Single-cell analysis illuminates dysfunctional CD8+T cells as a proliferative, dynamically regulated compartment within human melanoma

The immune cell composition within tumors plays a major role in response to immunotherapy. Therefore, comprehensive characterization of the diverse functional states exhibited by immune cell infiltrates, and their association with treatment outcome, is critical for the development of more effective immunotherapies. We combined single-cell RNA- and TCR-sequencing with an autologous tumor reactivity assay, tracing immune cell heterogeneity and dynamics in melanoma patients. Analysis of 70,000 cells revealed the presence of two effector T-cell subsets, of which only one transitions into a dysfunctional T-cell population, as based both on TCR sharing as well as a gradient of expression of dysfunction-associated genes present in virtually all samples. Notably, we denote dysfunctional T cells— and in particular early dysfunctional cells—as the major proliferating immune cell compartment. Furthermore, TCR-seq of autologous tumor reactive T cells illustrated that presence of reactive potential is associated with the magnitude of dysfunctional signature and is in concordance with response to immunotherapy. Data from 25 melanoma patients confirm the universality of these observations and distinguish shared and divergent regulatory modules between dysfunctional CD8 and regulatory T cells. Our analysis also puts forward novel candidate genes, which are highly correlated with known checkpoint targets within specific cellular subsets and may prove to be effective targets for checkpoint blockade. In conclusion, our findings proclaim that CD8 T cells previously associated with a dysfunctional or exhausted state are in fact a highly proliferating and dynamically interacting cell population within the human tumor microenvironment. This abstract is also being presented as Poster B58. Citation Format: Ido Yofe, Hanjie Li, Anne van der Leun, Yaniv Lubling, Dikla Gelbard Solodkin, Alexander van Akkooi, Hugo M. Horlings, Eyal David, Yael Baran, Akihad Berkovitz, Aviezer Lifshitz, Ton N. Schumacher, Amos Tanay, Ido Amit. Single-cell analysis illuminates dysfunctional CD8+ T cells as a proliferative, dynamically regulated compartment within human melanoma [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr PR04.