Genomics of bone and body composition traits in children

摘要 我们的目标是确定调控儿童骨密度、质量和强度发育的基因。 童年是终身肌肉骨骼健康的关键窗口。在治疗期间未能实现最佳骨增量 童年导致在以后的生活中的次优峰值骨量和骨脆性。超过5000万美国老年人 成年人有骨质疏松症或低骨量。骨质疏松症有很强的遗传成分，但只有20%的 成人骨矿物质密度（BMD）的变异性可以用迄今为止发现的遗传变异来解释。儿科研究 在提取这种复杂表型的遗传学方面应该是非常有效的，因为（a） 环境的影响是短期的，和（B）生长，身体组成和 成熟也影响骨生成。揭示儿童期骨骼增长的遗传结构至关重要 了解终身骨骼健康和确定预防和治疗骨脆弱性的目标。 双能X线骨密度仪（DXA）测量区域BMD广泛用于遗传研究。关于DXA 随着软件的进步，骨质量和结构强度的元素可以被提取，沿着 已知影响骨生成的组成参数。这些更深层次的DXA衍生表型具有很大的 有可能进一步揭示骨骼发育的遗传决定因素的重要、新颖的见解。我们有 NICHD儿童骨密度研究（BMDCS）队列的全基因组基因分型是独一无二的， 它具有规模大、年龄范围广、数据质量高、多样性和纵向设计等特点。我们将推出新的 表型从现有的DXA和X光片图像，并应用先进的多维表型和 多变量GWAS方法来鉴定新的基因座。GWAS仅报告与给定的 性状，而不一定是罪魁祸首基因的精确位置。因此，我们将使用高分辨率`变量来 我们的“空间和功能基因组学中心”建立了“基因作图”技术， 以前报道的儿科新基因座和我们预期的新基因座。我们的方法首先优先考虑假定的因果关系 使用开放染色质和增强子表观遗传签名的SNP，然后识别3D基因组接触 这些优先SNP和它们的靶基因启动子之间，使用基于高分辨率启动子的 染色质构象捕获技术。为了验证这些靶基因，我们将使用CRISPR/Cas9来编辑这些靶基因。 假定的调节SNP，并使用siRNA靶向基因，并显示对骨相关表型的影响。我们 将我们的技术应用于原代儿科人间充质祖细胞（MSC）衍生的成骨细胞， 非常相关的骨细胞模型，用于了解儿童骨量增加。 因此，我们的建议是一个无与伦比的机会，询问新的表型和功能特征， 实际的效应基因使用高分辨率染色质构象捕捉方法在这些新的， 以及先前已知的骨相关基因座。

ABSTRACT Our objective is to identify genes that regulate development of bone density, quality and strength in childhood. Childhood is a critical window for lifelong musculoskeletal health. Failure to achieve optimal bone accrual during childhood results in suboptimal peak bone mass and bone fragility later in life. In excess of 50 million older US adults have osteoporosis or low bone mass. Osteoporosis has a strong heritable component, yet only 20% of adult bone mineral density (BMD) variability is explained by genetic variants discovered to date. Pediatric studies should be highly effective in distilling the genetics of this complex phenotype, given (a) the duration of environmental influences is shorter, and (b) the genetic determinants of growth, body composition and maturation also influence bone accrual. Uncovering the genetic architecture of childhood bone accrual is critical for understanding lifelong skeletal health and identifying targets for preventing and treating bone fragility. Dual energy x-ray absorptiometry (DXA) measures of areal BMD are widely used in genetic studies. With DXA software advances, elements of bone quality and structural strength can be extracted, along with body composition parameters known to influence bone accrual. These deeper DXA-derived phenotypes have great potential to shed further important, novel insights into genetic determinants of the developing skeleton. We have genome-wide genotyped the NICHD Bone Mineral Density in Childhood Study (BMDCS) cohort which is unique for its large size, broad age range, high data quality, diversity and longitudinal design. We will derive new phenotypes from existing DXA and radiograph images, and apply advanced multidimensional phenotyping and multivariate GWAS methods to identify new loci. GWAS only reports genomic signals associated with a given trait and not necessarily the precise location of culprit genes. Therefore, we will use high-resolution `variant to gene mapping' techniques established in our `Center for Spatial and Functional Genomics' to investigate both previously reported pediatric novel loci and our anticipated new loci. Our approach first prioritizes putative causal SNPs using open chromatin and enhancer epigenetic signatures, and then identifies 3D genomic contacts between these prioritized SNPs and their target gene promoters, using a high-resolution promoter-based chromatin conformation capture technique. To validate these target genes, we will use CRISPR/Cas9 to edit the putative regulatory SNPs and use siRNA to target genes and show an effect on bone-relevant phenotypes. We will apply our techniques in primary pediatric human mesenchymal progenitor cell (MSC)-derived osteoblasts, a very relevant bone cellular model for understanding pediatric bone mass accrual. Thus, our proposal is an unparalleled opportunity to interrogate novel phenotypes and functionally characterize the actual effector genes using high resolution chromatin conformation capture approaches at these new, as well as previously known bone-related loci.