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

doi:10.1073/pnas.0401168101

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

^*Division of Pulmonary Allergy and Critical Care Medicine, Department of Medicine, and ^§Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213; ^¶Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15213; ^‡Jiangsu Key Laboratory for Molecular Medical Biotechnology, Nanjing Normal University, Nanjing 210097, China; ^∥Department of Pathology and Laboratory Medicine, St. Paul's Hospital-Providence Health Care, University of British Columbia, Vancouver, BC, Canada V6Z 1Y6; and ^**Department of Medicine, College of Physicians and Surgeons of Columbia University, New York, NY 10032

Edited by Bert Vogelstein, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, and approved August 30, 2004 (received for review February 19, 2004)

Abstract

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 α, IL-1β, and IFN-γ) 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.

Footnotes

↵ †† To whom correspondence should be addressed at: University of Pittsburgh, Division of Pulmonary Allergy and Critical Care Medicine, Montefiore University Hospital 628 NW, 3459 Fifth Avenue, Pittsburgh, PA 15213. E-mail: choiam{at}upmc.edu.
↵ † W.N. and C.-J.L. contributed equally to this work.
Author contributions: A.M.K.C. designed research; W.N., C.-J.L., S.M.A., S.L.O., and S.C.W. performed research; C.A.F.-B., Y.P.D., R.S., S.H., Z.Z., D.J.P., J.M.P., and J.C.H. contributed new reagents/analytic tools; W.N., C.-J.L., N.K., S.H., D.G.P., J.C.H., and A.M.K.C. analyzed data; W.N., C.-J.L., D.G.P., and A.M.K.C. wrote the paper.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: COPD, chronic obstructive pulmonary disease; SAGE, serial analysis of gene expression; QRT-PCR, real-time quantitative RT-PCR; CSE, cigarette smoke extract; MMP, matrix metalloproteinase; FEV₁, forced expiratory volume in 1 sec; TNF-α, tumor necrosis factor α; GO, gene ontology.