The identification and verification of hub genes associated with pulmonary arterial hypertension using weighted gene co-expression network analysis

Abstract

Background Pulmonary arterial hypertension (PAH) is characterized by a progressive increase in pulmonary vascular resistance and pulmonary arterial pressure, with complex etiology, difficult treatment and poor prognosis. The objective of this study was to investigate the potential biomarkers for PAH based on bioinformatics analysis. Methods The GSE117261 datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified by screening PAH patients and controls. Then the DEGs were analyzed using a Weighted Gene Co-expression Network Analysis (WGCNA) and the key modules were determined, and to further explore their potential biological functions via Gene Ontology analysis (GO), Kyoto Encyclopedia of Genes and Genomes Pathway analysis (KEGG), and Gene Set Enrichment Analysis (GSEA). Moreover, Protein–protein interaction (PPI) networks were constructed to identify hub gene candidates in the key modules. Finally, real-time quantitative polymerase chain reaction was supplied to detect the expressions of hub genes in human pulmonary arterial smooth cells treated with cobalt chloride (COCl2) which was used to mimic hypoxia. Results There were 2299 DEGs identified. WGCNA indicated that yellow module was the key one correlated with PAH. GO and KEGG analysis demonstrated that genes in the yellow module were mainly enriched in ‘Pathways in cancer’. GSEA revealed that ‘HALLMARK_MYC_TARGETS_V1’ was remarkably enriched in PAH. Based on the PPI network, vascular endothelial growth factor A, proto-oncogene receptor tyrosine kinase (KIT), PNN interacting serine and arginine rich protein (PNISR) and heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1) were identified as the hub genes. Additionally, the PCR indicated that the elevated expressions of PNISR and HNRNPH1 were in line with the bioinformatics analysis. ROC analysis determined that PNISR and HNRNPH1 may be potential biomarkers to provide better diagnosis of PAH. Conclusion PNISR and HNRNPH1 were potential biomarkers to diagnosis PAH. In summary, the identified DEGs, modules, pathways, and hub genes provide clues and shed light on the potential molecular mechanisms of PAH.

Comprehensive analyses of m6A RNA methylation patterns and related immune microenvironment in idiopathic pulmonary arterial hypertension

“…Sterile ophthalmic scissors were used to cut the pulmonary arteries of patients into small pieces. Then, small pieces of pulmonary arteries were cultured in DMEM/F12 containing 20% FBS in a humidified environment of 5% CO 2 at 37°C ( Wu et al, 2022 ). The medium was replaced by DMEM with 0.02% FBS and starved for 24 h when the cells were 70%–80% confluent.…”

Bioinformatics analysis of the immune cell infiltration characteristics and correlation with crucial diagnostic markers in pulmonary arterial hypertension

“…Gene expression profiles in patients with PAH were downloaded from the GEO database ( https://www.ncbi.nlm.nih.gov/geoprofiles/ ). Three datasets were selected, including GSE117261 [ 16 , 17 ], GSE113439 [ 18 ] and GSE53408 [ 19 – 21 ]. GSE117261 (58 patients with PAH and 25 control) was used as a training set, GSE113439 (15 patients with PAH and 11 control) and GSE53408 (12 patients with PAH and 11 control) were used as validation sets, and all three datasets were based on GLP6244 platform (Affymetrix Human Gene 1.0ST Array).…”

“…Previous studies have identified potential biomarkers and abnormal immune cell infiltration between PAH and normal control in different datasets downloaded for the GEO database using different bioinformatics methods [ 14 , 15 ]. Our previous studies have identified PNISR and HNRNPH1 may be potential biomarkers to provide a better diagnosis of PAH [ 16 ]. In this study, the GSE117261 were downloaded to screen differentially expressed genes (DEGs) between PAH and control and further explore their potential biological functions via enrichment analysis.…”

Canagliflozin inhibits PASMCs proliferation via regulating SGLT1/AMPK signaling and attenuates vascular remodeling in MCT-induced pulmonary arterial hypertension

“…Total RNA from pulmonary artery and PASMCs was isolated, and cDNA synthesis was performed as described previously [29]. Briefly, RNA extraction was carried out using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, Nanjing, China), and cDNA synthesis was performed using Hifair ® III 1st Strand cDNA Synthesis Kit (Yeasen Biotech, Shanghai, China) following the manufacturer's instructions.…”