Methylation Abnormalities in Mammary Carcinoma: The Methylation Suicide Hypothesis

Anne H. O’Donnell^1,2, John R. Edwards³, Robert A. Rollins^1,4, Nathan D. Vander Kraats³, Tao Su⁵, Hanina H. Hibshoosh⁵, Timothy H. Bestor^1*

¹Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, NY, USA.
²Division of Genetics, Boston Children’s Hospital, Boston, MA, USA.
³Center for Pharmacogenomics, Washington University School of Medicine, St. Louis, MO, USA.
⁴Pfizer BioTherapeutics Research and Development, Center for Integrative Biology and Biotherapeutics, Pearl River, NY, USA.
⁵Department of Pathology, College of Physicians and Surgeons of Columbia University, New York, NY, USA.

DOI: 10.4236/jct.2014.514131                

Abstract

Promoter silencing by ectopic de novo methylation of tumor suppressor genes has been proposed as comparable or equivalent to inactivating mutations as a factor in carcinogenesis. However, this hypotheses had not previously been tested by high resolution, high-coverage whole-genome methylation profiling in primary carcinomas. We have determined the genomic methylation status of a series of primary mammary carcinomas and matched control tissues by examination of more than 2.7 billion CpG dinucleotides. Most of the tumors showed variable losses of DNA methylation from all sequence compartments, but increases in promoter methylation were infrequent, very small in extent, and were observed largely at CpG-poor promoters. De novo methylation at the promoters of proto-oncogenes and tumor suppressor genes occurred at approximately the same frequency. The findings indicate that tumor suppressor silencing by de novo methylation is much less common than currently believed. We put forward a hypothesis under which the demethylation commonly observed in carcinomas is a manifestation of a defensive system that kills incipient cancer cells.

Keywords

DNA Methylation, Mammary Carcinoma

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Majuru, S. and Oyewumi, O. (2009) Nanotechnology in Drug Development and Life Cycle Management. Nanotechnology in Drug Delivery, 10, 597-619. http://dx.doi.org/10.1007/978-0-387-77668-2_20
[2]	Feinberg, A.P. and Vogelstein, B. (1983) Hypomethylation Distinguishes Genes of Some Human Cancers from Their Normal Counterparts. Nature, 301, 89-92. http://dx.doi.org/10.1038/301089a0
[3]	Greger, V., Passarge, E., Hopping, W., Messmer, E. and Horsthemke, B. (1989) Epigenetic Changes May Contribute to the Formation and Spontaneous Regression of Retinoblastoma. Human Genetics, 83, 155-158. http://dx.doi.org/10.1007/BF00286709
[4]	Smiraglia, D.J., Rush, L.J., Fruhwald, M.C., Dai, Z., Held, W.A., Costello, J.F., Lang, J.C., Eng, C., Li, B., Wright, F.A., Caligiuri, M.A. and Plass, C. (2001) Excessive CpG Island Hypermethylation in Cancer Cell Lines versus Primary Human Malignancies. Human Molecular Genetics, 10, 1413-1419. http://dx.doi.org/10.1093/hmg/10.13.1413
[5]	Rollins, R.A., Haghighi, F., Edwards, J.R., Das, R., Zhang, M.Q., Ju, J. and Bestor, T.H. (2006) Large-Scale Structure of Genomic Methylation Patterns. Genome Research, 16, 157-163.
[6]	Edwards, J.R., O’Donnell, A.H., Rollins, R.A., Peckham, H.E., Lee, C., Milekic, M.H., Chanrion, B., Fu, Y., Su, T., Hibshoosh, H., Gingrich, J.A., Haghighi, F., Nutter, R. and Bestor, T.H. (2010) Chromatin and Sequence Features That Define the Fine and Gross Structure of Genomic Methylation Patterns. Genome Research, 20, 972-980. http://dx.doi.org/10.1101/gr.101535.109
[7]	Warnecke, P.M., Stirzaker, C., Song, J., Grunau, C., Melki, J.R. and Clark, S.J. (2002) Identification and Resolution of Artifacts in Bisulfite Sequencing. Methods, 7, 101-107. http://dx.doi.org/10.1016/S1046-2023(02)00060-9
[8]	Forbes, S.A., Tang, G., Bindal, N., Bamford, S., Dawson, E., Cole, C., Kok, C.Y., Jia, M., Ewing, R., Menzies, A., et al. (2010) COSMIC (the Catalogue of Somatic Mutations in Cancer): A Resource to Investigate Acquired Mutations in Human Cancer. Nucleic Acids Research, 38, D652-D657. http://dx.doi.org/10.1093/nar/gkp995
[9]	Bernardino, J., Roux, C., Almeida, A., Vogt, N., Gibaud, A., Gerbault-Seureau, M., Magdelenat, H., Bourgeois, C.A., Malfoy, B. and Dutrillaux, B. (1997) DNA Hypomethylation in Breast Cancer: An Independent Parameter of Tumor Progression?” Cancer Genetics and Cytogenetics, 97, 83-89. http://dx.doi.org/10.1016/S0165-4608(96)00385-8
[10]	Soares, J., Pinto, A.E., Cunha, C.V., Andre, S., Barao, I., Sousa, J.M. and Cravo, M. (1999) Global DNA Hypomethylation in Breast Carcinoma: Correlation with Prognostic Factors and Tumor Progression. Cancer, 85, 112-118. http://dx.doi.org/10.1002/(SICI)1097-0142(19990101)85:1<112::AID-CNCR16>3.0.CO;2-T
[11]	Jackson, K., Yu, M.C., Arakawa, K., Fiala, E., Youn, B., Fiegl, H., Muller-Holzner, E., Widschwendter, M. and Ehrlich, M. (2004) DNA Hypomethylation Is Prevalent Even in Low-Grade Breast Cancers. Cancer Biology & Therapy, 3, 1225-1231. http://dx.doi.org/10.4161/cbt.3.12.1222
[12]	Holzmann, K., Welter, C., Klein, V., Pistorius, G., Seitz, G. and Blin, N. (1992) Tumor-Specific Methylation Patterns of erbB2 (HER2/neu) Sequences in Gastro-Intestinal Cancer. Anticancer Research, 12, 1013-1018.
[13]	Lapidus, R.G., Ferguson, A.T., Ottaviano, Y.L., Parl, F.F., Smith, H.S., Weitzman, S.A., Baylin, S.B., Issa, J.P. and Davidson, N.E. (1996) Methylation of Estrogen and Progesterone Receptor Gene 5’ CpG Islands Correlates with Lack of Estrogen and Progesterone Receptor Gene Expression in Breast Tumors. Clinical Cancer Research, 2, 805-810.
[14]	Irizarry, R.A., Ladd-Acosta, C., Wen, B., Wu, Z., Montano, C., Onyango, P., Cui, H., Gabo, K., Rongione, M., Webster, M., et al. (2009) The Human Colon Cancer Methylome Shows Similar Hypo- and Hypermethylation at Conserved Tissue-Specific CpG Island Shores. Nature Genetics, 41, 178-186. http://dx.doi.org/10.1038/ng.298
[15]	Busslinger, M., Hurst, J. and Flavell, R.A. (1983) DNA Methylation and the Regulation of Globin Gene Expression. Cell, 34, 197-206. http://dx.doi.org/10.1016/0092-8674(83)90150-2
[16]	Kass, S.U., Landsberger, N. and Wolffe, A.P. (1997) DNA Methylation Directs a Time-Dependent Repression of Transcription Initiation. Current Biology, 7, 157-165. http://dx.doi.org/10.1016/S0960-9822(97)70086-1
[17]	Honc, G.C., Hawkins, R.D., Caballero, O.L., Lo, C., Lister, R., Pelizzola, M., Valsesia, A., Ye, Z., Kuan, S., Edsall, L.E., Camargo, A.A., Stevenson, B.J., Ecker, J.R., Bafna, V., Strausberg, R.L., Simpson, A.J. and Ren, B. (2012) Global DNA Hypomethylation Coupled to Repressive Chromatin Domain Formation and Gene Silencing in Breast Cancer. Genome Research, 22, 246-258. http://dx.doi.org/10.1101/gr.125872.111
[18]	Antequera, F., Boyes, J. and Bird, A. (1990) High Levels of de novo Methylation and Altered Chromatin Structure at CpG Islands in Cell Lines. Cell, 62, 503-514. http://dx.doi.org/10.1016/0092-8674(90)90015-7
[19]	Jones, P.A., Wolkowicz, M.J., Rideout III, W.M., Gonzales, F.A., Marziasz, C.N., Coetzee, G.A. and Tapscott, S.J. (1990) De novo Methylation of the MyoD1 CpG Island during the Establishment of Immortal Cell Lines. Proceedings of the National Academy of Sciences of the United States of America, 87, 6117-6121. http://dx.doi.org/10.1073/pnas.87.16.6117
[20]	Robinson, M.D., Stirzaker, C., Statham, A.L., Coolen, M.W., Song, J.Z., Nair, S.S., Strbenac, D., Speed, T.P. and Clark, S.J. (2010) Evaluation of Affinity-Based Genome-Wide DNA Methylation Data: Effects of CpG Density, Amplification Bias, and Copy Number Variation. Genome Research, 20, 1719-1729. http://dx.doi.org/10.1101/gr.110601.110
[21]	Damelin, M. and Bestor, T.H. (2007) Biological Functions of DNA Methyltransferase 1 Require Its Methyltransferase Activity. Molecular and Cellular Biology, 27, 3891-3899. http://dx.doi.org/10.1128/MCB.00036-07
[22]	Chen, T., Hevi, S., Gay, F., Tsujimoto, N., He, T., Zhang, B., Ueda, Y. and Li, E. (2007) Complete Inactivation of DNMT1 Leads to Mitotic Catastrophe in Human Cancer Cells. Nature Genetics, 39, 391-396. http://dx.doi.org/10.1038/ng1982
[23]	Fratta, E., Coral, S., Covre, A., Parisi, G., Colizzi, F., Danielli, R., Marie Nicolay, H.J., Sigalotti, L. and Maio, M. (2011) The Biology of Cancer Testis Antigens: Putative Function, Regulation and Therapeutic Potential. Molecular Oncology, 5, 164-182. http://dx.doi.org/10.1016/j.molonc.2011.02.001
[24]	DeNardo, D.G. and Coussens, L.M. (2007) Inflammation and Breast Cancer. Balancing Immune Response: Crosstalk between Adaptive and Innate Immune Cells during Breast Cancer Progression. Breast Cancer Research, 9, 212. http://dx.doi.org/10.1186/bcr1746
[25]	Wagner, H. (2004) The Immunobiology of the TLR9 Subfamily. Trends in Immunology, 25, 381-386. http://dx.doi.org/10.1016/j.it.2004.04.011
[26]	Critchley-Thorne, R.J., Simons, D.L., Yan, N., Miyahira, A.K., Dirbas, F.M., Johnson, D.L., Swetter, S.M., Carlson, R.W., Fisher, G.A., Koong, A., et al. (2009) Impaired Interferon Signaling Is a Common Immune Defect in Human Cancer. Proceedings of the National Academy of Sciences of the United States of America, 106, 9010-9015. http://dx.doi.org/10.1073/pnas.0901329106