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Physiol. Genomics 5: 147-160, 2001;
1094-8341/01 $5.00
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Received 22 November 2000; accepted in final form 14 February 2001.
Physiological Genomics 5:147-160 (2001)
1094-8341/01 $5.00 © 2001 American Physiological Society

Time course of LPS-induced gene expression in a mouse model of genitourinary inflammation

MARCIA R. SABAN 1, HELEN HELLMICH 2, NGOC-BICH NGUYEN 1, JOHN WINSTON 2, TIMOTHY G. HAMMOND 3 and RICARDO SABAN 1

1 Department of Physiology, University Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73190
2 Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas 77555
3 Tulane Environmental Astrobiology Center, and Nephrology Section, Tulane University Medical Center, and Veterans Affairs Medical Center, New Orleans, Louisiana 70112

In this study, self-organizing map (SOM) gene cluster techniques are applied to the analysis of cDNA microarray analysis of gene expression changes occurring in the early stages of genitourinary inflammation. We determined the time course of lipopolysaccharide (LPS)-induced gene expression in experimental cystitis. Mice were euthanized 0.5, 1, 4, and 24 h after LPS instillation into the urinary bladder, and gene expression was determined using four replicate Atlas mouse cDNA expression arrays containing 588 known genes at each time point. SOM gene cluster analysis, performed without preconditions, identified functionally significant gene clusters based on the kinetics of change in gene expression. Genes were classified as follows: 1) expressed at time 0; 2) early genes (peak expression between 0.5 and 1 h); and 3) late genes (peak expression between 4 and 24 h). One gene cluster maintained a constant level of expression during the entire time period studied. In contrast, LPS treatment downregulated the expression of some genes expressed at time 0, in a cluster including transcription factors, protooncogenes, apoptosis-related proteins (cysteine protease), intracellular kinases, and growth factors. Gene upregulation in response to LPS was observed as early as 0.5 h in a cluster including the interleukin-6 (IL-6) receptor, {alpha}- and ß-nerve growth factor ({alpha}- and ß-NGF), vascular endothelial growth factor receptor-1 (VEGF R1), C-C chemokine receptor, and P-selectin. Another tight cluster of genes with marked expression at 1 h after LPS and insignificant expression at all other time points studied included the protooncogenes c-Fos, Fos-B, Fra-2, Jun-B, Jun-D, and Egr-1. Almost all interleukin genes were upregulated as early as 1 h after stimulation with LPS. Nuclear factor-{kappa}B (NF-{kappa}B) pathway genes collected in a single cluster with a peak expression 4 h after LPS stimulation. In contrast, most of the interleukin receptors and chemokine receptors presented a late peak of expression 24 h after LPS coinciding with the peak of neutrophil infiltration into the bladder wall. Selected cDNA microarray observations were confirmed by RNase protection assay. In conclusion, the cDNA array experimental approach provided a global profile of gene expression changes in bladder tissue after stimulation with LPS. SOM techniques identified functionally significant gene clusters, providing a powerful technical basis for future analysis of mechanisms of bladder inflammation.

gene array; mouse model of disease; urinary bladder inflammation; interstitial cystitis




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