Exploratory single-cell profiling of intrarenal B and T cell subsets in ANCA-associated glomerulonephritis

Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a small-vessel autoimmune vasculitis often accompanied by glomerulonephritis impacting kidney function. Although B and T cells are central to AAV pathogenesis, current knowledge is largely based on peripheral blood analyses, underscoring the need to define their subsets and interactions within target tissues. Core-needle kidney biopsies were obtained from five AAV patients with glomerulonephritis (AGN), one lupus nephritis (LN) and one nephrectomy control (NC). Live CD45 + immune cells were isolated for single-cell transcriptomic analysis, followed by B and T cells re-clustering and analysis of differential gene and protein expression, gene set enrichment and CellChat-based cell-cell communication. We identified 24 clusters and re-clustered B cell- and CD4 + /CD8 + T cell-enriched populations. B cell subpopulations included GC-like ( CXCR5 ; NF-κB signature), atypical memory (CD11c; antigen-presentation), uncharacterized with atypical/cytotoxic features ( HOPX , PRF1 ) and plasma ( SDC1 ) cells, with the latter two enriched in AGN. Among 11 CD4 + T cell clusters, Th1 ( TBX21 , IFNG ) and Th17 ( RORC , IL17A ) cells were increased in AGN versus NC and showed upregulated NF-κB signaling, two regulatory subsets ( FOXP3; IL-2/STAT5 signaling) and follicular T helper cells ( CXCL13 ), newly identified in AGN. CD8 + T cells included inflammatory Tc1 ( IFNG , TNF ) and Tc17 ( RORC , IL23R ) populations enriched in AGN, as well as 3 CD45RA-expressing effector memory (Temra) populations. CellChat analysis revealed distinct B-T cell communication networks in AGN. Exploratory single-cell profiling of B and T cells in AGN and NC kidney identified potentially pathogenic subsets and their signaling/communication patterns, offering novel targets for more directed therapies.