Gene Expression Profiles of Acute Exacerbations of Idiopathic Pulmonary Fibrosis

• Published in: American journal of respiratory and critical care medicine 2009-07, Vol.180 (2), p.167-175
• Main Authors: Konishi, Kazuhisa, Gibson, Kevin F, Lindell, Kathleen O, Richards, Thomas J, Zhang, Yingze, Dhir, Rajiv, Bisceglia, Michelle, Gilbert, Sebastien, Yousem, Samuel A, Song, Jin Woo, Kim, Dong Soon, Kaminski, Naftali
• Format: Article
• Language: English
• Subjects: Acute Disease; Aged; alpha-Defensins - genetics; alpha-Defensins - metabolism; Anesthesia. Intensive care medicine. Transfusions. Cell therapy and gene therapy; Antibodies; Apoptosis; Biological and medical sciences; Biomarkers; Case-Control Studies; Cyclin A - genetics; Cyclin A - metabolism; Cyclin A2; D. Interstitial Lung Disease; Dyspnea - etiology; Dyspnea - metabolism; Expected values; Female; Gene expression; Gene Expression Profiling; Genetic Markers; Humans; Idiopathic Pulmonary Fibrosis - complications; Idiopathic Pulmonary Fibrosis - genetics; Idiopathic Pulmonary Fibrosis - metabolism; Intensive care medicine; Labeling; Laboratories; Lungs; Male; Medical sciences; Middle Aged; Oligonucleotide Array Sequence Analysis; Pneumology; Polymerase chain reaction; Proteins; Pulmonary fibrosis; Pulmonary hypertension. Acute cor pulmonale. Pulmonary embolism. Pulmonary vascular diseases; RNA, Messenger - metabolism; Viral infections
• ISSN: 1073-449X; 1535-4970
• DOI: 10.1164/rccm.200810-1596OC

The molecular mechanisms underlying acute exacerbations of idiopathic pulmonary fibrosis (IPF) are poorly understood. We studied the global gene expression signature of acute exacerbations of IPF. To understand the gene expression patterns of acute exacerbations of IPF. RNA was extracted from 23 stable IPF lungs, 8 IPF lungs with acute exacerbation (IPF-AEx), and 15 control lungs and used for hybridization on Agilent gene expression microarrays. Functional analysis of genes was performed with Spotfire and Genomica. Gene validations for MMP1, MMP7, AGER, DEFA1-3, COL1A2, and CCNA2 were performed by real-time quantitative reverse transcription-polymerase chain reaction. Immunohistochemistry and in situ terminal deoxynucleotidyltransferase dUTP nick end-labeling assays were performed on the same tissues used for the microarray. ELISA for alpha-defensins was performed on plasma from control subjects, patients with stable IPF, and patients with IPF-AEx. Gene expression patterns in IPF-AEx and IPF samples were similar for the genes that distinguish IPF from control lungs. Five hundred and seventy-nine genes were differentially expressed (false discovery rate < 5%) between stable IPF and IPF-AEx. Functional analysis of these genes did not indicate any evidence of an infectious or overwhelming inflammatory etiology. CCNA2 and alpha-defensins were among the most up-regulated genes. CCNA2 and alpha-defensin protein levels were also higher and localized to the epithelium of IPF-AEx, where widespread apoptosis was also detected. alpha-Defensin protein levels were increased in the peripheral blood of patients with IPF-AEx. Our results indicate that IPF-AEx is characterized by enhanced epithelial injury and proliferation, as reflected by increases in CCNA2 and alpha-defensins and apoptosis of epithelium. The concomitant increase in alpha-defensins in the peripheral blood and lungs may suggest their use as biomarkers for this disorder.