- Open Access
Metabolic recoding of epigenetics in cancer
Cancer Communications volume 38, Article number: 25 (2018)
Dysregulation of metabolism allows tumor cells to generate needed building blocks as well as to modulate epigenetic marks to support cancer initiation and progression. Cancer-induced metabolic changes alter the epigenetic landscape, especially modifications on histones and DNA, thereby promoting malignant transformation, adaptation to inadequate nutrition, and metastasis. Recent advances in cancer metabolism shed light on how aberrations in metabolites and metabolic enzymes modify epigenetic programs. The metabolism-induced recoding of epigenetics in cancer depends strongly on nutrient availability for tumor cells. In this review, we focus on metabolic remodeling of epigenetics in cancer and examine potential mechanisms by which cancer cells integrate nutritional inputs into epigenetic modification.
Dysregulated metabolism is one of the most prominent features of cancer. Since the postulation of aerobic glycolysis (Warburg effect) in the early 20th century , metabolic reprogramming in cancer has been the subject of extensive research . Cellular metabolism is reprogrammed at multiple levels in cancer: genetic, epigenetic, transcriptional, posttranscriptional, translational control, and posttranslational [3,4,5,6,7,8,9,10]. Consequently, the expression of a wide range of metabolism-related proteins, such as metabolite transporters and metabolic enzymes, are dysregulated in cancer cells .
Metabolism is reprogrammed in cancer cells through the action of cell-intrinsic and -extrinsic factors. Alterations in oncogenes and tumor suppressor genes cooperatively remodel metabolic pathways to satisfy biosynthetic demands of cancer cells . At the same time, microenvironmental factors modulate metabolic reprogramming; these factors include nutritional , inflammatory, and immune elements in malignant tissue . For example, metabolic activity and nutritional status of cancer cells strongly influence epigenetics, especially modifications on histone and DNA . The metabolic reprogramming interacts with epigenetic regulation and signal transduction to promote cancer cell survival and proliferation [16, 17], and to influence a broad range of biological processes .
This review summarizes recent advances in our understanding of metabolic recoding of epigenetics in cancer, with particular emphasis on how cancer cells encode nutrient input into the epigenetic landscape.
Metabolites are key players in epigenetic remodeling in cancer
Cancer cells show a disordered landscape  of epigenetic enzymes that catalyze the addition and removal of epigenetic marks, such as modifications on histones and genomic DNA . This reshaping of epigenetics is driven by alterations in epigenetic machinery as well as in the metabolic network .
Metabolism and epigenetics are intimately connected, as epigenetic enzymes employ various metabolic intermediates as substrates . Dysregulation of metabolic pathways activates or suppresses epigenetic modifiers, leading to epigenetic remodeling. The interaction between cellular metabolism and epigenetics as well as the disease relevance of this interaction have recently been reviewed [15, 17]. The focus of the present review is how cancer metabolism modulates DNA methylation, histone methylation, and histone acetylation, as well as their connection with nutrient availability.
Acetyl-CoA, NAD+ and histone acetylation
The most extensively investigated epigenetic marks are DNA methylation and covalent modifications of histones . Histone tails are covalently modified by diverse post-translational modifications , of which the best understood are acetylation and methylation . Histone acetyltransferases (HATs) deliver an acetyl group from acetyl-CoA to lysine residues in histones , whereas histone deacetylases (HDACs) catalyze the reverse reaction (Fig. 1). HDACs can be divided into two families : classical HDACs directly hydrolyze acetyl-lysine ; SIRT-family HDACs deacetylate via an NAD+-dependent mechanism . Histone acetylation is linked to energy metabolism since acetyl-CoA and NAD+ are indicators of cellular energy status (Fig. 1).
SAM, α-KG, oxygen and histone/DNA methylation
Histones are methylated on lysine and arginine residues , and this methylation can repress or activate gene transcription . Lysine methyltransferase (KMT) and arginine methyltransferase (PRMT) utilize S-adenosyl homocysteine (SAM) as the methyl donor in histone methylation (Fig. 2a). The reverse reaction of lysine demethylation is catalyzed by the amine oxidases lysine demethylases (LSD) 1 and 2  in a reaction dependent on flavin adenine dinucleotide (FAD), as well as by an α-ketoglutarate (α-KG)-dependent dioxygenase, which produces succinate in an oxygen-dependent reaction  (Fig. 2a). Both α-KG and succinate are intermediates of the tricarboxylic acid (TCA) cycle, indicating a functional correlation between the TCA cycle and α-KG-dependent demethylation. The enzyme that demethylates histone arginine residues is being actively investigated [29, 30]. The protein has been proposed to be an oxygen- and α-KG-dependent dioxygenase similar to that responsible for lysine demethylation . In this case, too, demethylation is linked to oxygen levels and the TCA cycle (Fig. 2a).
In humans, DNA methylation occurs predominantly at CpG islands . In this process, DNA methyltransferase (DNMT) adds a methyl group—donated by SAM as in histone methylation—onto the cytosine of CpG dinucleotides (Fig. 2b). DNA methylation typically represses transcription of the marked genes, helping to stabilize the genome and promote cell differentiation . The reverse reaction of DNA demethylation is catalyzed by ten-eleven translocation (TET) family enzymes, including TET1, TET2, and TET3, which are α-KG- and oxygen-dependent dioxygenases . TET enzymes iteratively oxidize 5-methylcytosine (5mC) and convert α-KG into succinate (Fig. 2b).
Metabolic intermediates participate as substrates or coenzymes in nearly all epigenetic coding processes. In cancer, metabolic dysregulation interacts with nutritional status to modulate epigenetic marks on histones and DNA. This nutritional status is defined largely as the availability of carbon sources.
Nutrient availability affects epigenetic regulation in cancer
Glucose availability is reflected in histone and DNA modification in cancer
Glucose and glutamine are the major carbon sources of most mammalian cells, and glucose metabolism is closely related to histone acetylation and deacetylation. Glucose availability affects the intracellular pool of acetyl-CoA, a central metabolic intermediate that is also the acetyl donor in histone acetylation  (Fig. 1). Glucose is converted to acetyl-CoA by the pyruvate dehydrogenase complex (PDC), which produces acetyl-CoA from glucose-derived pyruvate; and by adenosine triphosphate-citrate lyase (ACLY), which generates acetyl-CoA from glucose-derived citrate. PDC and ACLY activity depend on glucose availability, which thereby influences histone acetylation and consequently modulates gene expression and cell cycle progression [34, 35]. Dysregulation of ACLY and PDC contributes to metabolic reprogramming and promotes the development of multiple cancers, such as lung cancer . At the same time, glucose metabolism maintains the NAD+/NADH ratio, and NAD+ participates in SIRT-mediated histone deacetylation  (Fig. 1). SIRT enzyme activity is altered in various malignancies [25, 36, 38,39,40,41], and inhibiting SIRT6, a histone deacetylase that acts on acetylated H3K9 and H3K56, promotes tumorigenesis [42, 43]. SIRT7, which deacetylates H3K18 and thereby represses transcription of target genes, is activated in cancer to stabilize cells in the transformed state [44,45,46]. Interestingly, nutrients appear to modulate SIRT activity. For example, long-chain fatty acids activate the deacetylase function of SIRT6, and this may affect histone acetylation [47, 48].
Glucose catabolism affects histone acetylation as well as histone and DNA methylation, since glucose-derived α-KG serves as a substrate in the reactions catalyzed by histone demethylases and TET family DNA dioxygenases  (Fig. 2a, b).
Glutamine metabolism modulates cancer epigenetics
Glutamine metabolism also contributes to the production of acetyl-CoA and α-KG, and glutamine oxidation correlates with the cell state-specific epigenetic landscape. Naive embryonic stem cells efficiently take up both glutamine and glucose to maintain a high level of α-KG to promote histone and DNA demethylation, which in turn helps maintain pluripotency . Inhibition of glutamine oxidation affects histone modifications including H4K16ac and H3K4me3 in breast cancer cell lines, altering the transcription of genes involved in apoptosis and metastasis .
Acetate and other carbon sources as epigenetic metabolites
Cancer cells absorb acetate and incorporate it into histones . Acetyl-CoA synthetases (ACSSs) convert acetate to acetyl-CoA, which in turn serves as a major carbon source in lower eukaryotes, but not mammals. However, glioma cells and hepatocellular cancer cells utilize acetate as an alternative carbon source to sustain acetyl-CoA production [52, 53] (Fig. 1). This compensates for the hypoxic, nutrient-poor microenvironment of solid tumors. Mammalian cells express three ACSS isozymes (ACSS1-3). The contribution of ACSS isozymes to histone acetylation varies across different cancers [54,55,56]. ACSS is highly expressed in glioma and hepatocellular cancer, which correlates with histone hyperacetylation [54,55,56]. ACLY functions as a switch and controls carbon source preference of cancer cells .
Other carbon sources, such as fatty acids, also regulate epigenetic modifications  (Fig. 1). A high-fat diet reduces the acetyl-CoA level and decreases acetylation of H3K23 in white adipose tissue but not liver. This suggests that lipids may affect cancer risk via an epigenetic mechanism, since obesity predisposes to the development of multiple cancers .
One-carbon metabolism modifies chromatin methylation
In one-carbon metabolism, the amino acids glycine and serine are converted via the folate and methionine cycles to nucleotide precursors and SAM. Multiple nutrients fuel one-carbon metabolism, including glucose, serine, glycine, and threonine  (Fig. 2a, b). High levels of the methyl donor SAM influence histone methylation , which may explain how high SAM levels prevent malignant transformation . Glucose availability is encoded in methylation of H3R17 by arginine methyltransferase CARM1 .
2-hydroxyglutarate and oncometabolites
In cancer, genetic alteration and microenvironment perturbation modify the catalytic properties of metabolic enzymes, reshaping epigenetics. Cancer-associated mutations in isocitrate dehydrogenase (IDH) 1 and 2 confer on the enzyme the ability to produce 2-hydroxyglutarate (2-HG), which is structurally analogous to α-KG  (Fig. 3). 2-HG competes with α-KG to bind to the catalytic pocket of several α-KG-dependent epigenetic enzymes, suppressing their catalytic activity and leading to genome-wide hypermethylation of histones and DNA [65, 66]. The resulting aberrant gene expression promotes tumorigenesis [67, 68]. The metabolic enzymes fumarate hydratase (FH) and succinate dehydrogenase (SDH) are also frequently mutated in certain cancers . Loss-of-function mutations in FH and SDH lead to accumulation of fumarate and succinate, which act as competitive inhibitors of α-KG-dependent dioxygenase  (Fig. 3). The oncogenic effect of α-KG, fumarate, and succinate via epigenetic regulation has led them to be named oncometabolites .
2-HG also accumulates in hypoxic cancer cells without IDH mutations, through a process mediated at least in part by the metabolic enzymes malate dehydrogenase (MDH) and lactate dehydrogenase (LDH). Hypoxia makes the tumor microenvironment acidic, which causes MDH and LDH to bind substrates promiscuously and generate 2-HG [71, 72] (Fig. 3). Under these conditions, more 2-HG is produced by LDH than by MDH . LDH may also modulate epigenetics in cancer cells independently of 2-HG, since tumor pH is highly heterogeneous and in fact only some cancer cell lines or tumor tissues reach the pH of 6 needed to trigger promiscuous 2-HG production [74,75,76]. The in vivo significance of substrate promiscuity-induced 2-HG production remains to be explored.
Other metabolites show oncogenic effects in certain tissues. For example, normal colonocytes utilize butyrate as a major carbon source. Glucose is used by a subtype of colon cancer cells as the carbon source, resulting in butyrate accumulation. Butyrate further inhibits HDAC to induce histone hyperacetylation and promote the proliferation of colon cancer cells  (Fig. 1).
Cellular metabolism is highly dynamic and compartmentalized. The accumulation of certain metabolites in cancer can target epigenetic enzymes to globally alter the epigenetic landscape. Evidence suggests that this alteration can be random. For example, cancer cells containing IDH mutations show highly variable DNA hypermethylation patterns, with effects on gene transcription difficult to predict . In this model of metabolic recoding of cancer epigenetics (Fig. 4a), fluctuations in the level of a metabolite produce metabolic noise and randomly modify epigenetic marks to generate diverse clonal epigenetic landscapes. This provides an opportunity for clonal selection during tumor growth, metastasis, and relapse (Fig. 4a). At the same time, recent studies have provided evidence supporting the idea that cancer-related metabolic changes lead to locus-specific recoding of epigenetic marks.
Reign of chaos: precise epigenetic reprogramming by cancer metabolism
Dose-responsive modulation of cancer epigenetics by metabolites
2-HG presumably inhibits all α-KG-dependent epigenetic enzymes, but its overall effects appear to depend strongly on its intracellular concentration. Cancer cells carrying IDH mutations, for example, vary significantly in 2-HG concentration , and this influences the resulting epigenetic recoding. Transient expression of mutant forms of IDH suppresses the H3K9 demethylase KDM4C more strongly than other demethylases . In addition, α-KG-dependent dioxygenases show diverse half-maximal inhibitory concentrations (IC50) of 2-HG . These findings suggest that metabolic alterations in cancer cells reshape epigenetics in a manner dependent on metabolite dose (Fig. 4b).
Histones are conjugated to a large number of metabolites . It is thus reasonable to expect that fluctuations of metabolites can broadly impact the epigenetic landscape. Understanding metabolism-induced epigenetic alterations requires the development of an atlas of interactions between key metabolites and epigenetic enzymes in cancer cells.
Sequence-specific recruitment of metabolic enzymes
Precise recoding of epigenetic marks requires recognition of a specific genomic locus or DNA sequence. Metabolic enzymes that have translocated to the nucleus may recognize specific DNA sequences by binding to transcription factors (Fig. 4c). Some metabolic enzymes translocate to the nucleus in response to stress or physiological signals. For example, glucose deprivation causes cytosolic ACSS2 to relocate to the nucleus, where it binds to transcription factor EB (TFEB). When TFEB binds to the promoter regions of lysosomal and autophagy genes, it brings ACSS2 with it; the ACSS2 produces acetyl-CoA and increases histone H3 acetylation, modulating the expression of TFEB-regulated genes . In a second example, glucose starvation enhances interaction between nuclear FH and ATF2. ATF2 recruits FH to its target genes, inhibiting H3K36me2 demethylation and increasing expression of those genes, ultimately arresting cell growth . Other metabolic enzymes may also translocate to the nucleus and associate with transcription factors to mediate specific epigenetic remodeling.
One hypothesis holds that the ability of nuclear ACSS2 to alter histone acetylation and of nuclear FH to alter methylation depend on high local concentrations of acetyl-CoA and fumarate, respectively, at the specific target DNA sequences [82, 83]. Testing this hypothesis requires metabolite quantification in subcellular compartments, which remains a challenging task . The engineering of artificial metabolite sensors may advance locus-specific and real-time monitoring of epigenetic metabolites . Studies are also needed to explore the possibility that nuclear metabolic enzymes modify epigenetic marks independently of their catalytic activity.
Targeting of epigenetic enzymes by nutritional signals
Nutrient sensing and signaling is a key regulator of epigenetic machinery in cancer. During glucose shortage, the energy sensor AMPK activates arginine methyltransferase CARM1 and mediates histone H3 hypermethylation (H3R17me2), leading to enhanced autophagy . In addition, O-GlcNAc transferase (OGT) signals glucose availability to TET3 and inhibits TET3 by both decreasing its dioxygenase activity and promoting its nuclear export . These observations strongly suggest that nutrient signaling directly targets epigenetic enzymes to control epigenetic modifications (Fig. 4d).
The nutritional status of cancer cells is highly dynamic during cancer development. How cancer cells coordinate nutrient status with epigenetic phenomena during cancer progression remains an open question.
Our understanding of cancer metabolism has increased tremendously in the last decade. What were once considered bystander cells in the tumor microenvironment—such as cancer-associated fibroblasts , immune cells, and inflammatory cells [88, 89]—are now recognized as contributors to metabolic remodeling of cancer . For example, oxidative cancer cells thrive on lactate in the tumor microenvironment , while pancreatic cancer cells depend on alanine secreted by stroma-associated pancreatic stellate cells . Metabolite transport within tumor tissue and crosstalk between cancer cells and “bystander” cells cooperatively remodel cancer metabolism, suggesting an intricate and complicated regulatory network in the tumor microenvironment.
Metabolic remodeling has also been implicated in a variety of human diseases other than cancer [17, 93]. Cellular metabolism is closely related to stem cell homeostasis and differentiation . Elucidating the connection between metabolism and epigenetics would provide mechanistic insights into these diseases and offer potential therapeutic opportunities for translational investigations.
flavin adenine dinucleotide
- TCA cycle:
tricarboxylic acid cycle
ten-eleven translocation family enzyme
pyruvate dehydrogenase complex
adenosine triphosphate-citrate lyase
transcription factor EB
Vander Heiden MG, Cantley LC, Thompson CB. Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science. 2009;324:1029–33. https://doi.org/10.1126/science.1160809.
Pavlova NN, Thompson CB. The Emerging Hallmarks of Cancer Metabolism. Cell Metab. 2016;23:27–47. https://doi.org/10.1016/j.cmet.2015.12.006.
Lin R, Zhou X, Huang W, Zhao D, Lv L, Xiong Y, et al. Acetylation control of cancer cell metabolism. Curr Pharm Des. 2014;20:2627–33.
Qiu Z, Guo W, Wang Q, Chen Z, Huang S, Zhao F, et al. MicroRNA-124 reduces the pentose phosphate pathway and proliferation by targeting PRPS1 and RPIA mRNAs in human colorectal cancer cells. Gastroenterology. 2015;149(1587–98):e11. https://doi.org/10.1053/j.gastro.2015.07.050.
DeBerardinis RJ, Chandel NS. Fundamentals of cancer metabolism. Sci Adv. 2016;2:e1600200. https://doi.org/10.1126/sciadv.1600200.
Fan J, Lin R, Xia S, Chen D, Elf SE, Liu S, et al. Tetrameric Acetyl-CoA Acetyltransferase 1 is important for tumor growth. Mol Cell. 2016;64:859–74. https://doi.org/10.1016/j.molcel.2016.10.014.
Wang J, Zhu ZH, Yang HB, Zhang Y, Zhao XN, Zhang M, et al. Cullin 3 targets methionine adenosyltransferase IIalpha for ubiquitylation-mediated degradation and regulates colorectal cancer cell proliferation. FEBS J. 2016;283:2390–402. https://doi.org/10.1111/febs.13759.
Wang YP, Zhou W, Wang J, Huang X, Zuo Y, Wang TS, et al. Arginine methylation of MDH1 by CARM1 inhibits glutamine metabolism and suppresses pancreatic cancer. Mol Cell. 2016;64:673–87. https://doi.org/10.1016/j.molcel.2016.09.028.
Zhang Y, Xu YY, Yao CB, Li JT, Zhao XN, Yang HB, et al. Acetylation targets HSD17B4 for degradation via the CMA pathway in response to estrone. Autophagy. 2017;13:538–53. https://doi.org/10.1080/15548627.2016.1268302.
Guo W, Qiu Z, Wang Z, Wang Q, Tan N, Chen T, et al. MiR-199a-5p is negatively associated with malignancies and regulates glycolysis and lactate production by targeting hexokinase 2 in liver cancer. Hepatology. 2015;62:1132–44. https://doi.org/10.1002/hep.27929.
Martinez-Outschoorn UE, Peiris-Pages M, Pestell RG, Sotgia F, Lisanti MP. Cancer metabolism: a therapeutic perspective. Nat Rev Clin Oncol. 2017;14:11–31. https://doi.org/10.1038/nrclinonc.2016.60.
Boroughs LK, DeBerardinis RJ. Metabolic pathways promoting cancer cell survival and growth. Nat Cell Biol. 2015;17:351–9. https://doi.org/10.1038/ncb3124.
Liang C, Qin Y, Zhang B, Ji S, Shi S, Xu W, et al. Metabolic plasticity in heterogeneous pancreatic ductal adenocarcinoma. Biochem Biophys Acta. 2016;1866:177–88. https://doi.org/10.1016/j.bbcan.2016.09.001.
Zhong Z, Sanchez-Lopez E, Karin M. Autophagy, inflammation, and immunity: a troika governing cancer and its treatment. Cell. 2016;166:288–98. https://doi.org/10.1016/j.cell.2016.05.051.
Kinnaird A, Zhao S, Wellen KE, Michelakis ED. Metabolic control of epigenetics in cancer. Nat Rev Cancer. 2016;16:694–707. https://doi.org/10.1038/nrc.2016.82.
Ferrer CM, Lynch TP, Sodi VL, Falcone JN, Schwab LP, Peacock DL, et al. O-GlcNAcylation regulates cancer metabolism and survival stress signaling via regulation of the HIF-1 pathway. Mol Cell. 2014;54:820–31. https://doi.org/10.1016/j.molcel.2014.04.026.
Kaelin WG Jr, McKnight SL. Influence of metabolism on epigenetics and disease. Cell. 2013;153:56–69. https://doi.org/10.1016/j.cell.2013.03.004.
Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW. Cancer Genome Landsc. Science. 2013;339:1546–58. https://doi.org/10.1126/science.1235122.
Easwaran H, Tsai HC, Baylin SB. Cancer epigenetics: tumor heterogeneity, plasticity of stem-like states, and drug resistance. Mol Cell. 2014;54:716–27. https://doi.org/10.1016/j.molcel.2014.05.015.
Du J, Johnson LM, Jacobsen SE, Patel DJ. DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol. 2015;16:519–32. https://doi.org/10.1038/nrm4043.
Baylin SB, Jones PA. A decade of exploring the cancer epigenome—biological and translational implications. Nat Rev Cancer. 2011;11:726–34. https://doi.org/10.1038/nrc3130.
Katada S, Imhof A, Sassone-Corsi P. Connecting threads: epigenetics and metabolism. Cell. 2012;148:24–8. https://doi.org/10.1016/j.cell.2012.01.001.
Rothbart SB, Strahl BD. Interpreting the language of histone and DNA modifications. Biochem Biophys Acta. 2014;1839:627–43. https://doi.org/10.1016/j.bbagrm.2014.03.001.
Li T, Liu M, Feng X, Wang Z, Das I, Xu Y, et al. Glyceraldehyde-3-phosphate dehydrogenase is activated by lysine 254 acetylation in response to glucose signal. J Biol Chem. 2014;289:3775–85. https://doi.org/10.1074/jbc.M113.531640.
Xu SN, Wang TS, Li X, Wang YP. SIRT2 activates G6PD to enhance NADPH production and promote leukaemia cell proliferation. Sci Rep. 2016;6:32734. https://doi.org/10.1038/srep32734.
Cheng X. Structural and functional coordination of DNA and histone methylation. Cold Spring Harbor Perspect Biol. 2014. https://doi.org/10.1101/cshperspect.a018747.
Fang R, Barbera AJ, Xu Y, Rutenberg M, Leonor T, Bi Q, et al. Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation. Mol Cell. 2010;39:222–33. https://doi.org/10.1016/j.molcel.2010.07.008.
Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, et al. Histone demethylation by a family of JmjC domain-containing proteins. Nature. 2006;439:811–6. https://doi.org/10.1038/nature04433.
Walport LJ, Hopkinson RJ, Chowdhury R, Schiller R, Ge W, Kawamura A, et al. Arginine demethylation is catalysed by a subset of JmjC histone lysine demethylases. Nat Commun. 2016;7:11974. https://doi.org/10.1038/ncomms11974.
Blanc RS, Richard S. Arginine methylation: the coming of age. Mol Cell. 2017;65:8–24. https://doi.org/10.1016/j.molcel.2016.11.003.
Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet. 2013;14:204–20. https://doi.org/10.1038/nrg3354.
Pastor WA, Aravind L, Rao A. TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol. 2013;14:341–56. https://doi.org/10.1038/nrm3589.
Cai L, Sutter BM, Li B, Tu BP. Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. Mol Cell. 2011;42:426–37. https://doi.org/10.1016/j.molcel.2011.05.004.
Wellen KE, Hatzivassiliou G, Sachdeva UM, Bui TV, Cross JR, Thompson CB. ATP-citrate lyase links cellular metabolism to histone acetylation. Science. 2009;324:1076–80. https://doi.org/10.1126/science.1164097.
Sutendra G, Kinnaird A, Dromparis P, Paulin R, Stenson TH, Haromy A, et al. A nuclear pyruvate dehydrogenase complex is important for the generation of acetyl-CoA and histone acetylation. Cell. 2014;158:84–97. https://doi.org/10.1016/j.cell.2014.04.046.
Lin R, Tao R, Gao X, Li T, Zhou X, Guan KL, et al. Acetylation stabilizes ATP-citrate lyase to promote lipid biosynthesis and tumor growth. Mol Cell. 2013;51:506–18. https://doi.org/10.1016/j.molcel.2013.07.002.
Saunders LR, Verdin E. Sirtuins: critical regulators at the crossroads between cancer and aging. Oncogene. 2007;26:5489–504. https://doi.org/10.1038/sj.onc.1210616.
Lv L, Li D, Zhao D, Lin R, Chu Y, Zhang H, et al. Acetylation targets the M2 isoform of pyruvate kinase for degradation through chaperone-mediated autophagy and promotes tumor growth. Mol Cell. 2011;42:719–30. https://doi.org/10.1016/j.molcel.2011.04.025.
Zhao D, Zou SW, Liu Y, Zhou X, Mo Y, Wang P, et al. Lysine-5 acetylation negatively regulates lactate dehydrogenase A and is decreased in pancreatic cancer. Cancer Cell. 2013;23:464–76. https://doi.org/10.1016/j.ccr.2013.02.005.
Wang YP, Zhou LS, Zhao YZ, Wang SW, Chen LL, Liu LX, et al. Regulation of G6PD acetylation by SIRT2 and KAT9 modulates NADPH homeostasis and cell survival during oxidative stress. EMBO J. 2014;33:1304–20. https://doi.org/10.1002/embj.201387224.
Yang HB, Xu YY, Zhao XN, Zou SW, Zhang Y, Zhang M, et al. Acetylation of MAT IIalpha represses tumour cell growth and is decreased in human hepatocellular cancer. Nat Commun. 2015;6:6973. https://doi.org/10.1038/ncomms7973.
Cai J, Zuo Y, Wang T, Cao Y, Cai R, Chen FL, et al. A crucial role of SUMOylation in modulating Sirt6 deacetylation of H3 at lysine 56 and its tumor suppressive activity. Oncogene. 2016;35:4949–56. https://doi.org/10.1038/onc.2016.24.
Kawahara TL, Michishita E, Adler AS, Damian M, Berber E, Lin M, et al. SIRT6 links histone H3 lysine 9 deacetylation to NF-κB-dependent gene expression and organismal life span. Cell. 2009;136:62–74. https://doi.org/10.1016/j.cell.2008.10.052.
Barber MF, Michishita-Kioi E, Xi Y, Tasselli L, Kioi M, Moqtaderi Z, et al. SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature. 2012;487:114–8. https://doi.org/10.1038/nature11043.
Vazquez BN, Thackray JK, Simonet NG, Kane-Goldsmith N, Martinez-Redondo P, Nguyen T, et al. SIRT7 promotes genome integrity and modulates non-homologous end joining DNA repair. EMBO J. 2016;35:1488–503. https://doi.org/10.15252/embj.201593499.
Li L, Shi L, Yang S, Yan R, Zhang D, Yang J, et al. SIRT7 is a histone desuccinylase that functionally links to chromatin compaction and genome stability. Nat Commun. 2016;7:12235. https://doi.org/10.1038/ncomms12235.
Feldman JL, Baeza J, Denu JM. Activation of the protein deacetylase SIRT6 by long-chain fatty acids and widespread deacylation by mammalian sirtuins. J Biol Chem. 2013;288:31350–6. https://doi.org/10.1074/jbc.C113.511261.
Jiang H, Khan S, Wang Y, Charron G, He B, Sebastian C, et al. SIRT6 regulates TNF-alpha secretion through hydrolysis of long-chain fatty acyl lysine. Nature. 2013;496:110–3. https://doi.org/10.1038/nature12038.
Carey BW, Finley LW, Cross JR, Allis CD, Thompson CB. Intracellular alpha-ketoglutarate maintains the pluripotency of embryonic stem cells. Nature. 2015;518:413–6. https://doi.org/10.1038/nature13981.
Simpson NE, Tryndyak VP, Pogribna M, Beland FA, Pogribny IP. Modifying metabolically sensitive histone marks by inhibiting glutamine metabolism affects gene expression and alters cancer cell phenotype. Epigenetics. 2012;7:1413–20. https://doi.org/10.4161/epi.22713.
Wilhelm JA, McCarty KS. The uptake and turnover of acetate in HeLa cell histone fractions. Cancer Res. 1970;30:418–25.
Mashimo T, Pichumani K, Vemireddy V, Hatanpaa KJ, Singh DK, Sirasanagandla S, et al. Acetate is a bioenergetic substrate for human glioblastoma and brain metastases. Cell. 2014;159:1603–14. https://doi.org/10.1016/j.cell.2014.11.025.
Comerford SA, Huang Z, Du X, Wang Y, Cai L, Witkiewicz AK, et al. Acetate dependence of tumors. Cell. 2014;159:1591–602. https://doi.org/10.1016/j.cell.2014.11.020.
Schug ZT, Peck B, Jones DT, Zhang Q, Grosskurth S, Alam IS, et al. Acetyl-CoA synthetase 2 promotes acetate utilization and maintains cancer cell growth under metabolic stress. Cancer Cell. 2015;27:57–71. https://doi.org/10.1016/j.ccell.2014.12.002.
Gao X, Lin SH, Ren F, Li JT, Chen JJ, Yao CB, et al. Acetate functions as an epigenetic metabolite to promote lipid synthesis under hypoxia. Nat Commun. 2016;7:11960. https://doi.org/10.1038/ncomms11960.
Bulusu V, Tumanov S, Michalopoulou E, van den Broek NJ, MacKay G, Nixon C, et al. Acetate recapturing by nuclear acetyl-coa synthetase 2 prevents loss of histone acetylation during oxygen and serum limitation. Cell Rep. 2017;18:647–58. https://doi.org/10.1016/j.celrep.2016.12.055.
Zhao S, Torres A, Henry RA, Trefely S, Wallace M, Lee JV, et al. ATP-citrate lyase controls a glucose-to-acetate metabolic switch. Cell Rep. 2016;17:1037–52. https://doi.org/10.1016/j.celrep.2016.09.069.
McDonnell E, Crown SB, Fox DB, Kitir B, Ilkayeva OR, Olsen CA, et al. Lipids reprogram metabolism to become a major carbon source for histone acetylation. Cell Rep. 2016;17:1463–72. https://doi.org/10.1016/j.celrep.2016.10.012.
Carrer A, Parris JL, Trefely S, Henry RA, Montgomery DC, Torres A, et al. Impact of a high-fat diet on tissue acyl-coa and histone acetylation levels. J Biol Chem. 2017;292:3312–22. https://doi.org/10.1074/jbc.M116.750620.
Newman AC, Maddocks ODK. One-carbon metabolism in cancer. Br J Cancer. 2017;116:1499–504. https://doi.org/10.1038/bjc.2017.118.
Teperino R, Schoonjans K, Auwerx J. Histone methyl transferases and demethylases; can they link metabolism and transcription? Cell Metab. 2010;12:321–7. https://doi.org/10.1016/j.cmet.2010.09.004.
Panopoulos AD, Yanes O, Ruiz S, Kida YS, Diep D, Tautenhahn R, et al. The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming. Cell Res. 2012;22:168–77. https://doi.org/10.1038/cr.2011.177.
Shin HJ, Kim H, Oh S, Lee JG, Kee M, Ko HJ, et al. AMPK-SKP2-CARM1 signalling cascade in transcriptional regulation of autophagy. Nature. 2016;534:553–7. https://doi.org/10.1038/nature18014.
Dang L, White DW, Gross S, Bennett BD, Bittinger MA, Driggers EM, et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature. 2009;462:739–44. https://doi.org/10.1038/nature08617.
Xu W, Yang H, Liu Y, Yang Y, Wang P, Kim SH, et al. Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of alpha-ketoglutarate-dependent dioxygenases. Cancer Cell. 2011;19:17–30. https://doi.org/10.1016/j.ccr.2010.12.014.
Lu C, Ward PS, Kapoor GS, Rohle D, Turcan S, Abdel-Wahab O, et al. IDH mutation impairs histone demethylation and results in a block to cell differentiation. Nature. 2012;483:474–8. https://doi.org/10.1038/nature10860.
Wang Y, Xiao M, Chen X, Chen L, Xu Y, Lv L, et al. WT1 recruits TET2 to regulate its target gene expression and suppress leukemia cell proliferation. Mol Cell. 2015;57:662–73. https://doi.org/10.1016/j.molcel.2014.12.023.
Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. New Engl J Med. 2009;361:1058–66. https://doi.org/10.1056/NEJMoa0903840.
Pollard PJ, Briere JJ, Alam NA, Barwell J, Barclay E, Wortham NC, et al. Accumulation of Krebs cycle intermediates and over-expression of HIF1alpha in tumours which result from germline FH and SDH mutations. Hum Mol Genet. 2005;14:2231–9. https://doi.org/10.1093/hmg/ddi227.
Xiao M, Yang H, Xu W, Ma S, Lin H, Zhu H, et al. Inhibition of alpha-KG-dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors. Genes Dev. 2012;26:1326–38. https://doi.org/10.1101/gad.191056.112.
Intlekofer AM, Dematteo RG, Venneti S, Finley LW, Lu C, Judkins AR, et al. Hypoxia induces production of L-2-hydroxyglutarate. Cell Metab. 2015;22:304–11. https://doi.org/10.1016/j.cmet.2015.06.023.
Oldham WM, Clish CB, Yang Y, Loscalzo J. Hypoxia-mediated increases in L-2-hydroxyglutarate coordinate the metabolic response to reductive stress. Cell Metab. 2015;22:291–303. https://doi.org/10.1016/j.cmet.2015.06.021.
Intlekofer AM, Wang B, Liu H, Shah H, Carmona-Fontaine C, Rustenburg AS, et al. L-2-hydroxyglutarate production arises from noncanonical enzyme function at acidic pH. Nat Chem Biol. 2017;13:494–500. https://doi.org/10.1038/nchembio.2307.
Gerweck LE, Seetharaman K. Cellular pH gradient in tumor versus normal tissue: potential exploitation for the treatment of cancer. Cancer Res. 1996;56:1194–8.
Hou H, Zhao Y, Li C, Wang M, Xu X, Jin Y. Single-cell pH imaging and detection for pH profiling and label-free rapid identification of cancer-cells. Sci Rep. 2017;7:1759. https://doi.org/10.1038/s41598-017-01956-1.
Schartner EP, Henderson MR, Purdey M, Dhatrak D, Monro TM, Gill PG, et al. Cancer detection in human tissue samples using a fiber-tip pH probe. Cancer Res. 2016;76:6795–801. https://doi.org/10.1158/0008-5472.CAN-16-1285.
Donohoe DR, Collins LB, Wali A, Bigler R, Sun W, Bultman SJ. The Warburg effect dictates the mechanism of butyrate-mediated histone acetylation and cell proliferation. Mol Cell. 2012;48:612–26. https://doi.org/10.1016/j.molcel.2012.08.033.
Cancer Genome Atlas Research N,, et al, Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. New Engl J Med. 2013;368:2059–74. https://doi.org/10.1056/NEJMoa1301689.
Wang JH, Chen WL, Li JM, Wu SF, Chen TL, Zhu YM, et al. Prognostic significance of 2-hydroxyglutarate levels in acute myeloid leukemia in China. Proc Natl Acad Sci USA. 2013;110:17017–22. https://doi.org/10.1073/pnas.1315558110.
Chowdhury R, Yeoh KK, Tian YM, Hillringhaus L, Bagg EA, Rose NR, et al. The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep. 2011;12:463–9. https://doi.org/10.1038/embor.2011.43.
Fan J, Krautkramer KA, Feldman JL, Denu JM. Metabolic regulation of histone post-translational modifications. ACS Chem Biol. 2015;10:95–108. https://doi.org/10.1021/cb500846u.
Li X, Yu W, Qian X, Xia Y, Zheng Y, Lee JH, et al. Nucleus-translocated ACSS2 promotes gene transcription for lysosomal biogenesis and autophagy. Mol Cell. 2017;66(684–97):e9. https://doi.org/10.1016/j.molcel.2017.04.026.
Wang T, Yu Q, Li J, Hu B, Zhao Q, Ma C, et al. O-GlcNAcylation of fumarase maintains tumour growth under glucose deficiency. Nat Cell Biol. 2017. https://doi.org/10.1038/ncb3562.
Bowsher CG, Tobin AK. Compartmentation of metabolism within mitochondria and plastids. J Exp Bot. 2001;52:513–27.
Rogers JK, Church GM. Genetically encoded sensors enable real-time observation of metabolite production. Proc Natl Acad Sci USA. 2016;113:2388–93. https://doi.org/10.1073/pnas.1600375113.
Zhang Q, Liu X, Gao W, Li P, Hou J, Li J, et al. Differential regulation of the ten-eleven translocation (TET) family of dioxygenases by O-linked beta-N-acetylglucosamine transferase (OGT). J Biol Chem. 2014;289:5986–96. https://doi.org/10.1074/jbc.M113.524140.
Koukourakis MI, Giatromanolaki A, Harris AL, Sivridis E. Comparison of metabolic pathways between cancer cells and stromal cells in colorectal carcinomas: a metabolic survival role for tumor-associated stroma. Cancer Res. 2006;66:632–7. https://doi.org/10.1158/0008-5472.CAN-05-3260.
Ho PC, Bihuniak JD, Macintyre AN, Staron M, Liu X, Amezquita R, et al. Phosphoenolpyruvate is a metabolic checkpoint of anti-tumor T cell responses. Cell. 2015;162:1217–28. https://doi.org/10.1016/j.cell.2015.08.012.
Wenes M, Shang M, Di Matteo M, Goveia J, Martin-Perez R, Serneels J, et al. Macrophage metabolism controls tumor blood vessel morphogenesis and metastasis. Cell Metab. 2016;24:701–15. https://doi.org/10.1016/j.cmet.2016.09.008.
Dickson I. Pancreatic cancer: stromal-cancer cell crosstalk supports tumour metabolism. Nat Rev Gastroenterol Hepatol. 2016;13:558–9. https://doi.org/10.1038/nrgastro.2016.137.
Brisson L, Banski P, Sboarina M, Dethier C, Danhier P, Fontenille MJ, et al. Lactate dehydrogenase B controls lysosome activity and autophagy in cancer. Cancer Cell. 2016;30:418–31. https://doi.org/10.1016/j.ccell.2016.08.005.
Sousa CM, Biancur DE, Wang X, Halbrook CJ, Sherman MH, Zhang L, et al. Pancreatic stellate cells support tumour metabolism through autophagic alanine secretion. Nature. 2016;536:479–83. https://doi.org/10.1038/nature19084.
Lu C, Thompson CB. Metabolic regulation of epigenetics. Cell Metab. 2012;16:9–17. https://doi.org/10.1016/j.cmet.2012.06.001.
Folmes CD, Dzeja PP, Nelson TJ, Terzic A. Metabolic plasticity in stem cell homeostasis and differentiation. Cell Stem Cell. 2012;11:596–606. https://doi.org/10.1016/j.stem.2012.10.002.
YPW and QYL formulated the idea for this review, which they co-wrote. Both authors read and approved the final manuscript.
We thank members of the Cancer Metabolism Laboratory for critical discussions and support throughout this work.
The authors declare that they have no competing interests.
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This work was supported by MOST (2015CB910401 to Q.-Y.L), the Natural Science Foundation of China (81790253, 81790250, and 81430057 to Q.-Y.L; 81772946 and 81502379 to Y.-P.W.), the Innovation Program of Shanghai Municipal Education Commission (N173606 to Q.-Y.L.), and the ‘‘Chenguang Program’’ of the Shanghai Education Development Foundation (14CG15 to Y.-P.W).
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Wang, YP., Lei, QY. Metabolic recoding of epigenetics in cancer. Cancer Commun 38, 25 (2018). https://doi.org/10.1186/s40880-018-0302-3
- Cancer metabolism
- Histone modification
- DNA methylation
- Cancer microenvironment
- Nutrient availability