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Pulmonary arterial hypertension (PAH) is a severe cardiovascular disorder with high mortality. Multiple clinical diseases can induce PAH, but the underlying molecular mechanisms shared in PAHs associated with different diseases remain unclear. The aim of this study is to explore the key candidate genes and pathways in PAH associated with congenital heart disease (CHD-PAH), PAH associated with connective tissue disease (CTD-PAH), and idiopathic PAH (IPAH). We performed differential expression analysis based on a public microarray dataset GSE113439 and identified 1,442 differentially expressed genes, of which 80.3% were upregulated. Subsequently, both pathway enrichment analysis and protein–protein interaction network analysis revealed that the “Cell cycle” and “DNA damage” processes were significantly enriched in PAH. The expression of seven upregulated candidate genes ( EIF2AK2 ,  TOPBP1 ,  CDC5L ,  DHX15 , and  CUL1 – 3 ) and three downregulated candidate genes ( DLL4 ,  EGFL7 , and  ACE ) were validated by qRT-PCR. Furthermore, cell cycle-related genes  Cul1  and  Cul2  were identified in pulmonary arterial endothelial cells (PAECs)  in vitro.  The result revealed an increased expression of  Cul2  in PAECs after hypoxic treatment. Silencing  Cul2  could inhibit overproliferation and migration of PAECs in hypoxia. Taken together, according to bioinformatic analyses, our work revealed that “Cell cycle” and “DNA damage” process-related genes and pathways were significantly dysregulated expressed in PAHs associated with three different diseases. This commonality in molecular discovery might broaden the genetic perspective and understanding of PAH. Besides, silencing  Cul2  showed a protective effect in PAECs in hypoxia. The results may provide new treatment targets in multiple diseases induced by PAH.

Comparative Transcriptional Analysis of Pulmonary Arterial Hypertension Associated With Three Different Diseases