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Bengani H, Grozeva D, Moyon L, Bhatia S, Louros SR, Hope J, Jackson A, Prendergast JG, Owen LJ, Naville M, Rainger J, Grimes G, Halachev M, Murphy LC, Spasic-Boskovic O, van Heyningen V, Kind P, Abbott CM, Osterweil E, Raymond FL, Roest Crollius H, FitzPatrick DR. Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability. PLoS One 2021; 16:e0256181. [PMID: 34388204 PMCID: PMC8362966 DOI: 10.1371/journal.pone.0256181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/14/2021] [Accepted: 08/01/2021] [Indexed: 11/18/2022] Open
Abstract
Identifying causative variants in cis-regulatory elements (CRE) in neurodevelopmental disorders has proven challenging. We have used in vivo functional analyses to categorize rigorously filtered CRE variants in a clinical cohort that is plausibly enriched for causative CRE mutations: 48 unrelated males with a family history consistent with X-linked intellectual disability (XLID) in whom no detectable cause could be identified in the coding regions of the X chromosome (chrX). Targeted sequencing of all chrX CRE identified six rare variants in five affected individuals that altered conserved bases in CRE targeting known XLID genes and segregated appropriately in families. Two of these variants, FMR1CRE and TENM1CRE, showed consistent site- and stage-specific differences of enhancer function in the developing zebrafish brain using dual-color fluorescent reporter assay. Mouse models were created for both variants. In male mice Fmr1CRE induced alterations in neurodevelopmental Fmr1 expression, olfactory behavior and neurophysiological indicators of FMRP function. The absence of another likely causative variant on whole genome sequencing further supported FMR1CRE as the likely basis of the XLID in this family. Tenm1CRE mice showed no phenotypic anomalies. Following the release of gnomAD 2.1, reanalysis showed that TENM1CRE exceeded the maximum plausible population frequency of a XLID causative allele. Assigning causative status to any ultra-rare CRE variant remains problematic and requires disease-relevant in vivo functional data from multiple sources. The sequential and bespoke nature of such analyses renders them time-consuming and challenging to scale for routine clinical use.
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Affiliation(s)
- Hemant Bengani
- MRC Human Genetics Unit, IGMM, University of Edinburgh (UoE), Edinburgh, United Kingdom
| | - Detelina Grozeva
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Institute of Psychological Medicine & Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Lambert Moyon
- Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France
| | - Shipra Bhatia
- MRC Human Genetics Unit, IGMM, University of Edinburgh (UoE), Edinburgh, United Kingdom
| | - Susana R. Louros
- Centre for Discovery Brain Sciences, Patrick Wild Centre, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
| | - Jilly Hope
- Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Adam Jackson
- Centre for Discovery Brain Sciences, Patrick Wild Centre, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Liusaidh J. Owen
- MRC Human Genetics Unit, IGMM, University of Edinburgh (UoE), Edinburgh, United Kingdom
| | - Magali Naville
- Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France
| | - Jacqueline Rainger
- MRC Human Genetics Unit, IGMM, University of Edinburgh (UoE), Edinburgh, United Kingdom
| | - Graeme Grimes
- Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Mihail Halachev
- Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura C. Murphy
- Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Olivera Spasic-Boskovic
- East Midlands and East of England NHS Genomic Laboratory Hub, Molecular Genetics, Adden brooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust Cambridge, Cambridge, United Kingdom
| | | | - Peter Kind
- Centre for Discovery Brain Sciences, Patrick Wild Centre, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
| | - Catherine M. Abbott
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Emily Osterweil
- Centre for Discovery Brain Sciences, Patrick Wild Centre, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
| | - F. Lucy Raymond
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | | | - David R. FitzPatrick
- MRC Human Genetics Unit, IGMM, University of Edinburgh (UoE), Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
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Halachev M, Meynert A, Taylor MS, Vitart V, Kerr SM, Klaric L, Aitman TJ, Haley CS, Prendergast JG, Pugh C, Hume DA, Harris SE, Liewald DC, Deary IJ, Semple CA, Wilson JF. Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions. PLoS Genet 2019; 15:e1008480. [PMID: 31765389 PMCID: PMC6901239 DOI: 10.1371/journal.pgen.1008480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 06/12/2019] [Revised: 12/09/2019] [Accepted: 10/15/2019] [Indexed: 01/03/2023] Open
Abstract
Human population isolates provide a snapshot of the impact of historical demographic processes on population genetics. Such data facilitate studies of the functional impact of rare sequence variants on biomedical phenotypes, as strong genetic drift can result in higher frequencies of variants that are otherwise rare. We present the first whole genome sequencing (WGS) study of the VIKING cohort, a representative collection of samples from the isolated Shetland population in northern Scotland, and explore how its genetic characteristics compare to a mainland Scottish population. Our analyses reveal the strong contributions played by the founder effect and genetic drift in shaping genomic variation in the VIKING cohort. About one tenth of all high-quality variants discovered are unique to the VIKING cohort or are seen at frequencies at least ten fold higher than in more cosmopolitan control populations. Multiple lines of evidence also suggest relaxation of purifying selection during the evolutionary history of the Shetland isolate. We demonstrate enrichment of ultra-rare VIKING variants in exonic regions and for the first time we also show that ultra-rare variants are enriched within regulatory regions, particularly promoters, suggesting that gene expression patterns may diverge relatively rapidly in human isolates.
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Affiliation(s)
- Mihail Halachev
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Alison Meynert
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Martin S. Taylor
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Shona M. Kerr
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Lucija Klaric
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | | | - Timothy J. Aitman
- Centre for Genomic and Experimental Medicine, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Chris S. Haley
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - James G. Prendergast
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Carys Pugh
- Centre for Clinical Brain Sciences, Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - David A. Hume
- Mater Research Institute, University of Queensland, Woolloongabba, Australia
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, George Square, Edinburgh, United Kingdom
| | - David C. Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, George Square, Edinburgh, United Kingdom
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, George Square, Edinburgh, United Kingdom
| | - Colin A. Semple
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - James F. Wilson
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom
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Kaiser VB, Svinti V, Prendergast JG, Chau YY, Campbell A, Patarcic I, Barroso I, Joshi PK, Hastie ND, Miljkovic A, Taylor MS, Enroth S, Memari Y, Kolb-Kokocinski A, Wright AF, Gyllensten U, Durbin R, Rudan I, Campbell H, Polašek O, Johansson Å, Sauer S, Porteous DJ, Fraser RM, Drake C, Vitart V, Hayward C, Semple CA, Wilson JF. Homozygous loss-of-function variants in European cosmopolitan and isolate populations. Hum Mol Genet 2015; 24:5464-74. [PMID: 26173456 PMCID: PMC4572071 DOI: 10.1093/hmg/ddv272] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 04/03/2015] [Accepted: 07/07/2015] [Indexed: 12/30/2022] Open
Abstract
Homozygous loss of function (HLOF) variants provide a valuable window on gene function in humans, as well as an inventory of the human genes that are not essential for survival and reproduction. All humans carry at least a few HLOF variants, but the exact number of inactivated genes that can be tolerated is currently unknown—as are the phenotypic effects of losing function for most human genes. Here, we make use of 1432 whole exome sequences from five European populations to expand the catalogue of known human HLOF mutations; after stringent filtering of variants in our dataset, we identify a total of 173 HLOF mutations, 76 (44%) of which have not been observed previously. We find that population isolates are particularly well suited to surveys of novel HLOF genes because individuals in such populations carry extensive runs of homozygosity, which we show are enriched for novel, rare HLOF variants. Further, we make use of extensive phenotypic data to show that most HLOFs, ascertained in population-based samples, appear to have little detectable effect on the phenotype. On the contrary, we document several genes directly implicated in disease that seem to tolerate HLOF variants. Overall HLOF genes are enriched for olfactory receptor function and are expressed in testes more often than expected, consistent with reduced purifying selection and incipient pseudogenisation.
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Affiliation(s)
- Vera B Kaiser
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine and
| | - Victoria Svinti
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine and
| | - James G Prendergast
- The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - You-Ying Chau
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine and
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Inga Patarcic
- Medical School, University of Split, Soltanska 2, Split 21000, Croatia
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Peter K Joshi
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Nicholas D Hastie
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine and
| | - Ana Miljkovic
- Medical School, University of Split, Soltanska 2, Split 21000, Croatia
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine and
| | | | | | - Stefan Enroth
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, Uppsala SE-75108, Sweden and
| | - Yasin Memari
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Alan F Wright
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine and
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, Uppsala SE-75108, Sweden and
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Igor Rudan
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Harry Campbell
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Ozren Polašek
- Medical School, University of Split, Soltanska 2, Split 21000, Croatia, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Åsa Johansson
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, Uppsala SE-75108, Sweden and
| | - Sascha Sauer
- Max-Planck-Institute for Molecular Genetics, Otto-Warburg-Laboratory, Berlin, Germany
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Ross M Fraser
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Camilla Drake
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine and
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine and
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine and
| | - Colin A Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine and
| | - James F Wilson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine and Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
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Reddington JP, Perricone SM, Nestor CE, Reichmann J, Youngson NA, Suzuki M, Reinhardt D, Dunican DS, Prendergast JG, Mjoseng H, Ramsahoye BH, Whitelaw E, Greally JM, Adams IR, Bickmore WA, Meehan RR. Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes. Genome Biol 2013; 14:R25. [PMID: 23531360 PMCID: PMC4053768 DOI: 10.1186/gb-2013-14-3-r25] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [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: 08/10/2012] [Revised: 02/14/2013] [Accepted: 03/25/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND DNA methylation and the Polycomb repression system are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their genomic targeting. However, whether this role of DNA methylation is important in the context of transcriptional regulation is unclear. RESULTS By genome-wide mapping of the Polycomb Repressive Complex 2-signature histone mark, H3K27me3, in severely DNA hypomethylated mouse somatic cells, we show that hypomethylation leads to widespread H3K27me3 redistribution, in a manner that reflects the local DNA methylation status in wild-type cells. Unexpectedly, we observe striking loss of H3K27me3 and Polycomb Repressive Complex 2 from Polycomb target gene promoters in DNA hypomethylated cells, including Hox gene clusters. Importantly, we show that many of these genes become ectopically expressed in DNA hypomethylated cells, consistent with loss of Polycomb-mediated repression. CONCLUSIONS An intact DNA methylome is required for appropriate Polycomb-mediated gene repression by constraining Polycomb Repressive Complex 2 targeting. These observations identify a previously unappreciated role for DNA methylation in gene regulation and therefore influence our understanding of how this epigenetic mechanism contributes to normal development and disease.
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Affiliation(s)
- James P Reddington
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sara M Perricone
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Colm E Nestor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Breakthrough Breast Cancer Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Judith Reichmann
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Neil A Youngson
- Queensland Institute of Medical Research, Herston, Queensland 4006, Australia
| | - Masako Suzuki
- Departments of Genetics (Computational Genetics) and Center for Epigenomics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, USA
| | - Diana Reinhardt
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Donncha S Dunican
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - James G Prendergast
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Heidi Mjoseng
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Bernard H Ramsahoye
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Emma Whitelaw
- Queensland Institute of Medical Research, Herston, Queensland 4006, Australia
| | - John M Greally
- Departments of Genetics (Computational Genetics) and Center for Epigenomics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, USA
| | - Ian R Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Breakthrough Breast Cancer Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
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Nimmo ER, Prendergast JG, Aldhous MC, Kennedy NA, Henderson P, Drummond HE, Ramsahoye BH, Wilson DC, Semple CA, Satsangi J. Genome-wide methylation profiling in Crohn's disease identifies altered epigenetic regulation of key host defense mechanisms including the Th17 pathway. Inflamm Bowel Dis 2012; 18:889-99. [PMID: 22021194 DOI: 10.1002/ibd.21912] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 09/08/2011] [Indexed: 02/05/2023]
Abstract
BACKGROUND Germline variation in the 71 Crohn's disease (CD) loci implicated by genome-wide association studies (GWAS) only accounts for approximately 25% of estimated heritability. The contribution of epigenetic alterations to disease pathogenesis is emerging as a research priority. MATERIALS AND METHODS The methylation status of 27,578 CpG sites across the genome was analyzed using the Illumina Human Methylation27 assay in DNA extracted from whole blood samples from 40 adult females (21 ileal CD, 19 healthy controls) and 16 girls with childhood-onset CD, all nonsmokers. Our primary analysis compared methylation profiles in adult cases and controls. RESULTS Our data define a global methylation profile characteristic of ileal CD. In all, 1117 sites were differentially methylated (corrected P < 0.01); 50 showed significantly altered methylation in cases compared with controls (uncorrected P < 10(-6), corrected P < 0.0006), including genes altering immune activation: MAPK13, FASLG, PRF1, S100A13, RIPK3, and IL-21R. Gene ontology analyses implicated immunity-related pathways as targets of epigenetic modification (immune system processes [P = 1.3 × 10(-22)], immune response [P = 8.1 × 10(-16)], defense responses to bacteria [P = 1.8 × 10(-15)]). Ingenuity canonical pathway analyses implicated dendritic cell activity (P = 2.4 × 10(-8)) and differential regulation of cytokines by interleukin (IL)-17A and IL-17F (P = 5.8 × 10(-7)). We identified a significant enrichment of methylation changes within 50 kb of CD GWAS loci (8.6-fold [P = 0.021] in adults; 2.4-fold [P = 0.009] in adults and children combined), including IL-27, IL-19, TNF, MST1, and NOD2. Methylation status was predictive of disease status (sensitivity 0.71, specificity 0.83). Disease activity, drug therapy, NOD2 and DNMT3A genotypes were not associated with methylation changes. CONCLUSIONS These data provide an important insight into the impact of epigenetic mechanisms in the pathogenesis of CD.
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Affiliation(s)
- Elaine R Nimmo
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
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Sivakumaran S, Agakov F, Theodoratou E, Prendergast JG, Zgaga L, Manolio T, Rudan I, McKeigue P, Wilson JF, Campbell H. Abundant pleiotropy in human complex diseases and traits. Am J Hum Genet 2011; 89:607-18. [PMID: 22077970 DOI: 10.1016/j.ajhg.2011.10.004] [Citation(s) in RCA: 364] [Impact Index Per Article: 28.0] [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] [Received: 07/05/2011] [Revised: 08/25/2011] [Accepted: 10/07/2011] [Indexed: 11/19/2022] Open
Abstract
We present a systematic review of pleiotropy among SNPs and genes reported to show genome-wide association with common complex diseases and traits. We find abundant evidence of pleiotropy; 233 (16.9%) genes and 77 (4.6%) SNPs show pleiotropic effects. SNP pleiotropic status was associated with gene location (p = 0.024; pleiotropic SNPs more often exonic [14.5% versus 4.9% for nonpleiotropic, trait-associated SNPs] and less often intergenic [15.8% versus 23.6%]), "predicted transcript consequence" (p = 0.001; pleiotropic SNPs more often predicted to be structurally deleterious [5% versus 0.4%] but not more often in regulatory sequences), and certain disease classes. We develop a method to calculate the likelihood that pleiotropic links between traits occurred more often than expected and demonstrate that this approach can identify etiological links that are already known (such as between fetal hemoglobin and malaria risk) and those that are not yet established (e.g., between plasma campesterol levels and gallstones risk; and between immunoglobulin A and juvenile idiopathic arthritis). Examples of pleiotropy will accumulate over time, but it is already clear that pleiotropy is a common property of genes and SNPs associated with disease traits, and this will have implications for identification of molecular targets for drug development, future genetic risk-profiling, and classification of diseases.
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Affiliation(s)
- Shanya Sivakumaran
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
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