Global Analyses of the Placental Epigenome in Preeclampsia

先兆子痫胎盘表观基因组的整体分析

• 批准号: 9369783
• 负责人: Joseph F Costello
• 金额: $ 59.08万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2022-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9369783
• 关键词: Address; Affect; Alternative Splicing; Appearance; Area; Biometry; Birth; Blood; Cessation of life; ChIP-seq; Chorion; Chorionic villi; CpG dinucleotide; DNA; DNA Methylation; Data; Decidua; Developed Countries; Diagnosis; Enhancers; Epigenetic Process; Gene Expression; Gene Expression Regulation; Generations; Genes; Genetic Fingerprintings; Genetic Transcription; Genome; Genomics; Gestational Age; Goals; Histones; Human; Immunohistochemistry; In Vitro; Infection; Invaded; Laboratories; Messenger RNA; Methylation; MicroRNAs; Modeling; Molecular; Morbidity - disease rate; Morphology; National Institute of Child Health and Human Development; Nucleic Acid Regulatory Sequences; Pathogenesis; Pathology; Pathway interactions; Patients; Pattern; Perinatology; Placenta; Placental Biology; Placentation; Plasma; Pre-Eclampsia; Pregnancy; Premature Birth; Premature Labor; Proteins; RNA; Regulation; Regulator Genes; Regulatory Element; Research; Research Design; Research Personnel; Role; Sampling; Small RNA; Testing; Time; Tissues; Transcript; United States National Institutes of Health; Universities; Washington; Woman; base; bisulfite sequencing; candidate marker; cytotrophoblast; data visualization; epigenome; epigenomics; fetal; histone modification; in vitro Assay; insight; knock-down; mortality; new therapeutic target; novel; overexpression; predictive marker; promoter; targeted biomarker; targeted treatment; theories; therapeutic biomarker; transcriptome; transcriptome sequencing; transcriptomics; whole genome

PROJECT SUMMARY/ABSTRACT We theorize that the placental epigenome and its relationship to the transcriptome hold the key to understanding pathways with important roles in the pathogenesis of severe preeclampsia (sPE). This hypothesis is based on the association of sPE with certain placental pathologies. The cytotrophoblasts (CTBs) that invade the uterine wall fail to differentiate properly; CTB invasion of the decidua is shallow and endovascular invasion is constrained. Recently we found that CTBs of the smooth chorion also have very significant sPE-associated morphological and molecular changes. Chorionic villi from affected pregnancies have overt abnormalities as well such as syncytial knots. The investigators on this proposal—experts in epigenomic analyses, biostatistics and bioinfomatics, data visualization and human placental biology— completed detailed transcriptomic and epigenomic profiling, in the 2nd and 3rd trimesters of normal pregnancy, of the areas that are disrupted in sPE—CTBs, the smooth chorion and chorionic villi. Whole genome bisulfite sequencing (WGBS) confirmed hypomethylation of placental DNA and showed, for the first time, that large blocks of hypomethylation were marked with gains in repressive H3K9me3. Patterns of DNA methylation were unique to each sample type and trimester, suggesting dynamic regulation. As gestation advanced, many regulatory regions of the CTB genome became methylated, suggesting epigenetic mechanisms regulating functional alterations. Analyses of the corresponding RNA-seq data showed that CTB transcripts that were highly expressed in 2nd trimester and downregulated at term included more genes that are overexpressed in sPE than would be expected by chance. Exciting immunoblot (IB) data, corroborated by immunohistochemistry, showed a novel and strong difference in histone modification levels between CTBs isolated from the placentas of women diagnosed with sPE and control samples, matched for gestational age, that were isolated from the placentas of women who had a preterm birth with no sign of infection (nPTL). We theorize that coalescing epigenomic and transcriptomic data from CTBs, the smooth chorion and chorionic villi in sPE will reveal the dysregulated pathways and new mechanistic insights. As to approach, we will use WGBS to profile DNA methylation (Aim 1). We will employ IB and ChIP-seq to assess histone modifications—H3k27me3, H3k9me3, H3K4me1, H3K4me3 and H3K27ac (Aim 2). Also, we will explore the translational potential of the findings by asking whether the sPE-associated profile of dysregulated histone modifications can be detected in maternal plasma. We will apply RNA-seq to investigate the consequences of epigenetic alterations at the mRNA level and test the significance of the findings by using in vitro assays of TB functions (Aim 3). Results will be publically available through the WashU Epigenome Browser. Thus, our results will reveal the role of the epigenome in sPE-related changes in placental gene expression and candidate biomarkers of this condition.

项目概要/摘要 我们推测胎盘表观基因组及其与转录组的关系是关键 了解在严重先兆子痫 (SPE) 发病机制中具有重要作用的途径。 该假设基于 sPE 与某些胎盘病理学的关联。 未能正确区分侵入子宫壁的 CTB 侵入蜕膜较浅； 最近我们发现光滑绒毛膜的CTBs也受到很大的限制。 受影响妊娠引起的与 sPE 相关的显着的绒毛膜绒毛形态和分子变化。 也有明显的异常，例如合胞体结。 表观基因组分析、生物统计学和生物信息学、数据可视化和人类胎盘生物学—— 在正常妊娠的第二和第三个月完成了详细的转录组和表观基因组分析， sPE 中被破坏的区域——CTB、平滑绒毛膜和绒毛膜绒毛全基因组亚硫酸氢盐。 测序（WGBS）对胎盘 DNA 的甲基化进行了低证实，并首次表明，大 低甲基化的阻断以抑制性 H3K9me3 的增加为标志。 每种样本类型和三个月期都是独一无二的，表明随着妊娠的进展，许多变化都是动态调节的。 CTB基因组的调控区域甲基化，表明表观遗传机制调控 对相应 RNA-seq 数据的分析表明，CTB 转录本是 在妊娠第二期高表达并在足月时下调包括更多在妊娠期过表达的基因 sPE 比预期的令人兴奋的免疫印迹 (IB) 数据，经免疫组织化学证实， 显示从胎盘分离的 CTB 之间的组蛋白修饰水平存在新颖且强烈的差异 被诊断为 SPE 的女性和与胎龄相匹配的对照样本，这些样本是从 没有感染迹象的早产妇女的胎盘（nPTL）我们推测这种融合。 来自CTB、sPE中的光滑绒毛膜和绒毛膜绒毛的表观基因组和转录组数据将揭示 失调的途径和新的机制见解 至于方法，我们将使用 WGBS 来分析 DNA。 我们将使用 IB 和 ChIP-seq 来评估组蛋白修饰 - H3k27me3、H3k9me3、 H3K4me1、H3K4me3 和 H3K27ac（目标 2）。 询问是否可以在母体中检测到与 sPE 相关的组蛋白修饰失调情况 我们将应用 RNA-seq 来研究 mRNA 水平的表观遗传改变的后果。 并通过结核病功能的体外测定来测试研究结果的重要性（目标 3）。 通过华盛顿大学表观基因组浏览器公开可用因此，我们的结果将揭示 的作用。 与 sPE 相关的胎盘基因表达的表观基因组变化以及这种情况的候选生物标志物。