Abstract 16996: Meta-Analysis of DNA Microarrays Reveals Dysregulation of DNA Repair Genes Downstream of BMPR2 in Pulmonary Arterial Hypertension
Rationale: Somatic mutations in endothelial cells (EC) are suggested to play a role in the pathogenesis of pulmonary arterial hypertension (PAH). We hypothesize that dysfunction of bone morphogenetic protein receptor 2 (BMPR2) can sensitize cells to DNA damage and somatic mutations, leading to apoptosis-resistant and highly proliferative cell types. Our goal was to identify DNA repair genes associated with PAH and downstream of BMPR2 signaling using meta-analysis of DNA microarrays, a novel strategy in the study of PAH.
Methods: We searched in NCBI’s GEO database for gene expression profiles of lung tissue in either PAH patients or in animals and cell cultures after BMPR2 dysfunction. As of July 2011, we found eight eligible DNA microarray datasets. Study-specific effect sizes were weighted by inverse-variance before being combined. Target genes were identified based on FDR-adjusted p-value threshold of 0.05 and presence in at least half of the original datasets. The same criteria were used in a subset analysis of the human datasets. BMPR2 siRNA was used to create BMPR2-deficient pulmonary ECs.
Results: Our meta-analysis and human subset analysis revealed hundreds of novel target genes. As confirmation, qPCR of BMPR2-deficient ECs revealed 6/7 (85%) randomly selected meta-analysis target genes with significant expression change. Similarly, in the human subset analysis, 6/18 (33%) target genes showed significant expression change. Pubmatrix analysis revealed that over 28% of all targets were associated with DNA damage or repair. Human subset analysis target genes were enriched for chromatin biology (p=1.7E-04) based on gene ontology analysis. In addition, oPOSSUM promoter analysis showed enrichment of SP1 binding sites in promoter regions of upregulated target genes (p=6.44E-04) and enrichment of Nkx3-1 binding sites in promoter regions of downregulated target genes (p=5.81E-06). qPCR of BMPR2-deficient ECs revealed upregulation of SP1 (p<0.001) and downregulation of tumor suppressor Nkx3-1 (p<0.05).
Conclusions: Our study reveals novel networks of chromatin regulators and DNA repair genes associated with PAH and BMPR2 signaling, thus improving our understanding of the pathogenesis of PAH.
- © 2012 by American Heart Association, Inc.