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

Gufeng Gao; Ai Chen; Jin Gong; Weijun Lin; Weibin Wu; Sagor Mohammad Ismail Hajary; Guili Lian; Li Luo; Liangdi Xie

doi:10.3389/fgene.2023.1222368

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

Front Genet. 2023 Sep 4:14:1222368. doi: 10.3389/fgene.2023.1222368. eCollection 2023.

Authors

Gufeng Gao^{1

2

3

4

5}, Ai Chen^{1

2

3

4

5}, Jin Gong^{1

2

3

4

5}, Weijun Lin^{1

2

3

4

5}, Weibin Wu^{1

2

3

4

5}, Sagor Mohammad Ismail Hajary^{1

2

3

4

5}, Guili Lian^{1

2

3

4

5}, Li Luo^{1

2

3

4

5}, Liangdi Xie^{1

2

3

4

5}

Affiliations

¹ Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China.
² Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China.
³ Clinical Research Center for Geriatric Hypertension Disease of Fujian Province, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China.
⁴ Branch of National Clinical Research Center for Aging and Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
⁵ Department of Geriatrics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China.

Abstract

Idiopathic pulmonary arterial hypertension (IPAH) is a life-threatening disease with a poor prognosis and high heritability, characterized by elevated pulmonary vascular resistance (PVR) and pulmonary artery pressure. N6-methyladenosine (m6A) RNA modification influences many RNA metabolism pathways. However, the position of m6A methylation regulators in IPAH remains unknown. Therefore, the study aims to disclose the function m6A regulators exert in the pathological mechanisms of IPAH and the immune microenvironment involved. The GSE117261 dataset was downloaded from the Gene Expression Omnibus (GEO) to screen the differentially expressed genes (DEGs) between normal and IPAH samples. Functional and pathway enrichment analyses of DEGs were then conducted by Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG). We also identified the differentially-expressed m6A (DEm6A) regulators between normal and IPAH samples. Key m6A regulators related to the prediction of IPAH were selected using the random forest model. The results showed that FMR1, RBM15, HNRNPA2B1 and IGFBP3 were upregulated in IPAH. In contrast, LRPPRC was downregulated. The single sample gene set enrichment analysis (ssGSEA) method was then adopted to estimate the immune microenvironment in distinct m6A clusters and m6A phenotype-related genes (PRGs) clusters, respectively. Furthermore, we calculated the m6A score via principal component analysis (PCA), and the Sankey diagram was selected to present the correlation among the m6A clusters, m6A PRGs clusters and m6A score. Finally, quantitative RT-PCR and Western blotting were used to validate the key genes in human pulmonary artery smooth muscle cells (HPASMCs) treated by human platelet-derived growth factor-BB (PDGF-BB). The relative mRNA and protein expression levels of FMR1 were significantly elevated, however, the relative mRNA and protein expression levels of LRPPRC were downregulated. Besides, the relative mRNA level of HNRNPA2B1 was increased. Generally, this bioinformatics analysis might provoke more insights into diagnosing and treating IPAH.

Keywords: human pulmonary artery smooth muscle cells; idiopathic pulmonary arterial hypertension; immune microenvironment; m6A methylation regulators; platelet-derived growth factor-BB.

Grants and funding

This work was supported by the National Natural Science Foundation of China (82170355), Joint Funds for the Innovation of Science and Technology, Fujian province (2019Y9124), Fujian Clinical Medical Research Center for Geriatric Hypertensive Disease (SLN-YJZX) and 2020 Joint Fund of the Provincial Science and Technology Department for the “Creation of Double Highs” (2020Y9108).