Molecular biomarkers for quantitative and discrete COPD phenotypes.
Chronic obstructive pulmonary disease (COPD) is an inflammatory lung disorder with complex pathological features and largely unknown etiology. The identification of biomarkers for this disease could aid the development of methods to facilitate earlier diagnosis, the classification of disease subtypes, and provide a means to define therapeutic response. To identify gene expression biomarkers, we completed expression profiling of RNA derived from the lung tissue of 56 subjects with varying degrees of airflow obstruction using the Affymetrix U133 Plus 2.0 array. We applied multiple, independent analytical methods to define biomarkers for either discrete or quantitative disease phenotypes. Analysis of differential expression between cases (n = 15) and controls (n = 18) identified a set of 65 discrete biomarkers. Correlation of gene expression with quantitative measures of airflow obstruction (FEV(1)%predicted or FEV(1)/FVC) identified a set of 220 biomarkers. Biomarker genes were enriched in functions related to DNA binding and regulation of transcription. We used this group of biomarkers to predict disease in an unrelated data set, generated from patients with severe emphysema, with 97% accuracy. Our data contribute to the understanding of gene expression changes occurring in the lung tissue of patients with obstructive lung disease and provide additional insight into potential mechanisms involved in the disease process. Furthermore, we present the first gene expression biomarker for COPD validated in an independent data set.
Bhattacharya
Soumyaroop
S
Division of Neonatology and Center for Pediatric Biomedical Research, Department of Pediatrics, University of Rochester, Box 703, 601 Elmwood Avenue, Rochester, NY 14642, USA.
Srisuma
Sorachai
S
Demeo
Dawn L
DL
Shapiro
Steven D
SD
Bueno
Raphael
R
Silverman
Edwin K
EK
Reilly
John J
JJ
Mariani
Thomas J
TJ
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D015415:Biomarkers / Q000378:metabolism*; D020869:Gene Expression Profiling; D006801:Humans; D046228:Microarray Analysis; D008875:Middle Aged; D010641:Phenotype; D029424:Pulmonary Disease, Chronic Obstructive / Q000175:diagnosis / Q000378:metabolism* / Q000503:physiopathology*; D012313:RNA / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results
D015415:Biomarkers; D012313:RNA