Epigenetic Pharmacology in Precision Oncology: DNA Methyltransferase and Histone-Targeting Therapies from Molecular Mechanisms to Clinical Translation — A Narrative Review
DOI:
https://doi.org/10.68041/medsc.v1i1/03Keywords:
Chromatin Assembly and Disassembly, DNA Methylation, Epigenomics, Histone Deacetylase Inhibitors, Molecular Targeted Therapy, Neoplasms, Precision MedicineAbstract
Epigenetic changes contribute to cancer initiation, progression, and therapeutic resistance, as they control the expression of genes without affecting their DNA sequence. Epigenetic regulators are potential targets for precision oncology as they are involved in the progression of tumors, immune escape, and resistance to therapy, all of which are associated with aberrant DNA methylation and chromatin modifications. DNA methyltransferase (DNMT) inhibitors and histone-targeting drugs like histone deacetylase (HDAC) inhibitors have been clinically beneficial, particularly in hematological malignancies. However, they have a limited number of drawbacks, such as lack of specificity, toxicity, resistance, and lack of predictive biomarkers. With recent developments in multi-omics profiling, single-cell epigenomics, and targeted epigenome editing, more personalized therapeutic strategies are becoming a reality. This narrative review outlines the molecular mechanisms, clinical applications, and drawbacks in the use of DNA methyltransferase and histone-targeting therapies, and introduces novel strategies for patient selection based on biomarkers and for combination therapy. The combination of epigenomic technologies and precision medicine strategies could enable more effective therapeutic strategies and help develop more targeted, more durable types of cancer therapies.
References
1. Kagohara LT, Stein-O’Brien GL, Kelley D, Flam E, Wick HC, Danilova LV, et al. Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. Brief Funct Genomics. 2018;17(1):49-63. https://doi.org/10.1093/bfgp/elx018
2. Pathania AS. Crosstalk between noncoding RNAs and the epigenetics machinery in pediatric tumors and their microenvironment. Cancers (Basel). 2023;15(10):2833. https://doi.org/10.3390/cancers15102833
3. Olawade DB, Rashad I, Egbon E, Teke J, Ovsepian SV, Boussios S. Reversing epigenetic dysregulation in neurodegenerative diseases: mechanistic and therapeutic considerations. Int J Mol Sci. 2025;26(10):4929. https://doi.org/10.3390/ijms26104929
4. Kim DJ. The role of the DNA methyltransferase family and the therapeutic potential of DNMT inhibitors in tumor treatment. Curr Oncol. 2025;32(2):88. https://doi.org/10.3390/curroncol32020088
5. Gu M, Ren B, Fang Y, Ren J, Liu X, Wang X, et al. Epigenetic regulation in cancer. MedComm (2020). 2024;5(2):e495. https://doi.org/10.1002/mco2.495
6. Vatapalli R, Rossi AP, Chan HM, Zhang J. Cancer epigenetic therapy: recent advances, challenges, and emerging opportunities. Epigenomics. 2025;17(1):59-74. https://doi.org/10.1080/17501911.2024.2430169
7. Iyer KA, Koynova-Tenchov R, Sasso JM, Thite T, Deng Y, Zhou QA. The future of epigenetics: emerging technologies and clinical applications. ACS Pharmacol Transl Sci. 2026;9(3):506-544. https://doi.org/10.1021/acsptsci.5c00729
8. Jamalinia M, Weiskirchen R. Advances in personalized medicine: translating genomic insights into targeted therapies for cancer treatment. Ann Transl Med. 2025;13(2):18. https://doi.org/10.21037/atm-25-34
9. Yousaf A, Ali F. Novel Insights into Preclinical Oncology: Can Blood-Based Genomics Predict Cancer Years in Advance?. Al Najam J Med Life Sci. 2026;1(2):1-3. https://doi.org/10.68041/anjmls.v1i2/01
10. Bouyahya A, Mechchate H, Oumeslakht L, Zeouk I, Aboulaghras S, Balahbib A, et al. The role of epigenetic modifications in human cancers and the use of natural compounds as epidrugs: mechanistic pathways and pharmacodynamic actions. Biomolecules. 2022;12(3):367. https://doi.org/10.3390/biom12030367
11. Zhang X, Zhou Y, Liu Y, Li B, Tian S, Zhang Z. Research progress on the mechanism and function of histone acetylation regulating the interaction between pathogenic fungi and plant hosts. J Fungi (Basel). 2024;10(8):522. https://doi.org/10.3390/jof10080522
12. Wang J, Wang GG. No easy way out for EZH2: its pleiotropic, noncanonical effects on gene regulation and cellular function. Int J Mol Sci. 2020;21(24):9501. https://doi.org/10.3390/ijms21249501
13. Fagbemi OA, Ojo-Omoniyi DS, Bassey SI, Ogbozor FI, Onyeyili IN, Okei NC, et al. Epigenetic therapies in cancer treatment: opportunities and challenges. World J Biol Pharm Health Sci. 2024;20(3):454-478. https://doi.org/10.30574/wjbphs.2024.20.3.1052
14. Lin L, Liu Y. Advances in epigenomic sequencing and their applications in cancer diagnostics. Precis Chem. 2025;3(10):581-603. https://doi.org/10.1021/prechem.5c00014
15. Short NJ, Dombret H, Adès L, Kantarjian H. The evolution of research and therapy with hypomethylating agents in acute myeloid leukemia and myelodysplastic syndrome: new directions for old drugs. Cancer J. 2022;28(1):29-36. https://doi.org/10.1097/PPO.0000000000000568
16. Kalinkova L, Sevcikova A, Stevurkova V, Fridrichova I, Ciernikova S. Targeting DNA methylation in leukemia, myelodysplastic syndrome, and lymphoma: a potential diagnostic, prognostic, and therapeutic tool. Int J Mol Sci. 2023;24(1):633. https://doi.org/10.3390/ijms24010633
17. Parveen R, Harihar D, Chatterji BP. Recent histone deacetylase inhibitors in cancer therapy. Cancer. 2023;129(21):3372-3380. https://doi.org/10.1002/cncr.34974
18. Julia E, Salles G. EZH2 inhibition by tazemetostat: mechanisms of action, safety and efficacy in relapsed/refractory follicular lymphoma. Future Oncol. 2021;17(17):2127-2140. https://doi.org/10.2217/fon-2020-1244
19. Morschhauser F, Tilly H, Chaidos A, McKay P, Phillips T, Assouline S, et al. Tazemetostat for patients with relapsed or refractory follicular lymphoma: an open-label, single-arm, multicentre, phase 2 trial. Lancet Oncol. 2020;21(11):1433-1442. https://doi.org/10.1016/S1470-2045(20)30441-1
20. Bhat KP, Kaniskan HÜ, Jin J, Gozani O. Epigenetics and beyond: targeting writers of protein lysine methylation to treat disease. Nat Rev Drug Discov. 2021;20(4):265-286. https://doi.org/10.1038/s41573-020-00108-x
21. Zhang J, Yang C, Wu C, Cui W, Wang L. DNA methyltransferases in cancer: biology, paradox, aberrations, and targeted therapy. Cancers (Basel). 2020;12(8):2123. https://doi.org/10.3390/cancers12082123
22. Sato T, Issa JPJ, Kropf P. DNA hypomethylating drugs in cancer therapy. Cold Spring Harb Perspect Med. 2017;7(5):a026948. https://doi.org/10.1101/cshperspect.a026948
23. Rembiałkowska N, Rekiel K, Urbanowicz P, Mamala M, Marczuk K, Wojtaszek M, et al. Epigenetic dysregulation in cancer: implications for gene expression and DNA repair-associated pathways. Int J Mol Sci. 2025;26(13):6531. https://doi.org/10.3390/ijms26136531
24. Wenger V, Garcia-Manero G, Zeiser R, Lübbert M. DNA methyltransferase inhibitors in hematological malignancies and solid tumors. Int J Cancer. 2026;158(2):433-461. https://doi.org/10.1002/ijc.70197
25. Vänttinen I, Saad J, Ruokoranta T, Kytölä S, Qin G, Tercan B, et al. Drivers of clinical resistance to venetoclax and hypomethylating agents in acute myeloid leukemia and strategies for improving efficacy. HemaSphere. 2026;10(1):e70282. https://doi.org/10.1002/hem3.70282
26. Bulygin AA, Davletgildeeva AT, Kuznetsov NA. Recent advances in searching for DNMT inhibitors and their potential application in treating human diseases. Int J Mol Sci. 2026;27(10):4560. https://doi.org/10.3390/ijms27104560
27. Lai TJ, Prins RM, Everson RG. Epigenetic reprogramming with DNMT inhibitors: a multi-mechanistic approach to enhance immunotherapy in glioblastoma. J Cancer Immunol (Wilmington). 2025;7(1):39-44. https://doi.org/10.33696/cancerimmunol.7.103
28. Huang Z, Hu L, Liu Z, Wang S. The functions and regulatory mechanisms of histone modifications in skeletal muscle development and disease. Int J Mol Sci. 2025;26(8):3644. https://doi.org/10.3390/ijms26083644
29. Milazzo G, Mercatelli D, Di Muzio G, Triboli L, De Rosa P, Perini G, et al. Histone deacetylases (HDACs): evolution, specificity, role in transcriptional complexes, and pharmacological actionability. Genes (Basel). 2020;11(5):556. https://doi.org/10.3390/genes11050556
30. Kavanaugh SM, White LA, Kolesar JM. Vorinostat: a novel therapy for the treatment of cutaneous T-cell lymphoma. Am J Health Syst Pharm. 2010;67(10):793-797. https://doi.org/10.2146/ajhp090247
31. Smolewski P, Robak T. The discovery and development of romidepsin for the treatment of T-cell lymphoma. Expert Opin Drug Discov. 2017;12(8):859-873. https://doi.org/10.1080/17460441.2017.1341487
32. Yudaev P, Aleksandrova Y, Neganova M. Current research in polypharmacology for cancer treatment using dual-target histone deacetylase inhibitors. Int J Mol Sci. 2026;27(15):6604. https://doi.org/10.3390/ijms27156604
33. Liu X, Yang H, Liu X, Mou M, Liu J, Yan W, et al. Discovery of selective HDAC6 inhibitors driven by artificial intelligence and molecular dynamics simulation approaches. J Pharm Anal. 2025;15(8):101338. https://doi.org/10.1016/j.jpha.2025.101338
34. Moraitis S, Piperi C. Multi-faceted role of histone methyltransferase enhancer of zeste 2 (EZH2) in neuroinflammation and emerging targeting options. Biology (Basel). 2025;14(7):749. https://doi.org/10.3390/biology14070749
35. Wu M, Guan G, Yin H, Niu Q. A review of the bromodomain and extraterminal domain epigenetic reader proteins: function on virus infection and cancer. Viruses. 2024;16(7):1096. https://doi.org/10.3390/v16071096
36. Srivastava R, Singh R, Jauhari S, Lodhi N, Srivastava R. Histone demethylase modulation: epigenetic strategy to combat cancer progression. Epigenomes. 2023;7(2):10. https://doi.org/10.3390/epigenomes7020010
37. Han R, Zhou H, Peng B, Yu S, Zhu J, Chen J. Synergistic integration of HDAC inhibitors and individualized neoantigen therapy (INT): a next-generation combinatorial approach for cancer immunotherapy. Vaccines (Basel). 2025;13(6):550. https://doi.org/10.3390/vaccines13060550
38. Baretti M, Yarchoan M. Epigenetic modifiers synergize with immune-checkpoint blockade to enhance long-lasting antitumor efficacy. J Clin Invest. 2021;131(16):e151002. https://doi.org/10.1172/JCI151002
39. Chaudhary A, Orchard KJA, Salani F, Partsou T, Eccleston M, Bocci G, et al. Precision epigenetic therapies in oncology. Cancer Metastasis Rev. 2025;44(4):71. https://doi.org/10.1007/s10555-025-10288-w
40. Baylin SB, Jones PA. Epigenetic determinants of cancer. Cold Spring Harb Perspect Biol. 2016;8(9):a019505. https://doi.org/10.1101/cshperspect.a019505
41. Xu B, Konze KD, Jin J, Wang GG. Targeting EZH2 and PRC2 dependence as novel anticancer therapy. Exp Hematol. 2015;43(8):698-712. https://doi.org/10.1016/j.exphem.2015.05.001
42. Das S. DNA methylation profiling in central nervous system tumors: where do we draw the line of clinical utility? World J Exp Med. 2026;16(1):115070. https://doi.org/10.5493/wjem.v16.i1.115070
43. Lo PK, Zhou Q. Emerging techniques in single-cell epigenomics and their applications to cancer research. J Clin Genom. 2018;1(1):10.4172/JCG.1000103. https://doi.org/10.4172/JCG.1000103
44. Mukherjee S, Khatun R, Sengupta S, Bhattacharya M. Artificial intelligence: in precision medicine. Int J Adv Res Eng Technol. 2025;16(2):356-375. https://doi.org/10.34218/IJARET_16_02_022
45. Majchrzak-Celińska A, Warych A, Szoszkiewicz M. Novel approaches to epigenetic therapies: from drug combinations to epigenetic editing. Genes (Basel). 2021;12(2):208. https://doi.org/10.3390/genes12020208
46. Wu Q, Nie DY, Ba-alawi W, Ji Y, Zhang Z, Cruickshank J, et al. PRMT inhibition induces a viral mimicry response in triple-negative breast cancer. Nat Chem Biol. 2022;18(8):821-830. https://doi.org/10.1038/s41589-022-01024-4
47. Carter J, Hulse M, Sivakumar M, Burtell J, Thodima V, Wang M, et al. PRMT5 inhibitors regulate DNA damage repair pathways in cancer cells and improve response to PARP inhibition and chemotherapies. Cancer Res Commun. 2023;3(11):2233-2243. https://doi.org/10.1158/2767-9764.CRC-23-0070
48. Chen J, Tang P, Wang Y, Wang J, Yang C, Li Y, et al. Targeting bromodomain-selective inhibitors of BET proteins in drug discovery and development. J Med Chem. 2022;65(7):5184-5211. https://doi.org/10.1021/acs.jmedchem.1c01835
49. Shen L, Wang B, Wang SP, Ji SK, Fu MJ, Wang SW, et al. Combination therapy and dual-target inhibitors based on LSD1: new emerging tools in cancer therapy. J Med Chem. 2024;67(2):922-951. https://doi.org/10.1021/acs.jmedchem.3c02133
50. Guan A, Quek C. Single-cell multi-omics: insights into therapeutic innovations to advance treatment in cancer. Int J Mol Sci. 2025;26(6):2447. https://doi.org/10.3390/ijms26062447
51. Wang D, Zhang Y, Li Q, Li Y, Li W, Zhang A, et al. Epigenetics: mechanisms, potential roles, and therapeutic strategies in cancer progression. Genes Dis. 2024;11(5):101020. https://doi.org/10.1016/j.gendis.2023.04.040
52. Mazhar N, Khan MA, Majeed A, Zafar K. Mitochondrial DNA Mutations and Oxidative Phosphorylation Reprogramming in Colorectal Cancer and Breast Cancer: Systematic Review of Distinct Mitochondrial Mechanisms in Tumor Progressions. Al Najam J Med Life Sci. 2026;1(2):49–55. https://doi.org/10.68041/anjmls.v1i1/08
53. Zhang H, Pang Y, Yi L, Wang X, Wei P, Wang H, et al. Epigenetic regulators combined with tumour immunotherapy: current status and perspectives. Clin Epigenet. 2025;17(1):51. https://doi.org/10.1186/s13148-025-01856-6
54. Khawaja A, Jehangir AM. Beyond PD-1/PD-L1: TME-Targeted Therapies in the Era of Immunotherapy Resistance. J Biomol Pathog Ther. 2026;2(1):1-3. https://doi.org/10.68041/jbpt.v2i1/06
55. MacDonald WJ, Purcell C, Pinho-Schwermann M, Stubbs NM, Srinivasan PR, El-Deiry WS. Heterogeneity in cancer. Cancers (Basel). 2025;17(3):441. https://doi.org/10.3390/cancers17030441
56. Feinberg AP, Levchenko A. Epigenetics as a mediator of plasticity in cancer. Science. 2023;379(6632):eaaw3835. https://doi.org/10.1126/science.aaw3835
57. Yuan L, Xiong Y, Zhang Y, Gu S, Lei Y. Epigenome editing based treatment: progresses and challenges. Mol Ther. 2026;34(1):46-67. https://doi.org/10.1016/j.ymthe.2025.08.047
58. Acharya D, Mukhopadhyay A. A comprehensive review of machine learning techniques for multi-omics data integration: challenges and applications in precision oncology. Brief Funct Genomics. 2024;23(5):549-560. https://doi.org/10.1093/bfgp/elae013
59. Lu T, Ang CE, Zhuang X. Spatially resolved epigenomic profiling of single cells in complex tissues. Cell. 2022;185(23):4448-4464.e17. https://doi.org/10.1016/j.cell.2022.09.035
Downloads
Published
Issue
Section
License
Copyright (c) 2026 Khalida Rizwan, Zafar Junaid (Author)

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
MSAR Medical Sciences (MSAR MS) follows the Attribution Creative Commons-Non commercial (CC BY-NC 4.0) license which allows the users to copy and redistribute the material in any medium or format, remix, transform and build upon the material. The users must give credit to the source and indicate, provide a link to the license, and indicate if changes were made. However, the CC BY-NC 4.0 license restricts the use of material for commercial purposes (Further details are available at website. The Editorial Board of the MSAR MS endeavors to ensure the accuracy, integrity, and quality of all published content. However, the responsibility of opinions, interpretations, and conclusions expressed in the published articles rests entirely with the authors and do not necessarily reflect the views of the Editorial Board, publisher, or affiliated institutions.