Abstract
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.
Highlights
Identification of transcription factors that can synergistically work together within the pluripotency circuitry
Manual curation gives us direct evidence for the directionality of the nodes/edges, (ii) second, we studied the logic of the network using the single cell gene expression data, (iii) third, we performed combinatorial knockdowns of specific nodes which were instrumental in the maintenance of human pluripotency to predict the role of important regulators of pluripotency
The interactions in the human pluripotency network were extracted from the criterion of loss of function or knockdown of the transcription factors and epigenetic factors
Summary
Identification of transcription factors that can synergistically work together within the pluripotency circuitry. In one of the other similar study Dunn et al.[18] constructed data constrained Boolean model which connected 12 transcription factors among 16 interactions that suggest the least circuitry required to maintain pluripotency of mESC. Xu et al.[19] constructed a directional network of 30 pluripotency genes that are useful in predicting stem cell fate decisions In comparison to these studies, we have considered data from total 1018 single cells from snapshot progenitors and 758 single cells from time course profiling. Manual curation gives us direct evidence for the directionality of the nodes/edges, (ii) second, we studied the logic of the network using the single cell gene expression data, (iii) third, we performed combinatorial knockdowns of specific nodes which were instrumental in the maintenance of human pluripotency to predict the role of important regulators (positive/negative) of pluripotency. Our computational perturbation experiments revealed a new set of interesting putative pluripotency regulating genes
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