Skip to main content

Pharmaco-epigenomics: On the Road of Translation Medicine

  • Chapter
  • First Online:

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1168))

Abstract

Epigenomics refers to the study of genome-wide changes in epigenetic mechanisms including DNA methylation, histone modifications and non-coding RNAs expression. The alterations in normal DNA methylation and histone acetylation/deacetylation patterns lead to deregulated transcription and chromatin organization resulting in altered gene expression profiles that facilitates tumor development and progression. In consequence, novel therapeutic strategies aimed at reversing aberrant epigenetic marks in cancer cells have been developed and used in recent molecular studies and clinical trials. Pharmaco-epigenomics is a research area, which refers to the study of epigenome changes in cancer development and how chemotherapeutic agents can reverse these aberrant epigenetic marks by targeting the epigenetic machinery. Besides, the effects of genome-wide polymorphisms in populations leading to variations in drug response are also study subject of pharmaco-epigenomics and are being studied extensively in cancer. Recent findings showed that drug response could be largely influenced by the presence of aberrant epigenetic marks of the whole genome. This implies that biological pathways and cellular processes are under the impact of epigenome status. However, data about the relationship between drug response and the epigenomic variations is still scarce mainly because the epigenome is highly variable between individuals. The present chapter reviewed the advances on the epigenetics changes mainly DNA methylation and histones modifications on cervical and breast human cancers. A special emphasis in how they could be used as targets for the development and use of novel drugs in cancer therapy is delineated.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  1. Luger K, Dechassa ML, Tremethick DJ (2012) New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat Rev Mol Cell Biol 13:436–447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Relling MV, Evans WE (2015) Pharmacogenomics in the clinic. Nature 526:343350

    Article  CAS  Google Scholar 

  3. Marks P, Rifkind RA, Richon VM, Breslow R, Miller T, Kelly WK (2001) Histone deacetylases and cancer: causes and therapies. Nat Rev Cancer 1:194–202

    Article  CAS  PubMed  Google Scholar 

  4. Campos EI, Reinberg D (2009) Histones: annotating chromatin. Annu Rev Genet 43:559–599

    Article  CAS  PubMed  Google Scholar 

  5. Eberharter A, Becker PB (2002) Histone acetylation: a switch between repressive and permissive chromatin. Second in review series on chromatin dynamics. EMBO Rep 3:224–229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Lee KK, Workman JL (2007) Histone acetyltransferase complexes: one size doesn’t fit all. Nat Rev Mol Cell Biol 8:284–295

    Article  CAS  PubMed  Google Scholar 

  7. Barneda-Zahonero B, Parra M (2012) Histone deacetylases and cancer. Mol Oncol 6:579–589

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Ropero S, Esteller M (2007) The role of histone deacetylases (HDACs) in human cancer. Mol Oncol 1:19–25

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144:646–674

    Article  CAS  PubMed  Google Scholar 

  10. Ellis L, Atadja PW, Johnstone RW (2009) Epigenetics in cancer: targeting chromatin modifications. Mol Cancer Therapeutics 8:1409–1420

    Article  CAS  Google Scholar 

  11. Portela A, Esteller M (2010) Epigenetic modifications and human disease. Nat Biotechnol 28:1057–1068

    Article  CAS  PubMed  Google Scholar 

  12. Chen T, Li E (2004) Structure and function of eukaryotic DNA methyltransferases. Curr Top Dev Biol 60:55–89

    Article  CAS  PubMed  Google Scholar 

  13. Goll MG, Kirpekar F, Maggert KA, Yoder JA, Hsieh CL, Zhang X, Golic KG, Jacobsen SE, Bestor TH (2006) Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 311:395–398

    Article  CAS  PubMed  Google Scholar 

  14. Lopez-Serra L, Esteller M (2008) Proteins that bind methylated DNA and human cancer: reading the wrong words. Br J Cancer 98:1881–1885

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Kuroda A, Rauch TA, Todorov I, Ku HT, Al-Abdullah IH, Kandeel F, Mullen Y, Pfeifer GP, Ferreri K (2009) Insulin gene expression is regulated by DNA methylation. PLoS One 4:e6953

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  16. Thomson JP, Skene PJ, Selfridge J, Clouaire T, Guy J, Webb S, Kerr AR, Deaton A, Andrews R, James KD, Turner DJ, Illingworth R, Bird A (2010) CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464:1082–1086

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Esteller M (2008) Epigenetics in cancer. N Engl J Med 358:1148–1159

    Article  CAS  PubMed  Google Scholar 

  18. Saito Y, Kanai Y, Nakagawa T, Sakamoto M, Saito H, Ishii H, Hirohashi S (2003) Increased protein expression of DNA methyltransferase (DNMT) 1 is significantly correlated with the malignant potential and poor prognosis of human hepatocellular carcinomas. Int J Cancer 105:527–532

    Article  CAS  PubMed  Google Scholar 

  19. Peng DF, Kanai Y, Sawada M, Ushijima S, Hiraoka N, Kitazawa S, Hirohashi S (2006) DNA methylation of multiple tumor-related genes in association with overexpression of DNA methyltransferase 1 (DNMT1) during multistage carcinogenesis of the pancreas. Carcinogenesis 27:1160–1168

    Article  CAS  PubMed  Google Scholar 

  20. Zhang W, Xu J (2017) DNA methyltransferases and their roles in tumorigenesis. Biomark Res 5:1

    Article  PubMed  PubMed Central  Google Scholar 

  21. Taby R, Issa JP (2010) Cancer epigenetics. CA Cancer J Clin 60:376–392

    Article  PubMed  Google Scholar 

  22. Fraga MF, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta G, Bonaldi T, Haydon C, Ropero S, Petrie K, Iyer NG, Pérez-Rosado A, Calvo E, Lopez JA, Cano A, Calasanz MJ, Colomer D, Piris MA, Ahn N, Imhof A, Caldas C, Jenuwein T, Esteller M (2005) Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat Genet 37(4):391–400

    Article  CAS  PubMed  Google Scholar 

  23. Seligson DB, Horvath S, Shi T, Yu H, Tze S, Grunstein M, Kurdistani SK (2005) Global histone modification patterns predict risk of prostate cancer recurrence. Nature 30:1262–12666

    Article  CAS  Google Scholar 

  24. Benard A, Goossens-Beumer IJ, van Hoesel AQ, de Graaf W, Horati H, Putter H, Zeestraten EC, van de Velde CJ, Kuppen PJ (2014) Histone trimethylation at H3K4, H3K9 and H4K20 correlates with patient survival and tumor recurrence in early-stage colon cancer. BMC Cancer 14:531

    Article  PubMed  PubMed Central  Google Scholar 

  25. Drummond DC, Noble CO, Kirpotin DB, Guo Z, Scott GK, Benz CC (2005) Clinical development of histone deacetylase inhibitors as anticancer agents. Annu Rev Pharmacol Toxicol 45:495–528

    Article  CAS  PubMed  Google Scholar 

  26. Finnin MS, Donigian JR, Cohen A, Richon VM, Rifkind RA, Marks PA, Breslow R, Pavletich NP (1999) Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature 401:188–193

    Article  CAS  PubMed  Google Scholar 

  27. Richon VV (2006) Cancer biology: mechanism of antitumour action of vorinostat (suberoylanilide hydroxamic acid), a novel histone deacetylase inhibitor. Br J Cancer 95(Suppl 1):S2–S6

    Article  CAS  PubMed Central  Google Scholar 

  28. Richon VM, Sandhoff TW, Rifkind RA, Marks PA (2000) Histone deacetylase inhibitor selectively induces p21WAF1 expression and gene-associated histone acetylation. Proc Natl Acad Sci U S A 97:10014–10019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Sakajiri S, Kumagai T, Kawamata N, Saitoh T, Said JW, Koeffler HP (2005) Histone deacetylase inhibitors profoundly decrease proliferation of human lymphoid cancer cell lines. Exp Hematol 33(1):53–61

    Article  CAS  PubMed  Google Scholar 

  30. Torre LA, Bray F, Siegel RL, Ferlay J, Lortet-Tieulent J, Jemal A (2012) Global cancer statistics. CA Cancer J Clin 65:87–108

    Article  Google Scholar 

  31. Small W Jr, Bacon MA, Bajaj A, Chuang LT, Fisher BJ, Harkenrider MM, Jhingran A, Kitchener HC, Mileshkin LR, Viswanathan AN, Gaffney DK (2017) Cervical cancer: a global health crisis. Cancer 123:2404–2412

    Article  PubMed  Google Scholar 

  32. Woodman CB, Collins SI, Young LS (2007) The natural history of cervical HPV infection: unresolved issues. Nat Rev Cancer 7:11–22

    Article  CAS  PubMed  Google Scholar 

  33. Kim YI, Giuliano A, Hatch KD, Schneider A, Nour MA, Dallal GE, Selhub J, Mason JB (1994) Global DNA hypomethylation increases progressively in cervical dysplasia and carcinoma. Cancer 74:893–899

    Article  CAS  PubMed  Google Scholar 

  34. de Capoa A, Musolino A, Della Rosa S, Caiafa P, Mariani L, Del Nonno F, Vocaturo A, Donnorso RP, Niveleau A, Grappelli C (2003) DNA demethylation is directly related to tumour progression: evidence in normal, pre-malignant and malignant cells from uterine cervix samples. Oncol Rep 10:545–549

    PubMed  Google Scholar 

  35. Wu Q, Shi H, Suo Z, Nesland JM (2003) 5-CpG island methylation of the FHIT gene is associated with reduced protein expression and higher clinical stage in cervical carcinomas. Ultrastruct Pathol 27:417–422

    PubMed  Google Scholar 

  36. Kitkumthorn N, Yanatatsanajit P, Kiatpongsan S, Phokaew C, Triratanachat S, Trivijitsilp P, Termrungruanglert W, Tresukosol D, Niruthisard S, Mutirangura A (2006) Cyclin A1 promoter hypermethylation in human papillomavirus-associated cervical cancer. BMC Cancer 6:55

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  37. Narayan G, Arias-Pulido H, Koul S, Vargas H, Zhang FF, Villella J, Schneider A, Terry MB, Mansukhani M, Murty VV (2003) Frequent promoter methylation of CDH1, DAPK, RARB, and HIC1 genes in carcinoma of cervix uteri: its relationship to clinical outcome. Mol Cancer 2:24

    Article  PubMed  PubMed Central  Google Scholar 

  38. Kuzmin I, Liu L, Dammann R, Geil L, Stanbridge EJ, Wilczynski SP, Lerman MI, Pfeifer GP (2003) Inactivation of RAS association domain family 1A gene in cervical carcinomas and the role of human papillomavirus infection. Cancer Res 63:1888–1893

    CAS  PubMed  Google Scholar 

  39. Ojesina AI, Lichtenstein L, Freeman SS, Pedamallu CS, Imaz-Rosshandler I, Pugh TJ, Cherniack AD, Ambrogio L, Cibulskis K, Bertelsen B, Romero-Cordoba S, Treviño V, Vazquez-Santillan K, Guadarrama AS, Wright AA, Rosenberg MW, Duke F, Kaplan B, Wang R, Nickerson E, Walline HM, Lawrence MS, Stewart C, Carter SL, McKenna A, Rodriguez-Sanchez IP, Espinosa-Castilla M, Woie K, Bjorge L, Wik E, Halle MK, Hoivik EA, Krakstad C, Gabiño NB, Gómez-Macías GS, Valdez-Chapa LD, Garza-Rodríguez ML, Maytorena G, Vazquez J, Rodea C, Cravioto A, Cortes ML, Greulich H, Crum CP, Neuberg DS, Hidalgo-Miranda A, Escareno CR, Akslen LA, Carey TE, Vintermyr OK, Gabriel SB, Barrera-Saldaña HA, Melendez-Zajgla J, Getz G, Salvesen HB, Meyerson M (2014) Landscape of genomic alterations in cervical carcinomas. Nature 506:371–375

    Article  CAS  PubMed  Google Scholar 

  40. Cancer Genome Atlas Research Network, Albert Einstein College of Medicine, Analytical Biological Services, Barretos Cancer Hospital, Baylor College of Medicine et al (2017) Integrated genomic and molecular characterization of cervical cancer. Nature 543:378–384

    Article  CAS  Google Scholar 

  41. Beyer S, Zhu J, Mayr D, Kuhn C, Schulze S, Hofmann S, Dannecker C, Jeschke U, Kost BP (2017) Histone H3 acetyl K9 and histone H3 tri methyl K4 as prognostic markers for patients with cervical cancer. Int J Mol Sci 18:E477

    Article  PubMed  CAS  Google Scholar 

  42. Liu N, Zhao LJ, Li XP, Wang JL, Chai GL, Wei LH (2012) Histone deacetylase inhibitors inducing human cervical cancer cell apoptosis by decreasing DNAmethyltransferase 3B. Chin Med J 125:3273–3278

    CAS  PubMed  Google Scholar 

  43. Li H, Wu X (2004) Histone deacetylase inhibitor, Trichostatin A, activates p21WAF1/CIP1 expression through downregulation of c-myc and release of the repression of c-myc from the promoter in human cervical cancer cells. Biochem Biophys Res Commun 324:860–867

    Article  CAS  PubMed  Google Scholar 

  44. Szalmás A, Kónya J (2009) Epigenetic alterations in cervical carcinogenesis. Semin Cancer Biol 19:144–152

    Article  PubMed  CAS  Google Scholar 

  45. Mukherjee N, Kumar AP, Ghosh R (2015) DNA methylation and flavonoids in genitourinary cancers. Curr Pharmacol Rep 1:112–120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Piyathilake CJ, Badiga S, Kabagambe EK, Azuero A, Alvarez RD, Johanning GL, Partridge EE (2012) A dietary pattern associated with LINE-1 methylation alters the risk of developing cervical intraepithelial neoplasia. Cancer Prev Res (Phila) 5:385–392

    Article  CAS  Google Scholar 

  47. Sundaram MK, Ansari MZ, Mutery AA, Ashraf M, Nasab R, Rai S, Rais N, Hussain A (2017) Genistein induces alterations of epigenetic modulatory signatures in human cervical cancer cells. Anti Cancer Agents Med Chem 18:412–421

    Article  CAS  Google Scholar 

  48. Ali Khan M, Kedhari Sundaram M, Hamza A, Quraishi U, Gunasekera D, Ramesh L, Goala P, Al Alami U, Ansari MZ, Rizvi TA, Sharma C, Hussain A (2015) Sulforaphane reverses the expression of various tumor suppressor genes by targeting DNMT3B and HDAC1 in human cervical Cancer cells. Evid Based Complement Alternat Med 2015:412149

    Article  PubMed  PubMed Central  Google Scholar 

  49. Jha AK, Nikbakht M, Parashar G, Shrivastava A, Capalash N, Kaur J (2010) Reversal of hypermethylation and reactivation of the RARβ2 gene by natural compounds in cervical cancer cell lines. Folia Biol (Praha) 56:195–200

    CAS  Google Scholar 

  50. Ferlay J, Shin HR, Bray F, Forman D, Mathers C, Parkin DM (2010) Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer 127:2893–2917

    Article  CAS  PubMed  Google Scholar 

  51. Schnitt SJ (2010) Classification and prognosis of invasive breast cancer: from morphology to molecular taxonomy. Mod Pathol 23:S60–S64

    Article  PubMed  Google Scholar 

  52. Bernardino J, Roux C, Almeida A, Vogt N, Gibaud A, Gerbault-Seureau M, Magdelenat H, Bourgeois CA, Malfoy B, Dutrillaux B (1997) DNA hypomethylation in breast cancer: an independent parameter of tumor progression? Cancer Genet Cytogenet 97:83–89

    Article  CAS  PubMed  Google Scholar 

  53. Soares J, Pinto AE, Cunha CV, André S, Barão I, Sousa JM, Cravo M (1999) Global DNA hypomethylation in breast carcinoma: correlation with prognostic factors and tumor progression. Cancer 85:112–118

    Article  CAS  PubMed  Google Scholar 

  54. Alves G, Tatro A, Fanning T (1996) Differential methylation of human LINE-1 retrotransposons in malignant cells. Gene 176:39–44

    Article  CAS  PubMed  Google Scholar 

  55. Bera TK, Tsukamoto T, Panda DK, Huang T, Guzman RC, Hwang SI, Nandi S (1998) Defective retrovirus insertion activates c-Ha-ras protooncogene in an MNUinduced rat mammary carcinoma. Biochem Biophys Res Commun 248:835–840

    Article  CAS  PubMed  Google Scholar 

  56. Guo Y, Pakneshan P, Gladu J, Slack A, Szyf M, Rabbani SA (2002) Regulation of DNA methylation in human breast cancer. Effect on the urokinase-type plasminogen activator gene production and tumor invasion. J Biol Chem 277:41571–41579

    Article  CAS  PubMed  Google Scholar 

  57. Weber J, Salgaller M, Samid D, Johnson B, Herlyn M, Lassam N, Treisman J, Rosenberg SA (1994) Expression of the MAGE-1 tumor antigen is upregulated by the demethylating agent 5-aza-2′-deoxycytidine. Cancer Res 54:1766–1771

    CAS  PubMed  Google Scholar 

  58. Gupta A, Godwin AK, Vanderveer L, Lu A, Liu J (2003) Hypomethylation of the synuclein gamma gene CpG island promotes its aberrant expression in breast carcinoma and ovarian carcinoma. Cancer Res 63:664–673

    CAS  PubMed  Google Scholar 

  59. Sharma G, Mirza S, Parshad R, Srivastava A, Datta Gupta S, Pandya P, Ralhan R (2009) CpG hypomethylation of MDR1 gene in tumor and serum of invasive ductal breast carcinoma patients. Clin Biochem 43:373–379

    Article  PubMed  CAS  Google Scholar 

  60. Locke WJ, Clark SJ (2012) Epigenome remodelling in breast cancer: insights from an early in vitro model of carcinogenesis. Breast Cancer Res 14:215

    Article  PubMed  PubMed Central  Google Scholar 

  61. Virmani AK, Rathi A, Sathyanarayana UG, Padar A, Huang CX, Cunnigham HT, Farinas AJ, Milchgrub S, Euhus DM, Gilcrease M, Herman J, Minna JD, Gazdar AF (2001) Aberrant methylation of the adenomatous polyposis coli (APC) gene promoter 1A in breast and lung carcinomas. Clin Cancer Res 7:1998–2004

    CAS  PubMed  Google Scholar 

  62. Martinet N, Michel BY, Bertrand P, Benhida R (2012) Small molecules DNA methyltransferases inhibitors. Med Chem Commun 3:263–273

    Article  CAS  Google Scholar 

  63. Tao Y, Liu S, Briones V, Geiman TM, Muegge K (2011) Treatment of breast cancer cells with DNA demethylating agents leads to a release of Pol II stalling at genes with DNA-hypermethylated regions upstream of TSS. Nucleic Acids Res 39:9508–9520

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Champion C, Guianvarc’h D, Sénamaud-Beaufort C, Jurkowska RZ, Jeltsch A, Ponger L, Arimondo PB, Guieysse-Peugeot AL (2010) Mechanistic insights on the inhibition of c5 DNA methyltransferases by zebularine. PLoS One 5:e12388

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  65. Chen M, Shabashvili D, Nawab A, Yang SX, Dyer LM, Brown KD, Hollingshead M, Hunter KW, Kaye FJ, Hochwald SN, Marquez VE, Steeg P, Zajac-Kaye M (2012) DNA methyltransferase inhibitor, zebularine, delays tumor growth and induces apoptosis in a genetically engineered mouse model of breast cancer. Mol Cancer Ther 11:370–382

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to César López-Camarillo .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

López-Camarillo, C., Gallardo-Rincón, D., Álvarez-Sánchez, M.E., Marchat, L.A. (2019). Pharmaco-epigenomics: On the Road of Translation Medicine. In: Ruiz-Garcia, E., Astudillo-de la Vega, H. (eds) Translational Research and Onco-Omics Applications in the Era of Cancer Personal Genomics. Advances in Experimental Medicine and Biology, vol 1168. Springer, Cham. https://doi.org/10.1007/978-3-030-24100-1_3

Download citation

Publish with us

Policies and ethics