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Bell CG. Quantifying stochasticity in the aging DNA methylome. Nat Aging 2024:10.1038/s43587-024-00634-y. [PMID: 38755436 DOI: 10.1038/s43587-024-00634-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK.
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Bell CG. Epigenomic insights into common human disease pathology. Cell Mol Life Sci 2024; 81:178. [PMID: 38602535 PMCID: PMC11008083 DOI: 10.1007/s00018-024-05206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The epigenome-the chemical modifications and chromatin-related packaging of the genome-enables the same genetic template to be activated or repressed in different cellular settings. This multi-layered mechanism facilitates cell-type specific function by setting the local sequence and 3D interactive activity level. Gene transcription is further modulated through the interplay with transcription factors and co-regulators. The human body requires this epigenomic apparatus to be precisely installed throughout development and then adequately maintained during the lifespan. The causal role of the epigenome in human pathology, beyond imprinting disorders and specific tumour suppressor genes, was further brought into the spotlight by large-scale sequencing projects identifying that mutations in epigenomic machinery genes could be critical drivers in both cancer and developmental disorders. Abrogation of this cellular mechanism is providing new molecular insights into pathogenesis. However, deciphering the full breadth and implications of these epigenomic changes remains challenging. Knowledge is accruing regarding disease mechanisms and clinical biomarkers, through pathogenically relevant and surrogate tissue analyses, respectively. Advances include consortia generated cell-type specific reference epigenomes, high-throughput DNA methylome association studies, as well as insights into ageing-related diseases from biological 'clocks' constructed by machine learning algorithms. Also, 3rd-generation sequencing is beginning to disentangle the complexity of genetic and DNA modification haplotypes. Cell-free DNA methylation as a cancer biomarker has clear clinical utility and further potential to assess organ damage across many disorders. Finally, molecular understanding of disease aetiology brings with it the opportunity for exact therapeutic alteration of the epigenome through CRISPR-activation or inhibition.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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van Duijvenboden S, Ramírez J, Young WJ, Olczak KJ, Ahmed F, Alhammadi MJAY, Bell CG, Morris AP, Munroe PB. Integration of genetic fine-mapping and multi-omics data reveals candidate effector genes for hypertension. Am J Hum Genet 2023; 110:1718-1734. [PMID: 37683633 PMCID: PMC10577090 DOI: 10.1016/j.ajhg.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
Genome-wide association studies of blood pressure (BP) have identified >1,000 loci, but the effector genes and biological pathways at these loci are mostly unknown. Using published association summary statistics, we conducted annotation-informed fine-mapping incorporating tissue-specific chromatin segmentation and colocalization to identify causal variants and candidate effector genes for systolic BP, diastolic BP, and pulse pressure. We observed 532 distinct signals associated with ≥2 BP traits and 84 with all three. For >20% of signals, a single variant accounted for >75% posterior probability, 65 were missense variants in known (SLC39A8, ADRB2, and DBH) and previously unreported BP candidate genes (NRIP1 and MMP14). In disease-relevant tissues, we colocalized >80 and >400 distinct signals for each BP trait with cis-eQTLs and regulatory regions from promoter capture Hi-C, respectively. Integrating mouse, human disorder, gene expression and tissue abundance data, and literature review, we provide consolidated evidence for 436 BP candidate genes for future functional validation and discover several potential drug targets.
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Affiliation(s)
- Stefan van Duijvenboden
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK; Institute of Cardiovascular Science, University College London, London, UK; Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Julia Ramírez
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK; Aragon Institute of Engineering Research, University of Zaragoza, Zaragoza, Spain; Centro de Investigación Biomédica en Red - Bioingeniería, Biomateriales y Nanomedicina, Zaragoza, Spain
| | - William J Young
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK; Barts Heart Centre, St Bartholomew's Hospital, EC1A 7BE London, UK
| | - Kaya J Olczak
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
| | - Farah Ahmed
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
| | | | - Christopher G Bell
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK; National Institute of Health and Care Research, Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
| | - Patricia B Munroe
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK; National Institute of Health and Care Research, Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, EC1M 6BQ London, UK.
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Maiarù M, Acton RJ, Woźniak EL, Mein CA, Bell CG, Géranton SM. A DNA methylation signature in the stress driver gene Fkbp5 indicates a neuropathic component in chronic pain. Clin Epigenetics 2023; 15:155. [PMID: 37777763 PMCID: PMC10543848 DOI: 10.1186/s13148-023-01569-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 09/17/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND Epigenetic changes can bring insight into gene regulatory mechanisms associated with disease pathogenicity, including chronicity and increased vulnerability. To date, we are yet to identify genes sensitive to epigenetic regulation that contribute to the maintenance of chronic pain and with an epigenetic landscape indicative of the susceptibility to persistent pain. Such genes would provide a novel opportunity for better pain management, as their epigenetic profile could be targeted for the treatment of chronic pain or used as an indication of vulnerability for prevention strategies. Here, we investigated the epigenetic profile of the gene Fkbp5 for this potential, using targeted bisulphite sequencing in rodent pre-clinical models of chronic and latent hypersensitive states. RESULTS The Fkbp5 promoter DNA methylation (DNAm) signature in the CNS was significantly different between models of persistent pain, and there was a significant correlation between CNS and peripheral blood Fkbp5 DNAm, indicating that further exploration of Fkbp5 promoter DNAm as an indicator of chronic pain pathogenic origin is warranted. We also found that maternal separation, which promotes the persistency of inflammatory pain in adulthood, was accompanied by long-lasting reduction in Fkbp5 DNAm, suggesting that Fkbp5 DNAm profile may indicate the increased vulnerability to chronic pain in individuals exposed to trauma in early life. CONCLUSIONS Overall, our data demonstrate that the Fkbp5 promoter DNAm landscape brings novel insight into the differing pathogenic origins of chronic pain, may be able to stratify patients and predict the susceptibility to chronic pain.
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Affiliation(s)
- Maria Maiarù
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
- Department of Pharmacology, School of Pharmacy, University of Reading, Reading, UK
| | - Richard J Acton
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, UK
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Eva L Woźniak
- Genome Centre, Faculty of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Charles A Mein
- Genome Centre, Faculty of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sandrine M Géranton
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
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Saunderson EA, Encabo HH, Devis J, Rouault-Pierre K, Piganeau M, Bell CG, Gribben JG, Bonnet D, Ficz G. CRISPR/dCas9 DNA methylation editing is heritable during human hematopoiesis and shapes immune progeny. Proc Natl Acad Sci U S A 2023; 120:e2300224120. [PMID: 37579157 PMCID: PMC10450654 DOI: 10.1073/pnas.2300224120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/26/2023] [Indexed: 08/16/2023] Open
Abstract
Aging is associated with an abnormal increase in DNA methylation (DNAm) in human gene promoters, including in bone marrow stem cells. DNAm patterns are further perturbed in hematological malignancies such as acute myeloid leukemia but the physiological significance of such epigenetic changes is unknown. Using epigenetic editing of human stem/progenitor cells (HSPCs), we show that p15 methylation affects hematopoiesis in vivo. We edited the CDKN2B (p15) promoter and ARF (p14) using dCas9-3A3L and observed DNAm spreading beyond the gRNA location. We find that despite a transient delivery system, DNAm is maintained during myeloid differentiation in vitro, and hypermethylation of the p15 promoter reduces gene expression. In vivo, edited human HSPCs can engraft the bone marrow of mice and targeted DNAm is maintained in HSPCs long term. Moreover, epigenetic changes are conserved and inherited in both myeloid and lymphoid lineages. Although the proportion of myeloid (CD33+) and lymphoid (CD19+) cells is unaffected, monocyte (CD14+) populations decreased and granulocytes (CD66b+) increased in mice engrafted with p15 hypermethylated HSPCs. Monocytes derived from p15 hypermethylated HSPCs appear to be activated and show increased inflammatory transcriptional programs. We believe these findings have clinical relevance since we found p15 promoter methylation in the peripheral blood of patients with clonal hematopoiesis. Our study shows DNAm can be targeted and maintained in human HSPCs and demonstrated functional relevance of aberrant DNAm on the p15 locus. As such, other aging-associated aberrant DNAm may impact hematopoiesis in vivo.
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Affiliation(s)
- Emily A. Saunderson
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, LondonEC1M 6BQ, United Kingdom
| | - Hector Huerga Encabo
- Haematopoietic Stem Cell Laboratory, Francis Crick Institute, LondonNW1 1AT, United Kingdom
| | - Julie Devis
- Group of Computational Biology and Bioinformatics, de Duve Institute, Université Catholique de Louvain, Brussels1200, Belgium
| | - Kevin Rouault-Pierre
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, LondonEC1M 6BQ, United Kingdom
| | - Marion Piganeau
- Haematopoietic Stem Cell Laboratory, Francis Crick Institute, LondonNW1 1AT, United Kingdom
| | - Christopher G. Bell
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, LondonEC1M 6BQ, United Kingdom
| | - John G. Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, LondonEC1M 6BQ, United Kingdom
| | - Dominique Bonnet
- Haematopoietic Stem Cell Laboratory, Francis Crick Institute, LondonNW1 1AT, United Kingdom
| | - Gabriella Ficz
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, LondonEC1M 6BQ, United Kingdom
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McErlean P, Bell CG, Hewitt RJ, Busharat Z, Ogger PP, Ghai P, Albers GJ, Calamita E, Kingston S, Molyneaux PL, Beck S, Lloyd CM, Maher TM, Byrne AJ. DNA Methylome Alterations are Associated with Airway Macrophage Differentiation and Phenotype During Lung Fibrosis. Am J Respir Crit Care Med 2021; 204:954-966. [PMID: 34280322 DOI: 10.1164/rccm.202101-0004oc] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Airway macrophages (AMs) are key regulators of the lung environment and are implicated in the pathogenesis of idiopathic pulmonary fibrosis (IPF), a fatal respiratory disease with no cure. However, knowledge of epigenetics of AMs in IPF are limited. METHODS We undertook DNA methylation profiling using Illumina EPIC (850k) arrays in sorted AMs from Healthy (n=14) and IPF (n=30) donors. Cell-type deconvolution was performed using reference myeloid-cell DNA methylomes. MEASUREMENTS AND MAIN RESULTS Our analysis revealed epigenetic heterogeneity was a key characteristic of IPF-AMs. DNAm 'clock' analysis indicated epigenetic alterations in IPF-AMs was not associated with accelerated ageing. In differential DNAm analysis, we identified numerous differentially methylated positions (DMPs, n=11) and regions (DMRs, n=49) between healthy and IPF AMs respectively. DMPs and DMRs encompassed genes involved in lipid (LPCAT1) and glucose (PFKFB3) metabolism and importantly, DNAm status was associated with disease severity in IPF. CONCLUSIONS Collectively, our data identify that changes in the epigenome are associated with development and function of AMs in the IPF lung.
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Affiliation(s)
- Peter McErlean
- Imperial College London, 4615, London, United Kingdom of Great Britain and Northern Ireland
| | - Christopher G Bell
- William Harvey Research Institute, 105713, London, United Kingdom of Great Britain and Northern Ireland
| | - Richard J Hewitt
- National Heart and Lung Institute, Inflammation, Repair & Development, London, United Kingdom of Great Britain and Northern Ireland
| | - Zabreen Busharat
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
| | - Patricia P Ogger
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
| | - Poonam Ghai
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
| | - Gesa J Albers
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
| | - Emily Calamita
- Imperial College London, 4615, London, United Kingdom of Great Britain and Northern Ireland
| | - Shaun Kingston
- Royal Brompton Hospital, 156726, Interstitial Lung Disease Unit, London, United Kingdom of Great Britain and Northern Ireland
| | - Philip L Molyneaux
- Imperial College London, National Heart and Lung Institute, London, United Kingdom of Great Britain and Northern Ireland
| | - Stephan Beck
- University College London, 4919, London, United Kingdom of Great Britain and Northern Ireland
| | - Clare M Lloyd
- Imperial College, Leukocyte Biology, London, United Kingdom of Great Britain and Northern Ireland
| | - Toby M Maher
- Royal Brompton Hospital, 156726, Interstitial Lung Disease Unit, London, United Kingdom of Great Britain and Northern Ireland;
| | - Adam J Byrne
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
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Acton RJ, Yuan W, Gao F, Xia Y, Bourne E, Wozniak E, Bell J, Lillycrop K, Wang J, Dennison E, Harvey NC, Mein CA, Spector TD, Hysi PG, Cooper C, Bell CG. The genomic loci of specific human tRNA genes exhibit ageing-related DNA hypermethylation. Nat Commun 2021; 12:2655. [PMID: 33976121 PMCID: PMC8113476 DOI: 10.1038/s41467-021-22639-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/05/2021] [Indexed: 02/03/2023] Open
Abstract
The epigenome has been shown to deteriorate with age, potentially impacting on ageing-related disease. tRNA, while arising from only ˜46 kb (<0.002% genome), is the second most abundant cellular transcript. tRNAs also control metabolic processes known to affect ageing, through core translational and additional regulatory roles. Here, we interrogate the DNA methylation state of the genomic loci of human tRNA. We identify a genomic enrichment for age-related DNA hypermethylation at tRNA loci. Analysis in 4,350 MeDIP-seq peripheral-blood DNA methylomes (16-82 years), identifies 44 and 21 hypermethylating specific tRNAs at study-and genome-wide significance, respectively, contrasting with none hypomethylating. Validation and replication (450k array and independent targeted Bisuphite-sequencing) supported the hypermethylation of this functional unit. Tissue-specificity is a significant driver, although the strongest consistent signals, also independent of major cell-type change, occur in tRNA-iMet-CAT-1-4 and tRNA-Ser-AGA-2-6. This study presents a comprehensive evaluation of the genomic DNA methylation state of human tRNA genes and reveals a discreet hypermethylation with advancing age.
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Affiliation(s)
- Richard J Acton
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Charterhouse Square, Queen Mary University of London, London, UK
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Wei Yuan
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, King's College London, London, UK
- Institute of Cancer Research, Sutton, UK
| | - Fei Gao
- BGI-Shenzhen, Shenzhen, China
| | | | - Emma Bourne
- Barts & The London Genome Centre, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Eva Wozniak
- Barts & The London Genome Centre, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jordana Bell
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, King's College London, London, UK
| | - Karen Lillycrop
- Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Jun Wang
- Shenzhen Digital Life Institute, Shenzhen, Guangdong, China
- iCarbonX, Zhuhai, Guangdong, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau, China
| | - Elaine Dennison
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Charles A Mein
- Barts & The London Genome Centre, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, King's College London, London, UK
| | - Pirro G Hysi
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, King's College London, London, UK
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Christopher G Bell
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Charterhouse Square, Queen Mary University of London, London, UK.
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Lechner M, Schartinger VH, Steele CD, Nei WL, Ooft ML, Schreiber LM, Pipinikas CP, Chung GTY, Chan YY, Wu F, To KF, Tsang CM, Pearce W, Morelli D, Philpott M, Masterson L, Nibhani R, Wells G, Bell CG, Koller J, Delecluse S, Yip YL, Liu J, Forde CT, Forster MD, Jay A, Dudás J, Krapp A, Wan S, Uprimny C, Sprung S, Haybaeck J, Fenton TR, Chester K, Thirlwell C, Royle G, Marafioti T, Gupta R, Indrasari SR, Herdini C, Slim MAM, Indrawati I, Sutton L, Fles R, Tan B, Yeong J, Jain A, Han S, Wang H, Loke KSH, He W, Xu R, Jin H, Cheng Z, Howard D, Hwang PH, Le QT, Tay JK, West RB, Tsao SW, Meyer T, Riechelmann H, Oppermann U, Delecluse HJ, Willems SM, Chua MLK, Busson P, Lo KW, Wollmann G, Pillay N, Vanhaesebroeck B, Lund VJ. Somatostatin receptor 2 expression in nasopharyngeal cancer is induced by Epstein Barr virus infection: impact on prognosis, imaging and therapy. Nat Commun 2021; 12:117. [PMID: 33402692 PMCID: PMC7785735 DOI: 10.1038/s41467-020-20308-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
Nasopharyngeal cancer (NPC), endemic in Southeast Asia, lacks effective diagnostic and therapeutic strategies. Even in high-income countries the 5-year survival rate for stage IV NPC is less than 40%. Here we report high somatostatin receptor 2 (SSTR2) expression in multiple clinical cohorts comprising 402 primary, locally recurrent and metastatic NPCs. We show that SSTR2 expression is induced by the Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1) via the NF-κB pathway. Using cell-based and preclinical rodent models, we demonstrate the therapeutic potential of SSTR2 targeting using a cytotoxic drug conjugate, PEN-221, which is found to be superior to FDA-approved SSTR2-binding cytostatic agents. Furthermore, we reveal significant correlation of SSTR expression with increased rates of survival and report in vivo uptake of the SSTR2-binding 68Ga-DOTA-peptide radioconjugate in PET-CT scanning in a clinical trial of NPC patients (NCT03670342). These findings reveal a key role in EBV-associated NPC for SSTR2 in infection, imaging, targeted therapy and survival.
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MESH Headings
- Animals
- Female
- Humans
- Male
- Mice
- Antineoplastic Agents/pharmacology
- Cell Line, Tumor
- Epstein-Barr Virus Infections/drug therapy
- Epstein-Barr Virus Infections/genetics
- Epstein-Barr Virus Infections/mortality
- Epstein-Barr Virus Infections/virology
- Gene Expression Regulation, Neoplastic
- Herpesvirus 4, Human/drug effects
- Herpesvirus 4, Human/growth & development
- Herpesvirus 4, Human/pathogenicity
- Host-Pathogen Interactions/genetics
- Lymphatic Metastasis
- Mice, Nude
- Molecular Targeted Therapy
- Nasopharyngeal Carcinoma/drug therapy
- Nasopharyngeal Carcinoma/genetics
- Nasopharyngeal Carcinoma/mortality
- Nasopharyngeal Carcinoma/virology
- Nasopharyngeal Neoplasms/drug therapy
- Nasopharyngeal Neoplasms/genetics
- Nasopharyngeal Neoplasms/mortality
- Nasopharyngeal Neoplasms/virology
- Neoplasm Recurrence, Local/drug therapy
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/mortality
- Neoplasm Recurrence, Local/virology
- NF-kappa B/genetics
- NF-kappa B/metabolism
- Octreotide/pharmacology
- Positron Emission Tomography Computed Tomography
- Receptors, Somatostatin/antagonists & inhibitors
- Receptors, Somatostatin/genetics
- Receptors, Somatostatin/metabolism
- Signal Transduction
- Survival Analysis
- Viral Matrix Proteins/antagonists & inhibitors
- Viral Matrix Proteins/genetics
- Viral Matrix Proteins/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Matt Lechner
- UCL Cancer Institute, University College London, London, UK.
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA.
- Barts Health NHS Trust, London, UK.
- Royal National Throat, Nose and Ear Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK.
| | - Volker H Schartinger
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Wen Long Nei
- Divisions of Radiation Oncology and Medical Sciences, National Cancer Centre, Singapore, Singapore
- Oncology Academic Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Marc Lucas Ooft
- King´s College Hospitals, NHS Foundation Trust, London, UK
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Liesa-Marie Schreiber
- Institute of Virology and Christian Doppler Laboratory for Viral Immunotherapy of Cancer, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Grace Tin-Yun Chung
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuk Yu Chan
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Feng Wu
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi Man Tsang
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wayne Pearce
- UCL Cancer Institute, University College London, London, UK
| | | | | | - Liam Masterson
- Department of Otolaryngology, Addenbrooke's Hospital, Cambridge, UK
| | - Reshma Nibhani
- Botnar Research Centre, University of Oxford, Oxford, UK
| | - Graham Wells
- Botnar Research Centre, University of Oxford, Oxford, UK
| | - Christopher G Bell
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Julia Koller
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
- Botnar Research Centre, University of Oxford, Oxford, UK
| | - Susanne Delecluse
- German Cancer Research Centre (DKFZ) and Inserm, Unit F100/U1074, Heidelberg, Germany
| | - Yim Ling Yip
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Jacklyn Liu
- UCL Cancer Institute, University College London, London, UK
| | - Cillian T Forde
- Royal National Throat, Nose and Ear Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Martin D Forster
- UCL Cancer Institute, University College London, London, UK
- Royal National Throat, Nose and Ear Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
| | - Amrita Jay
- Department of Histopathology, University College London Hospitals NHS Trust, Euston Road, London, UK
| | - József Dudás
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Annika Krapp
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Simon Wan
- Institute of Nuclear Medicine, University College Hospital, Euston Road, London, UK
| | - Christian Uprimny
- Department of Nuclear Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Susanne Sprung
- Department of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Haybaeck
- Department of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
- Diagnostic & Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, UK
| | - Kerry Chester
- UCL Cancer Institute, University College London, London, UK
| | - Christina Thirlwell
- UCL Cancer Institute, University College London, London, UK
- University of Exeter College of Medicine and Health, Exeter, UK
| | - Gary Royle
- UCL Cancer Institute, University College London, London, UK
| | | | - Rajeev Gupta
- UCL Cancer Institute, University College London, London, UK
| | - Sagung Rai Indrasari
- ENT Head and Neck Surgery Department, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Camelia Herdini
- ENT Head and Neck Surgery Department, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Mohd Afiq Mohd Slim
- Department of Ear, Nose and Throat, University Hospital Crosshouse, Crosshouse, Kilmarnock, UK
| | - I Indrawati
- Department of Anatomical Pathology, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | | | - Renske Fles
- Department of Head and Neck Surgery and Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bing Tan
- ENT Head and Neck Surgery Department, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
- Department of ENT/Head and Neck Surgery, Maastricht University Medical Center (MUMC), Maastricht, The Netherlands
| | - Joe Yeong
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Amit Jain
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Shuting Han
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Haitao Wang
- Divisions of Radiation Oncology and Medical Sciences, National Cancer Centre, Singapore, Singapore
| | - Kelvin S H Loke
- Department of Nuclear Medicine and Molecular Imaging, Singapore General Hospital, Singapore, Singapore
| | - Wan He
- Department of Oncology, The Second Clinical Medical College, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong, China
| | - Ruilian Xu
- Department of Oncology, The Second Clinical Medical College, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong, China
| | - Hongtao Jin
- Department of Pathology, The Second Clinical Medical College, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong, China
| | - Zhiqiang Cheng
- Department of Pathology, The Second Clinical Medical College, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong, China
| | - David Howard
- Royal National Throat, Nose and Ear Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK
- ENT Department, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Peter H Hwang
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Joshua K Tay
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore, Singapore
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sai Wah Tsao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Tim Meyer
- UCL Cancer Institute, University College London, London, UK
| | - Herbert Riechelmann
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Udo Oppermann
- Botnar Research Centre, University of Oxford, Oxford, UK
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, 79085, Freiburg, Germany
| | | | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Pathology, University Medical Center Groningen, Groningen, The Netherlands
| | - Melvin L K Chua
- Divisions of Radiation Oncology and Medical Sciences, National Cancer Centre, Singapore, Singapore
- Oncology Academic Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Pierre Busson
- CNRS-UMR 9018-METSY, Gustave Roussy and Université Paris-Saclay, Villejuif, France
| | - Kwok Wai Lo
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Guido Wollmann
- Institute of Virology and Christian Doppler Laboratory for Viral Immunotherapy of Cancer, Medical University of Innsbruck, Innsbruck, Austria
| | - Nischalan Pillay
- UCL Cancer Institute, University College London, London, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | | | - Valerie J Lund
- UCL Cancer Institute, University College London, London, UK.
- Royal National Throat, Nose and Ear Hospital and Head and Neck Centre, University College London Hospitals NHS Trust, London, UK.
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9
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Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JPJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK. DNA methylation aging clocks: challenges and recommendations. Genome Biol 2019; 20:249. [PMID: 31767039 PMCID: PMC6876109 DOI: 10.1186/s13059-019-1824-y] [Citation(s) in RCA: 410] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other vertebrates. Also, extensive research is aimed at their potential to quantify biological aging rates and test longevity or rejuvenating interventions. Here, we discuss key challenges to understand clock mechanisms and biomarker utility. This requires dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models. We also highlight important ethical issues in forensic age determination and predicting the trajectory of biological aging in an individual.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK.
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Stephan Beck
- Medical Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, London, UK.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
| | - Steve Horvath
- Department of Human Genetics, Gonda Research Center, David Geffen School of Medicine, Los Angeles, CA, USA.
- Department of Biostatistics, School of Public Health, University of California-Los Angeles, Los Angeles, CA, USA.
| | - Trey Ideker
- San Diego Center for Systems Biology, University of California-San Diego, San Diego, CA, USA.
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI, USA.
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.
- The Wellcome Trust Sanger Institute, Cambridge, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK.
| | | | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany.
| | - Kang Zhang
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau.
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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10
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Bowler EH, Smith-Vidal A, Lester A, Bell J, Wang Z, Bell CG, Wang Y, Divecha N, Skipp PJ, Ewing RM. Deep proteomic analysis of Dnmt1 mutant/hypomorphic colorectal cancer cells reveals dysregulation of epithelial-mesenchymal transition and subcellular re-localization of Beta-Catenin. Epigenetics 2019; 15:107-121. [PMID: 31448663 PMCID: PMC6961695 DOI: 10.1080/15592294.2019.1656154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
DNA methyltransferase I plays the central role in maintenance of CpG DNA methylation patterns across the genome and alteration of CpG methylation patterns is a frequent and significant occurrence across many cancers. Cancer cells carrying hypomorphic alleles of Dnmt1 have become important tools for understanding Dnmt1 function and CpG methylation. In this study, we analyse colorectal cancer cells with a homozygous deletion of exons 3 to 5 of Dnmt1, resulting in reduced Dnmt1 activity. Although this cell model has been widely used to study the epigenome, the effects of the Dnmt1 hypomorph on cell signalling pathways and the wider proteome are largely unknown. In this study, we perform the first quantitative proteomic analysis of this important cell model and identify multiple signalling pathways and processes that are significantly dysregulated in the hypomorph cells. In Dnmt1 hypomorph cells, we observed a clear and unexpected signature of increased Epithelial-to-Mesenchymal transition (EMT) markers as well as reduced expression and sub-cellular re-localization of Beta-Catenin. Expression of wild-type Dnmt1 in hypomorph cells or knock-down of wild-type Dnmt1 did not recapitulate or rescue the observed protein profiles in Dnmt1 hypomorph cells suggesting that hypomorphic Dnmt1 causes changes not solely attributable to Dnmt1 protein levels. In summary, we present the first comprehensive proteomic analysis of the widely studied Dnmt1 hypomorph colorectal cancer cells and identify redistribution of Dnmt1 and its interaction partner Beta-Catenin.
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Affiliation(s)
- Emily H Bowler
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Alex Smith-Vidal
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Alex Lester
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Joseph Bell
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Zhenghe Wang
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Christopher G Bell
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Yihua Wang
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Nullin Divecha
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Paul J Skipp
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Rob M Ewing
- School of Biological Sciences, University of Southampton, Southampton, UK
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11
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Curtis EM, Krstic N, Cook E, D'Angelo S, Crozier SR, Moon RJ, Murray R, Garratt E, Costello P, Cleal J, Ashley B, Bishop NJ, Kennedy S, Papageorghiou AT, Schoenmakers I, Fraser R, Gandhi SV, Prentice A, Javaid MK, Inskip HM, Godfrey KM, Bell CG, Lillycrop KA, Cooper C, Harvey NC. Gestational Vitamin D Supplementation Leads to Reduced Perinatal RXRA DNA Methylation: Results From the MAVIDOS Trial. J Bone Miner Res 2019; 34:231-240. [PMID: 30321476 PMCID: PMC6372078 DOI: 10.1002/jbmr.3603] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/10/2018] [Accepted: 10/06/2018] [Indexed: 11/20/2022]
Abstract
We have previously demonstrated inverse associations between maternal 25(OH)-vitamin D status and perinatal DNA methylation at the retinoid-X-receptor-alpha (RXRA) locus and between RXRA methylation and offspring bone mass. In this study, we used an existing randomized trial to test the hypothesis that maternal gestational vitamin D supplementation would lead to reduced perinatal RXRA locus DNA methylation. The Maternal Vitamin D Osteoporosis Study (MAVIDOS) was a multicenter, double-blind, randomized, placebo-controlled trial of 1000 IU/day cholecalciferol or matched placebo from 14 weeks' gestation until delivery. Umbilical cord (fetal) tissue was collected at birth and frozen at -80°C (n = 453). Pyrosequencing was used to undertake DNA methylation analysis at 10 CpG sites within the RXRA locus (identified previously). T tests were used to assess differences between treatment groups in methylation at the three most representative CpG sites. Overall, methylation levels were significantly lower in the umbilical cord from offspring of cholecalciferol-supplemented mothers, reaching statistical significance at four CpG sites, represented by CpG5: mean difference in % methylation between the supplemented and placebo groups was -1.98% (95% CI, -3.65 to -0.32, p = 0.02). ENCODE (Encyclopedia of DNA Elements) evidence supports the functionality of this locus with strong DNase hypersensitivity and enhancer chromatin within biologically relevant cell types including osteoblasts. Enrichment of the enhancer-related H3K4me1 histone mark is also seen in this region, as are binding sites for a range of transcription factors with roles in cell proliferation, response to stress, and growth factors. Our findings are consistent with previous observational results and provide new evidence that maternal gestational supplementation with cholecalciferol leads to altered perinatal epigenetic marking, informing mechanistic understanding of early life mechanisms related to maternal vitamin D status, epigenetic marks, and bone development. © 2018 The Authors. Journal of Bone and Mineral Research Published by Wiley Periodicals Inc.
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Affiliation(s)
| | - Nevena Krstic
- Institute of Developmental SciencesUniversity of SouthamptonUK
| | - Eloïse Cook
- Institute of Developmental SciencesUniversity of SouthamptonUK
| | | | | | - Rebecca J Moon
- MRC Lifecourse Epidemiology UnitUniversity of SouthamptonUK
- Paediatric EndocrinologyUniversity Hospitals Southampton NHS Foundation TrustSouthamptonUK
| | - Robert Murray
- Institute of Developmental SciencesUniversity of SouthamptonUK
| | - Emma Garratt
- Institute of Developmental SciencesUniversity of SouthamptonUK
| | - Paula Costello
- Institute of Developmental SciencesUniversity of SouthamptonUK
| | - Jane Cleal
- Institute of Developmental SciencesUniversity of SouthamptonUK
| | - Brogan Ashley
- Institute of Developmental SciencesUniversity of SouthamptonUK
| | - Nicholas J Bishop
- Academic Unit of Child HealthSheffield Children's HospitalUniversity of SheffieldSheffieldUK
| | - Stephen Kennedy
- Nuffield Department of Obstetrics and GynaecologyJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Aris T Papageorghiou
- Nuffield Department of Obstetrics and GynaecologyJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Inez Schoenmakers
- MRC Elsie Widdowson LaboratoryCambridgeUK
- Department of MedicineFaculty of Medicine and Health SciencesUniversity of East AngliaNorwichUK
| | - Robert Fraser
- Sheffield Hospitals NHS Trust(University of Sheffield)SheffieldUK
| | - Saurabh V Gandhi
- Sheffield Hospitals NHS Trust(University of Sheffield)SheffieldUK
| | | | - M Kassim Javaid
- NIHR Oxford Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Hazel M Inskip
- MRC Lifecourse Epidemiology UnitUniversity of SouthamptonUK
- NIHR Southampton Biomedical Research CentreUniversity of Southampton and University Hospital Southampton NHS Foundation TrustSouthamptonUK
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology UnitUniversity of SouthamptonUK
- NIHR Southampton Biomedical Research CentreUniversity of Southampton and University Hospital Southampton NHS Foundation TrustSouthamptonUK
| | - Christopher G Bell
- MRC Lifecourse Epidemiology UnitUniversity of SouthamptonUK
- Institute of Developmental SciencesUniversity of SouthamptonUK
| | | | - Cyrus Cooper
- MRC Lifecourse Epidemiology UnitUniversity of SouthamptonUK
- NIHR Oxford Biomedical Research CentreUniversity of OxfordOxfordUK
- NIHR Southampton Biomedical Research CentreUniversity of Southampton and University Hospital Southampton NHS Foundation TrustSouthamptonUK
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology UnitUniversity of SouthamptonUK
- NIHR Southampton Biomedical Research CentreUniversity of Southampton and University Hospital Southampton NHS Foundation TrustSouthamptonUK
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12
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Curtis EM, Titcombe P, Edwards M, Barton S, Tsai PC, Dennison EM, Bell J, Spector T, Valdes AM, Bell CG, Harvey NC, Cooper C. 090 DNA methylation and its relationship with musculoskeletal health in older adults from the Hertfordshire Cohort Study: findings from an epigenome-wide association study. Rheumatology (Oxford) 2018. [DOI: 10.1093/rheumatology/key075.314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Elizabeth M Curtis
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UNITED KINGDOM
| | - Philip Titcombe
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UNITED KINGDOM
| | - Mark Edwards
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UNITED KINGDOM
- Rheumatology Department, Portsmouth Hospitals NHS Trust, Portsmouth, UNITED KINGDOM
| | - Sheila Barton
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UNITED KINGDOM
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UNITED KINGDOM
| | - Elaine M Dennison
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UNITED KINGDOM
| | - Jordana Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UNITED KINGDOM
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UNITED KINGDOM
| | - Ana M Valdes
- Division of Rheumatology, Orthopaedics, and Dermatology, University of Nottingham, Nottingham, UNITED KINGDOM
| | - Christopher G Bell
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UNITED KINGDOM
- Institute of Developmental Sciences, University of Southampton, Southampton, UNITED KINGDOM
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UNITED KINGDOM
- NIHR Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, UNITED KINGDOM
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UNITED KINGDOM
- NIHR Oxford Musculoskeletal Biomedical Research Unit, University of Oxford, Oxford, UNITED KINGDOM
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13
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Bell CG, Gao F, Yuan W, Roos L, Acton RJ, Xia Y, Bell J, Ward K, Mangino M, Hysi PG, Wang J, Spector TD. Obligatory and facilitative allelic variation in the DNA methylome within common disease-associated loci. Nat Commun 2018; 9:8. [PMID: 29295990 PMCID: PMC5750212 DOI: 10.1038/s41467-017-01586-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 09/29/2017] [Indexed: 12/16/2022] Open
Abstract
Integrating epigenetic data with genome-wide association study (GWAS) results can reveal disease mechanisms. The genome sequence itself also shapes the epigenome, with CpG density and transcription factor binding sites (TFBSs) strongly encoding the DNA methylome. Therefore, genetic polymorphism impacts on the observed epigenome. Furthermore, large genetic variants alter epigenetic signal dosage. Here, we identify DNA methylation variability between GWAS-SNP risk and non-risk haplotypes. In three subsets comprising 3128 MeDIP-seq peripheral-blood DNA methylomes, we find 7173 consistent and functionally enriched Differentially Methylated Regions. 36.8% can be attributed to common non-SNP genetic variants. CpG-SNPs, as well as facilitative TFBS-motifs, are also enriched. Highlighting their functional potential, CpG-SNPs strongly associate with allele-specific DNase-I hypersensitivity sites. Our results demonstrate strong DNA methylation allelic differences driven by obligatory or facilitative genetic effects, with potential direct or regional disease-related repercussions. These allelic variations require disentangling from pure tissue-specific modifications, may influence array studies, and imply underestimated population variability in current reference epigenomes. Genomic polymorphisms affect the epigenome, which in turn influences how epigenome- and genome-wide analysis are interpreted. Here, the authors characterise allelic differences in DNA methylation driven by obligatory or facilitative genetic effects, which may affect disease-related loci.
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Affiliation(s)
- Christopher G Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK. .,MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK. .,Epigenomic Medicine, Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, SO17 1BJ, UK. .,Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, SO16 6YD, UK.
| | - Fei Gao
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Wei Yuan
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Leonie Roos
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Richard J Acton
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK.,Epigenomic Medicine, Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, SO17 1BJ, UK.,Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | | | - Jordana Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Kirsten Ward
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Pirro G Hysi
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Jun Wang
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK
| | - Timothy D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
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14
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Thurner M, van de Bunt M, Torres JM, Mahajan A, Nylander V, Bennett AJ, Gaulton KJ, Barrett A, Burrows C, Bell CG, Lowe R, Beck S, Rakyan VK, Gloyn AL, McCarthy MI. Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci. eLife 2018; 7:31977. [PMID: 29412141 PMCID: PMC5828664 DOI: 10.7554/elife.31977] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/06/2018] [Indexed: 12/30/2022] Open
Abstract
Human genetic studies have emphasised the dominant contribution of pancreatic islet dysfunction to development of Type 2 Diabetes (T2D). However, limited annotation of the islet epigenome has constrained efforts to define the molecular mechanisms mediating the, largely regulatory, signals revealed by Genome-Wide Association Studies (GWAS). We characterised patterns of chromatin accessibility (ATAC-seq, n = 17) and DNA methylation (whole-genome bisulphite sequencing, n = 10) in human islets, generating high-resolution chromatin state maps through integration with established ChIP-seq marks. We found enrichment of GWAS signals for T2D and fasting glucose was concentrated in subsets of islet enhancers characterised by open chromatin and hypomethylation, with the former annotation predominant. At several loci (including CDC123, ADCY5, KLHDC5) the combination of fine-mapping genetic data and chromatin state enrichment maps, supplemented by allelic imbalance in chromatin accessibility pinpointed likely causal variants. The combination of increasingly-precise genetic and islet epigenomic information accelerates definition of causal mechanisms implicated in T2D pathogenesis.
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Affiliation(s)
- Matthias Thurner
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom,Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Martijn van de Bunt
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom,Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Jason M Torres
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Anubha Mahajan
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Vibe Nylander
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Amanda J Bennett
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Kyle J Gaulton
- Department of PediatricsUniversity of California, San DiegoSan DiegoUnited States
| | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Carla Burrows
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Christopher G Bell
- Department of Twin Research and Genetic EpidemiologyKings College LondonLondonUnited Kingdom,MRC Lifecourse Epidemiology UnitUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Robert Lowe
- Centre for Genomics and Child Health, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUnited Kingdom
| | - Stephan Beck
- Department of Cancer Biology, UCL Cancer InstituteUniversity College LondonLondonUnited Kingdom
| | - Vardhman K Rakyan
- Centre for Genomics and Child Health, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUnited Kingdom
| | - Anna L Gloyn
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom,Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom,Oxford NIHR Biomedical Research CentreChurchill HospitalOxfordUnited Kingdom
| | - Mark I McCarthy
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom,Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom,Oxford NIHR Biomedical Research CentreChurchill HospitalOxfordUnited Kingdom
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15
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Simner C, Novakovic B, Lillycrop KA, Bell CG, Harvey NC, Cooper C, Saffery R, Lewis RM, Cleal JK. DNA methylation of amino acid transporter genes in the human placenta. Placenta 2017; 60:64-73. [PMID: 29208242 DOI: 10.1016/j.placenta.2017.10.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Placental transfer of amino acids via amino acid transporters is essential for fetal growth. Little is known about the epigenetic regulation of amino acid transporters in placenta. This study investigates the DNA methylation status of amino acid transporters and their expression across gestation in human placenta. METHODS BeWo cells were treated with 5-aza-2'-deoxycytidine to inhibit methylation and assess the effects on amino acid transporter gene expression. The DNA methylation levels of amino acid transporter genes in human placenta were determined across gestation using DNA methylation array data. Placental amino acid transporter gene expression across gestation was also analysed using data from publically available Gene Expression Omnibus data sets. The expression levels of these transporters at term were established using RNA sequencing data. RESULTS Inhibition of DNA methylation in BeWo cells demonstrated that expression of specific amino acid transporters can be inversely associated with DNA methylation. Amino acid transporters expressed in term placenta generally showed low levels of promoter DNA methylation. Transporters with little or no expression in term placenta tended to be more highly methylated at gene promoter regions. The transporter genes SLC1A2, SLC1A3, SLC1A4, SLC7A5, SLC7A11 and SLC7A10 had significant changes in enhancer DNA methylation across gestation, as well as gene expression changes across gestation. CONCLUSION This study implicates DNA methylation in the regulation of amino acid transporter gene expression. However, in human placenta, DNA methylation of these genes remains low across gestation and does not always play an obvious role in regulating gene expression, despite clear evidence for differential expression as gestation proceeds.
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Affiliation(s)
- C Simner
- The Institute of Developmental Sciences, University of Southampton, UK
| | - B Novakovic
- Cancer and Disease Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - K A Lillycrop
- The Institute of Developmental Sciences, University of Southampton, UK; Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - C G Bell
- The Institute of Developmental Sciences, University of Southampton, UK; MRC Lifecourse Epidemiology Unit, University of Southampton, UK
| | - N C Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK; NIHR Southampton Biomedical Research Centre, University of Southampton, University Hospital Southampton, NHS Foundation Trust, UK
| | - C Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK; NIHR Southampton Biomedical Research Centre, University of Southampton, University Hospital Southampton, NHS Foundation Trust, UK; NIHR Oxford Musculoskeletal Biomedical Research Unit, University of Oxford, UK
| | - R Saffery
- Cancer and Disease Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - R M Lewis
- The Institute of Developmental Sciences, University of Southampton, UK
| | - J K Cleal
- The Institute of Developmental Sciences, University of Southampton, UK.
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Bell CG, Seelanan P, O'Hare D. Microelectrode generator-collector systems for electrolytic titration: theoretical and practical considerations. Analyst 2017; 142:4048-4057. [PMID: 28980672 DOI: 10.1039/c7an01450c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electochemical generator-collector systems, where one electrode is used to generate a reagent, have a potentially large field of application in sensing and measurement. We present a new theoretical description for coplanar microelectrode disc-disc systems where the collector is passive (such as a potentiometric sensor) and the generator is operating at constant flux. This solution is then used to develop a leading order solution for such a system where the reagent reacts reversibly in solution, such as in acid-base titration, where a hydrogen ion flux is generated by electrolysis of water. The principal novel result of the theory is that such devices are constrained by a maximum reagent flux. The hydrogen ion concentration at the collector will only reflect the buffer capacity of the bulk solution if this constraint is met. Both mathematical solutions are evaluated with several microfabricated devices and reasonable agreement with theory is demonstrated.
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17
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Curtis EM, Murray R, Titcombe P, Cook E, Clarke-Harris R, Costello P, Garratt E, Holbrook JD, Barton S, Inskip H, Godfrey KM, Bell CG, Cooper C, Lillycrop KA, Harvey NC. Perinatal DNA Methylation at CDKN2A Is Associated With Offspring Bone Mass: Findings From the Southampton Women's Survey. J Bone Miner Res 2017; 32:2030-2040. [PMID: 28419547 PMCID: PMC5528139 DOI: 10.1002/jbmr.3153] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/28/2017] [Accepted: 04/07/2017] [Indexed: 12/21/2022]
Abstract
Poor intrauterine and childhood growth has been linked with the risk of osteoporosis in later life, a relationship that may in part be mediated through altered epigenetic regulation of genes. We previously identified a region within the promoter of the long non-coding RNA ANRIL encoded by the CDKN2A locus, at which differential DNA methylation at birth showed correlations with offspring adiposity. Given the common lineage of adipocytes and osteoblasts, we investigated the relationship between perinatal CDKN2A methylation and bone mass at ages 4 and 6 years. Using sodium bisulfite pyrosequencing, we measured the methylation status of the 9 CpGs within this region in umbilical cord samples from discovery (n = 332) and replication (n = 337) cohorts of children from the Southampton Women's Survey, whose bone mass was assessed by dual-energy X-ray absorptiomietry (DXA; Hologic Discovery). Inverse associations were found between perinatal CDKN2A methylation and whole-body minus head bone area (BA), bone mineral content (BMC), and areal bone mineral density (BMD). This was confirmed in replication and combined data sets (all p < 0.01), with each 10% increase in methylation being associated with a decrease in BMC of 4 to 9 g at age 4 years (p ≤ 0.001). Relationships were similar with 6-year bone mass. Functional investigation of the differentially methylated region in the SaOS-2 osteosarcoma cell line showed that transcription factors bound to the identified CpGs in a methylation-specific manner and that CpG mutagenesis modulated ANRIL expression. In conclusion, perinatal methylation at CDKN2A is associated with childhood bone development and has significance for cell function. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Elizabeth M Curtis
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Robert Murray
- Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Philip Titcombe
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Eloïse Cook
- Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | | | - Paula Costello
- Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Emma Garratt
- Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Joanna D Holbrook
- Institute of Developmental Sciences, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK.,Singapore Institute for Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
| | - Sheila Barton
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Hazel Inskip
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,Institute of Developmental Sciences, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Christopher G Bell
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,Institute of Developmental Sciences, University of Southampton, Southampton, UK.,Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK.,NIHR Oxford Musculoskeletal Biomedical Research Unit, University of Oxford, Oxford, UK
| | - Karen A Lillycrop
- Institute of Developmental Sciences, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK.,Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
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Abstract
OBJECTIVE Analysis of the epigenome-the chemical modifications and packaging of the genome that can influence or indicate its activity-enables molecular insight into cell type-specific machinery. It can, therefore, reveal the pathophysiological mechanisms at work in disease. Detected changes can also represent physiological responses to adverse environmental exposures, thus enabling the epigenetic mark of DNA methylation to act as an epidemiological biomarker, even in surrogate tissue. This makes epigenomic analysis an attractive prospect to further understand the pathobiology and epidemiological aspects of obesity. Furthermore, integrating epigenomic data with known obesity-associated common genetic variation can aid in deciphering their molecular mechanisms. METHODS AND CONCLUSIONS This review primarily examines epidemiological or population-based studies of epigenetic modifications in relation to adiposity traits, as opposed to animal or cell models. It discusses recent work exploring the epigenome with respect to human obesity, which to date has predominately consisted of array-based studies of DNA methylation in peripheral blood. It is of note that highly replicated BMI DNA methylation associations are not causal, but strongly driven by coassociations for more precisely measured intertwined outcomes and factors, such as hyperlipidemia, hyperglycemia, and inflammation. Finally, the potential for the future exploration of the epigenome in obesity and related disorders is considered.
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Affiliation(s)
- Christopher G Bell
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- Epigenomic Medicine, Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, UK
- Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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19
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Cook E, Curtis EM, Krstic N, D'Angelo S, Crozier SR, Moon RJ, Murray R, Garratt E, Costello P, Bishop NJ, Kennedy S, Papageorghiou AT, Schoenmakers I, Fraser R, Gandhi SV, Prentice A, Kassim Javaid M, Inskip HM, Godfrey KM, Bell CG, Cooper C, Lillycrop K, Harvey NC. 157. PERINATAL DNA METHYLATION AT THE RXRA PROMOTER IS ASSOCIATED WITH GESTATIONAL VITAMIN D SUPPLEMENTATION: RESULTS FROM THE MAVIDOS TRIAL. Rheumatology (Oxford) 2017. [DOI: 10.1093/rheumatology/kex062.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | | | | | - Rebecca J. Moon
- MRC Lifecourse Epidemiology Unit, University of Southampton
- Paediatric Endocrinology, University Hospitals Southampton NHS Foundation Trust, Southampton
| | | | | | | | - Nicholas J. Bishop
- Academic Unit of Child Health, Sheffield Children's Hospital, University of Sheffield, Sheffield
| | - Stephen Kennedy
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford
| | | | - Inez Schoenmakers
- MRC Elsie Widdowson
- Department of Medicine, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich
| | - Robert Fraser
- Sheffield Hospitals NHS Trust, University of Sheffield, Sheffield
| | | | | | - M Kassim Javaid
- NIHR Biomedical Research Centre, University of Oxford, Oxford
| | - Hazel M. Inskip
- MRC Lifecourse Epidemiology Unit, University of Southampton
- NIHR Southampton Nutrition Biomedical Research Centre, University of Southampton, Southampton, UNITED KINGDOM
| | - Keith M. Godfrey
- MRC Lifecourse Epidemiology Unit, University of Southampton
- NIHR Southampton Nutrition Biomedical Research Centre, University of Southampton, Southampton, UNITED KINGDOM
| | - Christopher G. Bell
- Institute of Developmental Sciences
- MRC Lifecourse Epidemiology Unit, University of Southampton
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton
- NIHR Biomedical Research Centre, University of Oxford, Oxford
| | | | - Nicholas C. Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton
- NIHR Southampton Nutrition Biomedical Research Centre, University of Southampton, Southampton, UNITED KINGDOM
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Roos L, Sandling JK, Bell CG, Glass D, Mangino M, Spector TD, Deloukas P, Bataille V, Bell JT. Higher Nevus Count Exhibits a Distinct DNA Methylation Signature in Healthy Human Skin: Implications for Melanoma. J Invest Dermatol 2016; 137:910-920. [PMID: 27993549 PMCID: PMC5754330 DOI: 10.1016/j.jid.2016.11.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/14/2016] [Accepted: 11/21/2016] [Indexed: 12/13/2022]
Abstract
High nevus count is the strongest risk factor for melanoma, and although gene variants have been discovered for both traits, epigenetic variation is unexplored. We investigated 322 healthy human skin DNA methylomes associated with total body nevi count, incorporating genetic and transcriptomic variation. DNA methylation changes were identified at genes involved in melanocyte biology, such as RAF1 (P = 1.2 × 10-6) and CTC1 (region: P = 6.3 × 10-4), and other genes including ARRDC1 (P = 3.1 × 10-7). A subset exhibited coordinated methylation and transcription changes within the same biopsy. The total analysis was also enriched for melanoma-associated DNA methylation variation (P = 6.33 × 10-6). In addition, we show that skin DNA methylation is associated in cis with known genome-wide association study single nucleotide polymorphisms for nevus count, at PLA2G6 (P = 1.7 × 10-49) and NID1 (P = 6.4 × 10-14), as well as melanoma risk, including in or near MC1R, MX2, and TERT/CLPTM1L (P < 1 × 10-10). Our analysis using a uniquely large dataset comprising healthy skin DNA methylomes identified known and additional regulatory loci and pathways in nevi and melanoma biology. This integrative study improves our understanding of predisposition to nevi and their potential contribution to melanoma pathogenesis.
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Affiliation(s)
- Leonie Roos
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; MRC London Institute of Medical Sciences, London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
| | - Johanna K Sandling
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Christopher G Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, UK; Epigenomic Medicine, Centre for Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, UK
| | - Daniel Glass
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Panos Deloukas
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Veronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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21
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Maiarù M, Tochiki KK, Cox MB, Annan LV, Bell CG, Feng X, Hausch F, Géranton SM. The stress regulator FKBP51 drives chronic pain by modulating spinal glucocorticoid signaling. Sci Transl Med 2016; 8:325ra19. [PMID: 26865567 DOI: 10.1126/scitranslmed.aab3376] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Polymorphisms in FKBP51 are associated with stress-related psychiatric disorders and influence the severity of pain symptoms experienced after trauma. We report that FKBP51 (FK506 binding protein 51) is crucial for the full development and maintenance of long-term pain states. Indeed, FKBP51 knockout mice, as well as mice in which silencing of FKBP51 is restricted to the spinal cord, showed reduced hypersensitivity in several persistent pain models in rodents. FKBP51 deletion did not compromise the detection of acute painful stimuli, a critical protective mechanism. Moreover, the intrathecal administration of the specific FKBP51 inhibitor SAFit2 reduced the severity of an established pain state, confirming the crucial role of spinal FKBP51 in nociceptive processing. Finally, glucocorticoid signaling, which is known to modulate persistent pain states in rodents, was impaired in FKBP51 knockout mice. This finding suggested that FKBP51 regulates chronic pain by modulation of glucocorticoid signaling. Thus, FKBP51 is a central mediator of chronic pain, likely in humans as well as rodents, and is a new pharmacologically tractable target for the treatment of long-term pain states.
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Affiliation(s)
- Maria Maiarù
- Cell and Developmental Biology, University College London (UCL), London WC1E 6BT, UK
| | - Keri K Tochiki
- Cell and Developmental Biology, University College London (UCL), London WC1E 6BT, UK
| | - Marc B Cox
- Border Biomedical Research Center and Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79902, USA
| | - Leonette V Annan
- Cell and Developmental Biology, University College London (UCL), London WC1E 6BT, UK
| | - Christopher G Bell
- Epigenomic Medicine, Centre for Biological Sciences, Institute of Developmental Sciences, S017 1BJ, and MRC (Medical Research Council) Lifecourse Epidemiology Unit, S016 6YD, University of Southampton, Southampton, UK
| | - Xixi Feng
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Felix Hausch
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Sandrine M Géranton
- Cell and Developmental Biology, University College London (UCL), London WC1E 6BT, UK.
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22
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Bell CG. Insights in human epigenomic dynamics through comparative primate analysis. Genomics 2016; 108:115-125. [DOI: 10.1016/j.ygeno.2016.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 08/03/2016] [Accepted: 09/29/2016] [Indexed: 12/11/2022]
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Bell CG, Xia Y, Yuan W, Gao F, Ward K, Roos L, Mangino M, Hysi PG, Bell J, Wang J, Spector TD. Novel regional age-associated DNA methylation changes within human common disease-associated loci. Genome Biol 2016; 17:193. [PMID: 27663977 PMCID: PMC5034469 DOI: 10.1186/s13059-016-1051-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/31/2016] [Indexed: 12/19/2022] Open
Abstract
Background Advancing age progressively impacts on risk and severity of chronic disease. It also modifies the epigenome, with changes in DNA methylation, due to both random drift and variation within specific functional loci. Results In a discovery set of 2238 peripheral-blood genome-wide DNA methylomes aged 19–82 years, we identify 71 age-associated differentially methylated regions within the linkage disequilibrium blocks of the single nucleotide polymorphisms from the NIH genome-wide association study catalogue. This included 52 novel regions, 29 within loci not covered by 450 k or 27 k Illumina array, and with enrichment for DNase-I Hypersensitivity sites across the full range of tissues. These age-associated differentially methylated regions also show marked enrichment for enhancers and poised promoters across multiple cell types. In a replication set of 2084 DNA methylomes, 95.7 % of the age-associated differentially methylated regions showed the same direction of ageing effect, with 80.3 % and 53.5 % replicated to p < 0.05 and p < 1.85 × 10–8, respectively. Conclusion By analysing the functionally enriched disease and trait-associated regions of the human genome, we identify novel epigenetic ageing changes, which could be useful biomarkers or provide mechanistic insights into age-related common diseases. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1051-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher G Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK. .,MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK. .,Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, UK. .,Epigenomic Medicine, Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, UK.
| | | | - Wei Yuan
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK.,Institute of Cancer Research, Sutton, UK
| | - Fei Gao
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Kirsten Ward
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Leonie Roos
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Pirro G Hysi
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jordana Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Timothy D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
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24
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Livshits G, Gao F, Malkin I, Needhamsen M, Xia Y, Yuan W, Bell CG, Ward K, Liu Y, Wang J, Bell JT, Spector TD. Contribution of Heritability and Epigenetic Factors to Skeletal Muscle Mass Variation in United Kingdom Twins. J Clin Endocrinol Metab 2016; 101:2450-9. [PMID: 27144936 PMCID: PMC4891794 DOI: 10.1210/jc.2016-1219] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
CONTEXT Skeletal muscle mass (SMM) is one of the major components of human body composition, with deviations from normal values often leading to sarcopenia. OBJECTIVE Our major aim was to conduct a genome-wide DNA methylation study in an attempt to identify potential genomic regions associated with SMM. DESIGN This was a mixed cross-sectional and longitudinal study. SETTING Community-based study. PARTICIPANTS A total of 1550 middle-aged United Kingdom twins (monozygotic [MZ] and dizygotic [DZ]), 297 of which were repeatedly measured participated in the study. MAIN OUTCOME MEASURE Appendicular lean mass assessed using dual-energy X-ray absorptiometry technology, and methylated DNA immunoprecipitation sequencing DNA methylation profiling genome-wide were obtained from each individual. RESULTS Heritability estimate of SMM, with simultaneous adjustment for covariates obtained using variance decomposition analysis, was h(2) = 0.809 ± 0.050. After quality control and analysis of longitudinal stability, the DNA methylation data comprised of 723 029 genomic sites, with positive correlations between repeated measurements (Rrepeated = 0.114-0.905). Correlations between MZ and DZ twins were 0.51 and 0.38 at a genome-wide average, respectively, and clearly increased with Rrepeated. Testing for DNA methylation association with SMM in 50 discordant MZ twins revealed 36 081 nominally significant results, of which the top-ranked 134 signals (P < .01 and Rrepeated > 0.40) were subjected to replication in the sample of 1196 individuals. Seven SMM methylation association signals replicated at a false discovery rate less than 0.1, and these were located in or near genes DNAH12, CAND1, CYP4F29P, and ZFP64, which have previously been highlighted in muscle-related studies. Adjusting for age, smoking, and blood cell heterogeneity did not alter significance of these associations. CONCLUSION This epigenome-wide study, testing longitudinally stable methylation sites, discovered and replicated a number of associations between DNA methylation at CpG loci and SMM. Four replicated signals were related to genes with potential muscle functions, suggesting that the methylome of whole blood may be informative of SMM variation.
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25
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Roos L, van Dongen J, Bell CG, Burri A, Deloukas P, Boomsma DI, Spector TD, Bell JT. Integrative DNA methylome analysis of pan-cancer biomarkers in cancer discordant monozygotic twin-pairs. Clin Epigenetics 2016; 8:7. [PMID: 26798410 PMCID: PMC4721070 DOI: 10.1186/s13148-016-0172-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/12/2016] [Indexed: 02/06/2023] Open
Abstract
Background A key focus in cancer research is the discovery of biomarkers that accurately diagnose early lesions in non-invasive tissues. Several studies have identified malignancy-associated DNA methylation changes in blood, yet no general cancer biomarker has been identified to date. Here, we explore the potential of blood DNA methylation as a biomarker of pan-cancer (cancer of multiple different origins) in 41 female cancer discordant monozygotic (MZ) twin-pairs sampled before or after diagnosis using the Illumina HumanMethylation450 BeadChip. Results We analysed epigenome-wide DNA methylation profiles in 41 cancer discordant MZ twin-pairs with affected individuals diagnosed with tumours at different single primary sites: the breast, cervix, colon, endometrium, thyroid gland, skin (melanoma), ovary, and pancreas. No significant global differences in whole blood DNA methylation profiles were observed. Epigenome-wide analyses identified one novel pan-cancer differentially methylated position at false discovery rate (FDR) threshold of 10 % (cg02444695, P = 1.8 × 10−7) in an intergenic region 70 kb upstream of the SASH1 tumour suppressor gene, and three suggestive signals in COL11A2, AXL, and LINC00340. Replication of the four top-ranked signals in an independent sample of nine cancer-discordant MZ twin-pairs showed a similar direction of association at COL11A2, AXL, and LINC00340, and significantly greater methylation discordance at AXL compared to 480 healthy concordant MZ twin-pairs. The effects at cg02444695 (near SASH1), COL11A2, and LINC00340 were the most promising in biomarker potential because the DNA methylation differences were found to pre-exist in samples obtained prior to diagnosis and were limited to a 5-year period before diagnosis. Gene expression follow-up at the top-ranked signals in 283 healthy individuals showed correlation between blood methylation and gene expression in lymphoblastoid cell lines at PRL, and in the skin tissue at AXL. A significant enrichment of differential DNA methylation was observed in enhancer regions (P = 0.03). Conclusions We identified DNA methylation signatures in blood associated with pan-cancer, at or near SASH1, COL11A2, AXL, and LINC00340. Three of these signals were present up to 5 years prior to cancer diagnosis, highlighting the potential clinical utility of whole blood DNA methylation analysis in cancer surveillance. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0172-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leonie Roos
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jenny van Dongen
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Christopher G Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK ; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK ; Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, UK ; Epigenomic Medicine, Centre for Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, UK
| | - Andrea Burri
- Department of Psychology, University of Zurich, Zurich, Switzerland
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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Abstract
Cancer is a set of diseases that exhibit not only genetic mutations but also a profoundly distorted epigenetic landscape. Over the last two decades, great advances have been made in identifying these alterations and their importance in the initiation and progression of cancer. Epigenetic changes can be seen from the very early stages in tumorigenesis and dysregulation of the epigenome has an increasingly acknowledged pathogenic role. Epigenomic twin studies have great potential to contribute to our understanding of complex diseases, such as cancer. This is because the use of monozygotic twins discordant for cancer enables epigenetic variation analysis without the confounding influence of the constitutive genetic background, age or cohort effects. It therefore allows the identification of susceptibility loci that may be sensitive to modification by the environment. These studies into cancer etiology will potentially lead to robust epigenetic markers for the detection and risk assessment of cancer.
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Affiliation(s)
- Leonie Roos
- Department of Twin Research & Genetic Epidemiology, St Thomas' Hospital, King's College London, London, SE1 7EH, UK
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Yuan W, Xia Y, Bell CG, Yet I, Ferreira T, Ward KJ, Gao F, Loomis AK, Hyde CL, Wu H, Lu H, Liu Y, Small KS, Viñuela A, Morris AP, Berdasco M, Esteller M, Brosnan MJ, Deloukas P, McCarthy MI, John SL, Bell JT, Wang J, Spector TD. An integrated epigenomic analysis for type 2 diabetes susceptibility loci in monozygotic twins. Nat Commun 2014; 5:5719. [PMID: 25502755 PMCID: PMC4284644 DOI: 10.1038/ncomms6719] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 10/31/2014] [Indexed: 01/05/2023] Open
Abstract
DNA methylation has a great potential for understanding the aetiology of common complex traits such as Type 2 diabetes (T2D). Here we perform genome-wide methylated DNA immunoprecipitation sequencing (MeDIP-seq) in whole-blood-derived DNA from 27 monozygotic twin pairs and follow up results with replication and integrated omics analyses. We identify predominately hypermethylated T2D-related differentially methylated regions (DMRs) and replicate the top signals in 42 unrelated T2D cases and 221 controls. The strongest signal is in the promoter of the MALT1 gene, involved in insulin and glycaemic pathways, and related to taurocholate levels in blood. Integrating the DNA methylome findings with T2D GWAS meta-analysis results reveals a strong enrichment for DMRs in T2D-susceptibility loci. We also detect signals specific to T2D-discordant twins in the GPR61 and PRKCB genes. These replicated T2D associations reflect both likely causal and consequential pathways of the disease. The analysis indicates how an integrated genomics and epigenomics approach, utilizing an MZ twin design, can provide pathogenic insights as well as potential drug targets and biomarkers for T2D and other complex traits. Type 2 diabetes (T2D) is a highly heterogeneous disease with a strong genetic component. Here the authors examine genome-wide methylation patterns in T2D-discordant, T2D-concordant and healthy concordant monozygotic twin pairs, and identify DNA methylation signals that may represent new biomarkers or drug targets for T2D.
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Affiliation(s)
- Wei Yuan
- Department of Twin Research &Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | | | - Christopher G Bell
- Department of Twin Research &Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Idil Yet
- Department of Twin Research &Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Teresa Ferreira
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Kirsten J Ward
- Department of Twin Research &Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Fei Gao
- BGI-Shenzhen, Shenzhen 518083, China
| | - A Katrina Loomis
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, USA
| | - Craig L Hyde
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, USA
| | | | - Hanlin Lu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yuan Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Kerrin S Small
- Department of Twin Research &Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Ana Viñuela
- Department of Twin Research &Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Andrew P Morris
- 1] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK [2] Department of Biostatistics, University of Liverpool, Liverpool L69 3GA, UK
| | - María Berdasco
- Cancer Epigenetics and Biology Program (PEBC), Hospital Duran i Reynals, Barcelona 08908, Spain
| | - Manel Esteller
- 1] Cancer Epigenetics and Biology Program (PEBC), Hospital Duran i Reynals, Barcelona 08908, Spain [2] Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia 08907, Spain [3] Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain
| | - M Julia Brosnan
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA
| | - Panos Deloukas
- 1] William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK [2] King Abdulaziz University, Jeddah 22254, Saudi Arabia
| | - Mark I McCarthy
- 1] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK [2] Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, oxford OX3 7LE, UK [3] Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford OX3 7LE, UK
| | - Sally L John
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA
| | - Jordana T Bell
- Department of Twin Research &Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Jun Wang
- 1] BGI-Shenzhen, Shenzhen 518083, China [2] King Abdulaziz University, Jeddah 22254, Saudi Arabia [3] Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark [4] The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Tim D Spector
- Department of Twin Research &Genetic Epidemiology, King's College London, London SE1 7EH, UK
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Abstract
BACKGROUND Targeted recruitment of chromatin-modifying enzymes to clusters of CpG dinucleotides contributes toward the formation of accessible chromatin. By interprimate comparison we previously identified the set of nonpolymorphic human-specific CpGs (CpG 'beacons') and revealed that these loci were enriched for human disease traits. Due to their human-specific CpG density change, extreme CpG 'beacon' clusters (≥20 CpG beacons/kb) were predicted to identify permissive chromatin peaks within the human genome. AIM We set out to explore these sequence-defined regions for evidence of an active chromatin signature. RESULTS Using available comparative primate epigenomic data from neurons of the prefrontal cortex, we show that these CpG 'beacon' clusters are indeed enriched for being human-specific H3K4me3 peaks (χ(2): p < 2.2 × 10(-16)) and thus predictive of permissive chromatin states. These sequence regions had a higher predictive value than previous selective analyses. We also show that both human-specific H3K4me3 and CpG 'beacon' clusters are increased within current and ancestral telomeric regions, supporting an association with recombination, which is higher towards the distal ends of chromosomes. CONCLUSION Therefore, CpG-focused comparative sequence analysis can precisely pinpoint chromatin structures that contribute to the human-specific phenotype and further supports an integrated approach in genomic and epigenomic studies.
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Affiliation(s)
- Christopher G Bell
- Medical Genomics, UCL Cancer Institute, University College London, London, UK
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Wilson GA, Butcher LM, Foster HR, Feber A, Roos C, Walter L, Woszczek G, Beck S, Bell CG. Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases. Genome Med 2014; 6:19. [PMID: 24598577 PMCID: PMC4062055 DOI: 10.1186/gm536] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 02/24/2014] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Common human diseases are caused by the complex interplay of genetic susceptibility as well as environmental factors. Due to the environment's influence on the epigenome, and therefore genome function, as well as conversely the genome's facilitative effect on the epigenome, analysis of this level of regulation may increase our knowledge of disease pathogenesis. METHODS In order to identify human-specific epigenetic influences, we have performed a novel genome-wide DNA methylation analysis comparing human, chimpanzee and rhesus macaque. RESULTS We have identified that the immunological Leukotriene B4 receptor (LTB4R, BLT1 receptor) is the most epigenetically divergent human gene in peripheral blood in comparison with other primates. This difference is due to the co-ordinated active state of human-specific hypomethylation in the promoter and human-specific increased gene body methylation. This gene is significant in innate immunity and the LTB4/LTB4R pathway is involved in the pathogenesis of the spectrum of human inflammatory diseases. This finding was confirmed by additional neutrophil-only DNA methylome and lymphoblastoid H3K4me3 chromatin comparative data. Additionally we show through functional analysis that this receptor has increased expression and a higher response to the LTB4 ligand in human versus rhesus macaque peripheral blood mononuclear cells. Genome-wide we also find human species-specific differentially methylated regions (human s-DMRs) are more prevalent in CpG island shores than within the islands themselves, and within the latter are associated with the CTCF motif. CONCLUSIONS This result further emphasises the exclusive nature of the human immunological system, its divergent adaptation even from very closely related primates, and the power of comparative epigenomics to identify and understand human uniqueness.
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Affiliation(s)
- Gareth A Wilson
- Medical Genomics, UCL Cancer Institute, University College London, London, UK ; Current address: Translational Cancer Therapeutics, CR-UK London Research Institute, Lincoln's Inn Fields, London, UK
| | - Lee M Butcher
- Medical Genomics, UCL Cancer Institute, University College London, London, UK
| | - Holly R Foster
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, Division of Asthma, Allergy and Lung Biology, King's College London, London, UK
| | - Andrew Feber
- Medical Genomics, UCL Cancer Institute, University College London, London, UK
| | - Christian Roos
- Genebank of Primates and Primate Genetics Laboratory, German Primate Centre, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Lutz Walter
- Genebank of Primates and Primate Genetics Laboratory, German Primate Centre, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Grzegorz Woszczek
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, Division of Asthma, Allergy and Lung Biology, King's College London, London, UK
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London, UK
| | - Christopher G Bell
- Medical Genomics, UCL Cancer Institute, University College London, London, UK ; Current address: Department of Twin Research & Genetic Epidemiology, St Thomas' Hospital, King's College London, London, UK
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Bell CG. The long-time chronoamperometric current at an inlaid microband (or laminar) electrode. Sensors (Basel) 2013; 13:626-47. [PMID: 23291578 PMCID: PMC3574695 DOI: 10.3390/s130100626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 12/20/2012] [Accepted: 12/21/2012] [Indexed: 11/22/2022]
Abstract
In this article, we derive an approximate asymptotic analytical expression for the long-time chronoamperometric current response at an inlaid microband (or laminar) electrode. The expression is applicable when the length of the microband is much greater than the width, so that the diffusion of the electrochemical species can be regarded as two-dimensional. We extend the previously known result for the diffusion-limited current response (Aoki, K. et al. J. Electroanal. Chem. 1987, 225, 19–32 and Phillips, C.G. J. Electroanal. Chem. 1992, 333, 11–32) to accommodate quasi-reversible reactions and unequal diffusion coefficients of the oxidant and the reductant. Comparison with numerical calculations validates the analytical expression, and we demonstrate that unequal diffusion coefficients can substantially change the current response. Finally, we discuss the form of the long-time current response for a one-step, one-electron redox reaction if the rate constants are modelled in the Butler–Volmer framework, and indicate the importance of choosing the width of the microband appropriately to allow accurate experimental determination of the standard kinetic rate constant and the electron transfer coefficient.
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Bell CG, Wilson GA, Butcher LM, Roos C, Walter L, Beck S. Human-specific CpG "beacons" identify loci associated with human-specific traits and disease. Epigenetics 2012; 7:1188-99. [PMID: 22968434 PMCID: PMC3469460 DOI: 10.4161/epi.22127] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Regulatory change has long been hypothesized to drive the delineation of the human phenotype from other closely related primates. Here we provide evidence that CpG dinucleotides play a special role in this process. CpGs enable epigenome variability via DNA methylation, and this epigenetic mark functions as a regulatory mechanism. Therefore, species-specific CpGs may influence species-specific regulation. We report non-polymorphic species-specific CpG dinucleotides (termed “CpG beacons”) as a distinct genomic feature associated with CpG island (CGI) evolution, human traits and disease. Using an inter-primate comparison, we identified 21 extreme CpG beacon clusters (≥ 20/kb peaks, empirical p < 1.0 × 10−3) in humans, which include associations with four monogenic developmental and neurological disease related genes (Benjamini-Hochberg corrected p = 6.03 × 10−3). We also demonstrate that beacon-mediated CpG density gain in CGIs correlates with reduced methylation in these species in orthologous CGIs over time, via human, chimpanzee and macaque MeDIP-seq. Therefore mapping into both the genomic and epigenomic space the identified CpG beacon clusters define points of intersection where a substantial two-way interaction between genetic sequence and epigenetic state has occurred. Taken together, our data support a model for CpG beacons to contribute to CGI evolution from genesis to tissue-specific to constitutively active CGIs.
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Affiliation(s)
- Christopher G Bell
- Medical Genomics, UCL Cancer Institute, University College London, London, UK.
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Bell CG, Anastassiou CA, O’Hare D, Parker KH, Siggers JH. Theory of large-amplitude sinusoidal voltammetry for reversible redox reactions. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.07.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Rakyan VK, Beyan H, Down TA, Hawa MI, Maslau S, Aden D, Daunay A, Busato F, Mein CA, Manfras B, Dias KRM, Bell CG, Tost J, Boehm BO, Beck S, Leslie RD. Identification of type 1 diabetes-associated DNA methylation variable positions that precede disease diagnosis. PLoS Genet 2011; 7:e1002300. [PMID: 21980303 PMCID: PMC3183089 DOI: 10.1371/journal.pgen.1002300] [Citation(s) in RCA: 271] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 08/03/2011] [Indexed: 12/24/2022] Open
Abstract
Monozygotic (MZ) twin pair discordance for childhood-onset Type 1 Diabetes (T1D) is ∼50%, implicating roles for genetic and non-genetic factors in the aetiology of this complex autoimmune disease. Although significant progress has been made in elucidating the genetics of T1D in recent years, the non-genetic component has remained poorly defined. We hypothesized that epigenetic variation could underlie some of the non-genetic component of T1D aetiology and, thus, performed an epigenome-wide association study (EWAS) for this disease. We generated genome-wide DNA methylation profiles of purified CD14+ monocytes (an immune effector cell type relevant to T1D pathogenesis) from 15 T1D–discordant MZ twin pairs. This identified 132 different CpG sites at which the direction of the intra-MZ pair DNA methylation difference significantly correlated with the diabetic state, i.e. T1D–associated methylation variable positions (T1D–MVPs). We confirmed these T1D–MVPs display statistically significant intra-MZ pair DNA methylation differences in the expected direction in an independent set of T1D–discordant MZ pairs (P = 0.035). Then, to establish the temporal origins of the T1D–MVPs, we generated two further genome-wide datasets and established that, when compared with controls, T1D–MVPs are enriched in singletons both before (P = 0.001) and at (P = 0.015) disease diagnosis, and also in singletons positive for diabetes-associated autoantibodies but disease-free even after 12 years follow-up (P = 0.0023). Combined, these results suggest that T1D–MVPs arise very early in the etiological process that leads to overt T1D. Our EWAS of T1D represents an important contribution toward understanding the etiological role of epigenetic variation in type 1 diabetes, and it is also the first systematic analysis of the temporal origins of disease-associated epigenetic variation for any human complex disease. Type 1 diabetes (T1D) is a complex autoimmune disease affecting >30 million people worldwide. It is caused by a combination of genetic and non-genetic factors, leading to destruction of insulin-secreting cells. Although significant progress has recently been made in elucidating the genetics of T1D, the non-genetic component has remained poorly defined. Epigenetic modifications, such as methylation of DNA, are indispensable for genomic processes such as transcriptional regulation and are frequently perturbed in human disease. We therefore hypothesized that epigenetic variation could underlie some of the non-genetic component of T1D aetiology, and we performed a genome-wide DNA methylation analysis of a specific subset of immune cells (monocytes) from monozygotic twins discordant for T1D. This revealed the presence of T1D–specific methylation variable positions (T1D–MVPs) in the T1D–affected co-twins. Since these T1D–MVPs were found in MZ twins, they cannot be due to genetic differences. Additional experiments revealed that some of these T1D–MVPs are found in individuals before T1D diagnosis, suggesting they arise very early in the process that leads to overt T1D and are not simply due to post-disease associated factors (e.g. medication or long-term metabolic changes). T1D–MVPs may thus potentially represent a previously unappreciated, and important, component of type 1 diabetes risk.
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Affiliation(s)
- Vardhman K Rakyan
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom.
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Abstract
The analysis of complex diseases was revolutionized by the ability to genotype at a genome-wide level tagging common SNPs in sufficiently large, and therefore adequately powered, population sample sets. This technological breakthrough has led to thousands of genetic variants being robustly associated with a multitude of phenotypic traits. These findings have illuminated novel genes and previously unknown pathways in the pathogenesis of disease, although in the majority of loci the functional mechanism remains unknown. The integration of this genomic information with epigenomic and transcriptomic data from these regions is one of the next steps in unraveling their biological significance. Allele-specific methylation influences allele-specific expression; therefore, the methylation state of the haplotypes within genetically associated regions can determine epigenetic differences with potential functional effects. DNA methylation data and association-determined risk and nonrisk haplotypes can be compared by a haplotype-specific methylation analysis. These are the first forays into what will become an increasingly routine multidimensional analysis as whole-genome, epigenome and transcriptome sequencing data become easily obtainable, with existing second- and soon to be available third-generation sequencing analyzers. Concise understanding of the functional implications of these genome-wide association-derived risk factors, plus rare variants discovered from deep sequencing experiments currently underway, will enable personalized risk and prevention profiling, as well as treatment, to come to fruition.
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Affiliation(s)
- Christopher G Bell
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6BT, UK.
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Bell CG, Finer S, Lindgren CM, Wilson GA, Rakyan VK, Teschendorff AE, Akan P, Stupka E, Down TA, Prokopenko I, Morison IM, Mill J, Pidsley R, Deloukas P, Frayling TM, Hattersley AT, McCarthy MI, Beck S, Hitman GA. Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus. PLoS One 2010; 5:e14040. [PMID: 21124985 PMCID: PMC2987816 DOI: 10.1371/journal.pone.0014040] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 10/27/2010] [Indexed: 01/04/2023] Open
Abstract
Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in the context of Type 2 Diabetes (T2D), focussing on known regions of genomic susceptibility. We assayed DNA methylation in 60 females, stratified according to disease susceptibility haplotype using previously identified association loci. CpG methylation was assessed using methylated DNA immunoprecipitation on a targeted array (MeDIP-chip) and absolute methylation values were estimated using a Bayesian algorithm (BATMAN). Absolute methylation levels were quantified across LD blocks, and we identified increased DNA methylation on the FTO obesity susceptibility haplotype, tagged by the rs8050136 risk allele A (p = 9.40×10−4, permutation p = 1.0×10−3). Further analysis across the 46 kb LD block using sliding windows localised the most significant difference to be within a 7.7 kb region (p = 1.13×10−7). Sequence level analysis, followed by pyrosequencing validation, revealed that the methylation difference was driven by the co-ordinated phase of CpG-creating SNPs across the risk haplotype. This 7.7 kb region of haplotype-specific methylation (HSM), encapsulates a Highly Conserved Non-Coding Element (HCNE) that has previously been validated as a long-range enhancer, supported by the histone H3K4me1 enhancer signature. This study demonstrates that integration of Genome-Wide Association (GWA) SNP and epigenomic DNA methylation data can identify potential novel genotype-epigenotype interactions within disease-associated loci, thus providing a novel route to aid unravelling common complex diseases.
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Affiliation(s)
- Christopher G Bell
- Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom.
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Abstract
The epigenome plays the pivotal role as interface between genome and environment. True genome-wide assessments of epigenetic marks, such as DNA methylation (methylomes) or chromatin modifications (chromatinomes), are now possible, either through high-throughput arrays or increasingly by second-generation DNA sequencing methods. The ability to collect these data at this level of resolution enables us to begin to be able to propose detailed questions, and interrogate this information, with regards to changes that occur due to development, lineage and tissue-specificity, and significantly those caused by environmental influence, such as ageing, stress, diet, hormones or toxins. Common complex traits are under variable levels of genetic influence and additionally epigenetic effect. The detection of pathological epigenetic alterations will reveal additional insights into their aetiology and how possible environmental modulation of this mechanism may occur. Due to the reversibility of these marks, the potential for sequence-specific targeted therapeutics exists. This review surveys recent epigenomic advances and their current and prospective application to the study of common diseases.
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Bell CG, Breward CJ, Howell PD, Penfold J, Thomas RK. A theoretical analysis of the surface tension profiles of strongly interacting polymer–surfactant systems. J Colloid Interface Sci 2010; 350:486-93. [DOI: 10.1016/j.jcis.2010.07.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 07/09/2010] [Accepted: 07/10/2010] [Indexed: 10/19/2022]
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Bell CG, Teschendorff AE, Rakyan VK, Maxwell AP, Beck S, Savage DA. Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus. BMC Med Genomics 2010. [PMID: 20687937 DOI: 10.1187/1755-8794-3-33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Diabetic nephropathy is a serious complication of diabetes mellitus and is associated with considerable morbidity and high mortality. There is increasing evidence to suggest that dysregulation of the epigenome is involved in diabetic nephropathy. We assessed whether epigenetic modification of DNA methylation is associated with diabetic nephropathy in a case-control study of 192 Irish patients with type 1 diabetes mellitus (T1D). Cases had T1D and nephropathy whereas controls had T1D but no evidence of renal disease. METHODS We performed DNA methylation profiling in bisulphite converted DNA from cases and controls using the recently developed Illumina Infinium HumanMethylation27 BeadChip, that enables the direct investigation of 27,578 individual cytosines at CpG loci throughout the genome, which are focused on the promoter regions of 14,495 genes. RESULTS Singular Value Decomposition (SVD) analysis indicated that significant components of DNA methylation variation correlated with patient age, time to onset of diabetic nephropathy, and sex. Adjusting for confounding factors using multivariate Cox-regression analyses, and with a false discovery rate (FDR) of 0.05, we observed 19 CpG sites that demonstrated correlations with time to development of diabetic nephropathy. Of note, this included one CpG site located 18 bp upstream of the transcription start site of UNC13B, a gene in which the first intronic SNP rs13293564 has recently been reported to be associated with diabetic nephropathy. CONCLUSION This high throughput platform was able to successfully interrogate the methylation state of individual cytosines and identified 19 prospective CpG sites associated with risk of diabetic nephropathy. These differences in DNA methylation are worthy of further follow-up in replication studies using larger cohorts of diabetic patients with and without nephropathy.
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Affiliation(s)
- Christopher G Bell
- Medical Genomics, UCL Cancer Institute, University College London, London, UK.
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Bell CG, Teschendorff AE, Rakyan VK, Maxwell AP, Beck S, Savage DA. Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus. BMC Med Genomics 2010; 3:33. [PMID: 20687937 PMCID: PMC2924253 DOI: 10.1186/1755-8794-3-33] [Citation(s) in RCA: 215] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 08/05/2010] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Diabetic nephropathy is a serious complication of diabetes mellitus and is associated with considerable morbidity and high mortality. There is increasing evidence to suggest that dysregulation of the epigenome is involved in diabetic nephropathy. We assessed whether epigenetic modification of DNA methylation is associated with diabetic nephropathy in a case-control study of 192 Irish patients with type 1 diabetes mellitus (T1D). Cases had T1D and nephropathy whereas controls had T1D but no evidence of renal disease. METHODS We performed DNA methylation profiling in bisulphite converted DNA from cases and controls using the recently developed Illumina Infinium HumanMethylation27 BeadChip, that enables the direct investigation of 27,578 individual cytosines at CpG loci throughout the genome, which are focused on the promoter regions of 14,495 genes. RESULTS Singular Value Decomposition (SVD) analysis indicated that significant components of DNA methylation variation correlated with patient age, time to onset of diabetic nephropathy, and sex. Adjusting for confounding factors using multivariate Cox-regression analyses, and with a false discovery rate (FDR) of 0.05, we observed 19 CpG sites that demonstrated correlations with time to development of diabetic nephropathy. Of note, this included one CpG site located 18 bp upstream of the transcription start site of UNC13B, a gene in which the first intronic SNP rs13293564 has recently been reported to be associated with diabetic nephropathy. CONCLUSION This high throughput platform was able to successfully interrogate the methylation state of individual cytosines and identified 19 prospective CpG sites associated with risk of diabetic nephropathy. These differences in DNA methylation are worthy of further follow-up in replication studies using larger cohorts of diabetic patients with and without nephropathy.
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Affiliation(s)
- Christopher G Bell
- Medical Genomics, UCL Cancer Institute, University College London, London, UK.
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Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, Shen H, Campan M, Noushmehr H, Bell CG, Maxwell AP, Savage DA, Mueller-Holzner E, Marth C, Kocjan G, Gayther SA, Jones A, Beck S, Wagner W, Laird PW, Jacobs IJ, Widschwendter M. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res 2010; 20:440-6. [PMID: 20219944 DOI: 10.1101/gr.103606.109] [Citation(s) in RCA: 613] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Polycomb group proteins (PCGs) are involved in repression of genes that are required for stem cell differentiation. Recently, it was shown that promoters of PCG target genes (PCGTs) are 12-fold more likely to be methylated in cancer than non-PCGTs. Age is the most important demographic risk factor for cancer, and we hypothesized that its carcinogenic potential may be referred by irreversibly stabilizing stem cell features. To test this, we analyzed the methylation status of over 27,000 CpGs mapping to promoters of approximately 14,000 genes in whole blood samples from 261 postmenopausal women. We demonstrate that stem cell PCGTs are far more likely to become methylated with age than non-targets (odds ratio = 5.3 [3.8-7.4], P < 10(-10)), independently of sex, tissue type, disease state, and methylation platform. We identified a specific subset of 69 PCGT CpGs that undergo hypermethylation with age and validated this methylation signature in seven independent data sets encompassing over 900 samples, including normal and cancer solid tissues and a population of bone marrow mesenchymal stem/stromal cells (P < 10(-5)). We find that the age-PCGT methylation signature is present in preneoplastic conditions and may drive gene expression changes associated with carcinogenesis. These findings shed substantial novel insights into the epigenetic effects of aging and support the view that age may predispose to malignant transformation by irreversibly stabilizing stem cell features.
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Bell CG, Wood DR, Cheong SJH, Kwan E, Sinosich M, Delprado W, Baumgart KW. Molecular confirmation of pathological specimen integrity in Australasia. Pathology 2009; 41:280-3. [PMID: 19291541 DOI: 10.1080/00313020902756311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AIM Investigations into 14 suspected pathology sample identification errors and mix-ups were performed, as a service for several public hospital and private laboratories, from 2005 to 2007. METHODS Analyses were performed with the forensic ABI Identifiler kit of 16 microsatellites (15 autosomal and amelogenin) on DNA from paraffin-embedded tissues or blood specimens and compared to independently verified (single or multiple) patient samples. RESULTS Of 23 unique patient specimens referred for sample integrity confirmation because of pathologist, clinician or patient concern, six (26.1%) were demonstrated to be discordant, indicating that specimen identification errors or mix-ups had occurred. CONCLUSIONS Due to their great sensitivity and high discrimination power, forensic identity multiplex systems using either microsatellites or single nucleotide polymorphisms (SNPs) can resolve concerns about pathology specimen identity and integrity.
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Affiliation(s)
- Christopher G Bell
- Sonic Clinical Institute, Douglass Hanly Moir Pathology, Sydney, NSW, Australia.
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Abstract
Allele-specific expression (ASE) is essential for normal development and many cellular processes but, if impaired, can result in disease. ASE is a feature of organisms with genomes consisting of more than one set of homologous chromosomes. The higher the number of chromosome sets (ploidy) per cell, the higher the potential complexity of ASE. Humans, for instance, are diploid (except germ cells, which are haploid), resulting in multiple possible expression states in time and space for each set of alleles. ASE is invoked and modulated by both genetic and epigenetic changes, affecting the underlying DNA sequence or chromatin of each allele, respectively. Although numerous methods have been developed to assay ASE, they usually require RNA to be available and are dependent upon genetic polymorphisms (such as single nucleotide polymorphisms (SNPs)) to differentiate between allelic transcripts. The rapid convergence to second-generation sequencing as the method of choice to examine genomic, epigenomic and transcriptomic data enables an integrated and more general approach to define and predict ASE, independent of SNPs. This 'Omni-Seq' approach has the potential to advance our understanding of the biology and pathophysiology of ASE-mediated processes by elucidating subtle combinatorial effects, leading to the accurate delineation of sub-phenotypes with consequential benefit for improved insight into disease etiology.
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Affiliation(s)
- Christopher G Bell
- Medical Genomics, University College London Cancer Institute, Huntley Street, London WC1E 6BT, UK
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Bell CG, Breward CJW, Howell PD, Penfold J, Thomas RK. Macroscopic modeling of the surface tension of polymer-surfactant systems. Langmuir 2007; 23:6042-52. [PMID: 17465579 DOI: 10.1021/la063714h] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Polymer-surfactant mixtures are increasingly being used in a wide range of applications. Weakly interacting systems, such as SDS/PEO and SDS/PVP, comprise ionic surfactants and neutral polymers, while strongly interacting systems, such as SDS/POLYDMDAAC and C12TAB/NaPSS, comprise ionic surfactants and oppositely charged ionic polymers. The complex nature of interactions in the mixtures leads to interesting and surprising surface tension profiles as the concentrations of polymer and surfactant are varied. The purpose of our research has been to develop a model to explain these surface tension profiles and to understand how they relate to the formation of different complexes in the bulk solution. In this paper we show how an existing model based on the law of mass action can be extended to model the surface tension of weakly interacting systems, and we also extend it further to produce a model for the surface tension of strongly interacting systems. Applying the model to a variety of strongly interacting systems gives remarkable agreement with the experimental results. The model provides a sound theoretical basis for comparing and contrasting the behavior of different systems and greatly enhances our understanding of the features observed.
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Affiliation(s)
- Christopher G Bell
- Mathematical Institute, University of Oxford, 24-29 St. Giles', Oxford, OX1 3LB, UK
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Taylor PJ, Maroulis S, Mullan GL, Pedersen RL, Baumli A, Elakis G, Piras S, Walsh C, Prósper-Gutiérrez B, De La Puente-Alonso F, Bell CG, Mowat DR, Johnston HM, Buckley MF. Measurement of the clinical utility of a combined mutation detection protocol in carriers of Duchenne and Becker muscular dystrophy. J Med Genet 2007; 44:368-72. [PMID: 17259292 PMCID: PMC2740880 DOI: 10.1136/jmg.2006.047464] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Recent methodological advances have improved the detection rate for dystrophin mutations, but there are no published studies that have measured the clinical utility of these protocols for carrier detection compared with conventional carrier testing protocols that use pedigree, serum creatine kinase levels and linkage analysis. METHODS AND SUBJECTS The clinical utility of a combined mutation detection protocol was measured. It involved quantitative PCR procedures followed by DNA sequence analysis for the identification of dystrophin mutation carriers in 2101 women at risk of being carriers from 348 mutation-known Duchenne or Becker muscular dystrophy pedigrees. RESULTS The combined mutation detection protocol identified a mutation in 96% and 82% of index cases of Duchenne muscular dystrophy and Becker muscular dystrophy, respectively. An additional 692 (33%) potential carriers were correctly classified by the combined mutation detection protocol compared with pedigree, serum creatine kinase levels and linkage analysis. Significantly lower mutation carrier rates were identified in the mothers of isolated cases with deletion mutations than predicted from theoretical considerations, but these findings were not confirmed for duplication and DNA sequence mutations. CONCLUSIONS There are significant clinical benefits to be gained from a combined mutation detection protocol for carrier detection. It is recommended that mutation-specific carrier frequencies for the different classes of dystrophin mutations should be taken into account in genetic counselling practice.
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Affiliation(s)
- Peter J Taylor
- Molecular and Cytogenetics Unit, Department of Haematology and Genetics, South Eastern Area Laboratory Services, Prince of Wales Hospital, Randwick, Sydney, Australia
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Bell CG, Meyre D, Petretto E, Levy-Marchal C, Hercberg S, Charles MA, Boyle C, Weill J, Tauber M, Mein CA, Aitman TJ, Froguel P, Walley AJ. No contribution of angiotensin-converting enzyme (ACE) gene variants to severe obesity: a model for comprehensive case/control and quantitative cladistic analysis of ACE in human diseases. Eur J Hum Genet 2006; 15:320-7. [PMID: 17164796 DOI: 10.1038/sj.ejhg.5201754] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Candidate gene analyses are often inconclusive owing to genetic or phenotypic heterogeneity, low statistical power, selection of nonfunctional SNPs, and inadequate statistical analysis of the genetic architecture. Angiotensin-converting enzyme (ACE) is involved in adipocyte growth and function and the ACE-processed angiotensin II inhibits adipocyte differentiation. Associations between body mass index (BMI) and ACE polymorphisms have been reported in general populations, but the contribution to severe obesity of this gene, which is located under an obesity genome-scan linkage peak on 17q23, is unknown. ACE is one of the most studied genes and markers responsible for variation in circulating ACE enzyme levels have been extensively characterised. Eight of these variants were genotyped in 1054 severely obese cases and 918 nonobese controls, as well as 116 nuclear families from the genome scan (n=447), enabling the known clades to be inferred. Qualitative analysis of individual single-nucleotide polymorphisms (SNPs), haplotypes, clades, and diploclades demonstrated no significant associations (P<0.05) after minimal correction for multiple testing. Quantitative analysis of clades and diploclades for BMI, waist-to-hip ratio, or ZBMI in children were also not significant. This rigorous, large-scale study of common, well-defined, severe polygenic obesity provides strong evidence that functionally relevant sequence variation in ACE, whether it is defined at the level of SNPs, haplotypes, or clades, is not associated with severe obesity in French Caucasians. Such a study design exemplifies the strategy needed to clearly define the contribution of the ACE gene to the plethora of complex genetic diseases where weak associations have been previously reported.
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Affiliation(s)
- Christopher G Bell
- Genomic Medicine, Hammersmith Hospital, Imperial College London, London, UK.
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Roscioli T, Cliffe ST, Bloch DB, Bell CG, Mullan G, Taylor PJ, Sarris M, Wang J, Donald JA, Kirk EP, Ziegler JB, Salzer U, McDonald GB, Wong M, Lindeman R, Buckley MF. Mutations in the gene encoding the PML nuclear body protein Sp110 are associated with immunodeficiency and hepatic veno-occlusive disease. Nat Genet 2006; 38:620-2. [PMID: 16648851 DOI: 10.1038/ng1780] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Accepted: 03/14/2006] [Indexed: 11/08/2022]
Abstract
We describe mutations in the PML nuclear body protein Sp110 in the syndrome veno-occlusive disease with immunodeficiency, an autosomal recessive disorder of severe hypogammaglobulinemia, combined T and B cell immunodeficiency, absent lymph node germinal centers, absent tissue plasma cells and hepatic veno-occlusive disease. This is the first report of the involvement of a nuclear body protein in a human primary immunodeficiency and of high-penetrance genetic mutations in hepatic veno-occlusive disease.
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Affiliation(s)
- Tony Roscioli
- Centre for Vascular Research, University of New South Wales, Sydney 2052, Australia.
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Bell CG, Meyre D, Samson C, Boyle C, Lecoeur C, Tauber M, Jouret B, Jaquet D, Levy-Marchal C, Charles MA, Weill J, Gibson F, Mein CA, Froguel P, Walley AJ. Association of melanin-concentrating hormone receptor 1 5' polymorphism with early-onset extreme obesity. Diabetes 2005; 54:3049-55. [PMID: 16186414 DOI: 10.2337/diabetes.54.10.3049] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Murine models have been highly effective in identifying the monogenic forms of human obesity discovered to date. Melanin-concentrating hormone receptor 1 (MCHR1) has been shown to be significant in the downstream orexigenic activity of the leptin-melanocortin pathway by such models. In this study, the human MCHR1 gene was extensively characterized by sequencing 3.5 kb of coding, untranslated and intronic regions plus 1 kb of putative promoter region in 180 morbidly obese adults and 87 morbidly obese children, a total of >2.4 Mb of sequencing. Thirty-nine single nucleotide polymorphisms (SNPs) were found, seven of which encode an amino acid change. One mutation, R248Q, appeared to cosegregate with the obesity trait in one pedigree but was also found to be a rare polymorphism in control samples. To investigate the possible polygenic role of MCHR1, the six common SNPs (minor allele frequency >5%) found in the sequenced regions were then screened in 557 morbidly obese adults, 552 obese children, and 1,195 nonobese nondiabetic control subjects. The plausible promoter SNP, rs133068, was found to be associated with protection against obesity in obese children only (allele frequency P = 0.006 and genotype frequency P = 0.004). Most significant results were found when using a dominant model (P = 0.001, odds ratio 0.695 [95% CI 0.560-0.863]). However, similar associations were found when both adults and children were analyzed together (P = 0.006, 0.783 [0.658-0.930]), suggesting that severe forms of obesity with early onset may be associated with SNPs in MCHR1.
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Affiliation(s)
- Christopher G Bell
- Section of Genomic Medicine, Faculty of Medicine, Imperial College, Hammersmith Hospital, London W12 0NN, UK
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Guérardel A, Barat-Houari M, Vasseur F, Dina C, Vatin V, Clément K, Eberlé D, Vasseur-Delannoy V, Bell CG, Galan P, Hercberg S, Helbecque N, Potoczna N, Horber FF, Boutin P, Froguel P. Analysis of sequence variability in the CART gene in relation to obesity in a Caucasian population. BMC Genet 2005; 6:19. [PMID: 15823203 PMCID: PMC1087839 DOI: 10.1186/1471-2156-6-19] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Accepted: 04/11/2005] [Indexed: 11/30/2022] Open
Abstract
Background Cocaine and amphetamine regulated transcript (CART) is an anorectic neuropeptide located principally in hypothalamus. CART has been shown to be involved in control of feeding behavior, but a direct relationship with obesity has not been established. The aim of this study was to evaluate the effect of polymorphisms within the CART gene with regards to a possible association with obesity in a Caucasian population. Results Screening of the entire gene as well as a 3.7 kb region of 5' upstream sequence revealed 31 SNPs and 3 rare variants ; 14 of which were subsequently genotyped in 292 French morbidly obese subjects and 368 controls. Haplotype analysis suggested an association with obesity which was found to be mainly due to SNP-3608T>C (rs7379701) (p = 0.009). Genotyping additional cases and controls also of European Caucasian origin supported further this possible association between the CART SNP -3608T>C T allele and obesity (global p-value = 0.0005). Functional studies also suggested that the SNP -3608T>C could modulate nuclear protein binding. Conclusion CART SNP -3608T>C may possibly contribute to the genetic risk for obesity in the Caucasian population. However confirmation of the importance of the role of the CART gene in energy homeostasis and obesity will require investigation and replication in further populations.
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Affiliation(s)
- Audrey Guérardel
- Institute of Biology-CNRS UMR 8090, Pasteur Institute, Lille, France
| | | | - Francis Vasseur
- Institute of Biology-CNRS UMR 8090, Pasteur Institute, Lille, France
- University Hospital, Lille, France
| | - Christian Dina
- Institute of Biology-CNRS UMR 8090, Pasteur Institute, Lille, France
| | - Vincent Vatin
- Institute of Biology-CNRS UMR 8090, Pasteur Institute, Lille, France
| | - Karine Clément
- Department of Nutrition-EA3502, Paris VI University, INSERM "Avenir" Hôtel-Dieu, Paris, France
| | - Delphine Eberlé
- Department of Nutrition-EA3502, Paris VI University, INSERM "Avenir" Hôtel-Dieu, Paris, France
| | | | - Christopher G Bell
- Imperial College genome Centre and Genomic Medicine, Hammersmith Campus, Imperial College London, UK
| | - Pilar Galan
- Scientific and Technical Institute of Nutrition and Food (ISTNA-CNAM), INSERM U557, INRA U1125, Paris, France
| | - Serge Hercberg
- Scientific and Technical Institute of Nutrition and Food (ISTNA-CNAM), INSERM U557, INRA U1125, Paris, France
| | - Nicole Helbecque
- Service d'Epidémiologie et de Santé Publique-INSERM U.508, Pasteur Institute, Lille, France
| | - Natascha Potoczna
- Dr. Horber Adipositas Stiftung, Hornbachstrasse 50, 8034, Zürich, Switzerland
| | - Fritz F Horber
- Dr. Horber Adipositas Stiftung, Hornbachstrasse 50, 8034, Zürich, Switzerland
| | - Philippe Boutin
- Institute of Biology-CNRS UMR 8090, Pasteur Institute, Lille, France
| | - Philippe Froguel
- Imperial College genome Centre and Genomic Medicine, Hammersmith Campus, Imperial College London, UK
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