Hu Kejin, Ianov Lara, Crossman David
Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
Heliyon. 2020 May 27;6(5):e04035. doi: 10.1016/j.heliyon.2020.e04035. eCollection 2020 May.
Pluripotent state can be established via reprogramming of somatic nuclei by factors within an oocyte or by ectopic expression of a few transgenes. Considered as being extensive and intensive, the full complement of genes to be reprogrammed, however, has never been defined, nor has the degree of reprogramming been determined quantitatively. Here, we propose a new concept of reprogramome, which is defined as the full complement of genes to be reprogrammed to the expression levels found in pluripotent stem cells (PSCs). This concept in combination with RNA-seq enables us to precisely profile reprogramome and sub-reprogramomes, and study the reprogramming process with the help of other available tools such as GO analyses. With reprogramming of human fibroblasts into PSCs as an example, we have defined the full complement of the human fibroblast-to-PSC reprogramome. Furthermore, our analyses of the reprogramome revealed that WNT pathways and genes with roles in cellular morphogenesis should be extensively and intensely reprogrammed for the establishment of pluripotency. We further developed a new mathematical model to quantitate the overall reprogramming, as well as reprogramming in a specific cellular feature such as WNT signaling pathways and genes regulating cellular morphogenesis. We anticipate that our concept and mathematical model may be applied to study and quantitate other reprogramming (pluripotency reprogramming from other somatic cells, and lineage reprogramming), as well as transcriptional and epigenetic differences between any two types of cells including cancer cells and their normal counterparts.
通过卵母细胞内的因子对体细胞核进行重编程或通过少数转基因的异位表达，可以建立多能状态。然而，需要重编程的完整基因集，尽管被认为是广泛且深入的，但从未被定义过，重编程的程度也未被定量确定。在这里，我们提出了一个新的重编程组概念，它被定义为需要重编程至多能干细胞（PSC）中所发现的表达水平的完整基因集。这个概念与RNA测序相结合，使我们能够精确描绘重编程组和亚重编程组，并借助其他可用工具（如GO分析）来研究重编程过程。以人类成纤维细胞重编程为PSC为例，我们已经定义了人类成纤维细胞向PSC重编程组的完整基因集。此外，我们对重编程组的分析表明，为了建立多能性，WNT信号通路和在细胞形态发生中起作用的基因应该被广泛且深入地重编程。我们进一步开发了一个新的数学模型来定量整体重编程，以及特定细胞特征（如WNT信号通路和调节细胞形态发生的基因）中的重编程。我们预计，我们的概念和数学模型可应用于研究和定量其他重编程（从其他体细胞进行多能性重编程以及谱系重编程），以及任何两种类型细胞（包括癌细胞及其正常对应细胞）之间的转录和表观遗传差异。
