Homologous recombination repair pathway mutations and genetic mechanisms shaping anti-tumor immunity and immunotherapy efficacy

Cleveland Clinic Lerner Com-Cwru, Cleveland OH

Investigators

Abstract

PROJECT SUMMARY Immune checkpoint blockade (ICB) therapies such as PD1/PD-L1-targeting antibodies activate the immune system to help eradicate tumor cells. However, treatment response varies dramatically across patients and cancer types. Genetic defects in DNA damage response pathways predispose to cancer and strongly influence tumor immunity. Our long-term goal is to understand how defects in DNA repair shape immunotherapy efficacy. A very important and commonly altered DNA repair pathway in human tumors is homologous recombination (HR) repair. The impact of mutations in this major repair pathway on tumor immunity is poorly understood and is an area of urgent need. Our preliminary data show that mutations in specific components of HR are strongly associated with superior response to ICB. Specifically, we showed that BRCA2 mutations are associated with improved survival while BRCA1 mutations are not. Syngeneic, isogenic mouse models recapitulate these findings. The central hypothesis of this application is that inactivation of specific portions of the HR repair pathway sensitizes tumors to ICB. Specifically, defects in the “upstream” parts of the HR pathway have distinct consequences on tumor immunity versus those that are “downstream” (post end-resection). The objective of this proposal is to characterize the mechanisms by which HR defects (HRD) influence ICB efficacy. We will accomplish our objective by pursuing 3 specific aims. In Aim 1, we will elucidate the mechanisms underlying differential immunogenicity between Brca2 and Brca1 mutant tumors in murine models. We will evaluate whether differences in response to ICB are due to (1) differences in intracellular immunologic signaling between upstream and downstream HR defects resulting in distinct effects on tumor immunity and (2) genetic alterations and generation of neoantigens vary based on the type of HR DNA repair defect. We will functionally examine cGAS/STING, the inflammasome, RIG-I and other relevant pathways, how BRCA1 and 2 inactivation influences these processes, and how they shape the tumor microenvironment. Aim 2 will characterize how HR repair pathway defects influence response to ICB in human tumors. We will expand our analysis to a larger cohort of patients, and test if “upstream” and “downstream” HR defects have distinct immunologic response. We will validate human observations by creating additional syngeneic murine models. We will use single cell sequencing on selected cases to delineate the functional divergence of distinct parts of the HR pathway in shaping the TME. In Aim 3, we will characterize the mechanisms of acquired resistance in HR defective tumors that progress after treatment with ICB. Using paired sets of samples, we will perform comprehensive evaluation of genetic and immunologic changes during acquired resistance. We will examine whether active HR deficiency is necessary for immunologic response, which will provide insight on the necessity of intracellular innate immunologic signaling in mediating response to therapy. We will comprehensively evaluate the TME to identify specific immunologic mediators of resistance.