Identification of Crucial Hub Genes and Differential T Cell Infiltration in Idiopathic Pulmonary Arterial Hypertension Using Bioinformatics Strategies

Abstract

Background: Idiopathic pulmonary arterial hypertension (IPAH) is a life-threatening disease. Growing evidence indicated that IPAH is a chronic immune disease. This study explored the molecular mechanisms and T cell infiltration of IPAH using integrated bioinformatics methods.Methods: Gene expression profiles of dataset GSE113439 were downloaded from the Gene Expression Omnibus and analyzed using R. Protein-protein interaction (PPI) network and gene set enrichment analysis (GSEA) were established by NetworkAnalyst. Gene Ontology enrichment analysis was performed using ClueGO. Transcription factors of differentially expressed genes (DEGs) were estimated using iRegulon. Transcription factors and selected hub genes were verified by real-time polymerase chain reaction (qPCR) in the lung tissues of rats with pulmonary artery hypertension. The least absolute shrinkage and selection operator regression model and the area under the receiver operating characteristic curve (AUC) were applied jointly to identify the crucial hub genes. Moreover, immune infiltration in IPAH was calculated using ImmuCellAI, and the correlation between key hub genes and immune cells was analyzed using R.Results: A total of 512 DEGs were screened, and ten hub genes and three transcription factors were filtered by the DEG PPI network. The DEGs were mainly enriched in mitotic nuclear division, chromosome organization, and nucleocytoplasmic transport. The ten hub genes and three transcription factors were confirmed by qPCR. Moreover, MAPK6 was identified as the most potent biomarker with an AUC of 100%, and ImmuCellAI immune infiltration analysis showed that a higher proportion of CD4-naive T cells and central memory T cells (Tcm) was apparent in the IPAH group, whereas the proportions of cytotoxic T cells (Tc), exhausted T cells (Tex), type 17 T helper cells, effector memory T cells, natural killer T cells (NKT), natural killer cells, gamma-delta T cells, and CD8 T cells were lower. Finally, MAPK6 was positively correlated with Tex and Tcm, and negatively correlated with Tc and NKT.Conclusion:MAPK6 was identified as a crucial hub gene to discriminate IPAH from the normal group. Dysregulated immune reactions were identified in the lung tissue of patients with IPAH.

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

“…In our study, CR1 was downregulated in PAH and positively correlated with monocytes and neutrophils, but negatively correlated with memory resting CD4 + T cells, which provided some evidence for future investigation of the mechanism of CR1-associated immune cell infiltration in PAH. TXNRD1, a member of the thioredoxin (Trx) system that catalyzes Trx1 reduction, plays a vital role in redox homeostasis [ 32 ]. In our study, it was shown that TXNRD1 mRNA was significantly decreased in human PAH lung samples by bioinformatics, which is consistent with previous reports [ 6 , 33 ].…”

Identification of Potential Biomarkers for Group I Pulmonary Hypertension Based on Machine Learning and Bioinformatics Analysis

“…As high-throughput technologies have been increasingly applied in PAH, largescale data can be obtained in publicly available databases. Moreover, many studies have been performed to identify molecular biomarkers and explore the underlying mechanisms of PAH based on public data [5,[14][15][16]. Despite the recently made great efforts, Group I PAH remains largely unexplored concerning its molecular mechanism and pathogenesis.…”

“…For instance, Nies et al found that the Insulin-like growth factor (IGF) axis could serve as a diagnostic biomarker for severe pulmonary hypertension [4]. Similarly, Yang et al uncovered mitogen-activated protein kinase 6 (MAPK6) to be an important gene for discriminating IPAH from healthy controls [5]. A few biological processes have been 2 of 24 reported to participate in developing Group I PAH; however, the search of biomarkers associated with this disease needs further exploitation.…”