Altered mRNA expression in renal biopsy tissue from patients with IgA nephropathy

Abstract

Immunoglobulin A (IgA) nephropathy (IgAN) is a renal disease characterized by glomerular deposition of IgA-dominant immune deposits that cause glomerular inflammation and sclerosis. Gene expression changes induced in renal tissues/cells as a result of the disease are largely uncharacterized. A sensitive differential mRNA display technique, restriction endonucleolytic analysis of differentially expressed sequences (READS) compared similarly processed normal renal tissue to renal biopsy RNA from patients with IgAN, minimal change disease, and necrotizing crescentic glomerulonephritis. A subset of genes with altered expression in IgAN as identified by the READS technology was further characterized and expression levels confirmed using real-time quantitative polymerase chain reaction (RT-PCR) analysis (TaqMan) in all RNA. Initial READS analysis showed IgAN samples have lower mRNA levels relative to normal renal tissue mRNA samples based upon total RNA as measured by ribosomal RNA. One hundred seventy-five differentially expressed non-redundant fragments were found from 860 initial candidate fragments. Twenty genes were selected for additional TaqMan analysis, and 13 of 20 genes showed statistically different expression when comparing biopsies from normal individuals and IgAN patients. Expression differences were seen in these genes in biopsies of IgAN of differing clinical activities. Gene expression cluster analysis using the Ward method detailed disease- and gene-related clusters. Detailed examination of the promoter regions of the genes within two gene clusters revealed common gene transcriptional regulatory protein-binding sites. IgAN leads to significant changes in overall mRNA transcription levels within the renal tissue, in addition to gene-specific mRNA level changes. Disease-related patterns of expression were identified and gene-specific clusters suggest common mechanisms of transcriptional alteration.