Gene expression profiling of anti-GBM glomerulonephritis model: the role of NFκB in immune complex–mediated kidney disease

JuHan Kim^1§, and Il Soo Ha^2§, Chang-Il Hwang³, Young-Ju Lee³, Jihoon Kim¹, Seung-Hee Yang⁴, Yon Su Kim⁴, Yun Anna Cao⁵, Sangdun Choi⁵, Woong-Yang Park³*

¹Seoul National University Biomedical Informatics (SNUBI), ²Departments of Pediatrics, ³Biochemistry and Molecular Biology, and ⁴Internal Medicine, Seoul National University College of Medicine, Seoul 110-799, Korea, ⁵Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA

Background. Immune complexes may cause an irreversible onset of chronic renal disease. Most patients with chronic renal disease undergo a final common pathway, marked by glomerulosclerosis and interstitial fibrosis. We attempted to draw a molecular map of anti-GBM glomerulonephritis (GN) in mice using oligonucleotide microarray technology. 
Methods. Kidneys were harvested at days 1, 3, 7, 11 and 16 after inducing GN by using anti-GBM antibody. In parallel with examining the biochemical and histological changes, gene expression profile was acquired against five pooled control kidneys. Gene expression levels were cross-validated by either RT-PCR or immunohistochemistry.
Results. Pathological changes in anti-GBM GN were confirmed in both BALB/c and C57BL/6 strains. Among the 13,680 spotted 65mer oligonucleotides, 1,112 (FDR < 0.05) genes showing significant temporal patterns by permutation ANOVA with multiple-testing correction were chosen for cluster analysis. From the expression profile, acute inflammatory reactions characterized by the elevation of various cytokines, including IL-1 and IL-6, were identified within 3 days of disease onset. After 7 days, tissue remodeling response was prominent with highly induced extracellular-matrix genes. Although cytokines related to lymphocyte activation were not detected, monocyte or mesangial cell proliferation-related genes were increased. TNF-α and NFκB pathway were consistently activated along the entire disease progression, inducing various target genes like complement 3, IL-1b, IL-6, Traf1 and Saa1. 
Conclusions. We made a large-scale gene expression timetable for mouse anti-GBM GN model, providing a comprehensive overview on the mechanism governing the initiation and the progression of inflammatory renal disease.

Kidney International 2004;66(5):1826-1837

Cluster Analysis

See the 50 clusters for the significant 1,112 gene.

Biological Pathway Analysis

We conducted biological interpretation analysis of the 50 clusters. 

The biological pathway analysis was conducted using ArrayXPath (accepted and will appear in Nucleic Acids Research, 2004 July), a recently developed bioinformatics tool by SNUBI.

Raw Data: 

The microarray data illustrated in this paper were submitted to the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession numbers GSM15078-GSM15092, GSE954-GSE958, and GSE969.

Quality Plot

Supplementary quality plot for the statistical significance analysis using permutation ANOVA.

GO Annotations

GO Annotations for the 50 clusters.