The metabolic network model of primed/naive human embryonic stem cells underlines the importance of oxidation-reduction potential and tryptophan metabolism in primed pluripotency

Abstract

Background Pluripotency is proposed to exist in two different stages: Naive and Primed. Conventional human pluripotent cells are essentially in the primed stage. In recent years, several protocols have claimed to generate naive human embryonic stem cells (hESCs). To the best of our knowledge, none of these protocols is currently recognized as the gold standard method. Furthermore, the consistency of the resulting cells from these diverse protocols at the molecular level is yet to be shown. Additionally, little is known about the principles that govern the metabolic differences between naive and primed pluripotency. In this work, using a computational approach, we tried to shed light on these basic issues. Results We showed that, after batch effect removal, the transcriptome data of eight different protocols which supposedly produce naive hESCs are clustered consistently when compared to the primed ones. Next, by integrating transcriptomes of all hESCs obtained by these protocols, we reconstructed p-hESCNet and n-hESCNet , the first metabolic network models representing hESCs. By exploiting reporter metabolite analysis we showed that the status of NAD and the metabolites involved in the TCA cycle are significantly altered between naive and primed hESCs. Furthermore, using flux variability analysis (FVA), the models showed that the kynurenine-mediated metabolism of tryptophan is remarkably downregulated in naive human pluripotent cells. Conclusion The aim of the present paper is twofold. Firstly, our findings confirm the applicability of all these protocols for generating naive hESCs, due to their consistency at the transcriptome level. Secondly, we showed that in silico metabolic models of hESCs can be used to simulate the metabolic states of naive and primed pluripotency. Our models confirmed the OXPHOS activation in naive cells and showed that oxidation-reduction potential vary between naive and primed cells. Tryptophan metabolism is also outlined as a key pathway in primed pluripotency and the models suggest that decrements in the activity of this pathway might be an appropriate marker for naive pluripotency.

Substrate stiffness facilitates improved induced pluripotent stem cell production through modulation of both early and late phases of cell reprogramming

“…At day 17, iPSCs on pAAm downregulated pathways related to cell adhesion (Focal adhesion, ECM-receptor interaction, and Cell adhesion molecules) as well as Axon guidance, and Antigen processing and presentation pathways compared to TCPS ( Figure 5 ), which are reported to be downregulated in mESC and naïve hESC. [31,34,35]…”

“…At day 17, iPSCs on pAAm downregulated pathways related to cell adhesion (Focal adhesion, ECM-receptor interaction, and Cell adhesion molecules) as well as Axon guidance, and Antigen processing and presentation pathways compared to TCPS (Figure 5), which are reported to be downregulated in mESC and naïve hESC. [31,34,35] At day 3, reprogramming cells in pAAm gel significantly downregulated many metabolism pathways (which included Glycolysis/Gluconeogenesis, Citrate cycle and oxidative phosphorylation) compared to TCPS (Figure 6). After Day 3, cells on the pAAm hydrogel started to upregulate various metabolic pathways, which were maximised at the end of reprogramming.…”

Superior induced pluripotent stem cell generation through phactr-3-driven mechano-modulation of both early and late phases of cell reprogramming

“…5), which are reported to be downregulated in mESC and naïve hESC. [31,34,35] At day 3, reprogramming cells in pAAm gel signi cantly downregulated many metabolism pathways (which included Glycolysis/Gluconeogenesis, Citrate cycle and oxidative phosphorylation) compared to TCPS (Fig. 6).…”

USP9X deubiquitinase couples the pluripotency network and cell metabolism to regulate ESC differentiation potential

“…The targets of this network affect different cellular features of ESC, including their interaction with the microenvironment, their shape and their cellular metabolism. In ESC compared to differentiated cells, oxidative phosphorylation (OXPHOS) is low and ATP synthesis is more dependent on glycolysis [16][17][18][19][20]. In addition, inhibition of pyruvate dehydrogenase (PDH) activity causes a significant increase in lactate levels and acidification of the microenvironment; while mTOR and HIF pathway activities favour glycolysis [21,22].…”

“…These changes in cell metabolism or microenvironment composition accompanying changes in pluripotency status might actually play a pivotal role in the regulation of cell fate and commitment. The coordination of the activity of the pluripotency network with other unique cellular features of ESC, including cell metabolism, remains to be clarified [17,21,23].…”