- About this Journal ·
- Abstracting and Indexing ·
- Advance Access ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Articles in Press ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 815894, 11 pages
Differentially Methylated Loci Distinguish Ovarian Carcinoma Histological Types: Evaluation of a DNA Methylation Assay in FFPE Tissue
1Department of Population Health Research, Alberta Health Services-Cancer Care, Calgary, AB, Canada T2S 3C3
2Departments of Medical Genetics and Oncology, University of Calgary, Calgary, AB, Canada T2N 4N2
3Department of Pathology and Laboratory Medicine, Calgary Laboratory Services, Calgary, AB, Canada T2N 2T9
4Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada T2N 4N2
5Department of Molecular Pathology, Tom Baker Cancer Centre, Alberta Health Services, Calgary, AB, Canada T2N 4N2
6Department of Public Health Sciences, University of Alberta, Edmonton, AB, Canada T6G 1C9
Received 4 July 2013; Accepted 19 August 2013
Academic Editor: John P. Geisler
Copyright © 2013 Linda E. Kelemen et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- P. A. Jones and S. B. Baylin, “The epigenomics of cancer,” Cell, vol. 128, no. 4, pp. 683–692, 2007.
- A. P. Feinberg, “Epigenetics at the epicenter of modern medicine,” Journal of the American Medical Association, vol. 299, no. 11, pp. 1345–1350, 2008.
- T. Mohandas, R. S. Sparkes, and L. J. Shapiro, “Reactivation of an inactive human X chromosome: evidence for X inactivation by DNA methylation,” Science, vol. 211, no. 4480, pp. 393–396, 1981.
- F. Antequerra, J. Boyes, and A. Bird, “High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines,” Cell, vol. 62, no. 3, pp. 503–514, 1990.
- D. J. Pulford, J. G. Falls, J. K. Killian, and R. L. Jirtle, “Polymorphisms, genomic imprinting and cancer susceptibility,” Mutation Research, vol. 436, no. 1, pp. 59–67, 1999.
- A. Bird, “DNA methylation patterns and epigenetic memory,” Genes and Development, vol. 16, no. 1, pp. 6–21, 2002.
- R. Lister, M. Pelizzola, R. H. Dowen et al., “Human DNA methylomes at base resolution show widespread epigenomic differences,” Nature, vol. 462, no. 7271, pp. 315–322, 2009.
- R. S. Illingworth and A. P. Bird, “CpG islands—‘a rough guide’,” FEBS Letters, vol. 583, no. 11, pp. 1713–1720, 2009.
- S. K. Murphy, “Targeting the epigenome in ovarian cancer,” Future Oncology, vol. 8, no. 2, pp. 151–164, 2012.
- R. A. Irizarry, C. Ladd-Acosta, B. Wen et al., “The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores,” Nature Genetics, vol. 41, no. 2, pp. 178–186, 2009.
- A. P. Feinberg, R. Ohlsson, and S. Henikoff, “The epigenetic progenitor origin of human cancer,” Nature Reviews Genetics, vol. 7, no. 1, pp. 21–33, 2006.
- K. D. Hansen, W. Timp, H. C. Bravo et al., “Increased methylation variation in epigenetic domains across cancer types,” Nature Genetics, vol. 43, no. 8, pp. 768–775, 2011.
- J. Ferlay, H.-R. Shin, F. Bray, D. Forman, C. Mathers, and D. M. Parkin, “Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008,” International Journal of Cancer, vol. 127, no. 12, pp. 2893–2917, 2010.
- N. Auersperg, A. S. T. Wong, K.-C. Choi, S. K. Kang, and P. C. K. Leung, “Ovarian surface epithelium: biology, endocrinology, and pathology,” Endocrine Reviews, vol. 22, no. 2, pp. 255–288, 2001.
- M. Köbel, S. E. Kalloger, D. G. Huntsman et al., “Differences in tumor type in low-stage versus high-stage ovarian carcinomas,” International Journal of Gynecological Pathology, vol. 29, no. 3, pp. 203–211, 2010.
- K.-K. Wong and D. Gershenson, “The continuum of serous tumors of low malignant potential and low-grade serous carcinomas of the ovary,” Disease Markers, vol. 23, no. 5-6, pp. 377–387, 2007.
- I.-M. Shih and R. J. Kurman, “Ovarian tumorigenesis: a proposed model based on morphological and molecular genetic analysis,” American Journal of Pathology, vol. 164, no. 5, pp. 1511–1518, 2004.
- G. Singer, R. Stöhr, L. Cope et al., “Patterns of p53 mutations separate ovarian serous borderline tumors and low- and high-grade carcinomas and provide support for a new model of ovarian carcinogenesis: a mutational analysis with immunohistochemical correlation,” American Journal of Surgical Pathology, vol. 29, no. 2, pp. 218–224, 2005.
- M. H. Roh, D. Kindelberger, and C. P. Crum, “Serous tubal intraepithelial carcinoma and the dominant ovarian mass: clues to serous tumor origin?” American Journal of Surgical Pathology, vol. 33, no. 3, pp. 376–383, 2009.
- C. A. Barton, N. F. Hacker, S. J. Clark, and P. M. O'Brien, “DNA methylation changes in ovarian cancer: implications for early diagnosis, prognosis and treatment,” Gynecologic Oncology, vol. 109, no. 1, pp. 129–139, 2008.
- D. Bell, A. Berchuck, M. Birrer, et al., “Integrated genomic analyses of ovarian carcinoma,” Nature, vol. 474, no. 7353, pp. 609–615, 2011.
- J. Z. Press, A. De Luca, N. Boyd et al., “Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities,” BMC Cancer, vol. 8, article 17, 2008.
- A. Rathi, A. K. Virmani, J. O. Schorge et al., “Methylation profiles of sporadic ovarian tumors and nonmalignant ovaries from high-risk women,” Clinical Cancer Research, vol. 8, no. 11, pp. 3324–3331, 2002.
- G. Strathdee, K. Appleton, M. Illand et al., “Primary ovarian carcinomas display multiple methylator phenotypes involving known tumor suppressor genes,” American Journal of Pathology, vol. 158, no. 3, pp. 1121–1127, 2001.
- M. Esteller, P. G. Corn, S. B. Baylin, and J. G. Herman, “A gene hypermethylation profile of human cancer,” Cancer Research, vol. 61, no. 8, pp. 3225–3229, 2001.
- C. Wang, A. Horiuchi, T. Imai et al., “Expression of BRCA1 protein in benign, borderline, and malignant epithelial ovarian neoplasms and its relationship to methylation and allelic loss of the BRCA1 gene,” Journal of Pathology, vol. 202, no. 2, pp. 215–223, 2004.
- N. Collins, R. Wooster, and M. R. Stratton, “Absence of methylation of CpG dinucleotides within the promoter of the breast cancer susceptibility gene BRCA2 in normal tissues and in breast and ovarian cancers,” British Journal of Cancer, vol. 76, no. 9, pp. 1150–1156, 1997.
- E. Gras, J. Cortes, O. Diez et al., “Loss of heterozygosity on chromosome 13q12-q14, BRCA-2 mutations and lack of BRCA-2 promoter hypermethylation in sporadic epithelial ovarian tumors,” Cancer, vol. 92, no. 4, pp. 787–795, 2001.
- J. L. Hilton, J. P. Geisler, J. A. Rathe, M. A. Hattermann-Zogg, B. Deyoung, and R. E. Buller, “Inactivation of BRCA1 and BRCA2 in ovarian cancer,” Journal of the National Cancer Institute, vol. 94, no. 18, pp. 1396–1406, 2002.
- J. F. Costello, M. C. Frühwald, D. J. Smiraglia et al., “Aberrant CpG-island methylation has non-random and tumour-type-specific patterns,” Nature Genetics, vol. 24, no. 2, pp. 132–138, 2000.
- J. K. Killian, S. Bilke, S. Davis et al., “In Genome-wide methylation profile of follicular lymphoma reveals distinct on- and off-island epigenotype [abstract no 32],” in Proceedings of the 99th Annual Meeting of the American Association for Cancer Research, AACR, San Diego, Calif, USA, April 2008.
- Illumina, Inc., Methylation profiling of FFPE samples. Technical Note: Illumina Epigenetics, 2008, http://www.illumina.com.
- M. Bibikova, Z. Lin, L. Zhou et al., “High-throughput DNA methylation profiling using universal bead arrays,” Genome Research, vol. 16, no. 3, pp. 383–393, 2006.
- C. Ladd-Acosta, J. Pevsner, S. Sabunciyan et al., “DNA methylation signatures within the human brain,” American Journal of Human Genetics, vol. 81, no. 6, pp. 1304–1315, 2007.
- The International HapMap Consortium, “The international HapMap project,” Nature, vol. 426, no. 6968, pp. 789–796, 2003.
- S. Houshdaran, S. Hawley, C. Palmer et al., “DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines,” PLoS ONE, vol. 5, no. 2, Article ID e9359, 2010.
- F. J. Steemers and K. L. Gunderson, “Illumina, Inc,” Pharmacogenomics, vol. 6, no. 7, pp. 777–782, 2005.
- A. Oliphant, D. L. Barker, J. R. Stuelpnagel, and M. S. Chee, “BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping,” BioTechniques, vol. 32, no. 6, pp. S56–S61, 2002.
- H. T. Bjornsson, M. I. Sigurdsson, M. D. Fallin et al., “Intra-individual change over time in DNA methylation with familial clustering,” Journal of the American Medical Association, vol. 299, no. 24, pp. 2877–2883, 2008.
- L. Carrel and H. F. Willard, “X-inactivation profile reveals extensive variability in X-linked gene expression in females,” Nature, vol. 434, no. 7031, pp. 400–404, 2005.
- V. G. Tusher, R. Tibshirani, and G. Chu, “Significance analysis of microarrays applied to the ionizing radiation response,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 9, pp. 5116–5121, 2001.
- F. A. Tavassoulu and P. Devilee, World Health Organization Classification of Tumors. Pathology and Genetics of Tumors of the Breast and Female Genital Organs, IARC Press, Lyon, France, 2003.
- S. E. Kalloger, M. Köbel, S. Leung et al., “Calculator for ovarian carcinoma subtype prediction,” Modern Pathology, vol. 24, no. 4, pp. 512–521, 2011.
- H. Shen, B. L. Fridley, H. Song et al., “Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer,” Nature Communications, vol. 4, article 1628, 2013.
- C. L. Pearce, C. Templeman, M. A. Rossing et al., “Association between endometriosis and risk of histological subtypes of ovarian cancer: a pooled analysis of case-control studies,” The Lancet Oncology, vol. 13, no. 4, pp. 385–394, 2012.
- R. J. Kurman and T. G. McConnell, “Characterization and comparison of precursors of ovarian and endometrial carcinoma: parts I and II,” International Journal of Surgical Pathology, vol. 18, no. 3, supplement, pp. 181S–189S, 2010.
- J. Liu, C. T. Albarracin, K.-H. Chang et al., “Microsatellite instability and expression of hMLH1 and hMSH2 proteins in ovarian endometrioid cancer,” Modern Pathology, vol. 17, no. 1, pp. 75–80, 2004.
- K. Q. Cai, C. Albarracin, D. Rosen et al., “Microsatellite instability and alteration of the expression of hMLH1 and hMSH2 in ovarian clear cell carcinoma,” Human Pathology, vol. 35, no. 5, pp. 552–559, 2004.
- K. C. Wiegand, S. P. Shah, O. M. Al-Agha et al., “ARID1A mutations in endometriosis-associated ovarian carcinomas,” The New England Journal of Medicine, vol. 363, no. 16, pp. 1532–1543, 2010.
- S. Jones, T.-L. Wang, I.-M. Shih et al., “Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma,” Science, vol. 330, no. 6001, pp. 228–231, 2010.
- M. Widschwendter, S. Apostolidou, A. A. Jones et al., “HOXA methylation in normal endometrium from premenopausal women is associated with the presence of ovarian cancer: a proof of principle study,” International Journal of Cancer, vol. 125, no. 9, pp. 2214–2218, 2009.
- Q. Wu, R. A. Lothe, T. Ahlquist et al., “DNA methylation profiling of ovarian carcinomas and their in vitro models identifies HOXA9, HOXB5, SCGB3A1, and CRABP1 as novel targets,” Molecular Cancer, vol. 6, article 45, 2007.
- T. Hawighorst, P. Velasco, M. Streit et al., “Thrombospondin-2 plays a protective role in multistep carcinogenesis: a novel host anti-tumor defense mechanism,” EMBO Journal, vol. 20, no. 11, pp. 2631–2640, 2001.
- A. Czekierdowski, S. Czekierdowska, J. Danilos et al., “Microvessel density and CPG island methylation of THBS2 gene in malignant ovarian tumors,” Journal of Physiology and Pharmacology, vol. 59, supplement 4, pp. 53–65, 2008.
- J. Kodama, I. Hashimoto, N. Seki et al., “Thrombospondin-1 and -2 messenger RNA expression in epithelial ovarian tumor,” Anticancer Research B, vol. 21, no. 4, pp. 2983–2987, 2001.
- N. Lopes, D. Gregg, S. Vasudevan, H. Hassanain, P. Goldschmidt-Clermont, and H. Kovacic, “Thrombospondin 2 regulates cell proliferation induced by Rac1 redox-dependent signaling,” Molecular and Cellular Biology, vol. 23, no. 15, pp. 5401–5408, 2003.
- V. Kulasingam, M. P. Pavlou, and E. P. Diamandis, “Integrating high-throughput technologies in the quest for effective biomarkers for ovarian cancer,” Nature Reviews Cancer, vol. 10, no. 5, pp. 371–378, 2010.
- R.-S. Mani, M. K. Iyer, Q. Cao et al., “TMPRSS2-ERG-mediated feed-forward regulation of wild-type ERG in human prostate cancers,” Cancer Research, vol. 71, no. 16, pp. 5387–5392, 2011.
- M. N. Davies, M. Volta, R. Pidsley et al., “Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood,” Genome Biology, vol. 13, no. 6, Article ID R43, 2012.
- A. K. Maunakea, R. P. Nagarajan, M. Bilenky et al., “Conserved role of intragenic DNA methylation in regulating alternative promoters,” Nature, vol. 466, no. 7303, pp. 253–257, 2010.
- S. B. Baylin and P. A. Jones, “A decade of exploring the cancer epigenome-biological and translational implications,” Nature Reviews Cancer, vol. 11, no. 10, pp. 726–734, 2011.
- Y. A. Medvedeva, M. V. Fridman, N. J. Oparina et al., “Intergenic, gene terminal, and intragenic CpG islands in the human genome,” BMC Genomics, vol. 11, no. 1, article 48, 2010.
- M. Gardiner-Garden and M. Frommer, “CpG islands in vertebrate genomes,” Journal of Molecular Biology, vol. 196, no. 2, pp. 261–282, 1987.
- M. Meyerson, S. Gabriel, and G. Getz, “Advances in understanding cancer genomes through second-generation sequencing,” Nature Reviews Genetics, vol. 11, no. 10, pp. 685–696, 2010.
- T. Wang, J. Zeng, C. B. Lowe et al., “Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 47, pp. 18613–18618, 2007.
- G. Bourque, “Transposable elements in gene regulation and in the evolution of vertebrate genomes,” Current Opinion in Genetics and Development, vol. 19, no. 6, pp. 607–612, 2009.
- S. J. Chanock, T. Manolio, M. Boehnke et al., “Replicating genotype-phenotype associations,” Nature, vol. 447, no. 7145, pp. 655–660, 2007.