Downloaded from genesdev.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW The metabolic programming of stem cells Ng Shyh-Chang and Huck-Hui Ng Genome Institute of Singapore, Singapore 138675 Advances in metabolomics have deepened our under- onic (or pluripotent) stem cells. Next, we focus on the ef- standing of the roles that specific modes of metabolism fects of metabolism on regulating the balance between play in programming stem cell fates. Here, we review re- quiescence and proliferation in some types of adult stem cent metabolomic studies of stem cell metabolism that cells. Finally, we describe the roles of metabolic signaling have revealed how metabolic pathways can convey chang- mechanisms in aging stem cells. es in the extrinsic environment or their niche to program stem cell fates. The metabolic programming of stem cells represents a fine balance between the intrinsic needs of a Metabolism to maintain stem cell pluripotency cellular state and the constraints imposed by extrinsic conditions. A more complete understanding of these OxPhos in pluripotency needs and constraints will afford us greater mastery over OxPhos refers to the mitochondrial oxygen-consuming our control of stem cell fates. series of reactions in the electron transport chain (ETC) and the ATP synthase complexes, which generate ATP us- ing energy produced by the oxidation of NADH, which is Stem cells are undifferentiated cells of multicellular or- in turn derived from the oxidation of nutrients through ganisms that possess long-term capacities for multipotent the mitochondrial Krebs cycle and other redox reactions. differentiation and self-renewal. Due to the limited life It is the main and most efficient source of energy for ’ span of most somatic cells, stem cells capacity to replen- most mammalian cells, although some cell types rely on ish damaged somatic cells and maintain a self-renewing glycolysis-driven substrate-level phosphorylation as the reservoir of progenitors is crucial for homeostasis in many alternative major source. tissues of many organisms. Thus, there is an immense in- Pluripotency emerges in the epiblast during mammali- terest in understanding the mechanisms for self-renewal an preimplantation development. The naïve state is asso- and differentiation in stem cells, given their potential ap- ciated with pluripotent stem cells (PSCs) in the plications in regenerative medicine and studies of human preimplantation epiblast of embryos, and these pluripo- development or aging. tent cells become primed during post-implantation devel- Recent advances in metabolomics and transcriptomics opment (Boroviak et al. 2015). In rodents, the naïve analyses have increased our understanding of stem cell preimplantation epiblast can be captured in vitro as em- self-renewal and lineage specification. These novel in- bryonic stem cells (ESCs) and sustained indefinitely as na- sights have shown that, besides morphogens and growth ïve PSCs using defined media containing LIF, GSK3β, and factors, various metabolic pathways also take part in the MEK inhibitors, also commonly known as the 2iL condi- regulation of stem cell fate. Besides their fine regulation tions (Ying et al. 2008). Naïve and primed PSCs display of glycolysis and oxidative phosphorylation (OxPhos) key differences in their derivation of germline-competent fluxes during self-renewal and differentiation, metabolites PSCs, epigenomic states, gene expression of naïve pluripo- that regulate epigenetic changes, including histone meth- tency markers and lineage-specific markers, signaling re- ylation and acetylation, have also been shown to be criti- quirements to maintain self-renewal, and central carbon cal regulators of stem cell fates. An emerging theme is that metabolism (Davidson et al. 2015). In particular, naïve metabolic pathways can also relay changing cues in the PSCs use more OxPhos, whereas primed PSCs rely almost extrinsic environment to regulate intrinsic cell fates. entirely on glycolysis (Zhou et al. 2012; Takashima et al. Stem cell metabolism represents a combination and bal- 2014; Sperber et al. 2015). Whether these changes re- ance of the intrinsic metabolic needs and extrinsic meta- semble the in vivo situation in which preimplantation bolic constraints. embryos preferentially use mitochondrial OxPhos but In this review, we first discuss the extensive studies of shift toward anaerobic glycolysis after implantation into the effects of metabolism on the maintenance of embry- © 2017 Shyh-Chang and Ng This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the [Keywords: oxidative phosphorylation; metabolomics; stem cell] full-issue publication date (see http://genesdev.cshlp.org/site/misc/ Corresponding authors: [email protected], [email protected] terms.xhtml). After six months, it is available under a Creative Commons Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.293167. License (Attribution-NonCommercial 4.0 International), as described at 116. http://creativecommons.org/licenses/by-nc/4.0/. 336 GENES & DEVELOPMENT 31:336–346 Published by Cold Spring Harbor Laboratory Press; ISSN 0890-9369/17; www.genesdev.org Downloaded from genesdev.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Metabolic programming the uterine wall (Barbehenn et al. 1978; Brinster and ic to naïve pluripotency, as it can also promote primed Troike 1979) remains unproven. In fact, a recent study PSC differentiation by regulating histone demethylation suggests that the OxPhos flux in PSCs is more dependent (Teslaa et al. 2016). on the medium composition and culture conditions than Thus, it appears that the mitochondrial Krebs cycle in- intrinsic changes in the pluripotency state (Zhang et al. termediate αKG and the αKG/Fe2+-dependent dioxyge- 2016). nases are critical for altering the epigenetic states of However, increasing evidence supports the idea that the both naïve pluripotency and differentiating PSCs. This shift in bioenergetic metabolism is intrinsically pro- could be one of the reasons why both naïve PSCs and dif- grammed by pluripotency factors and in turn regulates ferentiating PSCs activate mitochondrial OxPhos, where- some epigenetic machinery that is involved in the pro- as primed PSCs prefer glycolysis. However, more studies gramming of the naïve and primed pluripotency states are required to fully clarify the roles of these different (Takashima et al. 2014; Ware et al. 2014). For example, modes of metabolism for the different states of pluripo- both LIF-induced Stat3, which can promote mitochondri- tency. Moreover, the precise conditions for culturing hu- al transcription (Carbognin et al. 2016), and Esrrb, which man naïve PSCs remain controversial, and thus their can promote transcription of mitochondrial OxPhos metabolic needs are still not fully clarified. genes (Zhou et al. 2012), have been proposed as pluripo- Interestingly, another cofactor for the αKG/Fe2+-depen- tency factors that intrinsically promote OxPhos in naïve dent dioxygenases, ascorbate (or vitamin C), has also been PSCs. OxPhos regenerates NAD+ to keep the Krebs shown to improve reprogramming of somatic cells into in- cycle running and maintain sufficient cellular pools of duced PSCs (iPSCs) by promoting DNA 5-methyl-cyto- α-ketoglutarate (αKG) for use as a cofactor by epigenetic sine and H3K9me3 demethylation (Chen et al. 2013a,b). modifier enzymes, including the Jumonji domain- Unlike αKG, which can be synthesized and intrinsically containing (JmjC) histone demethylases and ten-eleven regulated in all mammalian cells, ascorbate cannot be translocation (TET) methylcytosine dioxygenases. These synthesized by human cells and must be supplemented 2+ Fe2+-dependent dioxygenases remove histone and DNA extrinsically. Hence, the human αKG/Fe -dependent methylation to regulate the chromatin state and thus dioxygenases represent a node that integrates both the in- pluripotency. trinsic metabolic needs and the extrinsic metabolic condi- For example, it was found that the 2i (GSK3β inhibitor + tions to determine human stem cell fate. MEK inhibitor) culture conditions rewired intrinsic glu- cose and glutamine metabolism to control intracellular Glycolysis in primed pluripotency and reprogramming αKG (Carey et al. 2015), an intermediate in the mitochon- drial Krebs cycle, which leads to the formation of succi- Glycolysis is the series of redox reactions in the cytosol nate (Fig. 1). Because αKG is a cofactor while succinate that rapidly catabolizes each six-carbon glucose molecule is a competitive inhibitor for the αKG/Fe2+-dependent to produce two three-carbon pyruvate molecules and two dioxygenases, increases in the αKG/succinate ratio were net ATP molecules as energy via substrate-level phos- sufficient to promote αKG/Fe2+-dependent dioxygenase phorylation. In most cell types, the pyruvate can be shunt- activities to erase multiple repressive chromatin modifi- ed into two metabolic fates: as either lactate via lactate cations (e.g., demethylation of H3K9me3, H3K27me3, dehydrogenase (LDH) or acetyl-CoA via pyruvate dehy- H4K20me3, and DNA) to promote naïve pluripotency drogenase (PDH). The intermediates in glycolysis can (Carey et al. 2015). In vitro supplementation with αKG also be shunted into macromolecule synthesis during rap- promoted naïve pluripotency, while succinate promoted id cell growth. Thus, while it is a less efficient source of differentiation of naïve PSCs.