Gene expression transcriptome of porcine induced pluripotent stem cell

Pig induced pluripotent stem cells (piPSCs) have significant biomedical and agricultural applications. We analyzed the transcriptional profiles of pig iPSC lines derived from different labs using Affymetrix GeneChip Pig Genome Array and published microarray datasets of mouse and human iPSCs. Our results demonstrated that cell surface proteins of EpCAM (epithelial cells adhesion molecule) were significantly upregulated in complete fully reprogrammed pig iPSCs, but not in partially reprogrammed cells. EpCAM could be markers for evaluating pig cell reprogramming and selecting successful reprogramming. We analyzed gene expression levels of the six key developmental signaling pathways, including JAK-STAT, NOTCH, TGF-βb, WNT, MAPK and VEGF in pig, human and mouse iPSCs, respectively. The result demonstrates that the core transcriptional network to maintain pluripotency and self-renewal in pig are different from mouse and human. Pig iPSCs lacked expression of specific naïve state markers (e.g. Klf family genes Klf2/4/5, Tbx3), but expressed unregulated primed state markers (e.g. Otx2 and Fabp7). Dlk1-Dio3 domain was silenced in piPSCs as previously seen in mouse and human iPSCs, which explains rare success of generation of pig chimeric and cloned offspring. Our analyses decipher pig somatic cells undergoes reprogramming into a primed state and maintains its regulatory network with define feature with human iPSCs and mouse EpiSCs. We compare gene expression profiles of pig iPS cell lines generated by our lab with cell lines derived from other labs with different levels of marker expression and plasticity.

猪诱导多能干细胞（pig induced pluripotent stem cells，piPSCs）具有重要的生物医学与农业应用价值。本研究采用Affymetrix GeneChip猪基因组芯片分析了不同实验室构建的猪iPSC系的转录组谱，并整合了已发表的小鼠和人iPSC的微阵列数据集。结果显示，在完全重编程的猪iPSC中，上皮细胞黏附分子（EpCAM，epithelial cell adhesion molecule）的细胞表面蛋白表达显著上调，而部分重编程细胞中无此变化。EpCAM可作为评估猪细胞重编程效率及筛选成功重编程细胞的标志物。本研究分别分析了猪、人及小鼠iPSC中6条关键发育信号通路的基因表达水平，包括JAK-STAT、NOTCH、TGF-β、WNT、MAPK及VEGF通路。结果表明，维持猪多能性与自我更新的核心转录调控网络与小鼠和人存在显著差异。猪iPSC未表达特异性的初始态标志物（如Klf家族基因Klf2/4/5、Tbx3），但可表达未受调控的始发态标志物（如Otx2与Fabp7）。与既往在小鼠和人iPSC中观察到的现象一致，piPSCs中的Dlk1-Dio3基因区域发生了沉默，这解释了猪嵌合体与克隆后代构建成功率极低的原因。本研究解析表明，猪体细胞经重编程后将进入始发态，并维持了与人类iPSC及小鼠上胚层干细胞（mouse epiblast stem cells，EpiSCs）相似的调控网络特征。本研究将本实验室构建的猪iPSC系的基因表达谱，与其他实验室构建的、具有不同标志物表达水平与可塑性的细胞系进行了对比分析。