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

In this study, self-organizing map (SOM) gene cluster techniques are applie d to the analysis of cDNA microarray analysis of gene expression changes oc curring in the early stages of genitourinary inflammation. We determined th e time course of lipopolysaccharide (LPS) induced gene expression in experi mental cystitis. Mice were euthanized 0.5, 1, 4, and 24 h after LPS instill ation into the urinary bladder, and gene expression was determined using fo ur replicate Atlas mouse cDNA expression arrays containing 588 known genes at each time point. SOM gene cluster analysis, performed without preconditi ons, identified functionally significant gene clusters based on the kinetic s of change in gene expression. Genes were classified as follows: 1) expres sed 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 maintain ed a constant level of expression during the entire time period studied. In contrast, LPS treatment downregulated the expression of some genes express ed 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 beta -nerve growth factor (alpha- and beta -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 pro tooncogenes c-Fos, Fos-B, Fra-2, Jun-B, Jun-D, and Egr-1. Almost all interl eukin genes were upregulated as early as 1 h after stimulation with LPS. Nu clear factor-kappaB (NF-kappaB) 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 exp ression 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 appr oach provided a global profile of gene expression changes in bladder tissue after stimulation with LPS. SOM techniques identified functionally signifi cant gene clusters, providing a powerful technical basis for future analysi s of mechanisms of bladder inflammation.