Comparison of Genome-Wide DNA Methylation Profiles of Fetal Tissues Conceived by In Vitro Fertilization and Natural Conception

Background: Assisted reproductive technology (ART) might induce adverse outcomes and increase the risk of metabolic disease in later life, suggesting epigenetic mechanisms, especially DNA methylation, might play a role. Methods: We compared the DNA methylation patterns of fetal tissues from abortions (50-60d, AB) and multifetal pregnancy reductions (MFPR) after multi-embryo transfer in patients undergoing in vitro fertility and embryo transfer (IVF-ET) between June 2008 and July 2016. Using a genome wide (450K loci) methylation analysis, we analyzed the differences in DNA methylation patterns between two groups. Findings: Global methylation levels were not significantly different between the AB and MFPR groups. The methylation levels were lower in the hypermethylated regions of the MFPR group than in those of the AB group, while the methylation levels were higher in the hypomethylated regions of the MFPR group. Heatmap visualization and hierarchical clustering of the sharp yes/no DMRs showed a difference between the DMRs in the AB and MFPR samples. In the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, skeletal system morphogenesis and type I diabetes mellitus ranked first. We identified 196 differentially methylated genes between the AB and MFPR groups. Ingenuity Pathway Analysis (IPA) revealed 8 disease and functional annotations associated with IVT-ET. In the MFPR group, the final validation showed lower BMP4 methylation levels in gene bodies, higher TPO methylation levels in the 1st exon and 5'UTR, and higher IL1B methylation levels in TSS1500 and TSS200. Interpretation: IVF-ET may alter global patterns of DNA methylation. These alterations may affect long-term patterns of gene expression, thus increasing the risk of adult diseases in offspring. Funding Statement: This work was supported by The National Key Research and Development Program of China (2017YFC1001301), International Cooperation Project of China and Canada NSFC (81661128010), National Natural Science Foundation of China (31471405), The National Key Basic Research Program (2013CB967404) and National Natural Science Foundation of China (81671456, 81671412), Doctoral Innovation Fund of School of Medicine, Shanghai Jiao Tong University(BXJ201640). Declaration of Interests: The authors state: none exist. Ethics Approval Statement: Written informed consent was obtained from all participating pregnant women. Epigenetic studies on fetal tissues were approved by the Ethics Committee of the International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, approval number (GKWL2017-81).