Human CD127+CD45RA+CCR7⁻CD8+ T cells represent an early-memory population governed by FOXP1 2250340

Abstract

Following viral infection, naïve CD8+ T cells differentiate into effector and memory populations that eliminate infected cells and establish long-term immunity. Yet, the regulatory mechanisms directing the differentiation toward a memory fate remain unclear. Here, we aim to delineate the differentiation trajectories of antigen-specific human CD8+ T cells following cognate antigen stimulation, and to identify an early-memory subset with a durable memory potential. Sequential peripheral blood samples were collected from healthy donors, vaccinated with BNT162b2 vaccine who subsequently experienced breakthrough infection, allowing longitudinal profiling of antigen-specific responses. Single-cell RNA sequencing integrated with DNA-barcoded MHC-I multimers was used to identify SARS-CoV-2 spike-specific CD8+ T cells. To further asses epigenetic regulation, parallel single-nucleus RNA and ATAC sequencing in a murine influenza A infection model was conducted. Regulatory network and trajectory analyses revealed a distinct early-memory population, uniquely exhibiting transcription factor FOXP1, within a spike-specific effector CD8 cluster. The analogous population in the murine model exhibited increased chromatin accessibility and FOXP1 motif enrichment. Phenotypically, FOXP1+ early-memory population showed a CD45RA+ effector memory T (TEMRA)-like surface expression with a loss of CCR7 expression while uniquely expressing CD127, suggesting functional heterogeneity within the TEMRA population. Functionally, FOXP1 knockdown reduced the expression level of TCF-1 in TCR-stimulated CD8+ T cells, implicating the role of FOXP1 in maintaining T-cell stemness. Our results identify that the CD127+CD45RA+CCR7⁻CD8+ T cell subset represents an early-memory population with the potential to generate durable memory responses, and FOXP1 is a key regulator of this population. Our findings provide mechanistic insights into transcriptional and epigenetic regulation of memory CD8+ T-cell generation. N/A Lymphocyte Differentiation and Peripheral Maintenance (LYM)