Single-cell RNA sequence (scRNAseq) analysis of T regulatory cells in relapsing remitting multiple sclerosis (RRMS)

Abstract Patients with RRMS have decreased numbers and function of Tregs, which may play a causative role in the pathogenesis of the disease. Here, we used scRNAseq to define Tregs populations in peripheral blood of 3 RRMS patients and 3 matched healthy controls (HCs) and compare their transcriptomes and function. We clustered sorted CD4+CD25+CD127− Tregs into active (a) and resting (r)Tregs. Our initial scRNAseq data analysis of the active Tregs identified 324 up-regulated differentially expressed genes (DEGs) and 208 down-regulated genes in RRMS in comparison to HCs. Upregulated genes include major histocompatibility complex (MHC) class I (HLAA, HLAB) and class II (HLADRB5) and TRCA gene, supportive of their activated status; ICAM2, involved in the migration to the CNS; ID3, involved in maintaining Treg pool and suppressive function; LAIR2, an indicator for exhaustive Tregs; NEAT1, whose silencing promotes Treg/Th17 balance, and TCF7, that limits Treg thymic generation. Genes with decreased expression include CD7, required for Treg homeostasis; costimulatory CD81; CTLA4 and JUNB required for optimal Treg function; IFTM1 and IF16 that may regulate IFN type I induction of Tregs; CXCR4; LGALS1 and LGALS3 coding for galectin 1 and 3 which inhibit Treg function; and NFKBIA and TNFAIP3, all suggestive of decreased Treg function in RRMS. Pathway enrichment analysis for DEGs in RRMS Tregs identified the strongest enrichment for type I IFN signaling pathway. Understanding the transcriptional changes involved in deficient Tregs functions in RRMS is crucial for better understanding of the disease pathogenesis and for a development of effective treatment for this disabling disease. State of Pennsylvania grant: Deficient T regulatory Cell (Treg) Function in Relapsing Remitting Multiple Sclerosis (RRMS)