Prostate Cancer Epigenetic Biomarkers: Next-generation Technologies

Overview

Journal Oncogene

Specialties Molecular Biology
Oncology

Date 2014 May 20

PMID 24837368

Citations 28

Authors

F Valdes-Mora

S J Clark

Affiliations

Soon will be listed here.

Abstract

Cancer is caused by a combination of genetic alterations and gross changes to the epigenetic landscape that together result in aberrant cancer gene regulation. Therefore, we need to fully sequence both the cancer genome and the matching cancer epigenomes before we can fully integrate the suite of molecular mechanisms involved in initiation and progression of cancer. A further understanding of epigenetic aberrations has a great potential in the next era of molecular genomic pathology in cancer detection and treatment in all types of cancer, including prostate cancer. In this review, we discuss the most common epigenetic aberrations identified in prostate cancer with the biomarker potential. We also describe the innovative and current epigenomic technologies used for the identification of epigenetic-associated changes in prostate cancer and future translational applications in molecular pathology for cancer detection and prognosis.

Citing Articles

A Model to Predict Prognosis of Renal Cell Clear Cell Carcinoma Based on 3 Angiogenesis-related Long Non-coding RNAs.

Chen G, Zhang T, Li F, Cui C, Huang Z, Gou X J Cancer. 2024; 15(11):3481-3494.

PMID: 38817877 PMC: 11134422. DOI: 10.7150/jca.94685.

Lineage Plasticity and Stemness Phenotypes in Prostate Cancer: Harnessing the Power of Integrated "Omics" Approaches to Explore Measurable Metrics.

Logotheti S, Papadaki E, Zolota V, Logothetis C, Vrahatis A, Soundararajan R Cancers (Basel). 2023; 15(17).

PMID: 37686633 PMC: 10486655. DOI: 10.3390/cancers15174357.

Prostate cancer in omics era.

Gholami N, Haghparast A, Alipourfard I, Nazari M Cancer Cell Int. 2022; 22(1):274.

PMID: 36064406 PMC: 9442907. DOI: 10.1186/s12935-022-02691-y.

The Role of Epigenetics in the Progression of Clear Cell Renal Cell Carcinoma and the Basis for Future Epigenetic Treatments.

Angulo J, Manini C, Lopez J, Pueyo A, Colas B, Ropero S Cancers (Basel). 2021; 13(9).

PMID: 33922974 PMC: 8123355. DOI: 10.3390/cancers13092071.

Integrative Analysis of Methylation and Copy Number Variations of Prostate Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis.

Hou Y, Hu J, Zhou L, Liu L, Chen K, Yang X Front Oncol. 2021; 11:647253.

PMID: 33869043 PMC: 8047072. DOI: 10.3389/fonc.2021.647253.

References

Robinson M, Stirzaker C, Statham A, Coolen M, Song J, Nair S . Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res. 2010; 20(12):1719-29. PMC: 2989998. DOI: 10.1101/gr.110601.110. View

Ruijter E, Van De Kaa C, Schalken J, Debruyne F, Ruiter D . Histological grade heterogeneity in multifocal prostate cancer. Biological and clinical implications. J Pathol. 1996; 180(3):295-9. DOI: 10.1002/(SICI)1096-9896(199611)180:3<295::AID-PATH663>3.0.CO;2-W. View

Wu H, Zhang Y . Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev. 2011; 25(23):2436-52. PMC: 3243055. DOI: 10.1101/gad.179184.111. View

Bae J . Perspectives of international human epigenome consortium. Genomics Inform. 2013; 11(1):7-14. PMC: 3630389. DOI: 10.5808/GI.2013.11.1.7. View

Prensner J, Rubin M, Wei J, Chinnaiyan A . Beyond PSA: the next generation of prostate cancer biomarkers. Sci Transl Med. 2012; 4(127):127rv3. PMC: 3799996. DOI: 10.1126/scitranslmed.3003180. View

Irizarry R, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg S, Jeddeloh J . Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 2008; 18(5):780-90. PMC: 2336799. DOI: 10.1101/gr.7301508. View

Li Y, Kong D, Ahmad A, Bao B, Dyson G, Sarkar F . Epigenetic deregulation of miR-29a and miR-1256 by isoflavone contributes to the inhibition of prostate cancer cell growth and invasion. Epigenetics. 2012; 7(8):940-9. PMC: 3427289. DOI: 10.4161/epi.21236. View

Cho N, Kim B, Choi M, Yoo E, Moon K, Cho Y . Hypermethylation of CpG island loci and hypomethylation of LINE-1 and Alu repeats in prostate adenocarcinoma and their relationship to clinicopathological features. J Pathol. 2006; 211(3):269-77. DOI: 10.1002/path.2106. View

Hua S, Kallen C, Dhar R, Baquero M, Mason C, Russell B . Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression. Mol Syst Biol. 2008; 4:188. PMC: 2394496. DOI: 10.1038/msb.2008.25. View

10.

Jeronimo C, Usadel H, Henrique R, Silva C, Oliveira J, Lopes C . Quantitative GSTP1 hypermethylation in bodily fluids of patients with prostate cancer. Urology. 2002; 60(6):1131-5. DOI: 10.1016/s0090-4295(02)01949-0. View

11.

Tong A, Fulgham P, Jay C, Chen P, Khalil I, Liu S . MicroRNA profile analysis of human prostate cancers. Cancer Gene Ther. 2008; 16(3):206-16. DOI: 10.1038/cgt.2008.77. View

12.

Tomizawa S, Kobayashi H, Watanabe T, Andrews S, Hata K, Kelsey G . Dynamic stage-specific changes in imprinted differentially methylated regions during early mammalian development and prevalence of non-CpG methylation in oocytes. Development. 2011; 138(5):811-20. PMC: 3035086. DOI: 10.1242/dev.061416. View

13.

Kriaucionis S, Heintz N . The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science. 2009; 324(5929):929-30. PMC: 3263819. DOI: 10.1126/science.1169786. View

14.

Bhusari S, Yang B, Kueck J, Huang W, Jarrard D . Insulin-like growth factor-2 (IGF2) loss of imprinting marks a field defect within human prostates containing cancer. Prostate. 2011; 71(15):1621-30. PMC: 3825178. DOI: 10.1002/pros.21379. View

15.

Schaefer A, Jung M, Mollenkopf H, Wagner I, Stephan C, Jentzmik F . Diagnostic and prognostic implications of microRNA profiling in prostate carcinoma. Int J Cancer. 2009; 126(5):1166-76. DOI: 10.1002/ijc.24827. View

16.

Hagman Z, Larne O, Edsjo A, Bjartell A, Ehrnstrom R, Ulmert D . miR-34c is downregulated in prostate cancer and exerts tumor suppressive functions. Int J Cancer. 2011; 127(12):2768-76. DOI: 10.1002/ijc.25269. View

17.

Fraga M, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta G . Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat Genet. 2005; 37(4):391-400. DOI: 10.1038/ng1531. View

18.

Ellinger J, Bastian P, Jurgan T, Biermann K, Kahl P, Heukamp L . CpG island hypermethylation at multiple gene sites in diagnosis and prognosis of prostate cancer. Urology. 2008; 71(1):161-7. DOI: 10.1016/j.urology.2007.09.056. View

19.

Jenuwein T, Allis C . Translating the histone code. Science. 2001; 293(5532):1074-80. DOI: 10.1126/science.1063127. View

20.

Devaney J, Stirzaker C, Qu W, Song J, Statham A, Patterson K . Epigenetic deregulation across chromosome 2q14.2 differentiates normal from prostate cancer and provides a regional panel of novel DNA methylation cancer biomarkers. Cancer Epidemiol Biomarkers Prev. 2010; 20(1):148-59. DOI: 10.1158/1055-9965.EPI-10-0719. View