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Kamal A, Awan AR, Rabbani M, Sheikh HR, Tayyab M, Firyal S, Khan IH, Wasim M. The interplay of PTEN and AKT nexus in breast cancer: a molecular perspective. Mol Biol Rep 2024; 51:345. [PMID: 38400870 DOI: 10.1007/s11033-024-09223-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/08/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND Breast cancer is a highly prevalent and life-threatening ailment that is commonly detected among the females. The downregulation of PTEN in breast cancer is associated with a poor prognosis, aggressive tumor type, and metastasis to lymph nodes, as it activates the pro-survival pathway PI3K/AKT, which is considered the ultimate proliferative pathway. MATERIAL AND METHODS The mRNA expression of PTEN and AKT genes was investigated using RT-qPCR and TaqMan primer probe chemistry. Moreover DNA was also isolated from the same tissue samples and exonic regions of both genes were amplified for mutational analysis. The proteins expression of PTEN and AKT from seven human breast cancer cell lines was checked through western blot experiments. RESULT The study revealed a decrease in PTEN expression in 73.3% of the samples, whereas an increase in AKT expression in 40% of samples was observed when compared to the distant normal breast tissue. Conversely, the remaining 60% of samples exhibited a decrease in AKT mRNA expression. There was no observed alteration in the genetic sequence of AKT and PTEN within the targeted amplified regions of breast cancer samples. The high levels of PTEN protein in T-47D and MDA-MB-453 resulted in a lower p-AKT. Two cell lines ZR-75-1 and MDA-MB-468 appeared to be PTEN negative on western blot but mRNA was detected on RT-qPCR. CONCLUSION In breast cancer the status/expression of PTEN & AKT at mRNA and protein level might be obliging in forecasting the path of disease progression, treatment and prognosis.
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Affiliation(s)
- Anum Kamal
- Lahore Garrison University, Lahore, Pakistan
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Ali Raza Awan
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Masood Rabbani
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | | | - Muhammad Tayyab
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Sehrish Firyal
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Imran H Khan
- Clinical Proteomics Core Lab, Department of Medical Pathology and Laboratory Medicine, University of California Davis Medical Center, Sacramento, CA, USA
| | - Muhammad Wasim
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
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2
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Norollahi SE, Vahidi S, Shams S, Keymoradzdeh A, Soleymanpour A, Solymanmanesh N, Mirzajani E, Jamkhaneh VB, Samadani AA. Analytical and therapeutic profiles of DNA methylation alterations in cancer; an overview of changes in chromatin arrangement and alterations in histone surfaces. Horm Mol Biol Clin Investig 2023; 44:337-356. [PMID: 36799246 DOI: 10.1515/hmbci-2022-0043] [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: 05/07/2022] [Accepted: 01/24/2023] [Indexed: 02/18/2023]
Abstract
DNA methylation is the most important epigenetic element that activates the inhibition of gene transcription and is included in the pathogenesis of all types of malignancies. Remarkably, the effectors of DNA methylation are DNMTs (DNA methyltransferases) that catalyze de novo or keep methylation of hemimethylated DNA after the DNA replication process. DNA methylation structures in cancer are altered, with three procedures by which DNA methylation helps cancer development which are including direct mutagenesis, hypomethylation of the cancer genome, and also focal hypermethylation of the promoters of TSGs (tumor suppressor genes). Conspicuously, DNA methylation, nucleosome remodeling, RNA-mediated targeting, and histone modification balance modulate many biological activities that are essential and indispensable to the genesis of cancer and also can impact many epigenetic changes including DNA methylation and histone modifications as well as adjusting of non-coding miRNAs expression in prevention and treatment of many cancers. Epigenetics points to heritable modifications in gene expression that do not comprise alterations in the DNA sequence. The nucleosome is the basic unit of chromatin, consisting of 147 base pairs (bp) of DNA bound around a histone octamer comprised of one H3/H4 tetramer and two H2A/H2B dimers. DNA methylation is preferentially distributed over nucleosome regions and is less increased over flanking nucleosome-depleted DNA, implying a connection between nucleosome positioning and DNA methylation. In carcinogenesis, aberrations in the epigenome may also include in the progression of drug resistance. In this report, we report the rudimentary notes behind these epigenetic signaling pathways and emphasize the proofs recommending that their misregulation can conclude in cancer. These findings in conjunction with the promising preclinical and clinical consequences observed with epigenetic drugs against chromatin regulators, confirm the important role of epigenetics in cancer therapy.
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Affiliation(s)
- Seyedeh Elham Norollahi
- Cancer Research Center and Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Shima Shams
- Student Research Committee, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Arman Keymoradzdeh
- Department of Neurosurgery, School of Medicine, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Armin Soleymanpour
- Student Research Committee, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Nazanin Solymanmanesh
- Student Research Committee, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Ebrahim Mirzajani
- Department of Biochemistry and Biophysics, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Vida Baloui Jamkhaneh
- Department of Veterinary Medicine, Islamic Azad University of Babol Branch, Babol, Iran
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Guilan University of Medical Sciences, Rasht, Iran
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3
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Bhat SM, Prasad PR, Joshi MB. Novel insights into DNA methylation-based epigenetic regulation of breast tumor angiogenesis. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 380:63-96. [PMID: 37657860 DOI: 10.1016/bs.ircmb.2023.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Breast tumors are highly vascularized and dependent on angiogenesis for growth, progression and metastasis. Like other solid tumors, vasculature in breast tumors also display leaky and tortuous phenotype and hence inhibit immune cell infiltration, show reduced efficacy to anticancer drugs and radiotherapy. Epigenetic reprogramming including significant alterations in DNA methylation in tumor and stromal cells generate an imbalance in expression of pro- and anti-angiogenic factors and subsequently lead to disordered angiogenesis. Hence, understanding DNA methylation-based regulation of angiogenesis in breast tumors may open new avenues for designing therapeutic targets. Our present review manuscript summarized contemporary knowledge of influence of DNA methylation in regulating angiogenesis. Further, we identified novel set of pro-angiogenic genes enriched in endothelial cells which are coregulated with DNMT isoforms in breast tumors and harboring CpG islands. Our analysis revealed promoters of pro-angiogenic genes were hypomethylated and anti-angiogenic genes were hypermethylated in tumors and further reflected on their expression patterns. Interestingly, promoter DNA methylation intensities of novel set of pro-angiogenic genes significantly correlated to patient survival outcome.
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Affiliation(s)
- Sharath Mohan Bhat
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Palla Ranga Prasad
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Manjunath B Joshi
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.
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Vietri MT, D'Elia G, Benincasa G, Ferraro G, Caliendo G, Nicoletti GF, Napoli C. DNA methylation and breast cancer: A way forward (Review). Int J Oncol 2021; 59:98. [PMID: 34726251 DOI: 10.3892/ijo.2021.5278] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/01/2021] [Indexed: 11/05/2022] Open
Abstract
The current management of breast cancer (BC) lacks specific non‑invasive biomarkers able to provide an early diagnosis of the disease. Epigenetic‑sensitive signatures are influenced by environmental exposures and are mediated by direct molecular mechanisms, mainly guided by DNA methylation, which regulate the interplay between genetic and non‑genetic risk factors during cancerogenesis. The inactivation of tumor suppressor genes due to promoter hypermethylation is an early event in carcinogenesis. Of note, targeted tumor suppressor genes are frequently hypermethylated in patient‑derived BC tissues and peripheral blood biospecimens. In addition, epigenetic alterations in triple‑negative BC, as the most aggressive subtype, have been identified. Thus, detecting both targeted and genome‑wide DNA methylation changes through liquid‑based assays appears to be a useful clinical strategy for early detection, more accurate risk stratification and a personalized prediction of therapeutic response in patients with BC. Of note, the DNA methylation profile may be mapped by isolating the circulating tumor DNA from the plasma as a more accessible biospecimen. Furthermore, the sensitivity to treatment with chemotherapy, hormones and immunotherapy may be altered by gene‑specific DNA methylation, suggesting novel potential drug targets. Recently, the use of epigenetic drugs administered alone and/or with anticancer therapies has led to remarkable results, particularly in patients with BC resistant to anticancer treatment. The aim of the present review was to provide an update on DNA methylation changes that are potentially involved in BC development and their putative clinical utility in the fields of diagnosis, prognosis and therapy.
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Affiliation(s)
- Maria Teresa Vietri
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giovanna D'Elia
- Unit of Clinical and Molecular Pathology, AOU, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giuseppe Ferraro
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Plastic Surgery Unit, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Gemma Caliendo
- Unit of Clinical and Molecular Pathology, AOU, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giovanni Francesco Nicoletti
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Plastic Surgery Unit, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
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Cheng J, Li M, Tzeng CM, Gou X, Chen S. Suppression of Tumorigenicity 5 Ameliorates Tumor Characteristics of Invasive Breast Cancer Cells via ERK/JNK Pathway. Front Oncol 2021; 11:621500. [PMID: 34395234 PMCID: PMC8356645 DOI: 10.3389/fonc.2021.621500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 06/04/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Suppression of tumorigenicity 5 (ST5) has been considered as a tumor suppressor gene in HeLa tumor cells. However, its role in the progression of breast cancer remains vague. METHODS Online database analysis was determined by Oncomine and Breast Cancer Gene-Expression Miner v4.4 (bc-GenExMiner v4.4). Tumor biology behaviors were measured by MTT assay, wound healing model, Transwell and Flow cytometry assays. Methylation-specific PCR (MSP) was employed to detect promoter methylation. RESULTS Low level of ST5 was observed in breast cancer specimens, particularly in recurrent, invasive breast cancer cases compared to para-carcinoma tissue or non-invasive breast cancer. The downregulation of ST5 was also proved in MDA-MB-231 and SKBR3 cell lines with a high invasive capability as compared to MCF-7 cell with a low invasive capability. ST5 was negatively associated with pathological stages of breast cancer. ST5-downregulation promoted, while ST5-upregulation inhibited the progression of cell proliferation, cell cycle and migration of MDA-MB-231 cells. Additionally, ST5 knockdown inhibited, whereas ST5 overexpression promoted apoptosis of MDA-MB-231 cells. However, ST5 modification, either upregulation or downregulation, had no significant impact on tumor behaviors of MCF-7 cells. Mechanistically, ST5 protein ablation activated, while ST5-upregulation repressed the activities of phosphorylated ERK1/2 and JNK, and subsequently the expression of c-Myc. PD98059-mediated ERK1/2 inhibition abolished the stimulatory effects of ST5-depletion on ERK1/2/JNK/c-Myc signaling axis, and ST5 depletion-mediated cell over-proliferation and migration. Of note, ST5 reduction in invasive breast cancer cells should implicate in the hypermethylation of ST5 promoter region. CONCLUSION Our findings suggest that ST5 potentially acts as a tumor suppressor gene in invasive breast cancer through regulating ERK/JNK signaling pathway and provide a novel insight for breast cancer treatment.
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Affiliation(s)
- Jianghong Cheng
- Shaanxi Key Laboratory of Brain Disorders and School of Basic Medical Science, Xi’an Medical University, Xi’an, China
| | - Mingli Li
- Translational Medicine Research Center (TMRC), School of Pharmaceutical Science, Xiamen University, Xiamen, China
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Otolaryngology Head and Neck Surgery, Xiamen, China
| | - Chi-Meng Tzeng
- Translational Medicine Research Center (TMRC), School of Pharmaceutical Science, Xiamen University, Xiamen, China
| | - Xingchun Gou
- Shaanxi Key Laboratory of Brain Disorders and School of Basic Medical Science, Xi’an Medical University, Xi’an, China
- Institute of Basic and Translational Medicine, Xi’an Medical University, Xi’an, China
- Academician Workstation of Chen Zhi-nan, Xi’an Medical University, Xi’an, China
| | - Shuai Chen
- Shaanxi Key Laboratory of Brain Disorders and School of Basic Medical Science, Xi’an Medical University, Xi’an, China
- Institute of Basic and Translational Medicine, Xi’an Medical University, Xi’an, China
- Academician Workstation of Chen Zhi-nan, Xi’an Medical University, Xi’an, China
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6
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Raafat N, Ismail K, Hawsawi NM, Saber T, Elsawy WH, Abdulmutaleb T, Raafat A, Gharib AF. Glutathione S transferase T1 gene polymorphism and its promoter methylation are associated with breast cancer susceptibility in Egyptian women. Biotechnol Appl Biochem 2021; 69:526-533. [PMID: 33600611 DOI: 10.1002/bab.2129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 02/07/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Breast cancer (BC) is one of the leading causes of cancer mortality in women. Glutathione S-transferase (GSTT1) is involved in activation of detoxification reactions and catalysis of chemicals conjugation with glutathione. GSTT1 genotype is a limiting factor for some environmental diseases. Epigenetic changes have an essential role in BC through inappropriate interaction between genomic and environmental risk factors. AIM This study was directed to explore the association of BC risk with GSTT1 genetic variations and its methylation status in Egyptian women. DESIGN AND METHODS This study included 100 healthy women as the control group and 100 patients were clinically and histologically diagnosed with breast cancer. All blood samples were used for genomic DNA extraction. GSTT1 genotyping was accomplished by multiplex PCR and methylation-specific PCR was used to analyze the GSTT1 promoter methylation status. RESULTS Breast cancer patients showed significant incidence of null GSTT1 in relation to controls (p = 0.004). GSTT1 gene promoter methylation status showed significant difference between hypermethylated and unmethylated patients when compared with healthy subjects (p = 0.005). GSTT1 promoter methylation status was not significantly associated with null genotype. There was no significant association between GSTT1-null genotypes and BC stage in cases with or without family history, but for promotor methylation, there was significant association with stage III and IV breast cancer disease. CONCLUSION GSTT1 null genetic variant and promoter hypermethylation in the GSTT region of the gene may be considered as critical risk factors for BC in Egyptian women.
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Affiliation(s)
- Nermin Raafat
- Medical Biochemistry Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Khadiga Ismail
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Nahed M Hawsawi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Taisir Saber
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Wael H Elsawy
- Department of Clinical Oncology and Nuclear Medicine, Faculty of Medicine, Zagazig University, Egypt
| | - Tariq Abdulmutaleb
- Ministry of Health, King Faisal Medical Complex Alpakistany, Taif, Saudi Arabia
| | - Ahmed Raafat
- General Surgery Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Amal F Gharib
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
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7
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Al-Eitan LN, Alghamdi MA, Tarkhan AH, Al-Qarqaz FA. Epigenome-wide analysis of common warts reveals aberrant promoter methylation. Int J Med Sci 2020; 17:191-206. [PMID: 32038103 PMCID: PMC6990892 DOI: 10.7150/ijms.39261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/08/2019] [Indexed: 12/13/2022] Open
Abstract
Epigenetic alteration of host DNA is a common occurrence in both low- and high-risk human papillomavirus (HPV) infection. Although changes in promoter methylation have been widely studied in HPV-associated cancers, they have not been the subject of much investigation in HPV-induced warts, which are a temporary manifestation of HPV infection. The present study sought to examine the differences in promoter methylation between warts and normal skin. To achieve this, DNA was extracted from 24 paired wart and normal skin samples and inputted into the Infinium MethylationEPIC BeadChip microarray. Differential methylation analysis revealed a clear pattern of hyper- and hypomethylation in warts compared to normal skin, and the most differentially methylated promoters were found within the EIF3EP2, CYSLTR1, C10orf99, KRT6B, LAMA4, and H3F3B genes as well as the C9orf30 pseudogene. Moreover, pathway analysis showed that the H3F3A, CDKN1A, and MAPK13 genes were the most common regulators among the most differentially methylated promoters. Since the tissue samples were excised from active warts, however, this differential methylation could either be a cellular response to HPV infection or an HPV-driven process to establish the wart and/or promote disease progression. Conclusively, it is apparent that HPV infection alters the methylation status of certain genes to possibly initiate the formation of a wart and maintain its presence.
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Affiliation(s)
- Laith N Al-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan.,Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Mansour A Alghamdi
- Department of Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia
| | - Amneh H Tarkhan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Firas A Al-Qarqaz
- Department of Internal Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan.,Division of Dermatology, Department of Internal Medicine, King Abdullah University Hospital, Jordan University of Science and Technology, Irbid 22110, Jordan
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8
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Mijnes J, Tiedemann J, Eschenbruch J, Gasthaus J, Bringezu S, Bauerschlag D, Maass N, Arnold N, Weimer J, Anzeneder T, Fasching PA, Rübner M, Bruno B, Heindrichs U, Freres J, Schulz H, Hilgers RD, Ortiz-Brüchle N, von Serenyi S, Knüchel R, Kloten V, Dahl E. SNiPER: a novel hypermethylation biomarker panel for liquid biopsy based early breast cancer detection. Oncotarget 2019; 10:6494-6508. [PMID: 31741713 PMCID: PMC6849652 DOI: 10.18632/oncotarget.27303] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/19/2019] [Indexed: 01/02/2023] Open
Abstract
Introduction Mammography is the gold standard for early breast cancer detection, but shows important limitations. Blood-based approaches on basis of cell-free DNA (cfDNA) provide minimally invasive screening tools to characterize epigenetic alterations of tumor suppressor genes and could serve as a liquid biopsy, complementing mammography. Methods Potential biomarkers were identified from The Cancer Genome Atlas (TCGA), using HumanMethylation450-BeadChip data. Promoter methylation status was evaluated quantitatively by pyrosequencing in a serum test cohort (n = 103), a serum validation cohort (n = 368) and a plasma cohort (n = 125). Results SPAG6, NKX2-6 and PER1 were identified as novel biomarker candidates. ITIH5 was included on basis of our previous work. In the serum test cohort, a panel of SPAG6 and ITIH5 showed 63% sensitivity for DCIS and 51% sensitivity for early invasive tumor (pT1, pN0) detection at 80% specificity. The serum validation cohort revealed 50% sensitivity for DCIS detection on basis of NKX2-6 and ITIH5. Furthermore, an inverse correlation between methylation frequency and cfDNA concentration was uncovered. Therefore, markers were tested in a plasma cohort, achieving a 64% sensitivity for breast cancer detection using SPAG6, PER1 and ITIH5. Conclusions Although liquid biopsy remains challenging, a combination of SPAG6, NKX2-6, ITIH5 and PER1 (SNiPER) provides a promising tool for blood-based breast cancer detection.
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Affiliation(s)
- Jolein Mijnes
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Janina Tiedemann
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Julian Eschenbruch
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Janina Gasthaus
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Sarah Bringezu
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Dirk Bauerschlag
- Department of Gynecology and Obstetrics, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Nicolai Maass
- Department of Gynecology and Obstetrics, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Norbert Arnold
- Department of Gynecology and Obstetrics, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Institute of Clinical Molecular Biology, University Medical Centre Schleswig-Holstein, Campus Kiel, Christian-Albrechts-University, Kiel, Germany
| | - Jörg Weimer
- Department of Gynecology and Obstetrics, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Tobias Anzeneder
- Patients' Tumor Bank of Hope (PATH-Biobank) Foundation, München, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Matthias Rübner
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Benjamin Bruno
- Department of Gynecology and Obstetrics Luisenhospital, Aachen, Germany
| | - Uwe Heindrichs
- Department of Gynecology and Obstetrics Luisenhospital, Aachen, Germany
| | - Jennifer Freres
- Department of Gynecology and Obstetrics Luisenhospital, Aachen, Germany
| | - Hanna Schulz
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Ralf-Dieter Hilgers
- Institute of Medical Statistics, University Hospital RWTH Aachen, Aachen, Germany
| | - Nadina Ortiz-Brüchle
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Sonja von Serenyi
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Ruth Knüchel
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Vera Kloten
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany.,Current address: Bayer AG, Pharmaceuticals Division, Biomarker Research, Wuppertal, Germany.,Share equal senior authorship
| | - Edgar Dahl
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany.,RWTH centralized Biomaterial Bank (RWTH cBMB) at the Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany.,Share equal senior authorship
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9
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Moghazy TF, ElAttar HA, Eldeeb MK, Rashad RM, Farouk AM, Farag AM. Methylation of Glutathione-S-Transferase P1 Promotor in Egyptian Females with Breast Cancer. Asian Pac J Cancer Prev 2019; 20:2523-2530. [PMID: 31450928 PMCID: PMC6852835 DOI: 10.31557/apjcp.2019.20.8.2523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Indexed: 12/24/2022] Open
Abstract
Background: Breast cancer (BC) is the second most common cancer after the lung cancer worldwide and number one killing cancer in Egyptian females . It is a multifactorial disease driven by different environmental, hormonal, genetic and epigenetic factors. Epigenetic alterations have been studied in cancer breast. Role of GSTP1 promotor methylation in breast cancer has been studied in different ethnic groups. Objectives: Current study aimed at studying the methylation status of the promotor region of glutathione-S-transferase P1 in breast ductal carcinoma of a cohort group of Egyptian females and its correlations with histopathological and prognostic parameters. Methods: Control group included 15 fresh normal breast tissues taken from BC female patients after leaving a clearly defined safety margin and a Patient group included confirmed 35 fresh breast ductal carcinoma tissue biopsies taken from female patients postoperatively. To all patients clinical examination, radiological examination (plain X-ray chest and or CT scan, ultrasonography of abdomen and pelvis were done), in addition to histopathological examination, typing, grading and staging of tumour, hormonal receptors status and molecular typing of breast mass. GSTP1 methylation status was evaluated using methyl specific polymerase chain reaction. Results: Statistical significant increase was found in methylation status of GSTP1 promotor gene in BC cases than that in control group, (60% of patients samples had methylated GSTP1 promotor vs only 6.7% of controls) (p= >0.001). No association was found between GSTP1 promotor methylation status and the poor prognostic factors neither with hormonal profile nor molecular type. However, GSTP1 promotor methylation were two times higher in postmenopausal than premenopausal cases and three times higher in late grade (III). Also GSTP1 promotor methylation was 2.4 times higher in Her2 positive cases than either ER or PR positive cases. Conclusion: Glutathione-S-Transferase P1 Promotor methylation plays a role in breast cancer development.
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Affiliation(s)
- Thanaa Fathy Moghazy
- Department of Chemical Pathology, Medical Research Institute, Alexandria University, Egypt.
| | - Hoda Aly ElAttar
- Department of Chemical Pathology, Medical Research Institute, Alexandria University, Egypt.
| | - Mona Kamal Eldeeb
- Department of Chemical Pathology, Medical Research Institute, Alexandria University, Egypt.
| | - Radwa Mohammed Rashad
- Department of Chemical Pathology, Medical Research Institute, Alexandria University, Egypt.
| | - Ayman Mohamed Farouk
- Department of Clinical and Rxperimental Surgery, Medical Research Institute, Alexandria University, Egypt
| | - Assmaa Mostafa Farag
- Department of Chemical Pathology, Medical Research Institute, Alexandria University, Egypt.
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10
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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 Almeida BP, Apolónio JD, Binnie A, Castelo-Branco P. Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers. BMC Cancer 2019; 19:219. [PMID: 30866861 PMCID: PMC6416975 DOI: 10.1186/s12885-019-5403-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Breast cancer is a highly heterogeneous disease resulting in diverse clinical behaviours and therapeutic responses. DNA methylation is a major epigenetic alteration that is commonly perturbed in cancers. The aim of this study is to characterize the relationship between DNA methylation and aberrant gene expression in breast cancer. METHODS We analysed DNA methylation and gene expression profiles from breast cancer tissue and matched normal tissue in The Cancer Genome Atlas (TCGA). Genome-wide differential methylation analysis and methylation-gene expression correlation was performed. Gene expression changes were subsequently validated in the METABRIC dataset. The Oncoscore tool was used to identify genes that had previously been associated with cancer in the literature. A subset of genes that had not previously been studied in cancer was chosen for further analysis. RESULTS We identified 368 CpGs that were differentially methylated between tumor and normal breast tissue (∆β > 0.4). Hypermethylated CpGs were overrepresented in tumor tissue and were found predominantly (56%) in upstream promoter regions. Conversely, hypomethylated CpG sites were found primarily in the gene body (66%). Expression analysis revealed that 209 of the differentially-methylated CpGs were located in 169 genes that were differently expressed between normal and breast tumor tissue. Methylation-expression correlations were predominantly negative (70%) for promoter CpG sites and positive (74%) for gene body CpG sites. Among these differentially-methylated and differentially-expressed genes, we identified 7 that had not previously been studied in any form of cancer. Three of these, TDRD10, PRAC2 and TMEM132C, contained CpG sites that showed diagnostic and prognostic value in breast cancer, particularly in estrogen-receptor (ER)-positive samples. A pan-cancer analysis confirmed differential expression of these genes together with diagnostic and prognostic value of their respective CpG sites in multiple cancer types. CONCLUSION We have identified 368 DNA methylation changes that characterize breast cancer tumor tissue, of which 209 are associated with genes that are differentially-expressed in the same samples. Novel DNA methylation markers were identified, of which cg12374721 (PRAC2), cg18081940 (TDRD10) and cg04475027 (TMEM132C) show promise as diagnostic and prognostic markers in breast cancer as well as other cancer types.
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Affiliation(s)
- Bernardo P. de Almeida
- Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Present address: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Joana Dias Apolónio
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center, Campus Gambelas, 8005-139 Faro, Portugal
| | - Alexandra Binnie
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center, Campus Gambelas, 8005-139 Faro, Portugal
- William Osler Health System, Brampton, ON Canada
| | - Pedro Castelo-Branco
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center, Campus Gambelas, 8005-139 Faro, Portugal
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Shukla S, Penta D, Mondal P, Meeran SM. Epigenetics of Breast Cancer: Clinical Status of Epi-drugs and Phytochemicals. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1152:293-310. [PMID: 31456191 DOI: 10.1007/978-3-030-20301-6_16] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetics refers to alterations in gene expression due to differential histone modifications and DNA methylation at promoter sites of genes. Epigenetic alterations are reversible and are heritable during somatic cell division, but do not involve changes in nucleotide sequence. Epigenetic regulation plays a critical role in normal growth and embryonic development by controlling transcriptional activities of several genes. In last two decades, these modifications have been well recognized to be involved in tumor initiation and progression, which has motivated many investigators to incorporate this novel field in cancer drug development. Recently, growing number of epigenetic changes have been reported that are involved in the regulations of genes involved in breast tumor growth and metastasis. Drugs possessing epigenetic modulatory activities known as epi-drugs, mainly the inhibitors of histone deacetylases (HDACs) and DNA methyltransferases (DNMTs). Some of these drugs are undergoing different clinical trials for breast cancer treatment. Several phytochemicals such as green tea polyphenols, curcumin, genistein, resveratrol and sulforaphane have also been shown to alter epigenetic modifications in multiple cancer types including breast cancer. In this chapter, we summarize the role of epigenetic changes in breast cancer progression and metastasis. We have also discussed about various epigenetic modulators possessing chemopreventive and therapeutic efficacy against breast cancer with future perspectives.
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Affiliation(s)
- Samriddhi Shukla
- Department of Paediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Dhanamjai Penta
- Laboratory of Cancer Epigenetics, Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, India
| | - Priya Mondal
- Laboratory of Cancer Epigenetics, Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, India
| | - Syed Musthapa Meeran
- Laboratory of Cancer Epigenetics, Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, India.
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13
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Tshering G, Dorji PW, Chaijaroenkul W, Na-Bangchang K. Biomarkers for the Diagnosis of Cholangiocarcinoma: A Systematic Review. Am J Trop Med Hyg 2018; 98:1788-1797. [PMID: 29637880 DOI: 10.4269/ajtmh.17-0879] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cholangiocarcinoma (CCA), a malignant tumor of the bile duct, is a major public health problem in many Southeast Asian countries, particularly Thailand. The slow progression makes it difficult for early diagnosis and most patients are detected in advanced stages. This study aimed to review all relevant articles related to the biomarkers for the diagnosis of CCA and point out potential biomarkers. A thorough search was performed in PubMed and ScienceDirect for CCA biomarker articles. Required data were extracted. A total of 46 articles that fulfilled the inclusion and had none of the exclusion criteria were included in the analysis (17, 22, 3, 4, and 1 articles on blood, tissue, bile, both blood and tissue, and urine biomarkers, respectively). Carbohydrate antigen 19-9 (CA19-9) and carcinoembryonic antigen (CEA), either alone or in combination with other biomarkers, are the most commonly studied biomarkers in the serum. Their sensitivity and specificity ranged from 47.2% to 98.2% and 89.7% to 100%, respectively. However, in the tissue, gene methylations and DNA-related markers were the most studied CCA biomarkers. Their sensitivity and specificity ranged from 58% to 87% and 98% to 100%, respectively. Some articles investigated biomarkers both in blood and tissues, particularly CA19-9 and CEA, with sensitivity and specificity ranging from 33% to 100% and 50% to 97.7%, respectively. Although quite a number of biomarkers with a potential role in the early detection of CCA have been established, it is difficult to single out any particular marker that could be used in the routine clinical settings.
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Affiliation(s)
- Gyem Tshering
- Chulabhorn International College of Medicine, Thammasat University, Rangsit Center, Klong Luang, Pathum Thani, Thailand
| | - Palden Wangyel Dorji
- Chulabhorn International College of Medicine, Thammasat University, Rangsit Center, Klong Luang, Pathum Thani, Thailand
| | - Wanna Chaijaroenkul
- Chulabhorn International College of Medicine, Thammasat University, Rangsit Center, Klong Luang, Pathum Thani, Thailand
| | - Kesara Na-Bangchang
- Center of Excellence in Pharmacology and Molecular Biology of Malaria and Cholangiocarcinoma, Chulabhorn International College of Medicine, Thammasat University, Rangsit Center, Klong Luang, Pathum Thani, Thailand.,Chulabhorn International College of Medicine, Thammasat University, Rangsit Center, Klong Luang, Pathum Thani, Thailand
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Sandbhor Gaikwad P, Banerjee R. Advances in point-of-care diagnostic devices in cancers. Analyst 2018; 143:1326-1348. [DOI: 10.1039/c7an01771e] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The early diagnosis and monitoring of the progress of cancers are limited due to the lack of adequate screening tools.
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Affiliation(s)
- Puja Sandbhor Gaikwad
- Research Scholar
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Bombay
- Mumbai
- India-400076
| | - Rinti Banerjee
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Bombay
- Mumbai
- India-400076
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15
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Targeting the Epigenome as a Novel Therapeutic Approach for Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1026:287-313. [DOI: 10.1007/978-981-10-6020-5_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Begam N, Jamil K, Raju SG. Promoter Hypermethylation of the ATM Gene as a Novel Biomarker for Breast Cancer. Asian Pac J Cancer Prev 2017; 18:3003-3009. [PMID: 29172272 PMCID: PMC5773784 DOI: 10.22034/apjcp.2017.18.11.3003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background: Breast cancer may be induced by activation of protooncogenes to oncogenes and in many cases inactivation of tumor suppressor genes. Ataxia telangiectasia mutated (ATM) is an important tumor suppressor gene which plays central roles in the maintenance of genomic integrity by activating cell cycle checkpoints and promoting repair of double-strand breaks of DNA. In breast cancer, decrease ATM expression correlates with a poor outcome; however, the molecular mechanisms underlying downregulation are still unclear. Promoter hypermethylation may contribute in downregulation. Hence the present investigation was designed to evaluate promoter methylation and expression of the ATM gene in breast cancer cases, and to determine links with clinical and demographic manifestations, in a South Indian population. Methods: Tumor biopsy samples were collected from 50 pathologically confirmed sporadic breast cancer cases. DNA was isolated from tumor and adjacent non-tumorous regions, and sodium bisulfite conversion and methylation-specific PCR were performed using MS-PCR primers for the ATM promoter region. In addition, ATM mRNA expression was also analyzed for all samples using real-time PCR. Results: Fifty eight percent (58%) of cancer tissue samples showed promoter hypermethylation for the ATM gene, in contrast to only 4.44% of normal tissues (p= 0.0001). Furthermore, ATM promoter methylation was positively associated with age (p = 0.01), tumor size (p=0.045) and advanced stage of disease i.e. stages III and IV (p =0.019). An association between promoter hypermethylation and lower expression of ATM mRNA was also found (p=0.035). Conclusion: We report for the first time that promoter hypermethylation of ATM gene may be useful as a potential new biomarker for breast cancer, especially in the relatively young patients.
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Affiliation(s)
- Nasrin Begam
- Jawaharlal Nehru Institute of Advanced Studies (JNIAS), School of Life Sciences, Centre for Biotechnology and Bioinformatics,Secunderabad- 500003,Telangana, India.
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Spitzwieser M, Entfellner E, Werner B, Pulverer W, Pfeiler G, Hacker S, Cichna-Markl M. Hypermethylation of CDKN2A exon 2 in tumor, tumor-adjacent and tumor-distant tissues from breast cancer patients. BMC Cancer 2017; 17:260. [PMID: 28403857 PMCID: PMC5389179 DOI: 10.1186/s12885-017-3244-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/29/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Breast carcinogenesis is a multistep process involving genetic and epigenetic changes. Tumor tissues are frequently characterized by gene-specific hypermethylation and global DNA hypomethylation. Aberrant DNA methylation levels have, however, not only been found in tumors, but also in tumor-surrounding tissue appearing histologically normal. This phenomenon is called field cancerization. Knowledge of the existence of a cancer field and its spread are of clinical relevance. If the tissue showing pre-neoplastic lesions is not removed by surgery, it may develop into invasive carcinoma. METHODS We investigated the prevalence of gene-specific and global DNA methylation changes in tumor-adjacent and tumor-distant tissues in comparison to tumor tissues from the same breast cancer patients (n = 18) and normal breast tissues from healthy women (n = 4). Methylation-sensitive high resolution melting (MS-HRM) analysis was applied to determine methylation levels in the promoters of APC, BRCA1, CDKN2A (p16), ESR1, HER2/neu and PTEN, in CDKN2A exon 2 and in LINE-1, as indicator for the global DNA methylation extent. The methylation status of the ESR2 promoter was determined by pyrosequencing. RESULTS Tumor-adjacent and tumor-distant tissues frequently showed pre-neoplastic gene-specific and global DNA methylation changes. The APC promoter (p = 0.003) and exon 2 of CDKN2A (p < 0.001) were significantly higher methylated in tumors than in normal breast tissues from healthy women. For both regions, significant differences were also found between tumor and tumor-adjacent tissues (p = 0.001 and p < 0.001, respectively) and tumor and tumor-distant tissues (p = 0.001 and p < 0.001, respectively) from breast cancer patients. In addition, tumor-adjacent (p = 0.002) and tumor-distant tissues (p = 0.005) showed significantly higher methylation levels of CDKN2A exon 2 than normal breast tissues serving as control. Significant correlations were found between the proliferative activity and the methylation status of CDKN2A exon 2 in tumor (r = -0.485, p = 0.041) and tumor-distant tissues (r = -0.498, p = 0.036). CONCLUSIONS From our results we can conclude that methylation changes in CDKN2A exon 2 are associated with breast carcinogenesis. Further investigations are, however, necessary to confirm that hypermethylation of CDKN2A exon 2 is associated with tumor proliferative activity.
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Affiliation(s)
- Melanie Spitzwieser
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Elisabeth Entfellner
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Bettina Werner
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Walter Pulverer
- Molecular Diagnostics, Austrian Institute of Technology, Muthgasse 11, 1190, Vienna, Austria
| | - Georg Pfeiler
- Department of Obstetrics and Gynecology, Division of Gynecology and Gynecological Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Stefan Hacker
- Department of Plastic and Reconstructive Surgery, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria.
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18
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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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Tang Q, Cheng J, Cao X, Surowy H, Burwinkel B. Blood-based DNA methylation as biomarker for breast cancer: a systematic review. Clin Epigenetics 2016; 8:115. [PMID: 27895805 PMCID: PMC5109688 DOI: 10.1186/s13148-016-0282-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/26/2016] [Indexed: 12/19/2022] Open
Abstract
Multiple studies have investigated global DNA methylation profiles and gene-specific DNA methylation in blood-based DNA to develop powerful screening markers for cancer. This systematic review summarizes the current evidence on methylation studies that investigated methylation level of blood-derived DNA of breast cancer (BC) patients in comparison to healthy controls by conducting a systematic literature review in PubMed and Web of Science. Essential results, such as methylation levels of BC cases and healthy controls, p values, and odds ratios, were extracted from these studies by two investigators independently. Overall, 45 publications met the inclusion criteria for this review. DNA from whole blood, as well as cell-free DNA (cfDNA) from serum or plasma, was used in these studies. The most common method used for measuring global DNA methylation was the investigation of repetitive elements as surrogates and the application of array-based genome-wide methylation analysis. For measuring gene-specific methylation level, methylation-specific PCR and pyrosequencing were the most frequently used methods. Epigenome-wide blood DNA hypomethylation in BC patients were reported in several studies; however, the evidence is still not conclusive. The most frequently investigated gene in whole blood was BRCA1, which was found more frequently methylated in patients compared to controls. RASSF1A was the most widely investigated gene in cfDNA of serum or plasma, which was also found more frequently methylated in patients compared to controls. Several of the eligible studies reported the associations of global hypomethylation and increased BC risk. Studies investigated associations between gene-specific methylation and BC risk, while got heterogeneous results. But two studies reported that hypermethylation of ATM gene was associated with increased BC risk, which suggest the potential use of this gene for BC risk stratification. Overall, our review suggests the possibility of using blood-based DNA methylation marker as promising marker for BC risk stratification, as several studies found associations between certain methylation level in blood and BC risk. However, so far, the evidence is still quite limited. Optimal markers are yet to be developed and promising results needed to be validated in prospective study cohorts and tested in large screening populations.
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Affiliation(s)
- Qiuqiong Tang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jie Cheng
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xue Cao
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Harald Surowy
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
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Wu L, Shen Y, Peng X, Zhang S, Wang M, Xu G, Zheng X, Wang J, Lu C. Aberrant promoter methylation of cancer-related genes in human breast cancer. Oncol Lett 2016; 12:5145-5155. [PMID: 28105221 PMCID: PMC5228392 DOI: 10.3892/ol.2016.5351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 10/18/2016] [Indexed: 12/15/2022] Open
Abstract
The clinical relevance of aberrant DNA methylation is being increasingly recognized in breast cancer. The present study aimed to evaluate the promoter methylation status of seven candidate genes and to explore their potential use as a biomarker for the diagnosis of breast cancer. A total of 70 Chinese patients with breast cancer were recruited, and matched with 20 patients with benign breast disease (BBD). Methylation-specific polymerase chain reaction was performed to measure the methylation status of selected genes. The protein expression of candidate genes was determined by immunohistochemistry. Hypermethylation of Breast cancer 1, early onset; DNA repair associated (BRCA1), glutathione S-transferase pi 1 (GSTP1), cyclin dependent kinase inhibitor 2A, O-6-methylguanine-DNA methyltransferase, phosphatase and tensin homolog, retinoic acid receptor beta 2 and cyclin D2 was observed to be more common in cancerous tissues (24.3, 31.4, 40.0, 27.1, 48.6, 55.7 and 67.1%, respectively) as compared with BBD controls (0.0, 0.0, 20.0, 25.0, 40.0, 40.0 and 45.0%, respectively). Immunohistochemical analysis demonstrated a correlation between the methylation of the target gene and downregulation of protein expression. When BRCA1 and GSTP1 were combined as the biomarker, the area under the receiver operating characteristic curve reached 0.721 (95% confidence interval, 0.616–0.827). The present findings indicated that promoter methylation of cancer-related genes was frequently observed in patients with breast cancer and was associated with various clinical features. Hypermethylation of BRCA1 and GSTP1 may be used as promising biomarkers for breast cancer.
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Affiliation(s)
- Liang Wu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Ye Shen
- Department of Gastrointestinal Surgery, Aoyoung Hospital, Zhangjiagang, Jiangsu 215617, P.R. China
| | - Xianzhen Peng
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Simin Zhang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Ming Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Guisheng Xu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Xianzhi Zheng
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Jianming Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China; Department of Social Medicine and Health Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P.R. China; The Innovation Center for Social Risk Governance in Health, Nanjing, Jiangsu, 211166, P.R. China
| | - Cheng Lu
- Department of Breast, Nanjing Maternity and Child Health Hospital of Nanjing Medical University, Nanjing, Jiangsu 210004, P.R. China
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White AJ, Chen J, Teitelbaum SL, McCullough LE, Xu X, Hee Cho Y, Conway K, Beyea J, Stellman SD, Steck SE, Mordukhovich I, Eng SM, Beth Terry M, Engel LS, Hatch M, Neugut AI, Hibshoosh H, Santella RM, Gammon MD. Sources of polycyclic aromatic hydrocarbons are associated with gene-specific promoter methylation in women with breast cancer. ENVIRONMENTAL RESEARCH 2016; 145:93-100. [PMID: 26671626 PMCID: PMC4706465 DOI: 10.1016/j.envres.2015.11.033] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/24/2015] [Accepted: 11/27/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Tobacco smoke, diet and indoor/outdoor air pollution, all major sources of polycyclic aromatic hydrocarbons (PAHs), have been associated with breast cancer. Aberrant methylation may be an early event in carcinogenesis, but whether PAHs influence the epigenome is unclear, particularly in breast tissue where methylation may be most relevant. We aimed to evaluate the role of methylation in the association between PAHs and breast cancer. METHODS In a population-based case-control study, we measured promoter methylation of 13 breast cancer-related genes in breast tumor tissue (n=765-851 cases) and global methylation in peripheral blood (1055 cases/1101 controls). PAH sources (current active smoking, residential environmental tobacco smoke (ETS), vehicular traffic, synthetic log burning, and grilled/smoked meat intake) were evaluated separately. Logistic regression was used to estimate adjusted odds ratios (ORs) and 95% confidence intervals (CIs). RESULTS When comparing methylated versus unmethylated genes, synthetic log use was associated with increased ORs for CDH1 (OR=2.26, 95%CI=1.06-4.79), HIN1 (OR=2.14, 95%CI=1.34-3.42) and RARβ (OR=1.80, 95%CI=1.16-2.78) and decreased ORs for BRCA1 (OR=0.44, 95%CI=0.30-0.66). Residential ETS was associated with decreased ORs for ESR1 (OR=0.74, 95%CI=0.56-0.99) and CCND2 methylation (OR=0.65, 95%CI=0.44-0.96). Current smoking and vehicular traffic were associated with decreased ORs for DAPK (OR=0.53, 95%CI=0.28-0.99) and increased ORs for TWIST1 methylation (OR=2.79, 95%CI=1.24-6.30), respectively. In controls, synthetic log use was inversely associated with LINE-1 (OR=0.59, 95%CI=0.41-0.86). DISCUSSION PAH sources were associated with hypo- and hypermethylation at multiple promoter regions in breast tumors and LINE-1 hypomethylation in blood of controls. Methylation may be a potential biologic mechanism for the associations between PAHs and breast cancer incidence.
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Affiliation(s)
- Alexandra J White
- Department of Epidemiology University of North Carolina, Chapel Hill, NC, USA.
| | - Jia Chen
- Departments of Preventive Medicine, New York, NY, USA; Departments of Oncological Science, New York, NY, USA; Departments of Pediatrics, Ichan School of Medicine at Mt. Sinai, New York, NY, USA
| | | | - Lauren E McCullough
- Department of Epidemiology University of North Carolina, Chapel Hill, NC, USA
| | - Xinran Xu
- Departments of Preventive Medicine, New York, NY, USA; Departments of Biometrics, Roche Product Development in Asia-Pacific, Shanghai, China
| | - Yoon Hee Cho
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT, USA
| | - Kathleen Conway
- Department of Epidemiology University of North Carolina, Chapel Hill, NC, USA
| | - Jan Beyea
- Department of Consulting in the Public Interest (CIPI), Lambertville, NJ, USA
| | | | - Susan E Steck
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC, USA
| | - Irina Mordukhovich
- Department of Epidemiology University of North Carolina, Chapel Hill, NC, USA
| | - Sybil M Eng
- Departments of Epidemiology, Columbia University, New York, NY, USA
| | - Mary Beth Terry
- Departments of Epidemiology, Columbia University, New York, NY, USA
| | - Lawrence S Engel
- Department of Epidemiology University of North Carolina, Chapel Hill, NC, USA
| | - Maureen Hatch
- Departments of Division of Cancer Epidemiology and Genetics, Radiation Epidemiology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Alfred I Neugut
- Departments of Epidemiology, Columbia University, New York, NY, USA; Departments of Medicine, Columbia University, New York, NY, USA
| | - Hanina Hibshoosh
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Regina M Santella
- Departments of Environmental Health Sciences; Columbia University, New York, NY, USA
| | - Marilie D Gammon
- Department of Epidemiology University of North Carolina, Chapel Hill, NC, USA
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Shakeri H, Gharesouran J, Fakhrjou A, Esfahani A, Mohaddes Ardebili SM. DNA methylation assessment as a prognostic factor in invasive breast cancer using methylation-specific multiplex ligation dependent probe amplification. EXCLI JOURNAL 2016; 15:11-20. [PMID: 27065772 PMCID: PMC4822054 DOI: 10.17179/excli2015-485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/05/2015] [Indexed: 12/17/2022]
Abstract
DNA methylation of promoter regions is a common molecular mechanism for inactivation of tumor suppressor genes that participates in carcinogenesis. Determining the methylation status of genes in cancer and their association with clinical features play an essential role in early diagnosis, prognosis and determine appropriate treatment for patients. The purpose of the present study was to evaluate the methylation of tumor suppressor genes in patients with invasive ductal carcinoma (IDC). Furthermore, we evaluated the association between clinical parameters and DNA methylation as a biomarker in diagnostic IDC patients. The methylation-specific multiplex ligation dependent probe amplification (MS-MLPA) assay was used to analyze the methylation profile of 24 genes in formalin-fixed paraffin embedded (FFPE) tissue samples from 75 patients with IDC. Each of the patients showed a distinctive methylation profile. We observed higher methylation in the RASSF1 (48 %), CDH13 (44 %) and GSTP1 (36 %) genes. Some of the methylated genes were associated with clinical features. Methylation of GSTP1 (P=0.028) and RASSF1 (P=0.012) were related with lymph node metastasis. Methylation of GSTP1 (P=0.005) was associated with high histological grade. Moreover, concurrent methylation of GSTP1 and CDH13 was observed in IDC patients (p<0.001). Hierarchical cluster analysis based on the methylation profile revealed two main clusters of patients, the highly methylated cluster being significantly associated with high histological grade and lymph node metastasis. The results of this study indicate that the methylation status of RASSF1 and CDH13 and GSTP1 can be a prognostic marker to better management of IDC patients.
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Affiliation(s)
- Halaleh Shakeri
- Hematology & Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biochemistry and Clinical Laboratories, Division of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalal Gharesouran
- Department of Biochemistry and Clinical Laboratories, Division of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ashraf Fakhrjou
- Department of Pathology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Esfahani
- Hematology & Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyyed Mojtaba Mohaddes Ardebili
- Hematology & Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biochemistry and Clinical Laboratories, Division of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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23
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White AJ, Chen J, McCullough LE, Xu X, Cho YH, Teitelbaum SL, Neugut AI, Terry MB, Hibshoosh H, Santella RM, Gammon MD. Polycyclic aromatic hydrocarbon (PAH)-DNA adducts and breast cancer: modification by gene promoter methylation in a population-based study. Cancer Causes Control 2015; 26:1791-802. [PMID: 26407953 DOI: 10.1007/s10552-015-0672-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 09/16/2015] [Indexed: 12/19/2022]
Abstract
PURPOSE Polycyclic aromatic hydrocarbon (PAH)-DNA adducts have been associated with breast cancer incidence. Aberrant changes in DNA methylation may be an early event in carcinogenesis. However, possible relations between PAH-DNA adducts, methylation, and breast cancer are unknown. The objectives of this study were to (1) assess associations between PAH-DNA adducts, and breast cancer, stratified by DNA methylation markers and (2) examine interactions between adducts and DNA methylation in association with breast cancer and tumor subtype. METHODS In a population-based case-control study, promoter methylation of 13 breast cancer-related genes was measured in tumor tissue (n = 765-851 cases). Blood DNA from breast cancer cases (n = 873) and controls (n = 941) was used to assess PAH-DNA adducts and global methylation. Logistic regression was used to estimate adjusted odds ratios (ORs) and 95% confidence intervals (CI); and the ratio of the OR (ROR) was used to assess heterogeneity. RESULTS Women with detectable PAH-DNA adducts and methylated RARβ (ROR 2.69, 95% CI 1.02-7.12; p for interaction = 0.03) or APC (ROR 1.76, 95% CI 0.87-3.58; p for interaction = 0.09) genes were more likely to have hormone receptor-positive tumors than other subtypes. Interactions with other methylation markers were not apparent (p ≥ 0.10). The association between adducts and breast cancer did not vary by methylation status of the tumor nor did adducts associate with global methylation in the controls. CONCLUSIONS Gene-specific methylation of RARβ, and perhaps APC, may interact with PAH-DNA adducts to increase risk of hormone receptor-positive breast cancer. There was little evidence that adducts were associated with or interacted with other methylation markers of interest.
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Affiliation(s)
- Alexandra J White
- Department of Epidemiology, University of North Carolina, CB#7435, McGavran-Greenberg Hall, Chapel Hill, NC, 27599-7435, USA.
| | - Jia Chen
- Departments of Preventive Medicine, Ichan School of Medicine at Mt. Sinai, New York, NY, USA.,Departments of Oncological Science, Ichan School of Medicine at Mt. Sinai, New York, NY, USA.,Departments of Pediatrics, Ichan School of Medicine at Mt. Sinai, New York, NY, USA
| | - Lauren E McCullough
- Department of Epidemiology, University of North Carolina, CB#7435, McGavran-Greenberg Hall, Chapel Hill, NC, 27599-7435, USA
| | - Xinran Xu
- Research Center for Translational Medicine, Shanghai East Hospital of Tongji University School of Medicine, Shanghai, China
| | - Yoon Hee Cho
- Department of Environmental Health Sciences, Columbia University, New York, NY, USA
| | - Susan L Teitelbaum
- Departments of Preventive Medicine, Ichan School of Medicine at Mt. Sinai, New York, NY, USA
| | - Alfred I Neugut
- Department of Epidemiology, Columbia University, New York, NY, USA.,Department of Medicine, Columbia University, New York, NY, USA
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University, New York, NY, USA
| | | | - Regina M Santella
- Department of Environmental Health Sciences, Columbia University, New York, NY, USA
| | - Marilie D Gammon
- Department of Epidemiology, University of North Carolina, CB#7435, McGavran-Greenberg Hall, Chapel Hill, NC, 27599-7435, USA
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24
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Spitzwieser M, Holzweber E, Pfeiler G, Hacker S, Cichna-Markl M. Applicability of HIN-1, MGMT and RASSF1A promoter methylation as biomarkers for detecting field cancerization in breast cancer. Breast Cancer Res 2015; 17:125. [PMID: 26370119 PMCID: PMC4570691 DOI: 10.1186/s13058-015-0637-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 08/27/2015] [Indexed: 12/18/2022] Open
Abstract
Introduction It has been shown in some articles that genetic and epigenetic abnormalities cannot only be found in tumor tissues but also in adjacent regions that appear histologically normal. This phenomenon is metaphorically called field cancerization or field defect. Field cancerization is regarded as clinically significant because it is assumed to be an important factor in local recurrence of cancer. As the field showing these molecular abnormalities may not be removed completely by surgery, these changes might lead to neoplasms and subsequent transformation to a tumor. We aimed to investigate the applicability of the methylation status of six tumor suppressor genes as biomarkers for detecting field cancerization in breast cancer. Methods The promoter methylation status of CCND2, DAPK1, GSTP1, HIN-1, MGMT and RASSF1A was determined by methylation-sensitive high-resolution melting (MS-HRM) analysis. MS-HRM methods for CCND2, MGMT and RASSF1A were developed in-house, primer sequences for DAPK1, GSTP1 and HIN-1 have already been published. Biopsy samples were taken from tumor, tumor-adjacent and tumor-distant tissue from 17 breast cancer patients. Normal breast tissues of four healthy women served as controls. Results All MS-HRM methods proved to be very sensitive. LODs were in the range from 0.1 to 1.5 %, LOQs ranged from 0.3 to 5.3 %. A total of 94 %, 82 % and 65 % of the tumors showed methylation of RASSF1A, HIN-1 and MGMT promoters, respectively. The methylation status of these promoters was significantly lower in tumor-distant tissues than in tumor tissues. Tumor-adjacent tissues showed higher methylation status of RASSF1A, HIN-1 and MGMT promoters than tumor-distant tissues, indicating field cancerization. The methylation status of the HIN-1 promoter in tumor-adjacent tissues was found to correlate strongly with that in the corresponding tumors (r = 0.785, p < 0.001), but not with that in the corresponding tumor-distant tissues (r = 0.312, p = 0.239). Conclusions Among the gene promoters investigated, the methylation status of the HIN-1 promoter can be considered the best suitable biomarker for detecting field cancerization. Further investigation is needed to test whether it can be used for defining surgical margins in order to prevent future recurrence of breast cancer.
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Affiliation(s)
- Melanie Spitzwieser
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria.
| | - Elisabeth Holzweber
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria.
| | - Georg Pfeiler
- Department of Obstetrics and Gynecology, Division of Gynecology and Gynecological Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
| | - Stefan Hacker
- Department of Plastic and Reconstructive Surgery, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria.
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25
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Delmonico L, Moreira ADS, Franco MF, Esteves EB, Scherrer L, Gallo CVDM, do Nascimento CM, Ornellas MHF, de Azevedo CM, Alves G. CDKN2A (p14(ARF)/p16(INK4a)) and ATM promoter methylation in patients with impalpable breast lesions. Hum Pathol 2015; 46:1540-7. [PMID: 26255234 DOI: 10.1016/j.humpath.2015.06.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 06/05/2015] [Accepted: 06/10/2015] [Indexed: 12/16/2022]
Abstract
Early detection of breast cancer increases the chances of cure, but the reliable identification of impalpable lesions is still a challenge. In spite of the advances in breast cancer detection, the molecular basis of impalpable lesions and the corresponding circulating biomarkers are not well understood. Impalpable lesions, classified by radiologists according to the Breast Imaging Reporting and Data System in the categories 3 and 4, can be either benign or malignant (slow growing or aggressive). In this article, we report the DNA methylation pattern in CDKN2A (p14(ARF)/p16(INK4a)) and in ATM gene promoters from 62 impalpable lesions, 39 peripheral blood samples, and 39 saliva samples, assessed by methylation-specific polymerase chain reaction method. ATM showed the greatest percentage of methylation in DNA from lesions (benign and malignant), blood (even with p16(INK4a)), and saliva, followed by p16(INK4a) and p14(ARF). Among the malignant cases, ATM promoter was the most hypermethylated in lesion DNA and in blood and saliva DNAs, and p14(ARF), the least. The highest percentage of p16(INK4a) methylation was found in the blood. Finally, our data are relevant because they were obtained using impalpable breast lesions from patients who were carefully recruited in 2 public hospitals of Rio de Janeiro.
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Affiliation(s)
- Lucas Delmonico
- Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil; Pós-Graduação em Ciências Médicas, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
| | - Aline dos Santos Moreira
- Laboratório de Genômica Funcional de Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Marco Felipe Franco
- Serviço de Radiologia, Hospital Universitário Gaffrée-Guinle, Rio de Janeiro 20270-004, Brazil
| | | | - Luciano Scherrer
- Sociedade Brasileira Oncologia Clínica, Belo Horizonte, Minas Gerais 30120-010, Brazil
| | - Claúdia Vitória de Moura Gallo
- Departamento de Genética, Instituto de Biologia Roberto Alcântara Gomes, Universidade Estadual do Rio de Janeiro, Rio de Janeiro 20550-900, Brazil
| | | | - Maria Helena Faria Ornellas
- Pós-Graduação em Ciências Médicas, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
| | | | - Gilda Alves
- Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil; Pós-Graduação em Ciências Médicas, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil.
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26
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Redshaw N, Huggett JF, Taylor MS, Foy CA, Devonshire AS. Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis. BMC Genomics 2014; 15:1174. [PMID: 25539843 PMCID: PMC4523014 DOI: 10.1186/1471-2164-15-1174] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/10/2014] [Indexed: 02/06/2023] Open
Abstract
Background DNA methylation is an important epigenetic mechanism in several human diseases, most notably cancer. The quantitative analysis of DNA methylation patterns has the potential to serve as diagnostic and prognostic biomarkers, however, there is currently a lack of consensus regarding the optimal methodologies to quantify methylation status. To address this issue we compared five analytical methods: (i) MethyLight qPCR, (ii) MethyLight digital PCR (dPCR), methylation-sensitive and -dependent restriction enzyme (MSRE/MDRE) digestion followed by (iii) qPCR or (iv) dPCR, and (v) bisulfite amplicon next generation sequencing (NGS). The techniques were evaluated for linearity, accuracy and precision. Results MethyLight qPCR displayed the best linearity across the range of tested samples. Observed methylation measured by MethyLight- and MSRE/MDRE-qPCR and -dPCR were not significantly different to expected values whilst bisulfite amplicon NGS analysis over-estimated methylation content. Bisulfite amplicon NGS showed good precision, whilst the lower precision of qPCR and dPCR analysis precluded discrimination of differences of < 25% in methylation status. A novel dPCR MethyLight assay is also described as a potential method for absolute quantification that simultaneously measures both sense and antisense DNA strands following bisulfite treatment. Conclusions Our findings comprise a comprehensive benchmark for the quantitative accuracy of key methods for methylation analysis and demonstrate their applicability to the quantification of circulating tumour DNA biomarkers by using sample concentrations that are representative of typical clinical isolates. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1174) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jim F Huggett
- LGC, Queens Road, Teddington, Middlesex, TW11 0LY, UK.
| | - Martin S Taylor
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK.
| | - Carole A Foy
- LGC, Queens Road, Teddington, Middlesex, TW11 0LY, UK.
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27
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Murria R, Palanca S, de Juan I, Egoavil C, Alenda C, García-Casado Z, Juan MJ, Sánchez AB, Santaballa A, Chirivella I, Segura Á, Hervás D, Llop M, Barragán E, Bolufer P. Methylation of tumor suppressor genes is related with copy number aberrations in breast cancer. Am J Cancer Res 2014; 5:375-385. [PMID: 25628946 PMCID: PMC4300703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 11/10/2014] [Indexed: 06/04/2023] Open
Abstract
This study investigates the relationship of promoter methylation in tumor suppressor genes with copy-number aberrations (CNA) and with tumor markers in breast cancer (BCs). The study includes 98 formalin fixed paraffin-embedded BCs in which promoter methylation of 24 tumour suppressor genes were assessed by Methylation-Specific Multiplex Ligation-dependent Probe Amplification (MS-MLPA), CNA of 20 BC related genes by MLPA and ER, PR, HER2, CK5/6, CK18, EGFR, Cadherin-E, P53, Ki-67 and PARP expression by immunohistochemistry (IHC). Cluster analysis classed BCs in two groups according to promoter methylation percentage: the highly-methylated group (16 BCs), containing mostly hyper-methylated genes, and the sparsely-methylated group (82 BCs) with hypo-methylated genes. ATM, CDKN2A, VHL, CHFR and CDKN2B showed the greatest differences in the mean methylation percentage between these groups. We found no relationship of the IHC parameters or pathological features with methylation status, except for Catherin-E (p = 0.008). However the highly methylated BCs showed higher CNA proportion than the sparsely methylated BCs (p < 0.001, OR = 1.62; IC 95% [1.26, 2.07]). CDC6, MAPT, MED1, PRMD14 and AURKA showed the major differences in the CNA percentage between the two groups, exceeding the 22%. Methylation in RASSF1, CASP8, DAPK1 and GSTP1 conferred the highest probability of harboring CNA. Our results show a new link between promoter methylation and CNA giving support to the importance of methylation events to establish new BCs subtypes. Our findings may be also of relevance in personalized therapy assessment, which could benefit the hyper methylated BC patients group.
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Affiliation(s)
- Rosa Murria
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La FeValencia, Spain
| | - Sarai Palanca
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La FeValencia, Spain
| | - Inmaculada de Juan
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La FeValencia, Spain
| | - Cecilia Egoavil
- Department of Pathology, University General HospitalAlicante, Spain
| | - Cristina Alenda
- Department of Pathology, University General HospitalAlicante, Spain
| | | | | | - Ana B Sánchez
- Genetic Counseling Unit, Elche HospitalAlicante, Spain
| | - Ana Santaballa
- Department of Oncology, University Hospital La FeValencia, Spain
| | | | - Ángel Segura
- Genetic Counseling Unit, University Hospital La FeValencia, Spain
| | - David Hervás
- Biostatistics Service, Health Research Institute La FeValencia, Spain
| | - Marta Llop
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La FeValencia, Spain
| | - Eva Barragán
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La FeValencia, Spain
| | - Pascual Bolufer
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La FeValencia, Spain
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28
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LAN VOTHITHUONG, HA NGOTHI, UYEN NGUYENQUYNH, DUONG NGUYENTHI, HUONG NGUYENTHITHU, THUAN TABICH, DUONG PHAMANHTHUY, VAN TO TA. Standardization of the methylation-specific PCR method for analyzing BRCA1 and ER methylation. Mol Med Rep 2014; 9:1844-50. [DOI: 10.3892/mmr.2014.1990] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 02/05/2014] [Indexed: 11/06/2022] Open
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29
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Wu HC, Delgado-Cruzata L, Machella N, Wang Q, Santella RM, Terry MB. DNA double-strand break repair genotype and phenotype and breast cancer risk within sisters from the New York site of the Breast Cancer Family Registry (BCFR). Cancer Causes Control 2013; 24:2157-68. [PMID: 24062231 DOI: 10.1007/s10552-013-0292-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 09/13/2013] [Indexed: 12/11/2022]
Abstract
PURPOSE We previously observed that poor DNA repair phenotype is associated with increased breast cancer (BC) risk within families. Here, we examined whether genetic variation in double-strand break repair (DSBR) genes is associated with BC risk and if genotypes are related to phenotype in unaffected women. METHODS Using data from the New York site of the Breast Cancer Family Registry, we investigated 25 single-nucleotide polymorphism (SNPs) involved in DSBR using biospecimens from 337 BC cases and 410 unaffected sister controls. RESULTS Genotypes in XRCC4 were associated with BC risk, with ORs of 1.67 (95 % CI 1.01-2.76) for the combined GA/AA of rs1805377 and 1.69 (95 % CI 1.03-2.77) for rs1056503 TG/GG; these associations were no longer statistically significant in multivariable conditional logistic regression models. When examining the association of SNPs with phenotype, we found that genotypes of XRCC5 rs3834 and rs1051685, which were highly correlated with each other, were associated with end-joining (EJ) capacity; women with the XRCC5 rs3834 GA genotype had better DNA repair as measured by higher levels of EJ capacity (37.8 ± 14.1 % for GA vs. 27.9 ± 11.8 % for GG carriers p = 0.0006). Women with the AA genotype of BRCA1 rs799917 also had higher EJ capacity (35.1 ± 9.2 %) than those with GG (26.4 ± 10.1 %, p = 0.02). CONCLUSIONS Overall, we found that selected DSBR genotypes were associated with phenotype, although they were not associated with BC risk itself, suggesting that phenotypic measures are influenced by endogenous and exogenous factors across the life course and may be better markers than genotypic measures for ascertaining BC risk.
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Affiliation(s)
- Hui-Chen Wu
- Department of Epidemiology, Mailman School of Public Health of Columbia University, 722 West 168th St., 724A, New York, NY, 10032, USA
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30
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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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Winardi W, Tsai CY, Chen WT, Tsai HP, Chung CL, Loh JK, Chai CY, Kwan AL. Reduced WWOX protein expression in human astrocytoma. Neuropathology 2013; 33:621-7. [PMID: 23675860 DOI: 10.1111/neup.12040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 03/26/2013] [Indexed: 11/29/2022]
Abstract
The WW domain-containing oxidoreductase (WWOX) functions as a tumor suppressor by interacting with various proteins in numerous important signaling pathways. WWOX silencing via homozygous deletion of its locus and/or promoter hypermethylation has been observed in various human cancers. However, the relationship between WWOX and tumors in the central nervous system has not been fully explored. In this study, the expression levels of WWOX protein in astrocytomas from 38 patients with different tumor grades were retrospectively analyzed by immunohistochemical staining. The results showed that 19 (50.0%) samples had highly reduced WWOX protein expression when compared with normal controls, while 14 (36.8%) and five (13.2%) cases exhibited moderate and mild decreases in WWOX expression, respectively. Reduction of the expression of WWOX protein correlated with patient age, supra-tentorial localization of the tumor and severity of the symptoms. Furthermore, loss of WWOX expression inversely correlated with survival time. No significant correlation was observed between the loss of WWOX expression and the gender of patients or the difference in pre-operative and post-operative karnofsky performance status scores. Surprisingly, there was no significant correlation between the loss of WWOX protein expression and overall tumor grades. Nevertheless, it was found that 63.6% (7/11) of the grade II astrocytomas had highly reduced WWOX expression and 36.4% (4/11) showed moderately reduced WWOX expression, while none of the samples exhibited mild reductions. Similar results were also found in grade III astrocytomas. The results from this small-size sample pilot study suggest that the loss of WWOX expression may be an early event in the pathogenesis of human astrocytoma.
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Kloten V, Becker B, Winner K, Schrauder MG, Fasching PA, Anzeneder T, Veeck J, Hartmann A, Knüchel R, Dahl E. Promoter hypermethylation of the tumor-suppressor genes ITIH5, DKK3, and RASSF1A as novel biomarkers for blood-based breast cancer screening. Breast Cancer Res 2013; 15:R4. [PMID: 23320751 PMCID: PMC3672828 DOI: 10.1186/bcr3375] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 01/09/2013] [Indexed: 12/14/2022] Open
Abstract
Introduction For early detection of breast cancer, the development of robust blood-based biomarkers that accurately reflect the host tumor is mandatory. We investigated DNA methylation in circulating free DNA (cfDNA) from blood of breast cancer patients and matched controls to establish a biomarker panel potentially useful for early detection of breast cancer. Methods We examined promoter methylation of seven putative tumor-suppressor genes (SFRP1, SFRP2, SFRP5, ITIH5, WIF1, DKK3, and RASSF1A) in cfDNA extracted from serum. Clinical performance was first determined in a test set (n = 261 sera). In an independent validation set (n = 343 sera), we validated the most promising genes for further use in early breast cancer detection. Sera from 59 benign breast disease and 58 colon cancer patients were included for additional specificity testing. Results Based on the test set, we determined ITIH5 and DKK3 promoter methylation as candidate biomarkers with the best sensitivity and specificity. In both the test and validation set combined, ITIH5 and DKK3 methylation achieved 41% sensitivity with a specificity of 93% and 100% in healthy and benign disease controls, respectively. Combination of these genes with RASSF1A methylation increased the sensitivity to 67% with a specificity of 69% and 82% in healthy controls and benign disease controls, respectively. Conclusions Tumor-specific methylation of the three-gene panel (ITIH5, DKK3, and RASSF1A) might be a valuable biomarker for the early detection of breast cancer.
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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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Lim SP, Wong NC, Suetani RJ, Ho K, Ng JL, Neilsen PM, Gill PG, Kumar R, Callen DF. Specific-site methylation of tumour suppressor ANKRD11 in breast cancer. Eur J Cancer 2012; 48:3300-9. [PMID: 22538187 DOI: 10.1016/j.ejca.2012.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 02/22/2012] [Accepted: 03/25/2012] [Indexed: 01/01/2023]
Abstract
ANKRD11 is a putative tumour suppressor gene in breast cancer, which has been shown in our laboratory to be a co-activator of p53. Our data suggest that down-regulation of ANKRD11 is associated with breast tumourigenesis. Breast cancer cell lines treated with DNA demethylating agents resulted in up-regulation of ANKRD11 expression suggesting that promoter DNA methylation may be responsible for its down-regulation. The transcriptional activity of a CpG-rich region 2kb upstream of the transcription initiation site of ANKRD11 was investigated using dual-luciferase reporter assays. The constructs carrying -661 to -571 bp promoter sequence showed significant transcriptional activity. Using the SEQUENOM Epityper Platform, the region between -770 and +399 bp was analysed in 25 breast tumours, four normal breast tissues and five normal blood samples. The region between -770 and -323 bp was shown to be frequently methylated in breast tumours. The methylation patterns of all analysed CpGs in this region were identical in the normal and tumour samples, except for a 19 bp region containing three CpG sites. These sites had significantly higher levels of methylation in tumours (40%) compared to normal samples (6%). Our findings support the role of ANKRD11 as a tumour suppressor gene and suggest that aberrant DNA methylation of three CpGs in a 19 bp region within the ANKRD11 promoter may be responsible for its down-regulation in breast cancer.
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Affiliation(s)
- Sue Ping Lim
- Cancer Therapeutics Laboratory, Discipline of Medicine, The University of Adelaide, South Australia, Australia.
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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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Abstract
Emerging evidence indicates that RUNX3 is a tumor suppressor in breast cancer. RUNX3 is frequently inactivated in human breast cancer cell lines and cancer samples by hemizygous deletion of the Runx3 gene, hypermethylation of the Runx3 promoter, or cytoplasmic sequestration of RUNX3 protein. Inactivation of RUNX3 is associated with the initiation and progression of breast cancer. Female Runx3(+/-) mice spontaneously develop ductal carcinoma, and overexpression of RUNX3 inhibits the proliferation, tumorigenic potential, and invasiveness of breast cancer cells. This review is intended to summarize these findings and discuss the tumor suppressor function of RUNX3 in breast cancer.
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Affiliation(s)
- Lin-Feng Chen
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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Andresen K, Boberg KM, Vedeld HM, Honne H, Hektoen M, Wadsworth CA, Clausen OP, Karlsen TH, Foss A, Mathisen O, Schrumpf E, Lothe RA, Lind GE. Novel target genes and a valid biomarker panel identified for cholangiocarcinoma. Epigenetics 2012; 7:1249-57. [PMID: 22983262 PMCID: PMC3499326 DOI: 10.4161/epi.22191] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cholangiocarcinoma is notoriously difficult to diagnose, and the mortality rate is high due to late clinical presentation. CpG island promoter methylation is frequently seen in cancer development. In the present study, we aimed at identifying novel epigenetic biomarkers with the potential to improve the diagnostic accuracy of cholangiocarcinoma. Microarray data analyses of cholangiocarcinoma cell lines treated with epigenetic drugs and their untreated counterparts were compared with previously published gene expression profiles of primary tumors and with non-malignant controls. Genes responding to the epigenetic treatment that were simultaneously downregulated in primary cholangiocarcinoma compared with controls (n = 43) were investigated for their promoter methylation status in cancer cell lines from the gastrointestinal tract. Genes commonly methylated in cholangiocarcinoma cell lines were subjected to quantitative methylation-specific polymerase chain reaction in a total of 93 clinical samples (cholangiocarcinomas and non-malignant controls). CDO1, DCLK1, SFRP1 and ZSCAN18, displayed high methylation frequencies in primary tumors and were unmethylated in controls. At least one of these four biomarkers was positive in 87% of the tumor samples, with a specificity of 100%. In conclusion, the novel methylation-based biomarker panel showed high sensitivity and specificity for cholangiocarcinoma. The potential of these markers in early diagnosis of this cancer type should be further explored.
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Affiliation(s)
- Kim Andresen
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radiumhospital, Oslo, Norway
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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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Xu Q, Jiang Y, Yin Y, Li Q, He J, Jing Y, Qi YT, Xu Q, Li W, Lu B, Peiper SS, Jiang BH, Liu LZ. A regulatory circuit of miR-148a/152 and DNMT1 in modulating cell transformation and tumor angiogenesis through IGF-IR and IRS1. J Mol Cell Biol 2012; 5:3-13. [PMID: 22935141 DOI: 10.1093/jmcb/mjs049] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Dysregulation of microRNAs is a common feature in human cancers, including breast cancer (BC). Here we describe the epigenetic regulation of miR-148a and miR-152 and their impact on BC cells. Due to the hypermethylation of CpG island, the expression levels of both miR-148a and miR-152 (miR-148a/152) are decreased in BC tissues and cells. DNMT1, the DNA methyltransferase 1 for the maintenance methylation, is aberrantly up-regulated in BC and its overexpression is responsible for hypermethylation of miR-148a and miR-152 promoters. Intriguingly, we found that DNMT1 expression, which is one of the targets of miR-148a/152, is inversely correlated with the expression levels of miR-148a/152 in BC tissues. Those results lead us to propose a negative feedback regulatory loop between miR-148a/152 and DNMT1 in BC. More importantly, we demonstrate that IGF-IR and IRS1, often overexpressed in BC, are two novel targets of miR-148a/152. Overexpression of miR-148a or miR-152 significantly inhibits BC cell proliferation, colony formation, and tumor angiogenesis via targeting IGF-IR and IRS1 and suppressing their downstream AKT and MAPK/ERK signaling pathways. Our results suggest a novel miR-148a/152-DNMT1 regulatory circuit and reveal that miR-148a and miR-152 act as tumor suppressors by targeting IGF-IR and IRS1, and that restoration of miR-148a/152 expression may provide a strategy for therapeutic application to treat BC patients.
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Affiliation(s)
- Qing Xu
- State Key Lab of Reproductive Medicine, and Department of Pathology, Cancer Center, Nanjing Medical University, Nanjing 210029, China
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Lian ZQ, Wang Q, Li WP, Zhang AQ, Wu L. Screening of significantly hypermethylated genes in breast cancer using microarray-based methylated-CpG island recovery assay and identification of their expression levels. Int J Oncol 2012; 41:629-38. [PMID: 22581028 DOI: 10.3892/ijo.2012.1464] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 04/17/2012] [Indexed: 11/06/2022] Open
Abstract
To screen candidate methylation markers for early detection of breast cancer and to explore the relationship between methylation and gene expression, we performed methylated-CpG island recovery assay (MIRA) combined with CpG island array on 61982 CpG sites across 4162 genes in 10 cancerous and 10 non-cancerous breast tissues. Direct bisulfite sequencing and combined bisulfite restriction analysis (COBRA) were carried out in independent cancerous and non-cancerous samples. Gene expression was analyzed by microarrays and validated using RT-PCR. We detected 70 significantly hypermethylated genes in breast cancer tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. Direct bisulfite sequencing showed widespread methylation occurring in intragenic regions of the WT1, PAX6 and ITGA4 genes and in the promoter region of the OTX2 gene in breast cancer tissues. COBRA assay confirmed that the WT1, OTX2 and PAX6 genes were hypermethylated in breast cancer tissues. Clustering analysis of the gene expression of 70 significantly hypermethylated genes revealed that most hypermethylated genes in breast cancer were not expressed in breast tissues. RT-PCR assay confirmed that WT1 and PITX2 were only weakly expressed in the breast cancer tissues and were not expressed in most non-cancerous breast tissues. OTX2 and PAX6 were not expressed in either breast cancer or non-cancerous tissues. In conclusion, these results will expand our knowledge of hypermethylated genes and methylation sites for early detection of breast cancer and deepen our understanding of the relationship between methylation and gene expression. The MIRA approach can screen candidate methylated genes for further clinical validation more effectively than gene expression microarray-based strategy.
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Affiliation(s)
- Zhen-Qiang Lian
- Guangdong Women and Children Hospital of Guangzhou Medical College, Guangzhou, People's Republic of China
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Iwasaki M, Ono H, Kuchiba A, Kasuga Y, Yokoyama S, Onuma H, Nishimura H, Kusama R, Yoshida T, Tsugane S. Association of postmenopausal endogenous sex hormones with global methylation level of leukocyte DNA among Japanese women. BMC Cancer 2012; 12:323. [PMID: 22839213 PMCID: PMC3481397 DOI: 10.1186/1471-2407-12-323] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 07/17/2012] [Indexed: 01/12/2023] Open
Abstract
Background Although global hypomethylation of leukocyte DNA has been associated with an increased risk of several sites of cancer, including breast cancer, determinants of global methylation level among healthy individuals remain largely unexplored. Here, we examined whether postmenopausal endogenous sex hormones were associated with the global methylation level of leukocyte DNA. Methods A cross-sectional study was conducted using the control group of a breast cancer case–control study in Nagano, Japan. Subjects were postmenopausal women aged 55 years or over who provided blood samples. We measured global methylation level of peripheral blood leukocyte DNA by luminometric methylation assay; estradiol, estrone, androstenedione, dehydroepiandrosterone sulfate, testosterone and free testosterone by radioimmunoassay; bioavailable estradiol by the ammonium sulfate precipitation method; and sex-hormone binding globulin by immunoradiometric assay. A linear trend of association between methylation and hormone levels was evaluated by regression coefficients in a multivariable liner regression model. A total of 185 women were included in the analyses. Results Mean global methylation level (standard deviation) was 70.3% (3.1) and range was from 60.3% to 79.2%. Global methylation level decreased 0.27% per quartile category for estradiol and 0.39% per quartile category for estrone while it increased 0.41% per quartile category for bioavailable estradiol. However, we found no statistically significant association of any sex hormone level measured in the present study with global methylation level of leukocyte DNA. Conclusions Our findings suggest that endogenous sex hormones are not major determinants of the global methylation level of leukocyte DNA.
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Affiliation(s)
- Motoki Iwasaki
- Epidemiology and Prevention Division, Research Center for Cancer Prevention and Screening, Tsukiji, Chuo-ku, Tokyo, Japan.
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Luna Coronell JA, Syed P, Sergelen K, Gyurján I, Weinhäusel A. The current status of cancer biomarker research using tumour-associated antigens for minimal invasive and early cancer diagnostics. J Proteomics 2012; 76 Spec No.:102-15. [PMID: 22842156 DOI: 10.1016/j.jprot.2012.07.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 06/22/2012] [Accepted: 07/16/2012] [Indexed: 11/30/2022]
Abstract
Tumour-associated antigens (TAA) can be detected prior to clinical diagnosis and thus would be ideal biomarkers for early detection of cancer using only a few microliters of a patient's serum. In this article we provide a summary of TAA screening and serum-profiling conducted for breast, prostate, lung and colon cancers. Different methodological approaches, including SEREX, SERPA, and phage display for TAA identification and TAA panels are summarised, and a revision of array based techniques is provided. The most promising studies performed on these cancers (performed with 80-400 serum samples, including controls) obtained sensitivities in a range of 44-95% and specificities of 80-100%. From the various studies reviewed, only one performed cross validation (AUC=0.71) in a prostate cancer study. Thus, albeit receiver operation characteristics are very promising, cross validation of most studies is still missing. Additionally, the concerted action of research groups for standardization of serum-TAA testing and cross validation is required. Along with today's technological options, the chances of establishing TAA biomarkers are now higher than ever before. This may also be true for confirmation and validation of already existing data, which is a prerequisite for implementation of TAA biomarkers into clinical diagnostics. This article is part of a Special Issue entitled: Integrated omics.
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Affiliation(s)
- Johana A Luna Coronell
- Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Muthgasse 11, 1190 Vienna, Austria.
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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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Xiang T, Li L, Yin X, Yuan C, Tan C, Su X, Xiong L, Putti TC, Oberst M, Kelly K, Ren G, Tao Q. The ubiquitin peptidase UCHL1 induces G0/G1 cell cycle arrest and apoptosis through stabilizing p53 and is frequently silenced in breast cancer. PLoS One 2012; 7:e29783. [PMID: 22279545 PMCID: PMC3261155 DOI: 10.1371/journal.pone.0029783] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 12/05/2011] [Indexed: 12/17/2022] Open
Abstract
Background Breast cancer (BrCa) is a complex disease driven by aberrant gene alterations and environmental factors. Recent studies reveal that abnormal epigenetic gene regulation also plays an important role in its pathogenesis. Ubiquitin carboxyl- terminal esterase L1 (UCHL1) is a tumor suppressor silenced by promoter methylation in multiple cancers, but its role and alterations in breast tumorigenesis remain unclear. Methodology/Principal Findings We found that UCHL1 was frequently downregulated or silenced in breast cancer cell lines and tumor tissues, but readily expressed in normal breast tissues and mammary epithelial cells. Promoter methylation of UCHL1 was detected in 9 of 10 breast cancer cell lines (90%) and 53 of 66 (80%) primary tumors, but rarely in normal breast tissues, which was statistically correlated with advanced clinical stage and progesterone receptor status. Pharmacologic demethylation reactivated UCHL1 expression along with concomitant promoter demethylation. Ectopic expression of UCHL1 significantly suppressed the colony formation and proliferation of breast tumor cells, through inducing G0/G1 cell cycle arrest and apoptosis. Subcellular localization study showed that UCHL1 increased cytoplasmic abundance of p53. We further found that UCHL1 induced p53 accumulation and reduced MDM2 protein level, and subsequently upregulated the expression of p21, as well as cleavage of caspase3 and PARP, but not in catalytic mutant UCHL1 C90S-expressed cells. Conclusions/Significance UCHL1 exerts its tumor suppressive functions by inducing G0/G1cell cycle arrest and apoptosis in breast tumorigenesis, requiring its deubiquitinase activity. Its frequent silencing by promoter CpG methylation may serve as a potential tumor marker for breast cancer.
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Affiliation(s)
- Tingxiu Xiang
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Xuedong Yin
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chenfu Yuan
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Cui Tan
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xianwei Su
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Lei Xiong
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Thomas C. Putti
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Michael Oberst
- Signal Transduction Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kathleen Kelly
- Signal Transduction Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Guosheng Ren
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- * E-mail: (GR); (QT)
| | - Qian Tao
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- * E-mail: (GR); (QT)
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Abstract
Breast cancer is caused by progressive genetic alterations and epigenetic changes that trigger tumor development. Among the epigenetic alterations descried in breast cancer, DNA promoter methylation has been extensively studied and observed in genes involved in several critical signaling pathways that initiate and promote breast tumorigenesis. In addition to DNA hypermethylation, global methylation levels have been observed to decrease with breast cancer progression. In close connection with DNA methylation changes, histone modifications, especially the acetylation and methylation of histone lysines, play an essential role in the nucleosomes remodeling and gene expression regulation in breast cancer.
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Affiliation(s)
- Ramona G Dumitrescu
- Saba University School of Medicine, Saba Island and Georgetown University Medical School, Washington, DC, USA.
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Brooks JD, Cairns P, Shore RE, Klein CB, Wirgin I, Afanasyeva Y, Zeleniuch-Jacquotte A. DNA methylation in pre-diagnostic serum samples of breast cancer cases: results of a nested case-control study. Cancer Epidemiol 2011; 34:717-23. [PMID: 20627767 DOI: 10.1016/j.canep.2010.05.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 05/06/2010] [Accepted: 05/08/2010] [Indexed: 11/27/2022]
Abstract
BACKGROUND Promoter methylation of tumor suppressor genes is a frequent and early event in breast carcinogenesis. Paired tumor tissue and serum samples from women with breast cancer show that promoter methylation is detectable in both sample types, with good concordance. This suggests the potential for these serum markers to be used for breast cancer detection. METHODS The current study was a case-control study nested within the prospective New York University Women's Health Study cohort aimed to assess the ability of promoter methylation in serum to detect pre-clinical disease. Cases were women with blood samples collected within the 6 months preceding breast cancer diagnosis (n=50). Each case was matched to 2 healthy cancer-free controls and 1 cancer-free control with a history of benign breast disease (BBD). RESULTS Promoter methylation analysis of four cancer-related genes: -RASSF1A, GSTP1, APC and RARβ2, - was conducted using quantitative methylation-specific PCR. Results showed that the frequency of methylation was lower than expected among cases and higher than expected among controls. Methylation was detected in the promoter region of: RASSF1A in 22.0%, 22.9% and 17.2% of cases, BBD controls and healthy controls respectively; GSTP1 in 4%, 10.4% and 7.1% respectively; APC in 2.0%, 4.4% and 4.2% respectively and RARβ2 in 6.7%, 2.3% and 1.1% respectively. CONCLUSION Methylation status of the four genes included in this study was unable to distinguish between cases and either control group. This study highlights some methodological issues to be addressed in planning prospective studies to evaluate methylation markers as diagnostic biomarkers.
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Affiliation(s)
- Jennifer D Brooks
- Division of Epidemiology, Department of Environmental Medicine, New York University School of Medicine, New York, NY 10016, United States.
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Pang D, Zhao Y, Xue W, Shan M, Chen Y, Zhang Y, Zhang G, Liu F, Li D, Yang Y. Methylation profiles of the BRCA1 promoter in hereditary and sporadic breast cancer among Han Chinese. Med Oncol 2011; 29:1561-8. [PMID: 22076508 DOI: 10.1007/s12032-011-0100-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Accepted: 10/25/2011] [Indexed: 01/18/2023]
Abstract
The development of breast cancer is a multistep process associated with complex changes in host gene expression patterns including inactivation of tumor suppressor genes and activation of oncogenes. Critically, hereditary predisposition plays a significant role in cancer susceptibility. However, mutation of the BRCA1 gene is found only in the minority of hereditary breast cancer, which indicates that there might be alternative, novel mechanisms contributing to inactivation of the BRCA1 gene. Studies have shown that aberrant methylation of genomic DNA plays an important role in carcinogenesis. The aim of this study was to investigate whether DNA methylation may be an alternative mechanism for the inactivation of BRCA1 as an epigenetic modification of the genome and whether hereditary breast cancer has a different BRCA1 methylation phenotype pattern than sporadic breast cancer. The pattern of CpG island methylation within the promoter region of BRCA1 was assessed by bisulfite sequencing DNA from peripheral blood cells of 72 patients with hereditary predisposition but without BRCA1 mutations and 30 sporadic breast cancer controls. The overall methylation level in patients with hereditary predisposition was significantly lower than that in the sporadic control group. However, patients with hereditary predisposition showed a significantly higher methylation susceptibility for the sites -518 when compared to controls. These results suggest that there might be different BRCA1 promoter methylation levels and patterns in sporadic and hereditary breast cancer in peripheral blood DNA. These findings may facilitate the early diagnosis of hereditary breast cancer.
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Affiliation(s)
- Da Pang
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, HaPing Road 158, Harbin, China.
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Xiang TX, Yuan Y, Li LL, Wang ZH, Dan LY, Chen Y, Ren GS, Tao Q. Aberrant promoter CpG methylation and its translational applications in breast cancer. CHINESE JOURNAL OF CANCER 2011; 32:12-20. [PMID: 22059908 PMCID: PMC3845590 DOI: 10.5732/cjc.011.10344] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Breast cancer is a complex disease driven by multiple factors including both genetic and epigenetic alterations. Recent studies revealed that abnormal gene expression induced by epigenetic changes, including aberrant promoter methylation and histone modification, plays a critical role in human breast Carcinogenesis. Silencing of tumor suppressor genes (TSGs) by promoter CpG methylation facilitates cells growth and survival advantages and further results in tumor initiation and progression, thus directly contributing to breast tumorigenesis. Usually, aberrant promoter methylation of TSGs, which can be reversed by pharmacological reagents, occurs at the early stage of tumorigenesis and therefore may serve as a potential tumor marker for early diagnosis and therapeutic targeting of breast cancer. In this review, we summarize the epigenetic changes of multiple TSGs involved in breast pathogenesis and their potential clinical applications as tumor markers for early detection and treatment of breast cancer.
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Affiliation(s)
- Ting-Xiu Xiang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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Wiechec E. Implications of genomic instability in the diagnosis and treatment of breast cancer. Expert Rev Mol Diagn 2011; 11:445-53. [PMID: 21545260 DOI: 10.1586/erm.11.21] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Tumorigenesis is a multistep process resulting from DNA mutations observed at the DNA sequence and chromosome level as well as epigenetic changes, which affect expression of oncogenes and tumor suppressor genes. Breast cancer is a very heterogeneous disease that manifests in various histological and clinical types. Defects in the biological action of the genome driven by various alterations, such as point mutations and chromosomal rearrangements, lead to the collapse of genome integrity, uncontrolled cell proliferation and failure in apoptotic cell death. Detailed profiling of breast cancer-associated genomic alterations is indispensable for the design of individualized anticancer therapy, by suggesting diagnostic and prognostic criteria as well as the outcome of applied treatment. Among various directions of cancer research, identification of genomic alterations in breast cancer and their translation into clinical applications is at the forefront.
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Affiliation(s)
- Emilia Wiechec
- Otto-von-Guericke University, Institute of Molecular and Clinical Immunology, Leipziger Str. 44, 39120 Magdeburg, Germany.
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Moelans CB, Verschuur-Maes AHJ, van Diest PJ. Frequent promoter hypermethylation of BRCA2, CDH13, MSH6, PAX5, PAX6 and WT1 in ductal carcinoma in situ and invasive breast cancer. J Pathol 2011; 225:222-31. [DOI: 10.1002/path.2930] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/08/2011] [Accepted: 04/25/2011] [Indexed: 12/25/2022]
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