Background Single-cell RNA-sequencing (scRNA-seq) has been recently applied in systemic lupus erythematosus (SLE) to define distinct cellular composition and transcriptional signatures, greatly expanding our understanding of SLE pathogenesis. However, since most of the studies were cross-sectional approach from a single moment in time, dynamic feature of immune cells over the disease course is yet to be revealed.

Methods We analyzed serial longitudinal PBMC samples (N=19) obtained at various time points of SLEDAI ranged from 4 to 19 in lupus nephritis (N=6) and from controls (N=33) using scRNA-seq (10X Chromium 5’, TCR sequencing).

Results SLE showed different cellular composition; reduction of CD4+ T, monocytes, cDC, pDC, and increases of CD8+ T and B cells compared to controls. Expression of type 1 IFN signatures were increased in the most cell clusters. Cell to cell interaction analysis revealed activated CD8+ T cells were the most interactive cell population. Further analysis of CD8+ T cell showed increased T cell exhaustion markers and highest cytotoxicity in GZMH+ CD8+ Tem population in SLE. We also observed significantly decreased CD8+ T cell TCR diversity in SLE. To investigate dynamic transformation of immune cells during flare, especially CD8+ T cells, we analyzed selected paired samples before and after flare of lupus nephritis (N=12). In flare state, GZMH+ CD8+ Tem were expanded, displaying increased cytotoxicity with reduction of TCR diversity. We also observed expression of T cell exhaustion markers, but reduced Type 1 IFN signalling in flare state. Interestingly, the paired TCR repertoire and mitochondrial mutation analysis reveals expanded effector CD8+ T cell clonotypes are heterogeneous in each flare from the same patient, directing towards unique antigen convergence in flare stage.

Conclusions These results uncover dynamic transition of peripheral blood immune cells during flare of lupus nephritis, especially in CD8+ T cell population, suggesting its pivotal roles in SLE pathogenesis.