Assistant Professor University of North Carolina at Chapel Hill Chapel Hill, North Carolina, United States
Disclosure(s):
H. Kay Chung, PhD: No financial relationships to disclose
Introduction/Rationale: CD8⁺ T cells differentiate into various states that affect immune responses in cancer and chronic infections. Our research focuses on T cell engineering to prevent the dysfunctional terminal exhaustion (TEXterm) while maintaining or enhancing their ability to develop protective tissue-resident memory (TRM). Since TEXterm and TRM have very similar transcriptomic and chromatin profiles, we aimed to identify specific transcription factors (TFs) that are key regulators uniquely defining each state.
Methods: To systematically define the TFs driving these states, we developed a comprehensive transcriptional and epigenetic atlas encompassing nine distinct CD8+ T cell differentiation states derived from 121 experiments across acute and chronic lymphocytic choriomeningitis virus (LCMV) infections.
Results: Our analysis catalogued TF activity fingerprints, uncovering regulatory mechanisms governing selective cell state differentiation. Global TF community analysis revealed distinct biological pathways underlying protective TRM versus dysfunctional TEXterm states, such as protein degradation. Through in vivo CRISPR screening integrated with single-cell RNA sequencing (in vivo Perturb-seq), we delineated that TFs selectively govern TEXterm. We identified HIC1 and GFI1 as shared regulators of TEXterm and TRM and KLF6 as a unique regulator of TRM. Importantly, we discovered novel TEXterm single-state TFs, including ZSCAN20 and JDP2 with no prior known function in T cells. Targeted deletion of these TFs enhanced tumor control and synergized with immune checkpoint blockade. Consistently, their depletion in human T cells reduces the expression of inhibitory receptors and improves effector function.
Conclusion: While our study primarily focuses on CD8+ TEXterm and TRM cell differentiation to enhance antitumor and antiviral immunity, our pipeline for identifying single-state TFs and ‘TF recipes’ can be adapted to program other cell types, ultimately advancing immune cell therapy in various applications.
