Spatially resolved transcriptomic profiling for glomerular and tubulointerstitial gene expression in C3 glomerulopathy

Abstract

AbstractIntroductionC3 glomerulopathy (C3G) is a rare but clinically significant glomerulopathy. However, little is known about its transcriptomic profile. We investigated the substructure-specific gene expression profile of C3G using the recently introduced spatial transcriptomics technology.MethodsWe performed spatial transcriptomic profiling using GeoMx Digital Spatial Profiler with formalin-fixed paraffin-embedded kidney biopsy specimens of three C3G cases and seven controls from donor kidney biopsy. Additionally, 41 samples of other glomerulonephritis, including focal segmental glomerulosclerosis, membranous nephropathy, and minimal change disease, were included as disease controls. Gene expression levels were compared by DESeq2 method to identify differentially expressed genes (DEGs). We performed gene ontology (GO) annotation through the ToppGene suite and mapped interactions among the DEGs using the STRING database.ResultsWe identified 229 and 157 highly expressed DEGs in the glomeruli of C3G compared to those of donor and disease controls, respectively, with consistently highest fold changes in POSTN, COL1A2, and IFI44L. Protease binding, structural molecule activity, and extracellular matrix structural constituent were among the top enriched GO terms in the glomeruli of C3G, with consistent features seen in the network analysis. In contrast, no significant GO enrichment was found among the 563 and 347 lowly expressed DEGs in the glomeruli of C3G compared to the controls. The tubulointerstitial transcriptomic profiles of C3G were similar to those of the controls.ConclusionIn the glomerulus of C3G, genes related to the extracellular matrix and interferon activity were the most upregulated. Significant disease-specific transcriptomic alterations in C3G provide potential insights into the pathophysiology.