Redefining the Foreign Antigen and Self-Driven Memory CD4+ T-Cell Compartments via Transcriptomic, Phenotypic, and Functional Analyses

Abstract

Under steady-state conditions, conventional CD4 + T lymphocytes are classically divided into naïve (CD44 lo CD62L hi ) and memory (CD44 hi CD62L lo ) cell compartments. While the latter population is presumed to comprise a mixture of distinct subpopulations of explicit foreign antigen (Ag)-specific “authentic” memory and foreign Ag-independent memory-phenotype (MP) cells, phenotypic markers differentially expressed in these two cell types have yet to be identified. Moreover, while MP cells themselves have been previously described as heterogeneous, it is unknown whether they consist of distinct subsets defined by marker expression. In this study, we demonstrate using combined single-cell RNA sequencing and flow cytometric approaches that self-driven MP CD4 + T lymphocytes are divided into CD127 hi Sca1 lo , CD127 hi Sca1 hi , CD127 lo Sca1 hi , and CD127 lo Sca1 lo subpopulations that are Bcl2 lo , while foreign Ag-specific memory cells are CD127 hi Sca1 hi Bcl2 hi . We further show that among the four MP subsets, CD127 hi Sca1 hi lymphocytes represent the most mature and cell division-experienced subpopulation derived from peripheral naïve precursors. Finally, we provide evidence arguing that this MP subpopulation exerts the highest responsiveness to Th1-differentiating cytokines and can induce colitis. Together, our findings define MP CD4 + T lymphocytes as a unique, self-driven population consisting of distinct subsets that differ from conventional foreign Ag-specific memory cells in marker expression and establish functional relevance for the mature subset of CD127 hi Sca1 hi MP cells.