Abstract
The aberrant DNA methylation has been noted to occur at promoter of tumor suppressor, cell adhesion, DNA repair, and other growth regulating genes during the progression of nonneoplastic esophageal mucosa to Barrett esophagus to esophageal adenocarcinoma. Methylation-mediated silencing of individual gene or concurrent loss of a number of genes plays crucial roles in dysplasia-metaplasia-neoplasia sequence of esophageal adenocarcinoma. In addition, promoter methylation of genes had shown significant prognostic potential in patients with esophageal adenocarcinoma. Thus, determination of methylation status of genes of interest can be used as a molecular marker for risk stratification and/or better prognosis of patients with esophageal adenocarcinoma. There are a number of methods including bead array, PCR and sequencing, pyrosequencing, methylation-specific PCR, and PCR with high-resolution melt curve available to determine the methylation status of particular gene of interest. Herein, we describe the polymerase chain reaction followed by sequencing-based protocol for identifying DNA methylation status in esophageal adenocarcinoma.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9:465–476
Sharma S, Kelly TK, Jones PA (2010) Epigenetics in cancer. Carcinogenesis 31:27–36
Feinberg AP, Tycko B (2004) The history of cancer epigenetics. Nat Rev Cancer 4:143–153
Kailasam A, Mittal SK, Agrawal DK (2015) Epigenetics in the pathogenesis of esophageal adenocarcinoma. Clin Transl Sci 8:394–402
Agarwal A, Polineni R, Hussein Z, Vigoda I, Bhagat TD, Bhattacharyya S, Maitra A, Verma A (2012) Role of epigenetic alterations in the pathogenesis of Barrett's esophagus and esophageal adenocarcinoma. Int J Clin Exp Pathol 5:382–396
Peng D, Hu TL, Jiang A, Washington MK, Moskaluk CA, Schneider-Stock R, El-Rifai W (2011) Location-specific epigenetic regulation of the metallothionein 3 gene in esophageal adenocarcinomas. PLoS One 6:e22009
Kaz AM, Grady WM (2014) Epigenetic biomarkers in esophageal cancer. Cancer Lett 342:193–199
Wong DJ, Barrett MT, Stoger R et al (1997) p16INK4a promoter is hypermethylated at a high frequency in esophageal adenocarcinomas. Cancer Res 57:2619–2622
Klump B, Hsieh CJ, Holzmann K, Gregor M, Porschen R (1998) Hypermethylation of the CDKN2/p16 promoter during neoplastic progression in Barrett’s esophagus. Gastroenterology 115:1381–1386
Eads CA, Lord RV, Wickramasinghe K, Long TI, Kurumboor SK, Bernstein L, Peters JH, DeMeester SR, DeMeester TR, Skinner KA, Laird PW (2001) Epigenetic patterns in the progression of esophageal adenocarcinoma. Cancer Res 61:3410–3418
Wild Christopher P, Hardie LJ (2003) Molecular events associated with the development of Barrett’s esophagus and esophageal adenocarcinoma. Nat Rev Cancer 3:676–684
Xu E, Gu J, Hawk ET, Wang KK, Lai M, Huang M, Ajani J, Wu X (2013) Genome-wide methylation analysis shows similar patterns in Barrett's esophagus and esophageal adenocarcinoma. Carcinogenesis 34:2750–2756
Corn PG, Heath EI, Heitmiller R, Fogt F, Forastiere AA, Herman JG, Wu TT (2001) Frequent hypermethylation of the 5′ CpG island of E-cadherin in esophageal adenocarcinoma. Clin Cancer Res 7:2765–2769
Kuester D, El-Rifai W, Peng D, Ruemmele P, Kroeckel I, Peters B, Moskaluk CA, Stolte M, Mönkemüller K, Meyer F, Schulz HU, Hartmann A, Roessner A, Schneider-Stock R (2009) Silencing of MGMT expression by promoter hypermethylation in the metaplasia-dysplasia-carcinoma sequence of Barrett’s esophagus. Cancer Lett 275:117–126
Smith E, Ruszkiewicz AR, Jamieson GG, Drew PA (2014) IGFBP7 is associated with poor prognosis in esophageal adenocarcinoma and is regulated by promoter DNA methylation. Br J Cancer 110:775–782
Brock MV, Gou M, Akiyama Y, Muller A, Wu TT, Montgomery E, Deasel M, Germonpré P, Rubinson L, Heitmiller RF, Yang SC, Forastiere AA, Baylin SB, Herman JG (2003) Prognostic importance of promoter hypermethylation of multiple genes in esophageal adenocarcinoma. Clin Cancer Res 9:2912–2919
Wang JS, Guo M, Montgomery EA, Thompson RE, Cosby H, Hicks L, Wang S, Herman JG, Canto MI (2009) DNA promoter hypermethylation of p16 and APC predicts neoplastic progression in Barrett’s esophagus. Am J Gastroenterol 104:2153–2160
Kuester D, Dar AA, Moskaluk CC, Krueger S, Meyer F, Hartig R, Stolte M, Malfertheiner P, Lippert H, Roessner A, El-Rifai W, Schneider-Stock R (2007) Early involvement of death-associated protein kinase promoter hypermethylation in the carcinogenesis of Barrett’s esophageal adenocarcinoma and its association with clinical progression. Neoplasia 9:236–245
Jin Z, Cheng Y, Olaru A, Kan T, Yang J, Paun B, Ito T, Hamilton JP, David S, Agarwal R, Selaru FM, Sato F, Abraham JM, Beer DG, Mori Y, Shimada Y, Meltzer SJ (2008) Promoter hypermethylation of CDH13 is a common, early event in human esophageal adenocarcinogenesis and correlates with clinical risk factors. Int J Cancer 123:2331–2336
Jin Z, Mori Y, Yang J, Sato F, Ito T, Cheng Y, Paun B, Hamilton JP, Kan T, Olaru A, David S, Agarwal R, Abraham JM, Beer D, Montgomery E, Meltzer SJ (2007) Hypermethylation of the nel-like 1 gene is a common and early event and is associated with poor prognosis in early-stage esophageal adenocarcinoma. Oncogene 26:6332–6340
Tischoff I, Hengge UR, Vieth M, Ell C, Stolte M, Weber A, Schmidt WE, Tannapfel A (2007) Methylation of SOCS-3 and SOCS-1 in the carcinogenesis of Barrett’s adenocarcinoma. Gut 56:1047–1053
Jin Z, Olaru A, Yang J, Sato F, Cheng Y, Kan T, Mori Y, Mantzur C, Paun B, Hamilton JP, Ito T, Wang S, David S, Agarwal R, Beer DG, Abraham JM, Meltzer SJ (2007) Hypermethylation of tachykinin-1 is a potential biomarker in human esophageal cancer. Clin Cancer Res 13:6293–6300
Clément G, Guilleret I, He B, Yagui-Beltrán A, Lin YC, You L, Xu Z, Shi Y, Okamoto J, Benhattar J, Jablons D (2008) Epigenetic alteration of the Wnt inhibitory factor-1 promoter occurs early in the carcinogenesis of Barrett’s esophagus. Cancer Sci 99:46–53
Acknowledgements
Farhadul Islam and Johnny C. Tang contributed equally to this work as first authors.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Islam, F., Tang, J.C., Gopalan, V., Lam, A.K. (2018). Epigenetics: DNA Methylation Analysis in Esophageal Adenocarcinoma. In: Lam, A. (eds) Esophageal Adenocarcinoma. Methods in Molecular Biology, vol 1756. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7734-5_21
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7734-5_21
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7733-8
Online ISBN: 978-1-4939-7734-5
eBook Packages: Springer Protocols