Abstract 4943: Leveraging single-cell sequencing to discover novel exhaustion markers of CD8 T cells

Therapeutic revival of tumor-specific exhausted T cells using checkpoint blockade antibodies has improved clinical outcomes in cancer significantly. Notwithstanding a high overall response rate to these drugs, long-term benefit is realized by a small fraction of the treated patients. A mechanistic explanation of relapse comes from the recent findings that in both murine and human cancers intratumoral T cells exist in a wide spectrum of functional states – from fully functional at one end of the spectrum, to fully dysfunctional at the other end. Therefore, tumor response to checkpoint inhibitors is determined by the ratio of functional to dysfunctional state of T cells, which in turn is modulated by a wide array of immune-suppressive signals present within the tumor microenvironment. Dissecting the T cell functional states can significantly enhance our understanding of patient responses to immunotherapy drugs and can be used to develop targeted and personalized strategies for restoring antitumor immunity. A key challenge to this problem is that the transcriptional signatures of dysfunctional exhausted T cells are closely intertwined with the activated/effector CD8+ T cell states. This is not surprising, since T cell dysfunction arises following chronic T cell activation. Developing unique markers of T cell exhaustion from in vivo models has not been successful. In this study, we present data to show how single cell transcriptomics on a 10x Genomics platform can identify T cell functional states following antigen-stimulation in an ex vivo T cell activation system. In particular, we identified functional gene clusters and molecular networks that are unique to CD8+ T cell exhausted state. The combined expression of our T cell exhaustion gene signature correlated with poor prognosis when applied to TCGA data of over 1500 tumors from many different cancers. Furthermore, the molecular pathways identified in this study provide opportunities to develop novel therapeutic interventions specially targeting dysfunctional T cells in cancers thereby enhancing the efficacy of checkpoint inhibitors. Citation Format: Xiaoshan Shi, Savita Jayaram, Kayla Lee, Keshav Bhojak, Vasumathi Kode, Mridul Chaudhary, Ashwini Patil, Ravi Gupta, Amit Chaudhuri, Papia Chakraborty. Leveraging single-cell sequencing to discover novel exhaustion markers of CD8 T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4943.