Single-cell transcriptomes and T cell receptor sequences of CD4 or CD8 single positive T lymphocytes from peripheral blood or urine of lupus nephritis patients at flare.

Although these T cells have been attributed with propagation of tissue injury, it is unclear how they are activated and whether T cell autoreactivity drives the local inflammation. Kidney-infiltrating T cells are also observed in urine, where they have high resemblance with interstitial T cells.

Therefore, urinary T cells are a proxy to investigate tissue pathogenesis. Here, we analyzed urinary T cells to elucidate if a kidney-specific T cell autoimmune reaction contributes to tubulointerstitial inflammation in LN. Using single cell RNA sequencing, we compared transcriptomes and clonotypes of T cells from blood and urine of patients with active LN and show that urinary T cells were mostly activated CD8 effector memory cells recruited from a circulating CX3CR1+ subset.