Amity Institute of Biotechnology, Amity University, Uttar Pradesh, India.
Sci Rep. 2018 Jul 23;8(1):11031. doi: 10.1038/s41598-018-29480-w.
A network consisting of 45 core genes was developed for the genes/proteins responsible for loss/gain of function in human pluripotent stem cells. The nodes were included on the basis of literature curation. The initial network topology was further refined by constructing an inferred Boolean model from time-series RNA-seq expression data. The final Boolean network was obtained by integration of the initial topology and the inferred topology into a refined model termed as the integrated model. Expression levels were observed to be bi-modular for most of the genes involved in the mechanism of human pluripotency. Thus, single and combinatorial perturbations/knockdowns were executed using an in silico approach. The model perturbations were validated with literature studies. A number of outcomes are predicted using the knockdowns of the core pluripotency circuit and we are able to establish the minimum requirement for maintenance of pluripotency in human. The network model is able to predict lineage-specific outcomes and targeted knockdowns of essential genes involved in human pluripotency which are challenging to perform due to ethical constraints surrounding human embryonic stem cells.
建立了一个由 45 个核心基因组成的网络，用于研究人类多能干细胞中功能丧失/获得的基因/蛋白质。节点是根据文献整理包含在内的。通过从时间序列 RNA-seq 表达数据构建推断的布尔模型，进一步细化初始网络拓扑结构。最终的布尔网络是通过将初始拓扑和推断拓扑集成到一个称为综合模型的细化模型中获得的。大多数参与人类多能性机制的基因的表达水平表现为双模块。因此，使用计算机模拟方法对其进行了单一和组合的扰动/敲低实验。通过文献研究验证了模型的扰动。使用核心多能性回路的敲低实验预测了许多结果，我们能够确定维持人类多能性的最低要求。该网络模型能够预测谱系特异性结果和针对涉及人类多能性的关键基因的靶向敲低，由于围绕人类胚胎干细胞的伦理限制，这些实验难以进行。
