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Yao H, Li H, Wang J, Wu T, Ning W, Diao K, Wu C, Wang G, Tao Z, Zhao X, Chen J, Sun X, Liu XS. Copy number alteration features in pan-cancer homologous recombination deficiency prediction and biology. Commun Biol 2023; 6:527. [PMID: 37193789 DOI: 10.1038/s42003-023-04901-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/02/2023] [Indexed: 05/18/2023] Open
Abstract
Homologous recombination deficiency (HRD) renders cancer cells vulnerable to unrepaired double-strand breaks and is an important therapeutic target as exemplified by the clinical efficacy of poly ADP-ribose polymerase (PARP) inhibitors as well as the platinum chemotherapy drugs applied to HRD patients. However, it remains a challenge to predict HRD status precisely and economically. Copy number alteration (CNA), as a pervasive trait of human cancers, can be extracted from a variety of data sources, including whole genome sequencing (WGS), SNP array, and panel sequencing, and thus can be easily applied clinically. Here we systematically evaluate the predictive performance of various CNA features and signatures in HRD prediction and build a gradient boosting machine model (HRDCNA) for pan-cancer HRD prediction based on these CNA features. CNA features BP10MB[1] (The number of breakpoints per 10MB of DNA is 1) and SS[ > 7 & <=8] (The log10-based size of segments is greater than 7 and less than or equal to 8) are identified as the most important features in HRD prediction. HRDCNA suggests the biallelic inactivation of BRCA1, BRCA2, PALB2, RAD51C, RAD51D, and BARD1 as the major genetic basis for human HRD, and may also be applied to effectively validate the pathogenicity of BRCA1/2 variants of uncertain significance (VUS). Together, this study provides a robust tool for cost-effective HRD prediction and also demonstrates the applicability of CNA features and signatures in cancer precision medicine.
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Affiliation(s)
- Huizi Yao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huimin Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyu Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wei Ning
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Kaixuan Diao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chenxu Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guangshuai Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ziyu Tao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiangyu Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jing Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiaoqin Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xue-Song Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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Lobanova O, Medvedieva N, Fishchuk L, Dubitska O, Cheshuk V, Vereshchako R, Zakhartseva L, Rossokha Z, Gorovenko N. Methylation of promoter region of BRCA1 gene versus pathogenic variants of gene: risk factor or clinical marker of breast cancer. Breast Cancer Res Treat 2022; 196:505-515. [DOI: 10.1007/s10549-022-06774-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/13/2022] [Indexed: 11/28/2022]
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3
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Pereira IC, Mascarenhas IF, Capetini VC, Ferreira PMP, Rogero MM, Torres-Leal FL. Cellular reprogramming, chemoresistance, and dietary interventions in breast cancer. Crit Rev Oncol Hematol 2022; 179:103796. [PMID: 36049616 DOI: 10.1016/j.critrevonc.2022.103796] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/16/2022] [Accepted: 08/21/2022] [Indexed: 10/31/2022] Open
Abstract
Breast cancer (BC) diagnosis has been associated with significant risk factors, including family history, late menopause, obesity, poor eating habits, and alcoholism. Despite the advances in the last decades regarding cancer treatment, some obstacles still hinder the effectiveness of therapy. For example, chemotherapy resistance is common in locally advanced or metastatic cancer, reducing treatment options and contributing to mortality. In this review, we provide an overview of BC metabolic changes, including the impact of restrictive diets associated with chemoresistance, the therapeutic potential of the diet on tumor progression, pathways related to metabolic health in oncology, and perspectives on the future in the area of oncological nutrition.
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Affiliation(s)
- Irislene Costa Pereira
- Department of Biophysics and Physiology, Center for Health Sciences, Federal University of Piauí, Teresina, Piauí, Brazil; Metabolic Diseases, Exercise and Nutrition Research Group (DOMEN), Center for Health Sciences, Federal University of Piauí, Teresina, Piauí, Brazil
| | - Isabele Frazão Mascarenhas
- Department of Biophysics and Physiology, Center for Health Sciences, Federal University of Piauí, Teresina, Piauí, Brazil
| | | | - Paulo Michel Pinheiro Ferreira
- Department of Biophysics and Physiology, Center for Health Sciences, Federal University of Piauí, Teresina, Piauí, Brazil
| | - Marcelo Macedo Rogero
- Department of Nutrition, School of Public Health, University of São Paulo, Sao Paulo, Brazil
| | - Francisco Leonardo Torres-Leal
- Department of Biophysics and Physiology, Center for Health Sciences, Federal University of Piauí, Teresina, Piauí, Brazil; Metabolic Diseases, Exercise and Nutrition Research Group (DOMEN), Center for Health Sciences, Federal University of Piauí, Teresina, Piauí, Brazil.
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Leibowitz BD, Dougherty BV, Bell JSK, Kapilivsky J, Michuda J, Sedgewick AJ, Munson WA, Chandra TA, Dry JR, Beaubier N, Igartua C, Taxter T. Validation of genomic and transcriptomic models of homologous recombination deficiency in a real-world pan-cancer cohort. BMC Cancer 2022; 22:587. [PMID: 35643464 PMCID: PMC9148513 DOI: 10.1186/s12885-022-09669-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Background With the introduction of DNA-damaging therapies into standard of care cancer treatment, there is a growing need for predictive diagnostics assessing homologous recombination deficiency (HRD) status across tumor types. Following the strong clinical evidence for the utility of DNA-sequencing-based HRD testing in ovarian cancer, and growing evidence in breast cancer, we present analytical validation of the Tempus HRD-DNA test. We further developed, validated, and explored the Tempus HRD-RNA model, which uses gene expression data from 16,750 RNA-seq samples to predict HRD status from formalin-fixed paraffin-embedded tumor samples across numerous cancer types. Methods Genomic and transcriptomic profiling was performed using next-generation sequencing from Tempus xT, Tempus xO, Tempus xE, Tempus RS, and Tempus RS.v2 assays on 48,843 samples. Samples were labeled based on their BRCA1, BRCA2 and selected Homologous Recombination Repair pathway gene (CDK12, PALB2, RAD51B, RAD51C, RAD51D) mutational status to train and validate HRD-DNA, a genome-wide loss-of-heterozygosity biomarker, and HRD-RNA, a logistic regression model trained on gene expression. Results In a sample of 2058 breast and 1216 ovarian tumors, BRCA status was predicted by HRD-DNA with F1-scores of 0.98 and 0.96, respectively. Across an independent set of 1363 samples across solid tumor types, the HRD-RNA model was predictive of BRCA status in prostate, pancreatic, and non-small cell lung cancer, with F1-scores of 0.88, 0.69, and 0.62, respectively. Conclusions We predict HRD-positive patients across many cancer types and believe both HRD models may generalize to other mechanisms of HRD outside of BRCA loss. HRD-RNA complements DNA-based HRD detection methods, especially for indications with low prevalence of BRCA alterations. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09669-z.
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Ho JCW, Chen J, Cheuk IWY, Siu MT, Shin VY, Kwong A. MicroRNA-199a-3p promotes drug sensitivity in triple negative breast cancer by down-regulation of BRCA1. Am J Transl Res 2022; 14:2021-2036. [PMID: 35422914 PMCID: PMC8991114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/07/2021] [Indexed: 06/14/2023]
Abstract
MiR-199a-3p was previously predicted to target tumor suppressor gene BRCA1, which has been linked to cancer onset and therapeutic response. In this study, the effects of miR-199a-3p-mediated BRCA1 dysfunction on triple-negative breast cancer (TNBC) progression and chemosensitivity were assessed. The association between miR-199a-3p and BRCA1 expression was examined in TNBC tumors and verified with luciferase reporter and protein assays. Tumorigenic functions of miR-199a-3p in TNBC cells were investigated by cell proliferation, clonogenic and migration assays. The sensitivities to chemotherapeutic drugs were tested with cisplatin and PARP inhibitor (veliparib) treatments. Mouse xenograft model was used to examine the effects of miR-199a-3p on tumor growth and drug response in vivo. MiR-199a-3p was shown to directly target BRCA1 in TNBC cells, resulting its downregulation and reduced luciferase reporter activity mediated by BRCA1 3'-UTR. Ectopic miR-199a-3p in TNBC cells exerted inhibitory effects on cell proliferation, migration and xenograft tumor growth. Moreover, miR-199a-3p was shown to reverse cisplatin-resistance and sensitize TNBC cells to veliparib, which might be due to repressed DNA repair ability and induced cell apoptosis. Our results demonstrated the tumor suppressive effects of miR-199a-3p on TNBC and induction on chemotherapeutic sensitivities, which were correlated with BRCA1 gene dysfunction. These findings may provide insights into the potential prognostic and therapeutic values of miR-199a-3p in patients with TNBC.
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Affiliation(s)
- John Chi-Wang Ho
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong, China
| | - Jiawei Chen
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong, China
| | - Isabella Wai-Yin Cheuk
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong, China
| | - Man-Ting Siu
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong, China
| | - Vivian Yvonne Shin
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong, China
| | - Ava Kwong
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong, China
- Department of Surgery, Hong Kong Sanatorium & HospitalHong Kong, China
- Hong Kong Hereditary Breast Cancer Family RegistryHong Kong, China
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6
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Ruscito I, Gasparri ML, De Marco MP, Costanzi F, Besharat AR, Papadia A, Kuehn T, Gentilini OD, Bellati F, Caserta D. The Clinical and Pathological Profile of BRCA1 Gene Methylated Breast Cancer Women: A Meta-Analysis. Cancers (Basel) 2021; 13:cancers13061391. [PMID: 33808555 PMCID: PMC8003261 DOI: 10.3390/cancers13061391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/09/2021] [Accepted: 03/16/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND DNA aberrant hypermethylation is the major cause of transcriptional silencing of the breast cancer gene 1 (BRCA1) gene in sporadic breast cancer patients. The aim of the present meta-analysis was to analyze all available studies reporting clinical characteristics of BRCA1 gene hypermethylated breast cancer in women, and to pool the results to provide a unique clinical profile of this cancer population. METHODS On September 2020, a systematic literature search was performed. Data were retrieved from PubMed, MEDLINE, and Scopus by searching the terms: "BRCA*" AND "methyl*" AND "breast". All studies evaluating the association between BRCA1 methylation status and breast cancer patients' clinicopathological features were considered for inclusion. RESULTS 465 studies were retrieved. Thirty (6.4%) studies including 3985 patients met all selection criteria. The pooled analysis data revealed a significant correlation between BRCA1 gene hypermethylation and advanced breast cancer disease stage (OR = 0.75: 95% CI: 0.58-0.97; p = 0.03, fixed effects model), lymph nodes involvement (OR = 1.22: 95% CI: 1.01-1.48; p = 0.04, fixed effects model), and pre-menopausal status (OR = 1.34: 95% CI: 1.08-1.66; p = 0.008, fixed effects model). No association could be found between BRCA1 hypermethylation and tumor histology (OR = 0.78: 95% CI: 0.59-1.03; p = 0.08, fixed effects model), tumor grading (OR = 0.78: 95% CI :0.46-1.32; p = 0.36, fixed effects model), and breast cancer molecular classification (OR = 1.59: 95% CI: 0.68-3.72; p = 0.29, random effects model). CONCLUSIONS hypermethylation of the BRCA1 gene significantly correlates with advanced breast cancer disease, lymph nodes involvement, and pre-menopausal cancer onset.
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Affiliation(s)
- Ilary Ruscito
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
- Correspondence: ; Tel.: +39-06-3377-5696
| | - Maria Luisa Gasparri
- Department of Gynecology and Obstetrics, Ente Ospedaliere Cantonale (EOC), Via Tesserete 46, 6900 Lugano, Switzerland; (M.L.G.); (A.P.)
- University of the Italian Switzerland (USI), Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
| | - Maria Paola De Marco
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Flavia Costanzi
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Aris Raad Besharat
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Andrea Papadia
- Department of Gynecology and Obstetrics, Ente Ospedaliere Cantonale (EOC), Via Tesserete 46, 6900 Lugano, Switzerland; (M.L.G.); (A.P.)
- University of the Italian Switzerland (USI), Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
| | - Thorsten Kuehn
- Interdisciplinary Breast Center, Department of Gynecology and Obstetrics, Klinikum Esslingen, 73730 Neckar, Germany;
| | - Oreste Davide Gentilini
- Breast Surgery Unit, San Raffaele University Hospital, via Olgettina 60, 20132 Milan, Italy;
| | - Filippo Bellati
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Donatella Caserta
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
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Arif T, Anwar N. Promoter Hypermethylation and Expression Changes of BRCA1 Gene in a Cohort of Sporadic Breast Cancer Cases among Pakistani Population. Asian Pac J Cancer Prev 2020; 21:2395-2401. [PMID: 32856871 PMCID: PMC7771953 DOI: 10.31557/apjcp.2020.21.8.2395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Indexed: 11/25/2022] Open
Abstract
Objective: The purpose of our study was to determine the frequency of BRCA1 promoter hypermethylation and its association with expression changes of BRCA1 and main morphological features in sporadic breast cancer. Methods: A retrospective review of cases was performed to select those with specific morphological features suggestive of breast cancer. BRCA1 promoter hypermethylation and changes in protein expression were evaluated in 30 cancerous and 30 non-cancerous tissue samples. A tissue microarray containing samples from normal and tumor tissue was prepared and stained for BRCA1 protein expression using a commercially available monoclonal antibody against BRCA1 (Ab-1) clone MS110 (mAb). DNA was extracted using modified protocol of Qiagen minikit. DNA was modified using a Bisulfite conversion kit and BRCA1 hypermethylation was detected using a methylation specific PCR. Results: Promoter hypermethylation was negative in 30 non-cancerous samples with retained BRCA1 protein expression. Methylation was positive in 82.6% (n=19/23) of the sporadic cancer samples that had loss of BRCA1 expression and 50% (n=2/4) of the samples with equivocal protein expression. Methylation was negative in all the sporadic breast cancer samples (n=3/3) with retained protein expression. Chi-square analysis showed significant association of BRCA1 promoter methylation with decreased protein expression (P=0.016) and co-existence of loss of BRCA1 and Her2neu at chromosome 17 (P=0.026) respectively. There was no significant association of BRCA1 methylation with morphological features excluding necrosis (P=0.035). Promoter hypermethylation was found to be most common (68.75%) among Triple Negative Breast Cancer (TNBC) females less than 45 years old. Conclusion: Our study suggests that BRCA1 promoter hypermethylation has significant contribution in sporadic breast carcinogenesis. This was our preliminary study in Pakistan. Further studies aimed to determine the in-depth mechanisms of BRCA1 epigenetics in TNBC. BRCAness enriched phenotype in TNBC might be used as a biomarker for the exploitation of therapeutic and clinical implications.
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Affiliation(s)
- Taqdees Arif
- MPhil Molecular Pathology and Genomics, Department of Biological Sciences, Forman Christian College, Lahore, Pakistan
| | - Natasha Anwar
- Consultant Molecular Pathologist, Agha Khan University Hospital Lahore Stat Lab, Lahore, Pakistan
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Li S, He Y, Li C, Liu X, Shen Y, Wu Y, Bai N, Li Q. The association between the methylation frequency of BRCA1/2 gene promoter and occurrence and prognosis of breast carcinoma: A meta-analysis. Medicine (Baltimore) 2020; 99:e19345. [PMID: 32150073 PMCID: PMC7478499 DOI: 10.1097/md.0000000000019345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Breast cancer susceptibility gene 1/2 (BRCA1/2) is a promising tumor marker in many types of cancer. However, the methylation frequency of BRCA1/2 gene with occurrence risk and survival benefit of patients with breast carcinoma remains controversy. The aim of the present study was to assess the relationship between BRCA1/2 gene promoter methylation and the occurrence and prognosis in breast carcinoma based on a meta-analysis, meanwhile, this article explored the differential expression levels of BRCA1/2 gene promoter methylation in peripheral blood and tumor tissues of breast cancer patients. METHODS Electronic databases (PubMed, Medline, Cochrane Library, and CNKI) were searched up to June 2019. The number of BRCA1/2 promoter methylation-positive and -negative patients in breast carcinoma patients were measured, and hazard ratio (HR) with 95% confidence interval (CI) for the association between BRCA1/2 gene promoter methylation and the prognosis of breast carcinoma patients. Primary end points were presence of breast cancer, overall survival (OS), disease-free survival (DFS). Statistical analysis was performed with STATA 12.0. RESULTS AND CONCLUSIONS Fifty-eight articles including 19,084 individuals met full eligibility criteria. We observed that the frequency of BRCA1 gene promoter methylation was higher in breast cancer tissues compared with normal tissues, and the prognostic analysis suggested that BRCA1 gene promoter methylation was significantly associated with poor overall survival and poor disease-free survival. This study also verified that there was no statistically significant difference in the methylation frequency of BRCA1 gene promoter between peripheral blood and tumor tissues in breast cancer patients, which suggests that the detection of BRCA1 promoter methylation in peripheral blood may be a non-invasive and rapid way to monitor the occurrence breast cancer.
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Affiliation(s)
- Shu Li
- Clinical Laboratory, Chongqing Health Center for Women and Children
| | - Yong He
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing
| | - Chunli Li
- Clinical Laboratory, Chongqing Health Center for Women and Children
| | - Xing Liu
- Clinical Laboratory, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Yan Shen
- Clinical Laboratory, Chongqing Health Center for Women and Children
| | - Yang Wu
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing
| | - Ningjing Bai
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing
| | - Qiuhong Li
- Clinical Laboratory, Chongqing Health Center for Women and Children
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Chen J, Haanpää MK, Gruber JJ, Jäger N, Ford JM, Snyder MP. High-Resolution Bisulfite-Sequencing of Peripheral Blood DNA Methylation in Early-Onset and Familial Risk Breast Cancer Patients. Clin Cancer Res 2019; 25:5301-5314. [PMID: 31175093 DOI: 10.1158/1078-0432.ccr-18-2423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 04/11/2019] [Accepted: 06/05/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Understanding and explaining hereditary predisposition to cancer has focused on the genetic etiology of the disease. However, mutations in known genes associated with breast cancer, such as BRCA1 and BRCA2, account for less than 25% of familial cases of breast cancer. Recently, specific epigenetic modifications at BRCA1 have been shown to promote hereditary breast cancer, but the broader potential for epigenetic contribution to hereditary breast cancer is not yet well understood. EXPERIMENTAL DESIGN We examined DNA methylation through deep bisulfite sequencing of CpG islands and known promoter or regulatory regions in peripheral blood DNA from 99 patients with familial or early-onset breast or ovarian cancer, 6 unaffected BRCA mutation carriers, and 49 unaffected controls. RESULTS In 9% of patients, we observed altered methylation in the promoter regions of genes known to be involved in cancer, including hypermethylation at the tumor suppressor PTEN and hypomethylation at the proto-oncogene TEX14. These alterations occur in the form of allelic methylation that span up to hundreds of base pairs in length. CONCLUSIONS Our observations suggest a broader role for DNA methylation in early-onset, familial risk breast cancer. Further studies are warranted to clarify these mechanisms and the benefits of DNA methylation screening for early risk prediction of familial cancers.
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Affiliation(s)
- Justin Chen
- Department of Genetics, Stanford University, Stanford, California
| | - Maria K Haanpää
- Department of Medicine, Oncology Division, Stanford University, Stanford, California
| | - Joshua J Gruber
- Department of Genetics, Stanford University, Stanford, California.,Department of Medicine, Oncology Division, Stanford University, Stanford, California
| | - Natalie Jäger
- Department of Genetics, Stanford University, Stanford, California
| | - James M Ford
- Department of Genetics, Stanford University, Stanford, California. .,Department of Medicine, Oncology Division, Stanford University, Stanford, California
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, California.
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10
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Paydar P, Asadikaram G, Nejad HZ, Akbari H, Abolhassani M, Moazed V, Nematollahi MH, Ebrahimi G, Fallah H. Epigenetic modulation of BRCA-1 and MGMT genes, and histones H4 and H3 are associated with breast tumors. J Cell Biochem 2019; 120:13726-13736. [PMID: 30938887 DOI: 10.1002/jcb.28645] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/03/2019] [Accepted: 02/14/2019] [Indexed: 12/11/2022]
Abstract
Aberrant patterns in promoter methylation of tumor-suppressor genes and posttranslational modifications of histone proteins are considered as major features of malignancy. In this study, we aimed to investigate promoter methylation of three tumor-suppressor genes (BRCA-1, MGMT, and P16) and three histone marks (H3K9ac, H3K18ac, and H4K20me3) in patients with breast tumors. This case-control study included 27 patients with malignant breast tumors (MBT) and 31 patients with benign breast tumors (BBT). The methylation-specific PCR was used for determining promoter methylation of BRCA-1, MGMT, and P16 genes. Western blot analysis was performed to detect histone lysine acetylation (H3K9ac and H3K18ac) and lysine methylation (H4K20me3). BRCA-1 promoter methylation was detected in 44.4% of the MBT whereas this alteration was found in 9.7% of BBT (P = 0.005). The Kaplan-Meier analysis indicated that hypermethylation in BRCA-1 promoter was significantly associated with poor overall survival of patients with breast cancer (P = 0.039). MGMT promoter methylation was identified in 18.5% of MBT and 0.0% of the BBT (P = 0.01). The frequency of P16 promoter methylation was 25.8% in BBT and 11.1% in MBT (P = 0.12). As compared with BBT, MBT samples displayed the aberrant patterns of histones marks with hypomethylation of H4K20 and hypoacetylation of H3K18 (P = 0.03 and P = 0.04, respectively). There was a negative significant correlation between H3K9ac levels and tumor size in MBT group (r = -0.672; P = 0.008). The present findings suggest that promoter hypermethylation of MGMT and BRCA-1 genes along with alterations in H3K18ac and H4K20me3 levels may have prognostic values in patients with breast cancer. Moreover, the detection of these epigenetic modifications in breast tumors could be helpful in finding new methods for breast cancer therapy.
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Affiliation(s)
- Parisa Paydar
- Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman, Iran.,Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Gholamreza Asadikaram
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Neuroscience Research Center, Institute of Neuropharmacology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Zeynali Nejad
- Department of Surgery, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamed Akbari
- Student Research Committee, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Moslem Abolhassani
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Vahid Moazed
- Department of Hematology and Oncology, Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hadi Nematollahi
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Ghasem Ebrahimi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Fallah
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
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NINDREA RD, ARYANDONO T, LAZUARDI L, DWIPRAHASTO I. Family History of Breast Cancer and Breast Cancer Risk between Malays Ethnicity in Malaysia and Indonesia: A Meta-Analysis. IRANIAN JOURNAL OF PUBLIC HEALTH 2019; 48:198-205. [PMID: 31205873 PMCID: PMC6556193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND Breast cancer is the most common cancer type in women not only in world but also in Malays ethnicity between Malaysia and Indonesia. Breast cancer has varying incidence in every country, but genetic factor by family history influence the incidence of breast cancer. This systematic review and meta-analysis was performed to determine family history of breast cancer and breast cancer risk between Malays ethnicity in Malaysia and Indonesia. METHODS This meta-analysis was conducted on published research articles on family history of breast cancer and breast cancer risk between Malays ethnicity in Malaysia and Indonesia published between Jan 1999 and Jul 2018 in the online article databases of PubMed, ProQuest and EBSCO. Pooled odds ratios (OR) were calculated with fixed and random-effect models. Publication bias was visually evaluated by using funnel plots and statistically assessed through Egger's and Begg's tests. Data were processed using Review Manager 5.3 (RevMan 5.3) and Stata version 14.2 (Stata Corporation). RESULTS We reviewed 1123 articles. There are 10 studies with number of samples 4511 conducted a systematic review and continued with Meta-analysis of relevant data. The results showed significant association between family history of breast cancer with breast cancer risk in Malays ethnicity in Malaysia and Indonesia (OR = 3.34 [95% CI 2.68-4.15, P<0.00001]). There was not significant publication bias for studies included in family history of breast cancer and breast cancer risk in Malays ethnicity in Malaysia and Indonesia. CONCLUSION This analysis confirmed the association of family history of breast cancer and breast cancer risk between Malays ethnicity in Malaysia and Indonesia.
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Affiliation(s)
- Ricvan Dana NINDREA
- Doctoral Program, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia, Department of Public Health, Faculty of Medicine, Universitas Andalas, Padang, Indonesia,Corresponding Author:
| | - Teguh ARYANDONO
- Department of Surgery, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Lutfan LAZUARDI
- Department of Health Policy and Management, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Iwan DWIPRAHASTO
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Active and secondhand smoke exposure throughout life and DNA methylation in breast tumors. Cancer Causes Control 2019; 30:53-62. [PMID: 30617699 DOI: 10.1007/s10552-018-1102-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 11/22/2018] [Indexed: 10/27/2022]
Abstract
PURPOSE Tobacco smoke exposure has been associated with altered DNA methylation. However, there is a paucity of information regarding tobacco smoke exposure and DNA methylation of breast tumors. METHODS We conducted a case-only analysis using breast tumor tissue from 493 postmenopausal and 225 premenopausal cases in the Western New York Exposures and Breast Cancer (WEB) study. Methylation of nine genes (SFN, SCGB3A1, RARB, GSTP1, CDKN2A, CCND2, BRCA1, FHIT, and SYK) was measured with pyrosequencing. Participants reported their secondhand smoke (SHS) and active smoking exposure for seven time periods. Unconditional logistic regression was used to estimate odds ratios (OR) of having methylation higher than the median. RESULTS SHS exposure was associated with tumor DNA methylation among postmenopausal but not premenopausal women. Active smoking at certain ages was associated with increased methylation of GSTP1, FHIT, and CDKN2A and decreased methylation of SCGB3A1 and BRCA1 among both pre- and postmenopausal women. CONCLUSION Exposure to tobacco smoke may contribute to breast carcinogenesis via alterations in DNA methylation. Further studies in a larger panel of genes are warranted.
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13
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Harahap WA, Sudji IR, Nindrea RD. BRCA1 Promoter Methylation and Clinicopathological Characteristics in Sporadic Breast Cancer Patients in Indonesia. Asian Pac J Cancer Prev 2018; 19:2643-2649. [PMID: 30256562 PMCID: PMC6249447 DOI: 10.22034/apjcp.2018.19.9.2643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Objective: The aim of this study was to investigate the BRCA1 promoter methylation and clinicopathological characteristics in sporadic breast cancer patients in Indonesia. Methods: In this cohort study, we selected 90 patients with stage I-III who had definitive surgery at our institution in 2011-2014. Demographic and clinical data regarding pathological stage, breast cancer treatment, outcome etc. were collected from the medical records. Twelve patients had incomplete information on follow up and 18 samples had insufficient tissues for the experiment. Sixty patients with adequate cancer tissues and complete follow up record were analyzed, only 56 patients were analyzed because 4 samples mRNA expression could not be detected. The Mann–Whitney U tests for non-normally distributed groups were used to compare the levels expression of BRCA1 mRNA between methylated and non-methylated samples. Chi-square tests were used to compare methylation status, BRCA1 mRNA expression and clinicopathological characteristics. P value < 0.05 was considered as statistically significant correlation. Data analysis was held by using the GraphPad PRISM 7 (GraphPad Software Inc., USA). Results: DNA and RNA were isolated from primary tumor tissues of 56 breast cancer patients. BRCA1 promoter methylation was detected in 48 of 56 patients (85%). Level of BRCA1 mRNA expression was associated with decreased methylation level in the BRCA1 promoter regions suggesting the role of epigenetic silencing. However, there was no statistically significant association among methylation levels, BRCA1 mRNA transcript level with clinicopathological factors. Conclusion: To our knowledge, this is the first study investigating methylation status and level of BRCA1 mRNA transcripts among breast cancer patients in Indonesia. We found that the prevalence of BRCA1 promoter methylation is higher than other studies from different populations. However, further investigation involving larger number of patients is required.
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Affiliation(s)
- Wirsma Arif Harahap
- Division of Surgical Oncology Medical School of Andalas University, M.Djamil Hospital, Padang, Indonesia.
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14
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Nindrea RD, Harahap WA, Aryandono T, Lazuardi L. Association of BRCA1 Promoter Methylation with Breast Cancer in Asia: A Meta- Analysis. Asian Pac J Cancer Prev 2018; 19:885-889. [PMID: 29693332 PMCID: PMC6031799 DOI: 10.22034/apjcp.2018.19.4.885] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Objective: The aim of this study was to determine the degree of association of BRCA1 promoter methylation with breast cancer in Asia. Methods: The study sample for the present meta-analysis was provided by published research articles on associations of BRCA1 promoter methylation with breast cancer in Asia accessed through databases on PubMed, ProQuest and EBSCO published between 1997 and November 2017. Pooled odds ratios (OR) were calculated with fixed and random-effect models. Data were processed using Review Manager 5.3 (RevMan 5.3). Results: Of a total of 475 articles, 11 studies were included in our systematic review with meta-analysis of relevant data. The results showed a highly significant association between BRCA1 promoter methylation with breast cancer in Asia (OR = 8.78 [95% CI 4.15-18.56, p < 0.00001]). Conclusion: This analysis confirmed association between BRCA1 promoter methylation and breast cancer in Asia. BRCA1 promoter assessment might be a predictive or diagnostic aid for breast cancer prediction.
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15
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Felicio PS, Melendez ME, Arantes LMRB, Kerr LM, Carraro DM, Grasel RS, Campacci N, Scapulatempo-Neto C, Fernandes GC, de Carvalho AC, Palmero EI. Genetic and epigenetic characterization of the BRCA1 gene in Brazilian women at-risk for hereditary breast cancer. Oncotarget 2018; 8:2850-2862. [PMID: 27926510 PMCID: PMC5356847 DOI: 10.18632/oncotarget.13750] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/22/2016] [Indexed: 01/13/2023] Open
Abstract
This study aimed to characterize women at-risk for hereditary BC regarding their clinical and molecular characteristics (mutation and methylation in the BRCA1 gene) and correlate the gene expression levels with histopathological, clinical and family history information. BRCA1 real time qPCR was performed to evaluate methylation status and gene expression. The study included 88 women grouped according to the BRCA1 mutational status: 23 BRCA1 mutated, 22 with a Variant of Unknown Significance (VUS) in BRCA1 and 43 BRCA1 WT. Most BRCA1 mutated tumors were triple negative (69.6%) and had histologic grade III (61.0%). Patients with VUS/WT BRCA1 were predominantly of luminal B subtype with histological grades I and II. Regarding the methylation profile, BRCA1 hypermethylation was observed in only two patients (both WT) and none had association with pathogenic BRCA1 mutation. In one patient methylation was present in both, tumor and normal tissues. Hypermethylated tumors had ductal histology, negativity for ER and occurred in < 50 years patients. Gene expression profile showed in all groups lower BRCA1 mRNA levels in tumor tissue compared to the adjacent breast tissue, thereby indicating the loss/decrease of gene function. No association was found between the levels of BRCA1 gene expression and family history of cancer. In summary, our findings suggested that methylation at the BRCA1 gene is not the “second” event in the development of BC in patients with germline mutations in BRCA1 and, although rare, BRCA1 epimutations can constitute an explanation for a fraction of HBOC families.
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Affiliation(s)
- Paula Silva Felicio
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | | | - Ligia Maria Kerr
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Dirce Maria Carraro
- International Research Center, AC Camargo Cancer Center, São Paulo, SP, Brazil
| | | | - Natalia Campacci
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | | | - Edenir Inêz Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
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16
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Yadav P, Masroor M, Nandi K, Kaza RCM, Jain SK, Khurana N, Saxena A. Promoter Methylation of BRCA1, DAPK1 and RASSF1A is
Associated with Increased Mortality among Indian Women
with Breast Cancer. Asian Pac J Cancer Prev 2018; 19:443-448. [PMID: 29480000 PMCID: PMC5980932 DOI: 10.22034/apjcp.2018.19.2.443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background: Promoter methylation has been observed for several genes in association with cancer development and
progression. Hypermethylation mediated-silencing of tumor suppressor genes (TSGs) may contribute to breast cancer
pathogenesis. The present study was conducted to investigate the promoter methylation status of BRCA1, DAPK1 and
RASSF1A genes in Indian women with breast cancer. Materials and Methods: Promoter methylation was evaluated
in DNA extracted from mononuclear cells (MNCs) in peripheral blood samples of 60 histopathologically confirmed
newly diagnosed, untreated cases of breast cancer as well as 60 age and sex matched healthy controls using MS-PCR.
Association of promoter methylation with breast cancer-specific mortality was analyzed with Cox proportional hazards
models. Kaplan-Meier survival analysis was performed for overall survival of the breast cancer patients. Results: We
observed a significant increase of BRCA1, DAPK1 and RASSF1A promoter methylation levels by 51.7% (P <0.001),
55.0% (P <0.001) and 46.6% (P <0.001), respectively, when compared to healthy controls. A strong correlation was
noted between hypermethylation of the tumor suppressor genes BRCA1 (P= 0.009), DAPK1 (P= 0.008) and RASSF1A
(P= 0.02)) with early and advanced stages of breast cancer patients. We also found that breast cancer-specific mortality
was significantly associated with promoter methylation of BRCA1 [HR and 95% CI: 3.25 (1.448-7.317)] and DAPK1
[HR and 95% CI: 2.32 (1.05-5.11)], whereas limited significant link was evident with RASSF1A [HR and 95% CI: 1.54
(0.697-3.413]. Conclusion: Our results suggest that promoter methylation of BRCA1, DAPK1 and RASSF1A genes
may be associated with disease progression and poor overall survival of Indian women with breast cancer.
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Affiliation(s)
- Prasant Yadav
- Department of Biochemistry, Maulana Azad Medical College, New Delhi, India.,Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India.
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17
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Callahan CL, Bonner MR, Nie J, Han D, Wang Y, Tao MH, Shields PG, Marian C, Eng KH, Trevisan M, Beyea J, Freudenheim JL. Lifetime exposure to ambient air pollution and methylation of tumor suppressor genes in breast tumors. ENVIRONMENTAL RESEARCH 2018; 161:418-424. [PMID: 29197760 PMCID: PMC5747980 DOI: 10.1016/j.envres.2017.11.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 06/01/2023]
Abstract
BACKGROUND We previously reported increased risk of breast cancer associated with early life exposure to two measures of air pollution exposure, total suspended particulates (TSP) and traffic emissions (TE), possible proxies for exposure to polycyclic aromatic hydrocarbons (PAHs). Exposure to PAHs has been shown to be associated with aberrant patterns of DNA methylation in peripheral blood of healthy individuals. Exposure to PAHs and methylation in breast tumor tissue has received little attention. We examined the association of early life exposure to TSP and TE with patterns of DNA methylation in breast tumors. METHODS We conducted a study of women enrolled in the Western New York Exposures and Breast Cancer (WEB) Study. Methylation of nine genes (SFN, SCGB3A1, RARB, GSTP1, CDKN2A CCND2, BRCA1, FHIT, and SYK) was assessed using bisulfite-based pyrosequencing. TSP exposure at each woman's home address at birth, menarche, and when she had her first child was estimated. TE exposure was modeled for each woman's residence at menarche, her first birth, and twenty and ten years prior to diagnosis. Unconditional logistic regression was employed to estimate odds ratios (OR) of having methylation greater than the median value, adjusting for age, secondhand smoke exposure before age 20, current smoking status, and estrogen receptor status. RESULTS Exposure to higher TSP at a woman's first birth was associated with lower methylation of SCGB3A1 (OR = 0.48, 95% CI: 0.23-0.99) and higher methylation of SYK (OR = 1.86, 95% CI: 1.03-3.35). TE at menarche was associated with increased methylation of SYK (OR = 2.37, 95% CI: 1.05-5.33). TE at first birth and ten years prior to diagnosis was associated with decreased methylation of CCND2 (OR ten years prior to diagnosis=0.48, 95% CI: 0.26-0.89). Although these associations were nominally significant, none were significant after adjustment for multiple comparisons (p < 0.01). CONCLUSIONS We observed suggestive evidence that exposure to ambient air pollution throughout life, measured as TSP and TE, may be associated with DNA methylation of some tumor suppressor genes in breast tumor tissue. Future studies with a larger sample size that assess methylation of more sites are warranted.
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Affiliation(s)
- Catherine L Callahan
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, United States.
| | - Matthew R Bonner
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, United States
| | - Jing Nie
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, United States
| | - Daikwon Han
- Department of Epidemiology and Biostatistics, Texas A&M Texas A&M University, College Station, TX, United States
| | - Youjin Wang
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, United States
| | - Meng-Hua Tao
- Department of Biostatistics and Epidemiology, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Peter G Shields
- Division of Cancer Prevention and Control, College of Medicine and The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Catalin Marian
- Division of Cancer Prevention and Control, College of Medicine and The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States; Department of Biochemistry and Pharmacology, University of Medicine an Pharmacy Timisoara, Timisoara, Romania
| | - Kevin H Eng
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, United States
| | | | - Jan Beyea
- Consulting in the Public Interest, Lambertville, NJ, United States
| | - Jo L Freudenheim
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, United States
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18
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Pyrosequencing quantified methylation level of BRCA1 promoter as prognostic factor for survival in breast cancer patient. Oncotarget 2018; 7:27499-510. [PMID: 27027444 PMCID: PMC5053667 DOI: 10.18632/oncotarget.8355] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 03/16/2016] [Indexed: 12/11/2022] Open
Abstract
BRCA1 promoter methylation is an essential epigenetic transcriptional silencing mechanism, related to breast cancer (BC) occurrence and progression. We quantified the methylation level of BRCA1 promoter and evaluated its significance as prognostic and predictive factor. BRCA1 promoter methylation level was quantified by pyrosequencing in surgical cancerous and adjacent normal specimens from 154 BC patients. A follow up of 98 months was conducted to assess the correlation between BRCA1-methylation level vs. overall survival (OS) and disease free survival (DFS). The mean methylation level in BC tissues was significantly higher (mean 32.6%; median 31.9%) than in adjacent normal samples (mean 16.2%; median 13.0%) (P < 0.0001). Tumor stage (R = 0.6165, P < 0.0001) and size (R = 0.7328, P < 0.0001) were significantly correlated with the methylation level. Patients with unmethylated BRCA1 had a better OS and DFS compared to the methylated group (each P < 0.0001). BRCA1 promoter methylation level has a statistically significance on survival in BC patients (HazR = 1.465, P = 0.000) and is an independent prognostic factor for OS in BC patients (HazR = 2.042, P = 0.000). Patients with ductal type, HER2 negative, lymph node negative stage 1+2 tumors had a better OS and DFS. Classification of grades and molecular subtypes did not show any prognostic significance. Pyrosequencing is a precise and efficient method to quantify BRCA1 promoter methylation level, with a high potential for future clinical implication, as it identifies subgroups of patients with poorer prognosis.
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Kumar M, Sahu RK, Goyal A, Sharma S, Kaur N, Mehrotra R, Singh UR, Hedau S. BRCA1 Promoter Methylation and Expression - Associations with ER+, PR+ and HER2+ Subtypes of Breast Carcinoma. Asian Pac J Cancer Prev 2017; 18:3293-3299. [PMID: 29286222 PMCID: PMC5980886 DOI: 10.22034/apjcp.2017.18.12.3293] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Introduction: Considering the increasing trend in incidence rates, morbidity and mortality of breast cancer, there is
an urgent need to identify and validate new biomarkers for early detection and better management. The purpose of the
study was to investigate BRCA1 protein expression and promoter methylation of the BRCA1 gene and their association
with molecular subtypes based on estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth
factor receptor 2 (HER2) positivity. Materials and Methods: A total of 114 breast cancer tissue biopsies were collected
for methylation specific PCR (MSP) and immunohistochemical (IHC) analysis. Results: Seven tissue microarrays were
constructed. BRCA1 protein expression was reduced in 55/114 (48.2%) and in the majority of ER-negative tumors
(73.3%) (p<0.001). Similarly BRCA1 expression was reduced in the majority of PR-negative tumors (69.2%) but
without statistical significance (p value=0.083). BRCA1 methylation was positive in 59.6% cases. A subset regarding
ER+, PR+ and HER2+ was identified which consisted of 31.6% in which an inverse relationship between BRCA1
methylation and protein expression was noted. Conclusion: Reduced expression was associated with ER and PR
negative status which is linked with a poor prognosis. BRCA1 protein expression might thus be used as a prognostic
indicator to predict treatment response to hormone therapy.
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Affiliation(s)
- Mohit Kumar
- Department of Pathology, University Of Delhi, Delhi, India.
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20
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Targeting the Epigenome as a Novel Therapeutic Approach for Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1026:287-313. [DOI: 10.1007/978-981-10-6020-5_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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21
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Fleisher B, Clarke C, Ait-Oudhia S. Current advances in biomarkers for targeted therapy in triple-negative breast cancer. BREAST CANCER (DOVE MEDICAL PRESS) 2016; 8:183-197. [PMID: 27785100 PMCID: PMC5063595 DOI: 10.2147/bctt.s114659] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Triple-negative breast cancer (TNBC) is a complex heterogeneous disease characterized by the absence of three hallmark receptors: human epidermal growth factor receptor 2, estrogen receptor, and progesterone receptor. Compared to other breast cancer subtypes, TNBC is more aggressive, has a higher prevalence in African-Americans, and more frequently affects younger patients. Currently, TNBC lacks clinically accepted targets for tailored therapy, warranting the need for candidate biomarkers. BiomarkerBase, an online platform used to find biomarkers reported in clinical trials, was utilized to screen all potential biomarkers for TNBC and select only the ones registered in completed TNBC trials through clinicaltrials.gov. The selected candidate biomarkers were classified as surrogate, prognostic, predictive, or pharmacodynamic (PD) and organized by location in the blood, on the cell surface, in the cytoplasm, or in the nucleus. Blood biomarkers include vascular endothelial growth factor/vascular endothelial growth factor receptor and interleukin-8 (IL-8); cell surface biomarkers include EGFR, insulin-like growth factor binding protein, c-Kit, c-Met, and PD-L1; cytoplasm biomarkers include PIK3CA, pAKT/S6/p4E-BP1, PTEN, ALDH1, and the PIK3CA/AKT/mTOR-related metabolites; and nucleus biomarkers include BRCA1, the gluco-corticoid receptor, TP53, and Ki67. Candidate biomarkers were further organized into a "cellular protein network" that demonstrates potential connectivity. This review provides an inventory and reference point for promising biomarkers for breakthrough targeted therapies in TNBC.
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Affiliation(s)
- Brett Fleisher
- Department of Pharmaceutics, Center for Pharmacometrics and Systems Pharmacology, College of Pharmacy, University of Florida, Orlando, FL
| | - Charlotte Clarke
- Department of Translational Research, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Sihem Ait-Oudhia
- Department of Pharmaceutics, Center for Pharmacometrics and Systems Pharmacology, College of Pharmacy, University of Florida, Orlando, FL
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Promoter Methylation Status of Breast Cancer Susceptibility Gene 1 and 17 Beta Hydroxysteroid Dehydrogenase Type 1 Gene in Sporadic Breast Cancer Patients. Int J Breast Cancer 2016; 2016:9545241. [PMID: 27413552 PMCID: PMC4931089 DOI: 10.1155/2016/9545241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/06/2016] [Accepted: 02/29/2016] [Indexed: 01/17/2023] Open
Abstract
Epigenetic modifications are involved in breast carcinogenesis. Identifying genes that are epigenetically silenced via methylation could select target patients for diagnostic as well as therapeutic potential. We assessed promoter methylation of breast cancer susceptibility gene 1 (BRCA1) and 17 Beta Hydroxysteroid Dehydrogenase Type 1 (17βHSD-1) in normal and cancer breast tissues of forty sporadic breast cancer (BC) cases using restriction enzyme based methylation-specific PCR (REMS-PCR). In cancerous tissues, BRCA1 and 17βHSD-1 were methylated in 42.5% and 97.5%, respectively, while normal tissues had 35% and 95% methylation, respectively. BRCA1 methylation in normal tissues was 12.2-fold more likely to associate with methylation in cancer tissues (p < 0.001). It correlated significantly with increased age at menopause, mitosis, the negative status of Her2, and the molecular subtype "luminal A" (p = 0.048, p = 0.042, p = 0.007, and p = 0.049, resp.). Methylation of BRCA1 and 17βHSD-1 related to luminal A subtype of breast cancer. Since a small proportion of normal breast epithelial cells had BRCA1 methylation, our preliminary findings suggest that methylation of BRCA1 may be involved in breast tumors initiation and progression; therefore, it could be used as a biomarker for the early detection of sporadic breast cancer. Methylation of 17βHSD-1 in normal and cancer tissue could save patients the long term use of adjuvant antiestrogen therapies.
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Callahan CL, Wang Y, Marian C, Weng DY, Eng KH, Tao MH, Ambrosone CB, Nie J, Trevisan M, Smiraglia D, Edge SB, Shields PG, Freudenheim JL. DNA methylation and breast tumor clinicopathological features: The Western New York Exposures and Breast Cancer (WEB) study. Epigenetics 2016; 11:643-652. [PMID: 27245195 DOI: 10.1080/15592294.2016.1192735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We evaluated the association between methylation of 9 genes, SCGB3A1, GSTP1, RARB, SYK, FHIT, CDKN2A, CCND2, BRCA1, and SFN in tumor samples from 720 breast cancer cases with clinicopathological features of the tumors and survival. Logistic regression was used to estimate odds ratios (OR) of methylation and Cox proportional hazards models to estimate hazard ratios (HR) between methylation and breast cancer related mortality. Estrogen receptor (ER) and progesterone receptor (PR) positivity were associated with increased SCGB3A1 methylation among pre- and post-menopausal cases. Among premenopausal women, compared with Stage 0 cases, cases of invasive cancer were more likely to have increased methylation of RARB (Stage I OR = 4.7, 95% CI: 1.1-19.0; Stage IIA/IIB OR = 9.7, 95% CI: 2.4-39.9; Stage III/IV OR = 5.6, 95% CI: 1.1-29.4) and lower methylation of FHIT (Stage I OR = 0.2, 95% CI: 0.1-0.9; Stage IIA/IIB OR = 0.2, 95% CI: 0.1-0.8; Stage III/IV OR = 0.6, 95% CI: 0.1-3.4). Among postmenopausal women, methylation of SYK was associated with increased tumor size (OR = 1.7, 95% CI: 1.0-2.7) and higher nuclear grade (OR = 2.0, 95% CI 1.2-3.6). Associations between methylation and breast cancer related mortality were observed among pre- but not post-menopausal women. Methylation of SCGB3A1 was associated with reduced risk of death from breast cancer (HR = 0.41, 95% CI: 0.17-0.99) as was BRCA1 (HR = 0.41, 95% CI: 0.16-0.97). CCND2 methylation was associated with increased risk of breast cancer mortality (HR = 3.4, 95% CI: 1.1-10.5). We observed differences in methylation associated with tumor characteristics; methylation of these genes was also associated with breast cancer survival among premenopausal cases. Understanding of the associations of DNA methylation with other clinicopathological features may have implications for prevention and treatment.
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Affiliation(s)
- Catherine L Callahan
- a Department of Epidemiology and Environmental Health , School of Public Health and Health Professions, University at Buffalo , Buffalo , NY , USA
| | - Youjin Wang
- a Department of Epidemiology and Environmental Health , School of Public Health and Health Professions, University at Buffalo , Buffalo , NY , USA
| | - Catalin Marian
- b Division of Cancer Prevention and Control , College of Medicine and The Ohio State University Comprehensive Cancer Center , Columbus , OH , USA.,c Department of Biochemistry and Pharmacology , University of Medicine and Pharmacy Timisoara , Timisoara , Romania
| | - Daniel Y Weng
- b Division of Cancer Prevention and Control , College of Medicine and The Ohio State University Comprehensive Cancer Center , Columbus , OH , USA
| | - Kevin H Eng
- d Department of Biostatistics and Bioinformatics , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Meng-Hua Tao
- e Department of Biostatistics and Epidemiology , University of North Texas Health Science Center , Fort Worth , TX , USA
| | - Christine B Ambrosone
- f Department of Cancer Prevention and Control , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Jing Nie
- a Department of Epidemiology and Environmental Health , School of Public Health and Health Professions, University at Buffalo , Buffalo , NY , USA
| | | | - Dominic Smiraglia
- h Department of Cancer Genetics , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Stephen B Edge
- i Department of Healthcare Outcomes and Policy , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Peter G Shields
- b Division of Cancer Prevention and Control , College of Medicine and The Ohio State University Comprehensive Cancer Center , Columbus , OH , USA
| | - Jo L Freudenheim
- a Department of Epidemiology and Environmental Health , School of Public Health and Health Professions, University at Buffalo , Buffalo , NY , USA
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Yang F, Chen F, Xu J, Guan X. Identification and frequency of the rs12516 and rs8176318 BRCA1 gene polymorphisms among different populations. Oncol Lett 2016; 11:2481-2486. [PMID: 27073502 DOI: 10.3892/ol.2016.4252] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 01/21/2016] [Indexed: 11/05/2022] Open
Abstract
Genetic mutation of breast cancer 1 (BRCA1) is one of the most notable factors responsible for a proportion of breast cancer cases. BRCA1 encodes a 1,863-amino acid protein and functions as a negative regulator of tumor growth. Thus, investigation of the underlying mechanisms that regulate BRCA1 gene expression provide further insight into possible targets for breast cancer therapy. Previous studies have demonstrated that the genetic variants in the BRCA1 3' untranslated region (3'UTR), in addition to the cytosine-phosphate-guanine (CpG) islands in the promoter region, are significantly associated with breast cancer risk; however, the role of single nucleotide polymorphisms (SNPs) in the BRCA1 3'UTR remains unclear. The present study aimed to investigate the association between SNPs and BRCA1 mRNA expression levels. Bioinformatics analysis demonstrated that 2 SNPs in the BRCA1 3'UTR (rs12516 and rs8176318 with putative microRNA binding sites) were significantly correlated with mRNA expression in lymphoblastoid cell lines (P=2.55×10-4 and P=8.78×10-5, respectively). Furthermore, the genotype frequency distribution varied between populations worldwide. In addition, 3 CpG islands and several transcription factor binding sites in the BRCA1 promoter region were established. The identification of such polymorphisms and CpG islands may aid in designing improved therapeutic strategies to treat patients with BRCA1-associated breast cancer.
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Affiliation(s)
- Fang Yang
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Fengxia Chen
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Jin Xu
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Xiaoxiang Guan
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
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Terry MB, McDonald JA, Wu HC, Eng S, Santella RM. Epigenetic Biomarkers of Breast Cancer Risk: Across the Breast Cancer Prevention Continuum. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 882:33-68. [PMID: 26987530 PMCID: PMC5305320 DOI: 10.1007/978-3-319-22909-6_2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Epigenetic biomarkers, such as DNA methylation, can increase cancer risk through altering gene expression. The Cancer Genome Atlas (TCGA) Network has demonstrated breast cancer-specific DNA methylation signatures. DNA methylation signatures measured at the time of diagnosis may prove important for treatment options and in predicting disease-free and overall survival (tertiary prevention). DNA methylation measurement in cell free DNA may also be useful in improving early detection by measuring tumor DNA released into the blood (secondary prevention). Most evidence evaluating the use of DNA methylation markers in tertiary and secondary prevention efforts for breast cancer comes from studies that are cross-sectional or retrospective with limited corresponding epidemiologic data, raising concerns about temporality. Few prospective studies exist that are large enough to address whether DNA methylation markers add to the prediction of tertiary and secondary outcomes over and beyond standard clinical measures. Determining the role of epigenetic biomarkers in primary prevention can help in identifying modifiable pathways for targeting interventions and reducing disease incidence. The potential is great for DNA methylation markers to improve cancer outcomes across the prevention continuum. Large, prospective epidemiological studies will provide essential evidence of the overall utility of adding these markers to primary prevention efforts, screening, and clinical care.
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Affiliation(s)
- Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
| | - Jasmine A McDonald
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Hui Chen Wu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sybil Eng
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Regina M Santella
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
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26
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Zhang L, Long X. Association of BRCA1 promoter methylation with sporadic breast cancers: Evidence from 40 studies. Sci Rep 2015; 5:17869. [PMID: 26643130 PMCID: PMC4672329 DOI: 10.1038/srep17869] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/04/2015] [Indexed: 12/01/2022] Open
Abstract
Breast cancer susceptibility gene 1 (BRCA1) located at chromosome 17q12-21 is a classic tumor suppressor gene, and has been considered as a significant role in hereditary breast cancers. Moreover, numerous studies demonstrated the methylation status of CpG islands in the promoter regions of BRCA1 gene was aberrant in patients with sporadic breast tumors compared with healthy females or patients with benign diseases. However, these conclusions were not always consistent. Hence, a meta-analysis was performed to get a more precise estimate for these associations. Crude odds ratio with 95% confidence interval were used to assess the association of BRCA1 promoter methylation and the risk or clinicopathologic characteristics of breast cancers under fixed or random effect model. A total of 40 studies were eligible for this present study. We observed the frequency of BRCA1 promoter methylation was statistically significant higher in breast cancers than non-cancer controls. Furthermore, BRCA1 methylation was statistically associated with lymph node metastasis, histological grade 3, ER(-), PR(-), triple-negative phenotype, and decreased or lack levels of BRCA1 protein expression. In conclusion, this study indicated that BRCA1 promoter methylation appeared to be a useful predictive or prognostic biomarker for breast cancers in clinical assessment.
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Affiliation(s)
- Li Zhang
- Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xinghua Long
- Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
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Thike AA, Tan PH, Ikeda M, Iqbal J. Increased ID4 expression, accompanied by mutant p53 accumulation and loss of BRCA1/2 proteins in triple-negative breast cancer, adversely affects survival. Histopathology 2015; 68:702-12. [PMID: 26259780 DOI: 10.1111/his.12801] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 08/06/2015] [Indexed: 01/08/2023]
Abstract
AIMS Breast cancer 1 (BRCA1) expression is down-regulated in a significant proportion of non-hereditary breast cancers, in the absence of any mutation. This phenomenon is more pronounced in oestrogen (ER)-negative tumours. Recent studies have suggested that inhibitor of DNA binding 4 (ID4), as well as p53, participate in the transcriptional regulation of BRCA1. METHODS Immunohistochemical expression of ID4, BRCA1, BRCA2 and p53 in 699 women with triple-negative breast cancer was investigated using tissue microarrays. The prognostic role of these biomarkers was also evaluated. Survival outcomes were estimated with the Kaplan-Meier method and compared between groups with log-rank statistics. RESULTS Loss of BRCA1 and BRCA2 expression and overexpression of ID4 and p53 was observed in 75%, 90%, 95% and 66% of tumours, respectively. ID4 expression was increased in higher tumour grade (P < 0.001) and was associated significantly with basal-like subtype (P < 0.001), BRCA2 down-regulation (P = 0.037) and p53 accumulation (P < 0.001). Patients with strong ID4 expression displayed worse disease-free survival in both triple-negative breast cancers (P = 0.041) and basal-like triple-negative breast cancers (P = 0.026). CONCLUSION There is frequent ID4 expression and concomitant loss of BRCA proteins in triple-negative breast cancer. We hypothesize that strong ID4 expression could be useful as a prognostic marker in triple-negative breast cancer, predicting early tumour recurrence.
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Affiliation(s)
- Aye A Thike
- Department of Pathology, Singapore General Hospital, Academia, Singapore, Singapore
| | - Puay H Tan
- Department of Pathology, Singapore General Hospital, Academia, Singapore, Singapore
| | - Murasaki Ikeda
- Department of Pathology, Singapore General Hospital, Academia, Singapore, Singapore
| | - Jabed Iqbal
- Department of Pathology, Singapore General Hospital, Academia, Singapore, Singapore
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Wong EM, Joo JE, McLean CA, Baglietto L, English DR, Severi G, Hopper JL, Milne RL, FitzGerald LM, Giles GG, Southey MC. Tools for translational epigenetic studies involving formalin-fixed paraffin-embedded human tissue: applying the Infinium HumanMethyation450 Beadchip assay to large population-based studies. BMC Res Notes 2015; 8:543. [PMID: 26438025 PMCID: PMC4595238 DOI: 10.1186/s13104-015-1487-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/21/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Large population-based translational epigenetic studies are emerging due to recent technological advances that have made molecular analyses possible. For example, the Infinium HumanMethylation450 Beadchip (HM450K) has enabled studies of genome-wide methylation on a scale not previously possible. However, application of the HM450K to DNA extracted from formalin-fixed paraffin-embedded (FFPE) tumour material has been more challenging than application to high quality DNA extracted from blood. To facilitate the application of this assay consistently across a large number of FFPE tumour-enriched DNA samples we have devised a modification to the HM450K protocol for FFPE that includes an additional quality control (QC) checkpoint. RESULTS QC checkpoint 3 was designed to assess the presence of DNA after bisulfite conversion and restoration, just prior to application of the HM450K assay. DNA was extracted from 474 archival FFPE breast tumour material. Five samples did not have a detectable amount of DNA with an additional 42 failing to progress past QC checkpoint 3. Genome-wide methylation was measured for the remaining 428 tumour-enriched DNA. Of these, only 4 samples failed our stringent HM450K data criteria thus representing a 99% success rate. Using prior knowledge about methylation marks associated with breast cancer we further explored the quality of the data. Twenty probes in the BRCA1 promoter region showed increased methylation in triple-negative breast cancers compared to Luminal A, Luminal B and HER2-positive breast cancer subtypes. Validation of this observation in published data from The Cancer Genome Atlas (TCGA) Network (obtained from DNA extracted from fresh frozen tumour samples) confirms the quality of the data obtained from the improved protocol. CONCLUSIONS The modified protocol is suitable for the analysis of FFPE tumour-enriched DNA and can be systematically applied to hundreds of samples. This protocol will have utility in population-based translational epigenetic studies and is applicable to a wide variety of translated studies interested in analysis of methylation and its role in the predisposition to disease and disease progression.
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Affiliation(s)
- Ee Ming Wong
- Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - JiHoon E Joo
- Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Catriona A McLean
- Anatomical Pathology, Alfred Health, The Alfred Hospital, Melbourne, VIC, 3181, Australia.
| | - Laura Baglietto
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia.
| | - Dallas R English
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia.
| | - Gianluca Severi
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia.
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia.
| | - Liesel M FitzGerald
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia.
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia.
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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Gong C, Fujino K, Monteiro LJ, Gomes AR, Drost R, Davidson-Smith H, Takeda S, Khoo US, Jonkers J, Sproul D, Lam EWF. FOXA1 repression is associated with loss of BRCA1 and increased promoter methylation and chromatin silencing in breast cancer. Oncogene 2015; 34:5012-24. [PMID: 25531315 PMCID: PMC4430311 DOI: 10.1038/onc.2014.421] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 10/01/2014] [Accepted: 11/15/2014] [Indexed: 12/11/2022]
Abstract
FOXA1 expression correlates with the breast cancer luminal subtype and patient survival. RNA and protein analysis of a panel of breast cancer cell lines revealed that BRCA1 deficiency is associated with the downregulation of FOXA1 expression. Knockdown of BRCA1 resulted in the downregulation of FOXA1 expression and enhancement of FOXA1 promoter methylation in MCF-7 breast cancer cells, whereas the reconstitution of BRCA1 in Brca1-deficent mouse mammary epithelial cells (MMECs) promoted Foxa1 expression and methylation. These data suggest that BRCA1 suppresses FOXA1 hypermethylation and silencing. Consistently, the treatment of MMECs with the DNA methylation inhibitor 5-aza-2'-deoxycitydine induced Foxa1 mRNA expression. Furthermore, treatment with GSK126, an inhibitor of EZH2 methyltransferase activity, induced FOXA1 expression in BRCA1-deficient but not in BRCA1-reconstituted MMECs. Likewise, the depletion of EZH2 by small interfering RNA enhanced FOXA1 mRNA expression. Chromatin immunoprecipitation (ChIP) analysis demonstrated that BRCA1, EZH2, DNA methyltransferases (DNMT)1/3a/3b and H3K27me3 are recruited to the endogenous FOXA1 promoter, further supporting the hypothesis that these proteins interact to modulate FOXA1 methylation and repression. Further co-immunoprecipitation and ChIP analysis showed that both BRCA1 and DNMT3b form complexes with EZH2 but not with each other, consistent with the notion that BRCA1 binds to EZH2 and negatively regulates its methyltransferase activity. We also found that EZH2 promotes and BRCA1 impairs the deposit of the gene silencing histone mark H3K27me3 on the FOXA1 promoter. These associations were validated in a familial breast cancer patient cohort. Integrated analysis of the global gene methylation and expression profiles of a set of 33 familial breast tumours revealed that FOXA1 promoter methylation is inversely correlated with the transcriptional expression of FOXA1 and that BRCA1 mutation breast cancer is significantly associated with FOXA1 methylation and downregulation of FOXA1 expression, providing physiological evidence to our findings that FOXA1 expression is regulated by methylation and chromatin silencing and that BRCA1 maintains FOXA1 expression through suppressing FOXA1 gene methylation in breast cancer.
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Affiliation(s)
- C Gong
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - K Fujino
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
- Department of Obstetrics & Gynecology, Faculty of Medicine, Juntendo University, Bunkyoku, Tokyo, Japan
| | - L J Monteiro
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - A R Gomes
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - R Drost
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - H Davidson-Smith
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - S Takeda
- Department of Obstetrics & Gynecology, Faculty of Medicine, Juntendo University, Bunkyoku, Tokyo, Japan
| | - U S Khoo
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - J Jonkers
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - D Sproul
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - E W-F Lam
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
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Truong PK, Lao TD, Doan TPT, Le TAH. BRCA1 promoter hypermethylation signature for early detection of breast cancer in the Vietnamese population. Asian Pac J Cancer Prev 2015; 15:9607-10. [PMID: 25520075 DOI: 10.7314/apjcp.2014.15.22.9607] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Breast cancer, a leading cause of death among women in most countries worldwide, is rapidly increasing in incidence in Vietnam. One of biomarkers is the disruption of the genetic material including epigenetic changes like DNA methylation. With the aim of finding hypermethylation at CpG islands of promoter of BRCA1 gene, belonged to the tumor suppressor gene family, as the biomarker for breast cancer in Vietnamese population, sensitive methyl specific PCR (MSP) was carried out on 115 samples including 95 breast cancer specimens and 20 normal breast tissues with other diseases which were obtained from Ho Chi Minh City Medical Hospital, Vietnam. The result indicated that the frequency of BRCA1 hypermethylation reached 82.1% in the cases (p<0.001). In addition, the DNA hypermethylation of this candidate gene increased the possibility to be breast cancer with high incidence via calculated odd ratios (p<0.05). In conclusion, hypermethylation of this candidate gene could be used as the promising biomarker application with Vietnamese breast cancer patients.
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Affiliation(s)
- Phuong Kim Truong
- Department of Biotechnology Applications in Medicine, Faculty of Biotechnology, Ho Chi Minh City Medicine and Pharmacy University, Vietnam E-mail :
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31
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Guo T, Ren Y, Wang B, Huang Y, Jia S, Tang W, Luo Y. Promoter methylation of BRCA1 is associated with estrogen, progesterone and human epidermal growth factor receptor-negative tumors and the prognosis of breast cancer: A meta-analysis. Mol Clin Oncol 2015; 3:1353-1360. [PMID: 26807247 DOI: 10.3892/mco.2015.620] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/18/2015] [Indexed: 11/06/2022] Open
Abstract
Aberrant methylation of the breast cancer susceptibility gene 1 (BRCA1) promoter is a mechanism for its functional inactivation. It may potentially be used as a prognostic marker in studies for patients with breast cancer and plays an important role in tumorigenesis. Numerous studies have suggested that the methylation of the BRCA1 promoter is associated with the prognosis of breast cancer. However, the prognosis of BRCA1 promoter methylation in breast cancer patients of different ethnicities remains ambiguous. The present meta-analysis was performed to adjust and augment a previously published study, which estimated the correlations between promoter methylation of BRCA1 and the clinical outcomes of breast cancer patients. These results indicated that BRCA1 methylation was significantly correlated with a poor prognosis of breast cancer, particularly for Asian patients, but the correlation was over-estimated in the previous study. The combined hazard ratios (HRs) in the present study were 1.76 (1.15-2.68) and 1.97 (1.12-3.44) for univariate and multivariate analysis of overall survival, which were different from 2.02 (1.35-3.03) and 1.38 (1.04-1.84) in the previous study. For studies of disease-free survival, the univariate and multivariate analyses also have different pooled HRs: 2.89 (1.73-4.83) and 3.92 (1.49-10.32) in the previously published study and 1.28 (0.68-2.43) and 1.64 (0.64-4.19) in the present study. In addition, the BRCA1 promoter regions used to detect the hypermethylation were different. All the studies using the Baldwin's primer reported that breast cancer patients with BRCA1 promoter methylation had a better prognosis. There were also correlations between BRCA1 promoter methylation and receptor-negativity of the estrogen receptors, progesterone receptor, human epidermal growth factor receptor 2 and a triple-negative status. Patients with the estrogen, progesterone and epidermal growth factor-related receptor-negative status were more likely to be negative for the BRCA1 protein.
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Affiliation(s)
- Taiyan Guo
- Laboratory of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Yongyong Ren
- Laboratory of Medical Genetics and Pharmacogenomics, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Boyuan Wang
- Laboratory of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Yingze Huang
- Laboratory of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Shuting Jia
- Laboratory of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Wenru Tang
- Laboratory of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Ying Luo
- Laboratory of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
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Xiong G, Liu J, Tang Q, Fan Y, Fang D, Yang K, Xie F, Zhang M, Zhang L, Liu L, Zhang C, Yao L, Yang L, Ci W, Zhao W, Gong Y, He Q, Gong K, He Z, Wang G, Li X, Guo Y, Zhou L. Prognostic and predictive value of epigenetic biomarkers and clinical factors in upper tract urothelial carcinoma. Epigenomics 2015; 7:733-44. [PMID: 25912368 DOI: 10.2217/epi.15.34] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We conducted this study to identify gene promoter methylation status and clinical predictors for upper tract urothelial carcinoma (UTUC) patients. Materials & methods: Using methylation-sensitive PCR, we examined ten genes promoter methylation status in 687 UTUC patients. Results: A methylated promoter of three genes to predict higher tumor stage (T3 and T4), five genes to predict higher tumor grade (G3) and one gene to predict pN+ were certified in this study. Nine factors were significantly associated with poor cancer-specific survival. Six factors were considered as predictors to develop bladder recurrence after surgery. Conclusion: Methylation occurs commonly in UTUCs, may affect carcinogenic mechanisms, and is a well predictive factor for cancer-specific survival and bladder recurrence in UTUCs.
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Affiliation(s)
- Gengyan Xiong
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Jin Liu
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Qi Tang
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Yu Fan
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Dong Fang
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Kaiwei Yang
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Feng Xie
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Min Zhang
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Lei Zhang
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Libo Liu
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Cuijian Zhang
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Li Yang
- Institute of Nephrology & Division of Nephrology, Peking University First Hospital, Beijing 100034, China
| | - Weimin Ci
- Laboratory of Disease Genomics & Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Zhao
- Department of Cell Biology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Qun He
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Kan Gong
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Zhisong He
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Gang Wang
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Yinglu Guo
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
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Abstract
Most recent investigations into cancer etiology have identified a key role played by epigenetics. Specifically, aberrant DNA and histone modifications which silence tumor suppressor genes or promote oncogenes have been demonstrated in multiple cancer models. While the role of epigenetics in several solid tumor cancers such as colorectal cancer are well established, there is emerging evidence that epigenetics also plays a critical role in breast and prostate cancer. In breast cancer, DNA methylation profiles have been linked to hormone receptor status and tumor progression. Similarly in prostate cancer, epigenetic patterns have been associated with androgen receptor status and response to therapy. The regulation of key receptor pathways and activities which affect clinical therapy treatment options by epigenetics renders this field high priority for elucidating mechanisms and potential targets. A new set of methylation arrays are now available to screen epigenetic changes and provide the cutting-edge tools needed to perform such investigations. The role of nutritional interventions affecting epigenetic changes particularly holds promise. Ultimately, determining the causes and outcomes from epigenetic changes will inform translational applications for utilization as biomarkers for risk and prognosis as well as candidates for therapy.
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Affiliation(s)
- Yanyuan Wu
- Division of Cancer Research and Training, Center to Eliminate Cancer Health Disparities, Department of Internal Medicine, Charles Drew University of Medicine and Science, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, USA
| | - Marianna Sarkissyan
- Division of Cancer Research and Training, Center to Eliminate Cancer Health Disparities, Department of Internal Medicine, Charles Drew University of Medicine and Science, Los Angeles, CA, USA
| | - Jaydutt V. Vadgama
- Division of Cancer Research and Training, Center to Eliminate Cancer Health Disparities, Department of Internal Medicine, Charles Drew University of Medicine and Science, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, USA
- Corresponding Author Contact Information: Division of Cancer Research and Training, Center to Eliminate Cancer Health Disparities, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, 1731 East 120th Street, Los Angeles, CA 90059, USA. Tele: 323-563-4853. Fax: 323-563-4859 ;
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Albarakati N, Abdel-Fatah TMA, Doherty R, Russell R, Agarwal D, Moseley P, Perry C, Arora A, Alsubhi N, Seedhouse C, Rakha EA, Green A, Ball G, Chan S, Caldas C, Ellis IO, Madhusudan S. Targeting BRCA1-BER deficient breast cancer by ATM or DNA-PKcs blockade either alone or in combination with cisplatin for personalized therapy. Mol Oncol 2015; 9:204-17. [PMID: 25205036 PMCID: PMC5528668 DOI: 10.1016/j.molonc.2014.08.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/23/2014] [Accepted: 08/11/2014] [Indexed: 11/17/2022] Open
Abstract
BRCA1, a key factor in homologous recombination (HR) repair may also regulate base excision repair (BER). Targeting BRCA1-BER deficient cells by blockade of ATM and DNA-PKcs could be a promising strategy in breast cancer. We investigated BRCA1, XRCC1 and pol β protein expression in two cohorts (n = 1602 sporadic and n = 50 germ-line BRCA1 mutated) and mRNA expression in two cohorts (n = 1952 and n = 249). Artificial neural network analysis for BRCA1-DNA repair interacting genes was conducted in 249 tumours. Pre-clinically, BRCA1 proficient and deficient cells were DNA repair expression profiled and evaluated for synthetic lethality using ATM and DNA-PKcs inhibitors either alone or in combination with cisplatin. In human tumours, BRCA1 negativity was strongly associated with low XRCC1, and low pol β at mRNA and protein levels (p < 0.0001). In patients with BRCA1 negative tumours, low XRCC1 or low pol β expression was significantly associated with poor survival in univariate and multivariate analysis compared to high XRCC1 or high pol β expressing BRCA1 negative tumours (ps < 0.05). Pre-clinically, BRCA1 negative cancer cells exhibit low mRNA and low protein expression of XRCC1 and pol β. BRCA1-BER deficient cells were sensitive to ATM and DNA-PKcs inhibitor treatment either alone or in combination with cisplatin and synthetic lethality was evidenced by DNA double strand breaks accumulation, cell cycle arrest and apoptosis. We conclude that XRCC1 and pol β expression status in BRCA1 negative tumours may have prognostic significance. BRCA1-BER deficient cells could be targeted by ATM or DNA-PKcs inhibitors for personalized therapy.
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Affiliation(s)
- Nada Albarakati
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG51PB, UK
| | | | - Rachel Doherty
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Roslin Russell
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Devika Agarwal
- School of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham NG11 8NS, UK
| | - Paul Moseley
- Department of Oncology, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Christina Perry
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Arvind Arora
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Nouf Alsubhi
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Claire Seedhouse
- Academic Haematology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Emad A Rakha
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Andrew Green
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Graham Ball
- School of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham NG11 8NS, UK
| | - Stephen Chan
- Department of Oncology, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Carlos Caldas
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Ian O Ellis
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Srinivasan Madhusudan
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG51PB, UK; Department of Oncology, Nottingham University Hospitals, Nottingham NG51PB, UK.
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Yao Y, Des Marais TL, Costa M. Chromatin Memory in the Development of Human Cancers. GENE TECHNOLOGY 2014; 3:114. [PMID: 25606572 PMCID: PMC4297643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cancer is a complex disease with acquired genomic and epigenomic alterations that affect cell proliferation, viability and invasiveness. Almost all the epigenetic mechanisms including cytosine methylation and hydroxymethylation, chromatin remodeling and non-coding RNAs have been found associate with carcinogenesis and cancer specific expression profile. Altered histone modification as an epigenetic hallmark is frequently found in tumors. Understanding the epigenetic alterations induced by carcinogens or infectious agents may help us understand early epigenetic changes prior to the development of cancer. In this review, we focus on chromatin remodeling and the associated histone modifiers in the development of cancer; the application of these modifiers as a cancer therapy target in different clinical trial phases is also discussed.
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Affiliation(s)
- Yixin Yao
- Department of Environmental Medicine New York University, New York, USA,Corresponding author: Yixin Yao, Department of Environmental Medicine, New York University, New York, USA; Tel: 845-731-3517;
| | | | - Max Costa
- Department of Environmental Medicine New York University, New York, USA,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, Tuxedo, New York, USA
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Barrow TM, Michels KB. Epigenetic epidemiology of cancer. Biochem Biophys Res Commun 2014; 455:70-83. [PMID: 25124661 DOI: 10.1016/j.bbrc.2014.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/15/2014] [Accepted: 08/01/2014] [Indexed: 02/06/2023]
Abstract
Epigenetic epidemiology includes the study of variation in epigenetic traits and the risk of disease in populations. Its application to the field of cancer has provided insight into how lifestyle and environmental factors influence the epigenome and how epigenetic events may be involved in carcinogenesis. Furthermore, it has the potential to bring benefit to patients through the identification of diagnostic markers that enable the early detection of disease and prognostic markers that can inform upon appropriate treatment strategies. However, there are a number of challenges associated with the conduct of such studies, and with the identification of biomarkers that can be applied to the clinical setting. In this review, we delineate the challenges faced in the design of epigenetic epidemiology studies in cancer, including the suitability of blood as a surrogate tissue and the capture of genome-wide DNA methylation. We describe how epigenetic epidemiology has brought insight into risk factors associated with lung, breast, colorectal and bladder cancer and review relevant research. We discuss recent findings on the identification of epigenetic diagnostic and prognostic biomarkers for these cancers.
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Affiliation(s)
- Timothy M Barrow
- Institute for Prevention and Tumor Epidemiology, Freiburg Medical Center, University of Freiburg, 79106, Germany; German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Karin B Michels
- Institute for Prevention and Tumor Epidemiology, Freiburg Medical Center, University of Freiburg, 79106, Germany; Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA.
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LAN VOTHITHUONG, HA NGOTHI, UYEN NGUYENQUYNH, DUONG NGUYENTHI, HUONG NGUYENTHITHU, THUAN TABICH, DUONG PHAMANHTHUY, VAN TO TA. Standardization of the methylation-specific PCR method for analyzing BRCA1 and ER methylation. Mol Med Rep 2014; 9:1844-50. [DOI: 10.3892/mmr.2014.1990] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 02/05/2014] [Indexed: 11/06/2022] Open
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Dimitrov SD, Lu D, Naetar N, Hu Y, Pathania S, Kanellopoulou C, Livingston DM. Physiological modulation of endogenous BRCA1 p220 abundance suppresses DNA damage during the cell cycle. Genes Dev 2013; 27:2274-91. [PMID: 24142877 PMCID: PMC3814647 DOI: 10.1101/gad.225045.113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BRCA1 p220 participates in DNA damage responses. Dimitrov et al. find that miR-545 directly reduces p220 expression. miR-545 inhibition increased p220 expression, and aberrant p220-associated DNA damage responses and de novo DNA strand breaks accumulated. Strand breaks were a product of p220 overexpression and were also dependent on aberrant, overexpressed p220-driven recruitment of RAD51 to DNA damage sites. These results suggest that, like its loss, an excess of p220 function represents a threat to genome integrity. Endogenous BRCA1 p220 expression peaks in S and G2 when it is activated, and the protein participates in certain key DNA damage responses. In contrast, its expression is markedly reduced in G0/G1. While variations in transcription represent a significant part of p220 expression control, there is at least one other relevant process. We found that a microRNA, miR-545, that is expressed throughout the cell cycle down-modulates endogenous p220 mRNA and protein abundance directly in both G0/G1 and S/G2. When miR-545 function was inhibited by a specific antagomir, endogenous p220 expression increased in G0/G1, and aberrant p220-associated DNA damage responses and de novo DNA strand breaks accumulated. Analogous results were observed upon inhibition of miR-545 function in S/G2. Both sets of antagomir effects were mimicked by infecting cells with a p220 cDNA-encoding adenoviral vector. Thus, strand breaks were a product of p220 overexpression, and their prevention by miR-545 depends on its modulation of p220 expression. Breaks were also dependent on aberrant, overexpressed p220-driven recruitment of RAD51 to either spontaneously arising or mutagen-based DNA damage sites. Hence, when its level is not physiologically maintained, endogenous p220 aberrantly directs at least one DNA repair protein, RAD51, to damage sites, where their action contributes to the development of de novo DNA damage. Thus, like its loss, a surfeit of endogenous p220 function represents a threat to genome integrity.
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Affiliation(s)
- Stoil D Dimitrov
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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Promoter methylation of BRCA1 in the prognosis of breast cancer: a meta-analysis. Breast Cancer Res Treat 2013; 142:619-27. [DOI: 10.1007/s10549-013-2774-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/10/2013] [Indexed: 10/26/2022]
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Watanabe Y, Maeda I, Oikawa R, Wu W, Tsuchiya K, Miyoshi Y, Itoh F, Tsugawa KI, Ohta T. Aberrant DNA methylation status of DNA repair genes in breast cancer treated with neoadjuvant chemotherapy. Genes Cells 2013; 18:1120-30. [PMID: 24581343 DOI: 10.1111/gtc.12100] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 09/06/2013] [Indexed: 12/14/2022]
Abstract
Dysregulation of homologous recombination (HR) DNA repair has been implicated in breast carcinogenesis and chemosensitivity. Here, we investigated the methylation status of sixteen HR genes and analyzed their association with tumor subtypes and responses to neoadjuvant chemotherapy. Core specimens were obtained before neoadjuvant chemotherapy from sixty cases of primary breast cancer of the following four subgroups: luminal breast cancer (LBC) with pathological complete response (pCR), LBC with stable disease, triple-negative breast cancer (TNBC) with pCR and TNBC with poor response. The aberrant DNA methylation status of the following HR related-genes was analyzed using bisulfite-pyrosequencing: BRCA1, BRCA2, BARD1, MDC1, RNF8, RNF168, UBC13, ABRA1, PALB2, RAD50, RAD51, RAD51C, MRE11, NBS1, CtIP and ATM. Among the genes analyzed, only the incidence of BRCA1 and RNF8 methylation was significantly higher in TNBC than that in LBC. Whereas the incidence of BRCA1 methylation was tended to be higher in pCR cases than in poor-response cases in TNBC, that of RNF8 was significantly lower in pCR cases than in poor-response cases. Our results indicate that the methylation status of HR genes was not generally associated with TNBC subtype or chemosensitivity although hypermethylation of BRCA1 is associated with TNBC subtype and may impact chemosensitivity.
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Affiliation(s)
- Yoshiyuki Watanabe
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, 216-8511, Japan
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