The Role of the Tumor Suppressor ARID1A in R loop Homeostasis and Tumor Immunity

PROJECT SUMMARY Cancer immunotherapy is the practice of harnessing the activity of the immune system to combat cancer. Immune checkpoint blockade (ICB) is a type of cancer immunotherapy that unleashes the activity of cytotoxic T cells by blocking the interaction of inhibitory receptors on T cells with ligands expressed on tumor cells. ICB

has been an effective treatment for many, resulting in durable, even curative anti-tumor immune responses. However, in most cancer types, less than 50% of patients respond, spurring efforts to understand genetic and molecular signatures associated with ICB response, as well as therapies that can be used in combination to

improve ICB efficacy. Retrospective studies have shown that mutations in the ARID1A gene are enriched among patients that respond to ICB in pan-cancer and cancer type specific trials. ARID1A is a subunit of the SWI/SNF chromatin remodeling complex, which utilizes energy derived from ATP hydrolysis to move

nucleosomes along DNA. Genes encoding subunits of the SWI/SNF complex are frequently mutated in human cancer, with ARID1A being the most frequently mutated subunit and the third most commonly mutated tumor suppressor behind TP53 and CDKN2A. ARID1A mutation could thus serve as an important biomarker for

cancer immunotherapy, potentially affecting treatment of hundreds of thousands of cancer patients. It is not known whether ARID1A mutation is causal or how ARID1A mutation sensitizes tumors to ICB treatment. Indeed, ARID1A mutation is commonly found in microsatellite unstable (MSI) or tumor mutation

burden-high (TMB-high) tumors, which are themselves independent predictors of ICB responsiveness. However, ARID1A mutation is beneficial independent of MSI and TMB status and additive for patients with MSI or TMB-high tumors. It was found that Arid1a mutant tumors grow more slowly than isogenic wild-type lines in

murine models, with increased immune infiltration and T cell activation. Further, Arid1a mutant cancer cells upregulate a subset of genes in the Type I Interferon response, including chemokines and antigen presentation and processing genes. Mechanistically, genetic or pharmacologic inhibition of ARID1A results in increased R

loops, as well as cytoplasmic accumulation of RNA:DNA hybrids and ssDNA. This proposal will utilize genetic deletion and small molecule inhibitors of ARID1A to determine 1) how ARID1A deficiency causes cytosolic nucleic acid release, 2) the pathway by which inflammatory genes are activated in ARID1A deficient cells, 3)

the role of R loop driven inflammatory responses in ARID1A mutant anti-tumor immunity and ICB response. This will be accomplished using ARID1A mutant human cancer cell lines and mouse models of Arid1a mutant cancer. Finally, studies pioneering the in vivo use of small molecule inhibitors of ARID1A in combination with

ICB will be performed. These studies will reveal the molecular mechanism by which ARID1A mutant cancers respond to ICB with the potential to improve patient selection for ICB and to augment ICB efficacy with ARID1A inhibitors.