Integrated analysis of transcriptome-wide m6A methylation in a Cd-induced kidney injury rat model

Shuangjing Li; Han Zhou; Yufen Liang; Qian Yang; Jiachen Zhang; Weitong Shen; Lijian Lei

Ecotoxicology and Environmental Safety (May 2023)

Integrated analysis of transcriptome-wide m6A methylation in a Cd-induced kidney injury rat model

Shuangjing Li,
Han Zhou,
Yufen Liang,
Qian Yang,
Jiachen Zhang,
Weitong Shen,
Lijian Lei

Affiliations

Shuangjing Li: Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
Han Zhou: Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
Yufen Liang: Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
Qian Yang: Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
Jiachen Zhang: Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
Weitong Shen: Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
Lijian Lei: Correspondence to: Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China.; Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China

Journal volume & issue: Vol. 256
p. 114903

Abstract

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Background: Accumulating evidence has demonstrated that N6-methyladenosine (m6A) plays important roles in a variety of diseases. However, the specific functions of m6A in CdCl2-induced kidney injury remain unclear. Objective: Here, we investigate a transcriptome-wide map of m6A modifications and explore the effects of m6A on Cd-induced kidney injury. Materials and methods: The rat kidney injury model was constructed by subcutaneous injection of CdCl2 (0.5, 1.0, and 2.0 mg/kg). The m6A levels were measured by colorimetry. The level of expression of m6A-related enzymes were detected by reverse transcription quantitative real-time PCR analysis. Transcriptome-wide m6A methylome in CdCl2 (2.0 mg/kg) and the control group were profiled by methylated RNA immunoprecipitation sequencing (MeRIP-seq). Subsequently, the sequencing data were analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), while gene set enrichment analysis (GSEA) confirmed the functional enrichment pathways of sequencing genes. In addition, a protein-protein interaction (PPI) network was applied to select hub genes. Results: The levels of m6A and m6A regulators (METTL3, METTL14, WTAP, YTHDF2) were significantly increased in CdCl2 groups. We identified a total of 2615 differentially expressed m6A peaks, 868 differentially expressed genes and 200 genes with significant changes in both m6A modification and gene expression levels. GO, KEGG, and GSEA analyses indicated that these genes were mainly enriched in inflammation and metabolism-related pathways such as in IL-17 signaling and fatty acid metabolism. According the result of the conjoint analysis, we identified the top ten hub genes (Fos, Hsp90aa1, Gata3, Fcer1g, Cftr, Cspg4, Atf3, Cdkn1a, Ptgs2, and Npy) which may be regulated by m6A and involve in CdCl2-induced kidney damage. Conclusion: This study established a m6A transcriptional map in a CdCl2-induced kidney injury model and suggested that m6A may affect CdCl2 induced kidney injury via regulated the inflammation and metabolism related gene.

Published in Ecotoxicology and Environmental Safety

ISSN: 0147-6513 (Print); 1090-2414 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Technology: Environmental technology. Sanitary engineering: Environmental pollution; Geography. Anthropology. Recreation: Environmental sciences
Website: https://www.journals.elsevier.com/ecotoxicology-and-environmental-safety

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