Abstract SY19-01: Investigating cancer determinants of tumor immune composition

Abstract

Abstract The cellular composition, spatial architecture, and tissue localization of a tumor have a major impact on a cancer’s progression and response to therapy. These factors are particularly relevant to tumor immunity as immune cell composition and localization within the tumor microenvironment (TME) is one of the major determinants of response to immunotherapy and patient outcome. Spatially resolved single cell genome sequencing has revealed that many genetically distinct sub-clones exist in proximity in tumors and can have different TME compositions, but how specific genes influence the TME, or how neighboring clones influence one another is not well-defined. Indeed, while some genes involved in orchestrating the TME have been identified, the potential roles of many genes in influencing the architecture and immune composition of different tumors are not established. To enable scale up studies to identify determinants of TME biology and tumor immunity, we established a first-of-its-kind in vivo spatial functional genomics platform called Perturb-map. We applied Perturb-map to knockout (KO) dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each KO influenced tumor growth, histopathology, and immune composition. Additionally, we paired Perturb-map and spatial transcriptomics for unbiased analysis of CRISPR-edited tumors. In contrast to in vitro CRISPR screens, we found KO of positive regulators of IFNγ signaling led to a major reduction of tumor burden, with varying impact from different pathway components. KO of Socs1, a negative regulator of IFNγ signaling, provided a growth advantage though was accompanied by increased T cell infiltration and notably, Socs1 KO tumors were more responsive to PDL1 blockade. Perturb-map also found that KO of the TGFβ Receptor 2 (Tgfbr2) resulted in a growth advantage, but unlike Socs1 KO, T cells were excluded from the lesions and the TME converted to a fibro-mucinous state. Spatial transcriptomics revealed TGFβ signaling was upregulated in Tgfbr2 KO tumors. Further analysis indicated this signal was from TGFβ-mediated activation of fibroblasts in tumors where cancer cells lost Tgfbr2, suggesting the mechanism for TME remodeling and T cell exclusion in Tgfbr2 KO tumors. These studies establish Perturb-map for functional genomics within tissue at single cell-resolution with spatial architecture preserved and provide insight into how TGFβ responsiveness of cancer cells can affect the TME (Dhainaut, Rose et al. BioRxiv 2021, doi.org/10.1101/2021.07.13.451021). Citation Format: Brian Brown. Investigating cancer determinants of tumor immune composition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr SY19-01.