Abstract

Abstract Background and Aims The ISN/RPS 2003 classification is the current gold standard histopathological classification for lupus nephritis (LN), and has important roles in guiding treatment and predicting prognosis. The classification system, largely based on light microscopy features, does not inform the underlying immunological aberrations. A classification based on molecular typing of immune-related pathways may better stratify LN patients and help select treatments that target specific immune cascades. Method The normalized expression matrix and clinical data were extracted from Gene Expression Omnibus database, Human Cell Atlas (Hacohen-Human-CELseq2) and Nephroseq. Four chip datasets (GSE127797, 32591, 69438 and 37463) and one single cell dataset were analyzed. Sample gene set enrichment analysis (ssGSEA) method was used to derive immune phenotype with gene expression data. The hierarchical clustering with ssGSEA scores of selected gene sets was used to classify LN tissues. Functional characterization and protein-protein interactions of the differential expression genes (DEGs) of three groups were compared with healthy donors using Metascape (absolute log FC > 1 and adjusted P-value < .05). Kruskal-Walli test and chi-square test were performed to compare the clinical parameters of the different groups. Results We analyzed 96 immune-related gene sets in the glomerular and tubulointerstitial regions of LN kidney biopsy samples. The immune-related genes were categorized into three clusters (Immune-Mild, Immune-Moderate and Immune-Severe) based on the degree of immune pathway activation. Interferon-stimulated genes are a hallmark of LN, with high signals in all three clusters. When compared to other groups, the Immune-Mild cluster from the glomerular region showed no T-cell activation or T cell receptor pathway. Also, the Immune-Mild (tubulointerstitial) group also showed minimal lymphocyte activation or migration. Protein-protein interactions networks with MOCDE components further suggested that STAT1 and ISG15 the hub genes in different clusters. The gene expressions of hub genes were then compared among epithelial cells and 21 immune cells from LN and heath controls. Immune clusters are correlated with clinical phenotypes, in which Immune-Mild Group (Glomerular) showed high prevalence of Class II and V LN, and Immune-Mild (Tubulointerstitial) showed more Class V LN. Immune-Severe group also showed higher degree of proteinuria and blood pressure but lower eGFR compared to Immune-Moderate and Immune-Mild groups. Conclusion A new molecular classification of LN based on the degree of immune pathway activation shows correlation with clinical manifestations and may potentially guide personalized therapy in LN patients.

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