Promoter- and Cell-specific Epigenetic Regulation of CD44, Cyclin D2, GLIPR1 and PTEN by Methyl-CpG Binding Proteins and Histone Modifications

Overview

Journal BMC Cancer

Publisher Biomed Central

Specialty Oncology

Date 2010 Jun 23

PMID 20565761

Citations 17

Authors

Imke Muller

Frank Wischnewski

Klaus Pantel

Heidi Schwarzenbach

Affiliations

Soon will be listed here.

Abstract

Background: The aim of the current study was to analyze the involvement of methyl-CpG binding proteins (MBDs) and histone modifications on the regulation of CD44, Cyclin D2, GLIPR1 and PTEN in different cellular contexts such as the prostate cancer cells DU145 and LNCaP, and the breast cancer cells MCF-7. Since global chromatin changes have been shown to occur in tumours and regions of tumour-associated genes are affected by epigenetic modifications, these may constitute important regulatory mechanisms for the pathogenesis of malignant transformation.

Methods: In DU145, LNCaP and MCF-7 cells mRNA expression levels of CD44, Cyclin D2, GLIPR1 and PTEN were determined by quantitative RT-PCR at the basal status as well as after treatment with demethylating agent 5-aza-2'-deoxycytidine and/or histone deacetylase inhibitor Trichostatin A. Furthermore, genomic DNA was bisulfite-converted and sequenced. Chromatin immunoprecipitation was performed with the stimulated and unstimulated cells using antibodies for MBD1, MBD2 and MeCP2 as well as 17 different histone antibodies.

Results: Comparison of the different promoters showed that MeCP2 and MBD2a repressed promoter-specifically Cyclin D2 in all cell lines, whereas in MCF-7 cells MeCP2 repressed cell-specifically all methylated promoters. Chromatin immunoprecipitation showed that all methylated promoters associated with at least one MBD. Treatment of the cells by the demethylating agent 5-aza-2'-deoxycytidine (5-aza-CdR) caused dissociation of the MBDs from the promoters. Only MBD1v1 bound and repressed methylation-independently all promoters. Real-time amplification of DNA immunoprecipitated by 17 different antibodies showed a preferential enrichment for methylated lysine of histone H3 (H3K4me1, H3K4me2 and H3K4me3) at the particular promoters. Notably, the silent promoters were associated with unmodified histones which were acetylated following treatment by 5-aza-CdR.

Conclusions: This study is one of the first to reveal the histone code and MBD profile at the promoters of CD44, Cyclin D2, GLIPR1 and PTEN in different tumour cells and associated changes after stimulation with methylation inhibitor 5-aza-CdR.

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References

Blanco-Aparicio C, Renner O, Leal J, Carnero A . PTEN, more than the AKT pathway. Carcinogenesis. 2007; 28(7):1379-86. DOI: 10.1093/carcin/bgm052. View

Al-Hajj M, Wicha M, Benito-Hernandez A, Morrison S, Clarke M . Prospective identification of tumorigenic breast cancer cells. Proc Natl Acad Sci U S A. 2003; 100(7):3983-8. PMC: 153034. DOI: 10.1073/pnas.0530291100. View

Jorgensen H, Ben-Porath I, Bird A . Mbd1 is recruited to both methylated and nonmethylated CpGs via distinct DNA binding domains. Mol Cell Biol. 2004; 24(8):3387-95. PMC: 381685. DOI: 10.1128/MCB.24.8.3387-3395.2004. View

Gotte M, Yip G . Heparanase, hyaluronan, and CD44 in cancers: a breast carcinoma perspective. Cancer Res. 2006; 66(21):10233-7. DOI: 10.1158/0008-5472.CAN-06-1464. View

Sharma G, Mirza S, Prasad C, Srivastava A, Gupta S, Ralhan R . Promoter hypermethylation of p16INK4A, p14ARF, CyclinD2 and Slit2 in serum and tumor DNA from breast cancer patients. Life Sci. 2007; 80(20):1873-81. DOI: 10.1016/j.lfs.2007.02.026. View

Dahl J, Collas P . Q2ChIP, a quick and quantitative chromatin immunoprecipitation assay, unravels epigenetic dynamics of developmentally regulated genes in human carcinoma cells. Stem Cells. 2007; 25(4):1037-46. DOI: 10.1634/stemcells.2006-0430. View

Verkaik N, van Steenbrugge G, van Weerden W, Bussemakers M, van der Kwast T . Silencing of CD44 expression in prostate cancer by hypermethylation of the CD44 promoter region. Lab Invest. 2000; 80(8):1291-8. DOI: 10.1038/labinvest.3780137. View

Esteller M, Herman J . Cancer as an epigenetic disease: DNA methylation and chromatin alterations in human tumours. J Pathol. 2001; 196(1):1-7. DOI: 10.1002/path.1024. View

Krishnan M, Singh A, Smith J, Sharma A, Chen X, Eschrich S . HDAC inhibitors regulate claudin-1 expression in colon cancer cells through modulation of mRNA stability. Oncogene. 2009; 29(2):305-12. PMC: 3388773. DOI: 10.1038/onc.2009.324. View

10.

Majumder P, Sellers W . Akt-regulated pathways in prostate cancer. Oncogene. 2005; 24(50):7465-74. DOI: 10.1038/sj.onc.1209096. View

11.

Radhakrishnan P, Basma H, Klinkebiel D, Christman J, Cheng P . Cell type-specific activation of the cytomegalovirus promoter by dimethylsulfoxide and 5-aza-2'-deoxycytidine. Int J Biochem Cell Biol. 2008; 40(9):1944-55. PMC: 4011493. DOI: 10.1016/j.biocel.2008.02.014. View

12.

Fujita H, Fujii R, Aratani S, Amano T, Fukamizu A, Nakajima T . Antithetic effects of MBD2a on gene regulation. Mol Cell Biol. 2003; 23(8):2645-57. PMC: 152551. DOI: 10.1128/MCB.23.8.2645-2657.2003. View

13.

Hirsch C, Bonham K . Histone deacetylase inhibitors regulate p21WAF1 gene expression at the post-transcriptional level in HepG2 cells. FEBS Lett. 2004; 570(1-3):37-40. DOI: 10.1016/j.febslet.2004.06.018. View

14.

Yu F, Zingler N, Schumann G, Stratling W . Methyl-CpG-binding protein 2 represses LINE-1 expression and retrotransposition but not Alu transcription. Nucleic Acids Res. 2001; 29(21):4493-501. PMC: 60185. DOI: 10.1093/nar/29.21.4493. View

15.

Sawa H, Murakami H, Ohshima Y, Sugino T, Nakajyo T, Kisanuki T . Histone deacetylase inhibitors such as sodium butyrate and trichostatin A induce apoptosis through an increase of the bcl-2-related protein Bad. Brain Tumor Pathol. 2002; 18(2):109-14. DOI: 10.1007/BF02479423. View

16.

Klose R, Bird A . Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci. 2006; 31(2):89-97. DOI: 10.1016/j.tibs.2005.12.008. View

17.

Zheng Y, Wu J, Chen Z, Goodman M . Chemical regulation of epigenetic modifications: opportunities for new cancer therapy. Med Res Rev. 2008; 28(5):645-87. DOI: 10.1002/med.20120. View

18.

El-Osta A, Kantharidis P, Zalcberg J, Wolffe A . Precipitous release of methyl-CpG binding protein 2 and histone deacetylase 1 from the methylated human multidrug resistance gene (MDR1) on activation. Mol Cell Biol. 2002; 22(6):1844-57. PMC: 135609. DOI: 10.1128/MCB.22.6.1844-1857.2002. View

19.

Lopez-Serra L, Ballestar E, Fraga M, Alaminos M, Setien F, Esteller M . A profile of methyl-CpG binding domain protein occupancy of hypermethylated promoter CpG islands of tumor suppressor genes in human cancer. Cancer Res. 2006; 66(17):8342-6. DOI: 10.1158/0008-5472.CAN-06-1932. View

20.

Hendrich B, Tweedie S . The methyl-CpG binding domain and the evolving role of DNA methylation in animals. Trends Genet. 2003; 19(5):269-77. DOI: 10.1016/S0168-9525(03)00080-5. View