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: 9920738
• 负责人: Joseph F Costello
• 金额: $ 55.61万
• 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/9920738
• 关键词: Address; Affect; Alternative Splicing; Appearance; Area; Biometry; Birth; Blood; 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; Maternal Mortality; 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; Second Pregnancy Trimester; Small RNA; Testing; Third Pregnancy Trimester; Time; Tissues; Transcript; United States National Institutes of Health; Universities; Uterus; Washington; Woman; base; bisulfite sequencing; candidate marker; cytotrophoblast; data visualization; epigenome; epigenomics; fetal; genomic locus; histone modification; in vitro Assay; insight; knock-down; miRNA expression profiling; mortality; new therapeutic target; novel; overexpression; predictive marker; promoter; targeted biomarker; targeted treatment; theories; 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.

项目总结/摘要 我们的理论是胎盘表观基因组及其与转录组的关系是 了解在重度子痫前期（sPE）发病机制中具有重要作用的途径。这 这一假说是基于sPE与某些胎盘病理学的关联。细胞滋养层细胞（CTB） CTB侵犯子宫壁不能正确区分; CTB对蜕膜的侵犯很浅， 血管内侵入受到限制。最近，我们发现光滑绒毛膜的CTB也有很大的 显著的sPE相关的形态学和分子变化。受影响妊娠的绒毛 也有明显的异常比如合胞体结这项提议的调查人员是 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- 完成了详细的转录组和表观基因组分析，在正常妊娠的第二和第三个三个月， 在sPE-CTB中被破坏的区域，即光滑绒毛膜和绒毛膜绒毛。全基因组亚硫酸氢盐 测序（WGBS）证实了胎盘DNA的低甲基化，并首次表明，大的 在抑制性H3 K9 me 3中，低甲基化的阻断标记有增益。DNA甲基化的模式是 每个样本类型和三个月都是独一无二的，这表明了动态调节。随着妊娠期的延长，许多 CTB基因组的调节区域甲基化，表明表观遗传机制调节 功能性改变相应RNA-seq数据的分析表明，CTB转录本， 在妊娠中期高表达，在足月时下调的基因中， 比预期的要好。令人兴奋的免疫印迹（IB）数据，经免疫组织化学证实， 显示了从胎盘分离的CTB之间组蛋白修饰水平的新的和强烈的差异 诊断为sPE的妇女和对照样本，胎龄匹配，从 早产妇女的胎盘，无感染迹象（nPTL）。我们的理论是 来自CTB的表观基因组和转录组数据，sPE中的光滑绒毛膜和绒毛膜绒毛将揭示 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 甲基化（目的1）。我们将使用IB和ChIP-seq来评估组蛋白修饰-H3 k27 me 3，H3 k9 me 3， H3 K4 me 1、H3 K4 me 3和H3 K27 ac（目标2）。此外，我们将通过以下方式探索这些发现的转化潜力： 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的特征， 等离子体我们将应用RNA-seq研究在mRNA水平上表观遗传改变的后果。 并通过使用TB功能的体外测定来测试这些发现的意义（目的3）。结果将 可通过WashU Epigenome Browser获得。因此，我们的结果将揭示的作用， 胎盘基因表达中sPE相关变化的表观基因组和这种疾病的候选生物标志物。