Project 2: Joint Transcriptomic and Epigenomic Studies for Male Osteoporosis

项目2：男性骨质疏松症的转录组和表观基因组联合研究

• 批准号: 10180819
• 负责人: ERIK K FLEMINGTON
• 金额: $ 22.53万
• 依托单位: TULANE UNIVERSITY OF LOUISIANA
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-15 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10180819
• 关键词: Affect; African American; Age; Apoptosis; Bioinformatics; Biological; Biological Assay; Bone Density; Bone Resorption; Caucasians; Cells; Chinese People; Clinical; DNA; DNA Methylation; Data; Data Set; Epigenetic Process; Ethnic Origin; Etiology; Female; Finite Element Analysis; Fracture; Gene Expression; Genes; Genetic Transcription; Genomics; Goals; In Vitro; Joints; Life; Luciferases; Measurement; Measures; Mediating; Messenger RNA; Metabolic Bone Diseases; MicroRNAs; Modification; Molecular; Osteoclasts; Osteoporosis; Outcome; Pathway Analysis; Play; Proteomics; Public Health; RNA; Reverse Transcriptase Polymerase Chain Reaction; Risk; Role; Signal Transduction; Small Interfering RNA; Specific qualifier value; Specificity; Testing; Time; Validation; Variant; Western Blotting; Woman; aged; base; bone cell; bone metabolism; bone quality; cell type; clinical phenotype; cohort; cytokine; differential expression; epigenomics; expectation; functional gain; functional genomics; genetic variant; genome wide association study; genomic data; human disease; in silico; insight; mRNA Expression; mRNA Stability; male; men; monocyte; multiple omics; neglect; novel; osteoclastogenesis; peripheral blood; recruit; risk variant; sex; transcriptome; transcriptome sequencing; transcriptomics

Osteoporosis is the most common metabolic bone disease mainly characterized by low bone mineral density (BMD,--areal BMD (aBMD) unless otherwise specified). Male osteoporosis is a major but most neglected public health problem. Peripheral blood monocytes (PBMs) may act as precursors of osteoclasts, the bone resorption cells, and produce cytokines important for osteoclast differentiation, activation, and apoptosis, and thus represent a major systemic cell for bone metabolism. micro-RNA (miRNAs)-mediated gene expression modifications are important transcriptomic dynamics underlying human diseases, and are involved in osteoclastogenesis in vitro. Next-G RNA- seq has an unparalleled power to comprehensively characterize transcriptome, in particular, revealing novel miRNAs. Therefore, our Hypothesis is: Changes in mRNA and miRNA expression profiles in PBMs underlie male BMD and bone quality/strength variation and can be identified most powerfully by the cutting edge Next-G RNA-seq. Through the Clinical Core, we will recruit and clinically phenotype 200 Caucasian and 100 African American (AA) men, aged 20-30, 150 (100 Caucasians and 50 AA) with high and 150 (100 Caucasians and 50 AA) with low BMD. Bone quality/strength (measured by quantitative CT [QCT] and finite element analyses [FEA]) will also be assessed on each subject. Half of the Caucasians (50 high vs. 50 low BMD subjects) will serve as a “discovery cohort” and the other half as a “replication cohort”. These same subjects will all be used in Proj 2 & 3. In Aim 1, we will comprehensively identify mRNAs important to male osteoporosis. We will use the PBMs total RNAs of the “discovery cohort” to perform RNA-seq-based transcriptome studies to identify mRNAs differentially expressed (DEx) in high vs. low BMD subjects. We will identify the top 10 DEx genes and validate them in the discovery cohort (within-cohort technical validation), the replication cohort (across-cohort biological validation), the AA cohort (across-ethnicity validation), and another independent set of 86 Caucasian female (46 high vs. 40 low BMD) subjects (from our SCOR, for across-sex validation). In silico replication in subjects of different sexes and/or ethnicities will be performed in existing functional genomics datasets. In Aim 2, we will identify/validate DEx miRNAs in high vs. low BMD subjects and the target genes of the top DEx miRNAs. We will identify the top 15 DEx miRNAs, and for each of which, identify top 5 potential target mRNAs through correlation and bioinformatics analyses and also validate their “targeting” relationship in the above mentioned cohorts/datasets as well as using luciferase-based functional assays. The significant mRNA/miRNA identified above will be tested for their significance for QTC and FEA measures. The data generated in this project will be used for more advanced analyses, such as eQTL/mQTL analyses, gene network analyses, causality analyses and other integrative analyses , e.g., to 1) gain functional insights into the genetic variants and DNA methylation marks identified in Proj 1 & 3; and 2) search for consistent signals of important risk genes through combined analyses of sub-signals at DNA and mRNA levels by data collected in Proj 1 & 2; 3) identify interactions of various epigenetic mechanisms such as miRNA and DNA methylation.

骨质疏松症是最常见的代谢骨病，主要以低骨矿物质密度为特征 （BMD，-areal BMD（ABMD），除非另有说明）。 健康问题。 并产生细胞因子对于破骨细胞差异，激活和appttosis的重要 骨代谢的全身细胞。 人类疾病的转录组动力学，并参与体外骨化剂。 SEQ具有全面的角色分类组，尤其是陶醉的小说的能力 因此，miRNA。 BMD和骨骼质量/强度变化，可以通过最尖端的Next-G RNA-Seq来确定最有力的最有力。 通过临床核心，我们将招募和临床表型200高加索和100名非裔美国人（AA） 男性，年龄在20-30、150（100名高加索人和50 AA），具有低BMD的150名（100名高加索人和50 AA）。 骨质量/强度（通过定量CT [QCT]和有限元分析[FEA]）也将beassssessessed 在每个主题上。 其他一半作为“复制队列”。 在AIM 1中，我们将全面识别对男性骨质疏松症重要的mRNA。 “发现队列”的RNA进行基于RNA-Seq的转录组，以鉴定mRNA 在高与低BMD受试者中表达（DEX）。 Discovery COHORT（核管内技术验证），复制队列（跨科罗特生物学验证）， AA队列（跨种族验证）和另一套独立的86名高加索女性（46个高与40 Loww BMD）受试者（来自我们的SCOR，为跨性别阀）。 种族将在现有的功能基因组数据集中进行。 在AIM 2中，我们将在高与低BMD受试者和最高DEX的靶基因中/验证/验证DEX miRNA miRNA。 通过相关性和生物信息学分析，并在上述中验证其“靶向”关系 介绍的队列/数据集以及基于荧光素酶的功能测定。 上面鉴定出的明显mRNA/miRNA将测试其对QTC和惠族的重要性。 该项目中生成的数据将用于更高级的分析，例如EQTL/MQTL分析， 基因网络分析，因果关系分析和其他综合分析，例如1）获得功能见解 遗传变异和DNA甲基化标记在ProJ 1和3中确定； 2）搜索一致的信号 重要的风险基因通过ProJ 1中的数据集体对DNA和mRNA水平的亚信号结合分析 ＆2; 3）确定各种表观遗传机制的相互作用，例如miRNA和DNA甲基化。