13 as a regulator of PD-L1 and CD276. Among DNAJC13-controlled surface proteins, we identify other known and proposed immune-checkpoint molecules. Based on this function, suppression of DNAJC13 strongly increases the sensitivity of human cancer cells to T-cell attack in vitro and prolongs survival of mice bearing pancreatic tumors. Together, our study establishes regulatory maps of major immune-modulatory surface molecules and identifies DNAJC13 as a potential target for the coordinated inhibition of multiple immunosuppressive signals.