The large ongoing NIH COPDGene(R) trial is a genome wide association study designed to elucidate the genetic basis of chronic obstructive pulmonary disease (COPD). This study also provides a unique opportunity to rapidly develop plasma biomarkers for COPD since the subjects enrolled are extremely well characterized phenotypically and plasma samples are being obtained. Our prior experience applying proteomic studies to the human lung in chronic smokers with and without COPD will allow us to efficiently carry out this objective. We found that chronic cigarette smoking increases the expression of proteins which mediate the unfolded protein response (UPR) and that the expression of these proteins differs qualitatively and quantitatively in ex- smokers with advanced COPD. Accordingly, we hypothesize that differentially expressed proteins including those which define the UPR can serve as candidate plasma biomarkers. In our 2 year GO proposal, we will use state-of-the-art proteomics approaches (i.e, iTRAQ and IPAS), to identify biomarkers in the plasma proteome which define COPD susceptibility and severity. These complementary methods are more sensitive than the traditional 2D gel approach in detecting low abundance proteins like cytokines, chemokines or growth factors in the picomolar range where biomarkers are likely to be found. Plasma samples will be obtained from the cohort of chronic smokers with and without COPD enrolled in the multi-center COPDGene(R) project. Candidate biomarkers will be identified in an initial observational group of 64 subjects - 32 subjects with advanced COPD (GOLD 4) and 32 smokers at risk but without COPD (GOLD 0). Candidate biomarkers will be correlated with clinical, radiological and physiological data using standard and novel bioinformatics techniques. Subsequently, candidate biomarkers will be validated in a separate, much larger group of 250 subjects having a wide range of COPD (i.e., GOLD stages 0, 1, 2, 3, and 4;n=50 subjects in each GOLD stage) using high throughput methods like ELISA or multiplex protein chip array. These comprehensive studies will be carried out simultaneously at two highly experienced proteomics facilities within the Temple University system -the Temple University School of Medicine which will perform the IPAS studies;and the Fox Chase Cancer Institute which will perform the iTRAQ studies. The use of two facilities with expertise in different mass spectroscopy technologies will allow the studies to be completed in a timely fashion. Since sample preparation and study population are important variables in the conduct of proteomic studies, the first year of the project will be used to: 1) validate the method of collecting, freezing and storing plasma;2) form the two cohorts of 64 subjects to be used as the observational group;and 3) analyze the samples from these 64 subjects. The second year of the project will be used to validate candidate biomarkers in the test group of 250 subjects with a range of COPD severity. The identification of sensitive and specific plasma biomarkers will enhance the understanding of COPD pathogenesis and the diagnosis and treatment of subjects affected with this important disease.
Chronic obstructive pulmonary disease (COPD), a disease characterized by inflammation, cell death and extensive lung tissue remodeling, is an increasingly important public health concern in the US and world-wide. The identification of sensitive and specific plasma biomarkers will enhance both the understanding of COPD pathogenesis and the diagnosis and treatment of subjects affected with this important disease. This study will use proteomics approaches on plasma samples obtained from subjects with and without COPD enrolled in the large ongoing NIH COPDGene(R) trial to accomplish this objective.
