| Part I DNA Methylome Profiling of Maternal Peripheral Blood and Placenta Reveal Potential Fetal DNA Markers for Noninvasive Prenatal TestingUtilizing epigenetic (DNA methylation) difference to differ maternal peripheral blood (PBL) and fetal (placental) DNA has been a promising strategy for noninvasive prenatal testing (NIPT). However, the differentially methylated regions (DMRs) have yet to be fully ascertained.In the present study, we performed the first genome-wide comparative methylome analysis between maternal PBL and fetal DNA from pregnancies of first trimester by methylated DNA immunoprecipitation sequencing (MeDIP-Seq) and Infinium HumanMethylation450 BeadChip.37112 DMRs and 46182 differentially methylated sites (DMSs) covering the whole genome, exclusive of Y chromosome, were identified by MeDIP-Seq and Infinium 450k array, respectively.3759 CpG sites in 2188 genomic regions were confirmed by both platforms. Not only did we find the previous reported potential fetal DNA markers in our identified DMRs/DMSs, but also we verified the identified DMRs/DMSs well in the validation round by MassARRAYTM pityper. The screened potential fetal DNA markers may be used for NIPT on aneuploidies and other chromosomal diseases, such as cri du chat syndrome (CdCs) and velo-cardio-facial syndrome (VCFS). In addition, these potential markers may also have application on early diagnosis of placental dysfunction, such as pre-eclampsia (PE).Part II Pathogenic Mechanism Analysis of Pre-eclampsiaPre-eclampsia (PE), a devastating pregnancy-associated disorder, is characterized by de-novo hypertension and proteinuria at or after 20 weeks’ gestation. PE puts a serious threat to maternal and fetal health and is a leading cause of maternal and fetal mortality and morbidity. A great deal of researches have been conducted to explore the precise etiology of PE over the past decades. Most theories on the etiology of PE suggested the central role of placenta in the development of PE. DNA methylation, the most extensively studied epigenetic modification, has been indicated to be involved in the development of PE. Consequently, it is essential to analyze the role of DNA methylation of PE in genome-wide scale, which would provide a novel perspective.In this study, DNA methylome analysis of 20 normal placentas and 22 placentas from pregnancies with PE were performed through Infinium HumanMethylation450 BeadChip. The differentially methylated genes were all hypomethylated in placentas from pregnancies with PE. Functional enrichment analysis indicated that all the differentially methylated genes were involved in cancer, cell movement, tissue/organ injuries and reproductive system development and function. Global DNA methylation analysis showed that placentas from pregnancies with PE were hypomethylated in comparison with normal placentas, but with no statistical significance, which might implicate the hypomethylation in PE would be an overall effect. Gene expression profile of 7 normal placentas and 5 placentas from pregnancies with PE indentified 162 genes that were differentially expressed (p<0.01 and fold change≥2) in PE placentas, of which 80 genes were up-regulated and 82 genes were down-regulated in PE. The screened genes with differential expression functionally enriched in cancer, cell growth and proliferation and tissue development. DNA methylation analysis of screened LEP and SH3PXD2A showed that the aberrant LEP promoter methylation and SH3PXD2A gene body methylation might take part in the regulation of gene expression and further participated in the pathogenesis.Overall consideration of DNA methylome and gene expression profile, we further confirmed that PE was a multi-factor and heterogeneous disease involved in multiple systems. Dysregulation of cell movement, dysregulation of cell growth and proliferation, failure of tissue development and function might be the core elements during PE development. DNA methylation might participate in the pathogenesis of PE through dysregulation of critical genes expression. |
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