Comprehensive gene expression profiles reveal pathways related to the pathogenesis of chronic obstructive pulmonary disease.

To better understand the molecular basis of chronic obstructive pulmonary disease (COPD), we used serial analysis of gene expression (SAGE) and microarray analysis to compare the gene expression patterns of lung tissues from COPD and control smokers. A total of 59,343 tags corresponding to 26,502 transcripts were sequenced in SAGE analyses. A total of 327 genes were differentially expressed (1.5-fold up- or down-regulated). Microarray analysis using the same RNA source detected 261 transcripts that were differentially expressed to a significant degree between GOLD-2 and GOLD-0 smokers. We confirmed the altered expression of a select number of genes by using real-time quantitative RT-PCR. These genes encode for transcription factors (EGR1 and FOS), growth factors or related proteins (CTGF, CYR61, CX3CL1, TGFB1, and PDGFRA), and extracellular matrix protein (COL1A1). Immunofluorescence studies on the same lung specimens localized the expression of Egr-1, CTGF, and Cyr61 to alveolar epithelial cells, airway epithelial cells, and stromal and inflammatory cells of GOLD-2 smokers. Cigarette smoke extract induced Egr-1 protein expression and increased Egr-1 DNA-binding activity in human lung fibroblast cells. Cytomix (tumor necrosis factor alpha, IL-1beta, and IFN-gamma) treatment showed that the activity of matrix metalloproteinase-2 (MMP-2) was increased in lung fibroblasts from EGR1 control (+/+) mice but not detected in that of EGR1 null (-/-) mice, whereas MMP-9 was regulated by EGR1 in a reverse manner. Our study represents the first comprehensive analysis of gene expression on GOLD-2 versus GOLD-0 smokers and reveals previously unreported candidate genes that may serve as potential molecular targets in COPD.

[1]  D. Peters,et al.  Genome-wide analysis of the endothelial transcriptome under short-term chronic hypoxia. , 2004, Physiological genomics.

[2]  Joaquín Dopazo,et al.  FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes , 2004, Bioinform..

[3]  Mi-Ock Lee,et al.  Identification of genes that are induced after cadmium exposure by suppression subtractive hybridization. , 2003, Toxicology.

[4]  Purvesh Khatri,et al.  Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate , 2003, Nucleic Acids Res..

[5]  Michael D Stern,et al.  The new role of SAGE in gene discovery. , 2003, Trends in biotechnology.

[6]  Mary E. Choi,et al.  TGF-β1 stimulates HO-1 via the p38 mitogen-activated protein kinase in A549 pulmonary epithelial cells , 2002 .

[7]  C. Zarins,et al.  Arterial enlargement in response to high flow requires early expression of matrix metalloproteinases to degrade extracellular matrix. , 2002, Experimental and molecular pathology.

[8]  A. Churg,et al.  Acute cigarette smoke-induced connective tissue breakdown requires both neutrophils and macrophage metalloelastase in mice. , 2002, American journal of respiratory cell and molecular biology.

[9]  Nir Friedman,et al.  Practical approaches to analyzing results of microarray experiments. , 2002, American journal of respiratory cell and molecular biology.

[10]  Liang Shi,et al.  Lipopolysaccharide stimulation of ERK1/2 increases TNF-α production via Egr-1 , 2002 .

[11]  M. Nugent,et al.  Elastase-released Epidermal Growth Factor Recruits Epidermal Growth Factor Receptor and Extracellular Signal-regulated Kinases to Down-regulate Tropoelastin mRNA in Lung Fibroblasts* , 2002, The Journal of Biological Chemistry.

[12]  T. Petty.  COPD in perspective. , 2002, Chest.

[13]  W. MacNee,et al.  Chronic Obstructive Lung Disease , 2002 .

[14]  M. Holtzman.  Improving Peer Review and Introducing Translational Review , 2002 .

[15]  M. Xiong,et al.  Systemic Sclerosis (Scleroderma): Specific Autoantigen Genes Are Selectively Overexpressed in Scleroderma Fibroblasts1 , 2001, The Journal of Immunology.

[16]  D. Romberger,et al.  Retinoic acid attenuates cytokine-driven fibroblast degradation of extracellular matrix in three-dimensional culture. , 2001, American journal of respiratory cell and molecular biology.

[17]  W. MacNee,et al.  Oxidative stress and lung inflammation in airways disease. , 2001, European journal of pharmacology.

[18]  L. Newman,et al.  Genetic and environmental modulation of chronic obstructive pulmonary disease. , 2001, Respiration physiology.

[19]  M. Kagnoff,et al.  Analysis of host responses to microbial infection using gene expression profiling. , 2001, Current opinion in microbiology.

[20]  Y. Ouchi,et al.  Tobacco smoke reduces viability in human lung fibroblasts: protective effect of glutathione S-transferase P1. , 2001, American journal of physiology. Lung cellular and molecular physiology.

[21]  F. Yamasawa,et al.  Increased expression of transforming growth factor-beta1 in small airway epithelium from tobacco smokers and patients with chronic obstructive pulmonary disease (COPD). , 2001, American journal of respiratory and critical care medicine.

[22]  D. Knight.  Epithelium–fibroblast interactions in response to airway inflammation , 2001, Immunology and cell biology.

[23]  R. Pauwels,et al.  Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease. NHLBI/WHO Global Initiative for Chronic Obstructive Lung Disease (GOLD) Workshop summary. , 2001, American journal of respiratory and critical care medicine.

[24]  D. Stevenson,et al.  Unique effects of zinc protoporphyrin on HO-1 induction and apoptosis. , 2001, Blood.

[25]  Y. Zou,et al.  Expression of Egr-1 in late stage emphysema. , 2000, The American journal of pathology.

[26]  Pat Levitt,et al.  Molecular Characterization of Schizophrenia Viewed by Microarray Analysis of Gene Expression in Prefrontal Cortex , 2000, Neuron.

[27]  T. Godfrey,et al.  Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5' nuclease quantitative reverse transcription-polymerase chain reaction. , 2000, The Journal of molecular diagnostics : JMD.

[28]  R. M. Senior.  Mechanisms of COPD: conference summary. , 2000, Chest.

[29]  B. Markoff,et al.  Who's smoking now? The epidemiology of tobacco use in the United States and abroad. , 2000, Clinics in chest medicine.

[30]  D. Pinsky,et al.  Egr-1: is it always immediate and early? , 2000, The Journal of clinical investigation.

[31]  Simon C Watkins,et al.  Caspase‐3 Mediated Neuronal Death After Traumatic Brain Injury in Rats , 2000, Journal of neurochemistry.

[32]  J. Rowley,et al.  Generation of longer cDNA fragments from serial analysis of gene expression tags for gene identification. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[33]  S. Apte,et al.  Egr-1 Mediates Extracellular Matrix-driven Transcription of Membrane Type 1 Matrix Metalloproteinase in Endothelium* , 1999, The Journal of Biological Chemistry.

[34]  V. de Waard,et al.  Serial analysis of gene expression to assess the endothelial cell response to an atherogenic stimulus. , 1999, Gene.

[35]  J. Milbrandt,et al.  Luteinizing Hormone Deficiency and Female Infertility in Mice Lacking the Transcription Factor NGFI-A (Egr-1) , 1996, Science.

[36]  K. Kinzler,et al.  Serial Analysis of Gene Expression , 1995, Science.

[37]  W. Stetler-Stevenson,et al.  Quantitative zymography: detection of picogram quantities of gelatinases. , 1994, Analytical biochemistry.

[38]  F. ManresaPresas.  Chronic obstructive lung diseases , 1983 .

[39]  J. Bishop,et al.  The expression of three abundance classes of messenger RNA in mouse tissues , 1976, Cell.