Metabolic switches during development and regeneration

Traditionally, cellular metabolism has been primarily studied for its fundamental role in supplying energy to the cell and supporting its overall function. However, both anabolic and catabolic metabolism have been implicated in controlling cellular proliferation, cell fate decisions and epigenetic control of gene expression through modulation of biosynthetic pathways, cell signaling and histone modifications (Martinez-Reyes and Chandel, 2020; Tarazona and Pourquie, 2020). As a result, cells switch their metabolism in response to different physiological and pathological conditions. Metabolic switches play a crucial role during mammalian development, from the earliest stages of embryogenesis to the postnatal period. The developing embryo relies primarily on glycolysis to support its rapid growth and differentiation (Smith and Sturmey, 2013). This is consistent with the role of glycolysis in production of nucleotides, amino acids and lipids, which are necessary for cell proliferation (Lunt and Vander Heiden, 2011; Vander Heiden et al., 2009). As the fetus approaches term, it adapts to the new environment after birth by an increase in mitochondrial biogenesis and a metabolic switch towards oxidative phosphorylation (Van Blerkom, 2009). Furthermore, the neonatal period is characterized by rapid growth, during which mitochondrial respiration and fatty acid oxidation become increasingly important owing to the energetic and biosynthetic needs of different cell types (Sieber and Spradling, 2017). This metabolic remodeling demonstrates that cellular metabolism plays a central role in mediating cell function and state.

In recent years, there has been a significant shift in the understanding of the role of metabolic transitions in cellular processes beyond being solely a response to energy demands. Instead, it is now recognized that cellular metabolism plays a central role in regulating cell fate during various developmental stages, neonatal growth, and tissue repair and regeneration (Mathieu and Ruohola-Baker, 2017; Sieber and Spradling, 2017). The existence of common mechanisms between development and regeneration suggests that metabolic transitions may also play a conserved role in regulating these processes (Bae et al., 2021a). This Review does not comprehensively cover the diverse roles that metabolism plays during development but aims to provide an overview of recent advancements in the essential roles that metabolic switches play in mammalian development and tissue regeneration. By identifying the underlying epigenetic and transcriptional mechanisms of this metabolic regulation, a better understanding of normal development, disease pathogenesis and tissue regeneration can be achieved.

The two main sources of ATP in cellular metabolism are glycolysis and oxidative phosphorylation (Fig. 1). Although less energy efficient, aerobic glycolysis is the main metabolic pathway during early development and proliferation. Initially, this was identified as a key driver of cancer cell proliferation on the basis of presumed mitochondrial defects (Warburg, 1956); however, extensive studies of this high glycolytic activity revealed that Warburg metabolism is integral to cancer pathogenesis (Pavlova and Thompson, 2016). Intriguingly, more recent studies demonstrated the indispensable role of aerobic glycolysis during normal development and cell proliferation (Lunt and Vander Heiden, 2011; Miyazawa and Aulehla, 2018). The exact rationale for relying on aerobic glycolysis during development and cell differentiation remains to be fully elucidated. Yet considerable research suggests various potential roles. One major possibility is that the increase in aerobic glycolysis caters to the demand for new biomass, such as phospholipids, nucleotides and amino acids, given that glycolysis is a central node for many anabolic pathways (Liberti and Locasale, 2016). These biomolecules are generated via two glycolysis shunts. The first glycolytic shunt is the pentose phosphate pathway (PPP), which includes an oxidative branch that breaks down the glycolysis intermediate glucose-6-phosphate into pentose sugars and NADPH (TeSlaa et al., 2023). NADPH is an important reducing agent used in many biosynthetic processes, and the pentose sugars are essential for nucleotide synthesis (Jiang et al., 2014; TeSlaa et al., 2023). The non-oxidative branch of the PPP involves the breakdown of fructose-6-phosphate and glyceraldehyde-3-phosphate into ribose-5-phosphate and erythrose-4-phosphate. Both branches of the PPP are involved in the biosynthesis of nucleotides and non-essential amino acids (TeSlaa et al., 2023).

The second glycolytic shunt is the serine synthesis pathway (SSP), through which the produced serine can be used to generate the amino acids, nucleotides and phospholipids needed for cell proliferation (Labuschagne et al., 2014; Mattaini et al., 2016). Additionally, the SSP can serve as a carbon donor for one-carbon metabolism, which contributes to nucleotide biosynthesis (Locasale, 2013). Importantly, one-carbon metabolism is required for the production of S-adenosyl methionine (SAM), which can methylate histones and DNA (Kaelin and McKnight, 2013).

Recent studies have suggested that biomass production via aerobic glycolysis might not reach levels sufficient to satisfy the biosynthetic demands necessary for cellular proliferation and development. This is because the majority of carbon derived from glucose is converted to lactate (DeBerardinis and Chandel, 2020). By contrast, both glycolytic and tricarboxylic acid (TCA) cycle metabolites can profoundly influence cellular fate and function by orchestrating post-translational modifications of proteins (Tarazona and Pourquie, 2020). Such modifications encompass alterations in chromatin structure, DNA methylation levels and protein acetylation, culminating in marked shifts in transcriptional regulation and cellular signaling pathways that control cell identity and differentiation during development. This metabolic control of epigenetic and transcriptional programs during development provides an important framework to target key pathways that can be harnessed to promote tissue regeneration.

One potential mechanism for the metabolic switch to aerobic glycolysis during development and regeneration could relate to the reported role of lactate, the end product of glycolysis, as a primary driver of cellular proliferation. A recent study provides evidence that lactate remodels the anaphase-promoting complex (APC/C) via inhibition of SENP1, which leads to the stabilization of post-translational modifications (SUMOylation) of the APC/C subunit APC4 (Liu et al., 2023). This process facilitates the binding of the ubiquitin-conjugating enzyme E2 C (UBE2C) to APC/C, subsequently activating it. As a result, lactate accumulation can bypass mitotic exit and stimulate cell proliferation in cancer cell lines. This study offers a new perspective on the preference for metabolic switching to glycolysis in cell cycle regulation. It remains to be determined whether this mechanism is pivotal for cell proliferation during the metabolic switch to aerobic glycolysis in development and regeneration.

Mitochondrial metabolism, especially oxidative phosphorylation, is a crucial energy-generating process, yielding a considerably higher number of ATP molecules per glucose molecule compared with glycolysis. Consequently, oxidative phosphorylation is typically linked with advanced developmental stages and postnatal maturation owing to the enhanced energy demands associated with these processes, such as cardiomyocyte maturation (Garbern and Lee, 2021). Although such metabolic switching has been recognized during development and regeneration, recent findings suggest that these metabolic switches actually play a decisive role in determining cellular fate, guiding developmental decisions and affecting abnormal physiology and disease progression (Cliff and Dalton, 2017; Ly et al., 2020; Tarazona and Pourquie, 2020).

Metabolic switches refer to the rewiring of the metabolic pathways within a cell or organism in response to changing environmental or physiological conditions. Several factors can influence the need for metabolic switches, including nutrient availability, energy demand, stress response, and developmental or hormonal changes (Etchegaray and Mostoslavsky, 2016). For example, in response to either extrinsic or intrinsic stimuli, cells can activate anabolic pathways to synthesize phospholipids, nucleotides and amino acids. Concurrently, they can induce catabolic pathways wherein individual metabolites influence the epigenetic and transcriptional state of the cell (Miyazawa and Aulehla, 2018; Tarazona and Pourquie, 2020). The dynamic interplay between these metabolic networks enables the precise coordination of energy production, cell proliferation and stem cell differentiation during development, thereby facilitating an organism's ability to thrive in diverse environments and adapt to diverse physiological states.

One important factor that has played a significant role in shaping metabolic adaptations during evolution is oxygen availability (Nakazawa et al., 2016). Oxygen is a key factor in cellular respiration, as it acts as the final electron acceptor in the mitochondrial electron transport chain, facilitating the production of ATP through oxidative phosphorylation. Over time, the gradual increase in atmospheric oxygen levels has allowed the evolution of aerobic organisms that can utilize oxygen in their metabolism, leading to the evolution of oxidative phosphorylation and complex multicellular life (Hedges et al., 2004). Interestingly, some organisms are obligate anaerobes, unable to survive in the presence of oxygen, whereas others, such as facultative anaerobes, can switch between aerobic and anaerobic metabolism depending on oxygen availability (Lu and Imlay, 2021). This suggests an evolutionary origin for metabolic adaptations that take place at both the organismal and cellular level.

Overall, metabolic switches serve to optimize cellular function and maintain organismal health by allowing cells and organisms to adapt to diverse environmental, developmental and physiological conditions. Our understanding of the complex regulatory networks underlying these switches continues to evolve as new molecular players and signaling pathways are discovered. More importantly, this underscores the importance of defining the mechanisms that control metabolic reprogramming to harness this knowledge for many translational purposes.

Metabolic intermediates from glycolysis, oxidative phosphorylation and fatty acid oxidation can orchestrate development, cell differentiation and proliferation. These metabolic switches can be triggered by growth factor stimulation and nutrient availability, leading to the intracellular activation of pivotal metabolic signaling pathways, such as the phosphoinositide 3-kinase (PI3K), mammalian target of rapamycin (mTOR) and hypoxia inducible factor 1, alpha (HIF1α) pathways (Liu and Sabatini, 2020). For instance, when a growth factor receptor is stimulated, it can initiate the PI3K/AKT pathway (Manning and Toker, 2017). This activation not only boosts the transcription and function of glycolytic enzymes but also triggers mTOR complex 1 (mTORC1), which in turn influences glucose metabolism via HIF1α (Liu and Sabatini, 2020; Mossmann et al., 2018). However, the majority of these mechanisms have been uncovered in cancer cells; the role of cell signaling pathways in controlling metabolic shifts during development, cell differentiation and regeneration remains to be explored.

One key mechanism by which metabolic intermediates control cell fate is by exerting epigenetic control over chromatin and gene transcription. Histone modifications, such as methylation and acetylation, along with DNA methylation, serve as central targets influenced by metabolic shifts. Additionally, these metabolites play an essential role in epigenetic control of cancer (Finley, 2023). Metabolic intermediates can act as substrates or co-factors for chromatin- and DNA-modifying enzymes (Kaelin and McKnight, 2013). For example, acetyl-CoA, primarily derived from pyruvate decarboxylation, can serve as an acetyl donor for histone acetylation by histone acetyltransferases (HATs) (Kinnaird et al., 2016). This results in enhancement of chromatin accessibility, facilitating transcription factor binding. Additionally, acetyl-CoA can also participate in post-translational modifications, either by promoting acetylation of lysine residues via lysine acetyl transferases (KATs) or aiding their deacetylation through lysine deacetylases (KDACs) (Marmorstein and Zhou, 2014; Seto and Yoshida, 2014).

Histone and DNA methylation can be influenced by metabolic intermediates. The metabolic intermediate SAM serves as a methyl donor for both histone and DNA methylation, facilitated by histone methyl transferases (HMTs) and DNA methyl transferases (DNMTs), respectively (Kaelin and McKnight, 2013). Meanwhile, the TCA cycle metabolite α-ketoglutarate (α-KG) serves as a key substrate for DNA and histone demethylation (Su et al., 2016). This demethylation is carried out by the α-KG-dependent dioxygenases, including the JmjC domain-containing family of histone demethylases (JHDMs) and ten-eleven translocation (TET) methylcytosine dioxygenases (Loenarz and Schofield, 2011). Notably, it is through this modulation of methylation status that α-KG influences self-renewal and differentiation of both murine and human pluripotent stem cells (PSCs), respectively (Carey et al., 2015; TeSlaa et al., 2016).

Interestingly, TCA cycle metabolites can influence each other's impact on epigenetic modifications. This interplay is evident in cancers driven by mutations in succinate dehydrogenase (SDH) and fumarate hydratase (FH), as these mutations lead to accumulation of succinate and fumarate (Isaacs et al., 2005; Selak et al., 2005). Consequently, this accumulation competes with α-KG, which inhibits the activity of α-KG-dependent dioxygenases, affecting both histone and DNA methylation levels (Xiao et al., 2012). This relationship between metabolism and epigenetics illustrates how imbalances in metabolite levels can instigate changes in gene expression that can drive cell proliferation. Elucidating the mechanisms by which these metabolites control cell proliferation could provide new avenues for the promotion of tissue regeneration.

The number of metabolites known to influence epigenetic modifications has grown significantly in recent years. Although this Review highlights many key metabolic intermediates, it does not provide an exhaustive list; the primary focus is to underscore the central role that metabolic control plays in epigenetic remodeling during development and differentiation. This serves as a foundational platform for further exploration into how these metabolites, and their epigenetic impacts, could pave the way for tissue regeneration.

Developmental events in both embryonic and postnatal development are regulated by metabolic switches, which influence cell fate, growth and differentiation to allow for proper development and tissue homeostasis (Chandel et al., 2016; Cliff and Dalton, 2017). Dysregulation of metabolic pathways can have profound effects on cellular function, potentially leading to developmental abnormalities or disease (Lu and Thompson, 2012; Teperino et al., 2010). Here, we highlight the instructive role that metabolic switches have at different developmental stages and processes.

Recent evidence underscores the regulatory role of cellular metabolism in dictating cell fate during development, stem cell fate differentiation and homeostasis. A metabolic shift between aerobic glycolysis and oxidative phosphorylation is identified during the transition between cell fates (Ly et al., 2020; Tarazona and Pourquie, 2020). Although glycolysis is typically elevated in undifferentiated cell states as well as during proliferation, and oxidative phosphorylation is predominantly active during differentiation and maturation, there are exceptions. For instance, glucose metabolism can influence cell fate determination not through glycolysis, but rather via glycolysis shunts, as seen during cell fate specification of the trophectoderm (Chi et al., 2020).

Cell fate determination is a complex, highly regulated process by which embryonic PSCs acquire specific identities and functions during the course of development (Smith, 2001). PSCs can self-renew and differentiate to all three germ layers during development. Initially, mouse and human PSCs exist in a naïve state during pre-implantation, and subsequently become primed during post-implantation (Zhao et al., 2023; Theunissen et al., 2016). Both naïve and primed PSCs demonstrate distinct epigenetic and transcriptional signatures to maintain pluripotency (Davidson et al., 2015). Importantly, PSCs exhibit metabolic shifts as they transition from a state of stemness to initiation of differentiation (Cliff and Dalton, 2017; Xu et al., 2013). A metabolic switch from oxidative phosphorylation to glycolysis takes places from naïve to primed human PSCs, which has been suggested to play an important role in embryo implantation (Gardner and Harvey, 2015; Sperber et al., 2015; Zhou et al., 2012).

Human PSCs are characterized by high rates of aerobic glycolysis, and reduced glycolysis results in loss of pluripotency and differentiation (Cliff and Dalton, 2017; Moussaieff et al., 2015). As PSCs produce acetyl-CoA via glycolysis, the acetyl-CoA substrate acetate blocks histone deacetylation, thereby maintaining pluripotency. However, early differentiation of PSCs takes place via downregulation of glycolysis, leading to reduced levels of acetyl-CoA and acetate. This decrease results in increased histone deacetylation, driving further differentiation (Moussaieff et al., 2015; Shyh-Chang and Daley, 2015). Landmark studies have uncovered that TCA cycle metabolites can influence cell fate determination by modulating chemical modifications, such as acetylation and methylation of DNA and histones, thus controlling the epigenetic and gene expression landscape that defines cellular identity (Baksh and Finley, 2021). For instance, the intracellular levels of the TCA cycle intermediate α-KG have been shown to maintain naïve murine embryonic stem cell pluripotency by regulating TET proteins, which maintains DNA and histone demethylation (Carey et al., 2015), but induce differentiation of primed human PSCs (TeSlaa et al., 2016). These studies demonstrate that the effect of α-KG on cell fate varies depending on the pluripotent state.

Another TCA cycle metabolite, succinate, has been found to inhibit the activity of α-KG-dependent dioxygenases, thus affecting the balance between pluripotency and differentiation (Chandel et al., 2016). Furthermore, fumarate and itaconate, additional TCA cycle intermediates, have been implicated in the regulation of cellular differentiation and function through their impact on various cellular processes, such as inflammation and hypoxia response (Mills and O'Neill, 2014; Murphy and O'Neill, 2018). Collectively, these findings highlight the multifaceted role of TCA cycle metabolites in controlling cell fate by modulating key signaling pathways and epigenetic processes.

During the first stage of embryonic development after fertilization, the single-cell embryo is dependent on pyruvate metabolism (Barbehenn et al., 1978). Interestingly, this unique dependence on pyruvate has been demonstrated to facilitate nuclear localization of TCA cycle enzymes, which are required for zygotic genome activation (Nagaraj et al., 2017). After subsequent divisions and blastocyst formation, the embryo becomes reliant on glucose metabolism (Leese and Barton, 1984). Importantly, the glycolytic metabolic state of early mammalian embryos is essential for biomass increase and cellular proliferation, which are necessary for proper tissue formation during embryonic development (Zhao et al., 2023; Lunt and Vander Heiden, 2011). For example, the embryonic heart utilizes glycolysis as a main energy source, which is essential for cardiomyocyte proliferation (Lopaschuk et al., 1992; Puente et al., 2014). Interestingly, this reliance on glycolysis is shared with cancer cells even in the presence of oxygen, which underscores the importance of defining developmental metabolism as an avenue that could provide insights into metabolic control of cancer (Smith and Sturmey, 2013).

Recent studies provided new insights into the dynamics of the key metabolic determinants during these early developmental stages. Specifically, a recent study performed ¹³C glucose labeling to track the metabolites from glucose breakdown by isotopolog analysis throughout the stages of pre-implantation development (Sharpley et al., 2021). This study supports the early dependence on pyruvate or lactate up to the two-cell-stage embryo. Interestingly, this early stage exhibits high levels of lactate dehydrogenase B (LDHB), which mediates the interconversion of lactate/pyruvate and NAD⁺/NADH and increased sensitivity to reductive stress by pyruvate withdrawal. However, the blastocyst stage is concomitant with significant reduction in LDHB levels and an increase in metabolic plasticity that is dependent on modulation of redox levels. This study demonstrates a highly rigid metabolic state during early development that is followed by high metabolic plasticity in later stages (Sharpley et al., 2021).

Metabolism can play a pivotal role in controlling development through the modulation of signaling pathways in a cell-intrinsic manner. One key instance of this is seen during trophectoderm formation, during which glucose metabolism is integral to cell fate specification. Specifically, glucose is metabolized towards the glycolytic shunts, including the hexosamine biosynthetic pathway (HBP), which leads to the nuclear translocation of yes-associated protein 1 (YAP1) (Chi et al., 2020). Additionally, the PPP is involved in nucleotide synthesis from glucose metabolism. This activates both mTOR and transcription factor AP-2, gamma (Tfap2c), culminating in the transcriptional activation of a trophectoderm gene program. Collectively, these findings illustrate a mechanistic role for developmental metabolism in shaping cell signaling and determining trophectoderm cell fate (Chi et al., 2020).

Another example of a cell-intrinsic mechanism involves the proliferation and differentiation of the embryonic Xenopus retina, which is dependent on aerobic glycolysis (Agathocleous et al., 2012). The cell-intrinsic control of the metabolic state is also elegantly demonstrated during somite development, as evidenced by the presence of a glycolytic activity gradient in the presomitic mesoderm. Specifically, the less-differentiated posterior presomitic mesoderm cells exhibit higher glycolytic activity than the more-differentiated anterior cells (Bulusu et al., 2017; Oginuma et al., 2017). Mechanistically, glycolytic activity is modulated by the fibroblast growth factor (FGF) signaling pathway. This, in turn, affects the WNT signaling pathway, which controls FGF signaling, illustrating a reciprocal feedback loop between glycolysis and growth factor signaling (Oginuma et al., 2017). This metabolic state is evident both in vivo and in vitro, underscoring a cell-intrinsic regulation of the metabolic gradient during somite segmentation (Bulusu et al., 2017). These studies demonstrate the central role that metabolic processes play in governing development, particularly in influencing cell differentiation, fate and proliferation (Fig. 1).

The redox state has long been recognized as a key regulator of development. During embryonic development, the intrauterine environment is characterized by mixing of arterial and venous blood that results in lower arterial partial pressure of oxygen (Dawes et al., 1954). The hypoxia-inducible factor (HIF) pathway plays an essential role in regulating metabolic re-wiring in response to low oxygen levels (hypoxia) during embryonic development. Activation of the HIF pathway promotes the transcription of genes involved in glycolysis, angiogenesis and erythropoiesis, enabling cells to adapt their metabolism and function under hypoxic conditions (Dunwoodie, 2009; Nakazawa et al., 2016). Thus, the redox state during development is an important sensor and mediator of metabolic states during embryonic development.

As embryonic development progresses, oxygen levels increase, and cells switch to oxidative phosphorylation to meet their growing energy demands during differentiation and maturation (Folmes and Terzic, 2014; Lange et al., 2016; Miyazawa et al., 2017). During postnatal development, nutrient availability and utilization undergo significant changes. For example, after birth, mammals switch from utilizing placental glucose to relying on milk-derived lactose and lipids, which is accompanied by metabolic and hormonal adaptations during growth and maturation after birth (Georgakopoulou et al., 2020; Hillman et al., 2012; Ward Platt and Deshpande, 2005). Thus, postnatal development represents an environment with specific cellular and functional requirements that are distinct from embryonic development.

Differentiating cells undergo metabolic adaptations to meet the specific energy and biosynthetic requirements of their mature cell types. For instance, the differentiation of human neural progenitor cells, derived from human induced PSCs (iPSCs), involves a metabolic switch from aerobic glycolysis to oxidative phosphorylation (Zheng et al., 2016). This process is characterized by a downregulation of hexokinase and lactate dehydrogenase. Subsequently, there is an increase in peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC1α; PPARGC1α) and estrogen-related receptor gamma (ERRγ; ESRRγ) levels, which helps sustain mitochondrial oxidative phosphorylation in post-mitotic differentiated neurons (Zheng et al., 2016). This reliance on glycolysis and subsequent metabolic switching to oxidative phosphorylation is also evident in the developing murine neocortex (Dong et al., 2022). Furthermore, postnatal brain development involves significant metabolic adaptations to support the high energy demands of processes such as synaptogenesis, myelination and neurotransmitter synthesis (Steiner, 2019). During this period, there is an increased reliance on oxidative phosphorylation and the use of ketone bodies as an energy source, especially during the early postnatal period (Cunnane and Crawford, 2014; Steiner, 2019).

Even more energetically demanding is the mammalian heart, which is considered to have the highest metabolic rate per gram of all organs (Wang et al., 2010). As a consequence, postnatal cardiomyocyte maturation is accompanied by a metabolic switch from glycolysis, which is the predominant energy source during development and the early neonatal period, to mitochondrial oxidative phosphorylation and fatty acid oxidation to meet the energy demands of the adult mature heart (Lalowski et al., 2018; Leone and Kelly, 2011; Lopaschuk et al., 1992; Piquereau and Ventura-Clapier, 2018). Interestingly, a recent study demonstrated that an increase in ketone body levels promotes postnatal metabolic maturation (Chong et al., 2022). Another study reveals that γ-linolenic acid from maternal milk controls postnatal cardiac metabolism by binding to retinoid X receptors, thereby promoting cardiomyocyte maturation (Paredes et al., 2023).

During this metabolic switch, cardiomyocytes exit the cell cycle and undergo a maturation cascade at the cellular and molecular level, including structural, metabolic and functional changes to support cardiac contractility (Guo and Pu, 2020; Puente et al., 2014). Importantly, this maturation process leads to loss of cardiomyocyte proliferative potential, which in turn results in the diminished cardiac regenerative ability of the mammalian heart. This emphasizes the idea that metabolic rewiring of the adult heart has the potential to promote endogenous heart regeneration (Bae et al., 2021a). Additionally, heart failure is characterized by distinct metabolic shifts and changes in metabolite utilization compared with the healthy heart. Whereas the human healthy heart predominantly utilizes fatty acids, the failing heart shifts its preference to ketones and lactate (Murashige et al., 2020). Thus, these studies demonstrate that cardiac metabolism plays a central role during mammalian cardiac maturation, disease and regeneration.

Also important during postnatal development is the immune system, which undergoes significant changes itself during this period (Henneke et al., 2021). Immune cells respond rapidly to molecular and pathogenic signals, initiating key transitions in their activation. Importantly, the immune response is crucial for tissue homeostasis and regeneration (Aurora and Olson, 2014). During these immune responses, these cells undergo significant metabolic switches. For instance, naïve T-cell activation is accompanied by an increase in aerobic glycolysis, which drives T-cell proliferation and anabolic growth (Buck et al., 2015; Chapman et al., 2020). Macrophage activation occurs in two stages: the first is mediated by metabolic reprogramming through the accumulation of the TCA cycle metabolites itaconate and succinate (Lampropoulou et al., 2016; Mills et al., 2016), followed by the decline of these metabolites (Seim et al., 2019). Numerous studies have demonstrated that metabolic regulation plays a broad role in modulating immune cell activation and function by influencing the epigenetic landscape (Britt et al., 2020).

In summary, metabolic switches are crucial for postnatal development, as they facilitate the adaptation of energy production, cellular growth and differentiation processes in response to the transition from the prenatal to the postnatal environment. These adaptations help ensure proper tissue and organ maturation, supporting the overall growth, development and function of the mature adult tissues after birth (Fig. 1).

Tissue regeneration represents a remarkable inherent capacity to replace damaged or lost tissue following injury via a highly coordinated series of cellular and molecular events (Poss, 2010). Regeneration can be mediated via activation and proliferation of quiescent adult stem cell populations, or via cellular proliferation of pre-existing cells to replenish the damaged tissue. Interestingly, cellular metabolism plays an important role in maintaining stem cell quiescence, as well as subsequent activation and proliferation during regeneration (Chandel et al., 2016; Ito and Suda, 2014; Shapira and Christofk, 2020; Shyh-Chang and Ng, 2017). For example, long-term hematopoietic stem cells (HSCs) depend on anerobic glycolysis during quiescence as they reside in a hypoxic niche, whereas loss of quiescence and differentiation of HSCs is accompanied by a metabolic switch to mitochondrial metabolism (Kocabas et al., 2012; Simsek et al., 2010). This is further evident in the dependence of HSC function on their metabolic state (Wang et al., 2014). Furthermore, recent evidence shows that inhibition of fatty acid oxidation by malonyl-CoA can promote proliferation and differentiation of both mouse and human hematopoietic stem/progenitor cells (HSPCs) (Giger et al., 2020). Similarly, increased fatty acid oxidation, as well as metabolic reprogramming to glycolysis, regulates intestinal stem cell function in homeostasis and aging (Mihaylova et al., 2018; Morris et al., 2020).

In some contexts, the metabolic regulation of stem cell quiescence and activation is complex. For example, during adult hippocampal neurogenesis, which is crucial for the learning and memory functions of the mammalian brain, the transition of neural stem cells (NSCs) from quiescence to proliferation is modulated by changes in fatty acid oxidation levels. Specifically, elevated levels of malonyl-CoA promote de novo lipogenesis and NSC activation and proliferation (Knobloch et al., 2013, 2017; Knobloch and Jessberger, 2017). Additionally, the activation of these NSCs is induced by lower mitochondrial pyruvate metabolism (Fig. 2A) (Petrelli et al., 2023). Subsequent differentiation of the activated NSC to an intermediate progenitor cell is driven by an increase in oxidative phosphorylation (Beckervordersandforth et al., 2017). These studies highlight the intricate role of metabolism in controlling NSC behavior (Scandella et al., 2023).

Muscle stem cells, known as satellite cells, remain quiescent in adult muscle. Upon activation, they can differentiate into new muscle fibers, contributing to postnatal muscle growth and repair (Yin et al., 2013). This transition of satellite cells from quiescence to activation ex vivo is mediated by a metabolic switch from fatty acid oxidation to glycolysis (Ryall et al., 2015; Tang and Rando, 2014). A decline in NAD⁺ concentration mediates this rise in glycolytic activity, which in turn reduces the activity of the histone deacetylase SIRT1 (Ryall et al., 2015). This decreased SIRT1 activity elevates H4K16ac levels, promoting muscle gene transcription (Ryall et al., 2015).

Beyond stem cell function during homeostasis and regeneration, metabolic switching also governs regenerative responses in various tissues and across different species after injury. The planarian Schmidtea mediterranea possesses extraordinary regenerative potential, in which amputated tissue fragments can regrow the entire worm (Reddien and Sanchez Alvarado, 2004). Remarkably, planarian regeneration is associated with the activation of aerobic glycolysis following amputation (Osuma et al., 2018). In axolotls, post-amputation limb regeneration is driven by the blastema, a structure that forms at the injury site and is composed of multipotent, lineage-restricted progenitors responsible for reconstructing the amputated limb (Min and Whited, 2023). Interestingly, limb regeneration is accompanied by dynamic changes in metabolite levels. During the early stages of blastema formation, an increase in glycolysis and anabolic metabolism is observed. However, during blastema proliferation and differentiation, there is a shift towards catabolic metabolism and an increase of TCA cycle metabolites. This highlights the fluctuating metabolic states that occur during axolotl limb regeneration (Varela-Rodriguez et al., 2020).

Another organism that can regenerate is the adult zebrafish Danio rerio, which is a common model for heart regeneration. Zebrafish can regenerate their hearts following injury via proliferation of pre-existing cardiomyocytes at the border zone of the injury site (Kikuchi et al., 2010). Remarkably, border zone cardiomyocytes undergo a metabolic reprogramming towards glycolysis to initiate cardiomyocyte proliferation and regeneration (Honkoop et al., 2019). Adult zebrafish can also regenerate their caudal fin, which is mediated by osteoblast de-differentiation and blastema formation that regenerates the bony rays of the amputated fin (Sehring and Weidinger, 2020). Similarly, this regenerative response is initiated by an increase in glycolysis, which in turn activates a transcriptional program essential for osteoblast dedifferentiation and blastema formation (Brandao et al., 2022). A similar switch to glucose metabolism is also observed in blastema formation during embryonic zebrafish tail regeneration (Sinclair et al., 2021).

Bones can regenerate throughout adulthood; however, this capacity decreases with age, which can lead to osteoporosis (Salhotra et al., 2020). A recent study demonstrates a distinct metabolic signature between the regenerating and non-regenerating bones in rats in the early phases of bone healing following fracture. Specifically, the metabolite succinate is upregulated during bone regeneration and is required for promoting pro-regenerative cellular responses (Loffler et al., 2023).

During muscle regeneration, satellite cell activation involves a metabolic switch to glycolysis, mirroring what is observed during ex vivo activation (Ryall et al., 2015). The transition of satellite cells between quiescence, proliferation and differentiation during muscle regeneration is driven by increased glycolysis, resulting in higher levels of histone acetylation (Yucel et al., 2019). Histone acetylation and chromatin accessibility is regulated by pyruvate dehydrogenase (PDH) activity as well, which is reduced during differentiation (Fig. 2B) (Yucel et al., 2019). Taken together, these findings underscore that metabolic switches, specifically towards glycolytic metabolism, are integral to multiple endogenous regenerative programs in response to injury. This includes the activation and proliferation of quiescent resident stem cell populations, as well as the cellular proliferation of pre-existing differentiated cells within injured tissues (Fig. 2).

Endogenous tissue regeneration does not exist in all adult tissues; thus, decoding the mechanisms through which metabolism controls development and endogenous regeneration could provide new avenues to promote regeneration in these adult non-regenerative tissues. For example, the metabolic switch from glycolysis to fatty acid oxidation that takes place during postnatal heart maturation results in loss of the ability of cardiomyocytes to enter the cell cycle and to subsequently regenerate following injury (Puente et al., 2014). Recent studies demonstrate that inducing glycolytic metabolism in the adult murine heart can promote adult cardiomyocyte cell cycle reentry via inhibition of pyruvate dehydrogenase kinase 4 (PDK4) (Fig. 2C) (Cardoso et al., 2020). Another important target that can promote adult heart regeneration is SDH, or mitochondrial complex II; mutations in Sdhb promote metabolic reprogramming in some types of cancer by inducing an epigenetic effect via DNA hypermethylation (Letouze et al., 2013; Morin et al., 2020). Remarkably, inhibition of SDH by the competitive inhibitor malonate-induced adult mouse cardiomyocyte proliferation, revascularization and restoration of cardiac function following adult cardiac injury (Fig. 2C) (Bae et al., 2021b). This inhibition of SDH resulted in a metabolic shift of cardiac metabolism towards glycolysis, demonstrating the metabolic reprogramming of the adult heart can promote adult cardiac regeneration (Bae et al., 2021b). The precise mechanisms through which glycolytic metabolism promotes cardiomyocyte proliferation and heart regeneration are yet to be unraveled. Insights gained from understanding metabolic control in development and cancer warrant exploration in the context of regeneration. Importantly, these results underscore the remarkable potential of inducing metabolic shifts in non-regenerative tissues to reawaken the regenerative mechanisms required to replenish the lost tissue following injury (Fig. 2).

In this Review, we have summarized our current understanding of metabolic switches and their roles in embryonic development, postnatal development, cell fate decisions and tissue regeneration. We further highlighted specific cell types and tissues in which metabolic pathways play an important role in orchestrating cell fate decisions and tissue organization, emphasizing the importance of understanding these mechanisms for potential therapeutic applications.

Although we have made significant strides in defining the role of metabolic switches over the past decade, our current understanding of metabolic rewiring remains limited. For instance, we have gained insights into the roles of glycolysis, oxidative phosphorylation and fatty acid oxidation in different developmental stages and cell types, but there is still much to learn about the complex interplay of these metabolic pathways and their regulation by various signaling molecules and transcription factors. Additionally, the molecular mechanisms underlying the metabolic switches between quiescence and activation in stem cells and the role of metabolism in lineage specification, cell fate determination and proliferation warrant further investigation.

As we move forward, technological advancements, such as single-cell transcriptomics, spatial transcriptomics and metabolomics, will be crucial in uncovering the complexity of metabolic networks during development and regeneration. These approaches will allow us to investigate the metabolic heterogeneity within a tissue, identify novel metabolic regulators and explore the metabolic crosstalk between different cell types. Moreover, future studies should further explore the potential of targeting metabolic pathways in regenerative medicine. Modulation of metabolic switches could provide a basis for innovative therapeutic strategies to promote tissue regeneration or prevent pathological processes, such as fibrosis and degeneration. Furthermore, understanding how metabolic alterations contribute to diseases, including cancer and metabolic disorders, could aid the development of targeted therapies in a tissue-specific and cell-specific manner. Thus, the future of metabolic research promises exciting discoveries and transformative implications for both basic and translational research.

I thank members of the Mahmoud Laboratory for critical reading of the manuscript and their insightful suggestions.