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Gordiyuk VV. Genetic and epigenetic changes of genes on chromosome 3 in human urogenital tumors. ACTA ACUST UNITED AC 2011. [DOI: 10.7124/bc.00007e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- V. V. Gordiyuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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Abstract
Background:DNA methylation regulates gene expression during development. The methylation pattern is established at the time of implantation. CpG islands are genome regions usually protected from methylation; however, selected islands are methylated later. Many undergo methylation in cancer, causing epigenetic gene silencing. Aberrant methylation occurs early in tumorigenesis, in a specific pattern, inhibiting differentiation.Although methylation of specific genes in ovarian tumors has been demonstrated in numerous studies, they represent only a fraction of all methylated genes in tumorigenesis.Objectives:To explore the hypermethylation design in ovarian cancer compared with the methylation profile of normal ovaries, on a genome-wide scale, thus shedding light on the role of gene silencing in ovarian carcinogenesis.Identifying genes that undergo de novo methylation in ovarian cancer may assist in creating biomarkers for disease diagnosis, prognosis, and treatment responsiveness.Methods:DNA was collected from human epithelial ovarian cancers and normal ovaries. Methylation was detected by immunoprecipitation using 5-methyl-cytosine-antibodies. DNA was hybridized to a CpG island microarray containing 237,220 gene promoter probes. Results were analyzed by hybridization intensity, validated by bisulfite analysis.Results:A total of 367 CpG islands were specifically methylated in cancer cells. There was enrichment of methylated genes in functional categories related to cell differentiation and proliferation inhibition. It seems that their silencing enables tumor proliferation.Conclusions:This study provides new perspectives on methylation in ovarian carcinoma, genome-wide. It illustrates how methylation of CpG islands causes silencing of genes that have a role in cell differentiation and functioning. It creates potential biomarkers for diagnosis, prognosis, and treatment responsiveness.
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Abstract
Ovarian cancer is the leading cause of death among gynecological cancers. It is now recognized that in addition to genetic alterations, epigenetic mechanisms, such as DNA methylation, histone modifications and nucleosome remodeling, play an important role in the development and progression of ovarian cancer by modulating chromatin structure, and gene and miRNA expression. Furthermore, epigenetic alterations have been recognized as useful tools for the development of novel biomarkers for diagnosis, prognosis, therapeutic prediction and monitoring of diseases. Moreover, new epigenetic therapies, such as DNA methyltransferase inhibitors and histone deacetylase inhibitors, have been found to be a potential therapeutic option, especially when used in combination with other agents. Here we discuss current developments in ovarian carcinoma epigenome research, the importance of the ovarian carcinoma epigenome for development of diagnostic and prognostic biomarkers, and the current epigenetic therapies used in ovarian cancer.
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Affiliation(s)
- Leonel Maldonado
- Department of Otolaryngology & Head & Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland 21231, USA
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Shih IM, Chen L, Wang CC, Gu J, Davidson B, Cope L, Kurman RJ, Xuan J, Wang TL. Distinct DNA methylation profiles in ovarian serous neoplasms and their implications in ovarian carcinogenesis. Am J Obstet Gynecol 2010; 203:584.e1-22. [PMID: 20965493 DOI: 10.1016/j.ajog.2010.08.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 05/19/2010] [Accepted: 08/09/2010] [Indexed: 11/17/2022]
Abstract
OBJECTIVE The purpose of this study was to analyze DNA methylation profiles among different types of ovarian serous neoplasm, which is a task that has not been performed. STUDY DESIGN The Illumina beads array (Illumina Inc, San Diego, CA) was used to profile DNA methylation in enriched tumor cells that had been isolated from 75 benign and malignant serous tumor tissues and 6 tumor-associated stromal cell cultures. RESULTS We found significantly fewer hypermethylated genes in high-grade serous carcinomas than in low-grade serous carcinoma and borderline tumors, which in turn had fewer hypermethylated genes than serous cystadenoma. Unsupervised analysis identified that serous cystadenoma, serous borderline tumor, and low-grade serous carcinomas tightly clustered together and were clearly different from high-grade serous carcinomas. We also performed supervised analysis to identify differentially methylated genes that may contribute to group separation. CONCLUSION The findings support the view that low-grade and high-grade serous carcinomas are distinctly different with low-grade, but not high-grade, serous carcinomas that are related to serous borderline tumor and cystadenoma.
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Affiliation(s)
- Ie-Ming Shih
- Division of Gynecologic Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
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Bol GM, Suijkerbuijk KPM, Bart J, Vooijs M, Van Der Wall E, Van Diest PJ. Methylation profiles of hereditary and sporadic ovarian cancer. Histopathology 2010; 57:363-70. [DOI: 10.1111/j.1365-2559.2010.03642.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sharma G, Mirza S, Parshad R, Srivastava A, Gupta SD, Pandya P, Ralhan R. Clinical significance of promoter hypermethylation of DNA repair genes in tumor and serum DNA in invasive ductal breast carcinoma patients. Life Sci 2010; 87:83-91. [PMID: 20470789 DOI: 10.1016/j.lfs.2010.05.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 04/23/2010] [Accepted: 04/29/2010] [Indexed: 10/19/2022]
Abstract
AIMS The clinical relevance of frequent methylation of CpG islands of key cancer genes in breast cancer is being increasingly recognized. Our study aimed to evaluate the promoter methylation status of DNA repair genes-BRCA1MGMT and GSTP1 in tumor and circulating DNA of invasive ductal breast carcinoma patients. MAIN METHODS Methylation-specific PCR was carried out to investigate the promoter methylation status of genes in tumor and circulating DNA of 100 breast cancer patients in a prospective study. The effect of promoter methylation on protein expression was evaluated by immunohistochemistry. KEY FINDINGS The frequency of tumor hypermethylation was 27% in BRCA1, 32% in MGMT and 25% in GSTP1 and correlated with methylation of these genes in paired serum DNA. Immunohistochemical analysis showed no detectable expression of BRCA1 and MGMT in 51/89 (57%) and 35/89 (39%) tumors, respectively. MGMT promoter methylation mediated gene silencing was associated with loss of its protein expression (p=0.002, O.R.=4.5, 95% C.I.=1.7-12.0). BRCA1 promoter methylation was not associated with loss of its protein expression, indicating that methylation is not the sole mechanism accounting for the loss/reduced BRCA1 protein expression. Importantly, GSTP1 and BRCA1 hypermethylation were found to be independent of other prognostic factors in predicting disease recurrence (p=0.02, HR=7.6, 95% C.I.=1.4-44.1; p=0.04, HR=6.2, 95% C.I.=1.1-35.7). SIGNIFICANCE Our study underscores the potential utility of DNA methylation of these genes in serum as a promising biomarker and can serve as a surrogate for tumor DNA methylation for diagnosis and prognosis of breast cancer.
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Affiliation(s)
- Gayatri Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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Kang S, Dong SM, Park NH. Frequent promoter hypermethylation of TGFBI in epithelial ovarian cancer. Gynecol Oncol 2010; 118:58-63. [PMID: 20421128 DOI: 10.1016/j.ygyno.2010.03.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 03/30/2010] [Accepted: 03/31/2010] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Using pharmacologic unmasking and genome-wide differential methylation analysis, we identified a novel methylated gene in ovarian cancers. METHODS Two ovarian cancer cells (OVCAR-3, ES-2) that showed synergistic growth inhibition by 5-aza-dC and cisplatin were selected. After treatment with 5-aza-dC, differential expression profiles were compared using microarray that contained 38,500 genes. Reactivation of candidate genes and their promoter methylation were validated by real-time RT-PCR, MS-PCR and bisulfite sequencing. Methylation status was tested by MS-PCR in 56 patients with epithelial ovarian cancer and compared to the 38 normal ovarian tissues. RESULTS We identified 103 candidate genes that were reactivated by 5-aza-dC treatment. Among those, SFN and TGFBI were commonly reactivated in both cells. Since SFN is a well known methylated marker, we selected TGFBI for further validation. Bisulfite sequencing revealed complete promoter methylation in ES-2 and partial methylation in OVCAR-3. In addition, silencing of TGFBI at the transcription level was reversed by 5-aza-dC treatment. TGFBI methylation was observed in 23 out of 38 (60.5%) cases of ovarian cancer, in no normal ovarian tissues (0 of 38, P=0.001), and in 5 out of 18 (27.8%) borderline tumors (P=0.044). In our cohort, we did not observe any association between methylation of TGFBI and clinicopathologic variables or clinical outcomes. CONCLUSION Our results confirm that TGFBI is frequently methylated in ovarian cancer. Its methylation can be used as a novel epigenetic biomarker in discriminating ovarian cancer from non-cancer or borderline tumors.
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Affiliation(s)
- Sokbom Kang
- Research Institute and Hospital, National Cancer Center, Goyang, Republic of Korea
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Dar AA, Majid S, Nosrati M, de Semir D, Federman S, Kashani-Sabet M. Functional modulation of IGF-binding protein-3 expression in melanoma. J Invest Dermatol 2010; 130:2071-9. [PMID: 20357812 DOI: 10.1038/jid.2010.70] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
IGF-binding protein-3 (IGFBP3) is a member of the IGFBP family, which regulates mitogenic and antiapoptotic effects of IGFs. In this report we evaluated the role of IGFBP3 in melanoma. Quantitative real-time PCR (qRT-PCR), western blot, and ELISA analyses indicated a significant downregulation of IGFBP3 expression in melanoma cell lines as compared with a normal melanocyte cell line. Melanoma cell lines treated with the demethylating agent 5-AZA-2'-deoxycytidine reexpressed IGFBP3 at the mRNA and protein levels. Chromatin immunoprecipitation assays revealed enrichment of acetylated histones H3 and H4, and H3 di- and tri-methylated lysine 4 on the unmethylated IGFBP3 promoter. The IGFBP3 promoter region was highly methylated in human melanoma samples as compared with normal nevi. Overexpression of IGFBP3 in melanoma cells in vitro suppressed tumor cell survival, induced apoptosis, reduced colony formation and invasion, and induced expression of the proapoptotic genes p21, PUMA, and BAX. IGFBP3 overexpression also resulted in cleavage of caspase 3 and reduced expression of phosphorylated AKT. Stable overexpression of IGFBP3 suppressed tumor cell growth in vivo. Our study results indicate that silencing of IGFBP3 in melanoma is due to the methylation of its promoter, and that overexpression of IGFBP3 induces apoptosis and suppresses cell survival and growth.
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Affiliation(s)
- Altaf A Dar
- Auerback Melanoma Research Laboratory, Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
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Mackay HJ, Hirte H, Colgan T, Covens A, MacAlpine K, Grenci P, Wang L, Mason J, Pham PA, Tsao MS, Pan J, Zwiebel J, Oza AM. Phase II trial of the histone deacetylase inhibitor belinostat in women with platinum resistant epithelial ovarian cancer and micropapillary (LMP) ovarian tumours. Eur J Cancer 2010; 46:1573-9. [PMID: 20304628 DOI: 10.1016/j.ejca.2010.02.047] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 02/16/2010] [Accepted: 02/24/2010] [Indexed: 11/15/2022]
Abstract
AIM Micropapillary/borderline (LMP) ovarian tumours are rarely included in clinical trials and are intrinsically resistant to radiation and chemotherapy. Platinum resistant epithelial ovarian cancer (EOC) has a poor prognosis. The histone deacetylase inhibitor belinostat demonstrated antitumour activity in pre-clinical ovarian cancer models. METHODS A phase II study was performed to evaluate the activity of belinostat in two patient populations: women with metastatic or recurrent platinum resistant (progression within 6 months) EOC and LMP ovarian tumours, both groups had received no more than 3 prior lines of chemotherapy. Belinostat 1000 mg/m(2)/d was administered iv days 1-5 of a 21 d cycle. Peripheral blood mononuclear cells (PBMCs) and tumour biopsies, where possible, for correlative studies were obtained prior to and following treatment. RESULTS Eighteen patients with EOC and 14 patients with LMP tumours were enrolled on study. Belinostat was well tolerated with no grade four toxicity (179 cycles). Grade 3 toxicity consisted of thrombosis (3 patients), hypersensitivity (1) and elevated ALP (1). One patient with LMP tumour had a partial response (unconfirmed) and 10 had stable disease (SD), 3 were non-evaluable. Median progression-free survival (PFS) was 13.4 months (95% confidence interval (CI), 5.6--not reached). Best response in patients with EOC was SD (nine patients) and median PFS was 2.3 months (95% CI, 1.2-5.7 months). An accumulation of acetylated histones H3 and H4 was noted in PBMCs and in tumour tissue. CONCLUSIONS Belinostat is well tolerated in both patient groups and shows some activity in patients with micropapillary (LMP) disease.
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Oy GF, Slipicevic A, Davidson B, Solberg Faye R, Maelandsmo GM, Flørenes VA. Biological effects induced by insulin-like growth factor binding protein 3 (IGFBP-3) in malignant melanoma. Int J Cancer 2010; 126:350-61. [PMID: 19588500 DOI: 10.1002/ijc.24727] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The insulin like growth factor (IGF) signaling pathway has been shown to contribute to melanoma progression, but little is known about the role of the IGF binding protein 3 (IGFBP-3) in melanoma biology. The aim of the present study was to characterize expression, function and regulation of IGFBP-3 in malignant melanomas and study its potential as a biomarker. The expression of IGFBP-3 varied between different human melanoma cell lines and reintroduction of the protein in non-expressing cells led to induction of apoptosis. Interestingly, in cell lines expressing endogenous IGFBP-3, siRNA silencing of the protein led to a cell line-dependent decrease in proliferation, but had no effect on apoptosis and invasion. Examination of patient material showed that IGFBP-3 is unexpressed in benign nevi while a slight increase in protein expression was seen in primary and metastatic melanoma. However, expression of the protein was low and no correlation was found with circulating levels of IGFBP-3 in serum, suggesting that IGFBP-3 has limited potential as a predictive marker in malignant melanoma. We showed that promoter methylation of IGFBP-3 occurred in both melanoma cell lines and patient material, implicating epigenetic silencing as a regulation mechanism. Furthermore, expression of the protein was shown to be regulated by the PI3-kinase/AKT and MAPK/ERK1/2 pathways. In summary, our findings suggest that IGFBP-3 can exert dual functional effects influencing both apoptosis and proliferation. Development of resistance to the antiproliferative effects of IGFBP-3 may be an important step in progression of malignant melanomas.
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Affiliation(s)
- Geir Frode Oy
- Department of Tumor Biology, Institute for Cancer Research, Oslo, Norway
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Torng PL, Lin CW, Chan MW, Yang HW, Huang SC, Lin CT. Promoter methylation of IGFBP-3 and p53 expression in ovarian endometrioid carcinoma. Mol Cancer 2009; 8:120. [PMID: 20003326 PMCID: PMC2799391 DOI: 10.1186/1476-4598-8-120] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 12/11/2009] [Indexed: 11/26/2022] Open
Abstract
Background Insulin-like growth factor binding protein (IGFBP-3) is an antiproliferative, pro-apoptotic and invasion suppressor protein which is transcriptionally regulated by p53. Promoter methylation has been linked to gene silencing and cancer progression. We studied the correlation between IGFBP-3 and p53 expression as well as IGFBP-3 promoter methylation in ovarian endometrioid carcinoma (OEC) by immunohistochemical staining and quantitative methylation-specific PCR (qMSP). Additionally, we assessed the molecular regulatory mechanism of wild type (wt) p53 on IGFBP-3 expression using two subclones of OEC, the OVTW59-P0 (low invasive) and P4 (high invasive) sublines. Results In 60 cases of OEC, 40.0% showed lower IGFBP-3 expression which was significantly correlated with higher IGFBP-3 promoter methylation. p53 overexpression was detected in 35.0% of OEC and was unrelated to clinical outcomes and IGFBP-3. By Kaplan-Meier analysis, patients with lower IGFBP-3, higher IGFBP-3 promoter methylation, and normal p53 were associated most significantly with lower survival rates. In OEC cell line, IGFBP-3 expression was correlated with IGFBP-3 promoter methylation. IGFBP-3 expression was restored after treatment with a DNA methy-transferase inhibitors (5-aza-deoxycytidine) and suppressed by a p53 inhibitor (pifithrin-α). The putative p53 regulatory sites on the promoter of IGFBP-3 were identified at -210, -206, -183 and -179 bases upstream of the transcription start site. Directed mutagenesis at these sites quantitatively reduced the transcription activity of IGFBP-3. Conclusion Our data suggests that IGFBP-3 silencing through IGFBP-3 promoter methylation in the absence of p53 overexpression is associated with cancer progression. These results support a potential role of IGFBP-3 methylation in the carcinogenesis of OEC.
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Affiliation(s)
- Pao-Ling Torng
- Department of Obstetric and Gynecology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwa.
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Chaudhry P, Srinivasan R, Patel FD. Utility of gene promoter methylation in prediction of response to platinum-based chemotherapy in epithelial ovarian cancer (EOC). Cancer Invest 2009; 27:877-84. [PMID: 19548140 DOI: 10.1080/07357900902849699] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The aim was to determine whether promoter methylation of BRCA1, MGMT, MLH1, RASSF1A, and p16 genes could predict response to platinum-based chemotherapy. Thirty-five subjects with epithelial ovarian cancer (EOC) treated by platinum-based chemotherapy were recruited. Methylation-specific polymerase chain reaction was carried out and the methylation index (MI) was also derived. Response to platinum-based chemotherapy was documented clinically, radiologically, and by serial CA125 levels. Methylated BRCA1 (p = .037) and a higher MI (p = .045) were associated with primary chemosensitivity. A better outcome was predicted by a higher MI (p = .032). In EOC, BRCA1 gene promoter methylation is useful in the prediction of response to chemotherapy.
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Affiliation(s)
- Parvesh Chaudhry
- Departments of Radiotherapy, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Yamada PM, Lee KW. Perspectives in mammalian IGFBP-3 biology: local vs. systemic action. Am J Physiol Cell Physiol 2009; 296:C954-76. [PMID: 19279229 DOI: 10.1152/ajpcell.00598.2008] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Insulin-like growth factor (IGF) binding protein (IGFBP)-3 has traditionally been defined by its role as a binding protein and its association with IGF delivery and availability. Development of non-IGF binding IGFBP-3 analogs and the use of cell lines devoid of type 1 IGF receptors (IGF-R) have led to critical advances in the field of IGFBP-3 biology. These studies show that IGFBP-3 has IGF-independent roles in inhibiting cell proliferation in cancer cell lines. Nuclear transcription factor, retinoid X receptor (RXR)-alpha, and IGFBP-3 functionally interact to reduce prostate tumor growth and prostate-specific antigen in vivo. Moreover, IGFBP-3 inhibits insulin-stimulated glucose uptake into adipocytes independent of IGF. The purpose of this review is to highlight IGFBP-3 as a novel effector molecule and not just another "binding protein" by discussing its IGF-independent actions on metabolism and cell growth. Although this review presents studies that assume the role of IGFBP-3 as either an endocrine or autocrine/paracrine molecule, these systems may not exist as distinct entities, justifying the examination of IGFBP-3 in an integrated model. Also, we provide an overview of factors that regulate IGFBP-3 availability, including its production, methylation, and ubiquitination. We conclude with the role of IGFBP-3 in whole body systems and possible future applications of IGFBP-3 in physiology.
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Affiliation(s)
- Paulette M Yamada
- Dept. of Pediatrics, Mattel Children's Hospital, Los Angeles, CA 90095-1752, USA
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[Promoter hypermethylation gene patterns in gynecological tumors]. Med Clin (Barc) 2009; 132:371-6. [PMID: 19268989 DOI: 10.1016/j.medcli.2008.05.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Accepted: 05/15/2008] [Indexed: 11/21/2022]
Abstract
BACKGROUND AND OBJECTIVE Gene silencing mediated by the aberrant methylation of the promoter region of DNA is involved in the inactivation of genes implicated in various metabolic pathways. Such a gene hypermethylation has become a useful molecular marker for the diagnosis, treatment and follow-up of cancer patients. Our objective is to analyze the patterns of gene hypermethylation in patients with gynecological tumors. PATIENTS AND METHODS We selected 115 patients with gynecological cancers: 22 ovarian; 13 endometrial, 11 cervical-uterine and 69 breast cancers. By testing methylation-specific PCR, we studied the methylation status of genes CDNK2A (p16), APC1A, FHIT, CDH1 and hMLH1. RESULTS The frequencies of gene methylation in genes p16, APC1A, FHIT, hMLH1 and CDH1 were 29.2%, 34%, 60.4%, 10.9% and 79.8%, respectively. 70% of cases showed at least two methylated genes, which means a rate of methylation >0.4. The lowest frequency of methylation was seen in ovarian cancer, while the highest one was observed in endometrial cancer. CONCLUSIONS The results indicate that the aberrant methylation of the promoter region is an important event in carcinogenesis of gynecological tumors and that the pattern of gene methylation is associated with the nature of the tumor. These particular characteristics can deliver relevant information on the major metabolic pathways altered in each tumor type. In addition to complementary studies (ie, loss of expression and/or function), this represents a clinical tool for the proper management of the disease.
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Affiliation(s)
- Carla Kurkjian
- Advanced Developmental Therapeutics Training Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, USA
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Affiliation(s)
- Zhen Lu
- Department of Experimental Therapeutics, M.D. Anderson Cancer Center, University of Texas, Houston, TX 77030-4009, USA
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Melnikov A, Scholtens D, Godwin A, Levenson V. Differential methylation profile of ovarian cancer in tissues and plasma. J Mol Diagn 2008; 11:60-65. [PMID: 19074590 DOI: 10.2353/jmoldx.2009.080072] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An accurate biomarker for detection of ovarian cancer may reduce cancer-related mortality. Using a previously developed microarray-based technique, we evaluated differences in DNA methylation profiles in a panel of 56 genes using sections of serous papillary adenocarcinomas and uninvolved ovaries (n=30) from women in a high-risk group. Methylation profiles were also generated for circulating DNA from blood of patients (n=33) and healthy controls (n=33). Using the most differentially methylated genes for naïve Bayesian analysis, we identified ten of these profiles as potentially informative in tissues. Various combinations of these genes produced 69% sensitivity and 70% specificity for cancer detection as estimated under a stratified, fivefold cross-validation protocol. In plasma, five genes were identified as informative; their combination had 85% sensitivity and 61% specificity for cancer detection. These results suggest that differential methylation profiling in heterogeneous samples has the potential to identify components of a composite biomarker that may detect ovarian cancer in blood with significant accuracy.
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Affiliation(s)
- Anatoliy Melnikov
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Denise Scholtens
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Andrew Godwin
- Fox Chase Cancer Center, Department of Medical Oncology, Philadelphia, Pennsylvania
| | - Victor Levenson
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
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DNA hypermethylation, Her-2/neu overexpression and p53 mutations in ovarian carcinoma. Gynecol Oncol 2008; 111:320-9. [PMID: 18757082 DOI: 10.1016/j.ygyno.2008.07.036] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Revised: 07/16/2008] [Accepted: 07/19/2008] [Indexed: 11/24/2022]
Abstract
OBJECTIVES To define patterns of aberrant DNA methylation, p53 mutation and Her-2/neu overexpression in tissues from benign (n=29), malignant (n=100), and border line malignant ovaries (n=10), as compared to normal (n=68) ovarian tissues. Further, to explore the relationship between the presence of genetic and epigenetic abnormalities in ovarian cancers, and assess the association between epigenetic changes and clinical stage of malignancy at presentation and response to therapy. METHODS The methylation status of 23 genes that were previously reported associated with various epithelial malignancies was assessed in normal and abnormal ovarian tissues by methylation-specific PCR. The presence of p53 mutation (n=82 cases) and Her-2/neu overexpression (n=51 cases) were assessed by DNA sequencing and immunohistochemistry, respectively. RESULTS Methylation of four genes (MINT31, HIC1, RASSF1, and CABIN1) was significantly associated with ovarian cancer but not other ovarian pathology. Her-2/neu overexpression was associated with aberrant methylation of three genes (MINT31, RASSF1, and CDH13), although aberrant methylation was not associated with p53 mutations. Methylation of RASSF1 and HIC1 was more frequent in early compared to late stage ovarian cancer, while methylation of CABIN1 and RASSF1 was associated with response to chemotherapy. CONCLUSION DNA methylation of tumor suppressor genes is a frequent event in ovarian cancer, and in some cases is associated with Her-2/neu overexpression. Methylation of CABIN1 and RASSF1 may have the utility to predict response to therapy.
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Gadducci A, Cosio S, Tana R, Genazzani AR. Serum and tissue biomarkers as predictive and prognostic variables in epithelial ovarian cancer. Crit Rev Oncol Hematol 2008; 69:12-27. [PMID: 18595727 DOI: 10.1016/j.critrevonc.2008.05.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Revised: 04/17/2008] [Accepted: 05/08/2008] [Indexed: 11/29/2022] Open
Abstract
Tumour stage, residual disease after initial surgery, histological type and tumour grade are the most important clinical-pathological factors related to the clinical outcome of patients with epithelial ovarian cancer. In the last years, several investigations have assessed different biological variables in sera and in tissue samples from patients with this malignancy in order to detect biomarkers able to reflect either the response to chemotherapy or survival. The present paper reviewed the literature data about the predictive or prognostic relevance of serum CA 125, soluble cytokeratin fragments, serum human kallikreins, serum cytokines, serum vascular endothelial growth factor and plasma d-dimer as well as of tissue expression of cell cycle- and apoptosis-regulatory proteins, human telomerase reverse transcriptase, membrane tyrosine kinase receptors and matrix metalloproteinases. A next future microarray technology will hopefully offer interesting perspectives of translational research for the identification of novel predictive and prognostic biomarkers for epithelial ovarian cancer.
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Affiliation(s)
- Angiolo Gadducci
- Department of Procreative Medicine, Division of Gynecology and Obstetrics, University of Pisa, Via Roma 56, Pisa 56127, Italy.
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Harley I, Rosen B, Risch HA, Siminovitch K, Beiner ME, McLaughlin J, Sun P, Narod SA. Ovarian cancer risk is associated with a common variant in the promoter sequence of the mismatch repair gene MLH1. Gynecol Oncol 2008; 109:384-7. [PMID: 18405947 PMCID: PMC3060029 DOI: 10.1016/j.ygyno.2007.11.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 11/23/2007] [Accepted: 11/29/2007] [Indexed: 10/22/2022]
Abstract
OBJECTIVES Inherited mutations in the MLH1 gene are associated with a proportion of families with the hereditary non-polyposis colon cancer syndrome (HNPCC). The cardinal features of the syndrome are a predisposition to colon, endometrial and ovarian cancers. Recently, it has been shown that a non-coding polymorphic variant in MLH1 (G>A nt-93) predisposes to colon and endometrial cancer, but with much reduced penetrance. We sought to establish whether or not this polymorphic variant also predisposes to ovarian cancer. METHODS We genotyped 899 women with invasive ovarian cancer and 931 controls for the G>A nt-93 variant. RESULTS The presence of the variant was associated with a modest, but highly significant risk of ovarian cancer (OR=1.5; 95% CI 1.3-1.9; p=0.00005). The association was present in cancers of all histologies except clear cell, and in all ethnic groups. CONCLUSIONS The G>A nt-93 variant of the MLH1 gene is associated with an increased risk of invasive ovarian cancer.
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Affiliation(s)
- Ian Harley
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Toronto, ON, Canada
| | - Barry Rosen
- Division of Gynecologic Oncology, Princess Margaret Hospital and University of Toronto, Toronto ON, Canada
| | - Harvey A. Risch
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kathy Siminovitch
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON, Canada
| | - Mario E. Beiner
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Toronto, ON, Canada
- Women’s College Research Institute, University of Toronto, Toronto ON, Canada
| | - John McLaughlin
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON, Canada
| | - Ping Sun
- Women’s College Research Institute, University of Toronto, Toronto ON, Canada
| | - Steven A. Narod
- Women’s College Research Institute, University of Toronto, Toronto ON, Canada
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Tao MH, Shields PG, Nie J, Millen A, Ambrosone CB, Edge SB, Krishnan SS, Marian C, Xie B, Winston J, Vito D, Trevisan M, Freudenheim JL. DNA hypermethylation and clinicopathological features in breast cancer: the Western New York Exposures and Breast Cancer (WEB) Study. Breast Cancer Res Treat 2008; 114:559-68. [PMID: 18463976 DOI: 10.1007/s10549-008-0028-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 04/11/2008] [Indexed: 10/22/2022]
Abstract
Aberrant DNA hypermethylation of gene promoter regions has been increasingly recognized as a common molecular alteration in carcinogenesis. We evaluated the association between major clinicopathological features and hypermethylation of genes in tumors among 803 incidence breast cancer cases from a large population-based case-control study conducted in Western New York State. DNA samples were isolated from archive paraffin embedded tumor tissue and were analyzed for hypermethylation status of the E-cadherin, p16, and RAR-beta(2) genes using real time methylation-specific polymerase chain reaction. The frequencies of hypermethylation were 20.0% for E-cadherin, 25.9% for p16, and 27.5% for RAR-beta(2) genes. For postmenopausal women, hypermethylation of E-cadherin tended to be more likely in progesterone receptor (PR) negative than in PR-positive tumors (odds ratio (OR), 1.41; 95% confidence interval (CI), 0.91-2.18). Hypermethylation of p16 tended to be more frequent among estrogen receptor (ER) negative cases than ER-positive cases (OR, 1.51; 95% CI, 1.01-2.32). Hypermethylation of RAR-beta(2) gene was inversely associated with histological and nuclear grade of breast cancer.
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Affiliation(s)
- Meng Hua Tao
- Department of Social and Preventive Medicine, School of Public Health and Health Professions, University at Buffalo, 270 Farber Hall, Buffalo, NY 14214, USA.
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73
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CpG island methylator phenotype (CIMP) in cancer: causes and implications. Cancer Lett 2008; 268:177-86. [PMID: 18471961 DOI: 10.1016/j.canlet.2008.03.022] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Revised: 03/19/2008] [Accepted: 03/19/2008] [Indexed: 12/31/2022]
Abstract
Strong evidence exists for a subgroup of tumours, from a variety of tissue types, exhibiting concordant tumour specific DNA methylation: the "CpG island methylator phenotype" (CIMP). Occurrence of CIMP is associated with a range of genetic and environmental factors, although the molecular causes are not well-understood. Both increased expression and aberrant targeting of DNA methyltransferases (DNMTs) could contribute to the occurrence of CIMP. One under-explored area is the possibility that DNA damage may induce or select for CIMP during carcinogenesis or treatment of tumours with chemotherapy. DNA damaging agents can induce DNA damage at guanine rich regions throughout the genome, including CpG islands. This DNA damage can result in stalled DNA synthesis, which will lead to localised increased DNMT1 concentration and therefore potentially increased DNA methylation at these sites. Chemotherapy can select for cells which have increased tolerance to DNA damage due to increased lesion bypass, in some cases by mechanisms which involve inactivation of genes by CpG island methylation. CIMP has been associated with worse patient prognosis, probably due to increased epigenetic plasticity. Therefore, further clinical testing of the diagnostic and prognostic value of the current CIMP markers, as well as increasing our understanding of the molecular causes underlying CIMP are required.
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74
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Barton CA, Hacker NF, Clark SJ, O'Brien PM. DNA methylation changes in ovarian cancer: implications for early diagnosis, prognosis and treatment. Gynecol Oncol 2008; 109:129-39. [PMID: 18234305 DOI: 10.1016/j.ygyno.2007.12.017] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 12/07/2007] [Accepted: 12/10/2007] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To review epigenetic changes identified in ovarian cancer, focusing on their potential as clinical markers for detection, monitoring of disease progression and as markers of therapeutic response. METHODS A comprehensive review of English language scientific literature on the topics of methylation and ovarian cancer was conducted. RESULTS Genome-wide demethylation of normally methylated and silenced chromosomal regions, and hypermethylation and silencing of genes including tumor suppressors are common features of cancer cells. Epigenetic alterations, including CpG island DNA methylation, occur in ovarian cancer and the identification of specific genes that are altered by epigenetic events is an area of intense research. Aberrant DNA methylation in ovarian cancer is observed in early cancer development, can be detected in DNA circulating in the blood and hence provides the promise of a non-invasive cancer detection test. In addition, identification of ovarian cancer-specific epigenetic changes has promise in molecular classification and disease stratification. CONCLUSIONS The detection of cancer-specific DNA methylation changes heralds an exciting new era in cancer diagnosis as well as evaluation of prognosis and therapeutic responsiveness and warrants further investigation.
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Affiliation(s)
- Caroline A Barton
- Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia
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75
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Press JZ, De Luca A, Boyd N, Young S, Troussard A, Ridge Y, Kaurah P, Kalloger SE, Blood KA, Smith M, Spellman PT, Wang Y, Miller DM, Horsman D, Faham M, Gilks CB, Gray J, Huntsman DG. Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities. BMC Cancer 2008; 8:17. [PMID: 18208621 PMCID: PMC2245962 DOI: 10.1186/1471-2407-8-17] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 01/22/2008] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Subclassification of ovarian carcinomas can be used to guide treatment and determine prognosis. Germline and somatic mutations, loss of heterozygosity (LOH), and epigenetic events such as promoter hypermethylation can lead to decreased expression of BRCA1/2 in ovarian cancers. The mechanism of BRCA1/2 loss is a potential method of subclassifying high grade serous carcinomas. METHODS A consecutive series of 49 ovarian cancers was assessed for mutations status of BRCA1 and BRCA2, LOH at the BRCA1 and BRCA2 loci, methylation of the BRCA1 promoter, BRCA1, BRCA2, PTEN, and PIK3CA transcript levels, PIK3CA gene copy number, and BRCA1, p21, p53, and WT-1 immunohistochemistry. RESULTS Eighteen (37%) of the ovarian carcinomas had germline or somatic BRCA1 mutations, or epigenetic loss of BRCA1. All of these tumours were high-grade serous or undifferentiated type. None of the endometrioid (n = 5), clear cell (n = 4), or low grade serous (n = 2) carcinomas showed loss of BRCA1, whereas 47% of the 38 high-grade serous or undifferentiated carcinomas had loss of BRCA1. It was possible to distinguish high grade serous carcinomas with BRCA1 mutations from those with epigenetic BRCA1 loss: tumours with BRCA1 mutations typically had decreased PTEN mRNA levels while those with epigenetic loss of BRCA1 had copy number gain of PIK3CA. Overexpression of p53 with loss of p21 expression occurred significantly more frequently in high grade serous carcinomas with epigenetic loss of BRCA1, compared to high grade serous tumors without loss of BRCA1. CONCLUSION High grade serous carcinomas can be subclassified into three groups: BRCA1 loss (genetic), BRCA1 loss (epigenetic), and no BRCA1 loss. Tumors in these groups show distinct molecular alterations involving the PI3K/AKT and p53 pathways.
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Affiliation(s)
- Joshua Z Press
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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Fridman AL, Rosati R, Li Q, Tainsky MA. Epigenetic and functional analysis of IGFBP3 and IGFBPrP1 in cellular immortalization. Biochem Biophys Res Commun 2007; 357:785-91. [PMID: 17451653 DOI: 10.1016/j.bbrc.2007.04.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 04/03/2007] [Accepted: 04/03/2007] [Indexed: 11/29/2022]
Abstract
Carcinogenic transformation of a cell requires bypassing senescence and becoming immortalized. A cellular senescence-like phenotype can be induced in immortal Li-Fraumeni syndrome (LFS) cells by treating them with the DNA methyltransferase inhibitor 5-aza-deoxycytidine. Our microarray-based expression profiling studies of spontaneously immortalized LFS cell lines identified genes that may provide the growth advantage required for the cells to become immortal. Several members of the IGFBP superfamily of genes fit the profile of genes involved in immortalization: silenced during immortalization and reactivated by 5-aza-deoxycytidine. Overexpression of IGFBP3 or IGFBPrP1 in the immortal LFS cell lines suppressed cell growth and inhibited colony formation. Both genes have the expression pattern of an epigenetically regulated gene and contain CpG islands suitable for methylation-dependent silencing. Analysis of how IGFBPs regulate immortalization will lead to a better understanding of this process and may lead to novel methods for the prevention and treatment of cancer.
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Affiliation(s)
- Aviva Levine Fridman
- Program in Molecular Biology and Genetics, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, 110 East Warren Avenue, Detroit, MI 48201, USA
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Perry AS, Loftus B, Moroose R, Lynch TH, Hollywood D, Watson RWG, Woodson K, Lawler M. In silico mining identifies IGFBP3 as a novel target of methylation in prostate cancer. Br J Cancer 2007; 96:1587-94. [PMID: 17453001 PMCID: PMC2359953 DOI: 10.1038/sj.bjc.6603767] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Promoter hypermethylation is central in deregulating gene expression in cancer. Identification of novel methylation targets in specific cancers provides a basis for their use as biomarkers of disease occurrence and progression. We developed an in silico strategy to globally identify potential targets of promoter hypermethylation in prostate cancer by screening for 5′ CpG islands in 631 genes that were reported as downregulated in prostate cancer. A virtual archive of 338 potential targets of methylation was produced. One candidate, IGFBP3, was selected for investigation, along with glutathione-S-transferase pi (GSTP1), a well-known methylation target in prostate cancer. Methylation of IGFBP3 was detected by quantitative methylation-specific PCR in 49/79 primary prostate adenocarcinoma and 7/14 adjacent preinvasive high-grade prostatic intraepithelial neoplasia, but in only 5/37 benign prostatic hyperplasia (P<0.0001) and in 0/39 histologically normal adjacent prostate tissue, which implies that methylation of IGFBP3 may be involved in the early stages of prostate cancer development. Hypermethylation of IGFBP3 was only detected in samples that also demonstrated methylation of GSTP1 and was also correlated with Gleason score ⩾7 (P=0.01), indicating that it has potential as a prognostic marker. In addition, pharmacological demethylation induced strong expression of IGFBP3 in LNCaP prostate cancer cells. Our concept of a methylation candidate gene bank was successful in identifying a novel target of frequent hypermethylation in early-stage prostate cancer. Evaluation of further relevant genes could contribute towards a methylation signature of this disease.
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Affiliation(s)
- A S Perry
- Department of Haematology and Academic Unit of Clinical and Molecular Oncology, Institute of Molecular Medicine, St James's Hospital and Trinity College Dublin, Ireland.
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