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Linowiecka K, Guz J, Dziaman T, Urbanowska-Domańska O, Zarakowska E, Szpila A, Szpotan J, Skalska-Bugała A, Mijewski P, Siomek-Górecka A, Różalski R, Gackowski D, Oliński R, Foksiński M. The level of active DNA demethylation compounds in leukocytes and urine samples as potential epigenetic biomarkers in breast cancer patients. Sci Rep 2024; 14:6481. [PMID: 38499584 PMCID: PMC10948817 DOI: 10.1038/s41598-024-56326-5] [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: 08/07/2023] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
The active DNA demethylation process, which involves TET proteins, can affect DNA methylation pattern. TET dependent demethylation results in DNA hypomethylation by oxidation 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) and its derivatives. Moreover, TETs' activity may be upregulated by ascorbate. Given that aberrant DNA methylation of genes implicated in breast carcinogenesis may be involved in tumor progression, we wanted to determine whether breast cancer patients exert changes in the active DNA demethylation process. The study included blood samples from breast cancer patients (n = 74) and healthy subjects (n = 71). We analyzed the expression of genes involved in the active demethylation process (qRT-PCR), and 5-mC and its derivatives level (2D-UPLC MS/MS). The ascorbate level was determined using UPLC-MS. Breast cancer patients had significantly higher TET3 expression level, lower 5-mC and 5-hmC DNA levels. TET3 was significantly increased in luminal B breast cancer patients with expression of hormone receptors. Moreover, the ascorbate level in the plasma of breast cancer patients was decreased with the accompanying increase of sodium-dependent vitamin C transporters (SLC23A1 and SLC23A2). The presented study indicates the role of TET3 in DNA demethylation in breast carcinogenesis.
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Affiliation(s)
- Kinga Linowiecka
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland.
- Department of Human Biology, Institute of Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland.
| | - Jolanta Guz
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Tomasz Dziaman
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Olga Urbanowska-Domańska
- Department of Oncology, Professor Franciszek Lukaszczyk Oncology Centre, Romanowskiej 2, 85-796, Bydgoszcz, Poland
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Anna Szpila
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Justyna Szpotan
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
- Department of Human Biology, Institute of Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
| | - Aleksandra Skalska-Bugała
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Paweł Mijewski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Agnieszka Siomek-Górecka
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Rafał Różalski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Ryszard Oliński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Marek Foksiński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland.
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Linowiecka K, Slominski AT, Reiter RJ, Böhm M, Steinbrink K, Paus R, Kleszczyński K. Melatonin: A Potential Regulator of DNA Methylation. Antioxidants (Basel) 2023; 12:1155. [PMID: 37371885 PMCID: PMC10295183 DOI: 10.3390/antiox12061155] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The pineal gland-derived indoleamine hormone, melatonin, regulates multiple cellular processes, ranging from chronobiology, proliferation, apoptosis, and oxidative damage to pigmentation, immune regulation, and mitochondrial metabolism. While melatonin is best known as a master regulator of the circadian rhythm, previous studies also have revealed connections between circadian cycle disruption and genomic instability, including epigenetic changes in the pattern of DNA methylation. For example, melatonin secretion is associated with differential circadian gene methylation in night shift workers and the regulation of genomic methylation during embryonic development, and there is accumulating evidence that melatonin can modify DNA methylation. Since the latter one impacts cancer initiation, and also, non-malignant diseases development, and that targeting DNA methylation has become a novel intervention target in clinical therapy, this review discusses the potential role of melatonin as an under-investigated candidate epigenetic regulator, namely by modulating DNA methylation via changes in mRNA and the protein expression of DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) proteins. Furthermore, since melatonin may impact changes in the DNA methylation pattern, the authors of the review suggest its possible use in combination therapy with epigenetic drugs as a new anticancer strategy.
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Affiliation(s)
- Kinga Linowiecka
- Department of Human Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
- Dr. Phillip Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL 33125, USA
| | - Andrzej T. Slominski
- Department of Dermatology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Pathology and Laboratory Medicine Service, VA Medical Center, Birmingham, AL 35294, USA
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health, Long School of Medicine, San Antonio, TX 78229, USA
| | - Markus Böhm
- Department of Dermatology, University of Münster, Von-Esmarch-Str. 58, 48149 Münster, Germany
| | - Kerstin Steinbrink
- Department of Dermatology, University of Münster, Von-Esmarch-Str. 58, 48149 Münster, Germany
| | - Ralf Paus
- Dr. Phillip Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL 33125, USA
| | - Konrad Kleszczyński
- Department of Dermatology, University of Münster, Von-Esmarch-Str. 58, 48149 Münster, Germany
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Fallet M, Blanc M, Di Criscio M, Antczak P, Engwall M, Guerrero Bosagna C, Rüegg J, Keiter SH. Present and future challenges for the investigation of transgenerational epigenetic inheritance. ENVIRONMENT INTERNATIONAL 2023; 172:107776. [PMID: 36731188 DOI: 10.1016/j.envint.2023.107776] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Epigenetic pathways are essential in different biological processes and in phenotype-environment interactions in response to different stressors and they can induce phenotypic plasticity. They encompass several processes that are mitotically and, in some cases, meiotically heritable, so they can be transferred to subsequent generations via the germline. Transgenerational Epigenetic Inheritance (TEI) describes the phenomenon that phenotypic traits, such as changes in fertility, metabolic function, or behavior, induced by environmental factors (e.g., parental care, pathogens, pollutants, climate change), can be transferred to offspring generations via epigenetic mechanisms. Investigations on TEI contribute to deciphering the role of epigenetic mechanisms in adaptation, adversity, and evolution. However, molecular mechanisms underlying the transmission of epigenetic changes between generations, and the downstream chain of events leading to persistent phenotypic changes, remain unclear. Therefore, inter-, (transmission of information between parental and offspring generation via direct exposure) and transgenerational (transmission of information through several generations with disappearance of the triggering factor) consequences of epigenetic modifications remain major issues in the field of modern biology. In this article, we review and describe the major gaps and issues still encountered in the TEI field: the general challenges faced in epigenetic research; deciphering the key epigenetic mechanisms in inheritance processes; identifying the relevant drivers for TEI and implement a collaborative and multi-disciplinary approach to study TEI. Finally, we provide suggestions on how to overcome these challenges and ultimately be able to identify the specific contribution of epigenetics in transgenerational inheritance and use the correct tools for environmental science investigation and biomarkers identification.
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Affiliation(s)
- Manon Fallet
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden; Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd, Oxford OX1 3QU, United Kingdom.
| | - Mélanie Blanc
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, INRAE, Palavas, France
| | - Michela Di Criscio
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Philipp Antczak
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Center for Molecular Medicine Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne, Germany
| | - Magnus Engwall
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | | | - Joëlle Rüegg
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Steffen H Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
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Guo Z, Zhao Y, Wu Y, Zhang Y, Wang R, Liu W, Zhang C, Yang X. Cellular retinol-binding protein 1: a therapeutic and diagnostic tumor marker. Mol Biol Rep 2023; 50:1885-1894. [PMID: 36515825 DOI: 10.1007/s11033-022-08179-2] [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: 09/18/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022]
Abstract
Cellular Retinol Binding Protein 1 (CRBP1) gene is a protein coding gene located on human chromosome 3q21, which codifies a protein named CRBP1. CRBP1 is widely expressed in many tissues as a chaperone protein to regulate the uptake, subsequent esterification and bioavailability of retinol. CRBP1 combines retinol and retinaldehyde with high affinity to protect retinoids from non-specific oxidation, and transports retinoids to specific enzymes to promote the biosynthesis of retinoic acid. The vital role of CRBP1 in retinoids metabolism has been gradually discovered, which has been implicated in tumorigenesis. However, the precise functions of CRBP1 in different diseases are still poorly understood. The purpose of this review is to provide an overview of the role of CRBP1 in various diseases, especially in both the promotion and inhibition of cancers, which may also offer a novel biomarker and potential therapeutic target for human diseases.
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Affiliation(s)
- Zhiyuan Guo
- College of Life Science, Henan Normal University, Xinxiang, 453007, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, China
| | - Yinshen Zhao
- College of Life Science, Henan Normal University, Xinxiang, 453007, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, China
| | - Yuqi Wu
- College of Life Science, Henan Normal University, Xinxiang, 453007, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, China
| | - Yuqi Zhang
- College of Life Science, Henan Normal University, Xinxiang, 453007, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, China
| | - Ruoyan Wang
- College of Life Science, Henan Normal University, Xinxiang, 453007, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, China
| | - Wan Liu
- College of Life Science, Henan Normal University, Xinxiang, 453007, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, China
| | - Chaoyang Zhang
- College of Life Science, Henan Normal University, Xinxiang, 453007, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, China
| | - Xianguang Yang
- College of Life Science, Henan Normal University, Xinxiang, 453007, China.
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, China.
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Tajbakhsh J, Mortazavi F, Gupta NK. DNA methylation topology differentiates between normal and malignant in cell models, resected human tissues, and exfoliated sputum cells of lung epithelium. Front Oncol 2022; 12:991120. [DOI: 10.3389/fonc.2022.991120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundGlobal DNA hypomethylation is a prominent feature of cancer cells including lung cancer, that has not been widely explored towards cancer diagnosis. In this study we assess the comparative distribution of global DNA methylation in normal cells versus cancer cells in various specimen models.MethodsWe used in situ immunofluorescence labeling of overall 5-methylcytosine (5mC) and covisualization of global DNA (gDNA) by 4’,6-diamidino-2-phenylindole (DAPI), confocal microscopy and 3D image analysis to derive 5mC/DAPI colocalization patterns in human cell lines (BEAS-2B, A549, H157) and upper respiratory epithelial cells derived from various sources (i.e., sputum from healthy and cancer patients, and resected tissues from normal parenchyma and lung tumors).ResultsBy introducing 5mC/DAPI colocalization index as a metric we could distinguish between normal epithelial cells and aberrantly hypomethylated cancer cells. Cultured lung cancer cells (H157 and A549) had significantly lower indices compared to normal cells (BEAS-2B). Furthermore, we were able to identify such extensively hypomethylated low-index cells in tumor tissues and the matching sputum from cancer patients. In contrast, the indices of cells derived from sputum of healthy individuals had more similarity to epithelial cells of normal parenchyma and the phenotypically normal BEAS-2B cells.ConclusionsThe results suggest that 5mC topology using high-resolution image cytometry shows potential for identifying hypomethylated cancerous cells in human tissues and amongst normal cells in matching sputum, which may render a valuable surrogate for biopsied tissues. This promising feature deserves further validation in more comprehensive studies.
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Switzer CH, Cho HJ, Eykyn TR, Lavender P, Eaton P. NOS2 and S-nitrosothiol signaling induces DNA hypomethylation and LINE-1 retrotransposon expression. Proc Natl Acad Sci U S A 2022; 119:e2200022119. [PMID: 35584114 PMCID: PMC9173756 DOI: 10.1073/pnas.2200022119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/29/2022] [Indexed: 12/31/2022] Open
Abstract
Inducible nitric oxide synthase (NOS2) produces high local concentrations of nitric oxide (NO), and its expression is associated with inflammation, cellular stress signals, and cellular transformation. Additionally, NOS2 expression results in aggressive cancer cell phenotypes and is correlated with poor outcomes in patients with breast cancer. DNA hypomethylation, especially of noncoding repeat elements, is an early event in carcinogenesis and is a common feature of cancer cells. In addition to altered gene expression, DNA hypomethylation results in genomic instability via retrotransposon activation. Here, we show that NOS2 expression and associated NO signaling results in substantial DNA hypomethylation in human cell lines by inducing the degradation of DNA (cytosine-5)–methyltransferase 1 (DNMT1) protein. Similarly, NOS2 expression levels were correlated with decreased DNA methylation in human breast tumors. NOS2 expression and NO signaling also resulted in long interspersed noncoding element 1 (LINE-1) retrotransposon hypomethylation, expression, and DNA damage. DNMT1 degradation was mediated by an NO/p38-MAPK/lysine acetyltransferase 5–dependent mechanism. Furthermore, we show that this mechanism is required for NO-mediated epithelial transformation. Therefore, we conclude that NOS2 and NO signaling results in DNA damage and malignant cellular transformation via an epigenetic mechanism.
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Affiliation(s)
- Christopher H. Switzer
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
| | - Hyun-Ju Cho
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
| | - Thomas R. Eykyn
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, SE1 7EH, United Kingdom
| | - Paul Lavender
- AsthmaUK Centre in Allergic Mechanisms of Asthma, School of Immunology and Microbial Science, King’s College London, Guy’s Hospital, London, SE1 9RT, United Kingdom
| | - Philip Eaton
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
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Diacofotaki A, Loriot A, De Smet C. Identification of Tissue-Specific Gene Clusters Induced by DNA Demethylation in Lung Adenocarcinoma: More Than Germline Genes. Cancers (Basel) 2022; 14:cancers14041007. [PMID: 35205751 PMCID: PMC8870412 DOI: 10.3390/cancers14041007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Loss of DNA methylation is often observed in human tumors, but how this epigenetic alteration impacts the transcriptome of cancer cells remains largely undefined. So far, DNA hypomethylation in tumors has been associated with aberrant activation of a germline-specific gene expression program. Here, we exploited transcriptomic and methylomic datasets of lung adenocarcinoma to investigate the possibility that other gene expression programs also become ectopically activated in hypomethylated tumors. Remarkably, we found that DNA hypomethylation in lung adenocarcinoma is associated with ectopic activation of not only germline-specific genes, but also gene clusters displaying specific expression in the gastrointestinal tract, or in stratified epithelia. Interestingly, expression of genes in this latter group was of prognostic value. Together, our study brings novel insight into the transcriptomic changes associated with DNA hypomethylation in tumors, and is an incentive to explore the value of hypomethylated DNA sequences as cancer biomarkers. Abstract Genome-wide loss of DNA methylation is commonly observed in human cancers, but its impact on the tumor transcriptome remains ill-defined. Previous studies demonstrated that this epigenetic alteration causes aberrant activation of a germline-specific gene expression program. Here, we examined if DNA hypomethylation in tumors also leads to de-repression of gene clusters with other tissue specificities. To this end, we explored transcriptomic and methylomic datasets from human lung adenocarcinoma (LUAD) cell lines, normal lung, and lung alveolar type II cells, considered as the origin of LUAD. Interestingly, DNA demethylation in LUAD cell lines was associated with activation of not only germline-specific (CG) genes, but also gene clusters displaying specific expression in the gastrointestinal tract (GI), or in stratified epithelia (SE). Consistently, genes from all three clusters showed highly specific patterns of promoter methylation among normal tissues and cell types, and were generally sensitive to induction by a DNA demethylating agent. Analysis of TCGA datasets confirmed that demethylation and activation of CG, GI and SE genes also occurs in vivo in LUAD tumor tissues, in association with global genome hypomethylation. For genes of the GI cluster, we demonstrated that HNF4A is a necessary factor for transcriptional activation following promoter demethylation. Interestingly, expression of several SE genes, in particular FAM83A, correlated with both tumor grade and reduced patient survival. Together, our study uncovers novel cell-type specific gene clusters that become aberrantly activated in LUAD tumors in association with genome-wide hypomethylation.
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Affiliation(s)
- Anna Diacofotaki
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (A.D.); (A.L.)
| | - Axelle Loriot
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (A.D.); (A.L.)
- Group of Computational Biology and Bioinformatics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Charles De Smet
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (A.D.); (A.L.)
- Correspondence:
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Chen QF, Gao H, Pan QY, Wang YJ, Zhong XN. Analysis at the single-cell level indicates an important role of heterogeneous global DNA methylation status on the progression of lung adenocarcinoma. Sci Rep 2021; 11:23337. [PMID: 34857857 PMCID: PMC8639744 DOI: 10.1038/s41598-021-02786-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 10/15/2021] [Indexed: 12/19/2022] Open
Abstract
Aberrant DNA modifications affect the tumorigenesis and progression of lung cancer. However, the global methylation status of tumor cells and the heterogeneous methylation status of cells within the same tumor need further study. We used publicly available single-cell RNAseq data to investigate the impact and diversity of global methylation status on lung adenocarcinoma. Clustering cells into subgroups and cell differentiation pseudotime analysis, based on expression profile, demonstrated that the global methylation status was crucial to lung adenocarcinoma function and progression. Hypermethylated tumor cells had increased activity related to the hypoxia response. Hyper- and hypomethylated cells indicated upregulation in pathways involving focal adhesion and cell junctions. Pseudotime analysis showed that cell clusters with unique methylation activities were located at the ends of the putative trajectories, suggesting that DNA methylation and demethylation activities were essential to tumor cell progression. Expression of SPP1 was associated with the global methylation status of tumor cells and with patient prognosis. Our study identified the importance and diversity of global DNA methylation status by analysis at the single-cell level. Our findings provide new information about the global DNA methylation status of tumor cells and suggest new approaches for precision medical treatments for lung adenocarcinoma.
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Affiliation(s)
- Quan-Fang Chen
- Department of Respiratory, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Han Gao
- Department of Respiratory, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Qing-Yun Pan
- Department of Respiratory, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Ying-Ju Wang
- Department of Respiratory, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Xiao-Ning Zhong
- Department of Respiratory, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China.
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Ruiz de la Cruz M, de la Cruz Montoya AH, Rojas Jiménez EA, Martínez Gregorio H, Díaz Velásquez CE, Paredes de la Vega J, de la Cruz Hernández-Hernández F, Vaca Paniagua F. Cis-Acting Factors Causing Secondary Epimutations: Impact on the Risk for Cancer and Other Diseases. Cancers (Basel) 2021; 13:cancers13194807. [PMID: 34638292 PMCID: PMC8508567 DOI: 10.3390/cancers13194807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/09/2021] [Accepted: 08/15/2021] [Indexed: 12/25/2022] Open
Abstract
Epigenetics affects gene expression and contributes to disease development by alterations known as epimutations. Hypermethylation that results in transcriptional silencing of tumor suppressor genes has been described in patients with hereditary cancers and without pathogenic variants in the coding region of cancer susceptibility genes. Although somatic promoter hypermethylation of these genes can occur in later stages of the carcinogenic process, constitutional methylation can be a crucial event during the first steps of tumorigenesis, accelerating tumor development. Primary epimutations originate independently of changes in the DNA sequence, while secondary epimutations are a consequence of a mutation in a cis or trans-acting factor. Secondary epimutations have a genetic basis in cis of the promoter regions of genes involved in familial cancers. This highlights epimutations as a novel carcinogenic mechanism whose contribution to human diseases is underestimated by the scarcity of the variants described. In this review, we provide an overview of secondary epimutations and present evidence of their impact on cancer. We propose the necessity for genetic screening of loci associated with secondary epimutations in familial cancer as part of prevention programs to improve molecular diagnosis, secondary prevention, and reduce the mortality of these diseases.
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Affiliation(s)
- Miguel Ruiz de la Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | | | - Ernesto Arturo Rojas Jiménez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Héctor Martínez Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Clara Estela Díaz Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
| | - Jimena Paredes de la Vega
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Fidel de la Cruz Hernández-Hernández
- Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | - Felipe Vaca Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México 14080, Mexico
- Correspondence: ; Tel.: +52-55-5623-1333 (ext. 39788)
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Epigenetic Regulation in Melanoma: Facts and Hopes. Cells 2021; 10:cells10082048. [PMID: 34440824 PMCID: PMC8392422 DOI: 10.3390/cells10082048] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 12/25/2022] Open
Abstract
Cutaneous melanoma is a lethal disease, even when diagnosed in advanced stages. Although recent progress in biology and treatment has dramatically improved survival rates, new therapeutic approaches are still needed. Deregulation of epigenetics, which mainly controls DNA methylation status and chromatin remodeling, is implied not only in cancer initiation and progression, but also in resistance to antitumor drugs. Epigenetics in melanoma has been studied recently in both melanoma preclinical models and patient samples, highlighting its potential role in different phases of melanomagenesis, as well as in resistance to approved drugs such as immune checkpoint inhibitors and MAPK inhibitors. This review summarizes what is currently known about epigenetics in melanoma and dwells on the recognized and potential new targets for testing epigenetic drugs, alone or together with other agents, in advanced melanoma patients.
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Adampourezare M, Dehghan G, Hasanzadeh M, Hosseinpoure Feizi MA. Application of lateral flow and microfluidic bio-assay and biosensing towards identification of DNA-methylation and cancer detection: Recent progress and challenges in biomedicine. Biomed Pharmacother 2021; 141:111845. [PMID: 34175816 DOI: 10.1016/j.biopha.2021.111845] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is an important epigenetic alteration that results from the covalent transfer of a methyl group to the fifth carbon of a cytosine residue in CpG dinucleotides by DNA methyltransferase. This modification mostly happens in the promoter region and the first exon of most genes and suppresses gene expression. Therefore, aberrant DNA methylation cause tumor progression, metastasis, and resistance to current anti-cancer therapies. So, the detection of DNA methylation is an important issue in diagnosis and therapy of most diseases. Conventional methods for the assay of DNA methylation and activity of DNA methyltransferases are time consuming. So, we need to multiplex operations and expensive instrumentation. To overcome the limitations of conventional methods, new methods such as microfluidic platforms and lateral flow tests have been developed to evaluate DNA methylation. The microfluidic tests are based on optical and electrical biosensing. These tests able us to can analyze DNA methylation with high efficiency and sensitivity without the need for expensive equipment and skilled people. Lateral flow strip tests are another type of rapid, simple, and sensitive test with advanced technology used to assess DNA methylation. Lateral flow strip tests are based on optical biosensors. This review attempts to evaluate new methods for assessing DNA extraction, DNA methylation and DNA methyltransferase activity as well as recent developments in microfluidic technology application for bisulfite treatment and restriction enzyme (bisulfite free), and lateral flow relying on their application in the field of recognition of DNA methylation in blood and body fluids. Also, the advantages and disadvantages of each test are reviewed. Finally, future prospects for the development of the microfluidics biodevices for the detection of DNA methylation is briefly discussed.
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Affiliation(s)
- Mina Adampourezare
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran; Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Gholamreza Dehghan
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran.
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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12
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Biondi LR, Tedardi MV, Gentile LB, Chamas PPC, Dagli MLZ. Quantification of Global DNA Methylation in Canine Mammary Gland Tumors via Immunostaining of 5-Methylcytosine: Histopathological and Clinical Correlations. Front Vet Sci 2021; 8:628241. [PMID: 33718471 PMCID: PMC7947677 DOI: 10.3389/fvets.2021.628241] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/04/2021] [Indexed: 11/26/2022] Open
Abstract
Mammary tumors are the most prevalent neoplasms in non-neutered female dogs, with genetic and epigenetic alterations contributing to canine mammary carcinogenesis. This study quantified global DNA methylation in 5-methylcytosine (5mC)-immunostained canine mammary tumor samples and established histopathological and clinical correlations. A total of 91 formalin-fixed paraffin-embedded mammary tumor samples from female dogs were retrospectively selected and subjected to immunohistochemistry using an anti-5mC mouse monoclonal antibody. We evaluated 5mC+ stained nuclei of neoplastic epithelial cells in canine mammary glands to obtain semiquantitative histoscores based on staining intensity. Survival rates were estimated based on owners' or veterinary records. Histological samples comprised 28 and 63 benign and malignant canine mammary gland tumors, respectively. Results revealed significant differences between global DNA methylation patterns when mammary samples were categorized as benign or malignant (p = 0.024), with hypomethylated patterns more prevalent in malignant tumors and those with higher relapse behavior (p = 0.011). Of note, large diameter (>5 cm) tumors revealed a lower methylation pattern (p = 0.028). Additionally, we found non-statistically significant differences when tumors were grouped by histopathological characteristics, clinical parameters, or survival. These findings propose global DNA methylation assessment as a promising tool for detecting canine mammary tumors with relapse propensity.
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Affiliation(s)
- Luiz Roberto Biondi
- Department of Small Animal Internal Medicine, School of Veterinary Medicine, Santos Metropolitan University, Universidade Metropolitana de Santos (UNIMES), São Paulo, Brazil
| | - Marcello Vannucci Tedardi
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Luciana Boffoni Gentile
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Patricia Pereira Costa Chamas
- Department of Small Animal Internal Medicine, School of Veterinary Medicine, Santos Metropolitan University, Universidade Metropolitana de Santos (UNIMES), São Paulo, Brazil
| | - Maria Lucia Zaidan Dagli
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
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Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13040728. [PMID: 33578793 PMCID: PMC7916622 DOI: 10.3390/cancers13040728] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Our research focuses in the elucidation of the nature of circulating cell-free DNA (ccfDNA) as a biological entity and its exploitation as a liquid biopsy biomaterial. Working on breast cancer, it became clear that although a promising biosource, its clinical exploitation is burdened mainly by gaps in knowledge about its biology and specific characteristics. The current review covers multiple aspects of ccfDNA in breast cancer. We cover key issues such as quantity, integrity, releasing structures, methylation specific changes, release mechanisms, biological role. Machine learning approaches for analyzing ccfDNA-generated data to produce classifiers for clinical use are also discussed. Abstract Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.
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Wei C, Liu X, Wang Q, Li Q, Xie M. Identification of Hypoxia Signature to Assess the Tumor Immune Microenvironment and Predict Prognosis in Patients with Ovarian Cancer. Int J Endocrinol 2021; 2021:4156187. [PMID: 34950205 PMCID: PMC8692015 DOI: 10.1155/2021/4156187] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The 5-year overall survival rate of ovarian cancer (OC) patients is less than 40%. Hypoxia promotes the proliferation of OC cells and leads to the decline of cell immunity. It is crucial to find potential predictors or risk model related to OC prognosis. This study aimed at establishing the hypoxia-associated gene signature to assess tumor immune microenvironment and predicting the prognosis of OC. METHODS The gene expression data of 378 OC patients and 370 OC patients were downloaded from datasets. The hypoxia risk model was constructed to reflect the immune microenvironment in OC and predict prognosis. RESULTS 8 genes (AKAP12, ALDOC, ANGPTL4, CITED2, ISG20, PPP1R15A, PRDX5, and TGFBI) were included in the hypoxic gene signature. Patients in the high hypoxia risk group showed worse survival. Hypoxia signature significantly related to clinical features and may serve as an independent prognostic factor for OC patients. 2 types of immune cells, plasmacytoid dendritic cell and regulatory T cell, showed a significant infiltration in the tissues of the high hypoxia risk group patients. Most of the immunosuppressive genes (such as ARG1, CD160, CD244, CXCL12, DNMT1, and HAVCR1) and immune checkpoints (such as CD80, CTLA4, and CD274) were upregulated in the high hypoxia risk group. Gene sets related to the high hypoxia risk group were associated with signaling pathways of cell cycle, MAPK, mTOR, PI3K-Akt, VEGF, and AMPK. CONCLUSION The hypoxia risk model could serve as an independent prognostic indicator and reflect overall immune response intensity in the OC microenvironment.
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Affiliation(s)
- Chunyan Wei
- Department of Gynaecology and Obstetrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoqing Liu
- Department of Gynaecology and Obstetrics, Maternal and Child Health Hospital of Shangzhou District, Shangluo, Shanxi Province, China
| | - Qin Wang
- Department of Gynaecology and Obstetrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qipei Li
- Department of Gynaecology and Obstetrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Min Xie
- Department of Gynaecology and Obstetrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Canberk S, Lima AR, Pinto M, Soares P, Máximo V. Epigenomics in Hurthle Cell Neoplasms: Filling in the Gaps Towards Clinical Application. Front Endocrinol (Lausanne) 2021; 12:674666. [PMID: 34108939 PMCID: PMC8181423 DOI: 10.3389/fendo.2021.674666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/03/2021] [Indexed: 12/29/2022] Open
Abstract
It has been widely described that cancer genomes have frequent alterations to the epigenome, including epigenetic silencing of various tumor suppressor genes with functions in almost all cancer-relevant signalling pathways, such as apoptosis, cell proliferation, cell migration and DNA repair. Epigenetic alterations comprise DNA methylation, histone modification, and microRNAs dysregulated expression and they play a significant role in the differentiation and proliferation properties of TC. In this review, our group assessed the published evidence on the tumorigenic role of epigenomics in Hurthle cell neoplasms (HCN), highlighting the yet limited, heteregeneous and non-validated data preventing its current use in clinical practice, despite the well developed assessment techniques available. The identified evidence gaps call for a joint endeavour by the medical community towards a deeper and more systematic study of HCN, aiming at defining epigenetic markers in early diagnose, allowing for accurate stratification of maligancy and disease risk and for effective systemic treatment.
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Affiliation(s)
- Sule Canberk
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Ana Rita Lima
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), Porto, Portugal
| | - Mafalda Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal
| | - Paula Soares
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Valdemar Máximo
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
- *Correspondence: Valdemar Máximo,
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Wielsøe M, Tarantini L, Bollati V, Long M, Bonefeld‐Jørgensen EC. DNA methylation level in blood and relations to breast cancer, risk factors and environmental exposure in Greenlandic Inuit women. Basic Clin Pharmacol Toxicol 2020; 127:338-350. [PMID: 32352194 PMCID: PMC7540549 DOI: 10.1111/bcpt.13424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/23/2020] [Accepted: 04/24/2020] [Indexed: 01/22/2023]
Abstract
Several studies have found aberrant DNA methylation levels in breast cancer cases, but factors influencing DNA methylation patterns and the mechanisms are not well understood. This case-control study evaluated blood methylation level of two repetitive elements and selected breast cancer-related genes in relation to breast cancer risk, and the associations with serum level of persistent organic pollutants (POPs) and breast cancer risk factors in Greenlandic Inuit. DNA methylation was determined using bisulphite pyrosequencing in blood from 74 breast cancer cases and 80 controls. Using first tertile as reference, the following was observed. Positive associations for ATM in second tertile (OR: 2.33, 95% CI: 1.04; 5.23) and ESR2 in third tertile (OR: 2.22, 95% CI: 0.97; 5.05) suggest an increased breast cancer risk with high DNA methylation. LINE-1 methylation was lower in cases than controls. In third tertile (OR: 0.42, 95% CI: 0.18; 0.98), associations suggest in accordance with the literature an increased risk of breast cancer with LINE-1 hypomethylation. Among controls, significant associations between methylation levels and serum level of POPs and breast cancer risk factors (age, body mass index, cotinine level) were found. Thus, breast cancer risk factors and POPs may alter the risk through changes in methylation levels; further studies are needed to elucidate the mechanisms.
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Affiliation(s)
- Maria Wielsøe
- Department of Public HealthCentre for Arctic Health & Molecular EpidemiologyAarhus UniversityAarhus CDenmark
| | - Letizia Tarantini
- EPIGET – Epidemiology, Epigenetics and Toxicology LaboratoryDepartment of Clinical Sciences and Community HealthUniversità degli Studi di MilanoMilanItaly
| | - Valentina Bollati
- EPIGET – Epidemiology, Epigenetics and Toxicology LaboratoryDepartment of Clinical Sciences and Community HealthUniversità degli Studi di MilanoMilanItaly
| | - Manhai Long
- Department of Public HealthCentre for Arctic Health & Molecular EpidemiologyAarhus UniversityAarhus CDenmark
| | - Eva Cecilie Bonefeld‐Jørgensen
- Department of Public HealthCentre for Arctic Health & Molecular EpidemiologyAarhus UniversityAarhus CDenmark
- Greenland Center for Health ResearchUniversity of GreenlandNuukGreenland
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Zal F, Yarahmadi A, Totonchi H, Barazesh M, Moradi Sarabi M. Nicotine attenuates global genomic DNA methylation by influencing DNMTs gene expression in human endometrial stromal cells. Genes Environ 2020; 42:6. [PMID: 32042366 PMCID: PMC7003317 DOI: 10.1186/s41021-020-0144-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/24/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND There is increasing evidence indicating an incidence of infertility and also the risk of endometrial cancers among smokers. However, the mechanism underlying nicotine adverse effect on female reproduction remains unclear. Growing evidence has suggested that environmental exposures such as nicotine could modulate the epigenome. No study has yet been published to evaluate the direct effect of nicotine on the epigenome profiling of human endometrial stromal cells (HESC). Herein, we decided to examine the direct effects of nicotine on global genomic DNA methylation status and DNA methyl- transferases (DNMTs) gene expression in HESC. HESC were treated with different doses of nicotine (0 or control, 10- 11, 10- 8 and 10- 6) M for 24 h and their genomic global DNA methylation and gene expression of DNMTs (DNMT1, DNMT3A, and DNMT3B) were investigated using ELISA and real-time PCR, respectively. RESULTS Nicotine treatments reduced the average level of DNMTs gene expression by 90, 79, and 73.4% in 10- 11, 10- 8 and 10- 6 M of nicotine treated cells as compared to control cells, respectively (p < 0.05). Also, 10- 8 and 10- 6 M of nicotine concentrations effectively reduced the amounts of 5-methylated cytosine (5-mC) by 1.09 and 1.87% compared to control cells, respectively (p < 0.05). The 5-mC percentages were positively correlated with the relative cellular DNMTs expression in HESC as verified by the Pearson correlation test. CONCLUSION An interesting possibility raised by the current study is that the reduced genomic global DNA methylation level in HESC may be partly due to the suppression of DNMTs gene expression caused by nicotine in these cells. GRAPHICAL ABSTRACT
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Affiliation(s)
- Fatemeh Zal
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Yarahmadi
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamidreza Totonchi
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahdi Barazesh
- Biotechnology Department, School of advanced medical sciences and technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mostafa Moradi Sarabi
- Department of Biochemistry and Genetics, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, 381251698 Iran
- Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
- Hepatitis Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
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18
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Interplay between BRCA1 and GADD45A and Its Potential for Nucleotide Excision Repair in Breast Cancer Pathogenesis. Int J Mol Sci 2020; 21:ijms21030870. [PMID: 32013256 PMCID: PMC7037490 DOI: 10.3390/ijms21030870] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/26/2020] [Accepted: 01/27/2020] [Indexed: 12/12/2022] Open
Abstract
A fraction of breast cancer cases are associated with mutations in the BRCA1 (BRCA1 DNA repair associated, breast cancer type 1 susceptibility protein) gene, whose mutated product may disrupt the repair of DNA double-strand breaks as BRCA1 is directly involved in the homologous recombination repair of such DNA damage. However, BRCA1 can stimulate nucleotide excision repair (NER), the most versatile system of DNA repair processing a broad spectrum of substrates and playing an important role in the maintenance of genome stability. NER removes carcinogenic adducts of diol-epoxy derivatives of benzo[α]pyrene that may play a role in breast cancer pathogenesis as their accumulation is observed in breast cancer patients. NER deficiency was postulated to be intrinsic in stage I of sporadic breast cancer. BRCA1 also interacts with GADD45A (growth arrest and DNA damage-inducible protein GADD45 alpha) that may target NER machinery to actively demethylate genome sites in order to change the expression of genes that may be important in breast cancer. Therefore, the interaction between BRCA1 and GADD45 may play a role in breast cancer pathogenesis through the stimulation of NER, increasing the genomic stability, removing carcinogenic adducts, and the local active demethylation of genes important for cancer transformation.
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Donovan MG, Wren SN, Cenker M, Selmin OI, Romagnolo DF. Dietary fat and obesity as modulators of breast cancer risk: Focus on DNA methylation. Br J Pharmacol 2020; 177:1331-1350. [PMID: 31691272 DOI: 10.1111/bph.14891] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022] Open
Abstract
Breast cancer (BC) is the most common cancer and second leading cause of cancer mortality in women worldwide. Validated biomarkers enhance efforts for early detection and treatment, which reduce the risk of mortality. Epigenetic signatures have been suggested as good biomarkers for early detection, prognosis and targeted therapy of BC. Here, we highlight studies documenting the modifying effects of dietary fatty acids and obesity on BC biomarkers associated with DNA methylation. We focus our analysis on changes elicited in writers of DNA methylation (i.e., DNA methyltransferases), global DNA methylation and gene-specific DNA methylation. To provide context, we precede this discussion with a review of the available evidence for an association between BC incidence and both dietary fat consumption and obesity. We also include a review of well-vetted BC biomarkers related to cytosine-guanine dinucleotides methylation and how they influence BC risk, prognosis, tumour characteristics and response to treatment. LINKED ARTICLES: This article is part of a themed section on The Pharmacology of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.6/issuetoc.
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Affiliation(s)
- Micah G Donovan
- Interdisciplinary Cancer Biology Graduate Program, University of Arizona, Tucson, Arizona
| | - Spencer N Wren
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona
| | - Mikia Cenker
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona
| | - Ornella I Selmin
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona.,The University of Arizona Cancer Center, Tucson, Arizona
| | - Donato F Romagnolo
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona.,The University of Arizona Cancer Center, Tucson, Arizona
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20
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Haim A, Boynao S, Elsalam Zubidat A. Consequences of Artificial Light at Night: The Linkage between Chasing Darkness Away and Epigenetic Modifications. Epigenetics 2019. [DOI: 10.5772/intechopen.84789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
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21
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Wang T, McCullough LE, White AJ, Bradshaw PT, Xu X, Cho YH, Terry MB, Teitelbaum SL, Neugut AI, Santella RM, Chen J, Gammon MD. Prediagnosis aspirin use, DNA methylation, and mortality after breast cancer: A population-based study. Cancer 2019; 125:3836-3844. [PMID: 31402456 DOI: 10.1002/cncr.32364] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 12/20/2018] [Accepted: 01/07/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND The authors hypothesized that epigenetic changes may help to clarify the underlying biologic mechanism linking aspirin use to breast cancer prognosis. To the authors' knowledge, this is the first epidemiologic study to examine whether global methylation and/or tumor promoter methylation of breast cancer-related genes interact with aspirin use to impact mortality after breast cancer. METHODS Prediagnosis aspirin use was assessed through in-person interviews within a population-based cohort of 1508 women diagnosed with a first primary breast cancer in 1996 and 1997. Global methylation in peripheral blood was assessed by long interspersed elements-1 (LINE-1) and the luminometric methylation assay. Promoter methylation of 13 breast cancer-related genes was measured in tumor by methylation-specific polymerase chain reaction and the MethyLight assay. Vital status was determined by the National Death Index through December 31, 2014 (N = 202/476 breast cancer-specific/all-cause deaths identified among 1266 women with any methylation assessment and complete aspirin data). Cox proportional hazards regression was used to estimate hazard ratios (HRs) and 95% CIs, and the likelihood ratio test was used to evaluate multiplicative interactions. RESULTS All-cause mortality was elevated among aspirin users who had methylated promotor of BRCA1 (HR, 1.67; 95% CI, 1.26-2.22), but not among those with unmethylated promoter of BRCA1 (HR, 0.99; 95% CI, 0.67-1.45; P for interaction ≤.05). Decreased breast cancer-specific mortality was observed among aspirin users who had unmethylated promotor of BRCA1 and PR and global hypermethylation of LINE-1 (HR, 0.60, 0.78, and 0.63, respectively; P for interaction ≤.05), although the 95% CIs included the null. CONCLUSIONS The current study suggests that the LINE-1 global methylation and promoter methylation of BRCA1 and PR in tumor may interact with aspirin use to influence mortality after breast cancer.
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Affiliation(s)
- Tengteng Wang
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | | | - Alexandra J White
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Patrick T Bradshaw
- Division of Epidemiology, University of California, Berkeley, California
| | - Xinran Xu
- Department of Biometrics, Roche Product Development in Asia-Pacific, Shanghai, China
| | - Yoon Hee Cho
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University, New York, New York
| | - Susan L Teitelbaum
- Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alfred I Neugut
- Department of Epidemiology, Columbia University, New York, New York.,Department of Medicine, Columbia University, New York, New York
| | | | - Jia Chen
- Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marilie D Gammon
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
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22
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Zubidat AE, Fares B, Fares F, Haim A. Artificial Light at Night of Different Spectral Compositions Differentially Affects Tumor Growth in Mice: Interaction With Melatonin and Epigenetic Pathways. Cancer Control 2019; 25:1073274818812908. [PMID: 30477310 PMCID: PMC6259078 DOI: 10.1177/1073274818812908] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Lighting technology is rapidly advancing toward shorter wavelength illuminations
that offer energy-efficient properties. Along with this advantage, the increased
use of such illuminations also poses some health challenges, particularly breast
cancer progression. Here, we evaluated the effects of artificial light at night
(ALAN) of 4 different spectral compositions (500-595 nm) at 350 Lux on melatonin
suppression by measuring its urine metabolite 6-sulfatoxymelatonin, global DNA
methylation, tumor growth, metastases formation, and urinary corticosterone
levels in 4T1 breast cancer cell-inoculated female BALB/c mice. The results
revealed an inverse dose-dependent relationship between wavelength and melatonin
suppression. Short wavelength increased tumor growth, promoted lung metastases
formation, and advanced DNA hypomethylation, while long wavelength lessened
these effects. Melatonin treatment counteracted these effects and resulted in
reduced cancer burden. The wavelength suppression threshold for
melatonin-induced tumor growth was 500 nm. These results suggest that short
wavelength increases cancer burden by inducing aberrant DNA methylation mediated
by the suppression of melatonin. Additionally, melatonin suppression and global
DNA methylation are suggested as promising biomarkers for early diagnosis and
therapy of breast cancer. Finally, ALAN may manifest other physiological
responses such as stress responses that may challenge the survival fitness of
the animal under natural environments.
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Affiliation(s)
- A E Zubidat
- 1 The Israeli Center for Interdisciplinary Research in Chronobiology, University of Haifa, Haifa, Israel
| | - B Fares
- 2 Department of Human Biology, University of Haifa, Haifa, Israel.,3 Department of Molecular Genetics, Carmel Medical Center, Haifa, Israel
| | - F Fares
- 2 Department of Human Biology, University of Haifa, Haifa, Israel.,3 Department of Molecular Genetics, Carmel Medical Center, Haifa, Israel
| | - A Haim
- 1 The Israeli Center for Interdisciplinary Research in Chronobiology, University of Haifa, Haifa, Israel
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23
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Harlid S, Xu Z, Kirk E, Wilson LE, Troester MA, Taylor JA. Hormone therapy use and breast tissue DNA methylation: analysis of epigenome wide data from the normal breast study. Epigenetics 2019; 14:146-157. [PMID: 30821641 PMCID: PMC6557608 DOI: 10.1080/15592294.2019.1580111] [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] [Indexed: 11/29/2022] Open
Abstract
Hormone therapy (HT) is associated with increased risk of breast cancer, strongly dependent on type, duration, and recency of use. HT use could affect cancer risk by changing breast tissue transcriptional programs. We hypothesize that these changes are preceded by changes in DNA methylation. To explore this hypothesis we used histologically normal-appearing breast tissue from the Normal Breast Study (NBS). DNA methylation β-values were obtained using the Illumina HumanMethylation 450 BeadChips for 90 samples including all NBS-participants who used HT within 5 y before surgery. Data were analyzed using the reference-free cell mixture method. Cancer Genome Atlas (TCGA) mRNA-Seq data were used to assess correlation between DNA methylation and gene expression. We identified 527 CpG sites in 403 genes that were associated with ever using HT at genome wide significance (FDR q < 0.05), of these, 68 sites were also significantly associated with duration of use or recency of use. Twelve sites reached significance in all analyses one of which was cg01382688 in ARHGEF4 (p < 1.2x10−7). Mutations in ARHGEF4 have been reported in breast tumors, but this is the first report of possible breast cancer-related DNA methylation changes. In addition, 22 genes included more than one significant CpG site and a majority of these sites were significantly correlated with gene expression. Although based on small numbers, these findings support the hypothesis that HT is associated with epigenetic alterations in breast tissue, and identifies genes with altered DNA methylation states which could be linked to breast cancer development.
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Affiliation(s)
- Sophia Harlid
- a Epigenetics & Stem Cell Biology Laboratory , National Institute of Environmental Health Sciences, NIH , Research Triangle Park , NC , USA.,b Department of Radiation Sciences, Oncology , Umeå University , Umeå , Sweden
| | - Zongli Xu
- c Epidemiology Branch , National Institute of Environmental Health Sciences, NIH , Research Triangle Park , NC , USA
| | - Erin Kirk
- d Department of Epidemiology , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
| | - Lauren E Wilson
- c Epidemiology Branch , National Institute of Environmental Health Sciences, NIH , Research Triangle Park , NC , USA.,e Department of Population Health Sciences , Duke University School of Medicine , Durham , NC , USA
| | - Melissa A Troester
- d Department of Epidemiology , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
| | - Jack A Taylor
- a Epigenetics & Stem Cell Biology Laboratory , National Institute of Environmental Health Sciences, NIH , Research Triangle Park , NC , USA.,c Epidemiology Branch , National Institute of Environmental Health Sciences, NIH , Research Triangle Park , NC , USA
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24
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Pharmaco-epigenomics: On the Road of Translation Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1168:31-42. [DOI: 10.1007/978-3-030-24100-1_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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25
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Tajbakhsh J. Covisualization of Global DNA Methylation/Hydroxymethylation and Protein Biomarkers for Ultrahigh-Definition Epigenetic Phenotyping of Stem Cells. Methods Mol Biol 2019; 2150:79-92. [PMID: 31768817 DOI: 10.1007/7651_2019_276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA methylation and DNA hydroxymethylation are genomic-scale key regulatory modifications in cellular differentiation and are skewed in complex diseases. Therefore, analyzing the nuclear distribution of globally methylated and hydroxymethylated DNA in conjunction with relevant cellular components, such as protein biomarkers, may well add cell-by-cell-specific spatial and temporal information to quantitative molecular data for the discovery of signaling networks in stem cell differentiation and their exploitation in the therapeutic reprogramming of cells. Fluorescence imaging provides an optical approach that has become an essential tool in this context. The in situ fluorescent covisualization of globally methylated and hydroxymethylated DNA (5-methylcytosine = 5mC, 5-hydroxymethylcytosine = 5hmC), global DNA (gDNA), and proteins can be challenging, as the immunofluorescence detection of 5mC and 5hmC sites requires thorough denaturing of double-stranded DNA for antigen retrieval. The protocol we present overcomes this obstacle through optimization of the necessary cell processing to delineate cytosine variants and gDNA while preserving the three-dimensional (3-D) structure of the cells and in connection the immunostaining of protein biomarkers and DNA counterstaining, making it suitable for ultrahigh definition (UHD) imaging of single cells by confocal and super-resolution microscopy, 3-D visualization, and high-content cytometry.
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26
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DeVaux RS, Herschkowitz JI. Beyond DNA: the Role of Epigenetics in the Premalignant Progression of Breast Cancer. J Mammary Gland Biol Neoplasia 2018; 23:223-235. [PMID: 30306389 PMCID: PMC6244889 DOI: 10.1007/s10911-018-9414-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/18/2018] [Indexed: 12/19/2022] Open
Abstract
Ductal Carcinoma in Situ (DCIS) is an early breast cancer lesion that is considered a nonobligate precursor to development of invasive ductal carcinoma (IDC). Although only a small subset of DCIS lesions are predicted to progress into a breast cancer, distinguishing innocuous from minacious DCIS lesions remains a clinical challenge. Thus, patients diagnosed with DCIS will undergo surgery with the potential for radiation and hormone therapy. This has led to a current state of overdiagnosis and overtreatment. Interrogating the transcriptome alone has yet to define clear functional determinants of progression from DCIS to IDC. Epigenetic changes, critical for imprinting and tissue specific development, in the incorrect context can lead to global signaling rewiring driving pathological phenotypes. Epigenetic signaling pathways, and the molecular players that interpret and sustain their signals, are critical to understanding the underlying pathology of breast cancer progression. The types of epigenetic changes, as well as the molecular players, are expanding. In addition to DNA methylation, histone modifications, and chromatin remodeling, we must also consider enhancers as well as the growing field of noncoding RNAs. Herein we will review the epigenetic interactions that have been uncovered in early stage lesions that impact breast cancer progression, and how these players may be utilized as biomarkers to mitigate overdiagnosis and overtreatment.
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Affiliation(s)
- Rebecca S DeVaux
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, USA
| | - Jason I Herschkowitz
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, USA.
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27
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Zakhari S, Hoek JB. Epidemiology of Moderate Alcohol Consumption and Breast Cancer: Association or Causation? Cancers (Basel) 2018; 10:E349. [PMID: 30249004 PMCID: PMC6210419 DOI: 10.3390/cancers10100349] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/20/2018] [Accepted: 09/20/2018] [Indexed: 02/07/2023] Open
Abstract
Epidemiological studies have been used to show associations between modifiable lifestyle habits and the incidence of breast cancer. Among such factors, a history of alcohol use has been reported in multiple studies and meta-analyses over the past decades. However, associative epidemiological studies that were interpreted as evidence that even moderate alcohol consumption increases breast cancer incidence have been controversial. In this review, we consider the literature on the relationship between moderate or heavy alcohol use, both in possible biological mechanisms and in variations in susceptibility due to genetic or epigenetic factors. We argue that there is a need to incorporate additional approaches to move beyond the associations that are reported in traditional epidemiological analyses and incorporate information on molecular pathologic signatures as a requirement to posit causal inferences. In particular, we point to the efforts of the transdisciplinary field of molecular pathological epidemiology (MPE) to evaluate possible causal relationships, if any, of alcohol consumption and breast cancer. A wider application of the principles of MPE to this field would constitute a giant step that could enhance our understanding of breast cancer and multiple modifiable risk factors, a step that would be particularly suited to the era of "personalized medicine".
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Affiliation(s)
- Samir Zakhari
- Science Office, Distilled Spirits Council, Washington, DC 20005, USA.
| | - Jan B Hoek
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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28
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Breast cancer subtype dictates DNA methylation and ALDH1A3-mediated expression of tumor suppressor RARRES1. Oncotarget 2018; 7:44096-44112. [PMID: 27286452 PMCID: PMC5190082 DOI: 10.18632/oncotarget.9858] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/09/2016] [Indexed: 11/25/2022] Open
Abstract
Breast cancer subtyping, based on the expression of hormone receptors and other genes, can determine patient prognosis and potential options for targeted therapy. Among breast cancer subtypes, tumors of basal-like and claudin-low subtypes are typically associated with worse patient outcomes, are primarily classified as triple-negative breast cancers (TNBC), and cannot be treated with existing hormone-receptor-targeted therapies. Understanding the molecular basis of these subtypes will lead to the development of more effective treatment options for TNBC. In this study, we focus on retinoic acid receptor responder 1 (RARRES1) as a paradigm to determine if breast cancer subtype dictates protein function and gene expression regulation. Patient tumor dataset analysis and gene expression studies of a 26 cell-line panel, representing the five breast cancer subtypes, demonstrate that RARRES1 expression is greatest in basal-like TNBCs. Cell proliferation and tumor growth assays reveal that RARRES1 is a tumor suppressor in TNBC. Furthermore, gene expression studies, Illumina HumanMethylation450 arrays, and chromatin immunoprecipitation demonstrate that expression of RARRES1 is retained in basal-like breast cancers due to hypomethylation of the promoter. Additionally, expression of the cancer stem cell marker, aldehyde dehydrogenase 1A3, which provides the required ligand (retinoic acid) for RARRES1 transcription, is also specific to the basal-like subtype. We functionally demonstrate that the combination of promoter methylation and retinoic acid signaling dictates expression of tumor suppressor RARRES1 in a subtype-specific manner. These findings provide a precedent for a therapeutically-inducible tumor suppressor and suggest novel avenues of therapeutic intervention for patients with basal-like breast cancer.
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29
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Zubidat AE, Haim A. Artificial light-at-night - a novel lifestyle risk factor for metabolic disorder and cancer morbidity. J Basic Clin Physiol Pharmacol 2017; 28:295-313. [PMID: 28682785 DOI: 10.1515/jbcpp-2016-0116] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 03/02/2017] [Indexed: 06/07/2023]
Abstract
Both obesity and breast cancer are already recognized worldwide as the most common syndromes in our modern society. Currently, there is accumulating evidence from epidemiological and experimental studies suggesting that these syndromes are closely associated with circadian disruption. It has been suggested that melatonin (MLT) and the circadian clock genes both play an important role in the development of these syndromes. However, we still poorly understand the molecular mechanism underlying the association between circadian disruption and the modern health syndromes. One promising candidate is epigenetic modifications of various genes, including clock genes, circadian-related genes, oncogenes, and metabolic genes. DNA methylation is the most prominent epigenetic signaling tool for gene expression regulation induced by environmental exposures, such as artificial light-at-night (ALAN). In this review, we first provide an overview on the molecular feedback loops that generate the circadian regulation and how circadian disruption by ALAN can impose adverse impacts on public health, particularly metabolic disorders and breast cancer development. We then focus on the relation between ALAN-induced circadian disruption and both global DNA methylation and specific loci methylation in relation to obesity and breast cancer morbidities. DNA hypo-methylation and DNA hyper-methylation, are suggested as the most studied epigenetic tools for the activation and silencing of genes that regulate metabolic and monostatic responses. Finally, we discuss the potential clinical and therapeutic roles of MLT suppression and DNA methylation patterns as novel biomarkers for the early detection of metabolic disorders and breast cancer development.
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30
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Shen J, Song R, Gong Y, Zhao H. Global DNA hypomethylation in leukocytes associated with glioma risk. Oncotarget 2017; 8:63223-63231. [PMID: 28968983 PMCID: PMC5609915 DOI: 10.18632/oncotarget.18739] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/21/2017] [Indexed: 11/25/2022] Open
Abstract
Global DNA hypomethylation in leukocytes has been associated with increased risk for a variety of cancers. However, the role of leukocyte global DNA hypomethylation in glioma development, if any, is largely unknown. To define this role, we performed a case-control study with 390 glioma patients and 390 controls with no known cancer. Levels of 5-methylcytosine (5-mC%), a marker for global DNA methylation, were measured in leukocyte DNA. Overall, median levels of 5-mC% were significantly lower in glioma cases than in controls (3.45 vs 3.82, P=0.001). Levels of 5-mC% differed significantly by age and sex among controls and by tumor subtype and grade among glioma cases. In multivariate analysis, lower levels of 5-mC% were associated with a 1.31-fold increased risk of glioma (odds ratio = 1.31, 95% confidence interval = 1.10-1.41). A significant dose-response trend was observed in quartile analysis (P=0.001). In an analysis further stratified by clinical characteristics at baseline, the association between lower levels of 5-mC% and glioma risk was evident only among younger participants (age <52 years), women, and those with aggressive tumor characteristics, such as glioblastoma subtype, high tumor grade (grade III or IV), and absence of IDH1 mutation. Our findings indicate that global DNA hypomethylation in leukocytes may contribute to the development of glioma and that the association is affected by age, sex, and tumor aggressiveness.
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Affiliation(s)
- Jie Shen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Renduo Song
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ye Gong
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hua Zhao
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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31
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Relationships between Global DNA Methylation in Circulating White Blood Cells and Breast Cancer Risk Factors. J Cancer Epidemiol 2017; 2017:2705860. [PMID: 28484492 PMCID: PMC5397634 DOI: 10.1155/2017/2705860] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 02/26/2017] [Accepted: 03/14/2017] [Indexed: 12/21/2022] Open
Abstract
It is not yet clear whether white blood cell DNA global methylation is associated with breast cancer risk. In this review we examine the relationships between multiple breast cancer risk factors and three markers of global DNA methylation: LINE-1, 5-mdC, and Alu. A literature search was conducted using Pubmed up to April 1, 2016, using combinations of relevant outcomes such as “WBC methylation,” “blood methylation,” “blood LINE-1 methylation,” and a comprehensive list of known and suspected breast cancer risk factors. Overall, the vast majority of reports in the literature have focused on LINE-1. There was reasonably consistent evidence across the studies examined that males have higher levels of LINE-1 methylation in WBC DNA than females. None of the other demographic, lifestyle, dietary, or health condition risk factors were consistently associated with LINE-1 DNA methylation across studies. With the possible exception of sex, there was also little evidence that the wide range of breast cancer risk factors we examined were associated with either of the other two global DNA methylation markers: 5-mdC and Alu. One possible implication of the observed lack of association between global WBC DNA methylation and known breast cancer risk factors is that the association between global WBC DNA methylation and breast cancer, if it exists, is due to a disease effect.
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32
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Shen J, Song R, Wan J, Huff C, Fang S, Lee JE, Zhao H. Global methylation of blood leukocyte DNA and risk of melanoma. Int J Cancer 2017; 140:1503-1509. [PMID: 28006848 DOI: 10.1002/ijc.30577] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/10/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022]
Abstract
Global DNA methylation, possibly influenced by lifestyle and environmental factors, has been suggested to play an active role in carcinogenesis. However, its role in melanoma has rarely been explored. The aims of this study were to evaluate the relationship between melanoma risk and levels of 5-methylcytosine (5-mC), a marker for global DNA methylation, in blood leukocyte DNA, and to determine whether this 5-mC level is influenced by pigmentation and sun exposure. This case-control study included 540 melanoma cases and 540 healthy controls. Overall, melanoma cases had significantly lower levels of 5-mC% than healthy controls (median: 3.24 vs. 3.91, p < 0.001). The significant difference between two groups did not differ by pigmentation or sun exposure. Among healthy controls, however, those who had fair skin color (p = 0.041) or light or no tanning after prolonged sun exposure (p = 0.031) or used a sunlamp (p = 0.028) had lower levels of 5-mC% than their counterparts. In addition, those with an intermediate or high phenotypic index, an indicator of cutaneous cancer susceptibility, had 2.58-fold greater likelihood of having a low level of 5-mC% [odds ratio (OR): 2.58; 95% confidence interval (CI): 1.72, 3.96] than those with a low phenotypic index. Lower levels of 5-mC% were associated with a 1.25-fold greater risk of melanoma (OR: 1.25; 95% CI: 1.08, 1.37). A significant dose-response relationship was observed in quartile analysis (p = 0.001). Our results suggest that global hypomethylation in blood leukocyte DNA is associated with increased risk of melanoma and that the level of methylation is influenced by pigmentation and sun exposure.
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Affiliation(s)
- Jie Shen
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Renduo Song
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Jie Wan
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Chad Huff
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Shenying Fang
- Departments of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Jeffrey E Lee
- Departments of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Hua Zhao
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
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33
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Qi D, Li J, Que B, Su J, Li M, Zhang C, Yang M, Zhou G, Ji W. Long non-coding RNA DBCCR1-003 regulate the expression of DBCCR1 via DNMT1 in bladder cancer. Cancer Cell Int 2016; 16:81. [PMID: 27777512 PMCID: PMC5069854 DOI: 10.1186/s12935-016-0356-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 10/03/2016] [Indexed: 01/17/2023] Open
Abstract
Background Many long non coding RNAs have been identified as key modulators in cancer development. A lncRNA, DBCCR1-003, derived from the locus of tumor suppressor gene DBCCR1 (deleted in bladder cancer chromosome region 1), has unknown function. In the present study, we explored function and molecular mechanism of DBCCR1-003 in bladder cancer (BC) development. Methods We evaluated the expression levels of DBCCR1-003 in tissues and cells with western blot and quantitative real-time polymerase chain reaction. Multiple approaches including chromatin immunoprecipitation assay and RNA immunoprecipitation were used to confirm the direct binding of DBCCR1-003 to DNMT1. The recombinant vector overexpressing DBCCR1-003 was constructed. Cell proliferation assay, colony formation assay and flow cytometric analysis were employed to measure the role of DBCCR1-003 in regulation of cell proliferation, cycle and apoptosis. Results Firstly we detected the expression of DBCCR1-003, DBCCR1, DNMT1 (DNA methyltransferase 1) and DNA methylation in the promoter of DBCCR1. We found low expression of DBCCR1-003, same as DBCCR1, while high expression of DNMT1 and hypermethylation of DBCCR1 gene promoter in BC tissues and T24 cells line. Further studies revealed that treatment of DNMT inhibitor, 5-aza-2-deoxycytidine(DAC), or overexpression of DBCCR1-003 led to increased DBCCR1 expression by reversion of promoter hypermethylation and DNMT1 binding to DBCCR1 promoter in T24 cells. Importantly, RNA immunoprecipitation (RIP) showed that DBCCR1-003 physically associates with DNMT1. The binding of them was increased with the inhibition of DBCCR1 promoter methylation, indicating that DBCCR1-003 may bind to DNMT1 and prevent DNMT1-mediated the methylation of DBCCR1. Furthermore, overexpression of DBCCR1-003 resulted in significant inhibition of T24 cells growth through the inducing G0/G1 arrest and apoptosis. Conclusions Taken together, these findings demonstrated that a novel tumor suppressor DBCCR1-003 regulates the expression of DBCCR1 via binding to DNMT1 and preventing DNMT1-mediated the methylation of DBCCR1 in BC. LncRNA DBCCR1-003 may serve as a novel biomarker and therapeutic target for BC in future cancer clinic. Electronic supplementary material The online version of this article (doi:10.1186/s12935-016-0356-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Defeng Qi
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Jinhui Li
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China.,The Affiliated Hospital of School of Medicine of Ningbo University, Zhejiang, 315000 China
| | - Biao Que
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Jialin Su
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China.,The First Affiliated Hospital, Center for Translational Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Mengxi Li
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Chaofeng Zhang
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Mei Yang
- Breast Disease Center, Guangdong Women and Children Hospital of Guangzhou Medical University, Guangzhou, 510010 Guangdong China.,Department of General Surgery, General Hospital of Guangzhou Military Command of PLA, Guangzhou, 510010 Guangdong China
| | - Guoren Zhou
- Department of Medical Oncology, Jiangsu Cancer Hospital, Nanjing, 210009 Jiangsu China
| | - Weidong Ji
- The First Affiliated Hospital, Center for Translational Medicine, Sun Yat-sen University, Guangzhou, 510080 China
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34
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Nasr R, Sleiman F, Awada Z, Zgheib NK. The pharmacoepigenetics of drug metabolism and transport in breast cancer: review of the literature and in silico analysis. Pharmacogenomics 2016; 17:1573-85. [DOI: 10.2217/pgs-2016-0081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The focus of this manuscript is on DNA methylation and miRNA regulation of drug-metabolizing enzymes and drug transporters involved in the disposition of drugs commonly used in breast cancer. We start with a review of the available scant literature and follow with an in silico analysis of the CpG islands and miRNA binding sites of genes of interest. We make the case that there is room for further research to include more genes and miRNAs despite the extensive sharing of miRNA targets by candidate genes of interest. We also stress on the role of peripheral blood as a source of pharmacoepigenetic biomarkers, and point out the lack of toxicoepigenetic studies in breast cancer.
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Affiliation(s)
- Rihab Nasr
- Department of Anatomy, Cell Biology & Physiology, American University of Beirut Faculty of Medicine (AUBFM), Beirut, Lebanon
| | - Fatima Sleiman
- Department of Pharmacology & Toxicology, American University of Beirut Faculty of Medicine (AUBFM), Beirut, Lebanon
| | - Zeinab Awada
- Department of Pharmacology & Toxicology, American University of Beirut Faculty of Medicine (AUBFM), Beirut, Lebanon
| | - Natalie K Zgheib
- Department of Pharmacology & Toxicology, American University of Beirut Faculty of Medicine (AUBFM), Beirut, Lebanon
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35
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Joyce BT, Gao T, Zheng Y, Liu L, Zhang W, Dai Q, Shrubsole MJ, Hibler EA, Cristofanilli M, Zhang H, Yang H, Vokonas P, Cantone L, Schwartz J, Baccarelli A, Hou L. Prospective changes in global DNA methylation and cancer incidence and mortality. Br J Cancer 2016; 115:465-72. [PMID: 27351216 PMCID: PMC4985350 DOI: 10.1038/bjc.2016.205] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/31/2016] [Accepted: 06/07/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Methylation of repetitive elements Alu and LINE-1 in humans is considered a surrogate for global DNA methylation. Previous studies of blood-measured Alu/LINE-1 and cancer risk are inconsistent. METHODS We studied 1259 prospective methylation measurements from blood drawn 1-4 times from 583 participants from 1999 to 2012. We used Cox regression to evaluate time-dependent methylation as a biomarker for cancer risk and mortality, and linear regression to compare mean differences in methylation over time by cancer status and analyse associations between rate of methylation change and cancer. RESULTS Time-dependent LINE-1 methylation was associated with prostate cancer incidence (HR: 1.38, 95% CI: 1.01-1.88) and all-cancer mortality (HR: 1.41, 95% CI: 1.03-1.92). The first measurement of Alu methylation (HR: 1.39, 95% CI: 1.08-1.79) was associated with all-cancer mortality. Participants who ultimately developed cancer had lower mean LINE-1 methylation than cancer-free participants 10+ years pre-diagnosis (P<0.01). Rate of Alu methylation change was associated with all-cancer incidence (HR: 3.62, 95% CI: 1.09-12.10). CONCLUSIONS Our results add longitudinal data on blood Alu and LINE-1 methylation and cancer, and potentially contribute to their use as early-detection biomarkers. Future larger studies are needed and should account for the interval between blood sample collection and cancer diagnosis.
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Affiliation(s)
- Brian T Joyce
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA.,Division of Epidemiology/Biostatistics, School of Public Health, University of Illinois-Chicago, 1603 W. Taylor Street, Chicago, IL 60612, USA
| | - Tao Gao
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA.,Institute for Public Health and Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA
| | - Lei Liu
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA
| | - Wei Zhang
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA
| | - Qi Dai
- Vanderbilt University Medical Center, 2525 West End Avenue, Suite 319, Nashville, TN 37203, USA
| | - Martha J Shrubsole
- Vanderbilt University Medical Center, 2525 West End Avenue, Suite 319, Nashville, TN 37203, USA
| | - Elizabeth A Hibler
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA
| | - Massimo Cristofanilli
- Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, 676 N. St Clair Street, 8th Floor, Chicago, IL 60611, USA
| | - Hu Zhang
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA
| | - Hushan Yang
- Department of Medical Oncology, Division of Population Science, Sidney Kimmel Cancer Center, Thomas Jefferson University, 834 Chestnut Street, Suite 314, Philadelphia, PA 19107, USA
| | - Pantel Vokonas
- VA Normative Aging Study, VA Boston Healthcare System, 150 South Huntington Avenue, Boston, MA 02130, USA.,Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Laura Cantone
- Molecular Epidemiology and Environmental Epigenetics Laboratory, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, San Barnaba 8, Milan 20122, Italy
| | - Joel Schwartz
- Department of Environmental Health, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA
| | - Andrea Baccarelli
- Department of Environmental Health, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Avenue, Olson Pavilion 8350, Chicago, IL 60611, USA
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McCullough LE, Chen J, Cho YH, Khankari NK, Bradshaw PT, White AJ, Garbowski G, Teitelbaum SL, Terry MB, Neugut AI, Hibshoosh H, Santella RM, Gammon MD. DNA methylation modifies the association between obesity and survival after breast cancer diagnosis. Breast Cancer Res Treat 2016; 156:183-94. [PMID: 26945992 DOI: 10.1007/s10549-016-3724-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/16/2016] [Indexed: 01/19/2023]
Abstract
Mechanisms underlying the poor breast cancer prognosis among obese women are unresolved. DNA methylation levels are linked to obesity and to breast cancer survival. We hypothesized that obesity may work in conjunction with the epigenome to alter prognosis. Using a population-based sample of women diagnosed with first primary breast cancer, we examined modification of the obesity-mortality association by DNA methylation. In-person interviews were conducted approximately 3 months after diagnosis. Weight and height were assessed [to estimate body mass index (BMI)], and blood samples collected. Promoter methylation of 13 breast cancer-related genes was assessed in archived tumor by methylation-specific PCR and Methyl Light. Global methylation in white blood cell DNA was assessed by analysis of long interspersed elements-1 (LINE-1) and with the luminometric methylation assay (LUMA). Vital status among 1308 patients (with any methylation biomarker and complete BMI assessment) was determined after approximately 15 years of follow-up (N = 194/441 deaths due to breast cancer-specific/all-cause mortality). We used Cox proportional hazards regression to estimate hazard ratios (HRs) and 95 % confidence intervals (CIs) using two-sided p values of 0.05. Breast cancer-specific mortality was higher among obese (BMI ≥ 30) patients with promoter methylation in APC (HR = 2.47; 95 % CI = 1.43-4.27) and TWIST1 (HR = 4.25; 95 % CI = 1.43-12.70) in breast cancer tissue. Estimates were similar, but less pronounced, for all-cause mortality. Increased all-cause (HR = 1.81; 95 % CI = 1.19-2.74) and breast cancer-specific (HR = 2.61; 95 % CI = 1.45-4.69) mortality was observed among obese patients with the lowest LUMA levels. The poor breast cancer prognosis associated with obesity may depend on methylation profiles, which warrants further investigation.
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Affiliation(s)
- Lauren E McCullough
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Jia Chen
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department Oncological Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yoon Hee Cho
- Department of Environmental Health Sciences, Columbia University, New York, NY, 10032, USA
| | - Nikhil K Khankari
- Division of Epidemiology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Patrick T Bradshaw
- School of Public Health Division of Epidemiology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Alexandra J White
- Epidemiology Branch National Institute of Environmental Health Science, Research Triangle Park, NC, 27709, USA
| | - Gail Garbowski
- Department of Environmental Health Sciences, Columbia University, New York, NY, 10032, USA
| | - Susan L Teitelbaum
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University, New York, NY, 10032, USA
| | - Alfred I Neugut
- Department of Epidemiology, Columbia University, New York, NY, 10032, USA.,Department of Medicine, Columbia University, New York, NY, 10032, USA
| | - Hanina Hibshoosh
- Department of Pathology, Columbia University, New York, NY, 10032, USA
| | - Regina M Santella
- Department of Environmental Health Sciences, Columbia University, New York, NY, 10032, USA
| | - Marilie D Gammon
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Du YF, Lin FY, Long WQ, Luo WP, Yan B, Xu M, Mo XF, Zhang CX. Serum betaine but not choline is inversely associated with breast cancer risk: a case-control study in China. Eur J Nutr 2016; 56:1329-1337. [PMID: 26897124 DOI: 10.1007/s00394-016-1183-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/06/2016] [Indexed: 02/02/2023]
Abstract
PURPOSE Choline and betaine are important for DNA methylation and synthesis, and may affect tumor carcinogenesis. To our knowledge, no previous study has examined the association between serum choline and betaine and breast cancer risk. This study aimed to examine whether serum choline and betaine were inversely associated with breast cancer risk among Chinese women. METHODS This hospital-based case-control study consecutively recruited 510 breast cancer cases and 518 frequency-matched (age and residence) controls, and blood samples were available for 500 cases and 500 controls. Serum choline and betaine were assayed by high-performance liquid chromatography-tandem mass spectrometry. Multiple unconditional logistic regression was used to estimate odds ratios (ORs) and 95 % confidence intervals (CIs). RESULTS An inverse association with breast cancer risk was observed for serum betaine (fourth vs first quartile adjusted OR 0.68, 95 % CI 0.47-0.97) and for the ratio of serum betaine to choline (fourth vs first quartile adjusted OR 0.70, 95 % CI 0.48-1.00), but not for serum choline (fourth vs first quartile adjusted OR 0.80, 95 % CI 0.56-1.15). Serum betaine was inversely associated with breast cancer risk in subjects with below-median dietary folate intake (fourth vs first quartile adjusted OR 0.48, 95 % CI 0.30-0.77). CONCLUSIONS This study suggested that serum betaine but not choline was inversely associated with breast cancer risk. This result needed to be further confirmed by the prospective studies.
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Affiliation(s)
- Yu-Feng Du
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Fang-Yu Lin
- Nursing Department, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Wei-Qing Long
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Wei-Ping Luo
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Bo Yan
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Ming Xu
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Xiong-Fei Mo
- Department of Vascular Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Cai-Xia Zhang
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China.
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Mendoza-Pérez J, Gu J, Herrera LA, Tannir NM, Matin SF, Karam JA, Huang M, Chang DW, Wood CG, Wu X. Genomic DNA Hypomethylation and Risk of Renal Cell Carcinoma: A Case-Control Study. Clin Cancer Res 2015; 22:2074-82. [PMID: 26655847 DOI: 10.1158/1078-0432.ccr-15-0977] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 11/22/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Genomic DNA hypomethylation is a hallmark of most cancer genomes, promoting genomic instability and cell transformation. In the present study, we sought to determine whether global DNA methylation in peripheral blood is associated with risk of renal cell carcinoma (RCC). EXPERIMENTAL DESIGN A retrospective case-control study consisting of 889 RCC cases and an equal number of age, gender, and ethnicity-matched controls was applied. Global DNA methylation was measured as 5-mC% content. Logistic regression was used to estimate odds ratio (OR) and 95% confidence interval (CI) for the association between DNA methylation level and the risk of RCC. RESULTS The median 5-mC% was significantly lower in cases than in healthy controls (P< 0.001). In multivariate logistic regression analysis, individuals in the lowest tertile (T1) of 5-mC% had higher risk of RCC with OR of 1.40 (95% CI, 1.06-1.84), compared with individuals in the highest tertile (T3;Pfor trend= 0.02). When stratified by RCC risk factors, associations between hypomethylation and increased RCC risk appeared to be stronger among males (OR, 1.61;Pfor trend= 0.01), younger age (OR, 1.47;Pfor trend= 0.03), never smokers (OR, 1.55;Pfor trend= 0.02), family history of other cancer (OR, 1.64;Pfor trend= 1.22E-03), and late stage (OR, 2.06,Pfor trend= 4.98E-04). Additionally, we observed significant interaction between gender and 5-mC% in elevating RCC risk (Pfor interaction= 0.03). CONCLUSIONS Our findings suggest an association between global DNA hypomethylation and RCC risk. To establish global DNA hypomethylation as a risk factor for RCC, future prospective studies are warranted. This study may provide further understanding of the etiology of RCC tumorigenesis.
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Affiliation(s)
- Julia Mendoza-Pérez
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Surena F Matin
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jose A Karam
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maosheng Huang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David W Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher G Wood
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Marzese DM, Hoon DS. Emerging technologies for studying DNA methylation for the molecular diagnosis of cancer. Expert Rev Mol Diagn 2015; 15:647-64. [PMID: 25797072 DOI: 10.1586/14737159.2015.1027194] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is an epigenetic mechanism that plays a key role in regulating gene expression and other functions. Although this modification is seen in different sequence contexts, the most frequently detected DNA methylation in mammals involves cytosine-guanine dinucleotides. Pathological alterations in DNA methylation patterns are described in a variety of human diseases, including cancer. Unlike genetic changes, DNA methylation is heavily influenced by subtle modifications in the cellular microenvironment. In all cancers, aberrant DNA methylation is involved in the alteration of a large number of oncological pathways with relevant theranostic utility. Several technologies for DNA methylation mapping have been developed recently and successfully applied in cancer studies. The scope of these technologies varies from assessing a single cytosine-guanine locus to genome-wide distribution of DNA methylation. Here, we review the strengths and weaknesses of these approaches in the context of clinical utility for the molecular diagnosis of human cancers.
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Affiliation(s)
- Diego M Marzese
- Department of Molecular Oncology, Saint John's Health Center, John Wayne Cancer Institute, 2200 Santa Monica Blvd, Santa Monica, CA 90404, USA
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40
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Herman D, Leakey TI, Behrens A, Yao-Borengasser A, Cooney CA, Jousheghany F, Phanavanh B, Siegel ER, Safar AM, Korourian S, Kieber-Emmons T, Monzavi-Karbassi B. CHST11 gene expression and DNA methylation in breast cancer. Int J Oncol 2015; 46:1243-51. [PMID: 25586191 PMCID: PMC4324579 DOI: 10.3892/ijo.2015.2828] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 12/03/2014] [Indexed: 01/09/2023] Open
Abstract
Our previously published data link P-selectin-reactive chondroitin sulfate structures on the surface of breast cancer cells to metastatic behavior of cells. We have shown that a particular sulfation pattern mediated by the expression of carbohydrate (chondroitin 4) sulfotransferase-11 (CHST11) correlates with P-selectin binding and aggressiveness of human breast cancer cell lines. The present study was performed to evaluate the prognostic value of CHST11 expression and determine whether aberrant DNA methylation controls CHST11 expression in breast cancer. Publicly available datasets were used to examine the association of CHST11 expression to aggressiveness and progression of breast cancer. Methylation status was analyzed using bisulfite genomic sequencing. 5-aza-2′-deoxycytidine (5AzadC) was used for DNA demethylation. Reduced representation bisulfite sequencing was performed in the CpG island of CHST11 with a minimum coverage of 10. Quantitative real-time RT-PCR was employed to confirm the expression profile of CHST11 in breast cancer cell lines. Flow cytometry was also used to confirm the expression of the CHST11 product, chondroitin sulfate A (CS-A). The expression of CHST11 was significantly higher in basal-like and Her2-amplified cell lines compared to luminal cell lines. CHST11 was also highly expressed in cancer tissues compared to normal tissues and the expression levels were significantly associated with tumor progression. We observed very low levels of DNA methylation in a CpG island of CHST11 in basal-like cells but very high levels in the same region in luminal cells. Treatment of MCF7 cells, a luminal cell line with very low expression of CHST11, with 5AzadC increased the expression of CHST11 and its immediate product, CS-A, in a dose-dependent manner. These results suggest that CHST11 may play a direct role in progression of breast cancer and that its expression is controlled by DNA methylation. Therefore, in addition to CHST11 mRNA levels, the methylation status of this gene also has potential as a prognostic biomarker.
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Affiliation(s)
- Damir Herman
- Division of Hematology/Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Tatiana I Leakey
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alice Behrens
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Aiwei Yao-Borengasser
- Department of Medical Genetics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Craig A Cooney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Fariba Jousheghany
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Bounleut Phanavanh
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Eric R Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - A Mazin Safar
- Division of Hematology/Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Soheila Korourian
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Thomas Kieber-Emmons
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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41
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Çelik S. Understanding the complexity of antigen retrieval of DNA methylation for immunofluorescence-based measurement and an approach to challenge. J Immunol Methods 2014; 416:1-16. [PMID: 25435341 DOI: 10.1016/j.jim.2014.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 10/31/2014] [Accepted: 11/21/2014] [Indexed: 12/28/2022]
Abstract
Cytosine methylation (5-methylcytosine, 5meC) in the CpG-rich regions of the mammalian genome is an important epigenetic mechanism playing roles in transcription regulation and genomic stability. The abnormalities in DNA methylation can occur in various types of cancer and some genetic diseases. The measurement of DNA methylation is therefore important and there is a range of methodologies used to detect DNA methylation. Many methods based on bisulfite treatment appeared with a lack of specificity after recent discoveries of various modifications of methylated cytosine, however there are new treatments developed to overcome this limitation. Immunofluorescence is currently known to be able to specifically detect DNA methylation as it uses different antibodies against 5meC and its derivatives, but it is a semi-quantitative method. Immunofluorescence protocols commonly include fixation of cells followed by permeabilisation, antigen retrieval, and treatments with antibodies. Establishing the strategy for antigen retrieval of immunofluorescence is important to unmask epitopes (i.e. 5meC) from other proteins, and therefore to access the antigen of interest. There are many approaches used for antigen retrieval induced by acid, enzyme and/or heat. The selection of antigen retrieval method can depend on a variety of such antigen-based or cell-based conditions, since the dynamic structure of DNA and chromatin accounts for the complexity of involved proteins to mask the epitope. This review aims to specifically focus on the complexity of in situ detection of DNA methylation by immunofluorescence-based methods using antigen retrieval with the current understanding of DNA methylation mechanism, and suggests conditions for antigenic retrieval of 5meC epitope.
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Affiliation(s)
- Selcen Çelik
- Human Reproduction and Development Unit, Kolling Institute for Medical Research, Sydney Medical School, University of Sydney, Sydney 2065, Australia.
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Melanoma epigenetics: novel mechanisms, markers, and medicines. J Transl Med 2014; 94:822-38. [PMID: 24978641 PMCID: PMC4479581 DOI: 10.1038/labinvest.2014.87] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/30/2014] [Accepted: 05/08/2014] [Indexed: 02/07/2023] Open
Abstract
The incidence and mortality rates of cutaneous melanoma continue to increase worldwide, despite the deployment of targeted therapies. Recently, there has been rapid growth and development in our understanding of epigenetic mechanisms and their role in cancer pathobiology. Epigenetics--defined as the processes resulting in heritable changes in gene expression beyond those caused by alterations in the DNA sequence--likely contain the information that encodes for such phenotypic variation between individuals with identical genotypes. By altering the structure of chromatin through covalent modification of DNA bases or histone proteins, or by regulating mRNA translation through non-coding RNAs, the epigenome ultimately determines which genes are expressed and which are kept silent. While our understanding of epigenetic mechanisms is growing at a rapid pace, the field of melanoma epigenomics still remains in its infancy. In this Pathology in Focus, we will briefly review the basics of epigenetics to contextualize and critically examine the existing literature using melanoma as a cancer paradigm. Our understanding of how dysregulated DNA methylation and DNA demethylation/hydroxymethylation, histone modification, and non-coding RNAs affect cancer pathogenesis and melanoma virulence, in particular, provides us with an ever-expanding repertoire of potential diagnostic biomarkers, therapeutic targets, and novel pathogenic mechanisms. The evidence reviewed herein indicates the critical role of epigenetic mechanisms in melanoma pathobiology and provides evidence for future targets in the development of next-generation biomarkers and therapeutics.
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Ronen M, Avrahami D, Gerber D. A sensitive microfluidic platform for a high throughput DNA methylation assay. LAB ON A CHIP 2014; 14:2354-2362. [PMID: 24841578 DOI: 10.1039/c4lc00150h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
DNA methylation is an epigenetic modification essential for normal development and maintenance of somatic biological functions. DNA methylation provides heritable, long-term chromatin regulation and the aberrant methylation pattern is associated with complex diseases including cancer. Discovering novel therapeutic targets demands development of high-throughput, sensitive and inexpensive screening platforms for libraries of chemical or biological matter involved in DNA methylation establishment and maintenance. Here, we present a universal, high-throughput, microfluidic-based fluorometric assay for studying DNA methylation in vitro. The enzymatic activity of bacterial HPAII DNA methyltransferase and its kinetic properties are measured using the assay (K(m)(DNA) = 5.8 nM, K(m)(SAM) = 9.8 nM and Kcat = 0.04 s(-1)). Using the same platform, we then demonstrate a two-step approach for high-throughput in vitro identification and characterization of small molecule inhibitors of methylation. The approach is examined using known non-nucleoside inhibitors, SGI-1027 and RG108, for which we measured IC50 of 4.5 μM and 87.5 nM, respectively. The dual role of the microfluidic-based methylation assay both for the quantitative characterization of enzymatic activity and high-throughput screening of non-nucleoside inhibitors coupled with quantitative characterization of the inhibition potential highlights the advantages of our system for epigenetic studies.
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Affiliation(s)
- Maria Ronen
- The Mina & Everard Goodman Faculty of Life Sciences, The Nanotechnology Institute, Bar-Ilan University, Ramat Gan, 5290002, Israel.
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44
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Li K, Li W, Dong X. Association of 677 C>T (rs1801133) and 1298 A>C (rs1801131) polymorphisms in the MTHFR gene and breast cancer susceptibility: a meta-analysis based on 57 individual studies. PLoS One 2014; 9:e71290. [PMID: 24945727 PMCID: PMC4063741 DOI: 10.1371/journal.pone.0071290] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 07/02/2013] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE The 677 C>T and 1298 A>C polymorphisms of methylenetetrahydrofolate reductase (MTHFR) gene have been widely reported and considered to have a significant effect on breast cancer risk, but the results are inconsistent. A meta-analysis based on 57 eligible studies was carried out to clarify the role of MTHFR gene polymorphisms in breast cancer. METHODS AND RESULTS Eligible articles were identified by searching databases including PubMed, Web of Science, EMBASE, CNKI and CBM for the period up to August 2012. Finally, a total of 57 studies were included in this meta-analysis. Crude ORs with 95% CIs were used to assess the association between the MTHFR polymorphisms and breast cancer risk. The pooled ORs were performed with additive model, dominant model and recessive model, respectively. Subgroup analysis was also performed by ethnicity. The statistical heterogeneity across studies was examined with χ2-based Q-test. A meta-analysis was performed using the Stata 12.0 software. Overall, the 677 C allele was significantly associated with breast cancer risk (OR = 0.942, 95%CI = 0.898 to 0.988) when compared with the 677 T allele in the additive model, and the same results were also revealed under other genetic models. Simultaneously, the 1298 A allele was not associated with the breast cancer susceptibility when compared with the 1298 C allele (OR = 0.993, 95%CI = 0.978 to 1.009). Furthermore, analyses under the dominant, recessive and the allele contrast model yielded similar results. CONCLUSIONS The results of this meta-analysis suggest that 677 C>T polymorphism in the MTHFR gene may contribute to breast cancer development. However, the 1298 A>C polymorphism is not significantly associated with increased risks of breast cancer.
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Affiliation(s)
- Kai Li
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, P. R. China
- * E-mail:
| | - Wusheng Li
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, P. R. China
| | - Xi Dong
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, P. R. China
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The nucleolar size is associated to the methylation status of ribosomal DNA in breast carcinomas. BMC Cancer 2014; 14:361. [PMID: 24884608 PMCID: PMC4062283 DOI: 10.1186/1471-2407-14-361] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 04/30/2014] [Indexed: 01/21/2023] Open
Abstract
Background There is a body of evidence that shows a link between tumorigenesis and ribosome biogenesis. The precursor of mature 18S, 28S and 5.8S ribosomal RNAs is transcribed from the ribosomal DNA gene (rDNA), which exists as 300–400 copies in the human diploid genome. Approximately one half of these copies are epigenetically silenced, but the exact role of epigenetic regulation on ribosome biogenesis is not completely understood. In this study we analyzed the methylation profiles of the rDNA promoter and of the 5’ regions of 18S and 28S in breast cancer. Methods We analyzed rDNA methylation in 68 breast cancer tissues of which the normal counterpart was partially available (45/68 samples) using the MassARRAY EpiTYPER assay, a sensitive and quantitative method with single base resolution. Results We found that rDNA locus tended to be hypermethylated in tumor compared to matched normal breast tissues and that the DNA methylation level of several CpG units within the rDNA locus was associated to nuclear grade and to nucleolar size of tumor tissues. In addition we identified a subgroup of samples in which large nucleoli were associated with very limited or absent rDNA hypermethylation in tumor respect to matched normal tissue. Conclusions In conclusion, we suggest that rDNA is an important target of epigenetic regulation in breast tumors and that rDNA methylation level is associated to nucleolar size.
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Global methylation levels in peripheral blood leukocyte DNA by LUMA and breast cancer: a case-control study in Japanese women. Br J Cancer 2014; 110:2765-71. [PMID: 24786600 PMCID: PMC4037832 DOI: 10.1038/bjc.2014.223] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Revised: 04/04/2014] [Accepted: 04/04/2014] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Global hypomethylation has been suggested to cause genomic instability and lead to an increased risk of cancer. We examined the association between the global methylation level of peripheral blood leukocyte DNA and breast cancer among Japanese women. METHODS We conducted a hospital-based case-control study of 384 patients aged 20-74 years with newly diagnosed, histologically confirmed invasive breast cancer, and 384 matched controls from medical checkup examinees in Nagano, Japan. Global methylation levels in leukocyte DNA were measured by LUminometric Methylation Assay. Odds ratios (ORs) and 95% confidence intervals (CIs) for the associations between global hypomethylation and breast cancer were estimated using a logistic regression model. RESULTS Compared with women in the highest tertile of global methylation level, ORs for the second and lowest tertiles were 1.87 (95% CI=1.20-2.91) and 2.86 (95% CI=1.85-4.44), respectively. Global methylation levels were significantly lower in cases than controls, regardless of the hormone receptor status of the cancer (all P values for trend <0.05). INTERPRETATION These findings suggest that the global methylation level of peripheral blood leukocyte DNA is low in patients with breast cancer and may be a potential biomarker for breast cancer risk.
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HAGE (DDX43) is a biomarker for poor prognosis and a predictor of chemotherapy response in breast cancer. Br J Cancer 2014; 110:2450-61. [PMID: 24755885 PMCID: PMC4021517 DOI: 10.1038/bjc.2014.168] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/28/2014] [Accepted: 03/05/2014] [Indexed: 01/10/2023] Open
Abstract
Background: HAGE protein is a known immunogenic cancer-specific antigen. Methods: The biological, prognostic and predictive values of HAGE expression was studied using immunohistochemistry in three cohorts of patients with BC (n=2147): early primary (EP-BC; n=1676); primary oestrogen receptor-negative (PER-BC; n=275) treated with adjuvant anthracycline-combination therapies (Adjuvant-ACT); and primary locally advanced disease (PLA-BC) who received neo-adjuvant anthracycline-combination therapies (Neo-adjuvant-ACT; n=196). The relationship between HAGE expression and the tumour-infiltrating lymphocytes (TILs) in matched prechemotherapy and postchemotherapy samples were investigated. Results: Eight percent of patients with EP-BC exhibited high HAGE expression (HAGE+) and was associated with aggressive clinico-pathological features (Ps<0.01). Furthermore, HAGE+expression was associated with poor prognosis in both univariate and multivariate analysis (Ps<0.001). Patients with HAGE+did not benefit from hormonal therapy in high-risk ER-positive disease. HAGE+and TILs were found to be independent predictors for pathological complete response to neoadjuvant-ACT; P<0.001. A statistically significant loss of HAGE expression following neoadjuvant-ACT was found (P=0.000001), and progression-free survival was worse in those patients who had HAGE+residual disease (P=0.0003). Conclusions: This is the first report to show HAGE to be a potential prognostic marker and a predictor of response to ACT in patients with BC.
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Raykov Z, Ivanov V, Raikova E, Galabov A. Folic Acid Role in Mutagenesis, Carcinogenesis, Prevention and Treatment of Cancer. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2004.10817133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Long XR, He Y, Huang C, Li J. MicroRNA-148a is silenced by hypermethylation and interacts with DNA methyltransferase 1 in hepatocellular carcinogenesis. Int J Oncol 2014; 44:1915-22. [PMID: 24714841 DOI: 10.3892/ijo.2014.2373] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 01/13/2014] [Indexed: 11/05/2022] Open
Abstract
In general, microRNAs, a class of small (~21 nucleotide) non-coding RNAs, negatively regulate the expression of their target genes. Dysregulation of miRNAs is a common feature in human cancers, but this phenomenon has not been studied extensively in hepatocellular carcinoma (HCC). miR‑148a, a member of the miR-148/152 family, has been found to be downregulated in several tumor types and has been suggested to be a tumor suppressor gene; however, its function in HCC remains unclear. Herein, we describe the epigenetic regulation of miR-148a and its impact on HCC cells. We found that, due to the hypermethylation of its CpG island, miR-148a undergoes methylation-mediated silencing in HCC cell lines. Additionally, DNMT1, the DNA methyltransferase that maintains methylation patterns, is aberrantly upregulated in HCC cell lines, and its overexpression is responsible for hypermethylation of the miR-148a promoter. Intriguingly, the expression of DNMT1, which is a target of miR-148a, is inversely correlated with the expression of miR-148a in HCC cells. These results lead us to propose the existence of a negative feedback regulatory loop between miR-148a and DNMT1 in HCC. Importantly, we demonstrate that the overexpression of miR-148a significantly inhibits HCC cell proliferation and cell cycle progression. Our results suggest the existence of a novel miR-148a-DNMT1 regulatory circuit and indicate that miR-148a acts as a tumor suppressor during hepatocellular carcinogenesis. These results may provide a promising alterative strategy for the therapeutic treatment of HCC.
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Affiliation(s)
- Xiao-Ran Long
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, P.R. China
| | - Yong He
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, P.R. China
| | - Cheng Huang
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, P.R. China
| | - Jun Li
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, P.R. China
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O'Donnell AH, Edwards JR, Rollins RA, Vander Kraats ND, Su T, Hibshoosh HH, Bestor TH. Methylation Abnormalities in Mammary Carcinoma: The Methylation Suicide Hypothesis. ACTA ACUST UNITED AC 2014; 5:1311-1324. [PMID: 25960928 PMCID: PMC4423420 DOI: 10.4236/jct.2014.514131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Promoter silencing by ectopic de novo methylation of tumor suppressor genes has been proposed as comparable or equivalent to inactivating mutations as a factor in carcinogenesis. However, this hypotheses had not previously been tested by high resolution, high-coverage whole-genome methylation profiling in primary carcinomas. We have determined the genomic methylation status of a series of primary mammary carcinomas and matched control tissues by examination of more than 2.7 billion CpG dinucleotides. Most of the tumors showed variable losses of DNA methylation from all sequence compartments, but increases in promoter methylation were infrequent, very small in extent, and were observed largely at CpG-poor promoters. De novo methylation at the promoters of proto-oncogenes and tumor suppressor genes occurred at approximately the same frequency. The findings indicate that tumor suppressor silencing by de novo methylation is much less common than currently believed. We put forward a hypothesis under which the demethylation commonly observed in carcinomas is a manifestation of a defensive system that kills incipient cancer cells.
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Affiliation(s)
- Anne H O'Donnell
- Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, NY, USA ; Division of Genetics, Boston Children's Hospital, Boston, MA, USA
| | - John R Edwards
- Center for Pharmacogenomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert A Rollins
- Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, NY, USA ; Pfizer BioTherapeutics Research and Development, Center for Integrative Biology and Biotherapeutics, Pearl River, NY, USA
| | - Nathan D Vander Kraats
- Center for Pharmacogenomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Tao Su
- Department of Pathology, College of Physicians and Surgeons of Columbia University, New York, NY, USA
| | - Hanina H Hibshoosh
- Department of Pathology, College of Physicians and Surgeons of Columbia University, New York, NY, USA
| | - Timothy H Bestor
- Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, NY, USA
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