van Vliet Marjolein M, Schoenmakers Sam, Boers Ruben G, van der Meeren Lotte E, Gribnau Joost, Steegers-Theunissen Régine P M
Department of Obstetrics and Gynaecology, Erasmus Medical Centre Rotterdam, Rotterdam, The Netherlands.
Department of Developmental Biology, Erasmus Medical Centre Rotterdam, Rotterdam, The Netherlands.
PLoS One. 2025 Jan 9;20(1):e0310019. doi: 10.1371/journal.pone.0310019. eCollection 2025.
Placental DNA methylation differences have been associated with timing in gestation and pregnancy complications. Maternal cell-free DNA (cfDNA) partly originates from the placenta and could enable the minimally invasive study of placental DNA methylation dynamics. We will for the first time longitudinally investigate cfDNA methylation during pregnancy by using Methylated DNA Sequencing (MeD-seq), which is compatible with low cfDNA levels and has an extensive genome-wide coverage. We aim to investigate DNA methylation in placental tissues and cfDNA during different trimesters in uncomplicated pregnancies, and in pregnancies with placental-related complications, including preeclampsia and fetal growth restriction. Identified gestational-age and disease-specific differentially methylated regions (DMRs) could lead to numerous applications including biomarker development.
Our study design involves three sub-studies. Sub-study 1 is a single-centre prospective, observational subcohort embedded within the Rotterdam Periconception cohort (Predict study). We will longitudinally collect maternal plasma in each trimester and during delivery, and sample postpartum placentas (n = 300). In sub-study 2, we will prospectively collect first and second trimester placental tissues (n = 10 per trimester). In sub-study 3 we will retrospectively collect plasma after non-invasive prenatal testing (NIPT) in an independent validation case-control cohort (n = 30-60). A methylation-dependent restriction enzyme (LpnPI) will be used to generate DNA fragments followed by sequencing on the Illumina NextSeq2000 platform. DMRs will be identified in placental tissues and cell types, and in cfDNA related to gestational-age or placental-related complications. (Paired) placental methylation profiles will be correlated to DMRs in cfDNA to aid tissue-of-origin analysis. We will establish a methylation score to predict associated diseases.
This study will provide insights in placental DNA methylation dynamics in health and disease, and could lead to clinical relevant biomarkers.
胎盘DNA甲基化差异与妊娠时间和妊娠并发症有关。母体游离DNA（cfDNA）部分来源于胎盘，可用于对胎盘DNA甲基化动态进行微创研究。我们将首次使用甲基化DNA测序（MeD-seq）纵向研究孕期cfDNA甲基化，该方法适用于低cfDNA水平且具有广泛的全基因组覆盖范围。我们旨在研究无并发症妊娠不同孕期以及患有胎盘相关并发症（包括先兆子痫和胎儿生长受限）的妊娠中胎盘组织和cfDNA中的DNA甲基化。识别出的孕周和疾病特异性差异甲基化区域（DMR）可能会带来包括生物标志物开发在内的众多应用。
我们的研究设计包括三个子研究。子研究1是一项嵌入鹿特丹围孕期队列（预测研究）的单中心前瞻性观察性子队列研究。我们将在每个孕期以及分娩时纵向收集母体血浆，并采集产后胎盘样本（n = 300）。在子研究2中，我们将前瞻性收集孕早期和孕中期的胎盘组织（每个孕期n = 10）。在子研究3中，我们将在一个独立的验证病例对照队列（n = 30 - 60）中回顾性收集无创产前检测（NIPT）后的血浆。将使用一种依赖甲基化的限制性内切酶（LpnPI）生成DNA片段，随后在Illumina NextSeq2000平台上进行测序。将在胎盘组织和细胞类型以及与孕周或胎盘相关并发症相关的cfDNA中识别DMR。（配对的）胎盘甲基化谱将与cfDNA中的DMR相关联，以辅助进行组织来源分析。我们将建立一个甲基化评分来预测相关疾病。
本研究将深入了解健康和疾病状态下胎盘DNA甲基化动态，并可能产生临床相关的生物标志物。
