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

• 批准号: 8368888
• 负责人: HONG-WEN DENG
• 金额: $ 65.12万
• 依托单位: TULANE UNIVERSITY OF LOUISIANA
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-01 至 2017-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8368888
• 关键词: Accounting; Affect; Apoptosis; Award; Biological Assay; Blood specimen; Bone Density; Bone Resorption; Caucasians; Caucasoid Race; 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; Genomics; Goals; Hereditary Disease; Heritability; Human; Immunoprecipitation; In Vitro; Knowledge; Lead; Life; Metabolic Bone Diseases; Methods; Modification; Molecular; Osteoclasts; Osteoporosis; Phenotype; Population Study; Predisposition; Premenopause; Prevention; Principal Investigator; Public Health; Quality of life; Recruitment Activity; Regulation; Regulator Genes; Research; Risk; Role; Sampling; Technology; Variant; Woman; aged; base; bisulfite; bone; bone loss; bone metabolism; cohort; cytokine; epidemiology study; epigenomics; expectation; genetic epidemiology; genome wide association study; human disease; in vitro Assay; in vivo; mRNA Expression; monocyte; next generation; novel; novel strategies; osteoclastogenesis; osteoporosis with pathological fracture; peripheral blood; programs; research study; sample collection

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. PUBLIC HEALTH RELEVANCE: Osteoporosis is a serious public health problem leading to severe bone loss and increased risk of fractures in elderly subjects, especially women. The proposed study will identify differentially methylated regions (DMRs) between subjects with discordant BMD phenotypes and reveal some epigenetic mechanisms of BMD variation and osteoporosis risk. The findings will contribute to a better and more comprehensive understanding of molecular mechanisms, and thus help prevention and treatment, of osteoporosis.

描述（由申请人提供）：骨质疏松症是一种常见疾病，主要以低骨矿物质密度（BMD）和裂缝风险增加为特征。外周血单核细胞（PBM）不仅可以充当破骨细胞，骨吸收细胞的前体，而且还产生对破骨细胞分化，激活和凋亡至关重要的细胞因子，从而代表骨代谢的主要全身细胞。 DNA甲基化作为基因表达的重要表观遗传调节剂的改变在病因中很重要 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，尚不清楚骨质疏松风险的人类中全球DNA甲基化谱（甲基化）的体内意义。 我们的假设是，PBMS中DNA甲基化谱的改变，基因表达和骨质质发生的相关变化有助于人类的峰值BMD变化。 我们的目标/期望是i）确定PBMS的差异性甲基化区域（DMR）在BMD极高的绝经前女性和BMD极低的峰值峰值的甲基甲基水平上的差异； ii）研究骨质疏松症的潜在表观遗传学机制，即，鉴定出DMRS可能如何通过影响相关基因的表达和随后的骨质质发生法来影响BMD峰值变异。 方法：1）PBM及其DNA和总RNA将从160个年度25-40岁的160个前高加索雌性中提取，其中包括80个具有极高的峰值BMD和80岁的峰值BMD，峰值BMD极低（但否则匹配）。 2）将通过在80个受试者的发现样本中（包括40名高和低BMD的40个受试者）中，通过最先进的技术MEDIP-SEQ（甲基化的DNA免疫沉淀测定法，然后是下一代测序）来确定DMR通过最先进的甲基化组分析研究（甲基化的DNA免疫沉淀测定法，然后是下一代测序）。 3）所鉴定的DMR将在独立复制样本中的亚硫酸盐测序（包括高40个和低BMD的40个）中得到确认，并且将通过将DNA甲基化数据与160名受试者PBMS潜在候选靶基因的mRNA表达水平相关的DNA甲基化数据来鉴定其靶基因。 4）鉴定出最显着的DMR相关靶基因在破骨细胞发生上的作用将通过基于细胞的体外测定进一步研究。 这个高度新颖的R01项目具有巨大的奖项，可以在骨质疏松研究领域产生突破。结果可能会通过扩展骨质疏松症的当前遗传流行病学研究，从经典DNA变异到新型表观遗传学/表观基因组学的机制，从而导致重大范式转移。因此，结果对于理解潜在的分子机制，从而有助于预防和治疗骨质疏松症将非常重要。 公共卫生相关性：骨质疏松症是一个严重的公共卫生问题，导致严重的骨质流失和老年受试者，尤其是女性骨折的风险增加。拟议的研究将在患有不一致的BMD表型的受试者之间确定差异化甲基化区域（DMR），并揭示了BMD变异和骨质疏松症风险的某些表观遗传机制。这些发现将有助于对分子机制的更好，更全面的了解，从而有助于预防和治疗骨质疏松症。