# The molecular mechanisms and potential therapeutic implications of the crosstalk between DNA methylation and metabolic reprogramming in thyroid cancer

**Authors:** Tianying Zhang, Hengtong Han, Yating Zhang, Tingting Zhang, Libin Ma, Ze Yang, Yong-xun Zhao

PMC · DOI: 10.1038/s41420-026-02981-8 · 2026-02-25

## TL;DR

This paper explores how DNA methylation and metabolic changes work together in thyroid cancer, offering new insights for better treatments.

## Contribution

The paper introduces a new theoretical framework called the 'DNA methylation-metabolism axis' to explain their crosstalk in thyroid cancer.

## Key findings

- DNA methylation and metabolic reprogramming form a self-reinforcing cycle in thyroid cancer.
- Metabolic changes influence DNA methylation through metabolites like SAM and α-KG.
- DNA methylation silences genes involved in metabolism and thyroid function, promoting tumor growth.

## Abstract

One of the fastest-growing malignant tumors in the world is thyroid cancer (TC), and there are currently no effective treatments for its aggressive subtypes, such as anaplastic carcinoma and radioactive iodine-refractory differentiated thyroid carcinoma. Recent investigations have shown that DNA methylation and metabolic reprogramming are not independent events, but rather create a closely interconnected, mutually reinforcing network of carcinogenic processes. On the one hand, metabolic reprogramming influences the methylation status of tumor suppressor genes and thyroid function genes by dynamically regulating the activity of DNA methyltransferases and demethylases through important metabolites (such as S-adenosylmethionine, or SAM, and α-KG) and oncogenic signaling pathways (like PI3K/AKT). Conversely, DNA methylation systematically remodels cellular glucose, lipid, and amino acid metabolism by directly silencing metabolic enzyme genes (such as FASN and GLS) and thyroid differentiation markers (such as NIS) to fulfill its proliferative demands. Tumor growth, treatment resistance, and the development of an immunosuppressive microenvironment are all fueled by this ongoing bidirectional interaction, which creates a self-reinforcing oncogenic cycle. As a result, the limitations of earlier discrete debates on DNA methylation or metabolic reprogramming are overcome in this review. To methodically clarify their crosstalk mechanisms, a theoretical framework based on the “DNA methylation-metabolism axis” is suggested. Additionally, it suggests multimodal therapy approaches that focus on this axis. Incorporating biomimetic delivery technologies, combined with epigenetic, metabolic, and immunotherapies, to lay the groundwork for comprehending TC causes and creating targeted treatments.

## Linked entities

- **Genes:** FASN (fatty acid synthase) [NCBI Gene 2194], GLS (glutaminase) [NCBI Gene 2744], SLC5A5 (solute carrier family 5 member 5) [NCBI Gene 6528]
- **Chemicals:** S-adenosylmethionine (PubChem CID 34755), α-KG (PubChem CID 51)
- **Diseases:** thyroid cancer (MONDO:0002108), anaplastic carcinoma (MONDO:0005617)

## Full-text entities

- **Genes:** BRAF (B-Raf proto-oncogene, serine/threonine kinase) [NCBI Gene 673] {aka B-RAF1, B-raf, BRAF-1, BRAF1, NS7, RAFB1}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, PTEN (phosphatase and tensin homolog) [NCBI Gene 5728] {aka 10q23del, BZS, CWS1, DEC, GLM2, MHAM}, DNMT3B (DNA methyltransferase 3 beta) [NCBI Gene 1789] {aka FSHD4, ICF, ICF1, M.HsaIIIB}, CDKN2A (cyclin dependent kinase inhibitor 2A) [NCBI Gene 1029] {aka ARF, CAI2, CDK4I, CDKN2, CMM2, INK4}, ACLY (ATP citrate lyase) [NCBI Gene 47] {aka ACL, ATPCL, CLATP}, PGK1 (phosphoglycerate kinase 1) [NCBI Gene 5230] {aka HEL-S-68p, MIG10, PGKA}, RET (ret proto-oncogene) [NCBI Gene 5979] {aka CDHF12, CDHR16, HSCR1, MEN2A, MEN2B, MTC1}, TET1 (tet methylcytosine dioxygenase 1) [NCBI Gene 80312] {aka CXXC6, LCX, bA119F7.1}, MLH1 (mutL homolog 1) [NCBI Gene 4292] {aka COCA2, FCC2, HNPCC, HNPCC2, LYNCH2, MLH-1}, TSHR (thyroid stimulating hormone receptor) [NCBI Gene 7253] {aka CHNG1, LGR3, hTSHR-I}, DNMT3A (DNA methyltransferase 3 alpha) [NCBI Gene 1788] {aka DNMT3A2, HESJAS, M.HsaIIIA, TBRS}, SLC1A3 (solute carrier family 1 member 3) [NCBI Gene 6507] {aka EA6, EAAT1, GLAST, GLAST1}, NFKB1 (nuclear factor kappa B subunit 1) [NCBI Gene 4790] {aka CVID12, EBP-1, KBF1, NF-kB, NF-kB1, NF-kappa-B1}, ZNF281 (zinc finger protein 281) [NCBI Gene 23528] {aka GZP1, ZBP-99, ZBP99, ZNP-99}, MECP2 (methyl-CpG binding protein 2) [NCBI Gene 4204] {aka AUTSX3, MRX16, MRX79, MRXS13, MRXSL, PPMX}, SFRP1 (secreted frizzled related protein 1) [NCBI Gene 6422] {aka FRP, FRP-1, FRP1, FrzA, SARP2}, SREBF1 (sterol regulatory element binding transcription factor 1) [NCBI Gene 6720] {aka HMD, IFAP2, SREBP1, bHLHd1}, ZHX2 (zinc fingers and homeoboxes 2) [NCBI Gene 22882] {aka AFR1, RAF}, PLAU (plasminogen activator, urokinase) [NCBI Gene 5328] {aka ATF, BDPLT5, QPD, UPA, URK, u-PA}, PPARGC1A (PPARG coactivator 1 alpha) [NCBI Gene 10891] {aka LEM6, PGC-1(alpha), PGC-1alpha, PGC-1v, PGC1, PGC1A}, LPL (lipoprotein lipase) [NCBI Gene 4023] {aka HDLCQ11, LIPD}, MAP2K7 (mitogen-activated protein kinase kinase 7) [NCBI Gene 5609] {aka JNKK2, MAPKK7, MEK, MEK 7, MKK7, PRKMK7}, PDCD1 (programmed cell death 1) [NCBI Gene 5133] {aka ADMIO4, AIMTBS, CD279, PD-1, PD1, SLEB2}, INS (insulin) [NCBI Gene 3630] {aka IDDM, IDDM1, IDDM2, ILPR, IRDN, MODY10}, ACACB (acetyl-CoA carboxylase beta) [NCBI Gene 32] {aka ACACbeta, ACC-beta, ACC2, ACCB, ACCbeta, HACC275}, FAM111B (FAM111 trypsin like peptidase B) [NCBI Gene 374393] {aka CANP, POIKTMP}, HOXD10 (homeobox D10) [NCBI Gene 3236] {aka HOX4, HOX4D, HOX4E, Hox-4.4}, PKM (pyruvate kinase M1/2) [NCBI Gene 5315] {aka CTHBP, HEL-S-30, OIP3, PK3, PKM2, TCB}, Sting1 (stimulator of interferon response cGAMP interactor 1) [NCBI Gene 72512] {aka 2610307O08Rik, ERIS, MPYS, Mita, STING, STING-beta}, TDG (thymine DNA glycosylase) [NCBI Gene 6996] {aka hTDG}, MAPK10 (mitogen-activated protein kinase 10) [NCBI Gene 5602] {aka JNK3, JNK3A, PRKM10, SAPK1b, p493F12, p54bSAPK}, STAT3 (signal transducer and activator of transcription 3) [NCBI Gene 6774] {aka ADMIO, ADMIO1, APRF, HIES}, MYC (MYC proto-oncogene, bHLH transcription factor) [NCBI Gene 4609] {aka MRTL, MYCC, bHLHe39, c-Myc}, BAX (BCL2 associated X, apoptosis regulator) [NCBI Gene 581] {aka BCL2L4}, SLC7A11 (solute carrier family 7 member 11) [NCBI Gene 23657] {aka CCBR1, xCT}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, CPT1A (carnitine palmitoyltransferase 1A) [NCBI Gene 1374] {aka CPT I, CPT1, CPT1-L, CPTI-L, L-CPT1}, TG (thyroglobulin) [NCBI Gene 7038] {aka AITD3, TGN}, SLC5A5 (solute carrier family 5 member 5) [NCBI Gene 6528] {aka NIS, TDH1}, HK1 (hexokinase 1) [NCBI Gene 3098] {aka CNSHA5, HK, HK1-ta, HK1-tb, HK1-tc, HKD}, SHMT1 (serine hydroxymethyltransferase 1) [NCBI Gene 6470] {aka CSHMT, SHMT, hcSHMT}, LDHA (lactate dehydrogenase A) [NCBI Gene 3939] {aka GSD11, HEL-S-133P, LDHM, PIG19}, TET2 (tet methylcytosine dioxygenase 2) [NCBI Gene 54790] {aka IMD75, KIAA1546, MDS}, FABP4 (fatty acid binding protein 4) [NCBI Gene 2167] {aka A-FABP, AFABP, ALBP, HEL-S-104, aP2}, PHGDH (phosphoglycerate dehydrogenase) [NCBI Gene 26227] {aka 3-PGDH, 3PGDH, HEL-S-113, NLS, NLS1, PDG}, CEBPA (CCAAT enhancer binding protein alpha) [NCBI Gene 1050] {aka C/EBP-alpha, CEBP}, NGFR (nerve growth factor receptor) [NCBI Gene 4804] {aka CD271, Gp80-LNGFR, TNFRSF16, p75(NTR), p75NTR}, G6PD (glucose-6-phosphate dehydrogenase) [NCBI Gene 2539] {aka CNSHA1, G6PD1}, ND6 (NADH dehydrogenase subunit 6) [NCBI Gene 4541] {aka MTND6}, Mdk (midkine) [NCBI Gene 17242] {aka MK, Mek}, CCND1 (cyclin D1) [NCBI Gene 595] {aka BCL1, D11S287E, PRAD1, U21B31}, GLS (glutaminase) [NCBI Gene 2744] {aka AAD20, CASGID, DEE71, EIEE71, GAC, GAM}, HIF1A (hypoxia inducible factor 1 subunit alpha) [NCBI Gene 3091] {aka HIF-1-alpha, HIF-1A, HIF-1alpha, HIF1, HIF1-ALPHA, MOP1}, LEP (leptin) [NCBI Gene 3952] {aka LEPD, OB, OBS}, DNMT1 (DNA methyltransferase 1) [NCBI Gene 1786] {aka ADCADN, AIM, CXXC9, DNMT, HSN1E, MCMT}, ACACA (acetyl-CoA carboxylase alpha) [NCBI Gene 31] {aka ACAC, ACACAD, ACACalpha, ACC, ACC1, ACCA}, SLC1A5 (solute carrier family 1 member 5) [NCBI Gene 6510] {aka AAAT, ASCT2, ATBO, M7V1, M7VS1, R16}, CIDEA (cell death inducing DFFA like effector a) [NCBI Gene 1149] {aka CIDE-A}, CDH1 (cadherin 1) [NCBI Gene 999] {aka Arc-1, BCDS1, CD324, CDHE, ECAD, LCAM}
- **Diseases:** MTC (MESH:C536914), metabolic diseases (MESH:D008659), hypoxia (MESH:D000860), hepatic steatosis (MESH:D005234), Hypoxic (MESH:D002534), gastric cancer (MESH:D013274), PTC (MESH:D000077273), fatigue (MESH:D005221), cholangiocarcinomas (MESH:D018281), carcinogenesis (MESH:D063646), retinopathy (MESH:D058437), ATC (MESH:D065646), Tumor (MESH:D009369), anaplastic carcinoma (MESH:D002277), melanoma (MESH:D008545), glioma (MESH:D005910), oral ulcers (MESH:D019226), undifferentiated and poorly differentiated (MESH:D020522), necrotic (MESH:D009336), thymic cancer (MESH:D013953), type 2 diabetes (MESH:D003924), breast cancer (MESH:D001943), lymph node metastasis (MESH:D008207), uveal melanoma (MESH:C536494), loss of appetite (MESH:D001068), iodine uptake disorder (MESH:D003409), T-ALL (MESH:D054218), bone marrow suppression (MESH:D001855), cytotoxic (MESH:D064420), metastasis (MESH:D009362), carcinogenic (MESH:D011230), deaths (MESH:D003643), TC (MESH:D013964), hypertension (MESH:D006973), colorectal cancer (MESH:D015179)
- **Chemicals:** etomidate (MESH:D005045), Decitabine (MESH:D000077209), leucine (MESH:D007930), 5-methylcytosine (MESH:D044503), acetyl coenzyme A (MESH:D000105), trametinib (MESH:C560077), S-adenosylmethionine (MESH:D012436), lactate (MESH:D019344), 2-DG (MESH:D003847), pentose phosphate (MESH:D010428), vemurafenib (MESH:D000077484), carbon (MESH:D002244), pyruvate (MESH:D019289), D-2-HG (MESH:C019417), proline (MESH:D011392), temsirolimus (MESH:C401859), LiCl (MESH:D018021), Azacitidine (MESH:D001374), Glucose (MESH:D005947), reactive oxygen species (MESH:D017382), CB-839 (MESH:C000593334), MG (MESH:D011765), ATP (MESH:D000255), sodium butyrate (MESH:D020148), glutamine (MESH:D005973), GSH (MESH:D005978), Dabrafenib (MESH:C561627), Lipid (MESH:D008055), LPS (MESH:D008070), JPH203 (MESH:C548172), palmitic acid (MESH:D019308), lenvatinib (MESH:C531958), iodine (MESH:D007455), purine (MESH:C030985), 5-formylcytosine (MESH:C560973), AZD3965 (MESH:C000592351), Amino acid (MESH:D000596), Iodine-131 (MESH:C000614965), 5-carboxylcytosine (MESH:C560974), NADPH (MESH:D009249), pembrolizumab (MESH:C582435), Serine (MESH:D012694), TCA (MESH:D014238), carbohydrate (MESH:D002241), fatty acid (MESH:D005227), MUFAs (MESH:D005229), selumetinib (MESH:C517975), Ldyyyn2020-98 (-), alpha-ketoglutarate (MESH:D007656), Tg (MESH:D013866), 5-hydroxymethylcytosine (MESH:C011865), everolimus (MESH:D000068338)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** B-RafV600E, serine-glycine, C5 position of cytosine
- **Cell lines:** DRO — Homo sapiens (Human), Amelanotic melanoma, Cancer cell line (CVCL_6286), 2-7 — Mus musculus (Mouse), Hybridoma (CVCL_C6KD)

## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12966297/full.md

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Source: https://tomesphere.com/paper/PMC12966297