Abstract

The goal of this study was to identify BPD markers by gene expression profiling in lung and peripheral blood mononuclear cell (PBMC) gene expression data. Studies of BPD are often focused on lung tissue, but rarely venture to find markers of the disease outside of the most affected tissue. Genes identified from these analyses can be used as markers of BPD, and may also be linked with causal mechanisms of the disease. First, we tested the biological relevance of BPD biomarkers previously identified in lung tissue by assessing their importance in normal lung development. Next, we identified sets of differentially expressed genes at 5±2 days (Near-birth) and 25±3 days (Near-diagnosis) post birth within a publicly-available microarray dataset utilizing RNA from the PBMCs from infants at high risk for a diagnosis of BPD. These lists provided markers of BPD including ARG1, MPO, OLFM4, CEACAM1, CEACAM6 and CEACAM8 that may provide further insight into the physiology of infants with BPD. Of these, ARG1, CEACAM1 and CEACAM6 were validated by qPCR using RNA samples from lung tissue. The identified genes and their associations with the inflammatory response and vascular development via the Urea cycle provide a basis for further investigation of these pathways within BPD pathogenesis. Another benefit of these markers has been explored: using PBMC gene expression to predict long-term outcome in the near-birth time point. These studies showed that a simple 3-fold cross-validation technique could provide a model with nearly 73% accurate classification of infants at less than 1 week after birth. These studies provide a strong motive for further analyses of these genes of interest and the predictive ability of biomarkers of BPD in PBMCs.

Library of Congress Subject Headings

Bronchopulmonary dysplasia--Genetics

Publication Date

7-11-2013

Document Type

Thesis

Student Type

Graduate

Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)

Advisor

Tom Mariani

Advisor/Committee Member

Soumyaroop Bhattacharya

Advisor/Committee Member

Michael Osier

Comments

Physical copy available from RIT's Wallace Library at RJ320.B75 M47 2013

Campus

RIT – Main Campus

Download

Share

COinS