Background/Purpose: Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a small-vessel autoimmune vasculitis, associated with severe lung and kidney impairment. B cells are crucial in AAV pathogenesis, further demonstrated by the beneficial clinical effects of rituximab (anti-CD20 B cell targeted) therapy. However, B lineage cell studies in AAV mostly rely on the peripheral blood, emphasizing the need to characterize these populations and their T cell counterparts in other compartments of the immune system and in the target tissues to understand their role in the pathogenesis. 

We aim to profile immune cells at single-cell resolution inkidney biopsies from AAV patients with active disease and a nephrectomy control, studying the resulting clusters of B and T lineage cells.

Methods: Core-needle kidney biopsies were obtained from 4 patients with AAV glomerulonephritis and a nephrectomy control. Live CD45⁺ immune cells from the kidney were sorted and processed for single-cell data generation and analysis. Annotation was based on the mature immune kidney cell atlas.

Results: We identified 24 clusters from which we focused on the main players of adaptive immunity: B and T lineage cells. Two B cell enriched clusters (based on CD19/CD20 expression; 5.07% of total) and one plasmablast/plasma cell cluster (based on CD38/CD138 expression; 0.45% of total) were re-clustered for further analysis. We obtained 4 subpopulations at low resolution, annotated as memory B cells (MS4A1, CD19, CD27, PAX5), naïve B cells (MS4A1, CD19, IGHD), plasmablast-like (MS4A1, CD19, CD27, TNFRSF13C, XBP1), and plasma cells (CD38, SDC1, IRF4, XBP1, PRDM1). The relative mean frequencies of the B lineage populations were 51.20% memory, 38.72% naïve , 5.24% plasmablasts, and 4.85% plasma cells. With higher resolution, 3 different subtypes of memory B cells were observed, in addition to 3 naïve/germinal center-like B cells, and the 2 previously well-defined plasmablast and plasma cell clusters. We identified 11 T cell enriched clusters (based on CD3 expression; 61.35% of total) and three NK/NKT cell clusters (based on CD16 expression; 14.24% of total), which were further re-clustered. Low resolution clustering resulted in 4 CD4 T cell clusters, 4 CD8 T cell clusters and 2 NK/NKT cell clusters, with a relative mean frequency of 34.06%, 50.19% and 15.75%, respectively. An increased resolution revealed 8 CD4 subpopulations, including one Treg cluster (based on FOXP3 and CTLA4 expression) and one T helper-like cluster (based on PDCD1 and CD40LG expression); 8 CD8 subpopulations, including one TEMRA-like subset (based on CD45RA, GZMH, GNLY, PRF1 expression); and 3 NK subclusters.

Conclusion: Our preliminary data profiles, for the first time, B and T cell populations in kidney biopsies from AAV patients with glomerulonephritis at single-cell resolution. Comprehensive examination of these clusters may reveal (pathogenic) subsets potentially specific for AAV or ANCA subtype that may contribute to kidney involvement. Subsequent gene set enrichment analysis may identify differential gene expression patterns and intracellular signalling pathways involved, offering potential targets for more directed therapies.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/profiling-of-b-and-t-cells-in-kidney-biopsies-from-anca-associated-vasculitis-patients-with-glomerulonephritis-at-single-cell-resolution/