Abstract PR005: Identification of DNA Damage Repair genes controlling the immune landscape of breast tumors via spatial functional genomics

Abstract

Abstract Immune checkpoint blockade (ICB) has revolutionized the field of cancer immunology, yet only 17-20% of patients who receive this treatment derive any clinical benefit. There is an unmet need to either identify the subset of patients who would respond to ICB or identify targets for combination therapies. By assessing frequently mutated pathways in these patients, we can identify potential biomarkers and candidates for combinatorial therapy. One such pathway is the DNA Damage Response (DDR) pathway. Faults in DDR pathways can lead to genome instability, higher tumor mutational burden (TMB), and accumulation of neoantigens in tumors. Consequently, tumors with one or more deficiencies in DDR (DDRd) have been shown to respond better to therapy and are associated with increased immune cell infiltration. However, previous work from our lab has shown that different gene alterations, even in the same DDR pathway, can polarize immune outcomes differently. To address this issue, we employed Perturb-map, a first-of-its-kind functional genomics approach, which utilizes protein barcodes (pro-Codes) to enable spatial resolution of CRISPR screens. We generated a Pro-Code/CRISPR library targeting frequently mutated DDR genes and introduced the library into 4T1 breast cancer cells, a syngeneic model of triple negative breast cancer. We introduced the cells into immunocompetent mice and performed multiplex imaging on metastatic lesions in the lung to spatially resolve each gene knockout tumor. We observed that loss of Rbbp8 and Polq led to larger tumors, whereas loss of Pms2 led to smaller tumors. Strikingly, Rbbp8 knockout tumors were also less infiltrated by CD4 T cells compared to control tumors. This system was also used to find therapeutic targets by performing synthetic lethality screens using mass cytometry. We transduced the library in isogenic Brca2 deficient 4T1 cells along with their wildtype (WT) counterparts and looked for enrichment or loss of pro-Codes across the different cell lines. These screens consistently identified known synthetic lethality partners like Parp1 in the Brca2 deficient cell lines and identified additional targets like Mre-11a, Bard1 and Rbbp8, which are being profiled further. Taken together, we have developed a scalable system to study the effect of DDR mutations on tumor cell intrinsic and extrinsic properties, which can not only help characterize immune outcomes but also identify potential therapeutic partners. This system proves to be a useful tool that can be leveraged to profile a number of different genes across multiple cancer types. Citation Format: Prerna Suri, Juhana Habib, Gurkan Mollaoglu, Luisanna Pia, Alessia Baccarini, Brian Brown, Robert Samstein. Identification of DNA Damage Repair genes controlling the immune landscape of breast tumors via spatial functional genomics [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr PR005.