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Liu J, Qu Y, Zhao Y, Liang F, Ji L, Wang Z, Li J, Zang Z, Huang H, Zhang J, Gu W, Dai L, Yang R. CCDC12 gene methylation in peripheral blood as a potential biomarker for breast cancer detection. Biomarkers 2024; 29:265-275. [PMID: 38776382 DOI: 10.1080/1354750x.2024.2358302] [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: 03/12/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Aberrant DNA methylation has been identified as biomarkers for breast cancer detection. Coiled-coil domain containing 12 gene (CCDC12) implicated in tumorigenesis. This study aims to investigate the potential of blood-based CCDC12 methylation for breast cancer detection. METHODS DNA methylation level of CpG sites (Cytosine-phosphate Guanine dinucleotides) in CCDC12 gene was measured by mass spectrometry in 255 breast cancer patients, 155 patients with benign breast nodules and 302 healthy controls. The association between CCDC12 methylation and breast cancer risk was evaluated by logistic regression and receiver operating characteristic curve analysis. RESULTS A total of eleven CpG sites were analyzed. The CCDC12 methylation levels were higher in breast cancer patients. Compared to the lowest tertile of methylation level in CpG_6,7, CpG_10 and CpG_11, the highest quartile was associated with 82, 91 and 95% increased breast cancer risk, respectively. The CCDC12 methylation levels were associated with estrogen receptor (ER) and human epidermal growth factor 2 (HER2) status. In ER-negative and HER2-positive (ER-/HER2+) breast cancer subtype, the combination of four sites CpG_2, CpG_5, CpG_6,7 and CpG_11 methylation levels could distinguish ER-/HER2+ breast cancer from the controls (AUC = 0.727). CONCLUSION The hypermethylation levels of CCDC12 in peripheral blood could be used for breast cancer detection.
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Affiliation(s)
- Jingjing Liu
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, China
| | - Yunhui Qu
- Department of Clinical Laboratory in the First Affiliated Hospital & Key Clinical Laboratory of Henan Province, Zhengzhou University, Zhengzhou, Henan, China
| | - Yutong Zhao
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, China
| | - Feifei Liang
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Longtao Ji
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Zhi Wang
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Jinyu Li
- Department of Otology, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, China
| | - Zishan Zang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Haixia Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jie Zhang
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
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Hawkins J, Browne EP, Arcaro KF, Sun Y. Rapid cell isolation in breastmilk in a non-clinical setting by a deterministic lateral displacement device and selective water and fat absorption. LAB ON A CHIP 2024; 24:604-614. [PMID: 38189141 DOI: 10.1039/d3lc00899a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Breastmilk is a reliable source of biomarker-containing, sloughed breast cells that have the potential to give valuable health insights to new mothers. Furthermore, known DNA-based markers for pregnancy-associated breast cancer are chemically stable and can be safely stored on a commercially available FTA® Elute Micro (EM) card, which can subsequently be mailed to a testing facility for the cost of a stamp. In theory, this archiving process can be performed by nonprofessionals in very low-resource settings as it simply requires placing a drop of breastmilk on an EM card. Although this level of convenience is paramount for new mothers, the low cell density of breastmilk complicates archiving on an EM card as such commercial products and associated protocols were designed for high-cell density physiological fluids such as blood. In this study, we present the use of a deterministic lateral displacement (DLD) device combined with porous superabsorbent polymers and hydrophobic sponges to achieve simple and low-cost cell enrichment in breastmilk. As the critical separation diameter in a DLD device is more heavily dependent on lithographically controlled pillar layout than fluid or flow properties, our use of DLD microfluidics allowed for the accommodation of both varying viscosities in human breastmilk samples and a varying pressure of actuation resulting from manual, syringe-driven operation. We demonstrate successful cell enrichment (>11×) and a corresponding increase in the DNA concentration of EM card elutions among breastmilk samples processed with our hybrid microfluidic system. As our device achieves sufficiently high cell enrichment in breastmilk samples while only requiring the user to push a syringe for 4 min with reasonable effort, we believe that it has high potential to expand EM card DNA archiving for diagnostic applications with low-cell density physiological fluids and in low-resource settings.
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Affiliation(s)
- Jamar Hawkins
- Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Eva P Browne
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Kathleen F Arcaro
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Yubing Sun
- Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA.
- Department of Biomedical Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
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Zhang C, Li J, Jiang H, Li M. Use of fiberoductoscopy for the management of pathological nipple discharge: ten years follow up of a single center in China. Gland Surg 2020; 9:2035-2043. [PMID: 33447554 PMCID: PMC7804554 DOI: 10.21037/gs-20-738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/29/2020] [Indexed: 11/06/2022]
Abstract
BACKGROUND Pathological nipple discharge (PND) is usually associated with benign intraductal papilloma, which has a higher malignant rate than other benign tumors in most cases. Fiberoductoscopy (FDS) is an alternative possibility in diagnostic and finding lesions in PND patients. Previously, the bloody discharge was presumed to show papilloma or breast cancer. However, as we started using FDS, papilloma or cancer also can be found in the cases with a transparent or yellow discharge. This study investigated the value of FDS for the diagnosis and locating of intraductal lesions in cases with nipple discharge. METHODS A retrospective analysis of 3,696 cases that initially presented with pathologic nipple discharge was performed. There were 4,456 FDSs performed, and the correlations between the FDS findings for distinct types of lesions and the pathological diagnosis were determined. RESULTS Among the 2,816 cases of elevated lesions, FDS confirmed 1,933 cases of intraductal papilloma, 584 cases of intraductal papillomatosis, and 299 cases of intraductal carcinoma. Among the 880 cases of non-elevated lesions, FDS confirmed 380 cases of duct dilation, 350 cases of duct inflammation, 136 cases of duct dilation and inflammation, and 14 cases of ductal carcinoma in situ (DCIS). All patients followed up 3 months to 12 years. There were 241 DCIS in total, and 8 cases had local recurrence, 2 cases had metastasis. Invasive ductal carcinoma, 41 cases, 3 had recurrence and 3 had metastases, and 1 for death. Invasive lobular carcinoma 23 cases, recurrence 2 cases, metastasis 1 case. CONCLUSIONS FDS has a high positive predictive rate and correlates well with the results of the pathological examination. The advantage of FDS is that it can observe the lesions, increasing the detection rate of early stage breast cancer, simple to operate, low cost, and no need for the appointment, appropriate for Chinese conditions.
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Affiliation(s)
- Chao Zhang
- Breast Cancer Department, Beijing Chaoyang Hospital, Beijing, China
| | - Jie Li
- Breast Cancer Department, Beijing Chaoyang Hospital, Beijing, China
| | - Hongchuan Jiang
- Breast Cancer Department, Beijing Chaoyang Hospital, Beijing, China
| | - Mengxin Li
- Breast Cancer Department, Beijing Chaoyang Hospital, Beijing, China
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The tumor suppressor Zinc finger protein 471 suppresses breast cancer growth and metastasis through inhibiting AKT and Wnt/β-catenin signaling. Clin Epigenetics 2020; 12:173. [PMID: 33203470 PMCID: PMC7672945 DOI: 10.1186/s13148-020-00959-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 10/26/2020] [Indexed: 12/24/2022] Open
Abstract
Background Zinc-finger protein 471 (ZNF471) is a member of the Krüppel-associated box domain zinc finger protein (KRAB-ZFP) family. ZNF471 is methylated in squamous cell carcinomas of tongue, stomach and esophageal. However, its role in breast carcinogenesis remains elusive. Here, we studied its expression, functions, and molecular mechanisms in breast cancer. Methods We examined ZNF471 expression by RT-PCR and qPCR. Methylation-specific PCR determined its promoter methylation. Its biological functions and related molecular mechanisms were assessed by CCK-8, clonogenicity, wound healing, Transwell, nude mice tumorigenicity, flow cytometry, BrdU-ELISA, immunohistochemistry and Western blot assays.
Results ZNF471 was significantly downregulated in breast cell lines and tissues due to its promoter CpG methylation, compared with normal mammary epithelial cells and paired surgical-margin tissues. Ectopic expression of ZNF471 substantially inhibited breast tumor cell growth in vitro and in vivo, arrested cell cycle at S phase, and promoted cell apoptosis, as well as suppressed metastasis. Further knockdown of ZNF471 verified its tumor-suppressive effects. We also found that ZNF471 exerted its tumor-suppressive functions through suppressing epithelial-mesenchymal transition, tumor cell stemness and AKT and Wnt/β-catenin signaling. Conclusions ZNF471 functions as a tumor suppressor that was epigenetically inactivated in breast cancer. Its inhibition of AKT and Wnt/β-catenin signaling pathways is one of the mechanisms underlying its anti-cancer effects.
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Waaijer L, Filipe MD, Simons J, van der Pol CC, de Boorder T, van Diest PJ, Witkamp AJ. Detection of breast cancer precursor lesions by autofluorescence ductoscopy. Breast Cancer 2020; 28:119-129. [PMID: 32725533 PMCID: PMC7796885 DOI: 10.1007/s12282-020-01136-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/16/2020] [Indexed: 12/26/2022]
Abstract
PURPOSE Autofluorescence is an image enhancement technique used for the detection of cancer precursor lesions in pulmonary and gastrointestinal endoscopy. This study evaluated the feasibility of addition of autofluorescence to ductoscopy for the detection of intraductal breast cancer precursor lesions. METHODS An autofluorescence imaging system, producing real-time computed images combining fluorescence intensities, was coupled to a conventional white light ductoscopy system. Prior to surgery, ductoscopy with white light and autofluorescence was evaluated under general anaesthesia in women scheduled for therapeutic or prophylactic mastectomy. Endoscopic findings in both modes were compared, marked and correlated with histology of the surgical specimen. RESULTS Four breast cancer patients and five high-risk women, with a median age of 47 years (range 23-62) were included. In autofluorescence mode, two intraductal lesions were seen in two breast cancer patients, which had an increase in the red-to-green fluorescence intensity compared with the surrounding tissue. One lesion had initially been missed by white light ductoscopy but was clearly visible in subsequent autofluorescence mode. One endoscopic finding was classified as suspicious by white light, but was negative in autofluorescence mode and showed normal histology. CONCLUSIONS This study demonstrates for the first time the in vivo feasibility of autofluorescence ductoscopy to detect pathologically confirmed breast cancer precursor lesions in both breast cancer patients and high-risk women that were occult under white light.
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Affiliation(s)
- Laurien Waaijer
- Department of Surgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Mando D Filipe
- Department of Surgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
| | - Janine Simons
- Department of Surgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Carmen C van der Pol
- Department of Surgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Tjeerd de Boorder
- Department of Medical Technology and Clinical Physics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Arjen Joost Witkamp
- Department of Surgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
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DNA Methylation Profiles and Their Diagnostic Utility in BC. DISEASE MARKERS 2019; 2019:6328503. [PMID: 31198475 PMCID: PMC6526564 DOI: 10.1155/2019/6328503] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/31/2019] [Accepted: 02/18/2019] [Indexed: 01/02/2023]
Abstract
Biomarkers, including DNA methylation, have shown a great potential for use in personalized medicine for BC and especially for the diagnosis of BC in developing countries. According to the bisulfite sequencing PCR in twelve specimens (BC and matched normal tissues), nine genetic probes were designed to detect the frequency of methylation of the promoters in a total of 302 paired cases of BC and matched normal breast tissues. Finally, a total of 900 serum samples were used to validate the use of these methylation biomarkers for clinical diagnosis of BC. A high frequency of promoter methylation of SFN, HOXA11, P16, RARβ, PCDHGB7, hMLH1, WNT5a, HOXD13, and RASSF1a was observed in BC tissues. The methylation frequencies of HOXD13 and hMLH1 increased with the progression of BC. The methylation frequencies of HOXD13 and WNT5a were significantly higher in BC. We found that methylation modification-positive samples were most consistently associated with luminal BC. Finally, we confirmed that RASSF1a, P16, and PCDHGB7 displayed a significant sensitivity and specificity as diagnostic biomarkers for BC (P < 0.001), and a panel that combined these three genes displayed increased significance (AUC, 0.781; P < 0.001). These data suggest that epigenetic markers in serum can potentially be used to diagnose BC. The identification of additional BC-specific methylated genes would improve the sensitivity and specificity of this approach. This study could also indicate that different molecular subtypes of BC are caused by distinct genetic and epigenetic mechanisms.
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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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de Boorder T, Waaijer L, van Diest PJ, Witkamp AJ. Ex vivo feasibility study of endoscopic intraductal laser ablation of the breast. Lasers Surg Med 2017; 50:137-142. [PMID: 28990682 DOI: 10.1002/lsm.22745] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2017] [Indexed: 12/22/2022]
Abstract
OBJECTIVE To determine the feasibility and safety of breast endoscopic thulium laser ablation for treatment of intraductal neoplasia. STUDY DESIGN Ductoscopy is a minimally invasive endoscopic approach of the milk ducts of the breast via the nipple. Besides diagnosis in women with pathologic nipple discharge (PND), it allows non-invasive removal of intraductal lesions with a stalk like papillomas. Removal, however, is often incomplete and flat lesions cannot be targeted. We therefore developed laser ductoscopy. METHODS Dosimetry of laser ductoscopy was assessed in thirteen mastectomy specimens, applying power settings of 1-5 W with 100-1000 ms pulsed exposure to a 375-μm outer diameter thulium fiber laser. Subsequently histology was obtained from the breast tissue that was treated with the Thulium laser. RESULTS Endoscopic view was maintained during ductoscopic laser ablation at 1-3 W. Increasing power to 4-5 W caused impaired vision due to shrinkage of the main duct around the ductoscope tip. Histology revealed localized ablation of the duct wall. CONCLUSION We show for the first time that laser ductoscopy is technically feasible. The Thulium laser enables a superficial intraductal ablation and is a useful tool for intraductal interventions. An in vivo prospective study is needed to further demonstrate its potential. Lasers Surg. Med. 50:137-142, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Tjeerd de Boorder
- Departments of Medical Technology and Clinical Physics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Laurien Waaijer
- Departments of Surgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Paul J van Diest
- Departments of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Arjen J Witkamp
- Departments of Surgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
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Vos S, Moelans CB, van Diest PJ. BRCA promoter methylation in sporadic versus BRCA germline mutation-related breast cancers. Breast Cancer Res 2017; 19:64. [PMID: 28569220 PMCID: PMC5452400 DOI: 10.1186/s13058-017-0856-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 05/16/2017] [Indexed: 02/08/2023] Open
Abstract
Background In breast cancer, BRCA promoter hypermethylation and BRCA germline mutations are said to occur together rarely, but this property has not yet been translated into a clinical test. Our aim in this study was to investigate the diagnostic value of BRCA1/2 methylation in distinguishing breast carcinomas of BRCA1 and BRCA2 germline mutation carriers from sporadic breast carcinomas using a recently developed BRCA methylation assay based on methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). Methods MS-MLPAs were performed to assess BRCA1 and BRCA2 methylation in breast carcinoma tissues from 39 BRCA1 and 33 BRCA2 germline mutation carriers, 80 patients with sporadic breast cancer, and normal breast tissues from 5 BRCA1 and 4 BRCA2 mutation carriers and 5 nonmutation carriers. Results Methylation frequencies varied considerably between CpG sites across the BRCA1 and BRCA2 promoters. Some CpG sites were methylated more frequently in BRCA1/2-related than in sporadic carcinomas, whereas other CpG sites were methylated more frequently in sporadic carcinomas, with large variances in sensitivity and specificity as a consequence. Conclusions The diagnostic value of BRCA promoter methylation analysis in distinguishing BRCA1/2-related from sporadic breast carcinomas seems to be considerably dependent on the targeted CpG sites. These findings are important for adequate use of BRCA methylation analysis as a prescreening tool for BRCA germline genetic testing or to identify BRCAness patients who may benefit from targeted therapies such as poly(adenosine diphosphate-ribose) polymerase inhibitors.
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Affiliation(s)
- Shoko Vos
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX, Utrecht, The Netherlands.
| | - Cathy Beatrice Moelans
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX, Utrecht, The Netherlands
| | - Paul Joannes van Diest
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX, Utrecht, The Netherlands
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Shan M, Yin H, Li J, Li X, Wang D, Su Y, Niu M, Zhong Z, Wang J, Zhang X, Kang W, Pang D. Detection of aberrant methylation of a six-gene panel in serum DNA for diagnosis of breast cancer. Oncotarget 2017; 7:18485-94. [PMID: 26918343 PMCID: PMC4951303 DOI: 10.18632/oncotarget.7608] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/11/2016] [Indexed: 01/05/2023] Open
Abstract
Detection of breast cancer at an early stage is the key for successful treatment and improvement of outcome. However the limitations of mammography are well recognized, especially for those women with premenopausal breast cancer. Novel approaches to breast cancer screening are necessary, especially in the developing world where mammography is not feasible. In this study, we examined the promoter methylation of six genes (SFN, P16, hMLH1, HOXD13, PCDHGB7 and RASSF1a) in circulating free DNA (cfDNA) extracted from serum. We used a high-throughput DNA methylation assay (MethyLight) to examine serum from 749 cases including breast cancer patients, patients with benign breast diseases and healthy women. The six-gene methylation panel test achieved 79.6% and 82.4% sensitivity with a specificity of 72.4% and 78.1% in diagnosis of breast cancer when compared with healthy and benign disease controls, respectively. Moreover, the methylation panel positive group showed significant differences in the following independent variables: (a) involvement of family history of tumors; (b) a low proliferative index, ki-67; (c) high ratios in luminal subtypes. Additionally the panel also complemented some breast cancer cases which were neglected by mammography or ultrasound. These data suggest that epigenetic markers in serum have potential for diagnosis of breast cancer.
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Affiliation(s)
- Ming Shan
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, P.R. China
| | - Huizi Yin
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China
| | - Junnan Li
- Department of Epidemiology and Biostatistics, Harbin Medical University, Harbin, P.R. China
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin, P.R. China
| | - Dong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P.R. China
| | - Yonghui Su
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China
| | - Ming Niu
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China
| | - Zhenbin Zhong
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China
| | - Ji Wang
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China
| | - Xianyu Zhang
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China
| | - Wenli Kang
- Department of Oncology, General Hospital of Heilongjiang Province Land Reclamation Headquarters, Harbin, P.R. China
| | - Da Pang
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, P.R. China
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Chong ETJ, Goh LPW, See EUH, Chuah JA, Chua KH, Lee PC. Association of CYP2E1, STK15 and XRCC1 Polymorphisms with Risk of Breast Cancer in Malaysian Women. Asian Pac J Cancer Prev 2017; 17:647-53. [PMID: 26925658 DOI: 10.7314/apjcp.2016.17.2.647] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Breast cancer is the most common type of cancer affecting Malaysian women. Recent statistics revealed that the cumulative probability of breast cancer and related deaths in Malaysia is higher than in most of the countries of Southeast Asia. Single nucleotide polymorphisms (SNPs) in CYP2E1 (rs6413432 and rs3813867), STK15 (rs2273535 and rs1047972) and XRCC1 (rs1799782 and rs25487) have been associated with breast cancer risk in a meta-analysis but any link in Southeast Asia, including Malaysia, remained to be determined. Hence, we investigated the relationship between these SNPs and breast cancer risk among Malaysian women in the present case-control study. MATERIALS AND METHODS Genomic DNA was isolated from peripheral blood of 71 breast cancer patients and 260 healthy controls and subjected to polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. RESULTS Our study showed that the c1/c2 genotype or subjects with at least one c2 allele in CYP2E1 rs3813867 SNP had significantly increased almost 1.8-fold higher breast cancer risk in Malaysian women overall. In addition, the variant Phe allele in STK15 rs2273535 SNP appeared to protect against breast cancer in Malaysian Chinese. No significance association was found between XRCC1 SNPs and breast cancer risk in the population. CONCLUSIONS This study provides additional knowledge on CYP2E1, STK15 and XRCC1 SNP impact of risk of breast cancer, particularly in the Malaysian population. From our findings, we also recommend Malaysian women to perform breast cancer screening before 50 years of age.
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Affiliation(s)
- Eric Tzyy Jiann Chong
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia E-mail :
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Nasr R, Sleiman F, Awada Z, Zgheib NK. The pharmacoepigenetics of drug metabolism and transport in breast cancer: review of the literature and in silico analysis. Pharmacogenomics 2016; 17:1573-85. [DOI: 10.2217/pgs-2016-0081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The focus of this manuscript is on DNA methylation and miRNA regulation of drug-metabolizing enzymes and drug transporters involved in the disposition of drugs commonly used in breast cancer. We start with a review of the available scant literature and follow with an in silico analysis of the CpG islands and miRNA binding sites of genes of interest. We make the case that there is room for further research to include more genes and miRNAs despite the extensive sharing of miRNA targets by candidate genes of interest. We also stress on the role of peripheral blood as a source of pharmacoepigenetic biomarkers, and point out the lack of toxicoepigenetic studies in breast cancer.
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Affiliation(s)
- Rihab Nasr
- Department of Anatomy, Cell Biology & Physiology, American University of Beirut Faculty of Medicine (AUBFM), Beirut, Lebanon
| | - Fatima Sleiman
- Department of Pharmacology & Toxicology, American University of Beirut Faculty of Medicine (AUBFM), Beirut, Lebanon
| | - Zeinab Awada
- Department of Pharmacology & Toxicology, American University of Beirut Faculty of Medicine (AUBFM), Beirut, Lebanon
| | - Natalie K Zgheib
- Department of Pharmacology & Toxicology, American University of Beirut Faculty of Medicine (AUBFM), Beirut, Lebanon
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13
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Abstract
Aberrant DNA methylation is considered to be one of the most common hallmarks of cancer. Several recent advances in assessing the DNA methylome provide great promise for deciphering the cancer-specific DNA methylation patterns. Herein, we present the current key technologies used to detect high-throughput genome-wide DNA methylation, and the available cancer-associated methylation databases. Additionally, we focus on the computational methods for preprocessing, analyzing and interpreting the cancer methylome data. It not only discusses the challenges of the differentially methylated region calling and the prediction model construction but also highlights the biomarker investigation for cancer diagnosis, prognosis and response to treatment. Finally, some emerging challenges in the computational analysis of cancer methylome data are summarized.
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14
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Waaijer L, Simons JM, Borel Rinkes IHM, van Diest PJ, Verkooijen HM, Witkamp AJ. Systematic review and meta-analysis of the diagnostic accuracy of ductoscopy in patients with pathological nipple discharge. Br J Surg 2016; 103:632-643. [DOI: 10.1002/bjs.10125] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/07/2015] [Accepted: 01/06/2016] [Indexed: 11/06/2022]
Abstract
Abstract
Background
Invasive surgery remains the standard for diagnosis of pathological nipple discharge (PND). Only a minority of patients with nipple discharge and an unsuspicious finding on conventional breast imaging have cancer. Ductoscopy is a minimally invasive alternative for evaluation of PND. This systematic review and meta-analysis was designed to evaluate the diagnostic accuracy of ductoscopy in patients with PND.
Methods
A systematic search of electronic databases for studies addressing ductoscopy in patients with PND was conducted. Two classification systems were assessed. For DSany, all visualized ductoscopic abnormalities were classified as positive, whereas for DSsusp, only suspicious findings were considered positive. After checking heterogeneity, pooled sensitivity and specificity of DSany and DSsusp were calculated.
Results
The search yielded 4642 original citations, of which 20 studies were included in the review. Malignancy rates varied from 0 to 27 per cent. Twelve studies, including 1994 patients, were eligible for meta-analysis. Pooled sensitivity and specificity of DSany were 94 (95 per cent c.i. 88 to 97) per cent and 47 (44 to 49) per cent respectively. Pooled sensitivity and specificity of DSsusp were 50 (36 to 64) and 83 (81 to 86) per cent respectively. Heterogeneity between studies was moderate to large for sensitivity (DSany: I2 = 17·5 per cent; DSsusp: I2 = 37·9 per cent) and very large for specificity (DSany: I2 = 96·8 per cent; DSsusp: I2 = 92·6 per cent).
Conclusion
Ductoscopy detects about 94 per cent of all underlying malignancies in patients with PND, but does not permit reliable discrimination between malignant and benign findings.
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Affiliation(s)
- L Waaijer
- Department of Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - J M Simons
- Department of Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - I H M Borel Rinkes
- Department of Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - P J van Diest
- Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - H M Verkooijen
- Imaging Division, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A J Witkamp
- Department of Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
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15
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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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16
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de Groot JS, Moelans CB, Elias SG, Hennink A, Verolme B, Suijkerbuijk KPM, Jager A, Seynaeve C, Bos P, Witkamp AJ, Ausems MGEM, van Diest PJ, van der Wall E. Repeated nipple fluid aspiration: compliance and feasibility results from a prospective multicenter study. PLoS One 2015; 10:e0127895. [PMID: 26000714 PMCID: PMC4441497 DOI: 10.1371/journal.pone.0127895] [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: 03/19/2014] [Accepted: 04/21/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Despite intensive surveillance, a high rate of interval malignancies is still seen in women at increased breast cancer risk. Therefore, novel screening modalities aiming at early detection remain needed. The intraductal approach offers the possibility to directly sample fluid containing cells, DNA and proteins from the mammary ductal system where, in the majority of cases, breast cancer originates. Fluid from the breast can non-invasively be obtained by oxytocin-assisted vacuum aspiration, called nipple fluid aspiration (NFA). The goal of this feasibility study was to evaluate the potential of repeated NFA, which is a critical and essential step to evaluate its possible value as a breast cancer screening method. METHODS In this multicenter, prospective study, we annually collected nipple fluid for up to 5 consecutive years from women at increased breast cancer risk, and performed a questionnaire-based survey regarding discomfort of the aspiration. Endpoints of the current interim analyses were the feasibility and results of 994 NFA procedures in 451 women with total follow-up of 560 person years of observation. RESULTS In this large group of women at increased risk of breast cancer, repetitive NFA appeared to be feasible and safe. In 66.4% of aspirated breasts, nipple fluid was successfully obtained. Independent predictive factors for successful NFA were premenopausal status, spontaneous nipple discharge, smaller breast size, bilateral oophorectomy and previous use of hormone replacement therapy or anti-hormonal treatment. The procedure was well tolerated with low discomfort. Drop-out rate was 20%, which was mainly due to repeated unsuccessful aspiration attempts. Only 1.6% of women prematurely declined further participation because of side effects. CONCLUSIONS Repeated NFA in women at increased breast cancer risk is feasible and safe. Therefore, NFA is a promising method to non-invasively obtain a valuable source of potential breast cancer specific biomarkers.
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Affiliation(s)
- J. S. de Groot
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C. B. Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - S. G. Elias
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - A. Hennink
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - B. Verolme
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - K. P. M. Suijkerbuijk
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - A. Jager
- Department of Medical Oncology, Erasmus University Medical Center, Daniel den Hoed Cancer Center, Rotterdam, The Netherlands
| | - C. Seynaeve
- Department of Medical Oncology, Erasmus University Medical Center, Daniel den Hoed Cancer Center, Rotterdam, The Netherlands
| | - P. Bos
- Department of Medical Oncology, Erasmus University Medical Center, Daniel den Hoed Cancer Center, Rotterdam, The Netherlands
| | - A. J. Witkamp
- Department of Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M. G. E. M. Ausems
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - P. J. van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - E. van der Wall
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
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17
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Methylation profiling of 48 candidate genes in tumor and matched normal tissues from breast cancer patients. Breast Cancer Res Treat 2015; 149:767-79. [DOI: 10.1007/s10549-015-3276-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/13/2015] [Indexed: 10/23/2022]
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18
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Toiyama Y, Okugawa Y, Goel A. DNA methylation and microRNA biomarkers for noninvasive detection of gastric and colorectal cancer. Biochem Biophys Res Commun 2014; 455:43-57. [PMID: 25128828 DOI: 10.1016/j.bbrc.2014.08.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 07/22/2014] [Accepted: 08/01/2014] [Indexed: 02/06/2023]
Abstract
Cancer initiation and progression is controlled by both genetic and epigenetic events. Epigenetics refers to the study of mechanisms that alter gene expression without permanently altering the DNA sequence. Epigenetic alterations are reversible and heritable, and include changes in histone modifications, DNA methylation, and non-coding RNA-mediated gene silencing. Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Aberrant epigenetic modifications occur at the earliest stages of neoplastic transformation and are now believed to be essential players in cancer initiation and progression. Recent advances in epigenetics have not only offered a deeper understanding of the underlying mechanism(s) of carcinogenesis, but have also allowed identification of clinically relevant putative biomarkers for the early detection, disease monitoring, prognosis and risk assessment of cancer patients. At this moment, DNA methylation and non-coding RNA including with microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) represent the largest body of available literature on epigenetic biomarkers with the highest potential for cancer diagnosis. Following identification of cell-free nucleic acids in systematic circulation, increasing evidence has demonstrated the potential of cell-free epigenetic biomarkers in the blood or other body fluids for cancer detection. In this article, we summarize the current state of knowledge on epigenetic biomarkers - primarily DNA methylation and non-coding RNAs - as potential substrates for cancer detection in gastric and colorectal cancer, the two most frequent cancers within the gastrointestinal tract. We also discuss the obstacles that have limited the routine use of epigenetic biomarkers in the clinical settings and provide our perspective on approaches that might help overcome these hurdles, so that these biomarkers can be readily developed for clinical management of cancer patients.
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Affiliation(s)
- Yuji Toiyama
- Gastrointestinal Cancer Research Laboratory, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, 3500 Gaston Avenue, Dallas, TX 75246, USA; Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Graduate School of Medicine, Mie University, Mie 514-8507, Japan
| | - Yoshinaga Okugawa
- Gastrointestinal Cancer Research Laboratory, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, 3500 Gaston Avenue, Dallas, TX 75246, USA; Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Graduate School of Medicine, Mie University, Mie 514-8507, Japan
| | - Ajay Goel
- Gastrointestinal Cancer Research Laboratory, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, 3500 Gaston Avenue, Dallas, TX 75246, USA.
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19
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van Kempen PMW, van Bockel L, Braunius WW, Moelans CB, van Olst M, de Jong R, Stegeman I, van Diest PJ, Grolman W, Willems SM. HPV-positive oropharyngeal squamous cell carcinoma is associated with TIMP3 and CADM1 promoter hypermethylation. Cancer Med 2014; 3:1185-96. [PMID: 25065733 PMCID: PMC4302669 DOI: 10.1002/cam4.313] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/03/2014] [Accepted: 07/07/2014] [Indexed: 12/30/2022] Open
Abstract
Oropharyngeal squamous cell carcinoma (OPSCC) is associated with human papillomavirus (HPV) in a proportion of tumors. HPV-positive OPSCC is considered a distinct molecular entity with a prognostic advantage compared to HPV-negative cases. Silencing of cancer-related genes by DNA promoter hypermethylation may play an important role in the development of OPSCC. Hence, we examined promoter methylation status in 24 common tumor suppressor genes in a group of 200 OPSCCs to determine differentially methylated genes in HPV-positive versus HPV-negative primary OPSCC. Methylation status was correlated with HPV status, clinical features, and patient survival using multivariate methods. Additionally, methylation status of 16 cervical squamous cell carcinomas (SCC) was compared with HPV-positive OPSCC. Using methylation-specific probe amplification, HPV-positive OPSCC showed a significantly higher cumulative methylation index (CMI) compared to HPV-negative OPSCC (P=0.008). For the genes CDH13, DAPK1, and RARB, both HPV-positive and HPV-negative OPSCC showed promoter hypermethylation in at least 20% of the tumors. HPV status was found to be an independent predictor of promoter hypermethylation of CADM1 (P < 0.001), CHFR (P = 0.027), and TIMP3 (P < 0.001). CADM1 and CHFR showed similar methylation patterns in OPSCC and cervical SCC, but TIMP3 showed no methylation in cervical SCC in contrast to OPSCC. Methylation status of neither individual gene nor CMI was associated with survival. These results suggest that HPV-positive tumors are to a greater extent driven by promotor hypermethylation in these tumor suppressor genes. Especially CADM1 and TIMP3 are significantly more frequently hypermethylated in HPV-positive OPSCC and CHFR in HPV-negative tumors.
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Affiliation(s)
- Pauline M W van Kempen
- Department of Otorhinolaryngology - Head and Neck Surgery, University Medical Center Utrecht, Utrecht, The Netherlands; Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
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Wojdacz TK, Windeløv JA, Thestrup BB, Damsgaard TE, Overgaard J, Hansen L. Identification and characterization of locus-specific methylation patterns within novel loci undergoing hypermethylation during breast cancer pathogenesis. Breast Cancer Res 2014; 16:R17. [PMID: 24490656 PMCID: PMC3978461 DOI: 10.1186/bcr3612] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 01/13/2014] [Indexed: 12/14/2022] Open
Abstract
Introduction Despite similar clinical and pathological features, large numbers of breast cancer patients experience different outcomes of the disease. This, together with the fact that the incidence of breast cancer is growing worldwide, emphasizes an urgent need for identification of new biomarkers for early cancer detection and stratification of patients. Methods We used ultrahigh-resolution microarrays to compare genomewide methylation patterns of breast carcinomas (n = 20) and nonmalignant breast tissue (n = 5). Biomarker properties of a subset of discovered differentially methylated regions (DMRs) were validated using methylation-sensitive high-resolution melting (MS-HRM) in a case–control study on a panel of breast carcinomas (n = 275) and non-malignant controls (n = 74). Results On the basis of microarray results, we selected 19 DMRs for large-scale screening of cases and controls. Analysis of the screening results showed that all DMRs tested displayed significant gains of methylation in the cancer tissue compared to the levels in control tissue. Interestingly, we observed two types of locus-specific methylation, with loci undergoing either predominantly full or heterogeneous methylation during carcinogenesis. Almost all tested DMRs (17 of 19) displayed low-level methylation in nonmalignant breast tissue, independently of locus-specific methylation patterns in cases. Conclusions Specific loci can undergo either heterogeneous or full methylation during carcinogenesis, and loci hypermethylated in cancer frequently show low-level methylation in nonmalignant tissue.
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van Veldhoven K, Rahman S, Vineis P. Epigenetics and epidemiology: models of study and examples. Cancer Treat Res 2014; 159:241-255. [PMID: 24114484 DOI: 10.1007/978-3-642-38007-5_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Epidemiological studies have successfully identified several environmental causes of disease, but often these studies are limited by methodological problems (e.g. lack of sensitivity and specificity in exposure assessment; confounding). Proposed approaches to improve observational studies of environmental associations are Mendelian randomization and the meet-in-the-middle (MITM) approach. The latter uses signals from the growing field of -omics as putative intermediate biomarkers in the pathogenetic process that links exposure with disease. The first part of this approach consists in the association between exposure and disease. The next step consists in the study of the relationship between (biomarkers of) exposure and intermediate -omic biomarkers of early effect; thirdly, the relation between the disease outcome and intermediate -omic biomarkers is assessed. We propose that when an association is found in all three steps it is possible that there is a casual association. One of the associations that have been investigated extensively in the recent years but is not completely understood is that between environmental endocrine disruptors and breast cancer. Here we present an example of how the "meet-in-the-middle" approach can be used to address the role of endocrine disruptors, by reviewing the relevant literature.
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22
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Rojo F, Domingo L, Sala M, Zazo S, Chamizo C, Menendez S, Arpi O, Corominas JM, Bragado R, Servitja S, Tusquets I, Nonell L, Macià F, Martínez J, Rovira A, Albanell J, Castells X. Gene expression profiling in true interval breast cancer reveals overactivation of the mTOR signaling pathway. Cancer Epidemiol Biomarkers Prev 2013; 23:288-99. [PMID: 24347552 DOI: 10.1158/1055-9965.epi-13-0761] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The development and progression of true interval breast cancers (tumors that truly appear after a negative screening mammogram) is known to be different from screen-detected cancers. However, the worse clinical behavior of true interval cancers is not fully understood from a biologic basis. We described the differential patterns of gene expression through microarray analysis in true interval and screen-detected cancers. METHODS An unsupervised exploratory gene expression profile analysis was performed on 10 samples (true interval cancers = 5; screen-detected cancers = 5) using Affymetrix Human Gene 1.0ST arrays and interpreted by Ingenuity Pathway Analysis. Differential expression of selected genes was confirmed in a validation series of 91 tumors (n = 12; n = 79) by immunohistochemistry and in 24 tumors (n = 8; n = 16) by reverse transcription quantitative PCR (RT-qPCR), in true interval and screen-detected cancers, respectively. RESULTS Exploratory gene expression analysis identified 1,060 differentially expressed genes (unadjusted P < 0.05) between study groups. On the basis of biologic implications, four genes were further validated: ceruloplasmin (CP) and ribosomal protein S6 kinase, 70 kDa, polypeptide 2 (RPS6KB2), both upregulated in true interval cancers; and phosphatase and tensin homolog (PTEN) and transforming growth factor beta receptor III (TGFBR3), downregulated in true interval cancers. Their differential expression was confirmed by RT-qPCR and immunohistochemistry, consistent with mTOR pathway overexpression in true interval cancers. CONCLUSIONS True interval and screen-detected cancers show differential expression profile both at gene and protein levels. The mTOR signaling is significantly upregulated in true interval cancers, suggesting this pathway may mediate their aggressiveness. IMPACT Linking epidemiologic factors and mTOR activation may be the basis for future personalized screening strategies in women at risk of true interval cancers.
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Affiliation(s)
- Federico Rojo
- Authors' Affiliations: Departments of Pathology and Immunology, IIS-Fundación Jiménez Díaz, Madrid; Cancer Research Program; Microarray Core Facility (SAM), IMIM (Hospital del Mar Medical Research Institute); Department of Epidemiology and Evaluation, Hospital del Mar; Research Network on Health Services in Chronic Diseases (REDISSEC); Departments of Pathology, Medical Oncology, and Radiology Department, Hospital del Mar; and Universitat Pompeu Fabra, Barcelona, Spain
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Sun S, Noviski A, Yu X. MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment. BMC Bioinformatics 2013; 14:259. [PMID: 23968174 PMCID: PMC3765750 DOI: 10.1186/1471-2105-14-259] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 08/09/2013] [Indexed: 11/10/2022] Open
Abstract
Background DNA methylation is an epigenetic event that adds a methyl-group to the 5’ cytosine. This epigenetic modification can significantly affect gene expression in both normal and diseased cells. Hence, it is important to study methylation signals at the single cytosine site level, which is now possible utilizing bisulfite conversion technique (i.e., converting unmethylated Cs to Us and then to Ts after PCR amplification) and next generation sequencing (NGS) technologies. Despite the advances of NGS technologies, certain quality issues remain. Some of the more prevalent quality issues involve low per-base sequencing quality at the 3’ end, PCR amplification bias, and bisulfite conversion rates. Therefore, it is important to conduct quality assessment before downstream analysis. To the best of our knowledge, no existing software packages can generally assess the quality of methylation sequencing data generated based on different bisulfite-treated protocols. Results To conduct the quality assessment of bisulfite methylation sequencing data, we have developed a pipeline named MethyQA. MethyQA combines currently available open-source software packages with our own custom programs written in Perl and R. The pipeline can provide quality assessment results for tens of millions of reads in under an hour. The novelty of our pipeline lies in its examination of bisulfite conversion rates and of the DNA sequence structure of regions that have different conversion rates or coverage. Conclusions MethyQA is a new software package that provides users with a unique insight into the methylation sequencing data they are researching. It allows the users to determine the quality of their data and better prepares them to address the research questions that lie ahead. Due to the speed and efficiency at which MethyQA operates, it will become an important tool for studies dealing with bisulfite methylation sequencing data.
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Affiliation(s)
- Shuying Sun
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland 44106, Ohio, USA.
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Starlard-Davenport A, Kutanzi K, Tryndyak V, Word B, Lyn-Cook B. Restoration of the methylation status of hypermethylated gene promoters by microRNA-29b in human breast cancer: A novel epigenetic therapeutic approach. J Carcinog 2013; 12:15. [PMID: 23961262 PMCID: PMC3746452 DOI: 10.4103/1477-3163.115720] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 12/13/2012] [Indexed: 01/08/2023] Open
Abstract
It is well established that transcriptional silencing of critical tumor-suppressor genes by DNA methylation is a fundamental component in the initiation of breast cancer. However, the involvement of microRNAs (miRNAs) in restoring abnormal DNA methylation patterns in breast cancer is not well understood. Therefore, we investigated whether miRNA-29b, due to its complimentarity to the 3’- untranslated region of DNA methyltransferase 3A (DNMT3A) and DNMT3B, could restore normal DNA methylation patterns in human breast cancers and breast cancer cell lines. We demonstrated that transfection of pre-miRNA-29b into less aggressive MCF-7 cells, but not MDA-MB-231 mesenchymal cells, inhibited cell proliferation, decreased DNMT3A and DNMT3B messenger RNA (mRNA), and decreased promoter methylation status of ADAM23 , CCNA1, CCND2, CDH1, CDKN1C, CDKN2A, HIC1, RASSF1, SLIT2, TNFRSF10D, and TP73 tumor-suppressor genes. Using methylation polymerase chain reaction (PCR) arrays and real-time PCR, we also demonstrated that the methylation status of several critical tumor-suppressor genes increased as stage of breast disease increased, while miRNA-29b mRNA levels were significantly decreased in breast cancers versus normal breast. This increase in methylation status was accompanied by an increase in DNMT1 and DNMT3B mRNA in advanced stage of human breast cancers and in MCF-7, MDA-MB-361, HCC70, Hs-578T, and MDA-MB-231 breast cancer cells as compared to normal breast specimens and MCF-10-2A, a non-tumorigenic breast cell line, respectively. Our findings highlight the potential for a new epigenetic approach in improving breast cancer therapy by targeting DNMT3A and DNMT3B through miRNA-29b in non-invasive epithelial breast cancer cells.
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25
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Yang BZ, Zhang H, Ge W, Weder N, Douglas-Palumberi H, Perepletchikova F, Gelernter J, Kaufman J. Child abuse and epigenetic mechanisms of disease risk. Am J Prev Med 2013; 44:101-7. [PMID: 23332324 PMCID: PMC3758252 DOI: 10.1016/j.amepre.2012.10.012] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 07/24/2012] [Accepted: 10/05/2012] [Indexed: 01/01/2023]
Abstract
BACKGROUND Child abuse is highly prevalent and associated with increased risk for a range of health problems, including cancer, cardiovascular disease, diabetes, psychiatric disorders, and other health problems. Little is currently known about the mechanism by which early adversity confers risk for health problems later in life. PURPOSE To determine if there are epigenetic differences associated with child maltreatment that may help explain association between adverse childhood experiences and later health problems. METHODS As part of a study examining genetic and environmental factors associated with depression, saliva DNA specimens were collected on 96 maltreated children removed from their parents due to abuse or neglect and 96 demographically matched control children between 2003 and 2010. In 2011, the Illumina 450K BeadChip was used on stored DNA specimens and analyzed to examine whole-genome methylation differences between maltreated and control children. RESULTS After controlling for multiple comparisons, maltreated and control children had significantly different methylation values at 2868 CpG sites (p<5.0 × 10(-7), all sites; average methylation difference per site=17%; range=1%-62%). The gene set contained numerous markers of diseases and biological processes related to the health problems associated with early childhood adversity. CONCLUSIONS Although replication is required, this study suggests that epigenetic mechanisms may be associated with risk for health problems later in life in maltreated children. This study lays the groundwork for future studies examining health and methylation measures to further characterize the role of epigenetic mechanisms in conferring risk for medical problems in individuals with histories of early adversity.
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Affiliation(s)
- Bao-Zhu Yang
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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26
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Epigenetics makes its mark on women-specific cancers—an opportunity to redefine oncological approaches? Gynecol Oncol 2013; 128:134-143. [DOI: 10.1016/j.ygyno.2012.09.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/21/2012] [Accepted: 09/22/2012] [Indexed: 01/21/2023]
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Mikeska T, Bock C, Do H, Dobrovic A. DNA methylation biomarkers in cancer: progress towards clinical implementation. Expert Rev Mol Diagn 2012; 12:473-87. [PMID: 22702364 DOI: 10.1586/erm.12.45] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Altered DNA methylation is ubiquitous in human cancers and specific methylation changes are often correlated with clinical features. DNA methylation biomarkers, which use those specific methylation changes, provide a range of opportunities for early detection, diagnosis, prognosis, therapeutic stratification and post-therapeutic monitoring. Here we review current approaches to developing and applying DNA methylation biomarkers in cancer therapy. We discuss the obstacles that have so far limited the routine use of DNA methylation biomarkers in clinical settings and describe ways in which these obstacles can be overcome. Finally, we summarize the current state of clinical implementation for some of the most widely studied and well-validated DNA methylation biomarkers, including SEPT9, VIM, SHOX2, PITX2 and MGMT.
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Affiliation(s)
- Thomas Mikeska
- Molecular Pathology Research & Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett Street, Melbourne, Victoria 8006, Australia
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Chen FM, Chang HW, Yang SF, Huang YF, Nien PY, Yeh YT, Hou MF. The mitogen-activated protein kinase phosphatase-1 (MKP-1) gene is a potential methylation biomarker for malignancy of breast cancer. Exp Mol Med 2012; 44:356-62. [PMID: 22333693 PMCID: PMC3366329 DOI: 10.3858/emm.2012.44.5.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The mitogen-activated protein kinase (MAPK) phosphatase- 1 (MKP-1) belongs to the MAPK cascades which are central to cell proliferation and apoptosis. The carcinogenic role of MKP-1 has been reported in many types of cancer but it has rarely been investigated in breast cancer. The present study was designed to evaluate the MKP-1 mRNA expression and its possible regulation by methylation of MKP-1 promoter in the model of several breast cancer cell lines and tissues as well as controls. Our data demonstrate MKP-1 mRNA expression significantly decreased in five breast cancer cell lines compared to breast controls (P<0.01). Using the methylation-specific PCR (MSP) analysis, the unmethylated reaction (U) is dominant in both normal cell lines and benign breast tumors (100% vs. 86.2%), whereas the methylated reaction (M) is dominant in both breast cancer cell lines and invasive breast tumors (100% vs. 57.2%). In terms of methylation ratio (M/M+U), methylation level in MKP-1 promoter is significantly higher in the invasive breast tumor tissues (n = 152) than in benign breast tumor tissues (n = 29) (P<0.0001). Assessing the methylation ratio of the promoter of MKP-1 gene to diagnose the breast malignancy (invasive vs. benign), the area under the receiver- operating characteristic (ROC) curve was 0.809 (95% CI: 0.711-0.906, P<0.001). The best performance for this prediction has a sensitivity of 76.32% and a specificity of 82.76% at the cutoff value of 0.38. Taken together, we firstly demonstrated that the promoter methylation of MKP-1 gene is a potential breast cancer biomarker for breast malignancy.
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Affiliation(s)
- Fang-Ming Chen
- Department of Surgery, School of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Epigenetic Methylation of Parathyroid CaR and VDR Promoters in Experimental Secondary Hyperparathyroidism. Int J Nephrol 2012; 2012:123576. [PMID: 23094155 PMCID: PMC3474253 DOI: 10.1155/2012/123576] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/04/2012] [Indexed: 11/25/2022] Open
Abstract
Secondary hyperparathyroidism (s-HPT) in uremia is characterized by decreased expression in the parathyroids of calcium sensing (CaR) and vitamin D receptors (VDR). Parathyroid hormone (PTH) is normalized despite low levels of CaR and VDR after experimental reversal of uremia. The expression of CaR in parathyroid cultures decreases rapidly. Methylation of promoter regions is often detected during epigenetic downregulation of gene expression. Therefore, using an experimental rat model, we examined changes in methylation levels of parathyroid CaR and VDR promoters in vivo and in vitro. Methods. Uremia was induced by 5/6 nephrectomy. Melting temperature profiling of CaR and VDR PCR products after bisulfite treatment of genomic DNA from rat parathyroids was performed. Real-time PCR measured expression of PTH, CaR, VDR, and klotho genes in vitro. Results. Parathyroids from uremic rats had similar low levels of methylation in vivo and in vitro. In culture, a significant downregulation of CaR, VDR, and klotho within two hours of incubation was observed, while housekeeping genes remained stable for 24 hours. Conclusion. In uremic s-HPT and in vitro, no overall changes in methylation levels in the promoter regions of parathyroid CaR and VDR genes were found. Thus, epigenetic methylation of these promoters does not explain decreased parathyroid expression of CaR and VDR genes in uremic s-HPT.
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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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Fujita N, Nakayama T, Yamamoto N, Kim SJ, Shimazu K, Shimomura A, Maruyama N, Morimoto K, Tamaki Y, Noguchi S. Methylated DNA and total DNA in serum detected by one-step methylation-specific PCR is predictive of poor prognosis for breast cancer patients. Oncology 2012; 83:273-82. [PMID: 22964822 DOI: 10.1159/000342083] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/13/2012] [Indexed: 01/05/2023]
Abstract
PURPOSE We recently developed the one-step methylation-specific PCR (OS-MSP) assay which can detect methylated DNA (met-DNA) in serum with high sensitivity. To examine its prognostic value, we applied this new assay to the detection of met-DNA in serum of breast cancer patients. METHODS Serum samples taken before surgery from 336 primary invasive breast cancer patients were subjected to the OS-MSP assay for the promoter regions of GSTP1, RASSF1A, and RARβ2. The assay outcome was considered positive when methylation was detected in at least one of these three genes. Total DNA content in serum was also determined. RESULTS Of the 336 stage I/II patients, 33 (10%) were positive for met-DNA in serum and showed a significantly worse overall survival (OS) rate at 100 months (78 vs. 95%; p = 0.002) than those with negative findings (n = 303). Patients with high total DNA in serum (n = 112) also showed a significantly worse OS rate at 100 months (86 vs. 97%; p = 0.001) than those with low total DNA in serum (n = 224). Moreover, patients both positive for met-DNA and with high total DNA in serum (n = 18) showed a much worse OS rate at 100 months (65 vs. 94%; p < 0.001) than the others (n = 318). CONCLUSIONS Met-DNA in serum detected with the OS-MSP assay constitutes a significant and independent prognostic factor, and its combination with total DNA in serum seems to be even more effective for prediction of prognosis for breast cancer patients.
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Affiliation(s)
- Noriko Fujita
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
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Diagnostic values of GHSR DNA methylation pattern in breast cancer. Breast Cancer Res Treat 2012; 135:705-13. [DOI: 10.1007/s10549-012-2197-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/03/2012] [Indexed: 11/25/2022]
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Bijron JG, Bol GM, Verheijen RH, van Diest PJ. Epigenetic biomarkers in the diagnosis of ovarian cancer. ACTA ACUST UNITED AC 2012; 6:421-38. [PMID: 23480807 DOI: 10.1517/17530059.2012.702105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Current diagnostic methods for ovarian cancer have limited performance. Recent advances within the field of epigenetics have shifted the clinical implementation of epigenetic biomarkers as a diagnostic approach from a dream for the future to a present-day consideration. Patients could potentially benefit greatly from this novel diagnostic approach. AREAS COVERED Epigenetic mechanisms in cancer are discussed, with a focus on potential diagnostic epigenetic biomarkers in ovarian cancer in tissue and body fluids. A literature search was undertaken (on 22-09-2011) for these subjects using the search syntax ((((((((((((((("ovarian") OR "ovary") OR "ovarian cancer") OR "ovarian cancers") OR "cancer of the ovary") OR "tumour of the ovary") OR "ovarian tumor") OR "ovarian tumors") OR "ovarian tumour") OR "ovarian tumours") OR "ovarian neoplasm") OR "ovarian neoplasms" OR "ovarian carcinoma") OR "ovarian carcinomas") OR "carcinoma of the ovary")) AND ((((((((("epigenetics") OR "epigenetic") OR "epigenome") OR "methylation") OR "hypermethylation") OR "chromatin modification") OR "histone") OR "histones") OR "acetylation") EXPERT OPINION To date no single epigenetic biomarker is able to accurately detect early ovarian cancer in either tissue or body fluids. A panel of epigenetic biomarkers based on aberrant DNA methylation in body fluids, especially blood, has the best chance of being implemented in clinical practice, as it is semi-invasive. However, progression toward clinical use is hampered by the lack of detection techniques combining high throughput and accuracy with low cost, by difficulties in establishing reliable reference values and by the heterogeneous nature of ovarian cancer. Until addressed, implementation as a diagnostic measure complimenting current techniques in select cases seems a far way to go, and implementation as a primary screening tool is yet even farther away.
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Affiliation(s)
- Jonathan G Bijron
- University Medical Center Utrecht, Department of Pathology , 3508 GA Utrecht , The Netherlands
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Van De Voorde L, Speeckaert R, Van Gestel D, Bracke M, De Neve W, Delanghe J, Speeckaert M. DNA methylation-based biomarkers in serum of patients with breast cancer. Mutat Res 2012; 751:304-325. [PMID: 22698615 DOI: 10.1016/j.mrrev.2012.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 06/03/2012] [Accepted: 06/05/2012] [Indexed: 12/18/2022]
Abstract
Alterations of genetic and epigenetic features can provide important insights into the natural history of breast cancer. Although DNA methylation analysis is a rapidly developing field, a reproducible epigenetic blood-based assay for diagnosis and follow-up of breast cancer has yet to be successfully developed into a routine clinical test. The aim of this study was to review multiple serum DNA methylation assays and to highlight the value of those novel biomarkers in diagnosis, prognosis and prediction of therapeutic outcome. Serum is readily accessible for molecular diagnosis in all individuals from a peripheral blood sample. The list of hypermethylated genes in breast cancer is heterogeneous and no single gene is methylated in all breast cancer types. There is increasing evidence that a panel of epigenetic markers is essential to achieve a higher sensitivity and specificity in breast cancer detection. However, the reported percentages of methylation are highly variable, which can be partly explained by the different sensitivities and the different intra-/inter-assay coefficients of variability of the analysis methods. Moreover, there is a striking lack of receiver operating characteristic (ROC) curves of the proposed biomarkers. Another point of criticism is the fact that 'normal' patterns of DNA methylation of some tumor suppressor and other cancer-related genes are influenced by several factors and are often poorly characterized. A relatively frequent methylation of those genes has been observed in high-risk asymptomatic women. Finally, there is a call for larger prospective cohort studies to determine methylation patterns during treatment and follow-up. Identification of patterns specific for a differential response to therapeutic interventions should be useful. Only in this way, it will be possible to evaluate the predictive and prognostic characteristics of those novel promising biomarkers.
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Affiliation(s)
- Lien Van De Voorde
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | | | - Dirk Van Gestel
- Department of Radiation Oncology, Antwerp University Hospital, Antwerp, Belgium
| | - Marc Bracke
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Wilfried De Neve
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Joris Delanghe
- Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium
| | - Marijn Speeckaert
- Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium; Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium.
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Avraham A, Uhlmann R, Shperber A, Birnbaum M, Sandbank J, Sella A, Sukumar S, Evron E. Serum DNA methylation for monitoring response to neoadjuvant chemotherapy in breast cancer patients. Int J Cancer 2012; 131:E1166-72. [PMID: 22407753 DOI: 10.1002/ijc.27526] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 02/21/2012] [Indexed: 01/09/2023]
Abstract
Patients with large or nonoperable breast cancers often receive neoadjuvant chemotherapy to facilitate full resection of the tumor and enable conservation of the breast. However, currently available methods for evaluation of response during therapy are limited and the actual effect of the treatment is only recognized at surgery upon completion of chemotherapy. Timely assessment of response could allow individual tailoring of the treatment and save noneffective drugs and unnecessary toxicity. Here, we suggest that tumor derived DNA methylation in the serum may reflect changes in tumor burden and allow early recognition of responders versus nonresponders. In this pilot study, we collected 7 consecutive serum samples from 52 patients with locally advanced breast cancer during neoadjuvant chemotherapy. We selected RASSF1, which was methylated in more than 80% of the tumors, for serum analysis. Using the "methylation sensitive PCR and high resolution melting," we detected RASSF1 methylation in the serum of 21 patients prior to therapy. In four patients who achieved complete pathological response, RASSF1 methylation in the serum became undetectable early during therapy. In contrast, in 17 patients that had partial or minimal pathological response, serum RASSF1 methylation persisted longer or throughout the treatment (complete versus partial response p = 0.02). These findings support further development of this assay for monitoring response during neoadjuvant therapy.
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Affiliation(s)
- Ayelet Avraham
- Oncology Department, Assaf Harofeh Medical Center, Zerifin, Israel
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Abstract
In the last 15 years, significant progress in the management of colorectal cancer (CRC) has been achieved with several new agents licensed extending median overall survival for stage IV disease to about 2 years. Treatment of CRC is stage-specific, multidisciplinary, and based on patient and tumor characteristics. Although especially early stages (0-III, according to Union for International Cancer Control) are treated with curative intent, patients with limited stage IV disease (liver and/or lung or localized peritoneal metastases) might still be curable in a multimodality approach including surgery, perioperative chemotherapy and/or radiotherapy. Despite the broad variety of prognostic factors, treatment decisions and selection of drugs are mainly based on clinicopathologic variables for early stage CRC, extent of disease, potential resectability, patients' eligibility to receive aggressive treatments including chemotherapy, surgery, and very few molecular markers such as KRAS mutational status for advanced disease. However, a tailored approach for the treatment of CRC taking into account all mentioned factors is currently recommended by national and international guidelines and will be discussed in this review.
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Affiliation(s)
- Dirk Arnold
- Hubertus Wald Tumour Center, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Germany.
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Current world literature. Curr Opin Oncol 2011; 23:700-9. [PMID: 21993416 DOI: 10.1097/cco.0b013e32834d384a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Koturbash I, Beland FA, Pogribny IP. Role of epigenetic events in chemical carcinogenesis—a justification for incorporating epigenetic evaluations in cancer risk assessment. Toxicol Mech Methods 2011; 21:289-97. [DOI: 10.3109/15376516.2011.557881] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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