Abstract IA25: Identification of essential genes for cancer immunotherapy

Abstract

Cancer immunotherapies can trigger dramatic responses in a subset of patients, but many patients with common types of cancer (e.g., breast, ovary, pancreatic, brain and colon) do not experience significant benefit from immunotherapy. The priority now must be determining what makes some cancers resist the immune system, even after treatments designed to fortify the body’s natural antitumor capabilities. Understanding the mechanisms of immune resistance and tumor escape could help enhance tumor immunotherapy. Virtually every cancer contains mutations within protein-encoding genes. These mutations can create targets that can be recognized by immune cells, but mutations may also impair immune recognition and enable immune escape. We have previously observed that cancer cells can escape immune recognition via loss of heterozygosity (LOH) and mutations in β2 microglobulin, which are common in human tumors. These historical findings are important because current cancer immunotherapies mostly rely on T cells, which are adept at recognizing cells in which genetic disruptions have generated aberrant proteins. Anti-CTLA-4 or PD1/PDL1 work in large part by releasing natural checkpoints that constrain T-cell activity. Chimeric antigen receptor T-cell therapies (CAR-T), generated by genetically altering a patient’s T cells, can trigger long-lasting remissions in some patients with blood cancers, but have not yet been definitively found to be effective in solid cancers. These therapies build on a deep understanding of T-cell biology gleaned from decades of basic research. To obtain a more complete, whole-genome visualization of why immunotherapies sometimes fail, we explored the factors that influence tumor cells’ vulnerability to T-cell killing. Using a library of 123,000 guide RNAs, we employed a CRISPR-Cas9 system to systematically eliminate the function of every protein-encoding gene. Surprisingly, this genome-wide screen identified dozens of new genes that potentially influence tumor cells’ susceptibility to T-cell attack. When these genes were knocked-out, tumor cells were significantly more likely to survive and continue to multiply after exposure to T cells that we had genetically engineered to recognize tumor-associated antigens. Many of the genes identified in our screen were previously known to be involved in T cell-tumor cell interactions, including those mediating antigen processing and presentation and responses to cytokines. However, dozens of unique “hits” from the CRISPR screen had not previously been linked to T cells’ ability to eliminate their targets. Loss-of-function mutations in these novel resistance genes were found at high rates in patients for whom immunotherapies failed. Given the diverse gene set revealed by our CRISPR screens and the complexity of the tumor microenvironment, which can include high levels of immunosuppressive potassium, it seems unlikely that a single “fix” will enhance immunotherapy. Instead, we must develop a new category of drugs that circumvent these escape mechanisms. We hope our findings will serve as a blueprint to guide comprehensive studies of what makes some tumors resist T-cell control. Ultimately, novel combination immunotherapies based on individual gene mutations may enable the expansion of curative immunotherapy. Selected References: 1. Restifo NP, Esquivel F, Asher AL, et al. Defective presentation of endogenous antigens by a murine sarcoma: Implications for the failure of an anti-tumor immune response. J Immunol 1991;147(4):1453-59. 2. Restifo NP, Spiess PJ, Karp SE, et al. 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