Characterizing Memory T Cells Associated with Systemic Lupus Erythematosus Pathogenesis
Systemic Lupus Erythematosus (SLE) is a chronic autoimmune disease associated with a severe morbidity and mortality. Around 70% of SLE patients follow a relapse-remitting pattern of disease characterized by flares of disease activity, followed by prolonged periods of disease quiescence. Memory CD4+ T cell subsets have been shown to play an important role in driving the autoantibody production which causes flares in SLE, however the precise T cell changes that accompany flares are unknown. CITE-seq and TCR-seq were performed to assess the transcriptomic profiles of CD4+ memory T cells in flaring and quiescent SLE patients. CD4+ memory T cells were isolated from PBMCs by negative selection using magnetic sorting, stained with oligo-conjugated antibodies against surface proteins for subset classification, and subsequently partitioned, barcoded, and sequenced. We examined samples from 15 distinct patients at 2 separate clinical visits spaced one year apart, yielding 30 samples. The longitudinal nature of our data allows us to inspect transcriptional changes both between and within patients. Integrated analysis of 30 samples identified 10 immune cell clusters (Figure 1A). At baseline, flaring patients (n=9) were significantly enriched for Tfh, Th2, Th17 cells, and a Treg subset, while quiescent patients (n=6) had increased Th1 cells. TCR repertoire analyses at baseline revealed a higher proportion of expanded clonotypes in flaring patients, which was not seen in quiescent patients. Interestingly, we also found that there was a higher proportion of expanded clonotypes at follow-up in various subsets of interest, particularly in flaring patients that later became quiescent, suggesting tissue egress and recirculation following resolution of inflammation. Clonal overlap among subsets was markedly greater in flaring patients, suggesting shared antigen specificity and differentiation from common progenitors. More specifically, we identified 2 functionally deviated/exhausted Treg subsets (ISGhi/ISGlo) (Figure 1B) and, at baseline, found notable clonal overlap between the ISGhi Treg subset and Th2/17 cells and between the ISGlo subset and Tfh/Tph cells in flaring patients, which was absent in quiescent patients (Figure 1C). This suggests that there are 2 distinct subsets of cells with shared antigen exposure and/or functional plasticity; one that is exposed to an IFN-rich environment in the tissue, and another that is more involved in T-B cell interactions within lymphoid compartments. We found abnormal Treg subsets with features of exhaustion and functional deviation that shared antigen specificity with other T helper cells. Their increased prevalence during flares suggests that dysregulated immunoregulation may contribute to SLE pathogenesis.