Heterogeneity and plasticity of the naive CD4+ T cell compartment

While naive 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 naive CD4+ T cell subsets that emerge within the single positive stage in the thymus: a quiescence cluster (TQ), a memory-like cluster (TMEM), a TCR reactive cluster (TTCR), an IFN responsive cluster (TIFN), and an undifferentiated cluster (TUND). Elevated expression of transcription factors KLF2, Mx1, and Nur77 within the TQ, TIFN, and TMEM clusters, respectively, allowed enrichment of these subsets for further analyses. Functional studies using sorted cells revealed that naive T cell subsets have distinctive functional biases upon stimulation. Furthermore, treatment of mice with inflammatory stimuli imparted a state of reduced responsiveness on naive T cells, evidenced by a reduction in cytokine production ex vivo. In human lupus patients, naive CD4+ T cell cluster frequencies were distorted, with the TIFN cluster expanding proportionately with disease score. Our data show that naive T cells are influenced by host environment, with functional consequences manifesting upon activation. These findings highlight a need to explore how naive T cells can become distorted in cancer, autoimmunity, and infectious diseases. SummaryThis study describes the transcriptional heterogeneity of murine and human naive CD4+ T cells as comprising of multiple discrete clusters that impact CD4+ T cell fate and trajectories. Naive CD4+ T cells experiencing inflammatory environments exhibit an altered transcriptional state that influences their functional trajectory.