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Mouat JS, Krigbaum NY, Hakam S, Thrall E, Mellis J, Yasui DH, Cirillo PM, Ludena Y, Schmidt RJ, La Merrill MA, Hertz-Picciotto I, Cohn BA, LaSalle JM. Females with autism spectrum disorders show stronger DNA methylation signatures than males in perinatal tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603098. [PMID: 39026708 PMCID: PMC11257592 DOI: 10.1101/2024.07.11.603098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Autism spectrum disorder (ASD) comprises a group of neurodevelopmental conditions currently diagnosed by behavioral assessment in childhood, with reported underdiagnosis in females. Though diagnosis in early life is linked to improved outcomes, we currently lack objective screening tools for newborns. To address this gap, we sought to identify a sex-specific DNA methylation signature for ASD using perinatal tissues that reflect dysregulation in the brain. DNA methylation was assayed from ASD and typically developing (TD) newborn blood, umbilical cord blood, placenta, and post-mortem cortex samples using whole genome bisulfite sequencing (WGBS) in a total of 511 samples. We found that methylation levels of differentially methylated regions (DMRs) differentiated samples by ASD diagnosis in females more than males across the perinatal tissues. We tested three theories for ASD sex differences in newborn blood, finding epigenetic support for an X chromosome-related female protective effect, as well as a high replication rate of DMRs (48.1%) in females across two independent cohorts. In our pan-tissue analysis, three genes (X-linked BCOR, GALNT9, OPCML) mapped to ASD DMRs replicated in all four female tissues. ASD DMRs from all tissues were enriched for neuro-related processes (females) and SFARI ASD-risk genes (females and males). Overall, we found a highly replicated methylation signature of ASD in females across perinatal tissues that reflected dysregulation in the brain and involvement of X chromosome epigenetics. This comparative study of perinatal tissues shows the promise of newborn blood DNA methylation biomarkers for early detection of females at risk for ASD and emphasizes the importance of sex-stratification in ASD studies.
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Affiliation(s)
- Julia S Mouat
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Nickilou Y Krigbaum
- Child Health and Development Studies, Public Health Institute, Berkeley, CA USA
| | - Sophia Hakam
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Emily Thrall
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Julia Mellis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Piera M Cirillo
- Child Health and Development Studies, Public Health Institute, Berkeley, CA USA
| | - Yunin Ludena
- MIND Institute, University of California, Davis, CA USA
- Department of Public Health Sciences, University of California, Davis, CA USA
| | - Rebecca J Schmidt
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
- Department of Public Health Sciences, University of California, Davis, CA USA
| | - Michele A La Merrill
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- Department of Environmental Toxicology, University of California, Davis, CA USA
- Environmental Health Sciences Center, University of California, Davis, CA USA
| | - Irva Hertz-Picciotto
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
- Department of Public Health Sciences, University of California, Davis, CA USA
- Environmental Health Sciences Center, University of California, Davis, CA USA
| | - Barbara A Cohn
- Child Health and Development Studies, Public Health Institute, Berkeley, CA USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
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Canning J, Strawbridge RJ, Miedzybrodzka Z, Marioni RE, Melbye M, Porteous DJ, Hurles ME, Sattar N, Sudlow CLM, Collins R, Padmanabhan S, Pell JP. Methods applied to neonatal dried blood spot samples for secondary research purposes: a scoping review. Crit Rev Clin Lab Sci 2024:1-24. [PMID: 38855982 DOI: 10.1080/10408363.2024.2360996] [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: 01/29/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
This scoping review aimed to synthesize the analytical techniques used and methodological limitations encountered when undertaking secondary research using residual neonatal dried blood spot (DBS) samples. Studies that used residual neonatal DBS samples for secondary research (i.e. research not related to newborn screening for inherited genetic and metabolic disorders) were identified from six electronic databases: Cochrane Library, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Embase, Medline, PubMed and Scopus. Inclusion was restricted to studies published from 1973 and written in or translated into English that reported the storage, extraction and testing of neonatal DBS samples. Sixty-seven studies were eligible for inclusion. Included studies were predominantly methodological in nature and measured various analytes, including nucleic acids, proteins, metabolites, environmental pollutants, markers of prenatal substance use and medications. Neonatal DBS samples were stored over a range of temperatures (ambient temperature, cold storage or frozen) and durations (two weeks to 40.5 years), both of which impacted the recovery of some analytes, particularly amino acids, antibodies and environmental pollutants. The size of DBS sample used and potential contamination were also cited as methodological limitations. Residual neonatal DBS samples retained by newborn screening programs are a promising resource for secondary research purposes, with many studies reporting the successful measurement of analytes even from neonatal DBS samples stored for long periods of time in suboptimal temperatures and conditions.
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Affiliation(s)
- Jordan Canning
- School of Health & Wellbeing, University of Glasgow, Glasgow, UK
| | - Rona J Strawbridge
- School of Health & Wellbeing, University of Glasgow, Glasgow, UK
- Division of Cardiovascular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Zosia Miedzybrodzka
- Department of Medical Genetics, Ashgrove House, NHS Grampian, Aberdeen, UK
- Medical Genetics Group, School of Medicine, Medical Sciences, Nutrition and Dentistry, University of Aberdeen, Aberdeen, UK
| | - Riccardo E Marioni
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Mads Melbye
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - David J Porteous
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Naveed Sattar
- School of Cardiovascular & Metabolic Health, University of Glasgow, Glasgow, UK
| | - Cathie L M Sudlow
- Usher Institute, University of Edinburgh, Edinburgh, UK
- Health Data Research UK, London, UK
| | - Rory Collins
- Clinical Trial Service Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Sandosh Padmanabhan
- School of Cardiovascular & Metabolic Health, University of Glasgow, Glasgow, UK
| | - Jill P Pell
- School of Health & Wellbeing, University of Glasgow, Glasgow, UK
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3
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Lee SM, Loo C, Prasasya R, Bartolomei M, Kohli R, Zhou W. Low-input and single-cell methods for Infinium DNA methylation BeadChips. Nucleic Acids Res 2024; 52:e38. [PMID: 38407446 PMCID: PMC11040145 DOI: 10.1093/nar/gkae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
The Infinium BeadChip is the most widely used DNA methylome assay technology for population-scale epigenome profiling. However, the standard workflow requires over 200 ng of input DNA, hindering its application to small cell-number samples, such as primordial germ cells. We developed experimental and analysis workflows to extend this technology to suboptimal input DNA conditions, including ultra-low input down to single cells. DNA preamplification significantly enhanced detection rates to over 50% in five-cell samples and ∼25% in single cells. Enzymatic conversion also substantially improved data quality. Computationally, we developed a method to model the background signal's influence on the DNA methylation level readings. The modified detection P-value calculation achieved higher sensitivities for low-input datasets and was validated in over 100 000 public diverse methylome profiles. We employed the optimized workflow to query the demethylation dynamics in mouse primordial germ cells available at low cell numbers. Our data revealed nuanced chromatin states, sex disparities, and the role of DNA methylation in transposable element regulation during germ cell development. Collectively, we present comprehensive experimental and computational solutions to extend this widely used methylation assay technology to applications with limited DNA.
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Affiliation(s)
- Sol Moe Lee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA 19104, USA
| | - Christian E Loo
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rexxi D Prasasya
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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4
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Lee SM, Loo CE, Prasasya RD, Bartolomei MS, Kohli RM, Zhou W. Low-input and single-cell methods for Infinium DNA methylation BeadChips. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558252. [PMID: 37786695 PMCID: PMC10541608 DOI: 10.1101/2023.09.18.558252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The Infinium BeadChip is the most widely used DNA methylome assay technology for population-scale epigenome profiling. However, the standard workflow requires over 200 ng of input DNA, hindering its application to small cell-number samples, such as primordial germ cells. We developed experimental and analysis workflows to extend this technology to suboptimal input DNA conditions, including ultra-low input down to single cells. DNA preamplification significantly enhanced detection rates to over 50% in five-cell samples and ∼25% in single cells. Enzymatic conversion also substantially improved data quality. Computationally, we developed a method to model the background signal's influence on the DNA methylation level readings. The modified detection p -values calculation achieved higher sensitivities for low-input datasets and was validated in over 100,000 public datasets with diverse methylation profiles. We employed the optimized workflow to query the demethylation dynamics in mouse primordial germ cells available at low cell numbers. Our data revealed nuanced chromatin states, sex disparities, and the role of DNA methylation in transposable element regulation during germ cell development. Collectively, we present comprehensive experimental and computational solutions to extend this widely used methylation assay technology to applications with limited DNA.
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Sasaki A, Murphy KE, Briollais L, McGowan PO, Matthews SG. DNA methylation profiles in the blood of newborn term infants born to mothers with obesity. PLoS One 2022; 17:e0267946. [PMID: 35500004 PMCID: PMC9060365 DOI: 10.1371/journal.pone.0267946] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/19/2022] [Indexed: 01/03/2023] Open
Abstract
Maternal obesity is an important risk factor for childhood obesity and influences the prevalence of metabolic diseases in offspring. As childhood obesity is influenced by postnatal factors, it is critical to determine whether children born to women with obesity during pregnancy show alterations that are detectable at birth. Epigenetic mechanisms such as DNA methylation modifications have been proposed to mediate prenatal programming. We investigated DNA methylation signatures in male and female infants from mothers with a normal Body Mass Index (BMI 18.5-24.9 kg/m2) compared to mothers with obesity (BMI≥30 kg/m2). BMI was measured during the first prenatal visit from women recruited into the Ontario Birth Study (OBS) at Mount Sinai Hospital in Toronto, ON, Canada. DNA was extracted from neonatal dried blood spots collected from heel pricks obtained 24 hours after birth at term (total n = 40) from women with a normal BMI and women with obesity matched for parity, age, and neonatal sex. Reduced representation bisulfite sequencing was used to identify genomic loci associated with differentially methylated regions (DMRs) in CpG-dense regions most likely to influence gene regulation. DMRs were predominantly localized to intergenic regions and gene bodies, with only 9% of DMRs localized to promoter regions. Genes associated with DMRs were compared to those from a large publicly available cohort study, the Avon Longitudinal Study of Parents and Children (ALSPAC; total n = 859). Hypergeometric tests revealed a significant overlap in genes associated with DMRs in the OBS and ALSPAC cohorts. PTPRN2, a gene involved in insulin secretion, and MAD1L1, which plays a role in the cell cycle and tumor suppression, contained DMRs in males and females in both cohorts. In males, KEGG pathway analysis revealed significant overrepresentation of genes involved in endocytosis and pathways in cancer, including IGF1R, which was previously shown to respond to diet-induced metabolic stress in animal models and in lymphocytes in the context of childhood obesity. These preliminary findings are consistent with Developmental Origins of Health and Disease paradigm, which posits that adverse prenatal exposures set developmental health trajectories.
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Affiliation(s)
- Aya Sasaki
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Kellie E. Murphy
- Department of Obstetrics & Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Laurent Briollais
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Patrick O. McGowan
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Psychology, University of Toronto, Toronto, Ontario, Canada
- Departments of Biological Sciences and Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Stephen G. Matthews
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Obstetrics & Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
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Veldman A, Kiewiet MBG, Heiner-Fokkema MR, Nelen MR, Sinke RJ, Sikkema-Raddatz B, Voorhoeve E, Westra D, Dollé MET, Schielen PCJI, van Spronsen FJ. Towards Next-Generation Sequencing (NGS)-Based Newborn Screening: A Technical Study to Prepare for the Challenges Ahead. Int J Neonatal Screen 2022; 8:ijns8010017. [PMID: 35323196 PMCID: PMC8949100 DOI: 10.3390/ijns8010017] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/28/2022] [Accepted: 02/08/2022] [Indexed: 01/27/2023] Open
Abstract
Newborn screening (NBS) aims to identify neonates with severe conditions for whom immediate treatment is required. Currently, a biochemistry-first approach is used to identify these disorders, which are predominantly inherited meta1bolic disorders (IMD). Next-generation sequencing (NGS) is expected to have some advantages over the current approach, for example the ability to detect IMDs that meet all screening criteria but lack an identifiable biochemical footprint. We have now designed a technical study to explore the use of NGS techniques as a first-tier approach in NBS. Here, we describe the aim and set-up of the NGS-first for the NBS (NGSf4NBS) project, which will proceed in three steps. In Step 1, we will identify IMDs eligible for NGS-first testing, based on treatability. In Step 2, we will investigate the feasibility, limitations and comparability of different technical NGS approaches and analysis workflows for NBS, eventually aiming to develop a rapid NGS-based workflow. Finally, in Step 3, we will prepare for the incorporation of this workflow into the existing Dutch NBS program and propose a protocol for referral of a child after a positive NGS test result. The results of this study will be the basis for an additional analytical route within NBS that will be further studied for its applicability within the NBS program, e.g., regarding the ethical, legal, financial and social implications.
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Affiliation(s)
- Abigail Veldman
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Correspondence: (A.V.); (M.B.G.K.)
| | - Mensiena B. G. Kiewiet
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (R.J.S.); (B.S.-R.)
- Correspondence: (A.V.); (M.B.G.K.)
| | - Margaretha Rebecca Heiner-Fokkema
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Marcel R. Nelen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (M.R.N.); (D.W.)
| | - Richard J. Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (R.J.S.); (B.S.-R.)
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (R.J.S.); (B.S.-R.)
| | - Els Voorhoeve
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands; (E.V.); (M.E.T.D.)
| | - Dineke Westra
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (M.R.N.); (D.W.)
| | - Martijn E. T. Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands; (E.V.); (M.E.T.D.)
| | - Peter C. J. I. Schielen
- Centre for Population Screening, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands;
| | - Francjan J. van Spronsen
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
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Tost J. Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:395-469. [DOI: 10.1007/978-3-031-11454-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Awada Z, Bouaoun L, Nasr R, Tfayli A, Cuenin C, Akika R, Boustany RM, Makoukji J, Tamim H, Zgheib NK, Ghantous A. LINE-1 methylation mediates the inverse association between body mass index and breast cancer risk: A pilot study in the Lebanese population. ENVIRONMENTAL RESEARCH 2021; 197:111094. [PMID: 33839117 DOI: 10.1016/j.envres.2021.111094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/28/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Lebanon is among the top countries worldwide in combined incidence and mortality of breast cancer, which raises concern about risk factors peculiar to this country. The underlying molecular mechanisms of breast cancer require elucidation, particularly epigenetics, which is recognized as a molecular sensor to environmental exposures. PURPOSE We aim to explore whether DNA methylation levels of AHRR (marker of cigarette smoking), SLC1A5 and TXLNA (markers of alcohol consumption), and LINE-1 (a genome-wide repetitive retrotransposon) can act as molecular mediators underlying putative associations between breast cancer risk and pertinent extrinsic (tobacco smoking and alcohol consumption) and intrinsic factors [age and body mass index (BMI)]. METHODS This is a cross-sectional pilot study which includes breast cancer cases (N = 65) and controls (N = 54). DNA methylation levels were measured using bisulfite pyrosequencing on available peripheral blood samples (N = 119), and Multivariate Imputation by Chained Equations (MICE) was used to impute missing DNA methylation values in remaining samples. Multiple mediation analysis was performed to assess direct and indirect (via DNA methylation) effects of intrinsic and extrinsic factors on breast cancer risk. RESULTS In relation to exposure, AHRR hypo-methylation was associated with cigarette but not waterpipe smoking, suggesting potentially different biomarkers of these two forms of tobacco use; SLC1A5 and TXLNA methylation were not associated with alcohol consumption; LINE-1 methylation was inversely associated with BMI (β-value [95% confidence interval (CI)] = -0.04 [-0.07, -0.02]), which remained significant after adjustment for age, smoking and alcohol consumption. In relation to breast cancer, there was no detectable association between AHRR, SLC1A5 or TXLNA methylation and cancer risk, but LINE-1 methylation was significantly higher in breast cancer cases when compared to controls (mean ± SD: 72.00 ± 0.66 versus 70.89 ± 0.73, P = 4.67 × 10-14). This difference remained significant after adjustment for confounders (odds ratio (OR) [95% CI] = 9.75[3.74, 25.39]). Moreover, LINE-1 hypo-methylation mediated 83% of the inverse effect of BMI on breast cancer risk. CONCLUSION This pilot study demonstrates that alterations in blood LINE-1 methylation mediate the inverse effect of BMI on breast cancer risk. This warrants large scale studies and stratification based on clinic-pathological types of breast cancer.
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Affiliation(s)
- Zainab Awada
- Department of Pharmacology and Toxicology, American University of Beirut Faculty of Medicine, Beirut, Lebanon; International Agency for Research on Cancer, Lyon, France
| | | | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Arafat Tfayli
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Cyrille Cuenin
- International Agency for Research on Cancer, Lyon, France
| | - Reem Akika
- Department of Pharmacology and Toxicology, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Rose-Mary Boustany
- Department of Biochemistry and Molecular Genetics, American University of Beirut Faculty of Medicine, Beirut, Lebanon; Department of Neurology, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Joelle Makoukji
- Department of Biochemistry and Molecular Genetics, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Hani Tamim
- Department of Internal Medicine and Clinical Research Institute, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Nathalie K Zgheib
- Department of Pharmacology and Toxicology, American University of Beirut Faculty of Medicine, Beirut, Lebanon.
| | - Akram Ghantous
- International Agency for Research on Cancer, Lyon, France.
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Gilbertson PK, Forrester S, Andrews L, McCann K, Rogers L, Park C, Moye J. The National Children's Study Archive Model: A 3-Tier Framework for Dissemination of Data and Specimens for General Use and Secondary Analysis. Front Public Health 2021; 9:526286. [PMID: 33748052 PMCID: PMC7973013 DOI: 10.3389/fpubh.2021.526286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 01/26/2021] [Indexed: 01/12/2023] Open
Abstract
The National Children's Study (NCS) Archive was created as a repository of samples, data, and information from the NCS Vanguard Study-a longitudinal pregnancy and birth cohort evaluating approaches to study influence of environmental exposures on child health and development-to provide qualified researchers with access to NCS materials for use in secondary research. The National Children's Study Archive (NCSA) model is a 3-tiered access model designed to make the wealth of information and materials gathered during the NCS Vanguard Study available at a user appropriate level. The NCSA model was developed as a 3-tier framework, for users of varying access levels, providing intuitive data exploration and visualization tools, an end-to-end data and sample request management system, and a restricted portal for participant-level data access with a team of experts available to assist users. This platform provides a model to accelerate transformation of information and materials from existing studies into new scientific discoveries. Trial Registration: ClinicalTrials.gov Identifier: NCT00852904 (first posted February 27, 2009).
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Affiliation(s)
| | - Susan Forrester
- Social & Scientific Systems Inc., Silver Spring, MD, United States
| | - Linda Andrews
- Social & Scientific Systems Inc., Silver Spring, MD, United States
| | - Kathleen McCann
- Social & Scientific Systems Inc., Silver Spring, MD, United States
| | - Lydia Rogers
- Social & Scientific Systems Inc., Silver Spring, MD, United States
| | - Christina Park
- National Institutes of Health, Office of the Director, Bethesda, MD, United States
| | - Jack Moye
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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10
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Fuss A, Mazigo HD, Mueller A. Detection of Schistosoma mansoni DNA using polymerase chain reaction from serum and dried blood spot card samples of an adult population in North-western Tanzania. Infect Dis Poverty 2021; 10:15. [PMID: 33622417 PMCID: PMC7901113 DOI: 10.1186/s40249-021-00798-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Real-time polymerase chain reaction (PCR) is a sensitive and specific method for diagnosing schistosomiasis. However, this method should be performed in a laboratory, usually located distant from the sample collection site. Therefore, it is important to have fast sampling preservation methods, which allow simple transport prior to DNA extraction and amplification. The aim of this study was to verify if blood samples applied to filter paper are suitable for analysis of Schistosoma mansoni DNA by real-time PCR. METHODS A cross-sectional study was conducted among 100 study participants aged 17 to 70 years in a fishing village on the southern shore of Lake Victoria, Tanzania. Serum samples and ethylenediaminetetraacetic acid (EDTA)-anticoagulated whole blood for preparation of dried blood spots (DBS) were collected to test for Schistosoma mansoni infection by real-time PCR. A combined diagnostic reference of positive results of serum-based real-time PCR and the Kato-Katz (KK) method was used for analysis. Sensitivity and negative predictive value (NPV) were calculated. The Wilcoxon signed-rank test was chosen to compare the mean cycle threshold (Ct) values from serum and DBS. RESULTS According to the reference, 92.5% S. mansoni positive samples were determined. The serum-based real-time PCR performed excellently with 95.4% sensitivity, whereas the DBS-based real-time PCR showed a low sensitivity (45.4%). The Ct-values were significantly higher in DBS (median: 37.3) than in serum samples (median: 27.5, P < 0.001), reflecting a lower parasite-specific DNA load on the filter cards. With increasing egg counts, an increase in sensitivity was observed for all methods. The POC-CCA test and the serum-based real-time PCR showed a sensitivity of 100% for medium and severe infections. The DBS real-time PCR showed a sensitivity of only 85.7% even for severe infections. CONCLUSIONS DBS-based real-time PCR did not provide good results in our study and therefore should not be recommended or must be tested concerning temperature of storage, storage duration, use of different filter papers and extraction methods before it is used in future studies. In contrast, our results showed that the POC-CCA test is a sensitive and precise test for detecting S. mansoni infections .
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Affiliation(s)
- Antje Fuss
- Medical Mission Institute, Hermann-Schell-Str. 7, 97074 Wuerzburg, Germany
| | - Humphrey D. Mazigo
- Department of Medical Parasitology and Entomology, School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
| | - Andreas Mueller
- Department of Tropical Medicine, Klinikum Wuerzburg Mitte gGmbH, Medical Mission Hospital, Wuerzburg, Germany
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11
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Laufer BI, Hwang H, Jianu JM, Mordaunt CE, Korf IF, Hertz-Picciotto I, LaSalle JM. Low-pass whole genome bisulfite sequencing of neonatal dried blood spots identifies a role for RUNX1 in Down syndrome DNA methylation profiles. Hum Mol Genet 2020; 29:3465-3476. [PMID: 33001180 PMCID: PMC7788293 DOI: 10.1093/hmg/ddaa218] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/16/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
Neonatal dried blood spots (NDBS) are a widely banked sample source that enables retrospective investigation into early life molecular events. Here, we performed low-pass whole genome bisulfite sequencing (WGBS) of 86 NDBS DNA to examine early life Down syndrome (DS) DNA methylation profiles. DS represents an example of genetics shaping epigenetics, as multiple array-based studies have demonstrated that trisomy 21 is characterized by genome-wide alterations to DNA methylation. By assaying over 24 million CpG sites, thousands of genome-wide significant (q < 0.05) differentially methylated regions (DMRs) that distinguished DS from typical development and idiopathic developmental delay were identified. Machine learning feature selection refined these DMRs to 22 loci. The DS DMRs mapped to genes involved in neurodevelopment, metabolism, and transcriptional regulation. Based on comparisons with previous DS methylation studies and reference epigenomes, the hypermethylated DS DMRs were significantly (q < 0.05) enriched across tissues while the hypomethylated DS DMRs were significantly (q < 0.05) enriched for blood-specific chromatin states. A ~28 kb block of hypermethylation was observed on chromosome 21 in the RUNX1 locus, which encodes a hematopoietic transcription factor whose binding motif was the most significantly enriched (q < 0.05) overall and specifically within the hypomethylated DMRs. Finally, we also identified DMRs that distinguished DS NDBS based on the presence or absence of congenital heart disease (CHD). Together, these results not only demonstrate the utility of low-pass WGBS on NDBS samples for epigenome-wide association studies, but also provide new insights into the early life mechanisms of epigenomic dysregulation resulting from trisomy 21.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Hyeyeon Hwang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Ian F Korf
- Genome Center, University of California, Davis, CA 95616, USA.,Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Irva Hertz-Picciotto
- MIND Institute, University of California, Davis, CA 95616, USA.,Department of Public Health Sciences, School of Medicine, University of California, Davis, CA 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
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12
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Sasaki A, Kim B, Murphy KE, Matthews SG. Impact of ex vivo Sample Handling on DNA Methylation Profiles in Human Cord Blood and Neonatal Dried Blood Spots. Front Genet 2020; 11:224. [PMID: 32265984 PMCID: PMC7106936 DOI: 10.3389/fgene.2020.00224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/26/2020] [Indexed: 11/13/2022] Open
Abstract
The profiling of DNA methylation modifications in peripheral blood has significant potential to determine risk factors for human disease. Little is known concerning the sensitivity of DNA methylation profiles to ex vivo sample handling. Here, we studied typical conditions prior to sample storage associated with cord blood samples obtained from clinical investigations using reduced representation bisulfite sequencing. We examined both whole blood collected shortly after birth and dried blood spots, a potentially important source of neonatal blood for investigation of the DNA methylome and the Developmental Origins of Health and Disease in human cohorts because they are routinely collected during clinical care. Samples were matched across different time conditions, as they were from the same cord blood samples obtained from the same individuals. Maintaining whole blood ex vivo up to 24 h (4°C) or dried blood spots up to 7 days (room temp.) had little effect on DNA methylation profiles. Minimal differences were detected between cord blood immediately frozen and dried blood spots. Our results indicate that DNA methylation profiles are resilient to ex vivo sample handling conditions prior to storage. These data will help guide future human studies focused toward determination of DNA methylation modifications in whole blood.
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Affiliation(s)
- Aya Sasaki
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Bona Kim
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Kellie E Murphy
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.,Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON, Canada
| | - Stephen G Matthews
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.,Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
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13
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Chung FFL, Herceg Z. The Promises and Challenges of Toxico-Epigenomics: Environmental Chemicals and Their Impacts on the Epigenome. ENVIRONMENTAL HEALTH PERSPECTIVES 2020; 128:15001. [PMID: 31950866 PMCID: PMC7015548 DOI: 10.1289/ehp6104] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND It has been estimated that a substantial portion of chronic and noncommunicable diseases can be caused or exacerbated by exposure to environmental chemicals. Multiple lines of evidence indicate that early life exposure to environmental chemicals at relatively low concentrations could have lasting effects on individual and population health. Although the potential adverse effects of environmental chemicals are known to the scientific community, regulatory agencies, and the public, little is known about the mechanistic basis by which these chemicals can induce long-term or transgenerational effects. To address this question, epigenetic mechanisms have emerged as the potential link between genetic and environmental factors of health and disease. OBJECTIVES We present an overview of epigenetic regulation and a summary of reported evidence of environmental toxicants as epigenetic disruptors. We also discuss the advantages and challenges of using epigenetic biomarkers as an indicator of toxicant exposure, using measures that can be taken to improve risk assessment, and our perspectives on the future role of epigenetics in toxicology. DISCUSSION Until recently, efforts to apply epigenomic data in toxicology and risk assessment were restricted by an incomplete understanding of epigenomic variability across tissue types and populations. This is poised to change with the development of new tools and concerted efforts by researchers across disciplines that have led to a better understanding of epigenetic mechanisms and comprehensive maps of epigenomic variation. With the foundations now in place, we foresee that unprecedented advancements will take place in the field in the coming years. https://doi.org/10.1289/EHP6104.
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Affiliation(s)
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
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14
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Awada Z, Nasr R, Akika R, Cahais V, Cuenin C, Zhivagui M, Herceg Z, Ghantous A, Zgheib NK. DNA methylome-wide alterations associated with estrogen receptor-dependent effects of bisphenols in breast cancer. Clin Epigenetics 2019; 11:138. [PMID: 31601247 PMCID: PMC6785895 DOI: 10.1186/s13148-019-0725-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/12/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Bisphenol A (BPA), an estrogen-like endocrine disruptor used in plastics, has been associated with development and promotion of breast cancer, so plastic manufacturers shifted towards less-studied analogs, BPF and BPS. Studying the associated DNA methylome-wide mechanisms of these derivatives is timely, particularly in comparison with BPA. METHODS We assessed proliferation, cell cycle, and migration of breast cancer cells (estrogen receptor (ER)-positive: MCF-7 and ER-negative: MDA-MB-231) treated with BPF and BPS ± estrogen receptor inhibitor (ERI) in comparison to BPA ± ERI. RNA expression and activity of DNA (de)methylation enzymes and LINE-1 methylation were quantified. DNA methylome-wide analysis was evaluated in bisphenol-exposed cells and compared to clinical breast cancer data. RESULTS The three bisphenols caused ER-dependent increased proliferation and migration of MCF-7 but not MDA-MB-231 cells, with BPS being 10 times less potent than BPA and BPF. Although they have similar chemical structures, the three bisphenols induced differential DNA methylation alterations at several genomic clusters of or single CpG sites, with the majority of these being ER-dependent. At equipotent doses, BPA had the strongest effect on the methylome, followed by BPS then BPF. No pathways were enriched for BPF while BPA- and BPS-induced methylome alterations were enriched in focal adhesion, cGMP-PKG, and cancer pathways, which were also dysregulated in methylome-wide alterations comparing ER-positive breast cancer samples to adjacent normal tissues. CONCLUSIONS The three bisphenols have important epigenetic effects in breast cell lines, with those of BPA and BPS overlapping with cancer-related pathways in clinical breast cancer models. Hence, further investigation of their safety is warranted.
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Affiliation(s)
- Z Awada
- Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Riad El-Solh, Beirut, 1107-2020, Lebanon
| | - R Nasr
- Anatomy, Cell Biology and Physiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - R Akika
- Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Riad El-Solh, Beirut, 1107-2020, Lebanon
| | - V Cahais
- Epigenetics group, International Agency for Research on Cancer, Cours Albert Thomas, 69372, Lyon, France
| | - C Cuenin
- Epigenetics group, International Agency for Research on Cancer, Cours Albert Thomas, 69372, Lyon, France
| | - M Zhivagui
- Epigenetics group, International Agency for Research on Cancer, Cours Albert Thomas, 69372, Lyon, France
| | - Z Herceg
- Epigenetics group, International Agency for Research on Cancer, Cours Albert Thomas, 69372, Lyon, France
| | - A Ghantous
- Epigenetics group, International Agency for Research on Cancer, Cours Albert Thomas, 69372, Lyon, France.
| | - N K Zgheib
- Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Riad El-Solh, Beirut, 1107-2020, Lebanon.
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15
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Walker RM, MacGillivray L, McCafferty S, Wrobel N, Murphy L, Kerr SM, Morris SW, Campbell A, McIntosh AM, Porteous DJ, Evans KL. Assessment of dried blood spots for DNA methylation profiling. Wellcome Open Res 2019; 4:44. [PMID: 30984878 PMCID: PMC6446498 DOI: 10.12688/wellcomeopenres.15136.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 11/26/2022] Open
Abstract
Background: DNA methylation reflects health-related environmental exposures and genetic risk, providing insights into aetiological mechanisms and potentially predicting disease onset, progression and treatment response. An increasingly recognised need for large-scale, longitudinally-profiled samples collected world-wide has made the development of efficient and straightforward sample collection and storage procedures a pressing issue. An alternative to the low-temperature storage of EDTA tubes of venous blood samples, which are frequently the source of the DNA used in such studies, is to collect and store at room temperature blood samples using purpose built filter paper, such as Whatman FTA® cards. Our goal was to determine whether DNA stored in this manner can be used to generate DNA methylation profiles comparable to those generated using blood samples frozen in EDTA tubes. Methods: DNA methylation profiles were obtained from matched EDTA tube and Whatman FTA® card whole-blood samples from 62 Generation Scotland: Scottish Family Health Study participants using the Infinium HumanMethylation450 BeadChip. Multiple quality control procedures were implemented, the relationship between the two sample types assessed, and epigenome-wide association studies (EWASs) performed for smoking status, age and the interaction between these variables and sample storage method. Results: Dried blood spot (DBS) DNA methylation profiles were of good quality and DNA methylation profiles from matched DBS and EDTA tube samples were highly correlated (mean
r = 0.991) and could distinguish between participants. EWASs replicated established associations for smoking and age, with no evidence for moderation by storage method. Conclusions: Our results support the use of Whatman FTA® cards for collecting and storing blood samples for DNA methylation profiling. This approach is likely to be particularly beneficial for large-scale studies and those carried out in areas where freezer access is limited. Furthermore, our results will inform consideration of the use of newborn heel prick DBSs for research use.
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Affiliation(s)
- Rosie M Walker
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Louise MacGillivray
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Sarah McCafferty
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Shona M Kerr
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Stewart W Morris
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Archie Campbell
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Division of Psychiatry, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - David J Porteous
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Kathryn L Evans
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
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16
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Genome-wide epigenetic signatures of childhood adversity in early life: Opportunities and challenges. J Dev Orig Health Dis 2019; 10:65-72. [PMID: 30744719 DOI: 10.1017/s2040174418000843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Maternal adversity and fetal glucocorticoid exposure has long-term effects on cardiovascular, metabolic and behavioral systems in offspring that can persist throughout the lifespan. These data, along with other environmental exposure data, implicate epigenetic modifications as potential mechanisms for long-term effects of maternal exposures on adverse health outcomes in offspring. Advances in microarray, sequencing and bioinformatic approaches have enabled recent studies to examine the genome-wide epigenetic response to maternal adversity. Studies of maternal exposures to xenobiotics such as arsenic and smoking have been performed at birth to examine fetal epigenomic signatures in cord blood relating to adult health outcomes. However, there have been no epigenomic studies examining these effects in animal models. On the other hand, to date, only a few studies of the effects of maternal psychosocial stress have been performed in human infants, and the majority of animal studies have examined epigenomic outcomes in adulthood. In terms of maternal exposure to excess glucocorticoids by synthetic glucocorticoid treatment, there has been no epigenetic study performed in humans and only a few studies undertaken in animal models. This review emphasizes the importance of examining biomarkers of exposure to adversity throughout development to identify individuals at risk and to target interventions. Thus, research performed at birth will be reviewed. In addition, potential subject characteristics associated with epigenetic modifications, technical considerations, the selection of target tissues and combining human studies with animal models will be discussed in relation to the design of experiments in this field of study.
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17
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Mostafavi N, Vermeulen R, Ghantous A, Hoek G, Probst-Hensch N, Herceg Z, Tarallo S, Naccarati A, Kleinjans JCS, Imboden M, Jeong A, Morley D, Amaral AFS, van Nunen E, Gulliver J, Chadeau-Hyam M, Vineis P, Vlaanderen J. Acute changes in DNA methylation in relation to 24 h personal air pollution exposure measurements: A panel study in four European countries. ENVIRONMENT INTERNATIONAL 2018; 120:11-21. [PMID: 30055357 DOI: 10.1016/j.envint.2018.07.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/17/2018] [Accepted: 07/17/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND One of the potential mechanisms linking air pollution to health effects is through changes in DNA-methylation, which so far has mainly been analyzed globally or at candidate sites. OBJECTIVE We investigated the association of personal and ambient air pollution exposure measures with genome-wide DNA-methylation changes. METHODS We collected repeated 24-hour personal and ambient exposure measurements of particulate matter (PM2.5), PM2.5 absorbance, and ultrafine particles (UFP) and peripheral blood samples from a panel of 157 healthy non-smoking adults living in four European countries. We applied univariate mixed-effects models to investigate the association between air pollution and genome-wide DNA-methylation perturbations at single CpG (cytosine-guanine dinucleotide) sites and in Differentially Methylated Regions (DMRs). Subsequently, we explored the association of air pollution-induced methylation alterations with gene expression and serum immune marker levels measured in the same subjects. RESULTS Personal exposure to PM2.5 was associated with methylation changes at 13 CpG sites and 69 DMRs. Two of the 13 identified CpG sites (mapped to genes KNDC1 and FAM50B) were located within these DMRs. In addition, 42 DMRs were associated with personal PM2.5 absorbance exposure, 16 DMRs with personal exposure to UFP, 4 DMRs with ambient exposure to PM2.5, 16 DMRs with ambient PM2.5 absorbance exposure, and 15 DMRs with ambient UFP exposure. Correlation between methylation levels at identified CpG sites and gene expression and immune markers was generally moderate. CONCLUSION This study provides evidence for an association between 24-hour exposure to air pollution and DNA-methylation at single sites and regional clusters of CpGs. Analysis of differentially methylated regions provides a promising avenue to further explore the subtle impact of environmental exposures on DNA-methylation.
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Affiliation(s)
- Nahid Mostafavi
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, the Netherlands.
| | - Roel Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, the Netherlands; Medical Research Council-Public Health England Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France.
| | - Gerard Hoek
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, the Netherlands.
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France.
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy.
| | | | - Jos C S Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, the Netherlands.
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Ayoung Jeong
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - David Morley
- Medical Research Council-Public Health England Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.
| | - Andre F S Amaral
- Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College London, London, UK.
| | - Erik van Nunen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, the Netherlands.
| | - John Gulliver
- Medical Research Council-Public Health England Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.
| | - Marc Chadeau-Hyam
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, the Netherlands; Medical Research Council-Public Health England Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.
| | - Paolo Vineis
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy; Medical Research Council-Public Health England Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.
| | - Jelle Vlaanderen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, the Netherlands.
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18
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Tikellis G, Dwyer T, Paltiel O, Phillips GS, Lemeshow S, Golding J, Northstone K, Boyd A, Olsen S, Ghantous A, Herceg Z, Ward MH, Håberg SE, Magnus P, Olsen J, Ström M, Mahabir S, Jones RR, Ponsonby AL, Clavel J, Charles MA, Trevathan E, Qian Z(M, Maule MM, Qiu X, Hong YC, Brandelise S, Roman E, Wake M, He JR, Linet MS. The International Childhood Cancer Cohort Consortium (I4C): A research platform of prospective cohorts for studying the aetiology of childhood cancers. Paediatr Perinat Epidemiol 2018; 32:568-583. [PMID: 30466188 PMCID: PMC11155068 DOI: 10.1111/ppe.12519] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/23/2018] [Accepted: 08/25/2018] [Indexed: 02/05/2023]
Abstract
BACKGROUND Childhood cancer is a rare but leading cause of morbidity and mortality. Established risk factors, accounting for <10% of incidence, have been identified primarily from case-control studies. However, recall, selection and other potential biases impact interpretations particularly, for modest associations. A consortium of pregnancy and birth cohorts (I4C) was established to utilise prospective, pre-diagnostic exposure assessments and biological samples. METHODS Eligibility criteria, follow-up methods and identification of paediatric cancer cases are described for cohorts currently participating or planning future participation. Also described are exposure assessments, harmonisation methods, biological samples potentially available for I4C research, the role of the I4C data and biospecimen coordinating centres and statistical approaches used in the pooled analyses. RESULTS Currently, six cohorts recruited over six decades (1950s-2000s) contribute data on 388 120 mother-child pairs. Nine new cohorts from seven countries are anticipated to contribute data on 627 500 additional projected mother-child pairs within 5 years. Harmonised data currently includes over 20 "core" variables, with notable variability in mother/child characteristics within and across cohorts, reflecting in part, secular changes in pregnancy and birth characteristics over the decades. CONCLUSIONS The I4C is the first cohort consortium to have published findings on paediatric cancer using harmonised variables across six pregnancy/birth cohorts. Projected increases in sample size, expanding sources of exposure data (eg, linkages to environmental and administrative databases), incorporation of biological measures to clarify exposures and underlying molecular mechanisms and forthcoming joint efforts to complement case-control studies offer the potential for breakthroughs in paediatric cancer aetiologic research.
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Affiliation(s)
- Gabriella Tikellis
- Population Epidemiology, Murdoch Children’s Research Institute, Royal Children’s Hospital, University of Melbourne, Melbourne, Australia
| | - Terence Dwyer
- Population Epidemiology, Murdoch Children’s Research Institute, Royal Children’s Hospital, University of Melbourne, Melbourne, Australia
- The George Institute for Global Health, University of Oxford, UK
| | - Ora Paltiel
- Braun School of Public Health, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Gary S. Phillips
- Center for Biostatistics, Department of Biomedical Informatics, Ohio State University, Columbus, Ohio, USA
| | - Stanley Lemeshow
- Division of Biostatistics, College of Public Health, Ohio State University, Columbus, Ohio, USA
| | - Jean Golding
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kate Northstone
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andy Boyd
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sjurdur Olsen
- Centre for Fetal Programming, Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Mary H. Ward
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Siri E. Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Norwat
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Norwat
| | - Jørn Olsen
- Department of Clinical Epidemiology, Aarhus University, Aarhus, Denmark
| | - Marin Ström
- Centre for Fetal Programming, Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Somdat Mahabir
- Division of Cancer Control and Population Sciences. National Cancer Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Rena R. Jones
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Anne-Louise Ponsonby
- Population Epidemiology, Murdoch Children’s Research Institute, Royal Children’s Hospital, University of Melbourne, Melbourne, Australia
| | - Jacqueline Clavel
- Institut National de la Santé et de la Recherche Médicale, Centre for Research in Epidemiology and Statistics Sorbonne Paris Cité, Villejuif, France
| | - Marie Aline Charles
- Institut National de la Santé et de la Recherche Médicale, Centre for Research in Epidemiology and Statistics Sorbonne Paris Cité, Villejuif, France
| | - Edwin Trevathan
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, USA
| | - Zhengmin (Min) Qian
- College for Public Health and Social Justice, Saint Louis University, Missouri, USA
| | - Milena M. Maule
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Xiu Qiu
- Department of Woman and Child Health Care, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yun-Chul Hong
- Institute of Environmental Medicine, College of Medicine, Seoul National University, South Korea
| | | | - Eve Roman
- Epidemiology and Cancer Statistics Group, Health Sciences, York University, UK
| | - Melissa Wake
- Population Epidemiology, Murdoch Children’s Research Institute, Royal Children’s Hospital, University of Melbourne, Melbourne, Australia
| | - Jian-Rong He
- Department of Woman and Child Health Care, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, UK
| | - Martha S. Linet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
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Lui G, Treluyer JM, Fresneau B, Piperno-Neumann S, Gaspar N, Corradini N, Gentet JC, Marec Berard P, Laurence V, Schneider P, Entz-Werle N, Pacquement H, Millot F, Taque S, Freycon C, Lervat C, Le Deley MC, Mahier Ait Oukhatar C, Brugieres L, Le Teuff G, Bouazza N. A Pharmacokinetic and Pharmacogenetic Analysis of Osteosarcoma Patients Treated With High-Dose Methotrexate: Data From the OS2006/Sarcoma-09 Trial. J Clin Pharmacol 2018; 58:1541-1549. [DOI: 10.1002/jcph.1252] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/08/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Gabrielle Lui
- EA 7323; Université Paris Descartes Sorbonne Paris Cité; Paris France
- Clinical Pharmacology Department; Cochin Hospital; Paris France
- CIC-1419 Inserm; Cochin-Necker; Paris France
| | - Jean-Marc Treluyer
- EA 7323; Université Paris Descartes Sorbonne Paris Cité; Paris France
- Clinical Pharmacology Department; Cochin Hospital; Paris France
- CIC-1419 Inserm; Cochin-Necker; Paris France
- URC; Tarnier Hospital; France
| | - Brice Fresneau
- Department of Children and Adolescents Oncology; Gustave Roussy; Villejuif France
- Paris-Saclay University; CESP; INSERM; Villejuif France
| | | | - Nathalie Gaspar
- Department of Children and Adolescents Oncology; Gustave Roussy; Villejuif France
| | - Nadège Corradini
- Pediatric Oncology Department; Mother-Children Hospital; Nantes France
| | - Jean-Claude Gentet
- Pediatric Oncology Department; La Timone Children's Hospital; Marseille France
| | - Perrine Marec Berard
- Pediatric Oncology Department; Institute of Pediatric Hematology and Oncology-Léon Bérard Anticancer Center; Lyon France
- Oncology Department; Institut Curie; Paris France
| | | | - Pascale Schneider
- Pediatric Hemato-Oncology Department; University Hospital; Rouen France
| | | | | | | | - Sophie Taque
- Department of Pediatric Hemato-Oncology; University Hospital; Rennes France
| | - Claire Freycon
- Pediatric Department; The Child and Family Hospital; University Hospital; Grenoble France
| | - Cyril Lervat
- Pediatric Oncology Unit; Centre Oscar Lambret; Lille France
| | - Marie Cécile Le Deley
- Paris-Saclay University; CESP; INSERM; Villejuif France
- Biostatistics Unit; Gustave Roussy; Villejuif France
| | | | - Laurence Brugieres
- Department of Children and Adolescents Oncology; Gustave Roussy; Villejuif France
| | - Gwénaël Le Teuff
- Paris-Saclay University; CESP; INSERM; Villejuif France
- Biostatistics Unit; Gustave Roussy; Villejuif France
| | - Naïm Bouazza
- EA 7323; Université Paris Descartes Sorbonne Paris Cité; Paris France
- CIC-1419 Inserm; Cochin-Necker; Paris France
- URC; Tarnier Hospital; France
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Serra O, Frazzi R, Perotti A, Barusi L, Buschini A. Use of FTA® classic cards for epigenetic analysis of sperm DNA. Biotechniques 2018; 64:45-51. [DOI: 10.2144/btn-2017-0101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/16/2018] [Indexed: 11/23/2022] Open
Abstract
FTA® technologies provide the most reliable method for DNA extraction. Although FTA technologies have been widely used for genetic analysis, there is no literature on their use for epigenetic analysis yet. We present for the first time, a simple method for quantitative methylation assessment based on sperm cells stored on Whatman FTA classic cards. Specifically, elution of seminal DNA from FTA classic cards was successfully tested with an elution buffer and an incubation step in a thermocycler. The eluted DNA was bisulfite converted, amplified by PCR, and a region of interest was pyrosequenced.
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Affiliation(s)
- Olga Serra
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Raffaele Frazzi
- Laboratory of Translational Research, Arcispedale S.Maria Nuova IRCCS, Reggio Emilia, Italy
| | - Alessio Perotti
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Lorenzo Barusi
- Procreazione Medicalmente Assistita (CPMA), Clinica Ostetrica e Ginecologica, Azienda Ospedaliero-Universitaria, Parma, Italy
| | - Annamaria Buschini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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21
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Méplan C. Association of Single Nucleotide Polymorphisms in Selenoprotein Genes with Cancer Risk. Methods Mol Biol 2018; 1661:313-324. [PMID: 28917054 DOI: 10.1007/978-1-4939-7258-6_22] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetic association studies have linked genetic variants in the Selenium (Se) metabolism with the development of complex diseases such as cancer and helped unravel novel mechanisms underlying cancer development. The chapter describes the specificity of genetic variants in the Se metabolism, the approaches used in association studies, and the limitations of such approaches.
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Affiliation(s)
- Catherine Méplan
- School of Biomedical Sciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK.
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22
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Ghantous A, Hernandez-Vargas H, Herceg Z. DNA Methylation Analysis from Blood Spots: Increasing Yield and Quality for Genome-Wide and Locus-Specific Methylation Analysis. Methods Mol Biol 2018; 1708:605-619. [PMID: 29224166 DOI: 10.1007/978-1-4939-7481-8_31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Blood represents an easily accessible human tissue for numerous research and clinical applications, including surrogate roles for biomarkers of other tissues. Dried blood spots (DBS) are space- and cost-efficient storage forms of blood while stably retaining many of its chemical constituents. Consequently, neonatal DBS are routinely collected in many countries, and their biobanks represent gold mines for research. However, the utility of DBS is restricted by the limited amount and quality of extractable biomolecules (including DNA), especially for genome-wide profiling. In particular, DNA methylome analysis in DBS has proven to be technically challenging, mainly due to the requirement for stringent preprocessing, such as bisulfite conversion. Moreover, DNA amplification, required to increase its yield, often leads to a bias in the analysis, particularly in methylome profiles. Thus, it is important to develop methodologies that maximize both the yield and quality of DNA from DBS for downstream analyses. Using a combination of in-house-derived and modified commercial extraction methods, we developed two robust protocols that produced increased DNA yield and quality from DBS. Though both protocols are more efficient relative to other published methods, one protocol yields less DNA compared to the other, but shows improved 260/280 spectrophotometric ratios, which are useful for sample quality assessment. Both protocols consist of two sequential phases, each involving several critical steps. Phase I comprises blood extraction off the filter papers, cell lysis, and protein digestion. Phase II involves DNA precipitation, purification, and elution. Results from subsequent locus-specific and genome-wide DNA methylation analyses demonstrate the high quality, reproducibility, and consistency of the data. This work may prove useful to meet the increased demand for research on DBS, particularly with a focus on the epigenetic origins of human diseases and newborn screening programs.
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Affiliation(s)
- Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 rue Albert-Thomas, 69008, Lyon, France
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 rue Albert-Thomas, 69008, Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 rue Albert-Thomas, 69008, Lyon, France.
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23
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Eze IC, Esse C, Bassa FK, Koné S, Acka F, Yao L, Imboden M, Jaeger FN, Schindler C, Dosso M, Laubhouet-Koffi V, Kouassi D, N'Goran EK, Utzinger J, Bonfoh B, Probst-Hensch N. Côte d'Ivoire Dual Burden of Disease (CoDuBu): Study Protocol to Investigate the Co-occurrence of Chronic Infections and Noncommunicable Diseases in Rural Settings of Epidemiological Transition. JMIR Res Protoc 2017; 6:e210. [PMID: 29079553 PMCID: PMC5681722 DOI: 10.2196/resprot.8599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Individual-level concomitance of infectious diseases and noncommunicable diseases (NCDs) is poorly studied, despite the reality of this dual disease burden for many low- and middle-income countries (LMICs). OBJECTIVE This study protocol describes the implementation of a cohort and biobank aiming for a better understanding of interrelation of helminth and Plasmodium infections with NCD phenotypes like metabolic syndrome, hypertension, and diabetes. METHODS A baseline cross-sectional population-based survey was conducted over one year, in the Taabo health and demographic surveillance system (HDSS) in south-central Côte d'Ivoire. We randomly identified 1020 consenting participants aged ≥18 years in three communities (Taabo-Cité, Amani-Ménou, and Tokohiri) reflecting varying stages of epidemiological transition. Participants underwent health examinations consisting of NCD phenotyping (anthropometry, blood pressure, renal function, glycemia, and lipids) and infectious disease testing (infections with soil-transmitted helminths, schistosomes, and Plasmodium). Individuals identified to have elevated blood pressure, glucose, lipids, or with infections were referred to the central/national health center for diagnostic confirmation and treatment. Aliquots of urine, stool, and venous blood were stored in a biobank for future exposome/phenome research. In-person interviews on sociodemographic attributes, risk factors for infectious diseases and NCDs, medication, vaccinations, and health care were also conducted. Appropriate statistical techniques will be applied in exploring the concomitance of infectious diseases and NCDs and their determinants. Participants' consent for follow-up contact was obtained. RESULTS Key results from this baseline study, which will be published in peer-reviewed literature, will provide information on the prevalence and co-occurrence of infectious diseases, NCDs, and their risk factors. The Taabo HDSS consists of rural and somewhat more urbanized areas, allowing for comparative studies at different levels of epidemiological transition. An HDSS setting is ideal as a basis for longitudinal studies since their sustainable field work teams hold close contact with the local population. CONCLUSIONS The collaboration between research institutions, public health organizations, health care providers, and staff from the Taabo HDSS in this study assures that the synthesized evidence will feed into health policy towards integrated infectious disease-NCD management. The preparation of health systems for the dual burden of disease is pressing in low- and middle-income countries. The established biobank will strengthen the local research capacity and offer opportunities for biomarker studies to deepen the understanding of the cross-talk between infectious diseases and NCDs. TRIAL REGISTRATION International Standard Randomized Controlled Trials Number (ISRCTN): 87099939; http://www.isrctn.com/ISRCTN87099939 (Archived by WebCite at http://www.webcitation.org/6uLEs1EsX).
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Affiliation(s)
- Ikenna C Eze
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Clémence Esse
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire.,Institut d'Ethnosociologie, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - Fidèle K Bassa
- Unite de Formation et de Recherche Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - Siaka Koné
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Felix Acka
- Institut National de Santé Publique, Abidjan, Côte d'Ivoire
| | - Loukou Yao
- Ligue Ivoirienne contre l'Hypertension Artérielle et les Maladies Cardiovasculaire, Abidjan, Côte d'Ivoire
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Fabienne N Jaeger
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Christian Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Mireille Dosso
- Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Véronique Laubhouet-Koffi
- Ligue Ivoirienne contre l'Hypertension Artérielle et les Maladies Cardiovasculaire, Abidjan, Côte d'Ivoire
| | - Dinard Kouassi
- Institut National de Santé Publique, Abidjan, Côte d'Ivoire
| | - Eliézer K N'Goran
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire.,Unite de Formation et de Recherche Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Bassirou Bonfoh
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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Tessitore MV, Sottini A, Roccaro AM, Ghidini C, Bernardi S, Martellosio G, Serana F, Imberti L. Detection of newly produced T and B lymphocytes by digital PCR in blood stored dry on nylon flocked swabs. J Transl Med 2017; 15:70. [PMID: 28381232 PMCID: PMC5381048 DOI: 10.1186/s12967-017-1169-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A normal number of T-cell receptor excision circles (TRECs) and K-deleting recombination excision circles (KRECs) is considered a biomarker for adequate new T- and B-cell production. In newborns, detection of TRECs and KRECs by real time PCR from dried blood spotted on filter paper is used for the screening of severe immunodeficiency. In adults, elderly and during diseases, where the number of TRECs is lower than in newborns and children, a large amount of DNA and a sensitive method of amplification are necessary to identify newly produced lymphocytes. METHODS DNA was prepared from blood of 203 healthy adults (range: 18-91 years old) absorbed for 10 s on flocked swabs and let to dry, or from peripheral blood mononuclear cells. DNA was subjected to digital PCR and to well established conventional real time PCR-based method using TREC- and KREC-specific primers and probes. The number of TRECs and KRECs was expressed per mL of blood. Statistical analysis was performed by nested ANOVA, Pearson coefficient of determination, and by linear regression tests. RESULTS The novel method for the storage of dried blood on nylon flocked swabs and the use of digital PCR allow quantification of TRECs and KRECs with high degree of sensitivity, specificity, accuracy, and precision. TRECs and KRECs were amplified by digital PCR in all tested blood samples, including those obtained from elderly individuals (>70 years old) and that were negative by real time PCR. Furthermore, values of TRECs and KRECs obtained by digital PCR were in the range of those acquired by real time PCR. CONCLUSIONS Our findings demonstrate that DNA isolation from dried blood on flocked swabs followed by digital PCR-based analysis represents a useful tool for studying new lymphocyte production in adults and elderly individuals. This suggests the potential use of the methodology when monitoring of clinical variables is limited by the number of molecules that can be amplified and detected, such as in patients with immunodeficiency or under immunosuppressive therapies.
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Affiliation(s)
- Marion Vaglio Tessitore
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Alessandra Sottini
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Aldo M Roccaro
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Claudia Ghidini
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Simona Bernardi
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Giovanni Martellosio
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Federico Serana
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Luisa Imberti
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy.
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25
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26
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Aguayo-Patrón S, Beltrán-Sauceda L, Calderón de la Barca AM. A population-wide applicable HLA-DQ2 and DQ8 genotyping using DNA from dried blood spots and duplex allele-specific qPCR amplification. Scandinavian Journal of Clinical and Laboratory Investigation 2016; 76:581-587. [PMID: 27670799 DOI: 10.1080/00365513.2016.1230773] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Genotyping of HLA-DQ2 and DQ8 haplotypes is important for diagnosis or for screening of early risk detection of celiac disease or type 1 diabetes. Usually, venous blood DNA extraction and expensive and time consuming amplification are used, that hinder population-wide studies. We assayed a friendly HLA-DQ2 and DQ8 genotyping procedure using a combination of DNA from dried blood spot (DBS) and duplex allele-specific qPCR amplification using SYBR Green. DNA was extracted using home-made buffers and compared to an extraction commercial kit. Duplex reactions by qPCR were designed using each Tm allele amplicon for reference samples (positive HLA-DQ2 or DQ8) with allele-specific primers. DBS samples from 558 children (7.99 ± 2.47 y) were collected. The DNA final yield obtained by the home-made extractive procedure was higher than from the commercial kit (1.11 ± 0.56 vs 0.23 ± 0.14 μg), while the quality was similar for both DNA samples. There was concordance in the amplification profiles for DNA samples obtained with both methods. All of four alleles from DQ2 and DQ8 haplotypes were accurately identified in duplex reactions. By using DBS samples and DNA extraction home-made procedure, the costs were reduced by 60%. The whole procedure is cost-effective for HLA-DQ2 and DQ8 genotyping.
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Affiliation(s)
- Sandra Aguayo-Patrón
- a Coordinación de Nutrición , Centro de Investigación en Alimentación y Desarrollo , Hermosillo , Sonora , México
| | - Lizbeth Beltrán-Sauceda
- a Coordinación de Nutrición , Centro de Investigación en Alimentación y Desarrollo , Hermosillo , Sonora , México
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Staunstrup NH, Starnawska A, Nyegaard M, Christiansen L, Nielsen AL, Børglum A, Mors O. Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots. Clin Epigenetics 2016; 8:81. [PMID: 27462375 PMCID: PMC4960904 DOI: 10.1186/s13148-016-0242-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed. RESULTS Here we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample. CONCLUSIONS In summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.
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Affiliation(s)
- Nicklas H Staunstrup
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; Translational Neuropsychiatric Unit, Aarhus University Hospital, Risskov, 8240 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark
| | - Anna Starnawska
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark ; Center for Integrative Sequencing, iSEQ, AU, Aarhus C, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark ; Center for Integrative Sequencing, iSEQ, AU, Aarhus C, Denmark
| | - Lene Christiansen
- Department of Public Health, University of Southern Denmark, Odense C, 5000 Denmark
| | - Anders L Nielsen
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark
| | - Anders Børglum
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; Research Department P, Aarhus University Hospital, Risskov, 8240 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark ; Center for Integrative Sequencing, iSEQ, AU, Aarhus C, Denmark
| | - Ole Mors
- Translational Neuropsychiatric Unit, Aarhus University Hospital, Risskov, 8240 Denmark ; Research Department P, Aarhus University Hospital, Risskov, 8240 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark
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28
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Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:343-430. [DOI: 10.1007/978-3-319-43624-1_15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Ghantous A, Hernandez-Vargas H, Byrnes G, Dwyer T, Herceg Z. Characterising the epigenome as a key component of the fetal exposome in evaluating in utero exposures and childhood cancer risk. Mutagenesis 2015; 30:733-42. [PMID: 25724893 PMCID: PMC4757935 DOI: 10.1093/mutage/gev010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Recent advances in laboratory sciences hold a promise for a 'leap forward' in understanding the aetiology of complex human diseases, notably cancer, potentially providing an evidence base for prevention. For example, remarkable advances in epigenomics have an important impact on our understanding of biological phenomena and importance of environmental stressors in complex diseases. Environmental and lifestyle factors are thought to be implicated in the development of a wide range of human cancers by eliciting changes in the epigenome. These changes, thus, represent attractive targets for biomarker discovery intended for the improvement of exposure and risk assessment, diagnosis and prognosis and provision of short-term outcomes in intervention studies. The epigenome can be viewed as an interface between the genome and the environment; therefore, aberrant epigenetic events associated with environmental exposures are likely to play an important role in the onset and progression of different human diseases. The advent of powerful technologies for analysing epigenetic patterns in both cancer tissues and normal cells holds promise that the next few years will be fundamental for the identification of critical cancer- and exposure-associated epigenetic changes and for their evaluation as new generation of biomarkers. Here, we discuss new opportunities in the current age of 'omics' technologies for studies with prospective design and associated biospecimens that represent exciting potential for characterising the epigenome as a key component of the fetal exposome and for understanding causal pathways and robust predictors of cancer risk and associated environmental determinants during in utero life. Such studies should improve our knowledge concerning the aetiology of childhood cancer and identify both novel biomarkers and clues to causation, thus, providing an evidence base for cancer prevention.
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Affiliation(s)
- Akram Ghantous
- Epigenetics and
- Biostatistics Groups, International Agency for Research on Cancer (IARC), 150 rue Albert-Thomas, F-69008 Lyon, France
- The George Institute for Global Health and Nuffield Department of Population Health, Oxford Martin School | University of Oxford, 34 Broad Street Oxford OX1 3BD, UK
| | - Hector Hernandez-Vargas
- Epigenetics and
- Biostatistics Groups, International Agency for Research on Cancer (IARC), 150 rue Albert-Thomas, F-69008 Lyon, France
- The George Institute for Global Health and Nuffield Department of Population Health, Oxford Martin School | University of Oxford, 34 Broad Street Oxford OX1 3BD, UK
| | - Graham Byrnes
- Biostatistics Groups, International Agency for Research on Cancer (IARC), 150 rue Albert-Thomas, F-69008 Lyon, France
| | - Terence Dwyer
- The George Institute for Global Health and Nuffield Department of Population Health, Oxford Martin School | University of Oxford, 34 Broad Street Oxford OX1 3BD, UK
| | - Zdenko Herceg
- *To whom correspondence should be addressed. Tel: +33-4-72 73 83 98; Fax: +33-4-72 73 83 29; E-mail:
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Abdul-Rahman OA, Rodriguez B, Wadlinger SR, Slutsman J, Boyle EB, Merrill LS, Botkin J, Moye J. Success rates for consent and collection of prenatal biological specimens in an epidemiologic survey of child health. ACTA ACUST UNITED AC 2015; 106:47-54. [PMID: 26407522 DOI: 10.1002/bdra.23455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND The National Children's Study (NCS) Vanguard Study began enrollment in January 2009 as an initial pilot study for a planned large-scale, longitudinal U.S. cohort study of the effect of environmental influences on child health and development, with biological and environmental sample collection conducted in seven locations from April 2009 to October 2010. We sought to determine rates of consent for, and success of collection of, maternal and paternal biospecimens before and during pregnancy in the NCS Vanguard Study. METHODS Samples of blood, saliva, vaginal swabs, urine, hair, and nails were collected before and during pregnancy. All specimens were sent to a central repository for processing, storage, and quality assessment. RESULTS Of 780 pregnant women asked to consent to sample collection, 773 (>99%) agreed, and of 295 nonpregnant women, 292 (99%) agreed. Of 440 fathers asked to consent to sample collection, 435 (99%) agreed. Frequency of successful collection of biospecimens varied depending on sample and visit type. In descending order, the ranges over all visit types of the proportion of expected samples successfully collected from women were: urine, 92.5 to 95.7%; hair, 89.6 to 92.5%; vaginal swab, 84.2 to 88.5%; blood, 74.9 to 78.5%; 2-day saliva, 65.8 to 81.6%; and nails, 76.4 to 76.7%. For fathers, rates were highest for urine (94.9%) and lowest for hair (63.0%). CONCLUSION High rates of consent for and collection of a wide variety of biospecimens can be achieved in prospective epidemiologic cohort studies of pregnant women. Ease of sample collection may be a primary factor influencing successful biospecimen collection.
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Affiliation(s)
- Omar A Abdul-Rahman
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, Mississippi
| | | | | | - Julia Slutsman
- National Children's Study Program Office, NICHD, NIH, Bethesda, Maryland
| | | | | | | | - Jack Moye
- National Children's Study Program Office, NICHD, NIH, Bethesda, Maryland
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Smith AK, Kilaru V, Klengel T, Mercer KB, Bradley B, Conneely KN, Ressler KJ, Binder EB. DNA extracted from saliva for methylation studies of psychiatric traits: evidence tissue specificity and relatedness to brain. Am J Med Genet B Neuropsychiatr Genet 2015; 168B:36-44. [PMID: 25355443 PMCID: PMC4610814 DOI: 10.1002/ajmg.b.32278] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/29/2014] [Indexed: 12/12/2022]
Abstract
DNA methylation has become increasingly recognized in the etiology of psychiatric disorders. Because brain tissue is not accessible in living humans, epigenetic studies are most often conducted in blood. Saliva is often collected for genotyping studies but is rarely used to examine DNA methylation because the proportion of epithelial cells and leukocytes varies extensively between individuals. The goal of this study was to evaluate whether saliva DNA is informative for studies of psychiatric disorders. DNA methylation (HumanMethylation450 BeadChip) was assessed in saliva and blood samples from 64 adult African Americans. Analyses were conducted using linear regression adjusted for appropriate covariates, including estimated cellular proportions. DNA methylation from brain tissues (cerebellum, frontal cortex, entorhinal cortex, and superior temporal gyrus) was obtained from a publically available dataset. Saliva and blood methylation was clearly distinguishable though there was positive correlation overall. There was little correlation in CpG sites within relevant candidate genes. Correlated CpG sites were more likely to occur in areas of low CpG density (i.e., CpG shores and open seas). There was more variability in CpG sites from saliva than blood, which may reflect its heterogeneity. Finally, DNA methylation in saliva appeared more similar to patterns from each of the brain regions examined overall than methylation in blood. Thus, this study provides a framework for using DNA methylation from saliva and suggests that DNA methylation of saliva may offer distinct opportunities for epidemiological and longitudinal studies of psychiatric traits.
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Affiliation(s)
- Alicia K. Smith
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia,Genetics and Molecular Biology Program, Emory University, Atlanta, Georgia,Correspondence to: Alicia K. Smith, Ph.D., Assistant Professor, Psychiatry & Behavioral Sciences, Emory University SOM, 101 Woodruff Circle NE; Ste 4113, Atlanta, GA 30322.
| | - Varun Kilaru
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia
| | - Torsten Klengel
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia,Max-Planck Institute of Psychiatry, Munich, Germany
| | - Kristina B. Mercer
- Genetics and Molecular Biology Program, Emory University, Atlanta, Georgia
| | - Bekh Bradley
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia,Clinical psychologist, Mental Health Service Line, Atlanta VA Medical Center, Decatur, Georgia
| | - Karen N. Conneely
- Genetics and Molecular Biology Program, Emory University, Atlanta, Georgia,Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Kerry J. Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Elisabeth B. Binder
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia,Max-Planck Institute of Psychiatry, Munich, Germany
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Comparison of customized spin-column and salt-precipitation finger-prick blood DNA extraction. Biosci Rep 2014; 34:BSR20140105. [PMID: 25222694 PMCID: PMC4206861 DOI: 10.1042/bsr20140105] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
gDNA (genomic DNA extraction from blood is a fundamental process in many diagnostic, identification and research applications. Numerous extraction methods have been reported and are available commercially. However, there is insufficient understanding of the impact of chemical buffers on DNA yield from either whole or nucleated blood. Moreover, these commercial kits are often costly, constraining less well-funded laboratories to traditional and more cost-effective salt-precipitation methods. Towards this, we compared a salt-precipitation and a customized cost-effective spin-column-based method, studying the impact of different chemical constituents on the yields. This customized method resulted in a shortening of the extraction process, higher gDNA yields, and more successful PCR amplification of gDNA genes compared with the salt-precipitation method. Optimizing different chemical buffers on whole- and nucleated blood materials further revealed that certain chemicals boosted extractions from whole- but not nucleated blood. These findings may be useful to laboratories that do not have ready access to commercial kits, and improve their nucleic acid extractions from blood economically. A customized spin-column finger-prick gDNA extraction yielded more DNA and gene amplification success than a salt-precipitation method. Further optimization showed certain buffers to augment whole, but not nucleated blood extractions.
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