Open Access

Genome‑wide methylation analysis reveals differentially methylated CpG sites and altered expression of heart development‑associated genes in fetuses with cardiac defects

  • Authors:
    • Jizi Zhou
    • Yu Xiong
    • Xinran Dong
    • Huijun Wang
    • Yanyan Qian
    • Duan Ma
    • Xiaotian Li
  • View Affiliations

  • Published online on: July 18, 2021     https://doi.org/10.3892/etm.2021.10464
  • Article Number: 1032
  • Copyright: © Zhou et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

DNA methylation, as an epigenetic mechanism, has a vital role in heart development. An increasing number of studies have investigated aberrant DNA methylation in pediatric or adult heart samples from patients with congenital heart defects (CHD). Placenta tissue, umbilical cord blood, or newborn blood have also been used to detect DNA methylation biomarkers for CHD. However, few studies have compared the methylation levels in fetal heart tissue with cardiac defects with that in normal controls. The present study conducted an integrative whole‑genome and CpG site‑specific DNA methylation analysis of fetal heart samples from 17 isolated cardiac defect cases, 14 non‑isolated cardiac defect cases, and 22 controls with normal hearts, using methylated DNA immunoprecipitation microarray and MassARRAY EpiTYPER assays. Expression of genes adjacent to differentially methylated regions (DMRs) was measured by RT‑qPCR and western blot analysis. The results revealed that fetuses with cardiac defects presented global hypomethylation. Genomic analysis of DMRs revealed that a proportion of DMRs were located in exons (12.4%), distal intergenic regions (11.14%), and introns (8.97%). Only 55.7% of DMRs were observed at promoter regions. Functional enrichment analysis for genes adjacent to these DMRs revealed that hypomethylated genes were involved in embryonic heart tube morphogenesis and immune‑related regulation functions. Intergenic hypermethylation of EGFR and solute carrier family 19 member 1 (SLC19A1), and intragenic hypomethylation of NOTCH1 were validated in fetal heart tissues with cardiac defects. Only SLC19A1 expression was significantly decreased at the mRNA level, while EGFR, NOTCH1, and SLC19A1 expression were all significantly decreased at the protein level. In conclusion, the present study demonstrated that fetal cardiac defects may be associated with alterations in regional and single CpG site methylation outside of promoter regions, resulting in differentiated expression of corresponding genes associated with heart development. These results present new insights into the epigenetic mechanisms underlying abnormal heart development.

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September-2021
Volume 22 Issue 3

Print ISSN: 1792-0981
Online ISSN:1792-1015

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Spandidos Publications style
Zhou J, Xiong Y, Dong X, Wang H, Qian Y, Ma D and Li X: Genome‑wide methylation analysis reveals differentially methylated CpG sites and altered expression of heart development‑associated genes in fetuses with cardiac defects. Exp Ther Med 22: 1032, 2021
APA
Zhou, J., Xiong, Y., Dong, X., Wang, H., Qian, Y., Ma, D., & Li, X. (2021). Genome‑wide methylation analysis reveals differentially methylated CpG sites and altered expression of heart development‑associated genes in fetuses with cardiac defects. Experimental and Therapeutic Medicine, 22, 1032. https://doi.org/10.3892/etm.2021.10464
MLA
Zhou, J., Xiong, Y., Dong, X., Wang, H., Qian, Y., Ma, D., Li, X."Genome‑wide methylation analysis reveals differentially methylated CpG sites and altered expression of heart development‑associated genes in fetuses with cardiac defects". Experimental and Therapeutic Medicine 22.3 (2021): 1032.
Chicago
Zhou, J., Xiong, Y., Dong, X., Wang, H., Qian, Y., Ma, D., Li, X."Genome‑wide methylation analysis reveals differentially methylated CpG sites and altered expression of heart development‑associated genes in fetuses with cardiac defects". Experimental and Therapeutic Medicine 22, no. 3 (2021): 1032. https://doi.org/10.3892/etm.2021.10464