MicroRNA signatures of CD4+ T cell subsets in healthy and multiple sclerosis subjects determined by small RNA-sequencing

Diverse CD4+ T cell subsets with specialized functions operate at different phases of the immune response. Among these are naïve, central memory (CM), effector memory (CM), and regulatory (Treg) cells that have been phenotypically and functionally characterized. To expand current knowledge and identify highly subset-selective markers, we have profiled miRNAs using small RNA-sequencing in FACS-sorted CD4+ T cell subsets from healthy subjects and untreated patients with relapsing-remitting multiple sclerosis (RRMS). Genomic clustering and abundance of the miRNAs were also investigated. From the 60 most differentially expressed miRNAs, broad signatures and highly selective core signatures were identified for naïve and memory CD4+ T cells at homeostasis, while miR-146a-5p was strongly upregulated in Treg cells. In line with other studies, a 5-miRNA core signature was identified for naïve cells (miR-125b-5p, miR-99a-5p, miR-365a-3p, miR-365b-3p, miR-193b-3p). Supporting the progressive memory T cell differentiation model, a number of miRNAs were upregulated in CM and EM cells and, notably, at higher level in EM cells. This was particularly the case for a miRNA core of 8 miRNAs from miR-23a~27a~24-2, miR-23b~27b~24-1, miR-221~222 clusters, and miR-22-3p, miR-181c-5p, with highly abundant miR-24-3p. In addition, we detected activation of the large ChrXq27.3 miR-506~514 cluster in EM cells. Interestingly, most of the miRNAs that were enriched in EM cells were shown to negatively regulate cell proliferation and survival. Finally, we found that the miRNA core signatures of naïve and memory CD4+ T cells were conserved in RRMS patients. Only few miRNAs were quantitatively modified, among these, miR-1248 was downregulated and may be a candidate disease marker. We have profiled miRNAs using small RNA-sequencing in FACS-sorted CD4+ T cell subsets from healthy subjects and untreated patients with relapsing-remitting multiple sclerosis (RRMS)