Comparison of the molecular profiles of human embryonic and isogenic induced pluripotent stem cells. [Illumina]. Homo sapiens

Many studies have compared the genetic and epigenetic profiles of human induced pluripotent stem cells (hiPSCs) to human embryonic stem cells (hESCs) and yet the picture remains unclear. To address this, we derived a population of neural precursor cells (NPCs) from the H1 (WA01) hESC line and generated isogenic iPSC lines by reprogramming. The gene expression and methylation profile of three lines were compared to the parental line and intermediate NPC population. We found no gene probe with expression that differed significantly between hESC and iPSC samples under undifferentiated or differentiated conditions. Analysis of the global methylation pattern also showed no significant difference between the two PSC populations. Both undifferentiated populations were distinctly different from the intermediate NPC population in both gene expression and methylation profiles. One point to note is that H1 is a male line and so extrapolation to female lines should be cautioned. However, these data confirm our previous findings that there are no significant differences between hESCs and hiPSCs at the gene expression or methylation level. Overall design: 12 samples: 1 human NPC, 5 human ESC (UNDIFF), 6 human iPSC (UNDIFF)

既往多项研究已对人类诱导多能干细胞（human induced pluripotent stem cells, hiPSCs）与人类胚胎干细胞（human embryonic stem cells, hESCs）的遗传及表观遗传谱展开比较，但相关研究结论仍未形成统一认知。为厘清这一问题，本研究从H1（WA01）人类胚胎干细胞系中诱导得到一批神经前体细胞（neural precursor cells, NPCs），并通过细胞重编程技术构建了同基因诱导多能干细胞系。随后，我们将3株细胞系的基因表达谱与甲基化谱，分别与亲本细胞系及中间态神经前体细胞群进行了比较。
结果显示，无论处于未分化还是分化状态，hESCs与hiPSCs样本间均未发现表达存在显著差异的基因探针。全基因组甲基化模式分析同样证实，两类多能干细胞（pluripotent stem cells, PSCs）群之间无显著差异。两类未分化细胞群的基因表达谱与甲基化谱，均与中间态神经前体细胞群存在显著差异。
需注意的是，H1为雄性细胞系，因此将本研究结论外推至雌性细胞系时应谨慎。但本研究数据验证了我们此前的结论：hESCs与hiPSCs在基因表达或甲基化水平上不存在显著差异。
整体实验设计：共纳入12个样本，包括1个人类神经前体细胞样本、5个未分化人类胚胎干细胞（UNDIFF）样本、6个未分化人类诱导多能干细胞（UNDIFF）样本。