Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Metformin regulates global DNA methylation via mitochondrial one-carbon metabolism

Abstract

The anti-diabetic biguanide metformin may exert health-promoting effects via metabolic regulation of the epigenome. Here we show that metformin promotes global DNA methylation in non-cancerous, cancer-prone and metastatic cancer cells by decreasing S-adenosylhomocysteine (SAH), a strong feedback inhibitor of S-adenosylmethionine (SAM)-dependent DNA methyltransferases, while promoting the accumulation of SAM, the universal methyl donor for cellular methylation. Using metformin and a mitochondria/complex I (mCI)-targeted analog of metformin (norMitoMet) in experimental pairs of wild-type and AMP-activated protein kinase (AMPK)-, serine hydroxymethyltransferase 2 (SHMT2)- and mCI-null cells, we provide evidence that metformin increases the SAM:SAH ratio-related methylation capacity by targeting the coupling between serine mitochondrial one-carbon flux and CI activity. By increasing the contribution of one-carbon units to the SAM from folate stores while decreasing SAH in response to AMPK-sensed energetic crisis, metformin can operate as a metabolo-epigenetic regulator capable of reprogramming one of the key conduits linking cellular metabolism to the DNA methylation machinery.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1
Figure 2
Figure 3

References

  1. 1

    Barzilai N, Crandall JP, Kritchevsky SB, Espeland MA . Metformin as a Tool to target aging. Cell Metab 2016; 23: 1060–1065.

    CAS  Article  Google Scholar 

  2. 2

    López-Otín C, Galluzzi L, Freije JM, Madeo F, Kroemer G . Metabolic control of longevity. Cell 2016; 166: 802–821.

    Article  Google Scholar 

  3. 3

    Kinnaird A, Zhao S, Wellen KE, Michelakis ED . Metabolic control of epigenetics in cancer. Nat Rev Cancer 2016; 16: 694–707.

    CAS  Article  Google Scholar 

  4. 4

    Sharma U, Rando OJ . Metabolic inputs into the epigenome. Cell Metab 2017; 25: 544–558.

    CAS  Article  Google Scholar 

  5. 5

    Zhong T, Men Y, Lu L, Geng T, Zhou J, Mitsuhashi A et al. Metformin alters DNA methylation genome-wide via the H19/SAHH axis. Oncogene 2017; 36: 2345–2354.

    CAS  Article  Google Scholar 

  6. 6

    Zhou J, Yang L, Zhong T, Mueller M, Men Y, Zhang N et al. H19 lncRNA alters DNA methylation genome wide by regulating S-adenosylhomocysteine hydrolase. Nat Commun 2015; 6: 10221.

    CAS  Article  Google Scholar 

  7. 7

    Caudill MA, Wang JC, Melnyk S, Pogribny IP, Jernigan S, Collins MD et al. Intracellular S-adenosylhomocysteine concentrations predict global DNA hypomethylation in tissues of methyl-deficient cystathionine beta-synthase heterozygous mice. J Nutr 2001; 131: 2811–2818.

    CAS  Article  Google Scholar 

  8. 8

    Owen MR, Doran E, Halestrap AP . Evidence that metformin exerts its anti-diabetic effects through inhibition of complex 1 of the mitochondrial respiratory chain. Biochem J 2000; 348: 607–614.

    CAS  Article  Google Scholar 

  9. 9

    Wheaton WW, Weinberg SE, Hamanaka RB, Soberanes S, Sullivan LB, Anso E et al. Metformin inhibits mitochondrial complex I of cancer cells to reduce tumorigenesis. Elife 2014; 3: e02242.

    Article  Google Scholar 

  10. 10

    Konishi H, Mohseni M, Tamaki A, Garay JP, Croessmann S, Karnan S et al. Mutation of a single allele of the cancer susceptibility gene BRCA1 leads to genomic instability in human breast epithelial cells. Proc Natl Acad Sci USA 2011; 108: 17773–17778.

    CAS  Article  Google Scholar 

  11. 11

    Menendez JA, Folguera-Blasco N, Cuyàs E, Fernández-Arroyo S, Joven J, Alarcón T . Accelerated geroncogenesis in hereditary breast-ovarian cancer syndrome. Oncotarget 2016; 7: 11959–11971.

    PubMed  PubMed Central  Google Scholar 

  12. 12

    Cuyàs E, Fernández-Arroyo S, Alarcón T, Lupu R, Joven J, Menendez JA . Germline BRCA1 mutation reprograms breast epithelial cell metabolism towards mitochondrial-dependent biosynthesis: evidence for metformin-based ‘starvation’ strategies in BRCA1 carriers. Oncotarget 2016; 7: 52974–52992.

    Article  Google Scholar 

  13. 13

    Sedic M, Skibinski A, Brown N, Gallardo M, Mulligan P, Martinez P et al. Haploinsufficiency for BRCA1 leads to cell-type-specific genomic instability and premature senescence. Nat Commun 2015; 6: 7505.

    CAS  Article  Google Scholar 

  14. 14

    Fernández-Arroyo S, Cuyàs E, Bosch-Barrera J, Alarcón T, Joven J, Menendez JA . Activation of the methylation cycle in cells reprogrammed into a stem cell-like state. Oncoscience 2016; 2: 958–967.

    PubMed  PubMed Central  Google Scholar 

  15. 15

    De Cecco M, Criscione SW, Peckham EJ, Hillenmeyer S, Hamm EA, Manivannan J et al. Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements. Aging Cell 2013; 12: 247–256.

    CAS  Article  Google Scholar 

  16. 16

    Miousse IR, Koturbash I . The Fine LINE: methylation drawing the cancer landscape. Biomed Res Int 2015; 2015: 131547.

    Article  Google Scholar 

  17. 17

    Kitkumthorn N, Mutirangura A . Long interspersed nuclear element-1 hypomethylation in cancer: biology and clinical applications. Clin Epigenet 2011; 2: 315–330.

    CAS  Article  Google Scholar 

  18. 18

    Pal S, Tyler JK . Epigenetics and aging. Sci Adv 2016; 2: e1600584.

    Article  Google Scholar 

  19. 19

    Mani SA, Guo W, Liao MJ, Eaton EN, Ayyanan A, Zhou AY et al. The epithelial-mesenchymal transition generates cells with properties of stem cells. Cell 2008; 133: 704–715.

    CAS  Article  Google Scholar 

  20. 20

    Gupta PB, Onder TT, Jiang G, Tao K, Kuperwasser C, Weinberg RA et al. Identification of selective inhibitors of cancer stem cells by high-throughput screening. Cell 2009; 138: 645–659.

    CAS  Article  Google Scholar 

  21. 21

    Vazquez-Martin A, Oliveras-Ferraros C, Cufí S, Del Barco S, Martin-Castillo B, Menendez JA . Metformin regulates breast cancer stem cell ontogeny by transcriptional regulation of the epithelial-mesenchymal transition (EMT) status. Cell Cycle 2010; 9: 3807–3814.

    CAS  Article  Google Scholar 

  22. 22

    Cuyàs E, Corominas-Faja B, Menendez JA . The nutritional phenome of EMT-induced cancer stem-like cells. Oncotarget 2014; 5: 3970–3982.

    Article  Google Scholar 

  23. 23

    Banerjee P, Surendran H, Chowdhury DR, Prabhakar K, Pal R . Metformin mediated reversal of epithelial to mesenchymal transition is triggered by epigenetic changes in E-cadherin promoter. J Mol Med (Berl) 2016; 94: 1397–1409.

    CAS  Article  Google Scholar 

  24. 24

    Yang M, Soga T, Pollard PJ . Oncometabolites: linking altered metabolism with cancer. J Clin Invest 2013; 123: 3652–3658.

    CAS  Article  Google Scholar 

  25. 25

    Duncan CG, Barwick BG, Jin G, Rago C, Kapoor-Vazirani P, Powell DR et al. A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation. Genome Res 2012; 22: 2339–2355.

    CAS  Article  Google Scholar 

  26. 26

    Menendez JA, Corominas-Faja B, Cuyàs E, García MG, Fernández-Arroyo S, Fernández AF et al. Oncometabolic nuclear reprogramming of cancer stemness. Stem Cell Rep 2016; 6: 273–283.

    CAS  Article  Google Scholar 

  27. 27

    Viollet B, Guigas B, Sanz Garcia N, Leclerc J, Foretz M, Andreelli F . Cellular and molecular mechanisms of metformin: an overview. Clin Sci (Lond) 2012; 122: 253–270.

    CAS  Article  Google Scholar 

  28. 28

    Foretz M, Guigas B, Bertrand L, Pollak M, Viollet B . Metformin: from mechanisms of action to therapies. Cell Metab 2014; 20: 953–966.

    CAS  Article  Google Scholar 

  29. 29

    Pollak M . Potential applications for biguanides in oncology. J Clin Invest 2013; 123: 3693–3700.

    CAS  Article  Google Scholar 

  30. 30

    Boukalova S, Stursa J, Werner L, Ezrova Z, Cerny J, Bezawork-Geleta A et al. Mitochondrial targeting of metformin enhances its activity against pancreatic cancer. Mol Cancer Ther 2016; 15: 2875–2886.

    CAS  Article  Google Scholar 

  31. 31

    Bridges HR, Sirviö VA, Agip AN, Hirst J . Molecular features of biguanides required for targeting of mitochondrial respiratory complex I and activation of AMP-kinase. BMC Biol 2016; 14: 65.

    Article  Google Scholar 

  32. 32

    Mattaini KR, Sullivan MR, Vander Heiden MG . The importance of serine metabolism in cancer. J Cell Biol 2016; 214: 249–257.

    CAS  Article  Google Scholar 

  33. 33

    Meiser J, Vazquez A . Give it or take it: the flux of one-carbon in cancer cells. FEBS J 2016; 283: 3695–3704.

    CAS  Article  Google Scholar 

  34. 34

    Meiser J, Tumanov S, Maddocks O, Labuschagne CF, Athineos D, Van Den Broek N et al. Serine one-carbon catabolism with formate overflow. Sci Adv 2016; 2: e1601273.

    Article  Google Scholar 

  35. 35

    Locasale JW . Serine, glycine and one-carbon units: cancer metabolism in full circle. Nat Rev Cancer 2013; 13: 572–583.

    CAS  Article  Google Scholar 

  36. 36

    Kotecki M, Reddy PS, Cochran BH . Isolation and characterization of a near-haploid human cell line. Exp Cell Res 1999; 252: 273–280.

    CAS  Article  Google Scholar 

  37. 37

    Essletzbichler P, Konopka T, Santoro F, Chen D, Gapp BV, Kralovics R et al. Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line. Genome Res 2014; 24: 2059–2065.

    CAS  Article  Google Scholar 

  38. 38

    Tan AS, Baty JW, Dong LF, Bezawork-Geleta A, Endaya B, Goodwin J et al. Mitochondrial genome acquisition restores respiratory function and tumorigenic potential of cancer cells without mitochondrial DNA. Cell Metab 2015; 21: 81–94.

    CAS  Article  Google Scholar 

  39. 39

    Cheng G, Zielonka J, Ouari O, Lopez M, McAllister D, Boyle K et al. Mitochondria-targeted analogues of metformin exhibit enhanced antiproliferative and radiosensitizing effects in pancreatic cancer cells. Cancer Res 2016; 76: 3904–1395.

    CAS  Article  Google Scholar 

  40. 40

    Ulanovskaya OA, Zuhl AM, Cravatt BF . NNMT promotes epigenetic remodeling in cancer by creating a metabolic methylation sink. Nat Chem Biol 2013; 9: 300–306.

    CAS  Article  Google Scholar 

  41. 41

    Yang Q, Liang X, Sun X, Zhang L, Fu X, Rogers CJ et al. AMPK/α-ketoglutarate axis dynamically mediates DNA demethylation in the Prdm16 promoter and brown adipogenesis. Cell Metab 2016; 24: 542–554.

    CAS  Article  Google Scholar 

  42. 42

    Kodiha M, Ho-Wo-Cheong D, Stochaj U . Pharmacological AMP-kinase activators have compartment-specific effects on cell physiology. Am J Physiol Cell Physiol 2011; 301: C1307–C1315.

    CAS  Article  Google Scholar 

  43. 43

    Miller RA, Chu Q, Xie J, Foretz M, Viollet B, Birnbaum MJ . Biguanides suppress hepatic glucagon signalling by decreasing production of cyclic AMP. Nature 2013; 494: 256–260.

    CAS  Article  Google Scholar 

  44. 44

    Talarico G, Orecchioni S, Dallaglio K, Reggiani F, Mancuso P, Calleri A et al. Aspirin and atenolol enhance metformin activity against breast cancer by targeting both neoplastic and microenvironment cells. Sci Rep 2016; 6: 18673.

    CAS  Article  Google Scholar 

  45. 45

    Huang X, Wullschleger S, Shpiro N, McGuire VA, Sakamoto K, Woods YL et al. Important role of the LKB1-AMPK pathway in suppressing tumorigenesis in PTEN-deficient mice. Biochem J 2008; 412: 211–221.

    CAS  Article  Google Scholar 

  46. 46

    Houde VP, Ritorto MS, Gourlay R, Varghese J, Davies P, Shpiro N et al. Investigation of LKB1 Ser431 phosphorylation and Cys433 farnesylation using mouse knockin analysis reveals an unexpected role of prenylation in regulating AMPK activity. Biochem J 2014; 458: 41–56.

    CAS  Article  Google Scholar 

  47. 47

    Ross FA, Jensen TE, Hardie DG . Differential regulation by AMP and ADP of AMPK complexes containing different γ subunitisoforms. Biochem J 2016; 473: 189–199.

    CAS  Article  Google Scholar 

  48. 48

    Gravel SP, Hulea L, Toban N, Birman E, Blouin MJ, Zakikhani M et al. Serine deprivation enhances antineoplastic activity of biguanides. Cancer Res 2014; 74: 7521–7533.

    CAS  Article  Google Scholar 

  49. 49

    Liu X, Romero IL, Litchfield LM, Lengyel E, Locasale JW . Metformin targets central carbon metabolism and reveals mitochondrial requirements in human cancers. Cell Metab 2016; 24: 728–739.

    CAS  Article  Google Scholar 

  50. 50

    Maddocks ODK, Athineos D, Cheung EC, Lee P, Zhang T, van den Broek NJF et al. Modulating the therapeutic response of tumours to dietary serine and glycine starvation. Nature 2017; 544: 372–376.

    CAS  Article  Google Scholar 

  51. 51

    Corominas-Faja B, Quirantes-Piné R, Oliveras-Ferraros C, Vazquez-Martin A, Cufí S, Martin-Castillo B et al. Metabolomic fingerprint reveals that metformin impairs one-carbon metabolism in a manner similar to the antifolate class of chemotherapy drugs. Aging (Albany NY) 2012; 4: 480–498.

    CAS  Article  Google Scholar 

  52. 52

    Cabreiro F, Au C, Leung KY, Vergara-Irigaray N, Cochemé HM, Noori T et al. Metformin retards aging in C. elegans by altering microbial folate and methionine metabolism. Cell 2013; 153: 228–239.

    CAS  Article  Google Scholar 

  53. 53

    Newman AC, Maddocks ODK . One-carbon metabolism in cancer. Br J Cancer 2017; 116: 1499–1504.

    CAS  Article  Google Scholar 

  54. 54

    Newman AC, Maddocks ODK . Serine and functional metabolites in cancer. Trends Cell Biol 2017; 27: 645–657.

    CAS  Article  Google Scholar 

  55. 55

    Laderoute KR, Amin K, Calaoagan JM, Knapp M, Le T, Orduna J et al. 5'-AMP-activated protein kinase (AMPK) is induced by low-oxygen and glucose deprivation conditions found in solid-tumor microenvironments. Mol Cell Biol 2006; 26: 5336–5347.

    CAS  Article  Google Scholar 

  56. 56

    Iglesias T, Espina M, Montes-Bayón M, Sierra LM, Blanco-González E . Anion exchange chromatography for the determination of 5-methyl-2'-deoxycytidine: application to cisplatin-sensitive and cisplatin-resistant ovarian cancer cell lines. Anal Bioanal Chem 2015; 407: 2423–2431.

    CAS  Article  Google Scholar 

Download references

Acknowledgements

This work was supported in part by grants from the Ministerio de Ciencia e Innovación (Grant SAF2016-80639-P), Plan Nacional de I+D+I, Spain and the Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR) (Grant 2014 SGR229), Department d’Economia I Coneixement, Catalonia, Spain, to Javier A Menendez and grants from the Czech Science Foundation (16-12816S) to Jan Stursa and Lukas Werner and the Czech Health Research Council (16-31704A) to Jiri Neuzil. Elisabet Cuyàs is supported by a Sara Borrell post-doctoral contract CD15/00033 from the Ministerio de Sanidad y Consumo, Fondo de Investigación Sanitaria (FIS), Spain, The Metabolism and Cancer laboratory is supported by an unrestricted grant from the Armangué family (Girona, Catalonia). This work is in memory of Joan Armangué who passed away after his brave fight against cancer in November 2016.

Author contributions

JAM conceived the idea, directed the project and wrote the manuscript. EC, SF-A, SV, RA-FG, MM-B and EB-G conducted metabolomic, ELISA-/HPLC-based DNA methylation and western blot experiments, and analyzed the data. JS and LW provided essential reagents. JN and BV provided essential reagents, intellectual insights and critical reading of the manuscript.

Author information

Affiliations

Authors

Corresponding author

Correspondence to J A Menendez.

Ethics declarations

Competing interests

The authors declare no conflict of interest.

Additional information

Supplementary Information accompanies this paper on the Oncogene website

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Cuyàs, E., Fernández-Arroyo, S., Verdura, S. et al. Metformin regulates global DNA methylation via mitochondrial one-carbon metabolism. Oncogene 37, 963–970 (2018). https://doi.org/10.1038/onc.2017.367

Download citation

Further reading

Search

Quick links