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Parada H, Sahrai L, Wolff MS, Santella RM, Chen J, Neugut AI, Teitelbaum SL. Urinary parabens and breast cancer risk: Modification by LINE-1 and LUMA global DNA methylation, and associations with breast cancer defined by tumor promoter methylation status. Mol Carcinog 2022; 61:1002-1015. [PMID: 35975911 PMCID: PMC9588525 DOI: 10.1002/mc.23456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/15/2022] [Accepted: 07/30/2022] [Indexed: 01/05/2023]
Abstract
Parabens are a group of alkyl esters of p-hydroxybenzoic acid added to consumer products to prevent the growth of harmful bacteria and molds. Parabens are hypothesized to increase the risk of breast cancer (BC); however, no study has examined the interactions between parabens, global DNA methylation (DNAm), and BC risk. We examined the modifying effects of DNAm on the associations between parabens and BC, and whether parabens were associated with BC defined by tumor promoter methylation status. Participants included 708 cases and 598 controls from the Long Island Breast Cancer Study Project. Methylparaben (MPB), propylparaben, and butylparaben levels were measured in spot urine samples. Global DNAm was measured by analysis of long interspersed elementes-1 (LINE-1) and the luminometric methylation assay (LUMA). The promoter methylation status of 13 genes was measured in tumor samples from 509 cases. We used logistic regression to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for the associations between parabens and BC stratified by LINE-1/LUMA, and between parabens and gene-specific promoter methylation-defined BC. Outcome heterogeneity was evaluated using ratios of ORs (RORs). We assessed the joint effects of the multiple parabens using quantile g-computation. The highest versus lowest tertile of MPB and a one-quantile increase in all parabens were associated with ORs of 1.46 (95% CI = 0.96-2.23) and 1.32 (95% CI = 1.02-1.71), respectively, among women with hypomethylated LINE-1. A one-ln unit increase in MPB was associated with a 25% increase in the odds of hypomethylated (vs. hypermethylated) CCND2 promoter-defined BC (ROR = 1.25, 95% CI = 1.06-1.48), and a one-quantile increase in all parabens was associated with a 55% increase in the odds of hypomethylated (vs. hypermethylated) CCND2 promoter-defined BC (ROR = 1.55, 95% CI = 1.04-2.32). Exposure to parabens may increase the risk of BC among women with hypomethylated global DNAm and may increase the risk of tumors with gene-specific hypomethylated promoter regions.
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Affiliation(s)
- Humberto Parada
- School of Public Health, Division of Epidemiology and BiostatisticsSan Diego State UniversitySan DiegoCaliforniaUSA,UC San Diego Moores Cancer CenterLa JollaCaliforniaUSA
| | - Leili Sahrai
- School of Public Health, Division of Epidemiology and BiostatisticsSan Diego State UniversitySan DiegoCaliforniaUSA
| | - Mary S. Wolff
- Department of Environmental Medicine and Public HealthIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Regina M. Santella
- Department of Environmental Health Sciences, Mailman School of Public HealthColumbia UniversityNew YorkNew YorkUSA
| | - Jia Chen
- UC San Diego Moores Cancer CenterLa JollaCaliforniaUSA
| | - Alfred I. Neugut
- Department of Medicine and Department of Epidemiology, Mailman School of Public Health, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
| | - Susan L. Teitelbaum
- Department of Environmental Medicine and Public HealthIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
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2
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Pham DAT, Le SD, Doan TM, Luu PT, Nguyen UQ, Ho SV, Vo LTT. Standardization of DNA amount for bisulfite conversion for analyzing the methylation status of LINE-1 in lung cancer. PLoS One 2021; 16:e0256254. [PMID: 34403448 PMCID: PMC8370637 DOI: 10.1371/journal.pone.0256254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/04/2021] [Indexed: 11/18/2022] Open
Abstract
Highly methylated Long Interspersed Nucleotide Elements 1 (LINE-1) constitute approximately 20% of the human genome, thus serving as a surrogate marker of global genomic DNA methylation. To date, there is still lacking a consensus about the precise location in LINE-1 promoter and its methylation threshold value, making challenging the use of LINE-1 methylation as a diagnostic, prognostic markers in cancer. This study reports on a technical standardization of bisulfite-based DNA methylation analysis, which ensures the complete bisulfite conversion of repeated LINE-1 sequences, thus allowing accurate LINE-1 methylation value. In addition, the study also indicated the precise location in LINE-1 promoter of which significant variance in methylation level makes LINE-1 methylation as a potential diagnostic biomarker for lung cancer. A serial concentration of 5-50-500 ng of DNA from 275 formalin-fixed paraffin-embedded lung tissues were converted by bisulfite; methylation level of two local regions (at nucleotide position 300–368 as LINE-1.1 and 368–460 as LINE-1.2) in LINE-1 promoter was measured by real time PCR. The use of 5 ng of genomic DNA but no more allowed to detect LINE-1 hypomethylation in lung cancer tissue (14.34% versus 16.69% in non-cancerous lung diseases for LINE-1.1, p < 0.0001, and 30.28% versus 32.35% for LINE-1.2, p < 0.05). Our study thus highlighted the optimal and primordial concentration less than 5 ng of genomic DNA guarantees the complete LINE-1 bisulfite conversion, and significant variance in methylation level of the LINE-1 sequence position from 300 to 368 allowed to discriminate lung cancer from non-cancer samples.
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Affiliation(s)
| | - Son Duc Le
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Trang Mai Doan
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Phuong Thu Luu
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Uyen Quynh Nguyen
- Department of Biology, VNU Institute of Microbiology and Biotechnology, Hanoi, Vietnam
| | - Son Van Ho
- Department of Biochemistry, 175 Hospital, Ho Chi Minh City, Vietnam
| | - Lan Thi Thuong Vo
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
- * E-mail:
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Cardelli M, Doorn RV, Larcher L, Donato MD, Piacenza F, Pierpaoli E, Giacconi R, Malavolta M, Rachakonda S, Gruis NA, Molven A, Andresen PA, Pjanova D, van den Oord JJ, Provinciali M, Nagore E, Kumar R. Association of HERV-K and LINE-1 hypomethylation with reduced disease-free survival in melanoma patients. Epigenomics 2020; 12:1689-1706. [PMID: 33125285 DOI: 10.2217/epi-2020-0127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To evaluate CpG methylation of long interspersed nuclear elements 1 (LINE-1) and human endogenous retrovirus K (HERV-K) retroelements as potential prognostic biomarkers in cutaneous melanoma. Materials & methods: Methylation of HERV-K and LINE-1 retroelements was assessed in resected melanoma tissues from 82 patients ranging in age from 14 to 88 years. In addition, nevi from eight patients were included for comparison with nonmalignant melanocytic lesions. Results: Methylation levels were lower in melanomas than in nevi. HERV-K and LINE-1 methylation were decreased in melanoma patients with clinical parameters associated with adverse prognosis, while they were independent of age and gender. Hypomethylation of HERV-K (but not LINE-1) was an independent predictor of reduced disease-free survival. Conclusion: HERV-K hypomethylation can be a potential independent biomarker of melanoma recurrence.
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Affiliation(s)
- Maurizio Cardelli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, 2300RC Leiden, The Netherlands
| | - Lares Larcher
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Michela Di Donato
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Elisa Pierpaoli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Sivaramakrishna Rachakonda
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany.,Division of Functional Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Nelleke A Gruis
- Department of Dermatology, Leiden University Medical Center, 2300RC Leiden, The Netherlands
| | - Anders Molven
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, N-5020 Bergen, Norway.,Department of Pathology, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Per Arne Andresen
- Department of Pathology, Oslo University Hospital, Rikshospitalet, 0424 Oslo, Norway
| | - Dace Pjanova
- Latvian Biomedical Research & Study Centre, LV-1067 Riga, Latvia
| | | | - Mauro Provinciali
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncología, 46009 València, Spain
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany.,Division of Functional Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
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4
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Kringel D, Kaunisto MA, Kalso E, Lötsch J. Machine-learned analysis of global and glial/opioid intersection-related DNA methylation in patients with persistent pain after breast cancer surgery. Clin Epigenetics 2019; 11:167. [PMID: 31775878 PMCID: PMC6881976 DOI: 10.1186/s13148-019-0772-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/23/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Glial cells in the central nervous system play a key role in neuroinflammation and subsequent central sensitization to pain. They are therefore involved in the development of persistent pain. One of the main sites of interaction of the immune system with persistent pain has been identified as neuro-immune crosstalk at the glial-opioid interface. The present study examined a potential association between the DNA methylation of two key players of glial/opioid intersection and persistent postoperative pain. METHODS In a cohort of 140 women who had undergone breast cancer surgery, and were assigned based on a 3-year follow-up to either a persistent or non-persistent pain phenotype, the role of epigenetic regulation of key players in the glial-opioid interface was assessed. The methylation of genes coding for the Toll-like receptor 4 (TLR4) as a major mediator of glial contributions to persistent pain or for the μ-opioid receptor (OPRM1) was analyzed and its association with the pain phenotype was compared with that conferred by global genome-wide DNA methylation assessed via quantification of the methylation in the retrotransposon LINE1. RESULTS Training of machine learning algorithms indicated that the global DNA methylation provided a similar diagnostic accuracy for persistent pain as previously established non-genetic predictors. However, the diagnosis can be based on a single DNA based marker. By contrast, the methylation of TLR4 or OPRM1 genes could not contribute further to the allocation of the patients to the pain-related phenotype groups. CONCLUSIONS While clearly supporting a predictive utility of epigenetic testing, the present analysis cannot provide support for specific epigenetic modulation of persistent postoperative pain via methylation of two key genes of the glial-opioid interface.
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Affiliation(s)
- Dario Kringel
- Institute of Clinical Pharmacology, Goethe-University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Mari A Kaunisto
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Eija Kalso
- Division of Pain Medicine, Department of Anesthesiology, Intensive Care and Pain Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe-University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- Fraunhofer Institute of Molecular Biology and Applied Ecology-Project Group Translational Medicine and Pharmacology (IME-TMP), Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
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Soler-Botija C, Gálvez-Montón C, Bayés-Genís A. Epigenetic Biomarkers in Cardiovascular Diseases. Front Genet 2019; 10:950. [PMID: 31649728 PMCID: PMC6795132 DOI: 10.3389/fgene.2019.00950] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/05/2019] [Indexed: 12/16/2022] Open
Abstract
Cardiovascular diseases are the number one cause of death worldwide and greatly impact quality of life and medical costs. Enormous effort has been made in research to obtain new tools for efficient and quick diagnosis and predicting the prognosis of these diseases. Discoveries of epigenetic mechanisms have related several pathologies, including cardiovascular diseases, to epigenetic dysregulation. This has implications on disease progression and is the basis for new preventive strategies. Advances in methodology and big data analysis have identified novel mechanisms and targets involved in numerous diseases, allowing more individualized epigenetic maps for personalized diagnosis and treatment. This paves the way for what is called pharmacoepigenetics, which predicts the drug response and develops a tailored therapy based on differences in the epigenetic basis of each patient. Similarly, epigenetic biomarkers have emerged as a promising instrument for the consistent diagnosis and prognosis of cardiovascular diseases. Their good accessibility and feasible methods of detection make them suitable for use in clinical practice. However, multicenter studies with a large sample population are required to determine with certainty which epigenetic biomarkers are reliable for clinical routine. Therefore, this review focuses on current discoveries regarding epigenetic biomarkers and its controversy aiming to improve the diagnosis, prognosis, and therapy in cardiovascular patients.
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Affiliation(s)
- Carolina Soler-Botija
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Carolina Gálvez-Montón
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Antoni Bayés-Genís
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain.,Cardiology Service, HUGTiP, Badalona, Spain.,Department of Medicine, Barcelona Autonomous University (UAB), Badalona, Spain
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6
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Deng Q, Huang W, Peng C, Gao J, Li Z, Qiu X, Yang N, Yuan B, Zheng F. Genomic 5-mC contents in peripheral blood leukocytes were independent protective factors for coronary artery disease with a specific profile in different leukocyte subtypes. Clin Epigenetics 2018; 10:9. [PMID: 29410709 PMCID: PMC5782379 DOI: 10.1186/s13148-018-0443-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/09/2018] [Indexed: 12/13/2022] Open
Abstract
Background Alterations in DNA methylation are demonstrated in atherosclerosis pathogenesis. However, changing rules of global DNA methylation and hydroxymethylation in peripheral blood leukocytes (PBLs) and different blood cell subtypes of coronary artery disease (CAD) patients are still inconclusive, and much less is known about mechanisms underlying. Results We recruited 265 CAD patients and 270 healthy controls with genomic DNA from PBLs, of which 50 patients and 50 controls were randomly chosen with DNA from isolated neutrophils, lymphocytes and monocytes, and RNA from PBLs. Genomic 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) contents were quantified by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) assay. Genomic 5-mC contents were negatively associated with the serum total cholesterol (TC) level (P = 0.010), age (P = 0.016), and PBL classifications (P = 0.023), explaining 6.8% individual variation in controls. Furthermore, genomic 5-mC contents were inversely associated with an increased risk of CAD (odds ratio (OR) = 0.325, 95% confidence interval (CI) = 0.237~0.445, P = 2.62 × 10− 12), independent of PBL counts and classifications, age, sex, histories of hyperlipidemia, hypertension, and diabetes. Within-individual analysis showed a general 5-mC decrease in PBL subtypes, but significant difference was found in monocytes only (P = 0.001), accompanied by increased 5-hmC (P = 3.212 × 10− 4). In addition, coincident to the reduced DNMT1 expression in patients’ PBLs, the expression level of DNMT1 was significantly lower (P = 0.022) in oxidized low-density lipoprotein (ox-LDL) stimulated THP-1-derived foam cells compared to THP-1 monocytes, with decreased genomic 5-mdC content (P = 0.038). Conclusions Global hypomethylation of blood cells defined dominantly by the monocyte DNA hypomethylation is independently associated with the risk of CAD in Chinese Han population. The importance of monocytes in atherosclerosis pathophysiology may demonstrate via an epigenetic pathway, but prospective studies are still needed to test the causality. Electronic supplementary material The online version of this article (10.1186/s13148-018-0443-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qianyun Deng
- 1Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071 China
| | - Wei Huang
- 2Department of Chemistry, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Wuhan University, Wuhan, 430071 China
| | - Chunyan Peng
- 1Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071 China.,3Department of Laboratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000 China
| | - Jiajia Gao
- 1Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071 China
| | - Zuhua Li
- 1Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071 China
| | - Xueping Qiu
- 1Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071 China
| | - Na Yang
- 1Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071 China
| | - Bifeng Yuan
- 1Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071 China.,2Department of Chemistry, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Wuhan University, Wuhan, 430071 China
| | - Fang Zheng
- 1Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071 China
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7
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Khan MFJ, Little J, Mossey PA, Steegers-Theunissen RPM, Autelitano L, Lombardo I, Andreasi RB, Rubini M. Evaluating LINE-1 methylation in cleft lip tissues and its association with early pregnancy exposures. Epigenomics 2018; 10:105-113. [DOI: 10.2217/epi-2017-0081] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Aim: To pilot investigation of methylation of long interspersed nucleotide element-1 in lip tissues from infants with nonsyndromic cleft lip, and its association with maternal periconceptional exposures. Methods: The lateral and medial sides of the cleft lips of 23 affected infants were analyzed for long interspersed nucleotide element-1 methylation by bisulfite conversion and pyrosequencing. Results: The medial side showed 1.8% higher methylation compared with the lateral side; p = 0.031, particularly in male infants (2.7% difference; p = 0.011) or when the mothers did not take folic acid during periconceptional period (2.4% difference; p = 0.011). These results were not statistically significant when Bonferroni adjustment was used. Conclusion: The observed differences in DNA methylation, although nonsignificant after correction for multiple comparisons, suggest that differential regulation of the two sides may impact lip fusion and warrant larger-scale replication.
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Affiliation(s)
- Mohammad Faisal J Khan
- Department of Biomedical & Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology & Genetics, University of Ferrara, Ferrara, Italy
| | - Julian Little
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Peter A Mossey
- Craniofacial Development at the WHO-collaborating Centre for Oral & Craniofacial Research, Dental Hospital & School, University of Dundee, Dundee, Scotland
| | - Régine PM Steegers-Theunissen
- Department of Obstetrics & Gynaecology, Department of Pediatrics, Division Neonatology Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Luca Autelitano
- Department of Cranio-Maxillo-Facial Surgery, Regional Centre for Orofacial Clefts & Craniofacial Anomalies, San Paolo Hospital, University of Milan, Milan, Italy
| | - Ilenia Lombardo
- Department of Biomedical & Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology & Genetics, University of Ferrara, Ferrara, Italy
| | - Rita Bassi Andreasi
- Department of Biomedical & Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology & Genetics, University of Ferrara, Ferrara, Italy
| | - Michele Rubini
- Department of Biomedical & Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology & Genetics, University of Ferrara, Ferrara, Italy
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Ghosh J, Coutifaris C, Sapienza C, Mainigi M. Global DNA methylation levels are altered by modifiable clinical manipulations in assisted reproductive technologies. Clin Epigenetics 2017; 9:14. [PMID: 28191261 PMCID: PMC5295214 DOI: 10.1186/s13148-017-0318-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 01/25/2017] [Indexed: 01/16/2023] Open
Abstract
Background We analyzed placental DNA methylation levels at repeated sequences (LINE1 elements) and all CCGG sites (the LUMA assay) to study the effect of modifiable clinical or laboratory procedures involved in in vitro fertilization. We included four potential modifiable factors: oxygen tension during embryo culture, fresh embryo transfer vs frozen embryo transfer, intracytoplasmic sperm injection (ICSI) vs conventional insemination or day 3 embryo transfer vs day 5 embryo transfer. Results Global methylation levels differed between placentas from natural conceptions compared to placentas conceived by IVF. Placentas from embryos cultured at 20% oxygen showed significant differences in LINE1 methylation compared to in vivo conceptions, while those from embryos cultured at 5% oxygen, did not have significant differences. In addition, placentas from fresh embryo transfer had significantly different LINE1 methylation compared to placentas from in vivo conceptions, while embryos resulting from frozen embryos were not significantly different from controls. On sex-stratified analysis, only males had significant methylation differences at LINE1 elements stratified for the modifiable factors. As expected, LINE1 methylation was significantly different between males and females in the control population. However, we did not observe sex-specific differences in the IVF group. We validated this sex-specific observation in an additional cohort and in opposite sex IVF twins. Conclusion We show that two clinically modifiable factors (embryo culture in 5 vs 20% oxygen tension and fresh vs frozen embryo transfer) are associated with global placental methylation differences. Interestingly, males appear more vulnerable to such treatment-related global changes in DNA methylation than do females. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0318-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jayashri Ghosh
- Center for Research on Reproduction and Women's Health, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 USA
| | - Christos Coutifaris
- Center for Research on Reproduction and Women's Health, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 USA.,Department of Obstetrics & Gynecology, University of Pennsylvania School of Medicine, 3701 Market Street, 8th Floor, Philadelphia, PA 19104 USA
| | - Carmen Sapienza
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140 USA.,Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140 USA
| | - Monica Mainigi
- Center for Research on Reproduction and Women's Health, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 USA.,Department of Obstetrics & Gynecology, University of Pennsylvania School of Medicine, 3701 Market Street, 8th Floor, Philadelphia, PA 19104 USA
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9
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Crary-Dooley FK, Tam ME, Dunaway KW, Hertz-Picciotto I, Schmidt RJ, LaSalle JM. A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies. Epigenetics 2017; 12:206-214. [PMID: 28055307 PMCID: PMC5406214 DOI: 10.1080/15592294.2016.1276680] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
DNA methylation is an epigenetic mark at the interface of genetic and environmental factors relevant to human disease. Quantitative assessments of global DNA methylation levels have therefore become important tools in epidemiology research, particularly for understanding effects of environmental exposures in complex diseases. Among the available methods of quantitative DNA methylation measurements, bisulfite sequencing is considered the gold standard, but whole-genome bisulfite sequencing (WGBS) has previously been considered too costly for epidemiology studies with high sample numbers. Pyrosequencing of repetitive sequences within bisulfite-treated DNA has been routinely used as a surrogate for global DNA methylation, but a comparison of pyrosequencing to WGBS for accuracy and reproducibility of methylation levels has not been performed. This study compared the global methylation levels measured from uniquely mappable (non-repetitive) WGBS sequences to pyrosequencing assays of several repeat sequences and repeat assay-matched WGBS data and determined uniquely mappable WGBS data to be the most reproducible and accurate measurement of global DNA methylation levels. We determined sources of variation in repetitive pyrosequencing assays to be PCR amplification bias, PCR primer selection bias in methylation levels of targeted sequences, and inherent variability in methylation levels of repeat sequences. Low-coverage, uniquely mappable WGBS showed the strongest correlation between replicates of all assays. By using multiplexing by indexed bar codes, the cost of WGBS can be lowered significantly to improve the accuracy of global DNA methylation assessments for human studies.
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Affiliation(s)
- Florence K Crary-Dooley
- a Department of Medical Microbiology and Immunology , Genome Center , University of California , Davis , CA , USA
| | - Mitchell E Tam
- a Department of Medical Microbiology and Immunology , Genome Center , University of California , Davis , CA , USA
| | - Keith W Dunaway
- a Department of Medical Microbiology and Immunology , Genome Center , University of California , Davis , CA , USA
| | - Irva Hertz-Picciotto
- b Department of Public Health Sciences , University of California , Davis , CA , USA.,c MIND Institute , University of California , Davis , CA , USA
| | - Rebecca J Schmidt
- b Department of Public Health Sciences , University of California , Davis , CA , USA.,c MIND Institute , University of California , Davis , CA , USA
| | - Janine M LaSalle
- a Department of Medical Microbiology and Immunology , Genome Center , University of California , Davis , CA , USA.,c MIND Institute , University of California , Davis , CA , USA
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10
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Shiratori H, Feinweber C, Knothe C, Lötsch J, Thomas D, Geisslinger G, Parnham MJ, Resch E. High-Throughput Analysis of Global DNA Methylation Using Methyl-Sensitive Digestion. PLoS One 2016; 11:e0163184. [PMID: 27749902 PMCID: PMC5066982 DOI: 10.1371/journal.pone.0163184] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 09/02/2016] [Indexed: 11/26/2022] Open
Abstract
DNA methylation is a major regulatory process of gene transcription, and aberrant DNA methylation is associated with various diseases including cancer. Many compounds have been reported to modify DNA methylation states. Despite increasing interest in the clinical application of drugs with epigenetic effects, and the use of diagnostic markers for genome-wide hypomethylation in cancer, large-scale screening systems to measure the effects of drugs on DNA methylation are limited. In this study, we improved the previously established fluorescence polarization-based global DNA methylation assay so that it is more suitable for application to human genomic DNA. Our methyl-sensitive fluorescence polarization (MSFP) assay was highly repeatable (inter-assay coefficient of variation = 1.5%) and accurate (r2 = 0.99). According to signal linearity, only 50–80 ng human genomic DNA per reaction was necessary for the 384-well format. MSFP is a simple, rapid approach as all biochemical reactions and final detection can be performed in one well in a 384-well plate without purification steps in less than 3.5 hours. Furthermore, we demonstrated a significant correlation between MSFP and the LINE-1 pyrosequencing assay, a widely used global DNA methylation assay. MSFP can be applied for the pre-screening of compounds that influence global DNA methylation states and also for the diagnosis of certain types of cancer.
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Affiliation(s)
- Hiromi Shiratori
- Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Frankfurt am Main, Germany
- * E-mail:
| | - Carmen Feinweber
- Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Frankfurt am Main, Germany
| | - Claudia Knothe
- Institute of Clinical Pharmacology, Goethe - University, Frankfurt am Main, Germany
| | - Jörn Lötsch
- Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Frankfurt am Main, Germany
- Institute of Clinical Pharmacology, Goethe - University, Frankfurt am Main, Germany
| | - Dominique Thomas
- Institute of Clinical Pharmacology, Goethe - University, Frankfurt am Main, Germany
| | - Gerd Geisslinger
- Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Frankfurt am Main, Germany
- Institute of Clinical Pharmacology, Goethe - University, Frankfurt am Main, Germany
| | - Michael J. Parnham
- Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Frankfurt am Main, Germany
| | - Eduard Resch
- Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Frankfurt am Main, Germany
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