Transcriptome-Wide N6-Methyladenosine Alternations in Pulmonary Arteries of Monocrotaline-Induced Pulmonary Arterial Hypertension in Rats and Novel Therapeutic Targets

Overview

Journal Biomedicines

Specialty Biomedical Engineering

Date 2024 Feb 24

PMID 38397966

Authors

Yilu Feng

Zaixin Yu

Mi Tang

Jiang Li

Baohua Peng

Mukamengjiang Juaiti

Yiyang Tang

Benhui Liang

Mingqi Ouyang

Qingqing Liu

Jie Song

Affiliations

Soon will be listed here.

Abstract

N6-methyladenosine (mA) is a post-transcriptional epigenetic change with transcriptional stability and functionality regulated by specific mA-modifying enzymes. However, the significance of genes modified by mA and enzymes specific to mA regulation in the context of pulmonary arterial hypertension (PAH) remains largely unexplored. MeRIP-seq and RNA-seq were applied to explore variances in mA and RNA expression within the pulmonary artery tissues of control and monocrotaline-induced PAH rats. Functional enrichments were analyzed using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. To screen candidate mA-related genes, the STRING and Metascape databases were used to construct a protein-protein interaction network followed by a real-time PCR validation of their expression. The expression level of an mA regulator was further investigated using immunohistochemical staining, immunofluorescence, and Western blot techniques. Additionally, proliferation assays were conducted on primary rat pulmonary artery smooth muscle cells (PASMCs). We identified forty-two differentially expressed genes that exhibited either hypermethylated or hypomethylated mA. These genes are predominantly related to the extracellular matrix structure, MAPK, and PI3K/AKT pathways. A candidate gene, centromere protein F (), was detected with increased expression in the PAH group. Additionally, we first identified an mA reader, leucine rich pentatricopeptide repeat containing (LRPPRC), which was downregulated in the PAH rat model. The in vitro downregulation of mediated by siRNA resulted in the enhanced proliferation and elevated expression of mRNA in primary rat PASMCs. Our study revealed a modified transcriptome-wide mA landscape and associated regulatory mechanisms in the pulmonary arteries of PAH rats, potentially offering a novel target for therapeutic strategies in the future.

References

He P, He C . m A RNA methylation: from mechanisms to therapeutic potential. EMBO J. 2021; 40(3):e105977. PMC: 7849164. DOI: 10.15252/embj.2020105977. View

Kim J, Lee A, Choi J, Park Y, Kang H, Chang W . Epigenetic modulation as a therapeutic approach for pulmonary arterial hypertension. Exp Mol Med. 2015; 47:e175. PMC: 4525299. DOI: 10.1038/emm.2015.45. View

Meng J, Cui X, Rao M, Chen Y, Huang Y . Exome-based analysis for RNA epigenome sequencing data. Bioinformatics. 2013; 29(12):1565-7. PMC: 3673212. DOI: 10.1093/bioinformatics/btt171. View

Xu S, Xu X, Zhang Z, Yan L, Zhang L, Du L . The role of RNA mA methylation in the regulation of postnatal hypoxia-induced pulmonary hypertension. Respir Res. 2021; 22(1):121. PMC: 8074209. DOI: 10.1186/s12931-021-01728-6. View

Meng J, Lu Z, Liu H, Zhang L, Zhang S, Chen Y . A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package. Methods. 2014; 69(3):274-81. PMC: 4194139. DOI: 10.1016/j.ymeth.2014.06.008. View

Wei W, Wang N, Deng M, Dong P, Liu J, Xiang Z . LRPPRC regulates redox homeostasis via the circANKHD1/FOXM1 axis to enhance bladder urothelial carcinoma tumorigenesis. Redox Biol. 2021; 48:102201. PMC: 8645923. DOI: 10.1016/j.redox.2021.102201. View

Eichstaedt C, Song J, Benjamin N, Harutyunova S, Fischer C, Grunig E . EIF2AK4 mutation as "second hit" in hereditary pulmonary arterial hypertension. Respir Res. 2016; 17(1):141. PMC: 5095976. DOI: 10.1186/s12931-016-0457-x. View

Xia Y, Zhang Y, Huang J, Chen B, Jiang Y, Sun Z . N6-Methyladenosine Modifications in Pulmonary Hypertension. Pharmacology. 2023; 108(6):497-503. DOI: 10.1159/000533588. View

Hansen T, Veno M, Damgaard C, Kjems J . Comparison of circular RNA prediction tools. Nucleic Acids Res. 2015; 44(6):e58. PMC: 4824091. DOI: 10.1093/nar/gkv1458. View

10.

Pinello N, Sun S, Jong-Leong Wong J . Aberrant expression of enzymes regulating mA mRNA methylation: implication in cancer. Cancer Biol Med. 2019; 15(4):323-334. PMC: 6372906. DOI: 10.20892/j.issn.2095-3941.2018.0365. View

11.

Siira S, Spahr H, Shearwood A, Ruzzenente B, Larsson N, Rackham O . LRPPRC-mediated folding of the mitochondrial transcriptome. Nat Commun. 2017; 8(1):1532. PMC: 5691074. DOI: 10.1038/s41467-017-01221-z. View

12.

Benincasa G, DeMeo D, Glass K, Silverman E, Napoli C . Epigenetics and pulmonary diseases in the horizon of precision medicine: a review. Eur Respir J. 2020; 57(6). DOI: 10.1183/13993003.03406-2020. View

13.

Song K, Li B, Chen Y, Wang H, Liu K, Tan W . LRPPRC regulates metastasis and glycolysis by modulating autophagy and the ROS/HIF1-α pathway in retinoblastoma. Mol Ther Oncolytics. 2021; 22:582-591. PMC: 8450181. DOI: 10.1016/j.omto.2021.06.009. View

14.

Tong J, Flavell R, Li H . RNA mA modification and its function in diseases. Front Med. 2018; 12(4):481-489. DOI: 10.1007/s11684-018-0654-8. View

15.

Le Ribeuz H, Courboulin A, Ghigna M, Lambert M, Hautefort A, Humbert M . In vivo miR-138-5p inhibition alleviates monocrotaline-induced pulmonary hypertension and normalizes pulmonary KCNK3 and SLC45A3 expression. Respir Res. 2020; 21(1):186. PMC: 7364627. DOI: 10.1186/s12931-020-01444-7. View

16.

Xu Z, Lv B, Qin Y, Zhang B . Emerging Roles and Mechanism of m6A Methylation in Cardiometabolic Diseases. Cells. 2022; 11(7). PMC: 8997388. DOI: 10.3390/cells11071101. View

17.

Thompson A, Lawrie A . Targeting Vascular Remodeling to Treat Pulmonary Arterial Hypertension. Trends Mol Med. 2016; 23(1):31-45. DOI: 10.1016/j.molmed.2016.11.005. View

18.

Dai Y, Liu L, Zeng T, Zhu Y, Li J, Chen L . Characterization of the oncogenic function of centromere protein F in hepatocellular carcinoma. Biochem Biophys Res Commun. 2013; 436(4):711-8. DOI: 10.1016/j.bbrc.2013.06.021. View

19.

Qin Y, Qiao Y, Li L, Luo E, Wang D, Yao Y . The mA methyltransferase METTL3 promotes hypoxic pulmonary arterial hypertension. Life Sci. 2021; 274:119366. DOI: 10.1016/j.lfs.2021.119366. View

20.

Zhang B, Wu Q, Li B, Wang D, Wang L, Zhou Y . mA regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in gastric cancer. Mol Cancer. 2020; 19(1):53. PMC: 7066851. DOI: 10.1186/s12943-020-01170-0. View