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Updated: Aug 6, 2026
Detection of MicroRNA Expression in the Kidneys of Immunoglobulin A Nephropathic Mice
Published on: July 8, 2020
A Combined Transcriptomics and Proteomics Approach to Identify Immune Signatures in ANCA-Associated
Ivana Stojkic1,2, John P Shapiro3, Arnon Arazi4
1Division of Pediatric Rheumatology, Nationwide Children's Hospital, Columbus, Ohio.
Objective:
Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis often leads to severe kidney damage. To better understand ANCA-associated glomerulonephritis (AAGN) and identify potential new therapeutic targets, we performed comprehensive transcriptomic and compartmental proteomic analysis of kidney biopsies from 23 patients in the transcriptomic cohort, 10 in the proteomic cohort, and 5 healthy controls for each comparison.
Methods:
Bulk RNA sequencing was performed on formalin-fixed paraffin-embedded kidney biopsies. Differentially expressed genes and pathways were identified using DESeq2, Ingenuity Pathway Analysis, and gene set enrichment analysis (GSEA). Correlations between gene expression and histologic features were assessed. Proteomic analysis was conducted via mass spectrometry of laser-microdissected glomerular and tubulointerstitial compartments to identify differentially abundant proteins and enriched pathways.
Results:
In AAGN, 347 genes were up-regulated and 134 down-regulated compared to controls, including IL17D, CXCR2, IL7R, and CD163. Notably, several tripartite motif (TRIM) family genes were up-regulated. GSEA revealed broad immune cell enrichment and activation of proinflammatory interleukin (IL)-12, IL-17, and IL-18 signaling. Additionally, specific pathways correlated with histologic features (r ≥ 0.6), including enrichment of the complement cascade in histologically normal glomeruli, suggesting complement activation precedes visible structural damage. Conversely, STAT3/TRIM25 signaling correlated with glomerulosclerosis, IL-23 with necrotizing glomeruli, and FAT10 (UBD) signaling with interstitial fibrosis and tubular atrophy. Proteomics identified 63 differentially abundant proteins in the tubulointerstitium and 271 in glomeruli, with key network activators overlapping across data sets.
Conclusion:
This study uncovered a complex intrarenal immune landscape in AAGN, featuring diverse immune cell involvement and pathways associated with progressive damage. Our findings highlight potential therapeutic targets for further investigation, including IL-17, IL-8, and IL-23.
