Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics (methylation array). Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics (methylation array)

Comparative studies in primates are extremely restricted because we only have access to a few types of cell lines from non-human apes and to a limited collection of frozen tissues. In order to gain better insight into regulatory processes that underlie variation in complex phenotypes, we must have access to faithful model systems for a wide range of tissues and cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee (Pan troglodytes) induced pluripotent stem cell (iPSC) lines derived from fibroblasts of healthy donors. All lines are free of integration from exogenous reprogramming vectors, can be maintained using standard iPSC culture techniques, and have proliferative and differentiation potential similar to human and mouse lines. To begin demonstrating the utility of comparative iPSC panels, we collected RNA-seq data and methylation profiles from the chimpanzee iPSCs and their corresponding fibroblast precursors, as well as from 7 human iPSCs and their precursors, which were of multiple cell type and population origins. Overall, we observed much less regulatory variation within species in the iPSCs than in the somatic precursors, indicating that the reprogramming process has erased many of the differences observed between somatic cells of different origins. We identified 4,918 differentially expressed genes and 1,986 differentially methylated regions between iPSCs of the two species, many of which are novel inter-species differences and not observed between the somatic cells of the two species. Our panel will help realise the potential of iPSCs, and in combination with genomic technologies, transform studies of comparative evolution in primates. Overall design: We obtained RNA sequencing and methylation profiles from 7 chimpanzee iPSCs and the fibroblasts used to generate them, as well as 7 human iPSCs and the LCLs and fibroblasts used to generate them.

灵长类动物的比较研究受到极大限制，因我们仅能获取少量非人猿类细胞系与有限的冰冻组织样本。为更深入解析复杂表型变异背后的调控机制，我们需要覆盖广泛组织与细胞类型的可靠模型系统。为此，我们从健康供体成纤维细胞中构建了7株完成全面表征的黑猩猩（Pan troglodytes）诱导多能干细胞（induced pluripotent stem cell，iPSC）系，形成一组细胞库。所有细胞系均未整合外源性重编程载体，可通过标准诱导多能干细胞培养技术进行维持，其增殖与分化潜能与人类、小鼠的诱导多能干细胞系相当。为验证比较用诱导多能干细胞库的应用价值，我们分别采集了黑猩猩诱导多能干细胞及其对应成纤维前体细胞、7株人类诱导多能干细胞及其前体细胞的RNA测序（RNA-seq）数据与甲基化谱，其中人类样本涵盖多种细胞类型与种群起源。整体分析显示，诱导多能干细胞的种内调控变异远少于体细胞前体，提示重编程过程消除了多数不同起源体细胞间的固有差异。我们在两个物种的诱导多能干细胞间鉴定出4918个差异表达基因与1986个差异甲基化区域，其中多数为全新的种间差异，未在两个物种的体细胞中被观测到。本细胞库将助力释放诱导多能干细胞的应用潜力，并结合基因组学技术革新灵长类比较进化研究。实验设计概述：我们获取了7株黑猩猩诱导多能干细胞及其构建所用成纤维细胞的RNA测序与甲基化谱数据，同时获取了7株人类诱导多能干细胞及其构建所用淋巴母细胞样细胞系（lymphoblastoid cell lines，LCLs）与成纤维细胞的相关数据。