Abstract
While naïve CD4(+) T cells have historically been considered a homogenous population, recent studies have provided evidence that functional heterogeneity exists within this population. Using single cell RNA sequencing (scRNAseq), we identify five transcriptionally distinct naïve CD4(+) T cell subsets that emerge within the single positive stage in the thymus: a quiescence cluster (T(Q)), a memory-like cluster (T(MEM)), a TCR reactive cluster (T(TCR)), an IFN responsive cluster (T(IFN)), and an undifferentiated cluster (T(UND)). Elevated expression of transcription factors KLF2, Mx1, and Nur77 within the T(Q), T(IFN), and T(MEM) clusters, respectively, allowed enrichment of these subsets for further analyses. Functional studies using sorted cells revealed that naïve T cell subsets have distinctive functional biases upon stimulation. Furthermore, treatment of mice with inflammatory stimuli imparted a state of reduced responsiveness on naïve T cells, evidenced by a reduction in cytokine production ex vivo. In human lupus patients, naïve CD4(+) T cell cluster frequencies were distorted, with the T(IFN) cluster expanding proportionately with disease score. Our data show that naïve T cells are influenced by host environment, with functional consequences manifesting upon activation. These findings highlight a need to explore how naïve T cells can become distorted in cancer, autoimmunity, and infectious diseases.