Metabolic remodeling during the loss and acquisition of pluripotency

Abstract

Pluripotent cells from the early stages of embryonic development have the unlimited capacity to self-renew and undergo differentiation into all of the cell types of the adult organism. These properties are regulated by tightly controlled networks of gene expression, which in turn are governed by the availability of transcription factors and their interaction with the underlying epigenetic landscape. Recent data suggest that, perhaps unexpectedly, some key epigenetic marks, and thereby gene expression, are regulated by the levels of specific metabolites. Hence, cellular metabolism plays a vital role beyond simply the production of energy, and may be involved in the regulation of cell fate. In this Review, we discuss the metabolic changes that occur during the transitions between different pluripotent states both in vitro and in vivo, including during reprogramming to pluripotency and the onset of differentiation, and we discuss the extent to which distinct metabolites might regulate these transitions.

Keywords: Epigenetics; Metabolic remodeling; Stem cell.

Fig. 1.

Overview of cellular metabolism. The major cellular metabolic pathways (indicated in red): glycolysis, pentose phosphate pathway, β-oxidation, TCA cycle and oxidative phosphorylation (OxPHOS). Each of these pathways produces metabolites that are required to fuel cell growth via the production of energy (ATP), nucleotides, lipids, amino acids and fatty acids (indicated in green). The most efficient pathway for the production of energy is OxPHOS, which produces significantly more ATP than glycolysis. Despite this difference, glycolysis is the main energy-producing pathway favored by pluripotent stem cells. ADP, adenosine diphosphate; ATP, adenosine triphosphate; ATPase, ATP synthase; ETC, electron transport chain; F6P, fructose 6 phosphate; G6P, glucose 6 phosphate; ROS, reactive oxygen species; TCA, tricarboxylic acid.

Fig. 2.

Dynamic changes in pluripotency in vivo and in vitro. (A) Pluripotent cells emerge from the inner cell mass (ICM) of the early blastocyst. These cells then segregate to form the primitive endoderm and the pluripotent, naïve epiblast. Following implantation, the epiblast begins to express specification factors, initiates gastrulation and goes on to differentiate into all the cells that will eventually make up the mature organism. (B) Distinct phases of pluripotency can be captured in vitro and have been shown to have characteristic metabolic profiles. Naïve embryonic stem cells (ESCs) are able to perform oxidative phosphorylation, glycolysis and fatty acid oxidation, whereas primed ESCs rely almost exclusively on glycolysis to meet their bioenergetic demands. Naïve ESCs contain mitochondria that are more spherical and contain less dense cristae, but as the cells transition to the primed state, a mixture of immature and relatively more mature mitochondria can be seen. Differentiated cells contain mitochondria with fully mature cristae. Differentiated cells rely primarily on oxidative phosphorylation. ICM, inner cell mass; PE, primitive endoderm; TE, trophectoderm.

Fig. 3.

Metabolic and transcriptional changes during entry into and exit from pluripotency. (A) A metabolic switch from mitochondrial oxidative phosphorylation to glycolysis takes place early during the acquisition of human pluripotency. The resulting human induced pluripotent stem cells (iPSCs) contain a mixture of immature and relatively more mature mitochondria, compared with the fully mature mitochondria of the original differentiated cell. (B) Changes in mitochondrial oxidative phosphorylation upon developmental progression and the re-acquisition of pluripotency during reprogramming. Mitochondrial respiration is significantly reduced during the transition from naïve to primed embryonic stem cells (ESCs) and increases during differentiation. Reprogramming of human differentiated cells leads to iPSCs that resemble primed ESCs, whereas mouse reprogramming leads to iPSCs in a naïve state. ERRα, estrogen-related receptor α; HIF, hypoxia inducible factor; NNMT, N-methyltransferase; OCR, oxygen consumption rate.

Fig. 4.

Metabolite levels influence the epigenetic landscape of ESCs. Cytoplasmic acetyl-CoA acetylates histones via histone acetyltransferase (HAT) activation. NAD+ inhibits DNA acetylation by activating sirtuin 1 (SIRT1). α-Ketoglutarate inhibits histone and DNA methylation by upregulating Jumonji-c domain histone demethylase (JMDH) and Tet methylcytosine dioxygenase (TET). High levels of nicotinamide N-methyltransferase (NNMT) activity prevent histone and DNA methylation by sequestering methyl groups from S-adenosyl methionine (SAM), forming 1-methylnicotinamide (1MNA), which acts as a powerful methyl sink. A depleted pool of methyl groups prevents DNA methyltransferase (DNMT) and histone methyltransferase (HMT) from methylating DNA and histones, respectively. High ATP levels block histone phosphorylation by inhibiting AMP-activated protein kinase (AMPK) activity (Bungard et al., 2010). ADP, adenosine diphosphate; ATP, adenosine triphosphate; ETC, electron transport chain; NA, nicotinamide; NAD+, oxidized nicotinamide adenine dinucleotide; NADH, reduced NAD; SAH, S-adenosyl-L-homocysteine; TCA, tricarboxylic acid.