Revealing the heterogeneity of CD4+ T cells through single-cell transcriptomics

Single-cell RNA sequencing (scRNA-seq) offers the ability to resolve whole transcriptomes of single cells with substantial throughput, and it has revolutionized studies of gene expression. The transcriptional resolution available can uncover fine structures of biologic heterogeneity that are manifest among cell populations. Here, we review the applications of scRNA-seq to profile the phenotypes and clonotypes of CD4+ T cells. First, we describe challenges inherent to scRNA-seq that are important for analysis of CD4+ T cells, as well as the technical solutions that are emerging to address these challenges. We then consider major themes of the application of scRNA-seq to CD4+ T cells, including investigation of CD4+ T-cell heterogeneity in model systems, analysis of populations from the peripheral blood, and the profiling of tissue-resident populations. We place emphasis on capabilities unique to scRNA-seq, such as the ability to obtain paired T-cell receptor and transcriptome information from single T cells and the potential to elucidate interactions between CD4+ T cells and other cells in their environment. Finally, we conclude by considering future areas of technologic advancement and innovation through which scRNA-seq may further shape our understanding of the roles of CD4+ T cells in health and disease.