A single-cell multiomic analysis of non-classical T cells reveals unique gene signatures 2588

Abstract Description Non-classical T cells are a heterogeneous population with both innate and adaptive features. KbDb-/- mice allow for the investigation of non-classical T cells in the absence of classical T cells. In this study, we performed single-cell RNA, TCR, and CITE-seq on splenic T cells from C57BL/6, KbDb-/-, and KbDb-/-Qa-1-/- mice at steady state and following viral infection. Our analysis reveals that non-classical T cells harbor unique gene signatures at homeostasis. Interestingly, a large population of naïve CD8+ T cells in KbDb-/- and KbDb-/-Qa-1-/- mice display a central memory-like phenotype and express the transcription factor Eomes. Following murine cytomegalovirus (MCMV) infection, a subset of non-classical CD8+ T cells, not observed in KbDb-/-Qa-1-/- mice, exhibit reduced metabolism and high expression of PD-1, TIGIT, and LAG-3. This exhausted Qa-1-restricted population exhibits limited αβ TCR diversity. CDR3 distance analysis reveals that these cells recognize related antigen(s). Additionally, we identified an innate-like double negative population that shares gene expression patterns with classical long-lived effector cells. However, expression of NKp46, inhibitory Ly49 receptors, and the transcription factor Helios suggest a regulatory role. Our work provides evidence of unique transcriptional states and repertoires of non-classical T cells, which may contribute to immunity when classical T cell responses are impaired. Funding Sources This work was supported by the NIH Research Grants R01 AI046709, R01 AI173163 (L.B.), R24 AI072073 (ImmGen) and T32HL134625 (S.P.R.). Topic Categories Computational and Systems Immunology (COMP)