W113 - Interconnected Differentiation Trajectories of Exhausted and Nk-like CD8+ T Cells Linked to Alefacept Therapy in Type 1 Diabetes

Kirsten Diggins, PhD – Systems Immunology – Benaroya Research Institute; Alice Wiedeman, PhD – Translational Immunology – Benaroya Research Institute; Elisavet Serti, MSc, PhD – Associate Director of Vaccines and Prevention, HJF | In support of the U.S. Military HIV Research Program (MHRP); Gerald Nepom – Immune Tolerance Network; Vivian Gersuk – Genomics Core – Benaroya Research Institute; Alice Long – Translational Immunology – Benaroya Research Institute; Peter Linsley – Systems Immunology – Benaroya Research Institute

Abstract Text: Better response to Alefacept (LFA3-Ig) in type 1 diabetes patients was previously linked to increased exhausted CD8+ T cells (Tex) with either a CD57+ or PD-1+ phenotype. Lineage relationships between CD57+ and PD-1+ cells and their importance in Alefacept response remained unknown. Here we used bulk ATAC-sequencing (n = 4 Alefacept responders, 0 wk and 104 wk) and single cell RNA-seq (scRNA-seq) combined with T cell receptor (TCR) sequencing (n = 12, 6 responders and 6 non-responders, 104 wk) to elucidate the lineage relationships and diversity of these populations. Bulk ATAC-seq revealed PD-1+ and CD57+ populations are epigenetically distinct and share increased accessibility of exhaustion-related genes and Natural Killer Cell Cytoxicity pathway genes. CD57+ cells, however, were distinguished by increased inhibitory Killer Cell Immunoglobulin-like Receptor (iKIR) accessibility. scRNA-seq with TCR seq identified previously unappreciated gene expression heterogeneity in CD57+ cells, characterized by iKIR and Interferon pathway expression diversity. CD57+ and PD-1+ populations also displayed reciprocal Inhibitory Receptor (IR) expression despite shared chromatin accessibility of exhaustion genes. Analysis of TCR sharing between PD-1+ and CD57+ populations revealed they share a common lineage and differentiate using four trajectories; Tex-PD-1+, Tex-CD57+, Tex-Branching, and Tex-Fluid, suggesting precursor cells differentiate into either the PD-1+ or CD57+ phenotype, or both. This pattern was supported by finding CMV/EBV-specific cells with both CD57+ and PD-1+ phenotypes in scRNA-seq data and sorted tetramer-specific cells. These findings demonstrate interconnections between exhausted and NK-like CD8+ cell populations and prompt investigation of cues driving their differentiation and role in response to therapy.