Skip to main content

DNA Methylation Analysis in Human Cancer

  • Protocol
  • First Online:
Pancreatic Cancer

Part of the book series: Methods in Molecular Biology ((MIMB,volume 980))

Abstract

The functional impact of aberrant DNA methylation and the widespread alterations in DNA methylation in cancer development have led to the development of a variety of methods to characterize the DNA methylation patterns. This chapter critiques and describes the major approaches to analyzing DNA methylation.

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

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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

Similar content being viewed by others

References

  1. Nanney DL (1958) Epigenetic control systems. Proc Natl Acad Sci USA 44:712–717

    Article  PubMed  CAS  Google Scholar 

  2. Choudhuri S (2011) From Waddington’s epigenetic landscape to small noncoding RNA: some important milestones in the history of epigenetics research. Toxicol Mech Methods 21:252–274

    Article  PubMed  CAS  Google Scholar 

  3. Shimabukuro M, Sasaki T, Imamura A, Tsujita T, Fuke C, Umekage T, Tochigi M, Hiramatsu K, Miyazaki T, Oda T, Sugimoto J, Jinno Y, Okazaki Y (2007) Global hypomethylation of peripheral leukocyte DNA in male patients with schizophrenia: a potential link between epigenetics and schizophrenia. J Psychiatr Res 41:1042–1046

    Article  PubMed  Google Scholar 

  4. Omura N, Goggins M (2009) Epigenetics and epigenetic alterations in pancreatic cancer. Int J Clin Exp Pathol 2:310–326, Epub 2008 Nov 15

    PubMed  CAS  Google Scholar 

  5. Chason RJ, Csokmay J, Segars JH, DeCherney AH, Armant DR (2011) Environmental and epigenetic effects upon preimplantation embryo metabolism and development. Trends Endocrinol Metab 22:412–420

    Article  PubMed  CAS  Google Scholar 

  6. Costenbader KH, Gay S, Riquelme ME, Iaccarino L, Doria A (2012) Genes, epigenetic regulation and environmental factors: which is the most relevant in developing autoimmune diseases? Autoimmun Rev 11(8):604–609

    Article  PubMed  Google Scholar 

  7. Szyf M, Slack AD (2000) Mechanisms of epigenetic silencing of the c21 gene in Y1 adrenocortical tumor cells. Endocr Res 26:921–930

    Article  PubMed  CAS  Google Scholar 

  8. Jirtle RL, Skinner MK (2007) Environmental epigenomics and disease susceptibility. Nat Rev Genet 8:253–262

    Article  PubMed  CAS  Google Scholar 

  9. 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 435:1262–1266

    Article  PubMed  CAS  Google Scholar 

  10. Seligson DB, Horvath S, McBrian MA, Mah V, Yu H, Tze S, Wang Q, Chia D, Goodglick L, Kurdistani SK (2009) Global levels of histone modifications predict prognosis in different cancers. Am J Pathol 174:1619–1628

    Article  PubMed  CAS  Google Scholar 

  11. Esteller M (2007) Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 8:286–298, Epub 2007 Mar 6

    Article  PubMed  CAS  Google Scholar 

  12. Beck S, Rakyan VK (2008) The methylome: approaches for global DNA methylation profiling. Trends Genet 24:231–237

    Article  PubMed  CAS  Google Scholar 

  13. Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196:261–282

    Article  PubMed  CAS  Google Scholar 

  14. Hendrich B, Tweedie S (2003) The methyl-CpG binding domain and the evolving role of DNA methylation in animals. Trends Genet 19:269–277

    Article  PubMed  CAS  Google Scholar 

  15. Takai D, Jones PA (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 99:3740–3745, Epub 2002 Mar 12

    Article  PubMed  CAS  Google Scholar 

  16. Ito S, D’Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y (2010) Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466:1129–1133

    Article  PubMed  CAS  Google Scholar 

  17. Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, Marques CJ, Andrews S, Reik W (2011) Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473:398–402

    Article  PubMed  CAS  Google Scholar 

  18. Xu W, Yang H, Liu Y, Yang Y, Wang P, Kim SH, Ito S, Yang C, Xiao MT, Liu LX, Jiang WQ, Liu J, Zhang JY, Wang B, Frye S, Zhang Y, Xu YH, Lei QY, Guan KL, Zhao SM, Xiong Y (2011) Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of alpha-ketoglutarate-dependent dioxygenases. Cancer Cell 19:17–30

    Article  PubMed  CAS  Google Scholar 

  19. Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, Li X, Li Y, Chen CH, Zhang W, Jian X, Wang J, Zhang L, Looney TJ, Zhang B, Godley LA, Hicks LM, Lahn BT, Jin P, He C (2011) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol 29: 68–72

    Article  PubMed  CAS  Google Scholar 

  20. Miranda TB, Jones PA (2007) DNA methylation: the nuts and bolts of repression. J Cell Physiol 213:384–390

    Article  PubMed  CAS  Google Scholar 

  21. Weber M, Schubeler D (2007) Genomic patterns of DNA methylation: targets and function of an epigenetic mark. Curr Opin Cell Biol 19:273–280

    Article  PubMed  CAS  Google Scholar 

  22. Zinn RL, Pruitt K, Eguchi S, Baylin SB, Herman JG (2007) hTERT is expressed in cancer cell lines despite promoter DNA methylation by preservation of unmethylated DNA and active chromatin around the transcription start site. Cancer Res 67:194–201

    Article  PubMed  CAS  Google Scholar 

  23. Newell-Price J, Clark AJ, King P (2000) DNA methylation and silencing of gene expression. Trends Endocrinol Metab 11:142–148

    Article  PubMed  CAS  Google Scholar 

  24. Wang YA, Kamarova Y, Shen KC, Jiang Z, Hahn MJ, Wang Y, Brooks SC (2005) DNA methyltransferase-3a interacts with p53 and represses p53-mediated gene expression. Cancer Biol Ther 4:1138–1143

    Article  PubMed  CAS  Google Scholar 

  25. Suzuki M, Yamada T, Kihara-Negishi F, Sakurai T, Hara E, Tenen DG, Hozumi N, Oikawa T (2006) Site-specific DNA methylation by a complex of PU.1 and Dnmt3a/b. Oncogene 25:2477–2488

    Article  PubMed  CAS  Google Scholar 

  26. Hervouet E, Vallette FM, Cartron PF (2009) Dnmt3/transcription factor interactions as crucial players in targeted DNA methylation. Epigenetics 4:487–499, Epub 2009 Oct 21

    Article  PubMed  CAS  Google Scholar 

  27. Kim JK, Samaranayake M, Pradhan S (2009) Epigenetic mechanisms in mammals. Cell Mol Life Sci 66:596–612

    Article  PubMed  CAS  Google Scholar 

  28. Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11:204–220

    Article  PubMed  CAS  Google Scholar 

  29. Esteller M (2006) The necessity of a human epigenome project. Carcinogenesis 27: 1121–1125

    Article  PubMed  CAS  Google Scholar 

  30. Callinan PA, Feinberg AP (2006) The emerging science of epigenomics. Hum Mol Genet 15 Spec No 1:R95–101

    Google Scholar 

  31. Rauscher FJ 3rd (2005) It is time for a human epigenome project. Cancer Res 65:11229

    Article  PubMed  CAS  Google Scholar 

  32. Laird PW (2003) The power and the promise of DNA methylation markers. Nat Rev Cancer 3:253–266

    Article  PubMed  CAS  Google Scholar 

  33. Schones DE, Zhao K (2008) Genome-wide approaches to studying chromatin modi-fications. Nat Rev Genet 9:179–191

    Article  PubMed  CAS  Google Scholar 

  34. Fraga MF, Esteller M (2002) DNA methylation: a profile of methods and applications. Biotechniques 33:632, 634, 636–649

    PubMed  CAS  Google Scholar 

  35. Pomraning KR, Smith KM, Freitag M (2009) Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47:142–150

    Article  PubMed  CAS  Google Scholar 

  36. Hatada I (2006) Emerging technologies for genome-wide DNA methylation profiling in cancer. Crit Rev Oncog 12:205–223

    Article  PubMed  Google Scholar 

  37. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89:1827–1831

    Article  PubMed  CAS  Google Scholar 

  38. Yang SF (1970) Sulfoxide formation from methionine or its sulfide analogs during ­aerobic oxidation of sulfite. Biochemistry 9: 5008–5014

    Article  PubMed  CAS  Google Scholar 

  39. Hayatsu H, Miller RC Jr (1972) The cleavage of DNA by the oxygen-dependent reaction of bisulfite. Biochem Biophys Res Commun 46: 120–124

    Article  PubMed  CAS  Google Scholar 

  40. Hayatsu H (2008) The bisulfite genomic sequencing used in the analysis of epigenetic states, a technique in the emerging environmental genotoxicology research. Mutat Res 659:77–82

    Article  PubMed  CAS  Google Scholar 

  41. Oda M, Glass JL, Thompson RF, Mo Y, Olivier EN, Figueroa ME, Selzer RR, Richmond TA, Zhang X, Dannenberg L, Green RD, Melnick A, Hatchwell E, Bouhassira EE, Verma A, Suzuki M, Greally JM (2009) High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res 37:3829–3839

    Article  PubMed  CAS  Google Scholar 

  42. Yegnasubramanian S, Lin X, Haffner MC, DeMarzo AM, Nelson WG (2006) Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation. Nucleic Acids Res 34:e19

    Article  PubMed  CAS  Google Scholar 

  43. Toyota M, Issa JP (2002) Methylated CpG island amplification for methylation analysis and cloning differentially methylated sequences. Methods Mol Biol 200:101–110

    PubMed  CAS  Google Scholar 

  44. Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, Greally JM (2006) Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res 16: 1046–1055

    Article  PubMed  CAS  Google Scholar 

  45. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schubeler D (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37:853–862, Epub 2005 Jul 10

    Article  PubMed  CAS  Google Scholar 

  46. Jacinto FV, Ballestar E, Esteller M (2008) Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. Biotechniques 44:35

    Article  PubMed  CAS  Google Scholar 

  47. Cross SH, Charlton JA, Nan X, Bird AP (1994) Purification of CpG islands using a methylated DNA binding column. Nat Genet 6:236–244

    Article  PubMed  CAS  Google Scholar 

  48. Rauch T, Li H, Wu X, Pfeifer GP (2006) MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res 66: 7939–7947

    Article  PubMed  CAS  Google Scholar 

  49. Rauch T, Pfeifer GP (2005) Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab Invest 85: 1172–1180

    Article  PubMed  CAS  Google Scholar 

  50. Gebhard C, Schwarzfischer L, Pham TH, Andreesen R, Mackensen A, Rehli M (2006) Rapid and sensitive detection of CpG-methylation using methyl-binding (MB)-PCR. Nucleic Acids Res 34:e82

    Article  PubMed  CAS  Google Scholar 

  51. Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG (2010) Whole-genome DNA methylation profiling using MethylCap-seq. Methods 52:232–236

    Article  PubMed  CAS  Google Scholar 

  52. Rauch TA, Pfeifer GP (2010) DNA methylation profiling using the methylated-CpG island recovery assay (MIRA). Methods 52: 213–217

    Article  PubMed  CAS  Google Scholar 

  53. Serre D, Lee BH, Ting AH (2010) MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res 38:391–399

    Article  PubMed  CAS  Google Scholar 

  54. Warnecke PM, Stirzaker C, Melki JR, Millar DS, Paul CL, Clark SJ (1997) Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. Nucleic Acids Res 25:4422–4426

    Article  PubMed  CAS  Google Scholar 

  55. Shen L, Guo Y, Chen X, Ahmed S, Issa JP (2007) Optimizing annealing temperature overcomes bias in bisulfite PCR methylation analysis. Biotechniques 42:48

    Article  PubMed  CAS  Google Scholar 

  56. Clark SJ, Harrison J, Paul CL, Frommer M (1994) High sensitivity mapping of ­methylated cytosines. Nucleic Acids Res 22: 2990–2997

    Article  PubMed  CAS  Google Scholar 

  57. Eads CA, Laird PW (2002) Combined bisulfite restriction analysis (COBRA). Methods Mol Biol 200:71–85

    PubMed  CAS  Google Scholar 

  58. Wojdacz TK, Dobrovic A, Hansen LL (2008) Methylation-sensitive high-resolution melting. Nat Protoc 3:1903–1908

    Article  PubMed  CAS  Google Scholar 

  59. Feng F, Liu L, Wang S (2010) Fluorescent conjugated polymer-based FRET technique for detection of DNA methylation of cancer cells. Nat Protoc 5:1255–1264

    Article  PubMed  CAS  Google Scholar 

  60. Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB (1996) Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 93:9821–9826

    Article  PubMed  CAS  Google Scholar 

  61. Campan M, Weisenberger DJ, Trinh B, Laird PW (2009) MethyLight. Methods Mol Biol 507:325–337

    Article  PubMed  CAS  Google Scholar 

  62. Worm J, Aggerholm A, Guldberg P (2001) In-tube DNA methylation profiling by fluorescence melting curve analysis. Clin Chem 47:1183–1189

    PubMed  CAS  Google Scholar 

  63. Mockler TC, Chan S, Sundaresan A, Chen H, Jacobsen SE, Ecker JR (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics 85:1–15

    Article  PubMed  CAS  Google Scholar 

  64. Hatada I, Kato A, Morita S, Obata Y, Nagaoka K, Sakurada A, Sato M, Horii A, Tsujimoto A, Matsubara K (2002) A microarray-based method for detecting methylated loci. J Hum Genet 47:448–451

    Article  PubMed  CAS  Google Scholar 

  65. Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, Shen R, Gunderson KL (2009) Genome-wide DNA methylation profiling using Infinium((R)) assay. Epigenomics 1:177–200

    Article  PubMed  CAS  Google Scholar 

  66. Bibikova M, Fan JB (2009) GoldenGate assay for DNA methylation profiling. Methods Mol Biol 507:149–163

    Article  PubMed  CAS  Google Scholar 

  67. Naef F, Lim DA, Patil N, Magnasco M (2002) DNA hybridization to mismatched templates: a chip study. Phys Rev E Stat Nonlin Soft Matter Phys 65:040902

    Article  PubMed  CAS  Google Scholar 

  68. Yan PS, Wei SH, Huang TH (2002) Differential methylation hybridization using CpG island arrays. Methods Mol Biol 200:87–100

    PubMed  CAS  Google Scholar 

  69. Huang TH, Laux DE, Hamlin BC, Tran P, Tran H, Lubahn DB (1997) Identification of DNA methylation markers for human breast carcinomas using the methylation-sensitive restriction fingerprinting technique. Cancer Res 57:1030–1034

    PubMed  CAS  Google Scholar 

  70. Ibrahim AE, Thorne NP, Baird K, Barbosa-Morais NL, Tavare S, Collins VP, Wyllie AH, Arends MJ, Brenton JD (2006) MMASS: an optimized array-based method for assessing CpG island methylation. Nucleic Acids Res 34:e136

    Article  PubMed  CAS  Google Scholar 

  71. Estecio MR, Yan PS, Ibrahim AE, Tellez CS, Shen L, Huang TH, Issa JP (2007) High-throughput methylation profiling by MCA coupled to CpG island microarray. Genome Res 17(10):1529–1536

    Article  PubMed  CAS  Google Scholar 

  72. Omura N, Li CP, Li A, Hong SM, Walter K, Jimeno A, Hidalgo M, Goggins M (2008) Genome-wide profiling of methylated promoters in pancreatic adenocarcinoma. Cancer Biol Ther 7:1146–1156, Epub 2008 Apr 29

    Article  PubMed  CAS  Google Scholar 

  73. Hayashi H, Nagae G, Tsutsumi S, Kaneshiro K, Kozaki T, Kaneda A, Sugisaki H, Aburatani H (2007) High-resolution mapping of DNA methylation in human genome using oligonucleotide tiling array. Hum Genet 120:701–711, Epub 2006 Sep 26

    Article  PubMed  CAS  Google Scholar 

  74. Tost J, Gut IG (2007) DNA methylation analysis by pyrosequencing. Nat Protoc 2:2265–2275

    Article  PubMed  CAS  Google Scholar 

  75. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315–322

    Article  PubMed  CAS  Google Scholar 

  76. Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 33:5868–5877

    Article  PubMed  CAS  Google Scholar 

  77. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766–770

    PubMed  CAS  Google Scholar 

  78. Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM (2009) Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res 19:1606–1615

    Article  PubMed  CAS  Google Scholar 

  79. Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks JB (2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res 19: 1593–1605

    Article  PubMed  CAS  Google Scholar 

  80. Suzuki H, Gabrielson E, Chen W, Anbazhagan R, van Engeland M, Weijenberg MP, Herman JG, Baylin SB (2002) A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet 31:141–149

    Article  PubMed  CAS  Google Scholar 

  81. Sato N, Fukushima N, Maitra A, Matsubayashi H, Yeo CJ, Cameron JL, Hruban RH, Goggins M (2003) Discovery of novel targets for aberrant methylation in pancreatic carcinoma using high-throughput microarrays. Cancer Res 63:3735–3742

    PubMed  CAS  Google Scholar 

  82. Sato N, Fukushima N, Chang R, Matsubayashi H, Goggins M (2006) Differential and epigenetic gene expression profiling identifies frequent disruption of the RELN pathway in pancreatic cancers. Gastroenterology 130:548–565

    Article  PubMed  CAS  Google Scholar 

  83. Lee BH, Yegnasubramanian S, Lin X, Nelson WG (2005) Procainamide is a specific inhibitor of DNA methyltransferase 1. J Biol Chem 280:40749–40756, Epub 2005 Oct 17

    Article  PubMed  CAS  Google Scholar 

  84. Datta J, Ghoshal K, Denny WA, Gamage SA, Brooke DG, Phiasivongsa P, Redkar S, Jacob ST (2009) A new class of quinoline-based DNA hypomethylating agents reactivates tumor suppressor genes by blocking DNA methyltransferase 1 activity and inducing its degradation. Cancer Res 69:4277–4285, Epub 2009 May 5

    Article  PubMed  CAS  Google Scholar 

  85. Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T, Xinarianos G, Cantor CR, Field JK, van den Boom D (2005) Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci USA 102:15785–15790

    Article  PubMed  CAS  Google Scholar 

  86. Coolen MW, Statham AL, Gardiner-Garden M, Clark SJ (2007) Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements. Nucleic Acids Res 35:e119

    Article  PubMed  CAS  Google Scholar 

  87. Tost J, Schatz P, Schuster M, Berlin K, Gut IG (2003) Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry. Nucleic Acids Res 31:e50

    Article  PubMed  Google Scholar 

  88. Piyathilake CJ, Frost AR, Bell WC, Oelschlager D, Weiss H, Johanning GL, Niveleau A, Heimburger DC, Grizzle WE (2001) Altered global methylation of DNA: an epigenetic difference in susceptibility for lung cancer is associated with its progression. Hum Pathol 32:856–862

    Article  PubMed  CAS  Google Scholar 

  89. Kobayakawa S, Miike K, Nakao M, Abe K (2007) Dynamic changes in the epigenomic state and nuclear organization of differentiating mouse embryonic stem cells. Genes Cells 12:447–460

    Article  PubMed  CAS  Google Scholar 

  90. Kovacova V, Janousek B (2012) Bisprimer—a program for the design of primers for bisulfite-based genomic sequencing of both plant and Mammalian DNA samples. J Hered 103: 308–312

    Article  PubMed  CAS  Google Scholar 

  91. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Graf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Backdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavare S, Beck S (2008) A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 26:779–785

    Article  PubMed  CAS  Google Scholar 

  92. Brena RM, Plass C (2009) Bio-COBRA: absolute quantification of DNA methylation in electrofluidics chips. Methods Mol Biol 507:257–269

    Article  PubMed  CAS  Google Scholar 

  93. Laird PW (2010) Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 11:191–203

    Article  PubMed  CAS  Google Scholar 

  94. Palmisano WA, Divine KK, Saccomanno G, Gilliland FD, Baylin SB, Herman JG, Belinsky SA (2000) Predicting lung cancer by detecting aberrant promoter methylation in sputum. Cancer Res 60:5954–5958

    PubMed  CAS  Google Scholar 

  95. Esteller M, Sanchez-Cespedes M, Rosell R, Sidransky D, Baylin SB, Herman JG (1999) Detection of aberrant promoter hypermethylation of tumor suppressor genes in serum DNA from non-small cell lung cancer patients. Cancer Res 59:67–70

    PubMed  CAS  Google Scholar 

  96. Sanchez-Cespedes M, Esteller M, Wu L, Nawroz-Danish H, Yoo GH, Koch WM, Jen J, Herman JG, Sidransky D (2000) Gene promoter hypermethylation in tumors and serum of head and neck cancer patients. Cancer Res 60:892–895

    PubMed  CAS  Google Scholar 

  97. Esteller M, Garcia-Foncillas J, Andion E, Goodman SN, Hidalgo OF, Vanaclocha V, Baylin SB, Herman JG (2000) Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med 343:1350–1354

    Article  PubMed  CAS  Google Scholar 

  98. Kantarjian HM, O’Brien S, Shan J, Aribi A, Garcia-Manero G, Jabbour E, Ravandi F, Cortes J, Davisson J, Issa JP (2006) Update of the decitabine experience in higher risk myelodysplastic syndrome and analysis of prognostic factors associated with outcome. Cancer 109:265–273

    Article  CAS  Google Scholar 

  99. Brabender J, Usadel H, Danenberg KD, Metzger R, Schneider PM, Lord RV, Wickramasinghe K, Lum CE, Park J, Salonga D, Singer J, Sidransky D, Holscher AH, Meltzer SJ, Danenberg PV (2001) Adenomatous polyposis coli gene promoter hypermethylation in non-small cell lung cancer is associated with survival. Oncogene 20:3528–3532

    Article  PubMed  CAS  Google Scholar 

  100. Bastian PJ, Palapattu GS, Lin X, Yegnasubramanian S, Mangold LA, Trock B, Eisenberger MA, Partin AW, Nelson WG (2005) Preoperative serum DNA GSTP1 CpG island hypermethylation and the risk of early prostate-specific antigen recurrence following radical prostatectomy. Clin Cancer Res 11:4037–4043

    Article  PubMed  CAS  Google Scholar 

  101. 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 11:8321–8325

    Article  PubMed  CAS  Google Scholar 

  102. Hoque MO, Begum S, Topaloglu O, Chatterjee A, Rosenbaum E, Van Criekinge W, Westra WH, Schoenberg M, Zahurak M, Goodman SN, Sidransky D (2006) Quantitation of promoter methylation of multiple genes in urine DNA and bladder cancer detection. J Natl Cancer Inst 98:996–1004

    Article  PubMed  CAS  Google Scholar 

  103. Li M, Chen WD, Papadopoulos N, Goodman SN, Bjerregaard NC, Laurberg S, Levin B, Juhl H, Arber N, Moinova H, Durkee K, Schmidt K, He Y, Diehl F, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW, Markowitz SD, Vogelstein B (2009) Sensitive digital quantification of DNA methylation in clinical samples. Nat Biotechnol 27:858–863

    Article  PubMed  CAS  Google Scholar 

  104. Clark SJ, Statham A, Stirzaker C, Molloy PL, Frommer M (2006) DNA methylation: bisulphite modification and analysis. Nat Protoc 1:2353–2364

    Article  PubMed  CAS  Google Scholar 

  105. Oda M, Greally JM (2009) The HELP assay. Methods Mol Biol 507:77–87

    Article  PubMed  CAS  Google Scholar 

  106. Taiwo O, Wilson GA, Morris T, Seisenberger S, Reik W, Pearce D, Beck S, Butcher LM (2012) Methylome analysis using MeDIP-seq with low DNA concentrations. Nat Protoc 7:617–636

    Article  PubMed  CAS  Google Scholar 

  107. Thu KL, Vucic EA, Kennett JY, Heryet C, Brown CJ, Lam WL, Wilson IM (2009) Methylated DNA immunoprecipitation. J Vis Exp e935107: J Vis Exp. 2009;(23). doi:pii: 935. 10.3791/935

    Google Scholar 

  108. Coffee B (2009) Methylation-specific PCR. Curr Protoc Hum Genet Chapter 10:Unit 10.6 61:10.6.1–10.6.14

    Google Scholar 

  109. Bormann Chung CA, Boyd VL, McKernan KJ, Fu Y, Monighetti C, Peckham HE, Barker M (2010) Whole methylome analysis by ultra-deep sequencing using two-base encoding. PLoS One 5:e9320

    Article  PubMed  CAS  Google Scholar 

  110. Ranade SS, Chung CB, Zon G, Boyd VL (2009) Preparation of genome-wide DNA fragment libraries using bisulfite in polyacrylamide gel electrophoresis slices with formamide denaturation and quality control for massively parallel sequencing by oligonucleotide ligation and detection. Anal Biochem 390:126–135

    Article  PubMed  CAS  Google Scholar 

  111. Applied Biosystems SOLiD™ 4 System SOLiD™ Bisulfite-Converted Fragment Library Preparation Protocol. http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_089329.pdf

Download references

Acknowledgments

This work was supported by NIH grants (CA62924, R01CA120432, RC2CA148376, and the Michael Rolfe Foundation).

Disclosures: None of the authors have any relevant potential conflicts.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Michael Goggins .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

O’Sullivan, E., Goggins, M. (2013). DNA Methylation Analysis in Human Cancer. In: Su, G. (eds) Pancreatic Cancer. Methods in Molecular Biology, vol 980. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-287-2_7

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-287-2_7

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-286-5

  • Online ISBN: 978-1-62703-287-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics