Description

A genome-scale CRISPR screen to identify essential genes for T cell based cancer therapies

Shashank Patel, Neville Sanjana, Maggie Cam, Feng Zhang, Nicholas Restifo

National Cancer Institute, NIH, USA

In responding to immune selection pressure mediated by T cells against cancer, somatic mutations can function in a bi-directional manner. On one hand, somatic mutations give rise to neoantigens capable of eliciting potent T cell responses. On the other hand, loss-of-function mutations or downregulation of gene expression in the tumor cell can contribute to an immune evasion against T cells. Limited evidence exists on which gene perturbations in human cancer can directly or indirectly impair T cell mediated cytolysis. To identify the genes essential in tumors to elicit a T cell-mediated cytolytic response, we developed a ‘two cell-type’ (2CT) CRISPR assay system consisting of human T cells as effectors and tumor cells as targets. We combined CRISPR-Cas9 screen datasets with TCGA gene expression datasets from >10,000 patient biopsies to study the patterns of immune sensitivity in human cancers. Using the 2CT genome-scale perturbation screen in melanoma cells, we identified and validated multiple genes whose loss impaired the effector function of T cells. Moreover, we uncover a group of core genes from these screens that correlates with cytolytic activity across the majority of the cancer types, reflecting context independence of these genes in the modulation of inherent T cell responses in multiple cancers. This dataset can be utilized to stratify patients for T-cell based immunotherapies, and also for studying emergence of novel immune escape mechanisms. This study demonstrates the broad applicability of 2CT CRISPR screens to study the interaction of cancer cells with immune cells and identify novel therapeutic targets for cellular therapies.

This research is supported by the Intramural Research Program of the NCI (ZIA BC 010763), Center for Cancer Research, NIH, Bethesda, MD, 20892.