Deep Immunophenotyping Reveals Cellular Phenotypes in Peripheral Blood Associated with Specific Patterns of Kidney Injury in Lupus Nephritis

Abstract Text: Lupus nephritis (LN) is a severe complication of systemic lupus requiring renal biopsy to guide treatment decisions. Defining LN heterogeneity using a non-invasive approach is a pressing need to improve treatment. We applied mass cytometry using four 48-marker panels to characterize peripheral blood mononuclear cells (PBMC) from 140 patients with biopsy-proven LN and 40 controls enrolled in the Accelerating Medicines Partnership RA/SLE Network. We projected cells in a reduced dimensional space and implemented covarying neighborhood analysis (CNA) to identify cell ‘neighborhoods’ associated with clinical features. Compared to controls, LN patients displayed significant enrichment of cells expressing interferon (IFN)-induced proteins including MX1 and Siglec1, reflecting a cytometric detection of an IFN signature. Comparing patients with proliferative LN (class III/IV+/-V, n=94) versus membranous LN (class V, n=46), we observed enrichment of a specific naive B cell population characterized as CD23- and CD21dim, in proliferative LN patients (p.adj=0.02). These cells were distinct from CD11c+ B cells and were also associated with increased histologic NIH activity index and with anti-dsDNA antibody, even after adjusting for immunosuppression. To further understand LN heterogeneity, we clustered patients and controls based on proportions of immune cell subsets using k-means clustering. We identified two major clusters: cluster1 included only LN patients, and cluster 2 included controls and 26 LN patients. Patients from cluster2 had significantly lower clinical extrarenal activity (p.adj=0.01) and IFN-induced protein expression (p.adj < 0.001) and higher histologic chronicity (p.adj < 0.001). These results nominate potential biomarkers associated with LN heterogeneity and highlight altered naive B cell activation in proliferative LN.