Epigenomewide DNA Methylation Study for Osteoporosis Risk

表观基因组 DNA 甲基化研究骨质疏松症风险

基本信息

批准号：
9138957
负责人：
HONG-WEN DENG
金额：
$ 60.55万
依托单位：
TULANE UNIVERSITY OF LOUISIANA
依托单位国家：
美国
项目类别：
财政年份：
2012
资助国家：
美国
起止时间：
2012-09-01 至 2019-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9138957
关键词：
Accounting Affect Apoptosis Award Biological Assay Blood specimen Bone Density Bone Resorption Caucasians Cell Line Cells Complex Cytosine DNA DNA Methylation DNA Modification Process DNA Sequence Data Disease Elderly Epigenetic Process Etiology Female Fracture Functional disorder Gene Expression Gene Expression Regulation Gene Targeting Genes Genetic Genomic DNA Goals Hereditary Disease Heritability Human Immunoprecipitation In Vitro Knowledge Lead Life Metabolic Bone Diseases Methods Modification Molecular Osteoclasts Osteoporosis Phenotype Predisposition Premenopause Prevention Principal Investigator Public Health Quality of life Recruitment Activity Regulator Genes Research Risk Role Sampling Technology Variant Woman aged base bisulfite sequencing bone bone loss bone metabolism cohort cytokine epidemiology study epigenetic regulation epigenomics expectation genetic epidemiology genome wide association study human disease in vitro Assay in vivo mRNA Expression methylome monocyte next generation sequencing novel novel strategies osteoclastogenesis osteoporosis with pathological fracture peripheral blood programs research study risk variant sample collection study population

项目摘要

DESCRIPTION (provided by applicant): Osteoporosis is a common disease mainly characterized by low bone mineral density (BMD) and increased risk of fractures. Peripheral blood monocytes (PBMs) may not only act as precursors of osteoclasts, the bone resorption cells, but also produce cytokines important for osteoclast differentiation, activation, and apoptosis, and thus represent major systemic cells for bone metabolism. Alterations in DNA methylation as an important epigenetic regulator of gene expression, is significant in the etiology of human complex diseases. In vitro studies have shown that DNA methylation is involved in osteoclastogenesis; however, the in vivo significance of global DNA methylation profiles (methylome) in humans underlying osteoporosis risk is unknown. Our Hypothesis is that altered DNA methylation profiles in PBMs and the associated changes in gene expression and osteoclastogenesis contribute to peak BMD variation in humans. Our Goal/Expectation is to i) identify differentially methylated regions (DMRs) in PBMs at the whole methylome level between premenopausal women with extremely high peak BMD and those with extremely low peak BMD; ii) study potential epigenetic mechanisms of osteoporosis, namely, how the DMRs identified may influence the peak BMD variation through affecting the expression of the relevant genes and subsequent osteoclastogenesis. Methods: 1) PBMs and their DNAs and total RNAs will be extracted from 160 premenopausal Caucasian females aged 25-40 years, including 80 with extremely high peak BMD and 80 with extremely low peak BMD (but otherwise matched). 2) DMRs will be identified by performing state-of-the-art methylome profiling studies with the cutting-edge technology MeDIP-seq (methylated DNA immunoprecipitation assays followed by next-generation sequencing) in a discovery sample of 80 subjects (including 40 with high and 40 with low BMD). 3) The identified DMRs will be subject to confirmation by bisulfite sequencing in an independent replication sample (including 40 with high and 40 with low BMD), and their target genes will be identified by correlating the DNA methylation data with the mRNA expression levels of the potential candidate target genes in PBMs of the total 160 subjects. 4) The roles of the identified most significant DMR-affiliated target genes on osteoclastogenesis will be further investigated by cell based in vitro assays. This highly novel R01 project holds great promise of award to generate breakthroughs in the osteoporosis research field. The results may lead to a major paradigm shift by expanding current genetic epidemiology studies of osteoporosis, from classical DNA variants to novel epigenetics/epigenomics mechanisms of DNA modification. Therefore, the results will be highly important for understanding the underlying molecular mechanisms, and thus help prevention and treatment, of osteoporosis.

描述（申请人提供）：骨质疏松症是一种常见疾病，主要特征是骨矿物质密度（BMD）低和骨折风险增加。外周血单核细胞（PBM）不仅可以作为破骨细胞（骨吸收细胞）的前体，还可以产生对破骨细胞分化、活化和凋亡重要的细胞因子，因此代表骨代谢的主要全身细胞。 DNA 甲基化的改变作为基因表达的重要表观遗传调节因子，在病因学中具有重要意义人类复杂疾病。体外研究表明DNA甲基化参与破骨细胞生成；然而，整体 DNA 甲基化谱（甲基化组）对人类骨质疏松症风险的体内意义尚不清楚。我们的假设是，PBM 中 DNA 甲基化谱的改变以及基因表达和破骨细胞生成的相关变化导致了人类 BMD 变化的峰值。我们的目标/期望是 i) 在具有极高峰值 BMD 和极低峰值 BMD 的绝经前女性之间的整个甲基化组水平上识别 PBM 中的差异甲基化区域 (DMR)； ii) 研究骨质疏松症潜在的表观遗传机制，即确定的 DMR 如何通过影响相关基因的表达和随后的破骨细胞生成来影响峰值 BMD 变化。方法： 1）从160名25-40岁绝经前白人女性中提取PBM及其DNA和总RNA，其中80名具有极高峰值BMD，80名具有极低峰值BMD（但其他方面匹配）。 2) 将通过使用尖端技术 MeDIP-seq（甲基化 DNA 免疫沉淀分析，然后进行下一代测序）在 80 名受试者（其中 40 名受试者）的发现样本中进行最先进的甲基化组分析研究来鉴定 DMR。高和 40，BMD 低）。 3) 鉴定出的DMR将在独立复制样本（包括40个高BMD和40个低BMD）中进行亚硫酸氢盐测序确认，并通过将DNA甲基化数据与目标基因的mRNA表达水平相关联来鉴定其靶基因。总共 160 名受试者的 PBM 中潜在的候选靶基因。 4）将通过基于细胞的体外测定进一步研究已确定的最重要的DMR相关靶基因对破骨细胞生成的作用。这个高度新颖的 R01 项目有望在骨质疏松症研究领域取得突破性进展。通过扩展当前骨质疏松症的遗传流行病学研究，从经典的 DNA 变异到 DNA 修饰的新型表观遗传学/表观基因组学机制，这些结果可能会导致重大范式转变。因此，这些结果对于了解骨质疏松症的潜在分子机制非常重要，从而有助于预防和治疗骨质疏松症。