Disruption of CTCF at the miR-125b1 locus in gynecological cancers

BMC Cancer

Ernesto Soto-Reyes¹  Rodrigo González-Barrios¹  Fernanda Cisneros-Soberanis¹  Roberto Herrera-Goepfert⁴  Víctor Pérez⁴  David Cantú¹  Diddier Prada¹  Clementina Castro¹  Félix Recillas-Targa³  Luis A Herrera² 

[1] Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México, DF, México

[2] Instituto de Investigaciones Biomédicas, UNAM, P.O. Box 70-228, Ciudad Universitaria, 04510 México, DF, México

[3] Instituto de Fisiología Celular, Departamento de Genética Molecular, UNAM, México, DF, México

[4] Departamento de Patología, INCan, México, DF, México

关键词: Breast cancer;    MicroRNA;    Promoter;    Cancer;    Epigenetic;    miR-125b1;    CTCF;   

Others  :  1080567
DOI  :  10.1186/1471-2407-12-40

 received in 2011-09-26, accepted in 2012-01-25,  发布年份 2012

【 摘 要 】

Background

In cancer cells, transcriptional gene silencing has been associated with genetic and epigenetic defects. The disruption of DNA methylation patterns and covalent histone marks has been associated with cancer development. Until recently, microRNA (miRNA) gene silencing was not well understood. In particular, miR-125b1 has been suggested to be an miRNA with tumor suppressor activity, and it has been shown to be deregulated in various human cancers. In the present study, we evaluated the DNA methylation at the CpG island proximal to the transcription start site of miR-125b1 in cancer cell lines as well as in normal tissues and gynecological tumor samples. In addition, we analyzed the association of CTCF and covalent histone modifications at the miR-125b1 locus.

Methods

To assess the DNA methylation status of the miR-125b1, genomic DNA was transformed with sodium bisulfite, and then PCR-amplified with modified primers and sequenced. The miR-125b1 gene expression was analyzed by qRT-PCR using U6 as a control for constitutive gene expression. CTCF repressive histone marks abundance was evaluated by chromatin immunoprecipitation assays.

Results

The disruption of CTCF in breast cancer cells correlated with the incorporation of repressive histone marks such H3K9me3 and H3K27me3 as well as with aberrant DNA methylation patterns. To determine the effect of DNA methylation at the CpG island of miR-125b1 on the expression of this gene, we performed a qRT-PCR assay. We observed a significant reduction on the expression of miR-125b1 in cancer cells in comparison with controls, suggesting that DNA methylation at the CpG island might reduce miR-125b1 expression. These effects were observed in other gynecological cancers, including ovarian and cervical tumors.

Conclusions

A reduction of miR-125b1 expression in cancers, correlated with methylation, repressive histone marks and loss of CTCF binding at the promoter region.

【 授权许可】

   
2012 Soto-Reyes et al; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [1]Medina PP, Slack F: MicroRNAs and cancer: an overview. Cell Cycle 2008, 7:2485-2492.
• [2]Melo SA, Esteller M: Dysregulation of microRNAs in cancer: playing with fire. FEBS Lett 2010, 585:2087-2099.
• [3]Sato F, Tsuchiya S, Meltzer SJ, Shimizu K: MicroRNAs and epigenetics. FEBS 2011, 278:1598-1609.
• [4]Lujambio A, Ropero S, Ballestar E, Fraga MF, Cerrato C, Setién F, Casado S, Suarez-Gauthier A, Sanchez-Cespedes M, Git A, Spiteri I, Das PP, Caldas C, Miska E, Esteller M: Genetic unmasking of an epigenetically silenced microRNA in human cancer cells. Cancer Res 2007, 67:1424-1429.
• [5]Laganà A, Russo F, Sismeiro C, Giugno R, Pulvirenti A, Ferro A: Variability in the incidence of miRNAs and genes in fragile sites and the role of repeats and CpG islands in the distribution of genetic material. PLoS One 2010, 5:e11166.
• [6]Ma L, Weinberg R: MicroRNAs in malignant progression. Cell Cycle 2008, 7:570-572.
• [7]Visone R, Croce CM: MiRNAs and cancer. Am J Pathol 2009, 174:1131-1138.
• [8]Zhang Y, Yan LX, Wu QN, Du ZM, Chen J, Liao DZ, Huang MY, Hou JH, Wu QL, Zeng MS, Huang WL, Zeng YX, Shao JY: miR-125b is methylated and functions as a tumor suppressor by regulating the ETS1 proto-oncogene in human invasive breast cancer. Cancer Res 2011, 71:3552-3562.
• [9]Feng J, Kim ST, Liu W, Kim JW, Zhang Z, Zhu Y, Berens M, Sun J, Xu J: An integrated analysis of germline and somatic, genetic and epigenetic alterations at 9p21.3 in glioblastoma. Cancer 2012, 118:232-240.
• [10]Scott GK, Goga A, Bhaumik D, Berger CE, Sullivan CS, Benz CC: Coordinate suppression of ERBB2 and ERBB3 by enforced expression of micro-RNA miR-125a or miR-125b. J BiolChem 2007, 282:1479-1486.
• [11]Zhou M, Liu Z, Zhao Y, Ding Y, Liu H, Xi Y, Xiong W, Li G, Lu J, Fodstad O, Riker AI, Tan M: MicroRNA-125b confers the resistance of breast cancer cells to paclitaxel through suppression of pro-apoptotic Bcl-2 antagonist killer 1 (Bak1) expression. J Biol Chem 2010, 285:21496-21507.
• [12]Recillas-Targa F, De La Rosa-Velázquez IA, Soto-Reyes E, Benítez-Bribiesca L: Epigenetic boundaries of tumour suppressor gene promoters: the CTCF connection and its role in carcinogenesis. J Cell Mol Med 2006, 10:554-568.
• [13]Recillas-Targa F, Soto-Reyes E, De la Rosa-Velazquez IA: Insulation of tumor suppressor genes by the nuclear factor CTCF. Biochem Cell Biol 2011, 89:479-488.
• [14]Butcher DT, Mancini-DiNardo DN, Archer TK, Rodenhiser DI: DNA binding sites for putative methylation boundaries in the unmethylated region of the BRCA1 promoter. Int J Cancer 2004, 111:669-678.
• [15]Butcher DT, Rodenhiser DI: Epigenetic inactivation of BRCA1 is associated with aberrant expression of CTCF and DNA methyltransferase (DNMT3B) in some sporadic breast tumours. Eur J Cancer 2007, 43:210-219.
• [16]De La Rosa-Velázquez IA, Rincón-Arano H, Benítez-Bribiesca L, Recillas-Targa F: Epigenetic regulation of the human retinoblastoma tumor suppressor gene promoter by CTCF. Cancer Res 2007, 67:2577-2585.
• [17]Witcher M, Emerson BM: Epigenetic silencing of the p16 (INK4a) tumor suppressor is associated with loss of CTCF binding and a chromatin boundary. Mol Cell 2009, 34:271-284.
• [18]Soto-Reyes E, Recillas-Targa F: Epigenetic regulation of the human p53 gene promoter by the CTCF transcription factor in transformed cell lines. Oncogene 2010, 29:2217-2227.
• [19]de Souza Rocha Simonini P, Breiling A, Gupta N, Malekpour M, Youns M, Omranipour R, Malekpour F, Volinia S, Croce CM, Najmabadi H, Diederichs S, Sahin O, Mayer D, Lyko F, Hoheisel JD, Riazalhosseini Y: Epigenetically deregulated microRNA-375 is involved in a positive feedback loop with estrogen receptor alpha in breast cancer cells. Cancer Res 2010, 70:9175-9184.
• [20]Kirmizis A, Bartley SM, Kuzmichev A, Margueron R, Reinberg D, Green R, Farnham PJ: Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev 2004, 18:1592-1605.
• [21]Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K: High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.
• [22]Hanahan D, Weinberg RA: Hallmarks of cancer: the next generation. Cell 2011, 144:646-674.
• [23]Iorio MV, Visone R, Di Leva G, Donati V, Petrocca F, Casalini P, Taccioli C, Volinia S, Liu CG, Alder H, Calin GA, Ménard S, Croce CM: MicroRNA signatures in human ovarian cancer. Cancer Res 2007, 67:8699-8707.
• [24]Lehmann U, Hasemeier B, Christgen M, Muller M, Romermann D, Langer F, Kreipe H: Epigenetic inactivation of microRNA gene hsa-mir-9-1 in human breast cancer. J Pathol 2008, 214:17-24.
• [25]Shi M, Liu D, Duan H, Shen B, Guo N: Metastasis-related miRNAs, active players in breast cancer invasion, and metastasis. Cancer Metastasis Rev 2010, 29:785-799.
• [26]Tolmachev V: Imaging of HER-2 overexpression in tumors for guiding therapy. Curr Pharm Des 2008, 14:2999-3019.
• [27]Phillips JE, Corces VG: CTCF: master weaver of the genome. Cell 2009, 26:1194-1211.
• [28]Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F, Wong E, Sheng J, Zhang Y, Poh T, Chan CS, Kunarso G, Shahab A, Bourque G, Cacheux-Rataboul V, Sung WK, Ruan Y, Wei CL: CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011, 43:630-638.
• [29]Espinoza CA, Ren B: Mapping higher order structure of chromatin domains. Nat Genet 2011, 43:615-616.