Weighted gene co-expression network analysis identifies dysregulated B-cell receptor signaling pathway and novel genes in pulmonary arterial hypertension

Abstract

BackgroundPulmonary arterial hypertension (PAH) is a devastating cardio-pulmonary vascular disease in which chronic elevated pulmonary arterial pressure and pulmonary vascular remodeling lead to right ventricular failure and premature death. However, the exact molecular mechanism causing PAH remains unclear.MethodsRNA sequencing was used to analyze the transcriptional profiling of controls and rats treated with monocrotaline (MCT) for 1, 2, 3, and 4 weeks. Weighted gene co-expression network analysis (WGCNA) was employed to identify the key modules associated with the severity of PAH. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the potential biological processes and pathways of key modules. Real-time PCR and western blot analysis were used to validate the gene expression. The hub genes were validated by an independent dataset obtained from the Gene Expression Omnibus database.ResultsA total of 26 gene modules were identified by WGCNA. Of these modules, two modules showed the highest correlation with the severity of PAH and were recognized as the key modules. GO analysis of key modules showed the dysregulated inflammation and immunity, particularly B-cell-mediated humoral immunity in MCT-induced PAH. KEGG pathway analysis showed the significant enrichment of the B-cell receptor signaling pathway in the key modules. Pathview analysis revealed the dysregulation of the B-cell receptor signaling pathway in detail. Moreover, a series of humoral immune response-associated genes, such as BTK, BAFFR, and TNFSF4, were found to be differentially expressed in PAH. Additionally, five genes, including BANK1, FOXF1, TLE1, CLEC4A1, and CLEC4A3, were identified and validated as the hub genes.ConclusionThis study identified the dysregulated B-cell receptor signaling pathway, as well as novel genes associated with humoral immune response in MCT-induced PAH, thereby providing a novel insight into the molecular mechanisms underlying inflammation and immunity and therapeutic targets for PAH.

B-cells in pulmonary arterial hypertension: friend, foe or bystander?

“…Gene expression studies performed on PBMCs from SSc-PAH patients and lungs from various PAH patients reveal a significant upregulation of genes involved in BCR signalling and the NF-κB pathway in the PAH groups [ 8 , 21 ]. In lungs from rats with monocrotaline (MCT)-induced PAH, genes related to B-cell activation, and especially BCR signalling mediators, display the strongest correlations with haemodynamic and histological markers of PAH severity [ 22 ]. These anomalies become more pronounced with the course of the experimental disease.…”

“…These anomalies become more pronounced with the course of the experimental disease. Pathway analysis reveals significant dysregulation of several key components of the BCR complex (such as upregulation of CD79A/B, BTK, CD19 and CD21) [ 22 ].…”

“…A pathogenic variant in the gene coding for TACI has been identified as a new causative mutation for PAH, possibly by promoting dysregulated vascular inflammation [ 46 ]. BAFF-R is one of the most upregulated gene in the lungs of MCT rats [ 22 ].…”