Skip to main content
SpringerLink
Log in

Methylation and MicroRNA Profiling to Understand Racial Disparities of Prostate Cancer

  • Protocol
  • First Online:
Cancer Epigenetics for Precision Medicine

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1856))

  • 2408 Accesses

Abstract

Prostate cancer is a serious disease in terms of its high incidence and mortality rate in the USA and around the world. The prostate specific antigen (PSA) has been used for prostate cancer diagnosis and follow-up of treatment but a number of challenges remain. Epigenetic biomarkers, especially methylation and microRNA (miR) biomarkers provide an opportunity for diagnosis, prognosis, and recurrence of prostate cancer. Differential global methylation has shown some promising results. In this chapter, the emphasis is given on those biomarkers which can be assayed noninvasively in a prospective study and in a clinic. Challenges in the field, especially the validation of potential biomarkers, and their potential solutions are provided in this chapter.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
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

Institutional subscriptions

Abbreviations

BPH:

Benign prostate hyperplasia

EMR:

Electronic medical records

HDM:

Histone demethylase

HMT:

Histone methyltransferase

MS-MLPA:

Methylation-specific multiplex ligation probe amplification

PBMC:

Peripheral mononuclear blood cells

References

  1. Ma G, Tang M, Wu Y, Xu X, Xu R (2016) LncRNAs and miRNAs: potential biomarkers and therapeutic targets for prostate cancer. Am J Transl Res 8(12):5141–5150

    Google Scholar 

  2. Srivastava A, Goldberger H, Afzal Z, Suy S, Collins SP, Kumar D (2015) Detection of circulatory microRNAs in prostate cancer. Methods Mol Biol 1238:523–538

    Google Scholar 

  3. Chiam K, Ricciardelli C, Bianco-Miotto T (2014) Epigenetic biomarkers in prostate cancer: current and future uses. Cancer Lett 342(2):248–256

    Google Scholar 

  4. Shui IM, Wong CJ, Zhao S, Kolb S, Ebot EM, Geybels MS, Rubicz R, Wright JL, Lin DW, Klotzle B, Bibikova M, Fan JB, Ostrander EA, Feng Z, Stanford JL (2016) Prostate tumor DNA methylation is associated with cigarette smoking and adverse prostate cancer outcomes. Cancer 122(14):2168–2177

    Google Scholar 

  5. Verma M (2016) Genome-wide association studies and epigenome-wide association studies go together in cancer control. Future Oncol 12(13):1645–1664

    Google Scholar 

  6. Blute ML, Damaschke NA Jr, Jarrard DF (2015) The epigenetics of prostate cancer diagnosis and prognosis: update on clinical applications. Curr Opin Urol 25(1):83–88

    Google Scholar 

  7. Brothman AR, Swanson G, Maxwell TM, Cui J, Murphy KJ, Herrick J, Speights VO, Isaac J, Rohr LR (2005) Global hypomethylation is common in prostate cancer cells: a quantitative predictor for clinical outcome? Cancer Genet Cytogenet 156(1):31–36

    Google Scholar 

  8. Mishra A, Verma M (2012) Epigenetics of solid cancer stem cells. Methods Mol Biol 863:15–31

    Google Scholar 

  9. Sethi S, Kong D, Land S, Dyson G, Sakr WA, Sarkar FH (2013) Comprehensive molecular oncogenomic profiling and miRNA analysis of prostate cancer. Am J Transl Res 5(2):200–211

    Google Scholar 

  10. Severi G, Southey MC, English DR, Jung CH, Lonie A, McLean C, Tsimiklis H, Hopper JL, Giles GG, Baglietto L (2014) Epigenome-wide methylation in DNA from peripheral blood as a marker of risk for breast cancer. Breast Cancer Res Treat 148(3):665–673

    Google Scholar 

  11. Shen J, LeFave C, Sirosh I, Siegel AB, Tycko B, Santella RM (2015) Integrative epigenomic and genomic filtering for methylation markers in hepatocellular carcinomas. BMC Med Genet 8:28

    Google Scholar 

  12. Smolle M, Uranitsch S, Gerger A, Pichler M, Haybaeck J (2014) Current status of long non-coding RNAs in human cancer with specific focus on colorectal cancer. Int J Mol Sci 15(8):13993–14013

    Google Scholar 

  13. Paone A, Galli R, Fabbri M (2011) MicroRNAs as new characters in the plot between epigenetics and prostate cancer. Front Genet 2:62

    Google Scholar 

  14. Skorodumova LO, Babalyan KA, Sultanov R, Vasiliev AO, Govorov AV, Pushkar DY, Prilepskaya EA, Danilenko SA, Generozov EV, Larin AK, Kostryukova ES, Sharova EI (2016) GSTP1, APC and RASSF1 gene methylation in prostate cancer samples: comparative analysis of MS-HRM method and Infinium HumanMethylation450 BeadChip beadchiparray diagnostic value. Biomed Khim 62(6):708–714

    Google Scholar 

  15. Jeronimo C, Henrique R, Hoque MO, Mambo E, Ribeiro FR, Varzim G, Oliveira J, Teixeira MR, Lopes C, Sidransky D (2004) A quantitative promoter methylation profile of prostate cancer. Clin Cancer Res 10(24):8472–8478

    Google Scholar 

  16. Ahmad AS, Vasiljevic N, Carter P, Berney DM, Moller H, Foster CS, Cuzick J, Lorincz AT (2016) A novel DNA methylation score accurately predicts death from prostate cancer in men with low to intermediate clinical risk factors. Oncotarget 7(44):71833–71840

    Google Scholar 

  17. Ellinger J, Haan K, Heukamp LC, Kahl P, Buttner R, Muller SC, von Ruecker A, Bastian PJ (2008) CpG island hypermethylation in cell-free serum DNA identifies patients with localized prostate cancer. Prostate 68(1):42–49

    Google Scholar 

  18. Rosenbaum E, Hoque MO, Cohen Y, Zahurak M, Eisenberger MA, Epstein JI, Partin AW, Sidransky D (2005) Promoter hypermethylation as an independent prognostic factor for relapse in patients with prostate cancer following radical prostatectomy. Clin Cancer Res 11(23):8321–8325

    Google Scholar 

  19. Yang B, Liu Z, Ning H, Zhang K, Pan D, Ding K, Huang W, Kang XL, Wang Y, Chen X (2016) MicroRNA-21 in peripheral blood mononuclear cells as a novel biomarker in the diagnosis and prognosis of prostate cancer. Cancer Biomark 17(2):223–230

    Google Scholar 

  20. Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O'Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, Tewari M (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 105(30):10513–10518

    Google Scholar 

  21. Wu Y, Davison J, Qu X, Morrissey C, Storer B, Brown L, Vessella R, Nelson P, Fang M (2016) Methylation profiling identified novel differentially methylated markers including OPCML and FLRT2 in prostate cancer. Epigenetics 11(4):247–258

    Google Scholar 

  22. Woodson K, O'Reilly KJ, Ward DE, Walter J, Hanson J, Walk EL, Tangrea JA (2006) CD44 and PTGS2 methylation are independent prognostic markers for biochemical recurrence among prostate cancer patients with clinically localized disease. Epigenetics 1(4):183–186

    Google Scholar 

  23. Bianco-Miotto T, Chiam K, Buchanan G, Jindal S, Day TK, Thomas M, Pickering MA, O'Loughlin MA, Ryan NK, Raymond WA, Horvath LG, Kench JG, Stricker PD, Marshall VR, Sutherland RL, Henshall SM, Gerald WL, Scher HI, Risbridger GP, Clements JA, Butler LM, Tilley WD, Horsfall DJ, Ricciardelli C, BioResource APC (2010) Global levels of specific histone modifications and an epigenetic gene signature predict prostate cancer progression and development. Cancer Epidemiol Biomark Prev 19(10):2611–2622

    Google Scholar 

  24. 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 435(7046):1262–1266

    Google Scholar 

  25. Tang X, Tang X, Gal J, Kyprianou N, Zhu H, Tang G (2011) Detection of microRNAs in prostate cancer cells by microRNA array. Methods Mol Biol 732:69–88

    Google Scholar 

  26. Almeida-Rios D, Graca I, Vieira FQ, Ramalho-Carvalho J, Pereira-Silva E, Martins AT, Oliveira J, Goncalves C, Costa BM, Henrique R, Jeronimo C (2016) Histone methyltransferase PRMT6 plays an oncogenic role of in prostate cancer. Oncotarget 7(33):53018–53028

    Google Scholar 

  27. Gaughan L, Stockley J, Wang N, McCracken SR, Treumann A, Armstrong K, Shaheen F, Watt K, McEwan IJ, Wang C, Pestell RG, Robson CN (2011) Regulation of the androgen receptor by SET9-mediated methylation. Nucleic Acids Res 39(4):1266–1279

    Google Scholar 

  28. Gurioli G, Salvi S, Martignano F, Foca F, Gunelli R, Costantini M, Cicchetti G, De Giorgi U, Sbarba PD, Calistri D, Casadio V (2016) Methylation pattern analysis in prostate cancer tissue: identification of biomarkers using an MS-MLPA approach. J Transl Med 14(1):249

    Google Scholar 

  29. Yegnasubramanian S, Haffner MC, Zhang Y, Gurel B, Cornish TC, Wu Z, Irizarry RA, Morgan J, Hicks J, TL DW, Isaacs WB, Bova GS, De Marzo AM, Nelson WG (2008) DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity. Cancer Res 68(21):8954–8967

    Google Scholar 

  30. Hashim D, Boffetta P, Galsky M, Oh W, Lucchini R, Crane M, Luft B, Moline J, Udasin I, Harrison D, Taioli E (2016) Prostate cancer characteristics in the world trade center cohort, 2002–2013. Eur J Cancer Prev. https://doi.org/10.1097/CEJ.0000000000000315

  31. Chen R, Sjoberg DD, Huang Y, Xie L, Zhou L, He D, Vickers AJ, Sun Y, Chinese Prostate Cancer, Prostate Biopsy Collaborative Group (2017) Prostate specific antigen and prostate cancer in Chinese men undergoing initial prostate biopsies compared with western cohorts. J Urol 197(1):90–96

    Google Scholar 

  32. Carrick DM, Black A, Gohagan JK, Khan A, Pettit K, Williams C, Yu K, Yurgalevitch S, Huang WY, Zhu C (2015) The PLCO biorepository: creating, maintaining, and administering a unique biospecimen resource. Rev Recent Clin Trials 10(3):212–222

    Google Scholar 

  33. Mullard A (2015) The roadmap Epigenomics project opens new drug development avenues. Nat Rev Drug Discov 14(4):223–225

    Google Scholar 

  34. Kirby MK, Ramaker RC, Roberts BS, Lasseigne BN, Gunther DS, Burwell TC, Davis NS, Gulzar ZG, Absher DM, Cooper SJ, Brooks JD, Myers RM (2017) Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns. BMC Cancer 17(1):273

    Google Scholar 

  35. Dezhong L, Xiaoyi Z, Xianlian L, Hongyan Z, Guohua Z, Bo S, Shenglei Z, Lian Z (2015) miR-150 is a factor of survival in prostate cancer patients. J BUON 20(1):173–179

    Google Scholar 

  36. Joyce BT, Gao T, Zheng Y, Liu L, Zhang W, Dai Q, Shrubsole MJ, Hibler EA, Cristofanilli M, Zhang H, Yang H, Vokonas P, Cantone L, Schwartz J, Baccarelli A, Hou L (2016) Prospective changes in global DNA methylation and cancer incidence and mortality. Br J Cancer 115(4):465–472

    Google Scholar 

  37. Xu S, Yi XM, Zhang ZY, Ge JP (2016) Zhou WQ, miR-129 predicts prognosis and inhibits cell growth in human prostate carcinoma. Mol Med Rep 14(6):5025-5032

    Google Scholar 

  38. Das DK, Naidoo M, Ilboudo A, Park JY, Ali T, Krampis K, Robinson BD, Osborne JR, Ogunwobi OO (2016) miR-1207-3p regulates the androgen receptor in prostate cancer via FNDC1/fibronectin. Exp Cell Res 348(2):190–200

    Google Scholar 

  39. Nikolic Z, Savic Pavicevic D, Vucic N, Cidilko S, Filipovic N, Cerovic S, Vukotic V, Romac S, Brajuskovic G (2015) Assessment of association between genetic variants in microRNA genes hsa-miR-499, hsa-miR-196a2 and hsa-miR-27a and prostate cancer risk in Serbian population. Exp Mol Pathol 99(1):145–150

    Google Scholar 

  40. Mihelich BL, Maranville JC, Nolley R, Peehl DM, Nonn L (2015) Elevated serum microRNA levels associate with absence of high-grade prostate cancer in a retrospective cohort. PLoS One 10(4):e0124245

    Google Scholar 

  41. Djulbegovic M, Beyth RJ, Neuberger MM, Stoffs TL, Vieweg J, Djulbegovic B, Dahm P (2010) Screening for prostate cancer: systematic review and meta-analysis of randomised controlled trials. BMJ 341:c4543

    Google Scholar 

Download references

Acknowledgments

We are thankful to Dr. L. Yan of EpigenDX Corporation (MA,USA). Portion of this work was supported by NIH-NIGMS grant# T34GM100831 and NIH-NCI grant# R01CA164318-03S1 to HNB.

Author information

Authors and Affiliations

  1. Department of Natural, Pharmacy and Health Sciences, Elizabeth City State University/University of North Carolina, Elizabeth City, NC, USA

    Hirendra Nath Banerjee & William Kahan

  2. Department of Pharmacology, National University of Singapore, Singapore, Singapore

    Vineet Kumar

  3. Methods and Technologies Branch, Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

    Mukesh Verma

Authors
  1. Hirendra Nath Banerjee
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. William Kahan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Vineet Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mukesh Verma
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hirendra Nath Banerjee .

Editor information

Editors and Affiliations

  1. Kelly Government Solutions, Bethesda, MD, USA

    Ramona G. Dumitrescu

  2. Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

    Mukesh Verma

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Banerjee, H.N., Kahan, W., Kumar, V., Verma, M. (2018). Methylation and MicroRNA Profiling to Understand Racial Disparities of Prostate Cancer. In: Dumitrescu, R., Verma, M. (eds) Cancer Epigenetics for Precision Medicine . Methods in Molecular Biology, vol 1856. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8751-1_15

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-8751-1_15

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8750-4

  • Online ISBN: 978-1-4939-8751-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation