Single-Cell Transcriptomics Of CD8 T Cells During CMV Viremia In Kidney Transplant Recipients Identify Transcriptional States Of Advanced Differentiation

Abstract Acute versus chronic viral infections define the dogma of strictly segregated pathways of generating memory or exhausted T cells. Paradoxically, chronic human cytomegalovirus (HCMV) infection elicits an inflationary T cell response with accumulation of progressively differentiated T cells occupying up to 30% of total CD8 T cells. The mechanisms of HCMV-driven memory T cell inflation remains poorly understood. HCMV infection is asymptomatic but immunocompromised transplant recipients often experience clinical episodes of CMV viremia correlating with graft injury and mortality. We leveraged a defined clinical cohort of renal transplant recipients and profiled the T cells from 31 CMV PCR+ patients with/without prior CMV exposure and 31 matched PCR− controls at baseline, longterm post-transplantation and at 1wk and 1month post-viremia for PCR+ patients. We observed contraction of naïve and central memory T cells and reciprocal expansion of terminal effector memory CD8 T cells post-viremia. ScRNASeq of CD8 T cells further defined early (CD28+CCR7+), transitional (CD28+GZMK+) and advanced (CD28-KLRG1+) stages of differentiation. Pseudotime analyses revealed specific transcriptomic modules and transcription factors associated with distinct CD8 T cell differentiation states. We report that HCMV induced progressively differentiated T cells with memory-progenitor features lacking inhibitory receptors but with stemness (kat6a, rnf138) and anti-apoptotic markers (bcl2, braf). Thus HCMV skewed the balance of CD8 T memory cells from pro-exhaustion to a prolonged non-classical memory phenotype. This study revealed important mechanisms underlying memory inflation over exhaustion in the setting of chronic antigen exposure. This work was funded by NIH grant U19AI128913 to EFR.