Abstract C034: Genome-wide CRISPR screen identifies novel immunotherapeutic targets in pancreatic cancer

Abstract

Abstract Background: Cancer-cell-intrinsic properties dictate the immune contexture of tumors, impacting the outcome of immunotherapy. Despite the increasing value of CRISPR/Cas9-based loss-of-function (LOF) genetic screens for systematically assessing gene knockout phenotype in tumor cells, it still present challenges, particularly when it comes to genomic editing in the context of large scale experiments and the identification of immunomodulatory genes in in vivo application. To address this, we have established an AsCpf1 (Cas12a)-based screen platform to enable comprehensive whole genome in vivo LOF screening and uncover novel immunotherapeutic targets for pancreatic cancer, which is notoriously resistant to current immunotherapies. Methods: We designed and constructed the optimized minimal CRISPR/AsCpf1 library that targets the entire mouse genome and is only one-fourth the size of the existing genome-wide Cas9-based library. To identify novel immune-related gene vulnerabilities in pancreatic cancer, we infected cell cultures derived from the classic p48-Cre KrasLSL-G12D/+ p53+/- genetically engineered pancreatic cancer mouse model with our AsCpf1 library for in vivo LOF screen in immune-competent and -incompetent mice. Next generation sequencing analysis was performed with the resulting tumors. The potential immunomodulatory hits were called out through BAGEL analysis, using a false discovery rate (FDR) < 0.05, and by comparing between the two mouse groups. Results: Our AsCpf1-based screen identified highly confident hits with potential immunomodulation properties. Notably, we observed depletions of various components of the MHC complex, including H13, specifically in the immune-competent background, implicating their requirement for the regulation of anti-tumor immunity. Depletion of H13 with CRISPR/Cas9 system significantly suppressed pancreatic tumor growth in T-cell dependent manner. Further immune profiling revealed that the loss of H13 triggered potent immune response which was featured by a substantial increase in effective CD8+ T cells and reduction in immunosuppressive macrophages in both subcutaneous and orthotopic models of pancreatic cancer. These findings are in accordance with our clinically relevant analysis showing that low expression of H13 is correlated with improved patient survival in pancreatic cancer and augmented responsiveness to immune checkpoint therapies in several cancer types. Conclusions: Our AsCpf1-based LOF screening platform enables unbiased exploration of in vivo functional players at whole-genome level, which can be applied to diverse disease context and models. In our lead screen, we have identified H13 as a promising immunomodulatory target for patients with pancreatic cancer. Citation Format: Xiaofei Wang, Jintan Liu, Giulio Draetta, Haoqiang Ying, Wantong Yao. Genome-wide CRISPR screen identifies novel immunotherapeutic targets in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C034.