Functional genomics of growth hormone response in a natural human model for short stature with comparisons to other populations and species

项目摘要/摘要 体型是生物学和健康的一个基本方面。然而，尽管最近在了解方面取得了许多进展- 在遗传变异的基础上，种群内和种群间变异的最接近的细胞原因 体型在很大程度上是未知的。在一个极端的情况下，身材矮小，或者说是“侏儒”表型，是一种特征-- TIC是世界各地热带雨林狩猎采集者(RHGs)的常见病，这种基因介导的特征很可能是对 热带雨林对人类居民的恶劣生态条件。RHG与RHG的比较 因此，非RHG群体为研究遗传、功能和进化提供了一个自然的人类模型。 生长和体型的基础。我建议研究全基因组对胰岛素样物质的调控反应 成纤维细胞生长因子1(IGF1)和成纤维细胞生长因子-9在软骨细胞培养中的作用 乌干达巴特瓦人(N=20)及其群体样本的诱导多能干细胞(IPSCs) 农学家与Bakiga相邻(N=20)。我将评估全基因组对IGF1的基因表达反应 和成纤维细胞生长因子-9通过RNAseq并通过治疗识别差异表达(DE)基因(基线与挑战)， 种群，以及种群x处理交互作用--即具有BATWA-specific的基因对IGF1或FGF9的反应。我 也将同时表征IGF1和成纤维细胞生长因子-9在黑猩猩和狒狒IPSC来源的反应 软骨细胞，从而允许将生长因子反应的变异划分为人类谱系特有的fic， 人类种群--特定于fic和共享组件。巴特瓦和巴克加fic-DE反应基因集 将与来自同一群体的SNP基因数据的群体基因组分析的结果交叉- 测试DE基因是否在包含阳性签名的基因组区域内显著富含fi 选择。与其他数据集的比较将有助于识别具有潜在表型和临床表型的基因座的fi阳离子。 ficance是一个标志。这是一种强大的、相关的体外系统的比较功能基因组学研究 一个自然的人体模型将促进我们对关键的人类成长和发展途径的理解。这个 建议的研究将是对first全基因组功能基因组在相关细胞类型中的生长情况进行调查 以侏儒表型为特征的人群中的因子反应。作为fi首批IPSC研究之一 非洲人和RHGs的第一个fi，该项目将人类细胞模型与种群基因组方法相结合，以 提供了人类基因组和功能多样性的扩展视图。与之前的研究不同，拟议的项目 将拥有探索生长因子途径中断所需的范围、相关的细胞类型和力量 在RHG中的侏儒表型中起作用。作为我NRSA奖学金的一部分提出的项目和培训 将推进我的职业目标，整合种群基因组和功能基因组方法，以了解 与生物医学相关的适应，将是我过渡到独立研究人员探索 过去进化适应的生物医学相关性。

PROJECT SUMMARY / ABSTRACT Body size is a fundamental aspect of biology and health. However, despite many recent gains in understand- ing its genetic variation underpinnings, the proximate cellular causes of variation in intra- and inter-population body size are largely unknown. At one extreme, small body size, or the “pygmy” phenotype, is a characteris- tic of rainforest hunter-gatherers (RHGs) worldwide, and this genetically-mediated trait is likely an adaptation to the harsh ecological conditions of tropical rainforests for human inhabitants. Comparisons between RHG and non-RHG populations thus present a natural human model for studying the genetic, functional, and evolutionary bases of growth and body size. I propose to investigate the genome-wide regulatory response to Insulin-like Growth Factor 1 (IGF1) and a Fibroblast Growth Factor (FGF-9) in experiments with chondrocytes derived from induced pluripotent stem cells (iPSCs) for population samples of the Batwa RHGs of Uganda (N=20) and their agriculturalist neighbors the Bakiga (N=20). I will estimate genome-wide gene expression responses to IGF1 and FGF-9 via RNAseq and identify differentially expressed (DE) genes by treatment (baseline vs. challenge), population, and population x treatment interaction–i.e. genes with Batwa-specific response to IGF1 or FGF-9. I will also simultaneously characterize the IGF1 and FGF-9 responses in chimpanzee and baboon iPSC-derived chondrocytes, thus allowing the partitioning of variation in growth factor response into human lineage-specific, human population-specific, and shared components. The sets of Batwa- and Bakiga-specific DE response genes will be intersected with results from population genomic analyses of SNP genotype data from the same popula- tions to test whether DE genes are significantly enriched within genome regions containing signatures of positive selection. Comparisons to other datasets will facilitate the identification of loci with potential phenotypic and clin- ical significance. This comparative functional genomics investigation of a powerful, relevant in vitro system from a natural human model will advance our understanding of critical human growth and development pathways. The proposed study will be the first genome-wide functional genomic investigation in a relevant cell type of the growth factor response in a human population characterized by the pygmy phenotype. As one of the first iPSC studies of Africans and the first of RHGs, the project integrates human cellular models with population genomic methods to afford an expanded view of human genomic and functional diversity. Unlike previous studies, the proposed project will have the scope, relevant cell type, and power necessary to explore the growth factor pathway disruptions that play a role in the pygmy phenotype in RHGs. The project and training proposed as part of my NRSA fellowship will advance my career goal of integrating population genomic and functional genomic approaches to understand biomedically relevant adaptations and will be ideal for my transition to an independent researcher exploring the biomedical relevance of past evolutionary adaptations.