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

Marcia R. Saban, Helen Hellmich, Ngoc Bich Nguyen, John Winston, Timothy G. Hammond, Ricardo Saban

Research output: Contribution to journalArticle

85 Citations (Scopus)

Abstract

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, α- and β-nerve growth factor (α- and β-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-κB (NF-κB) 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.

Original languageEnglish (US)
Pages (from-to)147-160
Number of pages14
JournalPhysiological Genomics
Volume2001
Issue number5
StatePublished - Jun 2001

Fingerprint

Lipopolysaccharides
Multigene Family
Inflammation
Gene Expression
Oligonucleotide Array Sequence Analysis
Urinary Bladder
Chemokine Receptors
Genes
Interleukin Receptors
Vascular Endothelial Growth Factor Receptor-1
Interleukin-6 Receptors
CC Chemokines
P-Selectin
Cystitis
Cysteine Proteases
Neutrophil Infiltration
Atlases
Interleukins
Nerve Growth Factor
Microarray Analysis

Keywords

  • Gene array
  • Interstitial cystitis
  • Mouse model of disease
  • Urinary bladder inflammation

ASJC Scopus subject areas

  • Genetics
  • Physiology

Cite this

Time course of LPS-induced gene expression in a mouse model of genitourinary inflammation. / Saban, Marcia R.; Hellmich, Helen; Nguyen, Ngoc Bich; Winston, John; Hammond, Timothy G.; Saban, Ricardo.

In: Physiological Genomics, Vol. 2001, No. 5, 06.2001, p. 147-160.

Research output: Contribution to journalArticle

Saban, Marcia R. ; Hellmich, Helen ; Nguyen, Ngoc Bich ; Winston, John ; Hammond, Timothy G. ; Saban, Ricardo. / Time course of LPS-induced gene expression in a mouse model of genitourinary inflammation. In: Physiological Genomics. 2001 ; Vol. 2001, No. 5. pp. 147-160.
@article{428f2074c8584799923e4f63ba05803d,
title = "Time course of LPS-induced gene expression in a mouse model of genitourinary inflammation",
abstract = "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, α- and β-nerve growth factor (α- and β-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-κB (NF-κB) 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.",
keywords = "Gene array, Interstitial cystitis, Mouse model of disease, Urinary bladder inflammation",
author = "Saban, {Marcia R.} and Helen Hellmich and Nguyen, {Ngoc Bich} and John Winston and Hammond, {Timothy G.} and Ricardo Saban",
year = "2001",
month = "6",
language = "English (US)",
volume = "2001",
pages = "147--160",
journal = "Physiological Genomics",
issn = "1094-8341",
publisher = "American Physiological Society",
number = "5",

}

TY - JOUR

T1 - Time course of LPS-induced gene expression in a mouse model of genitourinary inflammation

AU - Saban, Marcia R.

AU - Hellmich, Helen

AU - Nguyen, Ngoc Bich

AU - Winston, John

AU - Hammond, Timothy G.

AU - Saban, Ricardo

PY - 2001/6

Y1 - 2001/6

N2 - 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, α- and β-nerve growth factor (α- and β-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-κB (NF-κB) 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.

AB - 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, α- and β-nerve growth factor (α- and β-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-κB (NF-κB) 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.

KW - Gene array

KW - Interstitial cystitis

KW - Mouse model of disease

KW - Urinary bladder inflammation

UR - http://www.scopus.com/inward/record.url?scp=0347573332&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0347573332&partnerID=8YFLogxK

M3 - Article

VL - 2001

SP - 147

EP - 160

JO - Physiological Genomics

JF - Physiological Genomics

SN - 1094-8341

IS - 5

ER -