Multi-omics analysis reveals spatial heterogeneity of infiltrating T cells in high-grade serous ovarian cancer.

Abstract

e17603 Background: The effect of spatial immunologic variation, especially in T cell infiltration, recognition and expansion, across various tumor foci in the ovary (primary) and distant metastatic foci in the peritoneal cavity and their contribution to the limited response to immune therapy in High-Grade Serous Ovarian Cancer(HGSOC) remains unexplored. We aim to provide a detailed analysis of the landscape of heterogeneity of infiltrating T cells in primary and metastatic lesions and their differential characteristics in HGSOC. Methods: We performed multi-site sampling and simultaneous RNA sequencing (RNA-seq), whole-genome sequencing (WGS) and bulk T cell receptor (TCR) sequencing as well as single cell RNA sequencing (scRNA-seq) and paired TCR sequencing (scTCR-seq) in 9 patients (48 sites, including 19 ovarian, 11 omental, 18 other metastasis lesions) with untreated primary HGSOC. Validation by IHC, flow cytometry, another scRNA-seq data from 7 patients (32 sites, including 9 ovarian, 6 omental, 6 ascites and 11 other metastasis lesions) and spatial transcriptomics. Results: CD8 exhausted clusters that are enriched in ovarian tumors exhibited high exhaustion, tumor-specific score and low bystander score, whereas CD8 transition and NK-like clusters that are enriched in omental tumors exhibited the opposite characteristics, which was confirmed by flow cytometry. Of note, the exhausted CD8+ T cells exhibited GZMB, PRF1, FASLG and IFNG effector genes despite the expression of exhaustion markers, developing from an early differentiation state with high proliferative capacity and the process preferentially occurs in primary ovarian sites. Besides, T cells corresponding to the selected TCRs that had the same distribution as neoantigens were enriched in ovarian lesions, while the virus-specific TCR preferentially enriched in omentum samples. The association of TMB, HRD score, and COSMIC mutational signatures with antigen-engaged T cell subsets was not observed at the site level within individual patients. STARTRAC-migration analysis showed that T cell clusters in blood or other sites migrating to ovarian was extremely low or vice versa. The expression of MHC-I processing and presentation genes and MHC-I protein were higher in omental lesions, along with T cells were preferentially located in tumor region of ovarian tumors. Conclusions: We identify two different immune patterns in ovarian cancer: 1) ovarian lesions with low infiltration of mainly dysfunctional T cells and immunosuppressive Treg cells. These exhausted CD8 T cells with cytotoxic function are clonal expanded; 2) omental lesions infiltrated with non-tumor-specific bystander cells. Decreased major histocompatibility complex (MHC)-I antigen presentation ability and failure of T cell infiltration into omental tumors may contribute to lack of tumor-specific T cells in omental metastasis.