Development of iPSCs for comparative genomics in primates

灵长类动物比较基因组学 iPSC 的开发

基本信息

批准号：
10655911
负责人：
Yoav Gilad
金额：
$ 57.13万
依托单位：
UNIVERSITY OF CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-09-01 至 2027-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10655911
关键词：
ATAC-seq Address Adult Affect Autopsy Biocompatible Materials Biological Assay Biological Models Cardiac Catalogs Cell Differentiation process Cell Line Cells Chromatin Collection Communities Comparative Study Complex Data Data Set Development Disease Ethics Fibroblasts Foundations Freezing Future Gene Expression Gene Expression Regulation Genes Human Individual Letters Maps Mesenchymal Molecular Mutation Organoids Pan Genus Phenotype Pilot Projects Pongidae Population Primates Process Property Regulator Genes Research Research Personnel Resources Risk Sampling Series Tissue Sample Tissues cell type clinically relevant comparative comparative genomics differential expression differentiation protocol experience functional genomics genetic architecture human stem cells induced pluripotent stem cell insight lymphoblastoid cell line nonhuman tissue response single-cell RNA sequencing tool trait transcriptome sequencing virtual

项目摘要

Abstract This is a competitive renewal application for a second term of this project (years 5-8). Characterizing gene regulatory differences between humans and our close primate relatives is essential for understanding the molecular basis of human-specific traits. Comparative genomics provides us with the tools to identify both species-specific and conserved regulatory features, which has provided valuable insight into the genetic architecture of adaptation in gene regulation. However, ethical and practical considerations preclude comparative studies of molecular traits in live primates, particularly apes. Frozen post-mortem tissues from non-human apes are difficult to obtain, and even when they are available, they are not optimal templates for many functional genomic assays. Thus, we are generally unable to collect samples from enough individuals to map and study gene regulatory loci in non-human apes; we are unable to study gene regulation in more than a few tissues from apes; we are unable to study the dynamics of gene regulation during development; and we are unable to study regulatory responses to evolutionarily and clinically relevant exposures. In the first term of this project, we proposed to address this challenge by establishing a comparative panel of induced pluripotent stem cells (iPSCs) from humans and chimpanzees. We have successfully done this, and we have shared these lines freely and without restriction with more than 30 labs (see letters of support), facilitating comparative functional genomic studies by investigators who would not otherwise have been able to obtain appropriate samples to conduct their research. We now request support to continue to maintain and distribute this community resource, which we will expand in two ways. First, we will generate additional chimpanzee iPSC lines using the remaining samples we collected prior to the moratorium on chimpanzee research. We expect that these lines will soon become the only population-sample resource for future studies involving chimpanzees in the USA. Second, we will use human and chimpanzee iPSCs to develop a series of dynamically differentiating organoids, which we will also share freely to allow other groups to effectively utilize the comparative iPSC panel. The unique property of these dynamically differentiating organoids is that they contain asynchronously differentiating cells. While they do not produce pure cell populations that can be meaningfully analyzed with bulk RNA-seq data, single-cell RNA-seq can be used to deconvolve the organoids into dozens of cell types and developmental stages, allowing us to explore dynamic regulatory processes that cannot be observed in adult tissues10.

抽象的这是该项目第二个学期（第 5-8 年）的竞争性续签申请。表征人类和我们的灵长类近亲之间的基因调控差异对于了解人类特定特征的分子基础。比较基因组学为我们提供了工具识别物种特异性和保守的调控特征，这为遗传提供了宝贵的见解基因调控的适应结构。然而，伦理和实际考虑排除了比较对活体灵长类动物，特别是猿的分子特征的研究。非人类猿类的冷冻死后组织是很难获得，即使可以获得，它们也不是许多功能基因组的最佳模板化验。因此，我们通常无法从足够多的个体中收集样本来绘制和研究基因调控非人类猿类中的基因座；我们无法研究猿类的多种组织中的基因调控；我们无法研究发育过程中基因调控的动态；我们无法研究监管反应进化和临床相关的暴露。在该项目的第一阶段，我们建议通过建立诱导性比较小组来应对这一挑战来自人类和黑猩猩的多能干细胞（iPSC）。我们已经成功地做到了这一点，并且我们已经分享了这些线路可以自由且不受限制地与 30 多个实验室合作（参见支持信），从而促进比较由研究人员进行的功能基因组研究，否则他们无法获得适当的样本进行他们的研究。我们现在请求支持以继续维护和分发此社区资源，我们将以两种方式扩展。首先，我们将使用剩余的细胞生成额外的黑猩猩 iPSC 系。我们在暂停黑猩猩研究之前收集的样本。我们预计这些线路很快就会成为未来涉及美国黑猩猩的研究的唯一种群样本资源。其次，我们将使用人类和黑猩猩 iPSC 开发一系列动态分化的类器官，我们也将分享自由地允许其他团体有效地利用比较 iPSC 面板。这些的独特属性动态分化类器官的特点是它们包含异步分化的细胞。虽然他们不产生可以用大量 RNA-seq 数据进行有意义分析的纯细胞群，单细胞 RNA-seq 可以用于将类器官分解为数十种细胞类型和发育阶段，使我们能够探索在成人组织中无法观察到的动态调节过程10。