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Bhootra S, Jill N, Shanmugam G, Rakshit S, Sarkar K. DNA methylation and cancer: transcriptional regulation, prognostic, and therapeutic perspective. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2023; 40:71. [PMID: 36602616 DOI: 10.1007/s12032-022-01943-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 12/25/2022] [Indexed: 01/06/2023]
Abstract
DNA methylation is one among the major grounds of cancer progression which is characterized by the addition of a methyl group to the promoter region of the gene thereby causing gene silencing or increasing the probability of mutations; however, in bacteria, methylation is used as a defense mechanism where DNA protection is by addition of methyl groups making restriction enzymes unable to cleave. Hypermethylation and hypomethylation both pose as leading causes of oncogenesis; the former being more frequent which occurs at the CpG islands present in the promoter region of the genes, whereas the latter occurs globally in various genomic sequences. Reviewing methylation profiles would help in the detection and treatment of cancers. Demethylation is defined as preventing methyl group addition to the cytosine DNA base which could cause cancers in case of global hypomethylation, however, upon further investigation; it could be used as a therapeutic tool as well as for drug design in cancer treatment. In this review, we have studied the molecules that induce and enzymes (DNMTs) that bring about methylation as well as comprehend the correlation between methylation with transcription factors and various signaling pathways. DNA methylation has also been reviewed in terms of how it could serve as a prognostic marker and the various therapeutic drugs that have come into the market for reversing methylation opening an avenue toward curing cancers.
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Affiliation(s)
- Sannidhi Bhootra
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Nandana Jill
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Geetha Shanmugam
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Sudeshna Rakshit
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Koustav Sarkar
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India.
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Bücker L, Lehmann U. CDH1 (E-cadherin) Gene Methylation in Human Breast Cancer: Critical Appraisal of a Long and Twisted Story. Cancers (Basel) 2022; 14:cancers14184377. [PMID: 36139537 PMCID: PMC9497067 DOI: 10.3390/cancers14184377] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/27/2022] Open
Abstract
Simple Summary Genes can be inactivated by specific modifications of DNA bases, most often by adding a methyl group to the DNA base cytosine if it is followed by guanosine (CG methylation). This modification prevents gene expression and has been reported for many different genes in nearly all types of cancer. A prominent example is the gene CDH1, which encodes the cell-adhesion molecule E-cadherin. This is an important player in the spreading of tumor cells within the body (metastasis). Particularly in human breast cancer, many different research groups have studied the inactivation of the CDH1 gene via DNA methylation using various methods. Over the last 20 years, different, in part, even contradicting results have been published for the CDH1 gene in breast cancer. This review summarizes the most important publications and explains the bewildering heterogeneity of results through careful analysis of the methods which have been used. Abstract Epigenetic inactivation of a tumor suppressor gene by aberrant DNA methylation is a well-established defect in human tumor cells, complementing genetic inactivation by mutation (germline or somatic). In human breast cancer, aberrant gene methylation has diagnostic, prognostic, and predictive potential. A prominent example is the hypermethylation of the CDH1 gene, encoding the adhesion protein E-Cadherin (“epithelial cadherin”). In numerous publications, it is reported as frequently affected by gene methylation in human breast cancer. However, over more than two decades of research, contradictory results concerning CDH1 gene methylation in human breast cancer accumulated. Therefore, we review the available evidence for and against the role of DNA methylation of the CDH1 gene in human breast cancer and discuss in detail the methodological reasons for conflicting results, which are of general importance for the analysis of aberrant DNA methylation in human cancer specimens. Since the loss of E-cadherin protein expression is a hallmark of invasive lobular breast cancer (ILBC), special attention is paid to CDH1 gene methylation as a potential mechanism for loss of expression in this special subtype of human breast cancer. Proper understanding of the methodological basis is of utmost importance for the correct interpretation of results supposed to demonstrate the presence and clinical relevance of aberrant DNA methylation in cancer specimens.
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Affiliation(s)
| | - Ulrich Lehmann
- Correspondence: ; Tel.: +49-(0)511-532-4501; Fax: +49-(0)511-532-5799
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3
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Li J, Downs BM, Cope LM, Fackler MJ, Zhang X, Song CG, VandenBussche C, Zhang K, Han Y, Liu Y, Tulac S, Venkatesan N, de Guzman T, Chen C, Lai EW, Yuan J, Sukumar S. Automated and rapid detection of cancer in suspicious axillary lymph nodes in patients with breast cancer. NPJ Breast Cancer 2021; 7:89. [PMID: 34234148 PMCID: PMC8263765 DOI: 10.1038/s41523-021-00298-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/09/2021] [Indexed: 01/29/2023] Open
Abstract
Preoperative staging of suspicious axillary lymph nodes (ALNs) allows patients to be triaged to ALN dissection or to sentinel lymph node biopsy (SLNB). Ultrasound-guided fine needle aspiration (FNA) and cytology of ALN is moderately sensitive but its clinical utility relies heavily on the cytologist's experience. We proposed that the 5-h automated GeneXpert system-based prototype breast cancer detection assay (BCDA) that quantitatively measures DNA methylation in ten tumor-specific gene markers could provide a facile, accurate test for detecting cancer in FNA of enlarged lymph nodes. We validated the assay in ALN-FNA samples from a prospective study of patients (N = 230) undergoing SLNB. In a blinded analysis of 218 evaluable LN-FNAs from 108 malignant and 110 benign LNs by histology, BCDA displayed a sensitivity of 90.7% and specificity of 99.1%, achieving an area under the ROC curve, AUC of 0.958 (95% CI: 0.928-0.989; P < 0.0001). Next, we conducted a study of archival FNAs of ipsilateral palpable LNs (malignant, N = 72, benign, N = 53 by cytology) collected in the outpatient setting prior to neoadjuvant chemotherapy (NAC). Using the ROC-threshold determined in the prospective study, compared to cytology, BCDA achieved a sensitivity of 94.4% and a specificity of 92.5% with a ROC-AUC = 0.977 (95% CI: 0.953-1.000; P < 0.0001). Our study shows that the automated assay detects cancer in suspicious lymph nodes with a high level of accuracy within 5 h. This cancer detection assay, scalable for analysis to scores of LN FNAs, could assist in determining eligibility of patients to different treatment regimens.
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Affiliation(s)
- Juanjuan Li
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bradley M Downs
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leslie M Cope
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mary Jo Fackler
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiuyun Zhang
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chuan-Gui Song
- Department of Breast Surgery, Union Hospital Affiliated by Fujian Medical University, Fuzhou, China
| | | | - Kejing Zhang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yong Han
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital, Binzhou, China
| | - Yufei Liu
- Department of Pathology, Yichang Central People's Hospital, Yichang, China
| | | | | | | | - Chuang Chen
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | | | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Downs BM, Ding W, Cope LM, Umbricht CB, Li W, He H, Ke X, Holdhoff M, Bettegowda C, Tao W, Sukumar S. Methylated markers accurately distinguish primary central nervous system lymphomas (PCNSL) from other CNS tumors. Clin Epigenetics 2021; 13:104. [PMID: 33952317 PMCID: PMC8097855 DOI: 10.1186/s13148-021-01091-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/22/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Definitive diagnosis of primary central nervous system lymphoma (PCNSL) requires invasive surgical brain biopsy, causing treatment delays. In this paper, we identified and validated tumor-specific markers that can distinguish PCNSL from other CNS tumors in tissues. In a pilot study, we tested these newly identified markers in plasma. RESULTS The Methylation Outlier Detector program was used to identify markers in TCGA dataset of 48 diffuse large B-cell lymphoma (DLBCL) and 656 glioblastomas and lower-grade gliomas. Eight methylated markers clearly distinguished DLBCL from gliomas. Marker performance was verified (ROC-AUC of ≥ 0.989) in samples from several GEO datasets (95 PCNSL; 2112 other primary CNS tumors of 11 types). Next, we developed a novel, efficient assay called Tailed Amplicon Multiplexed-Methylation-Specific PCR (TAM-MSP), which uses two of the methylation markers, cg0504 and SCG3 triplexed with ACTB. FFPE tissue sections (25 cases each) of PCNSL and eight types of other primary CNS tumors were analyzed using TAM-MSP. TAM-MSP distinguished PCNSL from the other primary CNS tumors with 100% accuracy (AUC = 1.00, 95% CI 0.95-1.00, P < 0.001). The TAM-MSP assay also detected as few as 5 copies of fully methylated plasma DNA spiked into 0.5 ml of healthy plasma. In a pilot study of plasma from 15 PCNSL, 5 other CNS tumors and 6 healthy individuals, methylation in cg0504 and SCG3 was detectable in 3/15 PCNSL samples (20%). CONCLUSION The Methylation Outlier Detector program identified methylated markers that distinguish PCNSL from other CNS tumors with accuracy. The high level of accuracy achieved by these markers was validated in tissues by a novel method, TAM-MSP. These studies lay a strong foundation for a liquid biopsy-based test to detect PCNSL-specific circulating tumor DNA.
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Affiliation(s)
- Bradley M Downs
- Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Wanjun Ding
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, People's Republic of China.
| | - Leslie M Cope
- Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Christopher B Umbricht
- Departments of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Wenge Li
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Huihua He
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Xiaokang Ke
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Matthias Holdhoff
- Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Chetan Bettegowda
- Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Weiping Tao
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, People's Republic of China.
| | - Saraswati Sukumar
- Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
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Singh M, Kumar V, Sehrawat N, Yadav M, Chaudhary M, Upadhyay SK, Kumar S, Sharma V, Kumar S, Dilbaghi N, Sharma AK. Current paradigms in epigenetic anticancer therapeutics and future challenges. Semin Cancer Biol 2021; 83:422-440. [PMID: 33766649 DOI: 10.1016/j.semcancer.2021.03.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/14/2020] [Accepted: 03/16/2021] [Indexed: 12/16/2022]
Abstract
Any alteration at the genetic or epigenetic level, may result in multiplex of diseases including tumorigenesis which ultimately results in the cancer development. Restoration of the normal epigenome by reversing the epigenetic alterations have been reported in tumors paving the way for development of an effective epigenetic treatment in cancer. However, delineating various epigenetic events has been a challenging task so far despite substantial progress in understanding DNA methylation and histone modifications during transcription of genes. Many inhibitors in the form of epigenetic drugs mostly targeting chromatin and histone modifying enzymes including DNA methyltransferase (DNMT) enzyme inhibitors and a histone deacetylases (HDACs) inhibitor, have been in use subsequent to the approval by FDA for cancer treatment. Similarly, other inhibitory drugs, such as FK228, suberoylanilide hydroxamic acid (SAHA) and MS-275, have been successfully tested in clinical studies. Despite all these advancements, still we see a hazy view as far as a promising epigenetic anticancer therapy is concerned. The challenges are to have more specific and effective inhibitors with negligible side effects. Moreover, the alterations seen in tumors are not well understood for which one has to gain deeper insight into the tumor pathology as well. Current review focusses on such epigenetic alterations occurring in cancer and the effective strategies to utilize such alterations for potential therapeutic use and treatment in cancer.
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Affiliation(s)
- Manoj Singh
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Vikas Kumar
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Nirmala Sehrawat
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Mukesh Yadav
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Mayank Chaudhary
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Sushil K Upadhyay
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Sunil Kumar
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Varruchi Sharma
- Department of Biotechnology, Sri Guru Gobind Singh College Sector-26, Chandigarh, UT, 160019, India
| | - Sandeep Kumar
- Department of Bio& Nanotechnology, Guru Jambheshwar University of Science & Technology, Hisar, Haryana, 125001, India
| | - Neeraj Dilbaghi
- Department of Bio& Nanotechnology, Guru Jambheshwar University of Science & Technology, Hisar, Haryana, 125001, India
| | - Anil K Sharma
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India.
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Ahmadi M, Mohammadi Z, Azad M, Foroughi F, Khojastehpour S, Gheibi N, Samiee-Rad F, Maali A. Evaluation of expression level and methylation profile of CXX1 gene in breast cancer tissue blocks. J Cancer Res Ther 2021; 17:1328-1334. [DOI: 10.4103/jcrt.jcrt_27_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Azim R, Wang S, Zhou S, Zhong X. Purity estimation from differentially methylated sites using Illumina Infinium methylation microarray data. Cell Cycle 2020; 19:2028-2039. [PMID: 32627651 PMCID: PMC7469651 DOI: 10.1080/15384101.2020.1789315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/11/2020] [Accepted: 06/23/2020] [Indexed: 10/23/2022] Open
Abstract
Solid tissues collected from patient-driven clinical settings are composed of both normal and cancer cells, which often precede complications in data analysis and epigenetic findings. The Purity estimation of samples is crucial for reliable genomic aberration identification and uniform inter-sample and inter-patient comparisons as well. Here, an effective and flexible method has been developed and designed to estimate the level of methylation, which infers tumor purity without prior knowledge from the other datasets. The comprehensive analysis of our approach on Illumina Infinium 450 k methylation microarray explains that TCGA Breast Cancer data exhibits improved performance for purity assessment. This assessment has a strong correlation with other advanced methods.
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Affiliation(s)
- Riasat Azim
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, P.R. China
| | - Shulin Wang
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, P.R. China
| | - Su Zhou
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, P.R. China
| | - Xing Zhong
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, P.R. China
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Stastny I, Zubor P, Kajo K, Kubatka P, Golubnitschaja O, Dankova Z. Aberrantly Methylated cfDNA in Body Fluids as a Promising Diagnostic Tool for Early Detection of Breast Cancer. Clin Breast Cancer 2020; 20:e711-e722. [PMID: 32792225 DOI: 10.1016/j.clbc.2020.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/29/2020] [Accepted: 05/11/2020] [Indexed: 12/24/2022]
Abstract
Breast malignancies are the leading type of cancer among women. Its prevention and early detection, particularly in young women, remains challenging. To this end, cell-free DNA (cfDNA) detected in body fluids demonstrates great potential for early detection of tissue transformation and altered molecular setup, such as epigenetic profiles. Aberrantly methylated cfDNA in body fluids could therefore serve as a potential diagnostic and prognostic tool in breast cancer management. Abnormal methylation may lead to both an activation of oncogenes via hypomethylation and an inactivation of tumor suppressor genes by hypermethylation. We update the state of the art in the area of aberrant cfDNA methylation analyses as a diagnostic and prognostic tool in breast cancer, report on the main technological challenges, and provide an outlook for advancing the overall management of breast malignancies based on cfDNA as a target for diagnosis and tailored therapies.
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Affiliation(s)
- Igor Stastny
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Obstetrics and Gynaecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
| | - Pavol Zubor
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Gynecologic Oncology, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Karol Kajo
- Department of Pathology, St Elizabeth Cancer Institute Hospital, Bratislava, Slovak Republic; Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Kubatka
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Olga Golubnitschaja
- Radiological Hospital, Rheinische, Excellence University of Bonn, Bonn, Germany; Breast Cancer Research Centre, Rheinische, Excellence University of Bonn, Bonn, Germany; Centre for Integrated Oncology, Cologne-Bonn, Excellence University of Bonn, Bonn, Germany
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic
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Bin Y, Ding Y, Xiao W, Liao A. RASSF1A: A promising target for the diagnosis and treatment of cancer. Clin Chim Acta 2020; 504:98-108. [PMID: 31981586 DOI: 10.1016/j.cca.2020.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
Abstract
The Ras association domain family 1 isoform A (RASSF1A), a tumor suppressor, regulates several tumor-related signaling pathways and interferes with diverse cellular processes. RASSF1A is frequently demonstrated to be inactivated by hypermethylation in numerous types of solid cancers. It is also associated with lymph node metastasis, vascular invasion, and chemo-resistance. Therefore, reactivation of RASSF1A may be a viable strategy to block tumor progress and reverse drug resistance. In this review, we have summarized the clinical value of RASSF1A for screening, staging, and therapeutic management of human malignancies. We also highlighted the potential mechanism of RASSF1A in chemo-resistance, which may help identify novel drugs in the future.
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Affiliation(s)
- Yuling Bin
- Digestive System Department, the First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, China
| | - Yong Ding
- Department of Vascular Surgery, Zhongshan Hospital, Institue of Vascular Surgery, Fudan University, Shanghai 200032, China
| | - Weisheng Xiao
- Digestive System Department, the First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, China
| | - Aijun Liao
- Digestive System Department, the First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, China.
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Downs BM, Mercado-Rodriguez C, Cimino-Mathews A, Chen C, Yuan JP, Van Den Berg E, Cope LM, Schmitt F, Tse GM, Ali SZ, Meir-Levi D, Sood R, Li J, Richardson AL, Mosunjac MB, Rizzo M, Tulac S, Kocmond KJ, de Guzman T, Lai EW, Rhees B, Bates M, Wolff AC, Gabrielson E, Harvey SC, Umbricht CB, Visvanathan K, Fackler MJ, Sukumar S. DNA Methylation Markers for Breast Cancer Detection in the Developing World. Clin Cancer Res 2019; 25:6357-6367. [PMID: 31300453 DOI: 10.1158/1078-0432.ccr-18-3277] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/04/2019] [Accepted: 07/02/2019] [Indexed: 12/21/2022]
Abstract
PURPOSE An unmet need in low-resource countries is an automated breast cancer detection assay to prioritize women who should undergo core breast biopsy and pathologic review. Therefore, we sought to identify and validate a panel of methylated DNA markers to discriminate between cancer and benign breast lesions using cells obtained by fine-needle aspiration (FNA).Experimental Design: Two case-control studies were conducted comparing cancer and benign breast tissue identified from clinical repositories in the United States, China, and South Africa for marker selection/training (N = 226) and testing (N = 246). Twenty-five methylated markers were assayed by Quantitative Multiplex-Methylation-Specific PCR (QM-MSP) to select and test a cancer-specific panel. Next, a pilot study was conducted on archival FNAs (49 benign, 24 invasive) from women with mammographically suspicious lesions using a newly developed, 5-hour, quantitative, automated cartridge system. We calculated sensitivity, specificity, and area under the receiver-operating characteristic curve (AUC) compared with histopathology for the marker panel. RESULTS In the discovery cohort, 10 of 25 markers were selected that were highly methylated in breast cancer compared with benign tissues by QM-MSP. In the independent test cohort, this panel yielded an AUC of 0.937 (95% CI = 0.900-0.970). In the FNA pilot, we achieved an AUC of 0.960 (95% CI = 0.883-1.0) using the automated cartridge system. CONCLUSIONS We developed and piloted a fast and accurate methylation marker-based automated cartridge system to detect breast cancer in FNA samples. This quick ancillary test has the potential to prioritize cancer over benign tissues for expedited pathologic evaluation in poorly resourced countries.
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Affiliation(s)
- Bradley M Downs
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Ashley Cimino-Mathews
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chuang Chen
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Jing-Ping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Eunice Van Den Berg
- Department of Anatomical Pathology, University of Witwaterstrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Leslie M Cope
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Fernando Schmitt
- Medical Faculty of Porto University, Institute of Molecular Pathology and Immunology of Porto University, Porto, Portugal
| | - Gary M Tse
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Syed Z Ali
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Danielle Meir-Levi
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rupali Sood
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Juanjuan Li
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Andrea L Richardson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marina B Mosunjac
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Monica Rizzo
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia
| | | | | | | | | | | | | | - Antonio C Wolff
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Edward Gabrielson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Susan C Harvey
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher B Umbricht
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kala Visvanathan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Bloomberg School of Public Health, Baltimore, Maryland
| | - Mary Jo Fackler
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Alhudiri IM, Nolan CC, Ellis IO, Elzagheid A, Rakha EA, Green AR, Chapman CJ. Expression of Lamin A/C in early-stage breast cancer and its prognostic value. Breast Cancer Res Treat 2019; 174:661-668. [DOI: 10.1007/s10549-018-05092-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 10/27/2022]
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12
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de Groot JS, Moelans CB, Elias SG, Jo Fackler M, van Domselaar R, Suijkerbuijk KPM, Witkamp AJ, Sukumar S, van Diest PJ, van der Wall E. DNA promoter hypermethylation in nipple fluid: a potential tool for early breast cancer detection. Oncotarget 2017; 7:24778-91. [PMID: 27028854 PMCID: PMC5029741 DOI: 10.18632/oncotarget.8352] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/29/2016] [Indexed: 01/18/2023] Open
Abstract
Introduction Nipple fluid aspiration provides direct non-invasive sampling of fluid from the mammary ductal system, where the majority of breast cancers originate. DNA promoter hypermethylation (“methylation”) occurs early and at high frequency in breast carcinogenesis, bearing the potential as a biomarker for cancer detection at its earliest stages. We assessed methylation in nipple fluid from breasts of healthy women, of women with sporadic breast cancer and of their contralateral breasts. Our goal was to investigate whether nipple fluid can be used as a reliable methylation biomarker source. Methods Methylation levels of 13 genes were analysed by quantitative multiplex-methylation specific PCR (QM-MSP) in nipple fluid samples from breasts of healthy women, and from the affected and contralateral breasts of breast cancer patients. Results Methylation analysis of the low-volume nipple fluid samples was feasible. Despite the generally low methylation levels, cancerous and healthy breasts nipple fluid could be discriminated with an area under the receiver operating characteristic curve (AUC) of 0.64 (p<0.01) based on a multivariate model including AKR1B1, ALX1, RASSF1A and TM6SF1. Within-patient differences between cancerous and contralateral nipple fluid samples were less prominent. Conclusions Cancerous nipple fluid contains increased levels of methylation of tumor suppressor genes that potentially could serve as a biomarker for early breast cancer detection.
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Affiliation(s)
- Jolien S de Groot
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sjoerd G Elias
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mary Jo Fackler
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Robert van Domselaar
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Arjen J Witkamp
- Department of Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elsken van der Wall
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
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Moradi Sarabi M, Ghareghani P, Khademi F, Zal F. Oral Contraceptive Use May Modulate Global Genomic DNA Methylation and Promoter Methylation of APC1 and ESR1. Asian Pac J Cancer Prev 2017; 18:2361-2366. [PMID: 28950679 PMCID: PMC5720637 DOI: 10.22034/apjcp.2017.18.9.2361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background: There are challenging reports in the public health sphere regarding associations between oral contraceptive (OC) use and cancer risk. Methods: To evaluate possible effects of OCs on cancer susceptibility, we quantified of global 5-methyl cytosine (5-mC) levels and assessed methylation patterns of CpG islands of two key tumor suppressor genes, APC1 and ESR1, in serum of users by enzyme-linked immunosorbent assay and methylation specific PCR methods, respectively. Results: Our results indicated that OCs significantly decrease the level of global DNA methylation in users relative to control non-users. However, our data revealed no significant differences between CpG island methylation patterns for ESR1 and APC1 in healthy control and OC-treated women. However, we did find a trend for hypermethylation of both tumor suppressor genes in OC users. Conclusion: Our data suggest that the level of 5-mC but not individual CpG island patterns is significantly influenced by OCs in our cross-section of adult users.
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Affiliation(s)
- Mostafa Moradi Sarabi
- Biochemistry and Genetics Department, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.
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14
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Tumor and serum DNA methylation in women receiving preoperative chemotherapy with or without vorinostat in TBCRC008. Breast Cancer Res Treat 2017; 167:107-116. [PMID: 28918548 DOI: 10.1007/s10549-017-4503-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND Methylated gene markers have shown promise in predicting breast cancer outcomes and treatment response. We evaluated whether baseline and changes in tissue and serum methylation levels would predict pathological complete response (pCR) in patients with HER2-negative early breast cancer undergoing preoperative chemotherapy. METHODS The TBCRC008 trial investigated pCR following 12 weeks of preoperative carboplatin and albumin-bound paclitaxel + vorinostat/placebo (n = 62). We measured methylation of a 10-gene panel by quantitative multiplex methylation-specific polymerase chain reaction and expressed results as cumulative methylation index (CMI). We evaluated association between CMI level [baseline, day 15 (D15), and change] and pCR using univariate and multivariable logistic regression models controlling for treatment and hormone receptor (HR) status, and performed exploratory subgroup analyses. RESULTS In univariate analysis, one log unit increase in tissue CMI levels at D15 was associated with 40% lower chance of obtaining pCR (odds ratio, OR 0.60, 95% CI 0.37-0.97; p = 0.037). Subgroup analyses suggested a significant association between tissue D15 CMI levels and pCR in vorinostat-treated [OR 0.44 (0.20, 0.93), p = 0.03], but not placebo-treated patients. CONCLUSION In this study investigating the predictive roles of tissue and serum CMI levels in patients with early breast cancer for the first time, we demonstrate that high D15 tissue CMI levels may predict poor response. Larger studies and improved analytical procedures to detect methylated gene markers in early stage breast cancer are needed. TBCRC008 is registered on ClinicalTrials.gov (NCT00616967).
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Jezkova E, Zubor P, Kajo K, Grendar M, Dokus K, Adamkov M, Lasabova Z, Plank L, Danko J. Impact of RASSF1A gene methylation on the metastatic axillary nodal status in breast cancer patients. Oncol Lett 2017; 14:758-766. [PMID: 28693231 PMCID: PMC5494671 DOI: 10.3892/ol.2017.6204] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/31/2017] [Indexed: 12/13/2022] Open
Abstract
Hypermethylation of CpG islands is a hallmark of cancer and occurs at an early stage in breast tumorigenesis. To gain insight into the epigenetic switches that may promote and/or contribute to the initial neoplastic events during breast carcinogenesis, the present study focused on the DNA methylation profile of invasive breast carcinoma. The aim of the study was to evaluate the prognostic significance of Ras association domain family 1 isoform A (RASSF1A) promoter methylation status in operable breast cancer, and to analyze the utility of this biomarker regarding its association with metastatic and nonmetastatic axillary nodal status. For this purpose, formalin-fixed, paraffin-embedded tissue specimens from 116 breast cancer patients with known axillary nodal status were subjected to assessment of RASSF1A promoter methylation status by methylation-specific polymerase chain reaction (MSP) and methylation-sensitive high-resolution melting assay, and the results were subsequently validated by bisulfite sequencing. A multinomial logistic regression model was used to model the dependence of distinct levels of methylation status of the RASSF1A promoter on the nodal status. Promoter region CpG hypermethylation was identified by MSP in 97 (83.6%) of 116 primary breast tumors, while hypermethylation of RASSF1A was confirmed by MS-HRM in 107 (92.2%) of 116 cases of breast cancer. Based on the results of the multinomial logistic regression model, there was no significant difference between the frequency of RASSF1A promoter methylation and axillary lymph node status of patients in general. However, upon adjustment of pN stage, an association was identified between pN0 lymph node-negative status (without axillary metastases) and percentage of RASSF1A methylation in two groups of heterogeneous methylated alleles with ≤50% methylated (P<0.05) and >50% methylated alleles (P<0.0001). If a patients' nodal status changes from pN- to pN+ then the risk of having >50% methylated alleles increases by 7%. The present study revealed a specific phenomenon, suggesting that the presence of heterogeneous methylated alleles in the RASSF1A gene is significantly associated with lymph node-negative status in breast cancer patients. Furthermore, greater significance with negative axillary nodal status was observed with a higher level of heterogeneous methylated alleles in the RASSF1A gene.
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Affiliation(s)
- Eva Jezkova
- Department of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia.,Department of Histology and Embryology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Pavol Zubor
- Department of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia.,Department of Obstetrics and Gynaecology, Jessenius Faculty of Medicine, Martin University Hospital, 036 01 Martin, Slovakia
| | - Karol Kajo
- St. Elizabeth Cancer Institute Hospital, 812 50 Bratislava, Slovakia
| | - Marian Grendar
- Bioinformatic Unit, Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Karol Dokus
- Department of Obstetrics and Gynaecology, Jessenius Faculty of Medicine, Martin University Hospital, 036 01 Martin, Slovakia
| | - Marian Adamkov
- Department of Histology and Embryology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zora Lasabova
- Department of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Lukas Plank
- Department of Pathological Anatomy, Jessenius Faculty of Medicine, Martin University Hospital, 036 01 Martin, Slovakia
| | - Jan Danko
- Department of Obstetrics and Gynaecology, Jessenius Faculty of Medicine, Martin University Hospital, 036 01 Martin, Slovakia
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DUSP1 promoter methylation in peripheral blood leukocyte is associated with triple-negative breast cancer risk. Sci Rep 2017; 7:43011. [PMID: 28220843 PMCID: PMC5318948 DOI: 10.1038/srep43011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/18/2017] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is one of the most common epigenetic alterations, providing important information regarding cancer risk and prognosis. A case-control study (423 breast cancer cases, 509 controls) and a case-only study (326 cases) were conducted to evaluate the association of DUSP1 promoter methylation with breast cancer risk and clinicopathological characteristics. No significant association between DUSP1 methylation in peripheral blood leukocyte (PBL) DNA and breast cancer risk was observed. DUSP1 methylation was significantly associated with ER/PR-negative status; in particular, triple-negative breast cancer patients showed the highest frequency of DUSP1 methylation in both tumour DNA and PBL DNA. Soybean intake was significantly correlated with methylated DUSP1 only in ER-negative (OR 2.978; 95% CI 1.245-7.124) and PR negative (OR 2.735; 95% CI 1.315-5.692) patients. Irregular menstruation was significantly associated with methylated DUSP1 only in ER-positive (OR 3.564; 95% CI 1.691-7.511) and PR-positive (OR 3.902, 95% CI 1.656-9.194) patients. Thus, DUSP1 methylation is a cancer-associated hypermethylation event that is closely linked with triple-negative status. Further investigations are warranted to confirm the association of environmental factors, including fruit and soybean intake, irregular menstruation, and ER/PR status, with DUSP1 methylation in breast tumour DNA.
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17
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Jezkova E, Kajo K, Zubor P, Grendar M, Malicherova B, Mendelova A, Dokus K, Lasabova Z, Plank L, Danko J. Methylation in promoter regions of PITX2 and RASSF1A genes in association with clinicopathological features in breast cancer patients. Tumour Biol 2016; 37:10.1007/s13277-016-5324-3. [PMID: 27744628 DOI: 10.1007/s13277-016-5324-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/06/2016] [Indexed: 01/31/2023] Open
Abstract
Breast cancer is a heterogeneous disease with very different responses to therapy and different length of survival. In many cases, however, the determination of the stage and histopathological characteristics of breast cancer is insufficient to predict prognosis and response to treatment for the vast heterogeneity of the disease. To understand the molecular signature of subtypes of breast cancer, we attempted to identify the methylation status of key tumour suppressor gene Ras association (RalGDS/AF-6) domain family member 1 isoform a (RASSF1A) and a member of the paired-like homeodomain transcription factor family which functions in left-right asymmetry development (PITX2) and to correlate results with known clinicopathological features of breast cancer. Formalin-fixed, paraffin-embedded (FFPE) tissues of breast carcinomas (n = 149) were used for DNA extraction. DNA was modified by bisulphite conversion. Detection of the methylation level of the genes mentioned above was performed by methylation-sensitive high-resolution melting assay (MS-HRM). Based on MS-HRM results for RASSF1A and PITX2, we subdivided the samples into four groups according to methylation level (≤50 % methylated, >50 % methylated, 100 % methylated and completely unmethylated alleles). All degrees of methylation status for both genes underwent analysis of dependence with known clinicopathological features, and we found significant associations. In 134 of 149 (89.9 %) primary breast carcinomas, the RASSF1A promoter was methylated. Total hypermethylation of PITX2 was observed in 60 of 135 (44.4 %) breast cancer cases. RASSF1A hypermethylation had significant association with increased age (p < 0.05), tumour grade (p < 0.0001) and stage (p < 0.0001) in the 100 % methylated group. There was significant association of PITX2 hypermethylation with tumour grade (p < 0.0001) and stage (p < 0.0001). Association between the methylation level of both investigated genes and tumour type was significant for ductal invasive carcinoma cases only (p < 0.0001). This study shows different levels of heterogeneous methylation acquired by MS-HRM assay of the promoter region of RASSF1A and PITX2 and its relationship with clinicopathological features of 149 breast cancer patients. We noticed that immunohistopathological subtypes of breast cancer contain distinct promoter methylation patterns. All these data suggest that hypermethylation of the CpG island promoters of RASSF1A and PITX2 might play an essential role in the very early stages of breast cancer pathogenesis.
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Affiliation(s)
- Eva Jezkova
- Department of Oncology JFM CU, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 036 01, Martin, Slovakia.
- Clinic of Gynaecology and Obstetrics, Jessenius Faculty of Medicine, Martin University Hospital, Kollarova 2, 036 01, Martin, Slovakia.
| | - Karol Kajo
- St. Elizabeth Cancer Institute Hospital, Heydukova 10, 812 50, Bratislava, Slovakia
| | - Pavol Zubor
- Department of Oncology JFM CU, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 036 01, Martin, Slovakia
- Clinic of Gynaecology and Obstetrics, Jessenius Faculty of Medicine, Martin University Hospital, Kollarova 2, 036 01, Martin, Slovakia
| | - Marian Grendar
- Department of Oncology JFM CU, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 036 01, Martin, Slovakia
| | - Bibiana Malicherova
- Department of Oncology JFM CU, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 036 01, Martin, Slovakia
| | - Andrea Mendelova
- Department of Molecular Medicine JFM CU, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 036 01, Martin, Slovakia
| | - Karol Dokus
- Clinic of Gynaecology and Obstetrics, Jessenius Faculty of Medicine, Martin University Hospital, Kollarova 2, 036 01, Martin, Slovakia
| | - Zora Lasabova
- Department of Oncology JFM CU, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 036 01, Martin, Slovakia
| | - Lukas Plank
- Department of Pathological Anatomy, Jessenius Faculty of Medicine, Martin University Hospital, Kollarova 2, 036 01, Martin, Slovakia
| | - Jan Danko
- Clinic of Gynaecology and Obstetrics, Jessenius Faculty of Medicine, Martin University Hospital, Kollarova 2, 036 01, Martin, Slovakia
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Naghitorabi M, Mohammadi-Asl J, Sadeghi HMM, Rabbani M, Jafarian-Dehkordi A, Javanmard SH. Quantitation of CDH1 promoter methylation in formalin-fixed paraffin-embedded tissues of breast cancer patients using differential high resolution melting analysis. Adv Biomed Res 2016; 5:91. [PMID: 27308263 PMCID: PMC4908786 DOI: 10.4103/2277-9175.183139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/12/2014] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND E-cadherin (CDH1) plays an important role in cell-cell adhesion of epithelial tissues. Loss of E-cadherin expression can lead to loss of tissue integrity, metastasis, and cancer progression. Also loss of E-cadherin expression might be related to aberrant promoter methylation of the CDH1 gene. Many studies have been performed on CDH1 promoter methylation, especially in breast cancer. Although most of the studies have used qualitative methods for methylation analysis, this study is designed to quantitatively investigate CDH1 promoter methylation in breast cancer and its correlation with patients' clinicopathological features. MATERIALS AND METHODS Using differential high resolution melting analysis (D-HRMA), the methylation level of the CDH1 gene promoter was quantified in 98 breast cancer formalin-fixed paraffin-embedded (FFPE) tissues and also 10 fresh frozen normal breast tissues. RESULTS All samples were detected to be methylated at the CDH1 promoter region. About 74.5% of the breast cancer samples were hypermethylated with an average methylation level of around 60%, while 25.5% of the patients were methylated with the mean methylation level of about 33%, and 90% of the normal samples had a mean methylation level of about 18%. Statistical analyses represented a significant correlation between CDH1 promoter methylation and cancer progression hallmarks, such as, clinical stage, nodal involvement, tumor size, and histological grade. CONCLUSION In summary, quantitation of CDH1 promoter methylation can serve as a diagnostic and prognostic tool in breast cancer. Also D-HRMA can be used as a fast and reliable method for quantitation of promoter methylation.
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Affiliation(s)
- Mojgan Naghitorabi
- Department of Pharmaceutical Biotechnology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Javad Mohammadi-Asl
- Cancer, Petroleum and Environmental Pollutants Research Centre, Ahvaz Jundishapur University of Medical sciences, Ahvaz, Iran
| | | | - Mohammad Rabbani
- Department of Pharmaceutical Biotechnology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abbas Jafarian-Dehkordi
- Department of Pharmacology and Toxicology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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Cho YH, McCullough LE, Gammon MD, Wu HC, Zhang YJ, Wang Q, Xu X, Teitelbaum SL, Neugut AI, Chen J, Santella RM. Promoter Hypermethylation in White Blood Cell DNA and Breast Cancer Risk. J Cancer 2015; 6:819-24. [PMID: 26284132 PMCID: PMC4532978 DOI: 10.7150/jca.12174] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/07/2015] [Indexed: 12/31/2022] Open
Abstract
The role of gene-specific methylation in white blood cells (WBC) as a marker of breast cancer risk is currently unclear. We determined whether promoter hypermethylation in blood DNA of candidate tumor suppressor genes frequently methylated in breast tumors can be used as a surrogate biomarker for breast cancer risk. Promoter methylation of BRCA1, CDH1 and RARβ was analyzed in WBC DNA from a population-based sample of 1,021 breast cancer patients and 1,036 controls by the MethyLight assay. Gene-specific promoter methylation in the DNA of 569 tumor tissue samples was also analyzed to determine the correlation of methylation levels with blood from the same individual. Hypermethylation of BRCA1 (OR: 1.31; 95% CI: 0.98-1.75) in WBC was associated with an increased risk of breast cancer when positive methylation was defined as ≥0.1% methylated. There was lack of concordance between tumor tissue and paired WBC DNA methylation. These results provide limited support that hypermethylation of BRCA1 in WBC DNA may be useful for determination of breast cancer risk. Additional studies with larger numbers of genes are needed to fully understand the relationship between WBC methylation and breast cancer risk.
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Affiliation(s)
- Yoon Hee Cho
- 1. Department of Environmental Health Sciences, Columbia University, 630 West 168th St, New York, NY 10032, USA ; 8. Current address: Departments of Biomedical and Pharmaceutical Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Lauren E McCullough
- 2. Department of Epidemiology, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599, USA
| | - Marilie D Gammon
- 2. Department of Epidemiology, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599, USA
| | - Hui-Chen Wu
- 1. Department of Environmental Health Sciences, Columbia University, 630 West 168th St, New York, NY 10032, USA
| | - Yu-Jing Zhang
- 1. Department of Environmental Health Sciences, Columbia University, 630 West 168th St, New York, NY 10032, USA
| | - Qiao Wang
- 1. Department of Environmental Health Sciences, Columbia University, 630 West 168th St, New York, NY 10032, USA
| | - Xinran Xu
- 3. Department of Preventive Medicine, Mount Sinai School of Medicine, 1468 Madison Ave, New York, NY 10029, USA
| | - Susan L Teitelbaum
- 3. Department of Preventive Medicine, Mount Sinai School of Medicine, 1468 Madison Ave, New York, NY 10029, USA
| | - Alfred I Neugut
- 4. Department of Epidemiology, Columbia University, 722 West 168th St, New York, NY 10032, USA ; 5. Department of Medicine, Columbia University, 161 Fort Washington Ave at W 165th St, New York, NY 10032, USA
| | - Jia Chen
- 3. Department of Preventive Medicine, Mount Sinai School of Medicine, 1468 Madison Ave, New York, NY 10029, USA ; 6. Department of Pediatrics, Mount Sinai School of Medicine, One Gustave L. Levy Place
Box 1198, New York, NY 10029, USA ; 7. Department of Oncological Science, Mount Sinai School of Medicine, One Gustave L. Levy Place Box 1130, New York, NY 10029, USA
| | - Regina M Santella
- 1. Department of Environmental Health Sciences, Columbia University, 630 West 168th St, New York, NY 10032, USA
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Schrijver WAME, Jiwa LS, van Diest PJ, Moelans CB. Promoter hypermethylation profiling of distant breast cancer metastases. Breast Cancer Res Treat 2015; 151:41-55. [PMID: 25841351 PMCID: PMC4408366 DOI: 10.1007/s10549-015-3362-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/26/2015] [Indexed: 12/22/2022]
Abstract
Promoter hypermethylation of tumor suppressor genes seems to be an early event in breast carcinogenesis and is potentially reversible. This makes methylation a possible therapeutic target, a marker for treatment response and/or a prognostic factor. Methylation status of 40 tumor suppressor genes was compared between 53 primary breast tumors and their corresponding metastases to brain, lung, liver, or skin. In paired analyses, a significant decrease in methylation values was seen in distant metastases compared to their primaries in 21/40 individual tumor suppressor genes. Furthermore, primary tumors that metastasized to the liver clustered together, in line with the finding that primary breast carcinomas that metastasized to the brain, skin, or lung, showed higher methylation values in up to 27.5 % of tumor suppressor genes than primary carcinomas that metastasized to the liver. Conversion in methylation status of several genes from the primary tumor to the metastasis had prognostic value, and methylation status of some genes in the metastases predicted survival after onset of metastases. Methylation levels for most of the analyzed tumor suppressor genes were lower in distant metastases compared to their primaries, pointing to the dynamic aspect of methylation of these tumor suppressor genes during cancer progression. Also, specific distant metastatic sites seem to show differences in methylation patterns, implying that hypermethylation profiles of the primaries may steer site-specific metastatic spread. Lastly, methylation status of the metastases seems to have prognostic value. These promising findings warrant further validation in larger patient cohorts and more tumor suppressor genes.
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Affiliation(s)
| | - Laura S. Jiwa
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 Utrecht, CX The Netherlands
| | - Paul J. van Diest
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 Utrecht, CX The Netherlands
| | - Cathy B. Moelans
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 Utrecht, CX The Netherlands
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Swellam M, Abdelmaksoud MDE, Sayed Mahmoud M, Ramadan A, Abdel-Moneem W, Hefny MM. Aberrant methylation of APC and RARβ2 genes in breast cancer patients. IUBMB Life 2015; 67:61-8. [PMID: 25684670 DOI: 10.1002/iub.1346] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/30/2014] [Indexed: 01/22/2023]
Abstract
Changes in the status of DNA methylation are one of the most common molecular alterations in human neoplasia. We aimed to identify epigenetic molecular markers in serum for early detection of breast cancer. Authors analyzed retrospectively the methylation status of RARβ2 and APC genes in serum samples from 121 breast cancer patients, 79 patients with benign breast diseases, and 66 healthy volunteers using methylation-specific PCR. The methylated APC and RARβ2 were significantly higher in breast cancer patients (93.4%, 95.6%) than benign (7.8%, 14.5%) but not detected in healthy volunteers (0%) at (P < 0.0001). Both methylated genes showed no significant difference among clinicopathological factors apart from triple negative breast cancer patients as all of them (χ(2) = 7.4, P = 0.007) reported to be methylated RARβ2 genes. Both methylated genes were detected in all grades and stages. Both sensitivities and specificities of the methylated genes for breast cancer detection were superior to traditional tumor markers in detection of breast cancer, early stage, low grade tumors, and triple negative breast cancer patients. Thus methylated APC and RARβ2 genes might be valuable serum-based molecular markers for early detection of breast cancer.
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Affiliation(s)
- Menha Swellam
- Department of Biochemistry, Genetic Engineering and Biotechnology Research Division, National Research Centre, El Bohouth, Dokki, Giza, Egypt
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Host Factors and Risk of Breast Cancer Recurrence: Genetic, Epigenetic and Biologic Factors and Breast Cancer Outcomes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 862:143-53. [DOI: 10.1007/978-3-319-16366-6_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Validation of DNA promoter hypermethylation biomarkers in breast cancer--a short report. Cell Oncol (Dordr) 2014; 37:297-303. [PMID: 25123395 DOI: 10.1007/s13402-014-0189-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2014] [Indexed: 01/17/2023] Open
Abstract
PURPOSE DNA promoter hypermethylation of tumor suppressor genes is known to occur early in cancer development, including breast cancer. To improve early breast cancer detection, we aimed to investigate whether the identification of DNA promoter hypermethylation might be of added value. METHODS The methylation status of a panel of 19 candidate genes (AKR1B1, ALX1, ARHGEF7, FZD10, GHSR, GPX7, GREM1, GSTP1, HOXD1, KL, LHX2, MAL, MGMT, NDRG2, RASGRF2, SFRP1, SFRP2, TM6SF1 and TMEFF2) was determined in formalin-fixed paraffin-embedded normal breast and breast cancer tissue samples using gel-based methylation-specific PCR (MSP). RESULTS The promoters of the AKR1B1, ALX1, GHSR, GREM1, RASGRF2, SFRP2, TM6SF1 and TMEFF2 genes were found to be significantly differentially methylated in normal versus malignant breast tissues. Based on sensitivity, specificity and logistic regression analyses the best performing genes for detecting breast cancer were identified. Through multivariate analyses, we found that AKR1B1 and TM6SF1 could detect breast cancer with an area under the curve (AUC) of 0.986 in a receiver operating characteristic (ROC) assessment. CONCLUSIONS Based on our data, we conclude that AKR1B1 and TM6SF1 may serve as candidate methylation biomarkers for early breast cancer detection. Further studies are underway to evaluate the methylation status of these genes in body fluids, including nipple aspirates and blood.
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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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Chen QW, Zhu XY, Li YY, Meng ZQ. Epigenetic regulation and cancer (review). Oncol Rep 2013; 31:523-32. [PMID: 24337819 DOI: 10.3892/or.2013.2913] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 09/04/2013] [Indexed: 11/06/2022] Open
Abstract
'Epigenetics' is defined as the inheritable changes in gene expression with no alterations in DNA sequences. Epigenetics is a rapidly expanding field, and the study of epigenetic regulation in cancer is emerging. Disruption of the epigenome is a fundamental mechanism in cancer, and several epigenetic drugs have been proven to prolong survival and to be less toxic than conventional chemotherapy. Promising results from combination clinical trials with DNA methylation inhibitors and histone deacetylase inhibitors have recently been reported, and data are emerging that describe molecular determinants of clinical responses. Despite significant advances, challenges remain, including a lack of predictive markers, unclear mechanisms of response and resistance, and rare responses in solid tumors. Preclinical studies are ongoing with novel classes of agents that target various components of the epigenetic machinery. In the present review, examples of studies that demonstrate the role of epigenetic regulation in human cancers with the focus on histone modifications and DNA methylation, and the recent clinical and translational data in the epigenetics field that have potential in cancer therapy are discussed.
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Affiliation(s)
- Q W Chen
- Department of Integrated Oncology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - X Y Zhu
- Department of Integrated Oncology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Y Y Li
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Z Q Meng
- Department of Integrated Oncology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
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Differential methylation relative to breast cancer subtype and matched normal tissue reveals distinct patterns. Breast Cancer Res Treat 2013; 142:365-80. [PMID: 24212716 PMCID: PMC3832780 DOI: 10.1007/s10549-013-2738-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 10/12/2013] [Indexed: 11/17/2022]
Abstract
Due to the heterogeneous nature of breast cancer and the widespread use of single-gene studies, there is limited knowledge of multi-gene, locus-specific DNA methylation patterns in relation to molecular subtype and clinical features. We, therefore, quantified DNA methylation of 70 candidate gene loci in 140 breast tumors and matched normal tissues and determined associations with gene expression and tumor subtype. Using Sequenom’s EpiTYPER platform, approximately 1,200 CpGs were interrogated and revealed six DNA methylation patterns in breast tumors relative to matched normal tissue. Differential methylation of several gene loci was observed within all molecular subtypes, while other patterns were subtype-dependent. Methylation of numerous gene loci was inversely correlated with gene expression, and in some cases, this correlation was only observed within specific breast tumor subtypes. Our findings were validated on a larger set of tumors and matched adjacent normal tissue from The Cancer Genome Atlas dataset, which utilized methylation data derived from both Illumina Infinium 27 and 450 k arrays. These findings highlight the need to control for subtype when interpreting DNA methylation results, and the importance of interrogating multiple CpGs across varied gene regions.
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27
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Huang YT, Li FF, Ke C, Li Z, Li ZT, Zou XF, Zheng XX, Chen YP, Zhang H. PTPRO promoter methylation is predictive of poorer outcome for HER2-positive breast cancer: indication for personalized therapy. J Transl Med 2013; 11:245. [PMID: 24090193 PMCID: PMC3852714 DOI: 10.1186/1479-5876-11-245] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/25/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Protein Tyrosine Phosphatase Receptor-type O (PTPRO) has recently been in the spotlight as a tumor suppressor, whose encoding gene is frequently methylated in cancers. We examined the methylation status of the PTPRO gene promoter in breast cancer and evaluated the correlation between PTPRO promoter methylation and both clinicopathological parameters and prognosis of breast cancer patients. METHODS Two hundred twenty-one formalin-fixed, paraffin-embedded (FFPE) tumor tissues, 20 FFPE normal adjacent tissues and 24 matched plasma samples, collected from primary breast cancer patients, were assessed for PTPRO gene promoter methylation using methylation-specific PCR. Associations of promoter methylation with clinicopathological parameters were evaluated. Kaplan-Meier survival analysis and Cox proportional hazards models were used to estimate the effect on survival. RESULTS 175 samples gave identifiable PCR products, of which 130 cases (74.3%) had PTPRO gene promoter methylation. PTPRO methylation correlated with higher histological grade (P = 0.028), but not other clinical parameters. Multivariate analysis indicated that overall survival (OS) was significantly poorer in HER2-positive, but not ER-positive patients with methylated-PTPRO. Methylated-PTPRO was detectable in matched plasma samples and only observed in plasma from patients whose corresponding primary tumors were also methylated. CONCLUSIONS PTPRO methylation is a common event in the primary breast cancer and can be reliably detected in peripheral blood samples. PTPRO methylation is associated with poor survival only in HER2-positive patients, suggesting use of PTPRO methylation as a prognostic factor for breast cancer and for optimizing individualized therapy for HER2-positive patients.
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Affiliation(s)
- Yi-Teng Huang
- Department of Integrative Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou 515041, China
- Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Fei-Fei Li
- Department of Integrative Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou 515041, China
- Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Chen Ke
- Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Zhou Li
- Department of Integrative Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou 515041, China
- Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Zong-Tai Li
- Department of Integrative Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou 515041, China
- Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Xiao-Fang Zou
- Department of Integrative Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou 515041, China
- Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Xiao-Xuan Zheng
- Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Yu-Ping Chen
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Shantou University Medical College, Shantou 515041, China
| | - Hao Zhang
- Department of Integrative Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou 515041, China
- Tumor Tissue Bank, Affiliated Cancer Hospital of Shantou University Medical College, Shantou 515041, China
- Cancer Research Center, Shantou University Medical College, Shantou 515041, China
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28
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Pang JMB, Dobrovic A, Fox SB. DNA methylation in ductal carcinoma in situ of the breast. Breast Cancer Res 2013; 15:206. [PMID: 23826974 PMCID: PMC3707020 DOI: 10.1186/bcr3420] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ductal carcinoma in situ (DCIS) is a non-obligate precursor lesion of invasive carcinoma of the breast. Current prognostic markers based on histopathological examination are unable to accurately predict which DCIS cases will progress to invasive carcinoma or recur after surgical excision. Epigenetic changes have been shown to be a significant driver of tumorigenesis, and DNA methylation of specific gene promoters provides predictive and prognostic markers in many types of cancer, including invasive breast cancer. In general, the spectrum of genes that are methylated in DCIS strongly resembles that seen in invasive ductal carcinoma. The identification of specific prognostic markers in DCIS remains elusive and awaits additional work investigating a large panel of methylatable genes by using sensitive and reproducible technologies. This review critically appraises the role of methylation in DCIS and its use as a biomarker.
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TWIST1 promoter methylation is associated with prognosis in tonsillar squamous cell carcinoma. Hum Pathol 2013; 44:1722-9. [PMID: 23664538 DOI: 10.1016/j.humpath.2013.03.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 02/26/2013] [Accepted: 03/14/2013] [Indexed: 11/19/2022]
Abstract
Tonsillar squamous cell carcinomas (TSCC) frequently present with locally advanced diseases and cervical metastases, which are associated with poor prognoses. Epithelial-mesenchymal transition (EMT) is critical for tumor invasiveness and metastatic potential. Recent studies have shown that TWIST1-inducing EMT is overexpressed and hypermethylated in several cancers, indicating disease progression. The aim of the present study was to determine the clinical and prognostic significance of TWIST1 hypermethylation and EMT-related protein expression in TSCC. Methylation levels of TWIST1 promoter were analyzed by quantitative real-time methylation-specific polymerase chain reaction. Immunohistochemical analyses of TWIST1, Snail, and SMAD nuclear interacting protein-1 (SNIP1) were performed in 65 formalin-fixed, paraffin-embedded blocks of surgically resected specimens. TWIST1 promoter hypermethylation was found in 27.7% (18/65) of TSCCs. TWIST1 promoter hypermethylation was associated with poor differentiation (P = .012). Contralateral cervical lymph node metastasis was more frequently observed in TWIST1-methylated tumors (P = .029). High protein expressions of TWIST1, Snail, and SNIP1 were observed in 14 TSCC specimens (21.5%), 21 TSCC specimens (32.3%), and 38 TSCC specimens (58.5%), respectively. SNIP1 expression correlated significantly with TWIST1 methylation (P = .001), whereas TWIST1 protein expression did not. Contralateral cervical lymph node metastasis was an independent risk factor of the decreased overall survival rate (P = .002). TWIST1 methylation (P = .031) and pN stage (P = .037) were independent factors of poor prognoses affecting disease-free survival. TWIST1 promoter hypermethylation may be a useful molecular marker for predicting prognoses and contralateral cervical lymph node metastases in patients with TSCC.
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Witt D, Burfeind P, von Hardenberg S, Opitz L, Salinas-Riester G, Bremmer F, Schweyer S, Thelen P, Neesen J, Kaulfuss S. Valproic acid inhibits the proliferation of cancer cells by re-expressing cyclin D2. Carcinogenesis 2013; 34:1115-24. [PMID: 23349020 DOI: 10.1093/carcin/bgt019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In this study, primary murine prostate cancer (PCa) cells were derived using the well-established TRAMP model. These PCa cells were treated with the histone deacetylase inhibitor, valproic acid (VPA), and we demonstrated that VPA treatment has an antimigrative, antiinvasive and antiproliferative effect on PCa cells. Using microarray analyses, we discovered several candidate genes that could contribute to the cellular effects we observed. In this study, we could demonstrate that VPA treatment of PCa cells causes the re-expression of cyclin D2, a known regulator that is frequently lost in PCa as we could show using immunohistochemical analyses on PCa specimens. We demonstrate that VPA specifically induces the re-expression of cyclin D2, one of the highly conserved D-type cyclin family members, in several cancer cell lines with weak or no cyclin D2 expression. Interestingly, VPA treatment had no effect in fibroblasts, which typically have high basal levels of cyclin D2 expression. The re-expression of cyclin D2 observed in PCa cells is activated by increased histone acetylation in the promoter region of the Ccnd2 gene and represents one underlying molecular mechanism of VPA treatment that inhibits the proliferation of cancer cells. Altogether, our results confirm that VPA is an anticancer therapeutic drug for the treatment of tumors with epigenetically repressed cyclin D2 expression.
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Affiliation(s)
- Daria Witt
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
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Ulirsch J, Fan C, Knafl G, Wu MJ, Coleman B, Perou CM, Swift-Scanlan T. Vimentin DNA methylation predicts survival in breast cancer. Breast Cancer Res Treat 2012; 137:383-96. [PMID: 23239149 DOI: 10.1007/s10549-012-2353-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 11/21/2012] [Indexed: 11/30/2022]
Abstract
The Vimentin gene plays a pivotal role in epithelial-to-mesenchymal transition and is known to be overexpressed in the prognostically poor basal-like breast cancer subtype. Recent studies have reported Vimentin DNA methylation in association with poor clinical outcomes in other solid tumors, but not in breast cancer. We therefore quantified Vimentin DNA methylation using MALDI-TOF mass spectrometry in breast tumors and matched normal pairs in association with gene expression and survival in a hospital-based study of breast cancer patients. Gene expression data via qRT-PCR in cell lines and oligomicroarray data from breast tissues were correlated with percent methylation in the Vimentin promoter. A threshold of 20 percent average methylation compared with matched normal pairs was set for bivariate and multivariate tests of association between methylation and tumor subtype, tumor histopathology, and survival. Vimentin was differentially methylated in luminal breast cancer cell lines, and in luminal A, luminal B, and HER2-enriched breast tumor subtypes, but was rare in basal-like cell lines and tumors. Increased methylation was strongly correlated with decreased mRNA expression in cell lines, and had a moderate inverse correlation in breast tumors. Vimentin methylation predicted poor overall survival independent of race, subtype, stage, nodal status, or metastatic disease and holds promise as a new prognostic biomarker for breast cancer patients.
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Affiliation(s)
- Jacob Ulirsch
- The University of North Carolina at Chapel Hill School of Nursing, Lab 013, Carrington Hall, CB #7460, Chapel Hill, NC 27599-7460, USA
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Sturgeon SR, Balasubramanian R, Schairer C, Muss HB, Ziegler RG, Arcaro KF. Detection of promoter methylation of tumor suppressor genes in serum DNA of breast cancer cases and benign breast disease controls. Epigenetics 2012; 7:1258-67. [PMID: 22986510 DOI: 10.4161/epi.22220] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Tumors are capable of shedding DNA into the blood stream. This shed DNA may be recovered from serum or plasma. The objective of this study was to evaluate whether pyrosequencing promoter DNA in a panel of 12 breast cancer-related genes (APC, BRCA1, CCND2, CDH1, ESR1, GSTP1, HIN1, P16, RARβ, RASSF1, SFRP1 and TWIST) to measure the degree of methylation would lead to a useful serum-based marker of breast cancer. Serum was obtained from women who were about to undergo a breast biopsy or mastectomy at three hospitals from 1977 to 1987 in Grand Rapids, MI USA. We compared the methylation status of 12 genes in serum DNA obtained from three groups of postmenopausal women (mean age at blood collection: 63.0 y; SD 9.9; range 35-91): breast cancer cases with lymph node-positive disease (n = 241); breast cancer cases with lymph node-negative disease (n = 63); and benign breast disease control subjects (n = 234). Overall, median levels of promoter methylation were low, typically below 5%, for all genes in all study groups. For all genes, median levels of methylation were higher (by 3.3 to 47.6%) in lymph node-positive breast cancer cases than in the controls. Comparing mean methylation level between lymph-node positive cases and controls, the most statistically significant findings, after adjustment of the false-positive rate (q-value), were for TWIST (p = 0.04), SFRP1 (p = 0.16), ESR1 (p = 0.17), P16 (p = 0.19) and APC (p = 0.19). For two of these four genes (TWIST, P16), the median methylation level was also highest in lymph-node positive cases, intermediate in lymph node-negative cases and lowest in the controls. The percent of study subjects with mean methylation scores ≥ 5% was higher among lymph node-positive cases than controls for ten genes, and significantly higher for HIN1 and TWIST (22.0 vs. 12.2%, p = 0.04 and 37.9 vs. 24.5%, p = 0.004, respectively). Despite relatively consistent variation in methylation patterns among groups, these modest differences did not provide sufficient ability to distinguish between cases and controls in a clinical setting.
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Affiliation(s)
- Susan R Sturgeon
- Division of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, USA.
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Bijron JG, van der Groep P, van Dorst EB, Seeber LMS, Sie-Go DMDS, Verheijen RHM, van Diest PJ. Promoter hypermethylation patterns in fallopian tube epithelium of BRCA1 and BRCA2 germ line mutation carriers. Endocr Relat Cancer 2012; 19:69-81. [PMID: 22143498 DOI: 10.1530/erc-11-0338] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BRCA1/2 germ line mutation carriers have a high risk of developing fallopian tube carcinoma (FTC), thought to occur through different early (p53 signatures) and later (dysplasia, intra-epithelial carcinoma) premalignant stages. Promoter hypermethylation of tumour suppressor genes is known to play a key role in (early) carcinogenesis. However, little is known about methylation in normal and (pre)malignant fallopian tube tissue. We identified 14 areas of p53 accumulation in the fallopian tubes of BRCA mutation carriers. Cells from these areas were harvested together with cells from adjacent benign appearing areas. An age-matched non-BRCA sporadic control group (n=13) and eight sporadic FTCs were included as negative and positive controls respectively. Methylation-specific multiplex ligation-dependent probe amplification was used to assess promoter methylation of 70 tumour suppressor genes in all samples. We observed a gradual increase in methylation from sporadic control tissue (median cumulative methylation index (CMI) 568.19) through normal tissue and from areas of p53 accumulation in BRCA carriers (median CMI 687.54 and 676.72) to FTC (median CMI 780.97). Furthermore, the methylation percentage of many individual tumour suppressor genes differed significantly between these groups, gradually increasing as for CMI. Between areas with and without p53 accumulation in BRCA mutation carriers no significant differences were found. In this paper, we have shown that BRCA mutation carriers display increased methylation of tumour suppressor genes in their non-malignant fallopian tube epithelium, closer to methylation levels in FTC than to normal sporadic tissue. Methylation could, therefore, play an important role in the increased risk of gynaecological malignancies in BRCA mutation carriers.
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Affiliation(s)
- Jonathan G Bijron
- Department of Pathology, University Medical Centre Utrecht, PO Box 85500, 3508 GA Utrecht, The Netherlands
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Cho YH, Shen J, Gammon MD, Zhang YJ, Wang Q, Gonzalez K, Xu X, Bradshaw PT, Teitelbaum SL, Garbowski G, Hibshoosh H, Neugut AI, Chen J, Santella RM. Prognostic significance of gene-specific promoter hypermethylation in breast cancer patients. Breast Cancer Res Treat 2011; 131:197-205. [PMID: 21837480 DOI: 10.1007/s10549-011-1712-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/28/2011] [Indexed: 12/12/2022]
Abstract
The association between promoter methylation status and survival was investigated in a large cohort of women with breast cancer, participants in the Long Island Breast Cancer Study Project. Archived tumor tissues (n = 839) were collected from women diagnosed with a first primary invasive or in situ breast cancer in 1996-1997. Vital status was followed through the end of 2005 with a mean follow-up time of 8 years. Promoter methylation of eight breast cancer-related genes was assessed by MethyLight. The frequencies of methylation for HIN1, RASSF1A, DAPK1, GSTP1, CyclinD2, TWIST, CDH1 and RARβ were 62.9, 85.2, 14.1, 27.8, 19.6, 15.3, 5.8 and 27.6%, respectively. Since survival rates of in situ and invasive breast cancers are substantially different, survival analyses were conducted within 670 invasive cases with complete data on all genes. Age-adjusted Cox proportional hazards models revealed that GSTP1, TWIST and RARβ methylation was significantly associated with higher breast cancer-specific mortality. Methylation of GSTP1 and RARβ was significantly associated with higher all-cause mortality. To investigate the relationship between the number of methylated genes and breast cancer-specific mortality, we included previously published MethyLight data on p16 and APC methylation status. Breast cancer-specific mortality increased in a dose-dependent manner with increasing number of methylated genes (P (trend) = 0.002), although confidence intervals were wide. Our results suggest that promoter methylation, particularly for a panel of genes, has the potential to be used as a biomarker for predicting prognosis in breast cancer.
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Affiliation(s)
- Yoon Hee Cho
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 630 West 168th St, New York, NY 10032, USA
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