Discovery of osteoblast and osteoclast bone mass effector genes using advanced genomics

利用先进基因组学发现成骨细胞和破骨细胞骨量效应基因

• 批准号: 10675631
• 负责人: Struan F A Grant
• 金额: $ 66.98万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-03 至 2027-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10675631
• 关键词: ATAC-seq; Age Months; American; Bioinformatics; Biology; Bone Density; Bone Diseases; Bone Resorption; CRISPR/Cas technology; Cell Differentiation process; Cell Lineage; Cells; Child; Chromatin; Chromosome Mapping; Clustered Regularly Interspaced Short Palindromic Repeats; Collaborations; Collection; Communities; Complex; Data; Development; Disease; Enhancers; Etiology; Female; Fracture; Gene Expression; Genes; Genetic; Genetic Diseases; Genome; Genomics; Goals; Grant; Human; In Vitro; International; Knockout Mice; Laboratories; Link; Mechanics; Methods; Minerals; Mission; Modeling; Mus; Osteoblasts; Osteoclasts; Osteogenesis; Osteoporosis; Pathogenesis; Pathway Analysis; Phenotype; Physiology; Play; Process; Public Domains; Publishing; Regulation; Reporting; Research; Resolution; Role; Sample Size; Sampling; Signal Transduction; Small Interfering RNA; Testing; Time; Validation; Variant; Work; bone; bone geometry; bone loss; bone mass; causal variant; chromosome conformation capture; clinically relevant; follow-up; fracture risk; gene discovery; genetic variant; genome wide association study; genome-wide; genomic data; in vivo; interest; male; microCT; mouse model; novel; novel therapeutics; osteoblast differentiation; prevent; promoter; trait; transcriptome sequencing

Osteoporosis is a devastating disease of bone that impacts over 10 million Americans. While the cellular basis for osteoporosis includes an imbalance in bone formation by osteoblasts and bone resorption by osteoclasts, there are relatively few validated, clinically relevant genes directly linked to osteoporosis. There is a significant need to discover new genes that influence osteoporosis pathogenesis. Discovery of new osteoporosis genes will eventually permit the field of bone and mineral biology to achieve the long-term goal of developing new therapies to both prevent and treat this debilitating disease. The existing, long-term collaboration between the Hankenson and Grant laboratories has been focused on understanding the functional significance of genome wide association study (GWAS) signals associated with bone mass, osteoporosis and fracture risk. We have developed methods to use those signals to identify novel genes putatively involved in disease pathogenesis. While GWAS efforts by numerous research groups have been successful in discovering genomic variants robustly associated with bone mineral density (BMD) and fracture, GWAS only reports signals associated with a given trait and not necessarily culprit genes. In this proposal we utilize a computationally advanced, multi-step process that integrates genome level data to identify novel osteoblast and osteoclast genes. This bioinformatically-driven `genome-wide variant to gene mapping' effort combines RNA-seq, ATAC-seq and high-resolution chromatin conformation capture methods to implicate culprit effector genes. We have already used this approach in osteoblast lineage cells and 30% of osteoporosis-associated GWAS signals were shown to have direct physical contact with genes in these cells, totaling 86 putative target genes. Several of these targets (ex. EPDR1, ING3) have already had extensive functional follow-up. However, many more need functional follow-up and there are still 70% of osteoporosis associated GWAS loci that remain unresolved. Importantly, our initial work focused only on discovering osteoblast-associated genes, and thus genes that play a role in osteoclasts were not revealed. Furthermore, our published work to date has only focused on one time-point during the osteoblast differentiation process, thus genes that play roles at later points in cell differentiation have not been discovered. This comprehensive application will functionalize GWAS findings, and in doing so, reveal novel genes involved in regulating bone formation and resorption. Our established pipeline from gene discovery to gene validation has been robustly tested and thus far, although our sampling has been small, we have had a 100% hit rate for validating putative effector genes. Thus, it is our hypothesis that we can uncover many more BMD effector genes by conducting high resolution `genome-wide variant to gene mapping' in osteoclasts and osteoblasts. The relevance of genes will be validated using both in vitro and in vivo approaches in mouse models. Upon completion, we will provide the bone community with new targets to pursue for understanding mechanism.

骨质疏松症是一种毁灭性的骨骼疾病，影响了超过1000万美国人。而细胞基础 对于骨质疏松症，包括成骨细胞形成骨骼的不平衡和骨细胞的骨吸收， 与骨质疏松直接相关的临床相关基因相对较少。有重要的 需要发现影响骨质疏松发病机理的新基因。发现新的骨质疏松基因 最终将允许骨头和矿物生物学领域实现开发新的长期目标 预防和治疗这种使人衰弱的疾病的疗法。 Hankenson和Grant Laboratories之间现有的长期合作一直集中在 了解基因组广泛关联研究（GWAS）信号的功能意义 骨骼质量，骨质疏松和骨折风险。我们已经开发了使用这些信号来识别新颖的方法 基因参与疾病发病机理。众多研究小组的GWAS努力 成功地发现了与骨矿物质密度（BMD）和 裂缝，GWAS仅报告与给定性状相关的信号，而不一定是罪魁祸首。 在此建议中，我们利用一个计算高级的多步骤过程，将基因组级别的数据集成到 识别新型的成骨细胞和骨细胞基因。这种生物信息驱动的`基因组对基因的变体 映射的努力结合了RNA-seq，atac-seq和高分辨率染色质构象捕获方法 暗示罪魁祸首基因。我们已经在成骨细胞中使用了这种方法，30％ 骨质疏松相关的GWAS信号显示与这些细胞中的基因直接接触， 总计86个推定的靶基因。这些目标中的几个（例如EPDR1，ING3）已经有很大的 功能随访。但是，还有更多需要功能随访，还有70％的骨质疏松症 尚未解决的相关GWAS基因座。重要的是，我们最初的工作仅着重于发现 没有揭示与成骨细胞相关的基因，因此没有揭示在破骨细胞中起作用的基因。此外， 迄今 因此，尚未发现在细胞分化的后期角色中扮演角色的基因。 这种综合应用将使GWAS的发现功能函数，并在此过程中揭示涉及的新基因 在调节骨形成和吸收中。我们已建立的管道从基因发现到基因验证 已经经过了重新测试，到目前为止，尽管我们的采样很小，但我们的命中率为100％ 验证推定效应子基因。因此，我们的假设是我们可以发现更多的BMD效应器 通过在破骨细胞和成骨细胞中进行高分辨率的“全基因组变体对基因映射”的基因。 在小鼠模型中，使用体外和体内方法都将验证基因的相关性。之上 完成，我们将为骨头社区提供新的目标，以了解理解机制。