Genomics of bone and body composition traits in children

摘要 我们的目标是确定调节儿童时期骨密度、质量和强度发育的基因。 童年是终生肌肉骨骼健康的关键窗口。未能实现最佳的骨积累 童年导致在以后的生活中骨量和骨脆性低于最佳水平。超过5000万的美国老年人 成年人患有骨质疏松症或骨量低。骨质疏松症有很强的遗传成分，但只有20%的人 成人骨密度(BMD)的变异性可以用迄今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非常有效，因为(A)持续时间 环境影响较短，以及(B)生长、身体成分和 成熟度也会影响骨的累积。揭示儿童期骨积累的遗传结构是至关重要的 用于了解终生骨骼健康并确定预防和治疗骨脆性的目标。 双能X射线骨密度仪(DXA)测量面骨密度在遗传学研究中得到广泛应用。使用DXA 软件的进步，可以提取骨骼质量和结构强度的元素，以及身体 已知的影响骨累积的成分参数。这些更深层次的DXA衍生表型有很好的 有可能对发育中骨骼的遗传决定因素提供更重要的、新的见解。我们有 全基因组基因分型NICHD儿童骨密度研究(BMDCS)队列的独一无二 由于其体量大、年龄范围广、数据质量高、多样性和纵向设计。我们将衍生出新的 来自现有DXA和X光图像的表型，并应用先进的多维表型和 多变量广义遗传算法识别新的基因座。Gwas只报告与给定的 特征，而不一定是罪犯基因的准确位置。因此，我们将使用高分辨率`变量来 在我们的空间和功能基因组学研究中心建立的基因作图技术 先前报道的儿科新基因座和我们期待的新基因座。我们的方法首先优先考虑推定的因果关系 使用开放染色质和增强子表观遗传特征的SNPs，然后识别3D基因组接触 在这些优先SNPs和它们的目标基因启动子之间，使用基于高分辨率启动子的 染色质构象捕捉技术。为了验证这些靶基因，我们将使用CRISPR/Cas9编辑 推测的调节性SNPs，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儿童原代人间充质祖细胞(MSC)来源的成骨细胞 非常相关的骨细胞模型来理解儿童骨量的增加。 因此，我们的建议是一个无与伦比的机会来审问新的表型和功能特征 使用高分辨率染色质构象捕捉的实际效应基因在这些新的，如 以及之前已知的骨骼相关基因。

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.