Abstract 2627: PanCancer epigenetic regulators of lymphocyte activation states

Abstract Several immune cell types have been successfully targeted for immunomodulatory therapy; however, the efficacies of such therapies are hindered by incompatible immune cell activation states. CD8+ T-cell exhaustion is one of the most studied T-cell states in the context of cancer and was shown to limit checkpoint blockade efficacy. Although CD8+ T-cell exhaustion studies in mice showed this state is tightly regulated by chromatin accessibility of cis-regulatory elements (CREs) and transcription factor activation, the exploration of these mechanisms, their prevalence, and their specificity in human cancers remains limited. In addition, chromatin accessibility signatures of other lymphocyte (CD4+ and NK) states frequently found in solid tumors have not been carefully characterized in a pan-cancer setting. Here we introduce the first single-nuclei atlas of pan-cancer and disease-specific cis- and trans-regulatory elements in tumor infiltrating lymphocytes. We profiled ~140K T-cell and NK cell nuclei with snATAC-seq and snRNA-seq from 227 tumor and normal samples from eleven cancer types. We distinguished two major subpopulations among exhausted CD8+ T-cells: GZMK expressing (CD8+ GZMK+ Tex) and ITGAE+ tissue-resident (CD8+ Trm ex). CD8+ GZMK+ Tex was enriched in clear cell renal cell carcinoma, while CD8+ Trm ex was found in all other cancers. Both exhausted groups featured high motif accessibility and expression of NR4A1, NFATC2, and NFKB2 transcription factors (previously reported to regulate exhaustion), but differed in EOMES motif accessibility and gene expression. We have identified other lymphocyte subpopulations showing exhaustion signatures, including CD4+ follicular helpers (CD4+ Tfh), CD4+ regulatory cells (CD4+ Tregs), and weakly cytotoxic tissue-resident NK cells (trNK weak). All these subpopulations showed increased expression and motif accessibility of the NR4A1 transcription factor, highlighting its role in regulating dysfunctional states not only in CD8+ T-cells, but also in CD4+ and NK cells. Additionally, CD4+ Tfh and Tregs showed enhanced activity of NFKB1, NFKB2, and POU2F2, and trNK weak cells had increased activity of NR4A2 and NR2F2. To put our results into clinical perspective, we have collected cohorts of renal cancer, melanoma and triple-negative breast tumors treated with immunotherapy in clinical trial settings, and showed elevated GZMK expression in exhausted T-cells in responders compared to non-responders. Citation Format: Alla Karpova, Nadezhda V. Terekhanova, Siqi Chen, Reyka G. Jayasinghe, Andrew Houston, Wagma Caravan, Ryan C. Fields, Li Ding. PanCancer epigenetic regulators of lymphocyte activation states [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2627.