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Mackay DJG, Gazdagh G, Monk D, Brioude F, Giabicani E, Krzyzewska IM, Kalish JM, Maas SM, Kagami M, Beygo J, Kahre T, Tenorio-Castano J, Ambrozaitytė L, Burnytė B, Cerrato F, Davies JH, Ferrero GB, Fjodorova O, Manero-Azua A, Pereda A, Russo S, Tannorella P, Temple KI, Õunap K, Riccio A, de Nanclares GP, Maher ER, Lapunzina P, Netchine I, Eggermann T, Bliek J, Tümer Z. Multi-locus imprinting disturbance (MLID): interim joint statement for clinical and molecular diagnosis. Clin Epigenetics 2024; 16:99. [PMID: 39090763 PMCID: PMC11295890 DOI: 10.1186/s13148-024-01713-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Imprinting disorders are rare diseases resulting from altered expression of imprinted genes, which exhibit parent-of-origin-specific expression patterns regulated through differential DNA methylation. A subgroup of patients with imprinting disorders have DNA methylation changes at multiple imprinted loci, a condition referred to as multi-locus imprinting disturbance (MLID). MLID is recognised in most but not all imprinting disorders and is also found in individuals with atypical clinical features; the presence of MLID often alters the management or prognosis of the affected person. Some cases of MLID are caused by trans-acting genetic variants, frequently not in the patients but their mothers, which have counselling implications. There is currently no consensus on the definition of MLID, clinical indications prompting testing, molecular procedures and methods for epigenetic and genetic diagnosis, recommendations for laboratory reporting, considerations for counselling, and implications for prognosis and management. The purpose of this study is thus to cover this unmet need. METHODS A comprehensive literature search was conducted resulting in identification of more than 100 articles which formed the basis of discussions by two working groups focusing on clinical diagnosis (n = 12 members) and molecular testing (n = 19 members). Following eight months of preparations and regular online discussions, the experts from 11 countries compiled the preliminary documentation and determined the questions to be addressed during a face-to-face meeting which was held with the attendance of the experts together with four representatives of patient advocacy organisations. RESULTS In light of available evidence and expert consensus, we formulated 16 propositions and 8 recommendations as interim guidance for the clinical and molecular diagnosis of MLID. CONCLUSIONS MLID is a molecular designation, and for patients with MLID and atypical phenotypes, we propose the alternative term multi-locus imprinting syndrome. Due to the intrinsic variability of MLID, the guidelines underscore the importance of involving experts from various fields to ensure a confident approach to diagnosis, counselling, and care. The authors advocate for global, collaborative efforts in both basic and translational research to tackle numerous crucial questions that currently lack answers, and suggest reconvening within the next 3-5 years to evaluate the research advancements and update this guidance as needed.
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Affiliation(s)
| | - Gabriella Gazdagh
- Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Trust, Southampton, UK
| | - David Monk
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Frederic Brioude
- Centre de Recherche Saint Antoine, Endocrinologie Moléculaire et Pathologies d'empreinte, INSERMSorbonne Université, Hôpital Armand TrousseauAPHP, 75012, Paris, France
| | - Eloise Giabicani
- Centre de Recherche Saint Antoine, Endocrinologie Moléculaire et Pathologies d'empreinte, INSERMSorbonne Université, Hôpital Armand TrousseauAPHP, 75012, Paris, France
| | - Izabela M Krzyzewska
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jennifer M Kalish
- Division of Human Genetics and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Departments of Pediatrics and Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Saskia M Maas
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Jasmin Beygo
- Institut Für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Tiina Kahre
- Department of Laboratory Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Jair Tenorio-Castano
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Institute of Medical and Molecular Genetics, INGEMM-Idipaz, Madrid, Spain
| | - Laima Ambrozaitytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Birutė Burnytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Justin H Davies
- Faculty of Medicine, University of Southampton, Southampton, UK
- Regional Centre for Paediatric Endocrinology, Faculty of Medicine, Southampton Children's Hospital, University of Southampton, Southampton, UK
| | - Giovanni Battista Ferrero
- Department of Clinical and Biological Science, School of Medicine, Centre for Hemoglobinopathies, AOU San Luigi Gonzaga, University of Turin, Turin, Italy
| | - Olga Fjodorova
- Department of Laboratory Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - Africa Manero-Azua
- Rare Diseases Research Group, Molecular (Epi)Genetics Laboratory, Bioaraba Health Research Institute, Araba University Hospital-Txagorritxu, Vitoria-Gasteiz, Araba, Spain
| | - Arrate Pereda
- Rare Diseases Research Group, Molecular (Epi)Genetics Laboratory, Bioaraba Health Research Institute, Araba University Hospital-Txagorritxu, Vitoria-Gasteiz, Araba, Spain
| | - Silvia Russo
- IRCCS Research Laboratory of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, Milan, Italy
| | - Pierpaola Tannorella
- IRCCS Research Laboratory of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, Milan, Italy
| | - Karen I Temple
- Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Trust, Southampton, UK
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy
- Institute of Genetics and Biophysics (IGB),"Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), Naples, Italy
| | - Guiomar Perez de Nanclares
- Rare Diseases Research Group, Molecular (Epi)Genetics Laboratory, Bioaraba Health Research Institute, Araba University Hospital-Txagorritxu, Vitoria-Gasteiz, Araba, Spain
| | - Eamonn R Maher
- Aston Medical School, Aston University, Birmingham, UK
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Institute of Medical and Molecular Genetics, INGEMM-Idipaz, Madrid, Spain
| | - Irène Netchine
- Centre de Recherche Saint Antoine, Endocrinologie Moléculaire et Pathologies d'empreinte, INSERMSorbonne Université, Hôpital Armand TrousseauAPHP, 75012, Paris, France
| | - Thomas Eggermann
- Institute for Human Genetics and Genome Medicine. Faculty of Medicine, RWTH University Aachen, Aachen, Germany
| | - Jet Bliek
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Zeynep Tümer
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Habibi E, Miller MR, Schreier A, Campbell MA, Hung TC, Gille D, Baerwald M, Finger AJ. Single generation epigenetic change in captivity and reinforcement in subsequent generations in a delta smelt (Hypomesus transpacificus) conservation hatchery. Mol Ecol 2024; 33:e17449. [PMID: 38967124 DOI: 10.1111/mec.17449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 05/24/2024] [Accepted: 06/14/2024] [Indexed: 07/06/2024]
Abstract
A refugial population of the endangered delta smelt (Hypomesus transpacificus) has been maintained at the Fish Conservation and Culture Laboratory (FCCL) at UC Davis since 2008. Despite intense genetic management, fitness differences between wild and cultured fish have been observed at the FCCL. To investigate the molecular underpinnings of hatchery domestication, we used whole-genome bisulfite sequencing to quantify epigenetic differences between wild and hatchery-origin delta smelt. Differentially methylated regions (DMRs) were identified from 104 individuals by comparing the methylation patterns in different generations of hatchery fish (G1, G2, G3) with their wild parents (G0). We discovered a total of 132 significant DMRs (p < .05) between G0 and G1, 132 significant DMRs between G0 and G2, and 201 significant DMRs between G0 and G3. Our results demonstrate substantial differences in methylation patterns emerged between the wild and hatchery-reared fish in the early generations in the hatchery, with a higher proportion of hypermethylated DMRs in hatchery-reared fish. The rearing environment was found to be a stronger predictor of individual clustering based on methylation patterns than family, sex or generation. Our study indicates a reinforcement of the epigenetic status with successive generations in the hatchery environment, as evidenced by an increase in methylation in hypermethylated DMRs and a decrease in methylation in hypomethylated DMRs over time. Lastly, our results demonstrated heterogeneity in inherited methylation pattern in families across generations. These insights highlight the long-term consequences of hatchery practices on the epigenetic landscape, potentially impacting wild fish populations.
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Affiliation(s)
- Ensieh Habibi
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Michael R Miller
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Andrea Schreier
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Matthew A Campbell
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Tien-Chieh Hung
- Fish Conservation and Culture Laboratory, Biological and Agricultural Engineering Department, University of California Davis, Davis, California, USA
| | - Daphne Gille
- California Department of Water Resources, Division of Integrated Science and Engineering, West Sacramento, California, USA
| | - Melinda Baerwald
- California Department of Water Resources, Division of Integrated Science and Engineering, West Sacramento, California, USA
| | - Amanda J Finger
- Department of Animal Science, University of California Davis, Davis, California, USA
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Yadav B, Singh D, Mantri S, Rishi V. Genome-wide Methylation Dynamics and Context-dependent Gene Expression Variability in Differentiating Preadipocytes. J Endocr Soc 2024; 8:bvae121. [PMID: 38966711 PMCID: PMC11222978 DOI: 10.1210/jendso/bvae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Indexed: 07/06/2024] Open
Abstract
Obesity, characterized by the accumulation of excess fat, is a complex condition resulting from the combination of genetic and epigenetic factors. Recent studies have found correspondence between DNA methylation and cell differentiation, suggesting a role of the former in cell fate determination. There is a lack of comprehensive understanding concerning the underpinnings of preadipocyte differentiation, specifically when cells are undergoing terminal differentiation (TD). To gain insight into dynamic genome-wide methylation, 3T3 L1 preadipocyte cells were differentiated by a hormone cocktail. The genomic DNA was isolated from undifferentiated cells and 4 hours, 2 days postdifferentiated cells, and 15 days TD cells. We employed whole-genome bisulfite sequencing (WGBS) to ascertain global genomic DNA methylation alterations at single base resolution as preadipocyte cells differentiate. The genome-wide distribution of DNA methylation showed similar overall patterns in pre-, post-, and terminally differentiated adipocytes, according to WGBS analysis. DNA methylation decreases at 4 hours after differentiation initiation, followed by methylation gain as cells approach TD. Studies revealed novel differentially methylated regions (DMRs) associated with adipogenesis. DMR analysis suggested that though DNA methylation is global, noticeable changes are observed at specific sites known as "hotspots." Hotspots are genomic regions rich in transcription factor (TF) binding sites and exhibit methylation-dependent TF binding. Subsequent analysis indicated hotspots as part of DMRs. The gene expression profile of key adipogenic genes in differentiating adipocytes is context-dependent, as we found a direct and inverse relationship between promoter DNA methylation and gene expression.
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Affiliation(s)
- Binduma Yadav
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
- Regional Center for Biotechnology, Faridabad, Haryana 160014, India
| | - Dalwinder Singh
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
- Department of Anatomy and Cell Biology, Western University, London, Ontario N6A 5C1, Canada
| | - Shrikant Mantri
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
| | - Vikas Rishi
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
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Yu L, Ye J, Chen Q, Hong Q. lncRNA TTTY14 participates in the progression of repeated implantation failure by regulating the miR-6088/SEMA5A axis. J Assist Reprod Genet 2024; 41:727-737. [PMID: 38294620 PMCID: PMC10957803 DOI: 10.1007/s10815-024-03032-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024] Open
Abstract
PURPOSE To identify potential biomarkers and the molecular mechanisms associated with repeated implantation failure (RIF), three microarray datasets, GSE71331 (lncRNA + mRNA), GSE111974 (lncRNA + mRNA), and GSE71332 (miRNA), were retrieved from the Gene Expression Omnibus (GEO) database. METHODS The differentially expressed mRNAs (DEMs), lncRNAs (DElncRNAs), and miRNAs (DEmiRNAs) between normal control samples (C group) and RIF samples (RIF group) were identified, and then a module partition analysis was performed based on weighted correlation network analysis (WGCNA). Following enrichment analysis of the genes, the lncRNA-miRNA-mRNA interactions (ceRNA) were examined. The mRNAs in the ceRNA network were evaluated using the GSE58144 dataset. Finally, the key RNAs were verified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). RESULTS Fifty-three DEmiRNAs, 327 DEMs, and 13 DElncRNAs were identified between the C and RIF groups. According to WGCNA, the magenta module was positively correlated with RIF disease status. The lncRNA-mRNA interaction analysis based on genes in the magenta module revealed the intersecting lncRNAs, including peptidylprolyl isomerase E-like pseudogene (PPIEL) and the testis-specific transcript, y-Linked 14 (TTTY14); these lncRNAs are mainly involved in functions, such as plasma membrane organization. The ceRNA network analysis revealed several interactions, such as TTTY14-miR-6088-semaphorin 5 A (SEMA5A). Finally, SEMA5A and the zinc finger protein 555 (ZNF555) were identified to be significantly upregulated in the RIF group compared with those in the C group in the GSE58144 dataset. The RT-qPCR results aligned with the above results. CONCLUSIONS Overall, TTTY14, ZNF555, SEMA5A, PPIEL, and miR-6088 could serve as novel biomarkers of RIF.
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Affiliation(s)
- Lingzhu Yu
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, No.639 Zhizaoju Road, Huangpu District, Shanghai, 200011, P.R. China
| | - Jing Ye
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, No.639 Zhizaoju Road, Huangpu District, Shanghai, 200011, P.R. China
| | - Qiuju Chen
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, No.639 Zhizaoju Road, Huangpu District, Shanghai, 200011, P.R. China
| | - Qingqing Hong
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, No.639 Zhizaoju Road, Huangpu District, Shanghai, 200011, P.R. China.
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Kim HY, Shin CH, Shin CH, Ko JM. Uncovering the phenotypic consequences of multi-locus imprinting disturbances using genome-wide methylation analysis in genomic imprinting disorders. PLoS One 2023; 18:e0290450. [PMID: 37594968 PMCID: PMC10437897 DOI: 10.1371/journal.pone.0290450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/09/2023] [Indexed: 08/20/2023] Open
Abstract
Imprinted genes are regulated by DNA methylation of imprinted differentially methylated regions (iDMRs). An increasing number of patients with congenital imprinting disorders (IDs) exhibit aberrant methylation at multiple imprinted loci, multi-locus imprinting disturbance (MLID). We examined MLID and its possible impact on clinical features in patients with IDs. Genome-wide DNA methylation analysis (GWMA) using blood leukocyte DNA was performed on 13 patients with Beckwith-Wiedemann syndrome (BWS), two patients with Silver-Russell syndrome (SRS), and four controls. HumanMethylation850 BeadChip analysis for 77 iDMRs (809 CpG sites) identified three patients with BWS and one patient with SRS showing additional hypomethylation, other than the disease-related iDMRs, suggestive of MLID. Two regions were aberrantly methylated in at least two patients with BWS showing MLID: PPIEL locus (chromosome 1: 39559298 to 39559744), and FAM50B locus (chromosome 6: 3849096 to 3849469). All patients with BWS- and SRS-MLID did not show any other clinical characteristics associated with additional involved iDMRs. Exome analysis in three patients with BWS who exhibited multiple hypomethylation did not identify any causative variant related to MLID. This study indicates that a genome-wide approach can unravel MLID in patients with an apparently isolated ID. Patients with MLID showed only clinical features related to the original IDs. Long-term follow-up studies in larger cohorts are warranted to evaluate any possible phenotypic consequences of other disturbed imprinted loci.
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Affiliation(s)
- Hwa Young Kim
- Department of Pediatrics, Division of Pediatric Endocrinology and Metabolism, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Choong Ho Shin
- Department of Pediatrics, Division of Pediatric Endocrinology and Metabolism, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Ho Shin
- Department of Orthopaedics, Division of Pediatric Orthopedics, Seoul National University College of Medicine, Seoul, Korea
| | - Jung Min Ko
- Department of Pediatrics, Division of Clinical Genetics, Seoul National University College of Medicine, Seoul, Korea
- Rare Disease Center, Seoul National University Hospital, Seoul, Korea
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Wang SE, Jiang YH. Novel epigenetic molecular therapies for imprinting disorders. Mol Psychiatry 2023; 28:3182-3193. [PMID: 37626134 PMCID: PMC10618104 DOI: 10.1038/s41380-023-02208-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023]
Abstract
Genomic imprinting disorders are caused by the disruption of genomic imprinting processes leading to a deficit or increase of an active allele. Their unique molecular mechanisms underlying imprinted genes offer an opportunity to investigate epigenetic-based therapy for reactivation of an inactive allele or reduction of an active allele. Current treatments are based on managing symptoms, not targeting the molecular mechanisms underlying imprinting disorders. Here, we highlight molecular approaches of therapeutic candidates in preclinical and clinical studies for individual imprinting disorders. These include the significant progress of discovery and testing of small molecules, antisense oligonucleotides, and CRISPR mediated genome editing approaches as new therapeutic strategies. We discuss the significant challenges of translating these promising therapies from the preclinical stage to the clinic, especially for genome editing based approaches.
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Affiliation(s)
- Sung Eun Wang
- Department of Genetics, Yale University School of Medicine, 333 Cedar street, New Haven, CT, 06520, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, 333 Cedar street, New Haven, CT, 06520, USA.
- Department of Neuroscience, Yale University School of Medicine, 333 Cedar street, New Haven, CT, 06520, USA.
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar street, New Haven, CT, 06520, USA.
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Zhao Y, Peng F, Wang C, Murano T, Baba H, Ikematsu H, Li W, Goel A. A DNA Methylation-based Epigenetic Signature for the Identification of Lymph Node Metastasis in T1 Colorectal Cancer. Ann Surg 2023; 277:655-663. [PMID: 35837968 PMCID: PMC9840712 DOI: 10.1097/sla.0000000000005564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OBJECTIVE This study aimed to unravel the lymph node metastasis (LNM)-related methylated DNA (mDNA) landscape and develop a mDNA signature to identify LNM in patients with T1 colorectal cancers (T1 CRC). BACKGROUND Considering the invasiveness of T1 CRC, current guidelines recommend endoscopic resection in patients with LNM-negative, and radical surgical resection only for high-risk LNM-positive patients. Unfortunately, the clinicopathological criteria for LNM risk stratification are imperfect, resulting in frequent misdiagnosis leading to unnecessary radical surgeries and postsurgical complications. METHODS We conducted genome-wide methylation profiling of 39 T1 CRC specimens to identify differentially methylated CpGs between LNM-positive and LNM-negative, and performed quantitative pyrosequencing analysis in 235 specimens from 3 independent patient cohorts, including 195 resected tissues (training cohort: n=128, validation cohort: n=67) and 40 pretreatment biopsies. RESULTS Using logistic regression analysis, we developed a 9-CpG signature to distinguish LNM-positive versus LNM-negative surgical specimens in the training cohort [area under the curve (AUC)=0.831, 95% confidence interval (CI)=0.755-0.892; P <0.0001], which was subsequently validated in additional surgical specimens (AUC=0.825; 95% CI=0.696-0.955; P =0.003) and pretreatment biopsies (AUC=0.836; 95% CI=0.640-1.000, P =0.0036). This diagnostic power was further improved by combining the signature with conventional clinicopathological features. CONCLUSIONS We established a novel epigenetic signature that can robustly identify LNM in surgical specimens and even pretreatment biopsies from patients with T1 CRC. Our signature has strong translational potential to improve the selection of high-risk patients who require radical surgery while sparing others from its complications and expense.
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Affiliation(s)
- Yinghui Zhao
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fuduan Peng
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
| | - Chuanxin Wang
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, China
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tatsuro Murano
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroaki Ikematsu
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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Liang D, Aygün N, Matoba N, Ideraabdullah FY, Love MI, Stein JL. Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation. Hum Mol Genet 2023; 32:402-416. [PMID: 35994039 PMCID: PMC9851749 DOI: 10.1093/hmg/ddac207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 01/24/2023] Open
Abstract
Genomic imprinting results in gene expression bias caused by parental chromosome of origin and occurs in genes with important roles during human brain development. However, the cell-type and temporal specificity of imprinting during human neurogenesis is generally unknown. By detecting within-donor allelic biases in chromatin accessibility and gene expression that are unrelated to cross-donor genotype, we inferred imprinting in both primary human neural progenitor cells and their differentiated neuronal progeny from up to 85 donors. We identified 43/20 putatively imprinted regulatory elements (IREs) in neurons/progenitors, and 133/79 putatively imprinted genes in neurons/progenitors. Although 10 IREs and 42 genes were shared between neurons and progenitors, most putative imprinting was only detected within specific cell types. In addition to well-known imprinted genes and their promoters, we inferred novel putative IREs and imprinted genes. Consistent with both DNA methylation-based and H3K27me3-based regulation of imprinted expression, some putative IREs also overlapped with differentially methylated or histone-marked regions. Finally, we identified a progenitor-specific putatively imprinted gene overlapping with copy number variation that is associated with uniparental disomy-like phenotypes. Our results can therefore be useful in interpreting the function of variants identified in future parent-of-origin association studies.
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Affiliation(s)
- Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Folami Y Ideraabdullah
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Ku MS, Pan WC, Huang YT, Hsieh WS, Hsu YH, Chen PC, Liu CY. Associations between prenatal exposure to perfluoroalkyl substances, hypomethylation of MEST imprinted gene and birth outcomes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 304:119183. [PMID: 35331797 DOI: 10.1016/j.envpol.2022.119183] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Prenatal perfluoroalkyl substance (PFAS) exposure has been linked to adverse birth outcomes, but the underlying mechanism has yet to be elucidated. DNA methylation changes in mesoderm-specific transcript (MEST) imprinted gene may be a mechanism of the prenatal exposure effects of PFASs on fetal growth. The aim was to investigate the prenatal PFASs exposure effects on DNA methylation changes in MEST imprinted gene involved in fetal growth. Among 486 mother-infant pairs from the Taiwan Birth Panel Study, PFASs and DNA methylation levels at 5 CpG sites of MEST promoter region were measured in cord blood. Univariable and multivariable linear regressions were performed to estimate the associations between prenatal PFAS exposure, MEST DNA methylation levels, and child birth outcomes. Mediation analysis was performed to examine the potential pathway of MEST methylation between PFASs and birth outcomes. We found that higher prenatal perfluorooctyl sulfonate (PFOS) exposure was significantly associated with lower methylation levels at 5 CpG sites of MEST promoter region (an adjusted β range: -1.56, -2.22). Significant negative associations were also found between MEST methylation levels and child birth weight. Furthermore, the associations between PFOS and perfluorooctanoic acid (PFOA) exposure and MEST methylation levels were more profound in girls than in boys. The mediated effect of average MEST methylation level between PFOS exposure and birth weight was 18.3 (95% CI = 2.1, 40.2; p = 0.014). The direct effect of PFOS exposure to birth weight independent to average MEST methylation level was -93.2 (95% CI = -170.5, -17.8; p = 0.018). In conclusion, our results suggest that prenatal PFAS exposure, especially PFOS, is associated with lower methylation levels at MEST promoter region, which not only leverages the role of imprinted gene in ensuring the integrity of fetal growth but also provides a potential mechanism for evaluating the prenatal exposure effect.
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Affiliation(s)
- Mei-Sheng Ku
- Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei, Taiwan; Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Wen-Chi Pan
- Institute of Environmental and Occupational Health Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Yen-Tsung Huang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Wu-Shiun Hsieh
- Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine and Hospital, Taipei, Taiwan
| | - Yi-Hsiang Hsu
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, 02131, USA; Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02215, USA; Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
| | - Pau-Chung Chen
- Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei, Taiwan; Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan; Department of Environmental and Occupational Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan; National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Chen-Yu Liu
- Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei, Taiwan; Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan.
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10
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Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells. Nat Commun 2021; 12:6718. [PMID: 34795250 PMCID: PMC8602306 DOI: 10.1038/s41467-021-26949-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
In mammals, imprinted genes are regulated by differentially methylated regions (DMRs) that are inherited from germ cells, leading to monoallelic expression in accordance with parent-of-origin. Yet, it is largely unknown how imprinted DMRs are maintained in human embryos despite global DNA demethylation following fertilization. Here, we explored the mechanisms involved in imprinting regulation by employing human parthenogenetic embryonic stem cells (hpESCs), which lack paternal alleles. We show that although global loss of DNA methylation in hpESCs affects most imprinted DMRs, many paternally-expressed genes (PEGs) remain repressed. To search for factors regulating PEGs, we performed a genome-wide CRISPR/Cas9 screen in haploid hpESCs. This revealed ATF7IP as an essential repressor of a set of PEGs, which we further show is also required for silencing sperm-specific genes. Our study reinforces an important role for histone modifications in regulating imprinted genes and suggests a link between parental imprinting and germ cell identity. Genetic imprinting ensures monoallelic gene expression critical for normal embryonic development. Here the authors take advantage of human haploid parthenogenic embryonic stem cells lacking paternal alleles to identify, by genome-wide screening, factors involved in the regulation of imprinted genes.
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11
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Yeung EH, Mendola P, Sundaram R, Zeng X, Guan W, Tsai MY, Robinson SL, Stern JE, Ghassabian A, Lawrence D, O'Connor TG, Segars J, Gore-Langton RE, Bell EM. Conception by fertility treatment and offspring deoxyribonucleic acid methylation. Fertil Steril 2021; 116:493-504. [PMID: 33823999 PMCID: PMC8349775 DOI: 10.1016/j.fertnstert.2021.03.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVE To investigate whether deoxyribonucleic acid (DNA) methylation at birth and in childhood differ by conception using assisted reproductive technologies (ART) or ovulation induction compared with those in children conceived without fertility treatment. DESIGN Upstate KIDS is a matched exposure cohort which oversampled on newborns conceived by treatment. SETTING New York State (excluding New York City). PATIENT(S) This analysis included 855 newborns and 152 children at approximately 9 years of age. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) DNA methylation levels were measured using the Illumina EPIC platform. Single CpG and regional analyses at imprinting genes were conducted. RESULT(S) Compared to no fertility treatment, ART was associated with lower mean DNA methylation levels at birth in 11 CpGs (located in/near SYCE1, SPRN, KIAA2013, MYO1D, GET1/WRB-SH4BGR, IGF1R, SORD, NECAB3/ACTL10, and GET1) and higher mean methylation level in 1 CpG (KLK4; all false discovery rate P<.05). The strongest association (cg17676129) was located at SYCE1, which codes for a synaptonemal complex that plays a role in meiosis and therefore infertility. This CpG remained associated with newborn hypomethylation when the analysis was limited to those conceived with ICSI, but this may be because of underlying male infertility. In addition, nine regions in maternally imprinted genes (IGF1R, PPIEL, SVOPL GNAS, L3MBTL, BLCAP, HYMAI/PLAGL1, SNU13, and MEST) were observed to have decreased mean DNA methylation levels among newborns conceived by ART. In childhood, hypomethylation of the maternally imprinted gene, GNAS, persisted. No CpGs or regions were associated with ovulation induction. CONCLUSION(S) ART but not ovulation induction was associated with hypomethylation at birth, but only one difference at an imprinting region appeared to persist in childhood.
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Affiliation(s)
- Edwina H Yeung
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland.
| | - Pauline Mendola
- Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, New York
| | - Rajeshwari Sundaram
- Biostatistics and Bioinformatics Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland
| | | | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Sonia L Robinson
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland
| | - Judy E Stern
- Department of Obstetrics and Gynecology, Dartmouth-Hitchcock, Lebanon, New Hampshire
| | - Akhgar Ghassabian
- Departments of Pediatrics, Population Health, and Environmental Medicine, New York University School of Medicine, New York, New York
| | - David Lawrence
- Department of Environmental Health Sciences, University at Albany School of Public Health, Albany, New York
| | - Thomas G O'Connor
- Departments of Psychiatry, Psychology, Neuroscience, Obstetrics and Gynecology, University of Rochester, Rochester, New York
| | - James Segars
- Howard W. and Georgeanna Seegar Jones Laboratory of Reproductive Sciences and Women's Health Research, Department of Obstetrics and Gynecology, Johns Hopkins Medical University, Baltimore, Maryland
| | | | - Erin M Bell
- Department of Epidemiology and Biostatistics, University at Albany School of Public Health, Albany, New York
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12
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Yang Z, Zhao J, Li J, Wang J, Wang W. Genome-wide DNA methylation profiling of high-fat emulsion-induced hyperlipidemia mice intervened by a polysaccharide from Cyclocarya paliurus (Batal) Iljinskaja. Food Chem Toxicol 2021. [DOI: https://doi.org/10.1016/j.fct.2021.112230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Yang Z, Zhao J, Li J, Wang J, Wang W. Genome-wide DNA methylation profiling of high-fat emulsion-induced hyperlipidemia mice intervened by a polysaccharide from Cyclocarya paliurus (Batal) Iljinskaja. Food Chem Toxicol 2021; 152:112230. [PMID: 33878369 DOI: 10.1016/j.fct.2021.112230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023]
Abstract
Genome-wide DNA methylation was used to study the lipid-lowering effect of Cyclocarya paliurus (Batal) Iljinskaja polysaccharide (CPP). The objective of this study was to investigate the hypolipidemic effects and the potential underlying mechanisms of action of CPP-2 in high-fat emulsion (HFE)-induced mice. The results showed that CPP-2 reduced the level of genome-wide DNA methylation in the liver of HFE-induced mice, which had a lipid-lowering effect by regulating the AMP-activated protein kinase (AMPK) signaling-, fatty acid metabolism-, fatty acid biosynthesis- and adipocytokine signaling pathways. A series of lipid metabolism genes were screened out by conjoint analysis of the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Hereafter, fatty acid synthase (FAS) and peroxisome proliferators-activated receptor α (PPARα) as target genes were selected to validate the accuracy of the results. The findings demonstrated that CPP-2 might be effective in lowering the lipid content, thereby protecting against HFE-induced hyperlipidemia.
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Affiliation(s)
- Zhanwei Yang
- Key Lab for Agro-product Processing and Quality Control of Nanchang City, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China; School of Food Sciences and Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Jing Zhao
- Guang' an Vocation &Technical College, Guang' an 638000, China
| | - Jing'en Li
- Key Lab for Agro-product Processing and Quality Control of Nanchang City, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jin Wang
- The State Centre of Quality Supervision and Inspection for Camellia Products (Jiangxi), Ganzhou 341000, China
| | - Wenjun Wang
- Key Lab for Agro-product Processing and Quality Control of Nanchang City, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China.
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14
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Kagami M, Hara-Isono K, Matsubara K, Nakabayashi K, Narumi S, Fukami M, Ohkubo Y, Saitsu H, Takada S, Ogata T. ZNF445: a homozygous truncating variant in a patient with Temple syndrome and multilocus imprinting disturbance. Clin Epigenetics 2021; 13:119. [PMID: 34039421 PMCID: PMC8157728 DOI: 10.1186/s13148-021-01106-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/18/2021] [Indexed: 11/12/2022] Open
Abstract
Background ZNF445, as well as ZFP57, is involved in the postfertilization methylation maintenance of multiple imprinting-associated differentially methylated regions (iDMRs). Thus, ZNF445 pathogenic variants are predicted to cause multilocus imprinting disturbances (MLIDs), as do ZFP57 pathogenic variants. In particular, the MEG3/DLK1:IG-DMR would be affected, because the postzygotic methylation imprint of the MEG3/DLK1:IG-DMR is maintained primarily by ZNF445, whereas that of most iDMRs is preserved by both ZFP57 and ZNF445 or primarily by ZFP57. Results We searched for a ZNF445 variant(s) in six patients with various imprinting disorders (IDs) caused by epimutations and MLIDs revealed by pyrosequencing for nine iDMRs, without a selection for the original IDs. Re-analysis of the previously obtained whole exome sequencing data identified a homozygous ZNF445 variant (NM_181489.6:c.2803C>T:p.(Gln935*)) producing a truncated protein missing two of 14 zinc finger domains in a patient with Temple syndrome and MLID. In this patient, array-based genomewide methylation analysis revealed severe hypomethylation of most CpGs at the MEG3:TSS-DMR, moderate hypomethylation of roughly two-thirds of CpGs at the H19/IGF2:IG-DMR, and mild-to-moderate hypomethylation of a few CpGs at the DIRAS3:TSS-DMR, MEST:alt-TSS-DMR, IGF2:Ex9-DMR, IGF2:alt-TSS, and GNAS-AS1:TSS-DMR. Furthermore, bisulfite sequencing analysis for the MEG3/DLK1:IG-DMR delineated a markedly hypomethylated segment (CG-A). The heterozygous parents were clinically normal and had virtually no aberrant methylation pattern. Conclusions We identified a ZNF445 pathogenic variant for the first time. Since ZNF445 binds to the MEG3/DLK1:IG-DMR and other iDMRs affected in this patient, the development of Temple syndrome and MLID would primarily be explained by the ZNF445 variant. Furthermore, CG-A may be the target site for ZNF445 within the MEG3/DLK1:IG-DMR. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01106-5.
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Affiliation(s)
- Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
| | - Kaori Hara-Isono
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Yumiko Ohkubo
- Department of Pediatrics, Shizuoka Saiseikai Hospital, Oshika 1-1-1, Suruga-ku, Shizuoka, 422-8527, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan. .,Department of Pediatrics, Shizuoka Saiseikai Hospital, Oshika 1-1-1, Suruga-ku, Shizuoka, 422-8527, Japan. .,Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan. .,Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan. .,Department of Pediatrics, Hamamatsu Medical Center, Tomitsuka 328, Naka-ku, Hamamatsu, 432-8580, Japan.
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15
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Clinical and Molecular Diagnosis of Beckwith-Wiedemann Syndrome with Single- or Multi-Locus Imprinting Disturbance. Int J Mol Sci 2021; 22:ijms22073445. [PMID: 33810554 PMCID: PMC8036922 DOI: 10.3390/ijms22073445] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/22/2022] Open
Abstract
Beckwith-Wiedemann syndrome (BWS) is a clinically and genetically heterogeneous overgrowth disease. BWS is caused by (epi)genetic defects at the 11p15 chromosomal region, which harbors two clusters of imprinted genes, IGF2/H19 and CDKN1C/KCNQ1OT1, regulated by differential methylation of imprinting control regions, H19/IGF2:IG DMR and KCNQ1OT1:TSS DMR, respectively. A subset of BWS patients show multi-locus imprinting disturbances (MLID), with methylation defects extended to other imprinted genes in addition to the disease-specific locus. Specific (epi)genotype-phenotype correlations have been defined in order to help clinicians in the classification of patients and referring them to a timely diagnosis and a tailored follow-up. However, specific phenotypic correlations have not been identified among MLID patients, thus causing a debate on the usefulness of multi-locus testing in clinical diagnosis. Finally, the high incidence of BWS monozygotic twins with discordant phenotypes, the high frequency of BWS among babies conceived by assisted reproductive technologies, and the female prevalence among BWS-MLID cases provide new insights into the timing of imprint establishment during embryo development. In this review, we provide an overview on the clinical and molecular diagnosis of single- and multi-locus BWS in pre- and post-natal settings, and a comprehensive analysis of the literature in order to define possible (epi)genotype-phenotype correlations in MLID patients.
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16
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Katrinli S, Zheng Y, Gautam A, Hammamieh R, Yang R, Venkateswaran S, Kilaru V, Lori A, Hinrichs R, Powers A, Gillespie CF, Wingo AP, Michopoulos V, Jovanovic T, Wolf EJ, McGlinchey RE, Milberg WP, Miller MW, Kugathasan S, Jett M, Logue MW, Ressler KJ, Smith AK. PTSD is associated with increased DNA methylation across regions of HLA-DPB1 and SPATC1L. Brain Behav Immun 2021; 91:429-436. [PMID: 33152445 PMCID: PMC7749859 DOI: 10.1016/j.bbi.2020.10.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/09/2020] [Accepted: 10/27/2020] [Indexed: 12/21/2022] Open
Abstract
Posttraumatic stress disorder (PTSD) is characterized by intrusive thoughts, avoidance, negative alterations in cognitions and mood, and arousal symptoms that adversely affect mental and physical health. Recent evidence links changes in DNA methylation of CpG cites to PTSD. Since clusters of proximal CpGs share similar methylation signatures, identification of PTSD-associated differentially methylated regions (DMRs) may elucidate the pathways defining differential risk and resilience of PTSD. Here we aimed to identify epigenetic differences associated with PTSD. DNA methylation data profiled from blood samples using the MethylationEPIC BeadChip were used to perform a DMR analysis in 187 PTSD cases and 367 trauma-exposed controls from the Grady Trauma Project (GTP). DMRs were assessed with R package bumphunter. We identified two regions that associate with PTSD after multiple test correction. These regions were in the gene body of HLA-DPB1 and in the promoter of SPATC1L. The DMR in HLA-DPB1 was associated with PTSD in an independent cohort. Both DMRs included CpGs whose methylation associated with nearby sequence variation (meQTL) and that associated with expression of their respective genes (eQTM). This study supports an emerging literature linking PTSD risk to genetic and epigenetic variation in the HLA region.
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Affiliation(s)
- Seyma Katrinli
- Emory University, Department of Gynecology and Obstetrics, Atlanta, GA, USA
| | - Yuanchao Zheng
- Boston University School of Public Health, Department of Biostatistics, Boston, MA, USA
| | - Aarti Gautam
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ruoting Yang
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Suresh Venkateswaran
- Emory University School of Medicine Department of Pediatrics, Division of Pediatric Gastroenterology & Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Varun Kilaru
- Emory University, Department of Gynecology and Obstetrics, Atlanta, GA, USA
| | - Adriana Lori
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Rebecca Hinrichs
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Abigail Powers
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Charles F Gillespie
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Aliza P Wingo
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA; Division of Mental Health, Atlanta VA Medical Center, Decatur, GA, USA
| | - Vasiliki Michopoulos
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Tanja Jovanovic
- Wayne State University, Department of Psychiatry & Behavioral Neurosciences, Detroit, MI, USA
| | - Erika J Wolf
- National Center for PTSD at VA Boston Healthcare System, Boston, MA, USA; Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Regina E McGlinchey
- Geriatric Research Educational and Clinical Center and Translational Research Center for TBI and Stress Disorders, Boston, USA; VA Boston Health Care System, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - William P Milberg
- Geriatric Research Educational and Clinical Center and Translational Research Center for TBI and Stress Disorders, Boston, USA; VA Boston Health Care System, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Mark W Miller
- National Center for PTSD at VA Boston Healthcare System, Boston, MA, USA; Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Subra Kugathasan
- Emory University School of Medicine Department of Pediatrics, Division of Pediatric Gastroenterology & Children's Healthcare of Atlanta, Atlanta, GA, USA; Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Marti Jett
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mark W Logue
- Boston University School of Public Health, Department of Biostatistics, Boston, MA, USA; National Center for PTSD at VA Boston Healthcare System, Boston, MA, USA; Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA; Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
| | - Kerry J Ressler
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA; Department of Psychiatry, Harvard Medical School and McLean Hospital, Belmont, MA, USA
| | - Alicia K Smith
- Emory University, Department of Gynecology and Obstetrics, Atlanta, GA, USA; Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA.
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17
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Schoorlemmer J, Macías-Redondo S, Strunk M, Ramos-Ruíz R, Calvo P, Benito R, Paules C, Oros D. Altered DNA methylation in human placenta after (suspected) preterm labor. Epigenomics 2020; 12:1769-1782. [PMID: 33107765 DOI: 10.2217/epi-2019-0346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: The aim of this study was to determine if alterations in DNA methylation in the human placenta would support suspected preterm labor as a pathologic insult associated with diminished placental health. Methods: We evaluated placental DNA methylation at seven loci differentially methylated in placental pathologies using targeted bisulfite sequencing, in placentas associated with preterm labor (term birth after suspected preterm labor [n = 15] and preterm birth [n = 15]), and controls (n = 15). Results: DNA methylation levels at the NCAM1 and PLAGL1 loci in placentas associated with preterm labor did differ significantly (p < 0.05) from controls. Discussion: Specific alterations in methylation patterns indicative of an unfavourable placental environment are associated with preterm labor per se and not restricted to preterm birth.
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Affiliation(s)
- Jon Schoorlemmer
- Instituto Aragonés de Ciencias de la Salud (IACS) & Aragon Institute for Health Research (IIS Aragón), Zaragoza, Spain.,Placental pathophysiology & fetal programming research group, B05 DGA & GIIS-028 del IISA.,ARAID Foundation, Zaragoza, Spain
| | - Sofía Macías-Redondo
- Instituto Aragonés de Ciencias de la Salud (IACS) & Aragon Institute for Health Research (IIS Aragón), Zaragoza, Spain
| | - Mark Strunk
- Instituto Aragonés de Ciencias de la Salud (IACS), Sequencing & Functional Genomics, Aragon Biomedical Research Center (CIBA), Zaragoza, Spain
| | - Ricardo Ramos-Ruíz
- Unidad de Genómica, Fundación Parque Científico de Madrid, Madrid, Spain
| | - Pilar Calvo
- Placental pathophysiology & fetal programming research group, B05 DGA & GIIS-028 del IISA.,Aragon Institute for Health Research (IIS Aragón), Obstetrics Department, Hospital Clínico Universitario Zaragoza, Spain
| | - Rafael Benito
- Aragon Institute for Health Research (IIS Aragón), Microbiology Department, Hospital Clínico Universitario Zaragoza, Spain
| | - Cristina Paules
- Placental pathophysiology & fetal programming research group, B05 DGA & GIIS-028 del IISA.,Aragon Institute for Health Research (IIS Aragón), Obstetrics Department, Hospital Clínico Universitario Zaragoza, Spain
| | - Daniel Oros
- Placental pathophysiology & fetal programming research group, B05 DGA & GIIS-028 del IISA.,Aragon Institute for Health Research (IIS Aragón), Obstetrics Department, Hospital Clínico Universitario Zaragoza, Spain.,Red de Salud Materno Infantil y del Desarrollo (SAMID), RETICS, Instituto de Salud Carlos III (ISCIII), Subdirección General de Evaluación y Fomento de la Investigación, Fondo Europeo de Desarrollo Regional (FEDER), Spain
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18
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Hara-Isono K, Matsubara K, Fuke T, Yamazawa K, Satou K, Murakami N, Saitoh S, Nakabayashi K, Hata K, Ogata T, Fukami M, Kagami M. Genome-wide methylation analysis in Silver-Russell syndrome, Temple syndrome, and Prader-Willi syndrome. Clin Epigenetics 2020; 12:159. [PMID: 33092629 PMCID: PMC7583213 DOI: 10.1186/s13148-020-00949-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/13/2020] [Indexed: 12/19/2022] Open
Abstract
Background Imprinting disorders (IDs) show overlapping phenotypes, particularly in Silver–Russell syndrome (SRS), Temple syndrome (TS14), and Prader–Willi syndrome (PWS). These three IDs include fetal and postnatal growth failure, feeding difficulty, and muscular hypotonia as major clinical features. However, the mechanism that causes overlapping phenotypes has not been clarified. To investigate the presence or absence of methylation signatures associated with overlapping phenotypes, we performed genome-wide methylation analysis (GWMA). Results GWMA was carried out on 36 patients with three IDs (SRS [n = 16], TS14 [n = 7], PWS [n = 13]) and 11 child controls using HumanMethylation450 BeadChip including 475,000 CpG sites across the human genome. To reveal an aberrantly methylated region shared by SRS, TS14, and PWS groups, we compared genome-wide methylation data of the three groups with those of control subjects. All the identified regions were known as SRS-, TS14-, and PWS-related imprinting-associated differentially methylated regions (iDMRs), and there was no hypermethylated or hypomethylated region shared by different ID groups. To examine the methylation pattern shared by SRS, TS14, and PWS groups, we performed clustering analysis based on GWMA data. The result focusing on 620 probes at the 62 known iDMRs (except for SRS-, TS14-, and PWS-related iDMRs) classified patients into two categories: (1) category A, grossly normal methylation patterns mainly consisting of SRS group patients; and (2) category B, broad and mild hypermethylation patterns mainly consisting of TS14 and PWS group patients. However, we found no obvious relationship between these methylation patterns and phenotypes of patients. Conclusions GWMA in three IDs found no methylation signatures shared by SRS, TS14, and PWS groups. Although clustering analysis showed similar mild hypermethylation patterns in TS14 and PWS groups, further study is needed to clarify the effect of methylation patterns on the overlapping phenotypes.
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Affiliation(s)
- Kaori Hara-Isono
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.,Department of Pediatrics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Tomoko Fuke
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Kazuki Yamazawa
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.,Medical Genetics Center, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan
| | - Kazuhito Satou
- Department of Genome Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Nobuyuki Murakami
- Department of Pediatrics, Dokkyo Medical University Saitama Medical Center, 2-1-50 Minami Koshigaya, Koshigaya, 343-8555, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Kenichiro Hata
- Department of Maternal Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.,Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
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19
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Papulino C, Chianese U, Nicoletti MM, Benedetti R, Altucci L. Preclinical and Clinical Epigenetic-Based Reconsideration of Beckwith-Wiedemann Syndrome. Front Genet 2020; 11:563718. [PMID: 33101381 PMCID: PMC7522569 DOI: 10.3389/fgene.2020.563718] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/26/2020] [Indexed: 12/26/2022] Open
Abstract
Epigenetics has achieved a profound impact in the biomedical field, providing new experimental opportunities and innovative therapeutic strategies to face a plethora of diseases. In the rare diseases scenario, Beckwith-Wiedemann syndrome (BWS) is a pediatric pathological condition characterized by a complex molecular basis, showing alterations in the expression of different growth-regulating genes. The molecular origin of BWS is associated with impairments in the genomic imprinting of two domains at the 11p15.5 chromosomal region. The first domain contains three different regions: insulin growth like factor gene (IGF2), H19, and abnormally methylated DMR1 region. The second domain consists of cell proliferation and regulating-genes such as CDKN1C gene encoding for cyclin kinase inhibitor its role is to block cell proliferation. Although most cases are sporadic, about 5-10% of BWS patients have inheritance characteristics. In the 11p15.5 region, some of the patients have maternal chromosomal rearrangements while others have Uniparental Paternal Disomy UPD(11)pat. Defects in DNA methylation cause alteration of genes and the genomic structure equilibrium leading uncontrolled cell proliferation, which is a typical tumorigenesis event. Indeed, in BWS patients an increased childhood tumor predisposition is observed. Here, we summarize the latest knowledge on BWS and focus on the impact of epigenetic alterations to an increased cancer risk development and to metabolic disorders. Moreover, we highlight the correlation between assisted reproductive technologies and this rare disease. We also discuss intriguing aspects of BWS in twinning. Epigenetic therapies in clinical trials have already demonstrated effectiveness in oncological and non-oncological diseases. In this review, we propose a potential "epigenetic-based" approaches may unveil new therapeutic options for BWS patients. Although the complexity of the syndrome is high, patients can be able to lead a normal life but tumor predispositions might impair life expectancy. In this sense epigenetic therapies should have a supporting role in order to guarantee a good prognosis.
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Affiliation(s)
- Chiara Papulino
- Department of Precision Medicine, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Ugo Chianese
- Department of Precision Medicine, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Maria Maddalena Nicoletti
- Department of Precision Medicine, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Rosaria Benedetti
- Department of Precision Medicine, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Lucia Altucci
- Department of Precision Medicine, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
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20
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Fontana L, Bedeschi MF, Cagnoli GA, Costanza J, Persico N, Gangi S, Porro M, Ajmone PF, Colapietro P, Santaniello C, Crippa M, Sirchia SM, Miozzo M, Tabano S. (Epi)genetic profiling of extraembryonic and postnatal tissues from female monozygotic twins discordant for Beckwith-Wiedemann syndrome. Mol Genet Genomic Med 2020; 8:e1386. [PMID: 32627967 PMCID: PMC7507324 DOI: 10.1002/mgg3.1386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/26/2020] [Accepted: 06/01/2020] [Indexed: 12/19/2022] Open
Abstract
Background Beckwith–Wiedemann syndrome (BWS) is an overgrowth disorder caused by defects at the 11p15.5 imprinted region. Many cases of female monozygotic (MZ) twins discordant for BWS have been reported, but no definitive conclusions have been drawn regarding the link between epigenetic defects, twinning process, and gender. Here, we report a comprehensive characterization and follow‐up of female MZ twins discordant for BWS. Methods Methylation pattern at 11p15.5 and multilocus methylation disturbance (MLID) profiling were performed by pyrosequencing and MassARRAY in placental/umbilical cord samples and postnatal tissues. Whole‐exome sequencing was carried out to identify MLID causative mutations. X‐chromosome inactivation (XCI) was determined by HUMARA test. Results Both twins share KCNQ1OT1:TSS‐DMR loss of methylation (LOM) and MLID in blood and the epigenetic defect remained stable in the healthy twin over time. KCNQ1OT1:TSS‐DMRLOM was nonhomogeneously distributed in placental samples and the twins showed the same severely skewed XCI pattern. No MLID‐causative mutations were identified. Conclusion This is the first report on BWS‐discordant twins with methylation analyses extended to extraembryonic tissues. The results suggest that caution is required when attempting prenatal diagnosis in similar cases. Although the causative mechanism underlying LOM remains undiscovered, the XCI pattern and mosaic LOM suggest that both twinning and LOM/MLID occurred after XCI commitment.
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Affiliation(s)
- Laura Fontana
- Medical Genetics, Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Milano, Italy.,Research Laboratories Coordination Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Maria F Bedeschi
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Giulia A Cagnoli
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Jole Costanza
- Research Laboratories Coordination Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Nicola Persico
- Obstetrics and Gynecology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy.,Department of ClinicalSciences and Community Health, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Silvana Gangi
- NICU, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Matteo Porro
- Pediatric Physical Medicine & Rehabilitation Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Paola F Ajmone
- Child and AdolescentNeuropsychiatric Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Patrizia Colapietro
- Medical Genetics, Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Milano, Italy.,Research Laboratories Coordination Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Carlo Santaniello
- Research Laboratories Coordination Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Milena Crippa
- Medical Cytogenetics& Human Molecular Genetics, Istituto Auxologico Italiano-IRCCS, Milano, Italy
| | - Silvia M Sirchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | - Monica Miozzo
- Medical Genetics, Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Milano, Italy.,Research Laboratories Coordination Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Silvia Tabano
- Medical Genetics, Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Milano, Italy.,Laboratory of Medical Genetics, Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico, Milan, Italy
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21
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Imprinted genes in clinical exome sequencing: Review of 538 cases and exploration of mouse-human conservation in the identification of novel human disease loci. Eur J Med Genet 2020; 63:103903. [PMID: 32169557 DOI: 10.1016/j.ejmg.2020.103903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 01/20/2020] [Accepted: 03/09/2020] [Indexed: 01/01/2023]
Abstract
Human imprinting disorders cause a range of dysmorphic and neurocognitive phenotypes, and they may elude traditional molecular diagnosis such exome sequencing. The discovery of novel disorders related to imprinted genes has lagged behind traditional Mendelian disorders because current diagnostic technology, especially unbiased testing, has limited utility in their discovery. To identify novel imprinting disorders, we reviewed data for every human gene hypothesized to be imprinted, identified each mouse ortholog, determined its imprinting status in the mouse, and analyzed its function in humans and mice. We identified 17 human genes that are imprinted in both humans and mice, and have functional data in mice or humans to suggest that dysregulated expression would lead to an abnormal phenotype in humans. These 17 genes, along with known imprinted genes, were preferentially flagged 538 clinical exome sequencing tests. The identified genes were: DIRAS3 [1p31.3], TP73 [1p36.32], SLC22A3 [6q25.3], GRB10 [7p12.1], DDC [7p12.2], MAGI2 [7q21.11], PEG10 [7q21.3], PPP1R9A [7q21.3], CALCR [7q21.3], DLGAP2 [8p23.3], GLIS3 [9p24.2], INPP5F [10q26.11], ANO1 [11q13.3], SLC38A4 [12q13.11], GATM [15q21.1], PEG3 [19q13.43], and NLRP2 [19q13.42]. In the 538 clinical cases, eight cases (1.7%) reported variants in a causative known imprinted gene. There were 367/758 variants (48.4%) in imprinted genes that were not known to cause disease, but none of those variants met the criteria for clinical reporting. Imprinted disorders play a significant role in human disease, and additional human imprinted disorders remain to be discovered. Therefore, evolutionary conservation is a potential tool to identify novel genes involved in human imprinting disorders and to identify them in clinical testing.
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22
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Guelfi S, D'Sa K, Botía JA, Vandrovcova J, Reynolds RH, Zhang D, Trabzuni D, Collado-Torres L, Thomason A, Quijada Leyton P, Gagliano Taliun SA, Nalls MA, Small KS, Smith C, Ramasamy A, Hardy J, Weale ME, Ryten M. Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information. Nat Commun 2020; 11:1041. [PMID: 32098967 PMCID: PMC7042265 DOI: 10.1038/s41467-020-14483-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 12/20/2019] [Indexed: 12/30/2022] Open
Abstract
Genome-wide association studies have generated an increasing number of common genetic variants associated with neurological and psychiatric disease risk. An improved understanding of the genetic control of gene expression in human brain is vital considering this is the likely modus operandum for many causal variants. However, human brain sampling complexities limit the explanatory power of brain-related expression quantitative trait loci (eQTL) and allele-specific expression (ASE) signals. We address this, using paired genomic and transcriptomic data from putamen and substantia nigra from 117 human brains, interrogating regulation at different RNA processing stages and uncovering novel transcripts. We identify disease-relevant regulatory loci, find that splicing eQTLs are enriched for regulatory information of neuron-specific genes, that ASEs provide cell-specific regulatory information with evidence for cellular specificity, and that incomplete annotation of the brain transcriptome limits interpretation of risk loci for neuropsychiatric disease. This resource of regulatory data is accessible through our web server, http://braineacv2.inf.um.es/. Regulation of gene expression and splicing are thought to be tissue-specific. Here, the authors obtain genomic and transcriptomic data from putamen and substantia nigra of 117 neurologically healthy human brains and find that splicing eQTLs are enriched for neuron-specific regulatory information.
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Affiliation(s)
- Sebastian Guelfi
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Karishma D'Sa
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK.,Department of Medical & Molecular Genetics, School of Medical Sciences, King's College London, Guy's Hospital, London, UK
| | - Juan A Botía
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK.,Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - Jana Vandrovcova
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Regina H Reynolds
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - David Zhang
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Daniah Trabzuni
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK.,Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | | | | | | | | | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, US National Institutes of Health, Bethesda, MD, USA.,Data Tecnica International, Glen Echo, MD, USA
| | | | | | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Colin Smith
- Department of Neuropathology, MRC Sudden Death Brain Bank Project, University of Edinburgh, Edinburgh, UK
| | - Adaikalavan Ramasamy
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK.,Department of Medical & Molecular Genetics, School of Medical Sciences, King's College London, Guy's Hospital, London, UK.,Singapore Institute for Clinical Sciences, Brenner Centre for Molecular Medicine, Singapore, Singapore
| | - John Hardy
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Michael E Weale
- Department of Medical & Molecular Genetics, School of Medical Sciences, King's College London, Guy's Hospital, London, UK.,Genomics plc, Oxford, UK
| | - Mina Ryten
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK.
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23
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Bahado-Singh RO, Vishweswaraiah S, Aydas B, Mishra NK, Yilmaz A, Guda C, Radhakrishna U. Artificial intelligence analysis of newborn leucocyte epigenomic markers for the prediction of autism. Brain Res 2019; 1724:146457. [DOI: 10.1016/j.brainres.2019.146457] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 01/05/2023]
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24
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Xavier MJ, Roman SD, Aitken RJ, Nixon B. Transgenerational inheritance: how impacts to the epigenetic and genetic information of parents affect offspring health. Hum Reprod Update 2019; 25:518-540. [DOI: 10.1093/humupd/dmz017] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/19/2019] [Accepted: 04/04/2019] [Indexed: 12/18/2022] Open
Abstract
Abstract
BACKGROUND
A defining feature of sexual reproduction is the transmission of genomic information from both parents to the offspring. There is now compelling evidence that the inheritance of such genetic information is accompanied by additional epigenetic marks, or stable heritable information that is not accounted for by variations in DNA sequence. The reversible nature of epigenetic marks coupled with multiple rounds of epigenetic reprogramming that erase the majority of existing patterns have made the investigation of this phenomenon challenging. However, continual advances in molecular methods are allowing closer examination of the dynamic alterations to histone composition and DNA methylation patterns that accompany development and, in particular, how these modifications can occur in an individual’s germline and be transmitted to the following generation. While the underlying mechanisms that permit this form of transgenerational inheritance remain unclear, it is increasingly apparent that a combination of genetic and epigenetic modifications plays major roles in determining the phenotypes of individuals and their offspring.
OBJECTIVE AND RATIONALE
Information pertaining to transgenerational inheritance was systematically reviewed focusing primarily on mammalian cells to the exclusion of inheritance in plants, due to inherent differences in the means by which information is transmitted between generations. The effects of environmental factors and biological processes on both epigenetic and genetic information were reviewed to determine their contribution to modulating inheritable phenotypes.
SEARCH METHODS
Articles indexed in PubMed were searched using keywords related to transgenerational inheritance, epigenetic modifications, paternal and maternal inheritable traits and environmental and biological factors influencing transgenerational modifications. We sought to clarify the role of epigenetic reprogramming events during the life cycle of mammals and provide a comprehensive review of how the genomic and epigenomic make-up of progenitors may determine the phenotype of its descendants.
OUTCOMES
We found strong evidence supporting the role of DNA methylation patterns, histone modifications and even non-protein-coding RNA in altering the epigenetic composition of individuals and producing stable epigenetic effects that were transmitted from parents to offspring, in both humans and rodent species. Multiple genomic domains and several histone modification sites were found to resist demethylation and endure genome-wide reprogramming events. Epigenetic modifications integrated into the genome of individuals were shown to modulate gene expression and activity at enhancer and promoter domains, while genetic mutations were shown to alter sequence availability for methylation and histone binding. Fundamentally, alterations to the nuclear composition of the germline in response to environmental factors, ageing, diet and toxicant exposure have the potential to become hereditably transmitted.
WIDER IMPLICATIONS
The environment influences the health and well-being of progeny by working through the germline to introduce spontaneous genetic mutations as well as a variety of epigenetic changes, including alterations in DNA methylation status and the post-translational modification of histones. In evolutionary terms, these changes create the phenotypic diversity that fuels the fires of natural selection. However, rather than being adaptive, such variation may also generate a plethora of pathological disease states ranging from dominant genetic disorders to neurological conditions, including spontaneous schizophrenia and autism.
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Affiliation(s)
- Miguel João Xavier
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Shaun D Roman
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Chemical Biology and Clinical Pharmacology, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - R John Aitken
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Brett Nixon
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
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25
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Tissue-Specific Monoallelic Expression of Bovine AXL is Associated with DNA Methylation of Promoter DMR. Biochem Genet 2019; 57:801-812. [PMID: 31073794 DOI: 10.1007/s10528-019-09925-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 05/02/2019] [Indexed: 12/31/2022]
Abstract
The AXL protein is a receptor tyrosine kinase and is often implicated in proliferation, migration and therapy resistance in various cancers. The AXL gene in humans is maternally expressed and paternally imprinted with differentially methylated regions (DMR) surrounding the promoter region. However, the imprinting status and epigenetic regulation of AXL gene in cattle remain unclear. Therefore, we explored the molecular structure along with the patterns of allelic expression and DNA methylation of the bovine AXL gene. First, the complete cDNA sequence of bovine AXL was gathered by Sanger method, from transcripts obtained from RT-PCR, 5' and 3' -RACE. In silico BLAST alignments showed that the longest mRNA sequence of bovine AXL consists of 19 exons and encodes a protein of 887 amino acids. We further analyzed the allelic expression of bovine AXL by employing single-nucleotide polymorphism (SNP)-based sequencing method. A SNP site (GenBank Accession no: rs210020651) found in exon 7 allowed us to distinguish the two parental alleles. Monoallelic expression of AXL was observed in four adult bovine tissues (heart, liver, spleen and fat), while biallelic expression was found in the other adult tissues such as the lung, kidney, muscle, brain and placenta. To determine whether the DNA methylation played a role in the tissue-specific imprinting of bovine AXL, we performed bisulfite sequencing of two regions: region 1 was a CpG island (CGI) in AXL promoter, mapping to 643 bp upstream of the transcription start site of AXL 5'-v1 transcripts, while region two was homologous to the region of human AXL DMR, with 10 CpG sites overlapping the first translation start site (TSS1) of bovine AXL. In region 2, DNA from both monoallelic and biallelic expressed tissues were mostly found to be completely unmethylated. However, tissue-specific differential methylation patterns were found in monoallelic expressed tissues such as the heart and liver while hypomethylation was noted in the promoter CpG island in biallelic expressed tissues such as the lung. These observations demonstrated that the tissue-specific monoallelic expression of bovine AXL is dependent on the DNA methylation of its promoter region.
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26
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Krzyzewska IM, Alders M, Maas SM, Bliek J, Venema A, Henneman P, Rezwan FI, Lip KVD, Mul AN, Mackay DJG, Mannens MMAM. Genome-wide methylation profiling of Beckwith-Wiedemann syndrome patients without molecular confirmation after routine diagnostics. Clin Epigenetics 2019; 11:53. [PMID: 30898153 PMCID: PMC6429826 DOI: 10.1186/s13148-019-0649-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/06/2019] [Indexed: 11/16/2022] Open
Abstract
Beckwith-Wiedemann syndrome (BWS) is caused due to the disturbance of imprinted genes at chromosome 11p15. The molecular confirmation of this syndrome is possible in approximately 85% of the cases, whereas in the remaining 15% of the cases, the underlying defect remains unclear. The goal of our research was to identify new epigenetic loci related to BWS. We studied a group of 25 patients clinically diagnosed with BWS but without molecular conformation after DNA diagnostics and performed a whole genome methylation analysis using the HumanMethylation450 Array (Illumina).We found hypermethylation throughout the methylome in two BWS patients. The hypermethylated sites in these patients overlapped and included both non-imprinted and imprinted regions. This finding was not previously described in any BWS-diagnosed patient.Furthermore, one BWS patient exhibited aberrant methylation in four maternally methylated regions-IGF1R, NHP2L1, L3MBTL, and ZDBF2-that overlapped with the differentially methylated regions found in BWS patients with multi-locus imprinting disturbance (MLID). This finding suggests that the BWS phenotype can result from MLID without detectable methylation defects in the primarily disease-associated loci (11p15). Another patient manifested small but significant aberrant methylation in disease-associated loci at 11p near H19, possibly confirming the diagnosis in this patient.
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Affiliation(s)
- I M Krzyzewska
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - M Alders
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - S M Maas
- Amsterdam UMC, University of Amsterdam, Department of Pediatrics, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - J Bliek
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - A Venema
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - P Henneman
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - F I Rezwan
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - K V D Lip
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - A N Mul
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - D J G Mackay
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - M M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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27
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Epigenetically dysregulated genes and pathways implicated in the pathogenesis of non-syndromic high myopia. Sci Rep 2019; 9:4145. [PMID: 30858441 PMCID: PMC6411983 DOI: 10.1038/s41598-019-40299-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/30/2018] [Indexed: 12/20/2022] Open
Abstract
Myopia, commonly referred to as nearsightedness, is one of the most common causes of visual disability throughout the world. It affects more people worldwide than any other chronic visual impairment condition. Although the prevalence varies among various ethnic groups, the incidence of myopia is increasing in all populations across globe. Thus, it is considered a pressing public health problem. Both genetics and environment play a role in development of myopia. To elucidate the epigenetic mechanism(s) underlying the pathophysiology of high-myopia, we conducted methylation profiling in 18 cases and 18 matched controls (aged 4–12 years), using Illumina MethylationEPIC BeadChips array. The degree of myopia was variable among subjects, ranging from −6 to −15D. We identified 1541 hypermethylated CpGs, representing 1745 genes (2.0-fold or higher) (false discovery rate (FDR) p ≤ 0.05), multiple CpGs were p < 5 × 10−8 with a receiver operating characteristic area under the curve (ROC-AUC) ≥ 0.75 in high-myopia subjects compared to controls. Among these, 48 CpGs had excellent correlation (AUC ≥ 0.90). Herein, we present the first genome-wide DNA methylation analysis in a unique high-myopia cohort, showing extensive and discrete methylation changes relative to controls. The genes we identified hold significant potential as targets for novel therapeutic intervention either alone, or in combination.
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Touati A, Errea-Dorronsoro J, Nouri S, Halleb Y, Pereda A, Mahdhaoui N, Ghith A, Saad A, Perez de Nanclares G, H'mida Ben Brahim D. Transient neonatal diabetes mellitus and hypomethylation at additional imprinted loci: novel ZFP57 mutation and review on the literature. Acta Diabetol 2019; 56:301-307. [PMID: 30315371 DOI: 10.1007/s00592-018-1239-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 09/29/2018] [Indexed: 11/28/2022]
Abstract
AIM 6q24-related transient neonatal diabetes mellitus (6q24-TNDM) is a rare imprinting disorder characterized by uncontrolled hyperglycemia during the first 6 months of life. The molecular etiology of 6q24-TNDM is attributable to overexpression of the paternally inherited PLAGL1 and HYMAI genes located on the 6q24 locus. One of these major defects is maternal loss of methylation (LOM) at 6q24. In addition, approximately 50% of TNDM patients that present LOM at 6q24 can also display hypomethylation at additional imprinted loci (multilocus imprinting disturbances, MLID). Interestingly, the majority of these patients carry mutations in the ZFP57 gene, a transcription factor required for the adequate maintenance of methylation during early embryonic development. METHODS Methylation analysis of 6q24 and additional imprinted loci was carried out by MS-MLPA in a Tunisian male patient with clinical diagnosis of TNMD. For the same patient, mutation analysis of the ZFP57 gene was conducted by direct Sanger sequencing. RESULTS We report a novel nonsense mutation (c.373C > T; p.R125*; ENST00000376883.1) at the ZFP57 gene causing TNDM-MLID and describe detailed phenotype/epigenotype analysis of TNMD patients carrying ZFP57 mutations. CONCLUSION We provide additional support to the role of ZFP57 as a genetic determinant cause of MLID in patients with TNMD.
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Affiliation(s)
- Ameni Touati
- Department of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia
- High Institute of Biotechnology, Monastir University, Monastir, Tunisia
| | - Javier Errea-Dorronsoro
- Molecular (Epi)Genetic Lab, BioAraba National Health Institute, OSI Araba University Hospital, 01009, Vitoria-Gasteiz, Alava, Spain
| | - Sonia Nouri
- Department of Neonatology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia
- Faculty of Medicine, Sousse University, Sousse, Tunisia
| | - Yosra Halleb
- Department of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia
- Faculty of Medicine, Sousse University, Sousse, Tunisia
| | - Arrate Pereda
- Molecular (Epi)Genetic Lab, BioAraba National Health Institute, OSI Araba University Hospital, 01009, Vitoria-Gasteiz, Alava, Spain
| | - Nabiha Mahdhaoui
- Department of Neonatology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia
- Faculty of Medicine, Sousse University, Sousse, Tunisia
| | - Aida Ghith
- Department of Neonatology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia
- Faculty of Medicine, Sousse University, Sousse, Tunisia
| | - Ali Saad
- Department of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia
- Faculty of Medicine, Sousse University, Sousse, Tunisia
| | - Guiomar Perez de Nanclares
- Molecular (Epi)Genetic Lab, BioAraba National Health Institute, OSI Araba University Hospital, 01009, Vitoria-Gasteiz, Alava, Spain
| | - Dorra H'mida Ben Brahim
- Department of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia.
- Faculty of Medicine, Sousse University, Sousse, Tunisia.
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29
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Germline Epigenetic Testing of Imprinting Disorders in a Diagnostic Setting. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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30
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Insights into imprinting from parent-of-origin phased methylomes and transcriptomes. Nat Genet 2018; 50:1542-1552. [PMID: 30349119 DOI: 10.1038/s41588-018-0232-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 08/08/2018] [Indexed: 01/23/2023]
Abstract
Imprinting is the preferential expression of one parental allele over the other. It is controlled primarily through differential methylation of cytosine at CpG dinucleotides. Here we combine 285 methylomes and 11,617 transcriptomes from peripheral blood samples with parent-of-origin phased haplotypes, to produce a new map of imprinted methylation and gene expression patterns across the human genome. We demonstrate how imprinted methylation is a continuous rather than a binary characteristic. We describe at high resolution the parent-of-origin methylation pattern at the 15q11.2 Prader-Willi/Angelman syndrome locus, with nearly confluent stochastic paternal methylation punctuated by 'spikes' of maternal methylation. We find examples of polymorphic imprinted methylation unrelated (at VTRNA2-1 and PARD6G) or related (at CHRNE) to nearby SNP genotypes. We observe RNA isoform-specific imprinted expression patterns suggestive of a methylation-sensitive transcriptional elongation block. Finally, we gain new insights into parent-of-origin-specific effects on phenotypes at the DLK1/MEG3 and GNAS loci.
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31
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Fontana L, Bedeschi MF, Maitz S, Cereda A, Faré C, Motta S, Seresini A, D'Ursi P, Orro A, Pecile V, Calvello M, Selicorni A, Lalatta F, Milani D, Sirchia SM, Miozzo M, Tabano S. Characterization of multi-locus imprinting disturbances and underlying genetic defects in patients with chromosome 11p15.5 related imprinting disorders. Epigenetics 2018; 13:897-909. [PMID: 30221575 PMCID: PMC6284780 DOI: 10.1080/15592294.2018.1514230] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The identification of multilocus imprinting disturbances (MLID) appears fundamental to uncover molecular pathways underlying imprinting disorders (IDs) and to complete clinical diagnosis of patients. However, MLID genetic associated mechanisms remain largely unknown. To characterize MLID in Beckwith-Wiedemann (BWS) and Silver-Russell (SRS) syndromes, we profiled by MassARRAY the methylation of 12 imprinted differentially methylated regions (iDMRs) in 21 BWS and 7 SRS patients with chromosome 11p15.5 epimutations. MLID was identified in 50% of BWS and 29% of SRS patients as a maternal hypomethylation syndrome. By next-generation sequencing, we searched for putative MLID-causative mutations in genes involved in methylation establishment/maintenance and found two novel missense mutations possibly causative of MLID: one in NLRP2, affecting ADP binding and protein activity, and one in ZFP42, likely leading to loss of DNA binding specificity. Both variants were paternally inherited. In silico protein modelling allowed to define the functional effect of these mutations. We found that MLID is very frequent in BWS/SRS. In addition, since MLID-BWS patients in our cohort show a peculiar pattern of BWS-associated clinical signs, MLID test could be important for a comprehensive clinical assessment. Finally, we highlighted the possible involvement of ZFP42 variants in MLID development and confirmed NLRP2 as causative locus in BWS-MLID.
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Affiliation(s)
- L Fontana
- a Laboratory of Molecular Pathology, Department of Pathophysiology and Transplantation , Università degli Studi di Milano , Milano , Italy
| | - M F Bedeschi
- b Clinical Genetics Unit , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - S Maitz
- c Clinical Pediatric, Genetics Unit , MBBM Foundation, San Gerardo Monza , Monza , Italy
| | - A Cereda
- d Medical Genetics Unit , Papa Giovanni XXIII Hospital , Bergamo , Italy
| | - C Faré
- e Division of Pathology , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - S Motta
- e Division of Pathology , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - A Seresini
- f Medical Genetics Laboratory , Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico , Milano , Italy.,g Fondazione Grigioni per il Morbo di Parkinson , Milano , Italy
| | - P D'Ursi
- h Department of Biomedical Sciences National Research Council , Institute for Biomedical Technologies , Segrate , Italy
| | - A Orro
- h Department of Biomedical Sciences National Research Council , Institute for Biomedical Technologies , Segrate , Italy
| | - V Pecile
- i Medical Genetics Division , Institute for maternal and child health IRCCS Burlo Garofolo , Trieste , Italy
| | - M Calvello
- e Division of Pathology , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy.,j Division of Cancer Prevention and Genetics, IEO , European Institute of Oncology IRCCS , Milano , Italy
| | - A Selicorni
- k UOC Pediatria , ASST Lariana , Como , Italy
| | - F Lalatta
- b Clinical Genetics Unit , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - D Milani
- l Pediatric Highly Intensive Care Unit , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - S M Sirchia
- m Medical Genetics, Department of Health Sciences , Università degli Studi di Milano , Milano , Italy
| | - M Miozzo
- a Laboratory of Molecular Pathology, Department of Pathophysiology and Transplantation , Università degli Studi di Milano , Milano , Italy.,e Division of Pathology , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - S Tabano
- a Laboratory of Molecular Pathology, Department of Pathophysiology and Transplantation , Università degli Studi di Milano , Milano , Italy
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32
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Mozaffari SV, Stein MM, Magnaye KM, Nicolae DL, Ober C. Parent of origin gene expression in a founder population identifies two new candidate imprinted genes at known imprinted regions. PLoS One 2018; 13:e0203906. [PMID: 30204804 PMCID: PMC6133383 DOI: 10.1371/journal.pone.0203906] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/29/2018] [Indexed: 11/18/2022] Open
Abstract
Genomic imprinting is the phenomena that leads to silencing of one copy of a gene inherited from a specific parent. Mutations in imprinted regions have been involved in diseases showing parent of origin effects. Identifying genes with evidence of parent of origin expression patterns in family studies allows the detection of more subtle imprinting. Here, we use allele specific expression in lymphoblastoid cell lines from 306 Hutterites related in a single pedigree to provide formal evidence for parent of origin effects. We take advantage of phased genotype data to assign parent of origin to RNA-seq reads in individuals with gene expression data. Our approach identified known imprinted genes, two putative novel imprinted genes, PXDC1 and PWAR6, and 14 genes with asymmetrical parent of origin gene expression. We used gene expression in peripheral blood leukocytes (PBL) to validate our findings, and then confirmed imprinting control regions (ICRs) using DNA methylation levels in the PBLs.
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Affiliation(s)
- Sahar V. Mozaffari
- Committee on Genetics, Genomics & Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Michelle M. Stein
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Kevin M. Magnaye
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Dan L. Nicolae
- Committee on Genetics, Genomics & Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - Carole Ober
- Committee on Genetics, Genomics & Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
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33
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A genome-wide search for new imprinted genes in the human placenta identifies DSCAM as the first imprinted gene on chromosome 21. Eur J Hum Genet 2018; 27:49-60. [PMID: 30206355 DOI: 10.1038/s41431-018-0267-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 07/16/2018] [Accepted: 08/23/2018] [Indexed: 11/08/2022] Open
Abstract
We identified, through a genome-wide search for new imprinted genes in the human placenta, DSCAM (Down Syndrome Cellular Adhesion Molecule) as a paternally expressed imprinted gene. Our work revealed the presence of a Differentially Methylated Region (DMR), located within intron 1 that might regulate the imprinting in the region. This DMR showed a maternal allele methylation, compatible with its paternal expression. We showed that DSCAM is present in endothelial cells and the syncytiotrophoblast layer of the human placenta. In mouse, Dscam expression is biallelic in foetal brain and placenta excluding any possible imprinting in these tissues. This gene encodes a cellular adhesion molecule mainly known for its role in neurone development but its function in the placenta remains unclear. We report here the first imprinted gene located on human chromosome 21 with potential clinical implications.
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34
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Cuellar Partida G, Laurin C, Ring SM, Gaunt TR, McRae AF, Visscher PM, Montgomery GW, Martin NG, Hemani G, Suderman M, Relton CL, Davey Smith G, Evans DM. Genome-wide survey of parent-of-origin effects on DNA methylation identifies candidate imprinted loci in humans. Hum Mol Genet 2018; 27:2927-2939. [PMID: 29860447 PMCID: PMC6077796 DOI: 10.1093/hmg/ddy206] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/23/2018] [Indexed: 12/14/2022] Open
Abstract
Genomic imprinting is an epigenetic mechanism leading to parent-of-origin silencing of alleles. So far, the precise number of imprinted regions in humans is uncertain. In this study, we leveraged genome-wide DNA methylation in whole blood measured longitudinally at three time points (birth, childhood and adolescence) and genome-wide association studies (GWAS) data in 740 mother-child duos from the Avon Longitudinal Study of parents and children to identify candidate imprinted loci. We reasoned that cis-meQTLs at genomic regions that were imprinted would show strong evidence of parent-of-origin associations with DNA methylation, enabling the detection of imprinted regions. Using this approach, we identified genome-wide significant cis-meQTLs that exhibited parent-of-origin effects (POEs) at 82 loci, 34 novel and 48 regions previously implicated in imprinting (3.7-10<P < 10-300). Using an independent dataset from the Brisbane Systems Genetic Study, we replicated 76 out of the 82 identified loci. POEs were remarkably consistent across time points and were so strong at some loci that methylation levels enabled good discrimination of parental transmissions at these and surrounding genomic regions. The implication is that parental allelic transmissions could be modelled at many imprinted (and linked) loci in GWAS of unrelated individuals given a combination of genetic and methylation data. Novel regions showing parent of origin effects on methylation will require replication using a different technology and further functional experiments to confirm that such effects arise through a genomic imprinting mechanism.
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Affiliation(s)
- Gabriel Cuellar Partida
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, Australia
| | - Charles Laurin
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Susan M Ring
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tom R Gaunt
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Allan F McRae
- The Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Peter M Visscher
- The Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.,Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
| | - Grant W Montgomery
- The Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.,Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
| | | | - Gibran Hemani
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew Suderman
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline L Relton
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - David M Evans
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, Australia.,Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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35
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Shaaban S, MacKinnon S, Andrews C, Staffieri SE, Maconachie GDE, Chan WM, Whitman MC, Morton SU, Yazar S, MacGregor S, Elder JE, Traboulsi EI, Gottlob I, Hewitt AW, Hunter DG, Mackey DA, Engle EC. Genome-Wide Association Study Identifies a Susceptibility Locus for Comitant Esotropia and Suggests a Parent-of-Origin Effect. Invest Ophthalmol Vis Sci 2018; 59:4054-4064. [PMID: 30098192 PMCID: PMC6088800 DOI: 10.1167/iovs.18-24082] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/19/2018] [Indexed: 11/24/2022] Open
Abstract
Purpose To identify genetic variants conferring susceptibility to esotropia. Esotropia is the most common form of comitant strabismus, has its highest incidence in European ancestry populations, and is believed to be inherited as a complex trait. Methods White European American discovery cohorts with nonaccommodative (826 cases and 2991 controls) or accommodative (224 cases and 749 controls) esotropia were investigated. White European Australian and United Kingdom cohorts with nonaccommodative (689 cases and 1448 controls) or accommodative (66 cases and 264 controls) esotropia were tested for replication. We performed a genome-wide case-control association study using a mixed linear additive model. Meta-analyses of discovery and replication cohorts were then conducted. Results A significant association with nonaccommodative esotropia was discovered (odds ratio [OR] = 1.41, P = 2.84 × 10-09) and replicated (OR = 1.23, P = 0.01) at rs2244352 [T] located within intron 1 of the WRB (tryptophan rich basic protein) gene on chromosome 21 (meta-analysis OR = 1.33, P = 9.58 × 10-11). This single nucleotide polymorphism (SNP) is differentially methylated, and there is a statistically significant skew toward paternal inheritance in the discovery cohort. Meta-analysis of the accommodative discovery and replication cohorts identified an association with rs912759 [T] (OR = 0.59, P = 1.89 × 10-08), an intergenic SNP on chromosome 1p31.1. Conclusions This is the first genome-wide association study (GWAS) to identify significant associations in esotropia and suggests a parent-of-origin effect. Additional cohorts will permit replication and extension of these findings. Future studies of rs2244352 and WRB should provide insight into pathophysiological mechanisms underlying comitant strabismus.
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Affiliation(s)
- Sherin Shaaban
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Neurology, Harvard Medical School, Boston, Massachusetts, United States
- Dubai Harvard Foundation for Medical Research, Boston, Massachusetts, United States
| | - Sarah MacKinnon
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Caroline Andrews
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| | - Sandra E. Staffieri
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
- Department of Ophthalmology, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Gail D. E. Maconachie
- Department of Neuroscience, The University of Leicester Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - Wai-Man Chan
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| | - Mary C. Whitman
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - Sarah U. Morton
- Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Seyhan Yazar
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Western Australia, Australia
| | - Stuart MacGregor
- Stastical Genetics Laboratory, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - James E. Elder
- Department of Ophthalmology, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Elias I. Traboulsi
- Department of Ophthalmology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, United States
| | - Irene Gottlob
- Department of Neuroscience, The University of Leicester Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - Alex W. Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Western Australia, Australia
- Department of Ophthalmology, School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
| | - Strabismus Genetics Research Consortium
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Neurology, Harvard Medical School, Boston, Massachusetts, United States
- Dubai Harvard Foundation for Medical Research, Boston, Massachusetts, United States
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
- Department of Ophthalmology, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
- Department of Neuroscience, The University of Leicester Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
- Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts, United States
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Western Australia, Australia
- Stastical Genetics Laboratory, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Ophthalmology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, United States
- Department of Ophthalmology, School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, United States
| | - David G. Hunter
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - David A. Mackey
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Western Australia, Australia
- Department of Ophthalmology, School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
| | - Elizabeth C. Engle
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Neurology, Harvard Medical School, Boston, Massachusetts, United States
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, United States
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Mantovani G, Bastepe M, Monk D, de Sanctis L, Thiele S, Usardi A, Ahmed SF, Bufo R, Choplin T, De Filippo G, Devernois G, Eggermann T, Elli FM, Freson K, García Ramirez A, Germain-Lee EL, Groussin L, Hamdy N, Hanna P, Hiort O, Jüppner H, Kamenický P, Knight N, Kottler ML, Le Norcy E, Lecumberri B, Levine MA, Mäkitie O, Martin R, Martos-Moreno GÁ, Minagawa M, Murray P, Pereda A, Pignolo R, Rejnmark L, Rodado R, Rothenbuhler A, Saraff V, Shoemaker AH, Shore EM, Silve C, Turan S, Woods P, Zillikens MC, Perez de Nanclares G, Linglart A. Diagnosis and management of pseudohypoparathyroidism and related disorders: first international Consensus Statement. Nat Rev Endocrinol 2018; 14:476-500. [PMID: 29959430 PMCID: PMC6541219 DOI: 10.1038/s41574-018-0042-0] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This Consensus Statement covers recommendations for the diagnosis and management of patients with pseudohypoparathyroidism (PHP) and related disorders, which comprise metabolic disorders characterized by physical findings that variably include short bones, short stature, a stocky build, early-onset obesity and ectopic ossifications, as well as endocrine defects that often include resistance to parathyroid hormone (PTH) and TSH. The presentation and severity of PHP and its related disorders vary between affected individuals with considerable clinical and molecular overlap between the different types. A specific diagnosis is often delayed owing to lack of recognition of the syndrome and associated features. The participants in this Consensus Statement agreed that the diagnosis of PHP should be based on major criteria, including resistance to PTH, ectopic ossifications, brachydactyly and early-onset obesity. The clinical and laboratory diagnosis should be confirmed by a molecular genetic analysis. Patients should be screened at diagnosis and during follow-up for specific features, such as PTH resistance, TSH resistance, growth hormone deficiency, hypogonadism, skeletal deformities, oral health, weight gain, glucose intolerance or type 2 diabetes mellitus, and hypertension, as well as subcutaneous and/or deeper ectopic ossifications and neurocognitive impairment. Overall, a coordinated and multidisciplinary approach from infancy through adulthood, including a transition programme, should help us to improve the care of patients affected by these disorders.
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Affiliation(s)
- Giovanna Mantovani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Endocrinology Unit, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Murat Bastepe
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Barcelona, Spain
| | - Luisa de Sanctis
- Pediatric Endocrinology Unit, Department of Public Health and Pediatric Sciences, University of Torino, Turin, Italy
| | - Susanne Thiele
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - Alessia Usardi
- APHP, Reference Center for Rare Disorders of Calcium and Phosphate Metabolism, Platform of Expertise Paris-Sud for Rare Diseases and Filière OSCAR, Bicêtre Paris Sud Hospital (HUPS), Le Kremlin-Bicêtre, France
- APHP, Endocrinology and diabetes for children, Bicêtre Paris Sud Hospital (HUPS), Le Kremlin-Bicêtre, France
| | - S Faisal Ahmed
- Developmental Endocrinology Research Group, School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, UK
| | - Roberto Bufo
- IPOHA, Italian Progressive Osseous Heteroplasia Association, Cerignola, Foggia, Italy
| | - Timothée Choplin
- K20, French PHP and related disorders patient association, Jouars Pontchartrain, France
| | - Gianpaolo De Filippo
- APHP, Department of medicine for adolescents, Bicêtre Paris Sud Hospital (HUPS), Le Kremlin-Bicêtre, France
| | - Guillemette Devernois
- K20, French PHP and related disorders patient association, Jouars Pontchartrain, France
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Francesca M Elli
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Endocrinology Unit, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, Gasthuisberg, University of Leuven, Leuven, Belgium
| | - Aurora García Ramirez
- AEPHP, Spanish PHP and related disorders patient association, Huércal-Overa, Almería, Spain
| | - Emily L Germain-Lee
- Albright Center & Center for Rare Bone Disorders, Division of Pediatric Endocrinology & Diabetes, Connecticut Children's Medical Center, Farmington, CT, USA
- Department of Pediatrics, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Lionel Groussin
- APHP, Department of Endocrinology, Cochin Hospital (HUPC), Paris, France
- University of Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Neveen Hamdy
- Department of Medicine, Division of Endocrinology and Centre for Bone Quality, Leiden University Medical Center, Leiden, Netherlands
| | - Patrick Hanna
- INSERM U1169, Bicêtre Paris Sud, Paris Sud - Paris Saclay University, Le Kremlin-Bicêtre, France
| | - Olaf Hiort
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - Harald Jüppner
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter Kamenický
- APHP, Reference Center for Rare Disorders of Calcium and Phosphate Metabolism, Platform of Expertise Paris-Sud for Rare Diseases and Filière OSCAR, Bicêtre Paris Sud Hospital (HUPS), Le Kremlin-Bicêtre, France
- APHP, Department of Endocrinology and Reproductive Diseases, Bicêtre Paris Sud Hospital (HUPS), Le Kremlin-Bicêtre, France
- INSERM U1185, Paris Sud - Paris Saclay University, Le Kremlin-Bicêtre, France
| | - Nina Knight
- UK acrodysostosis patients' group, London, UK
| | - Marie-Laure Kottler
- Department of Genetics, Reference Centre for Rare Disorders of Calcium and Phosphate Metabolism, Caen University Hospital, Caen, France
- BIOTARGEN, UNICAEN, Normandie University, Caen, France
| | - Elvire Le Norcy
- University of Paris Descartes, Sorbonne Paris Cité, Paris, France
- APHP, Department of Odontology, Bretonneau Hospital (PNVS), Paris, France
| | - Beatriz Lecumberri
- Department of Endocrinology and Nutrition, La Paz University Hospital, Madrid, Spain
- Department of Medicine, Autonomous University of Madrid (UAM), Madrid, Spain
- Endocrine Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Michael A Levine
- Division of Endocrinology and Diabetes and Center for Bone Health, Children's Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Outi Mäkitie
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Regina Martin
- Osteometabolic Disorders Unit, Hormone and Molecular Genetics Laboratory (LIM/42), Endocrinology Division, Hospital das Clínicas HCFMUSP, Faculty of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Gabriel Ángel Martos-Moreno
- Department of Endocrinology, Hospital Infantil Universitario Niño Jesús, CIBERobn, ISCIII, Madrid, Spain
- Department of Pediatrics, Autonomous University of Madrid (UAM), Madrid, Spain
- Endocrine Diseases Research Group, Hospital La Princesa Institute for Health Research (IIS La Princesa), Madrid, Spain
| | | | - Philip Murray
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Arrate Pereda
- Molecular (Epi)Genetics Laboratory, BioAraba National Health Institute, Hospital Universitario Araba-Txagorritxu, Vitoria-Gasteiz, Alava, Spain
| | | | - Lars Rejnmark
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Rebecca Rodado
- AEPHP, Spanish PHP and related disorders patient association, Huércal-Overa, Almería, Spain
| | - Anya Rothenbuhler
- APHP, Reference Center for Rare Disorders of Calcium and Phosphate Metabolism, Platform of Expertise Paris-Sud for Rare Diseases and Filière OSCAR, Bicêtre Paris Sud Hospital (HUPS), Le Kremlin-Bicêtre, France
- APHP, Endocrinology and diabetes for children, Bicêtre Paris Sud Hospital (HUPS), Le Kremlin-Bicêtre, France
| | - Vrinda Saraff
- Department of Endocrinology and Diabetes, Birmingham Children's Hospital, Birmingham, UK
| | - Ashley H Shoemaker
- Pediatric Endocrinology and Diabetes, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eileen M Shore
- Departments of Orthopaedic Surgery and Genetics, Center for Research in FOP and Related Disorders, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Caroline Silve
- APHP, Service de Biochimie et Génétique Moléculaires, Hôpital Cochin, Paris, France
| | - Serap Turan
- Department of Pediatrics, Division of Endocrinology and Diabetes, Marmara University, Istanbul, Turkey
| | | | - M Carola Zillikens
- Department of Internal Medicine, Bone Center Erasmus MC - University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Guiomar Perez de Nanclares
- Molecular (Epi)Genetics Laboratory, BioAraba National Health Institute, Hospital Universitario Araba-Txagorritxu, Vitoria-Gasteiz, Alava, Spain.
| | - Agnès Linglart
- APHP, Reference Center for Rare Disorders of Calcium and Phosphate Metabolism, Platform of Expertise Paris-Sud for Rare Diseases and Filière OSCAR, Bicêtre Paris Sud Hospital (HUPS), Le Kremlin-Bicêtre, France.
- APHP, Endocrinology and diabetes for children, Bicêtre Paris Sud Hospital (HUPS), Le Kremlin-Bicêtre, France.
- INSERM U1169, Bicêtre Paris Sud, Paris Sud - Paris Saclay University, Le Kremlin-Bicêtre, France.
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37
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Yeung KS, Ho MSP, Lee SL, Kan ASY, Chan KYK, Tang MHY, Mak CCY, Leung GKC, So PL, Pfundt R, Marshall CR, Scherer SW, Choufani S, Weksberg R, Hon-Yin Chung B. Paternal uniparental disomy of chromosome 19 in a pair of monochorionic diamniotic twins with dysmorphic features and developmental delay. J Med Genet 2018; 55:847-852. [PMID: 30007940 DOI: 10.1136/jmedgenet-2018-105328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/05/2018] [Accepted: 06/27/2018] [Indexed: 01/23/2023]
Abstract
BACKGROUND We report here clinical, cytogenetic and molecular data for a pair of monochorionic diamniotic twins with paternal isodisomy for chromosome 19. Both twins presented with dysmorphic features and global developmental delay. This represents, to our knowledge, the first individual human case of paternal uniparental disomy for chromosome 19 (UPD19). METHODS Whole-exome sequencing, together with conventional karyotype and SNP array analysis were performed along with genome-wide DNA methylation array for delineation of the underlying molecular defects. RESULTS Conventional karyotyping on amniocytes and lymphocytes showed normal karyotypes for both twins. Whole-exome sequencing did not identify any pathogenic sequence variants but >5000 homozygous exonic variants on chromosome 19, suggestive of UPD19. SNP arrays on blood and buccal DNA both showed paternal isodisomy for chromosome 19. Losses of imprinting for known imprinted genes on chromosome 19 were identified, including ZNF331, PEG3, ZIM2 and MIMT1. In addition, imprinting defects were also identified in genes located on other chromosomes, including GPR1-AS, JAKMP1 and NHP2L1. CONCLUSION Imprinting defects are the most likely cause for the dysmorphism and developmental delay in this first report of monozygotic twins with UPD19. However, epigenotype-phenotype correlation will require identification of additional individuals with UPD19 and further molecular analysis.
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Affiliation(s)
- Kit San Yeung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Matthew Sai Pong Ho
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - So Lun Lee
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.,Department of Paediatrics and Adolescent Medicine, The Duchess of Kent Children's Hospital, Hong Kong
| | - Anita Sik Yau Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Hong Kong.,Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | - Kelvin Yuen Kwong Chan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Hong Kong.,Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | - Mary Hoi Yin Tang
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Christopher Chun Yu Mak
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Gordon Ka Chun Leung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Po Lam So
- Department of Obstetrics and Gynecology, Tuen Mun Hospital, Hong Kong
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian R Marshall
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics and Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.,McLaughlin Centre and Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sanaa Choufani
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science and Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Brian Hon-Yin Chung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.,Department of Paediatrics and Adolescent Medicine, The Duchess of Kent Children's Hospital, Hong Kong.,Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
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38
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Hernandez Mora JR, Tayama C, Sánchez-Delgado M, Monteagudo-Sánchez A, Hata K, Ogata T, Medrano J, Poo-Llanillo ME, Simón C, Moran S, Esteller M, Tenorio J, Lapunzina P, Kagami M, Monk D, Nakabayashi K. Characterization of parent-of-origin methylation using the Illumina Infinium MethylationEPIC array platform. Epigenomics 2018; 10:941-954. [PMID: 29962238 DOI: 10.2217/epi-2017-0172] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
AIM This study aimed to establish a catalog of probes corresponding to imprinted differentially methylated regions (DMRs) on the Infinium HumanMethylationEPIC BeadChip. MATERIALS & METHODS Reciprocal uniparental diploidies with low normal biparental mosaic contribution, together with normal diploid controls, were subjected to EPIC BeadChip hybridization. The methylation profiles were assessed for imprinted differential methylation. Top candidates were validated using locus-specific PCR-based assays. RESULTS Seven hundred and eighty-nine CpG probes coincided with 50 known imprinted DMRs and 467 CpG probes corresponding to 124 novel imprinted DMR candidates were identified. Validation led to identification of several subtle DMRs within known imprinted domains as well as novel maternally methylated regions associated with PTCHD3 and JAKMIP1. CONCLUSION Our comprehensive list of bona fide-imprinted DMR probes will simplify and facilitate methylation profiling of individuals with imprinting disorders and is applicable to other diseases in which aberrant imprinting has been implicated, such as cancer and fetal growth.
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Affiliation(s)
- Jose R Hernandez Mora
- Imprinting & Cancer group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health & Development, Tokyo, Japan
| | - Marta Sánchez-Delgado
- Imprinting & Cancer group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ana Monteagudo-Sánchez
- Imprinting & Cancer group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health & Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Jose Medrano
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Valencia, Spain
| | | | - Carlos Simón
- Igenomix SL, Valencia, Spain.,Department of Obs/Gyn, Valencia University, Valencia, Spain.,Department of Obs/Gyn, Stanford University, Palo Alto, CA 94305, USA
| | - Sebastian Moran
- Cancer Epigenetics group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Jair Tenorio
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health & Development, Tokyo, Japan
| | - David Monk
- Imprinting & Cancer group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health & Development, Tokyo, Japan
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39
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Xu D, Zhang C, Li J, Wang G, Chen W, Li D, Li S. Polymorphic Imprinting of SLC38A4 Gene in Bovine Placenta. Biochem Genet 2018; 56:639-649. [PMID: 29785670 DOI: 10.1007/s10528-018-9866-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/18/2018] [Indexed: 01/20/2023]
Abstract
Imprinted genes are characterized by monoallelic expression that is dependent on parental origin. Comparative analysis of imprinted genes between species is a powerful tool for understanding the biological significance of genomic imprinting. The slc38a4 gene encodes a neutral amino acid transporter and is identified as imprinted in mice. In this study, the imprinting status of SLC38A4 was assessed in bovine adult tissues and placenta using a polymorphism-based approach. Results indicate that SLC38A4 is not imprinted in eight adult bovine tissues including heart, liver, spleen, lung, kidney, muscle, fat, and brain. It was interesting to note that SLC38A4 showed polymorphic status in five heterogeneous placentas, with three exhibiting paternal monoallelic expression and two exhibiting biallelic expression. Monoallelic expression of imprinted genes is generally associated with allele-specific differentially methylation regions (DMRs) of CpG islands (CGIs)-encompassed promoter; therefore, the DNA methylation statuses of three CGIs in the SLC38A4 promoter and exon 1 region were tested in three placentas (two exhibiting paternal monoallelic and one showing biallelic expression of SLC38A4) and their corresponding paternal sperms. Unexpectedly, extreme hypomethylation (< 3%) of the DNA was observed in all the three detected placentas and their corresponding paternal sperms. The absence of DMR in bovine SLC38A4 promoter region implied that DNA methylation of these three CGIs does not directly or indirectly affect the polymorphic imprinting of SLC38A4 in bovine placenta. This suggested other epigenetic features other than DNA methylation are needed in regulating the imprinting of bovine SLC38A4, which is different from that of mouse with respect to a DMR existence at the mouse's slc38a4 promoter region. Although further work is needed, this first characterization of polymorphic imprinting status of SLC38A4 in cattle placenta provides valuable information on investigating the genomic imprinting phenomenon itself.
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Affiliation(s)
- Da Xu
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - Cui Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - Junliang Li
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - Guannan Wang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - Weina Chen
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China.,College of Chinese Medicine, Hebei University, Baoding, 071000, China
| | - Dongjie Li
- College of Life Science and Life Engineering, Hebei Science and Technology University, Shijiazhuang, 050018, China
| | - Shijie Li
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China.
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40
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Brioude F, Kalish JM, Mussa A, Foster AC, Bliek J, Ferrero GB, Boonen SE, Cole T, Baker R, Bertoletti M, Cocchi G, Coze C, De Pellegrin M, Hussain K, Ibrahim A, Kilby MD, Krajewska-Walasek M, Kratz CP, Ladusans EJ, Lapunzina P, Le Bouc Y, Maas SM, Macdonald F, Õunap K, Peruzzi L, Rossignol S, Russo S, Shipster C, Skórka A, Tatton-Brown K, Tenorio J, Tortora C, Grønskov K, Netchine I, Hennekam RC, Prawitt D, Tümer Z, Eggermann T, Mackay DJG, Riccio A, Maher ER. Expert consensus document: Clinical and molecular diagnosis, screening and management of Beckwith-Wiedemann syndrome: an international consensus statement. Nat Rev Endocrinol 2018; 14:229-249. [PMID: 29377879 PMCID: PMC6022848 DOI: 10.1038/nrendo.2017.166] [Citation(s) in RCA: 314] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Beckwith-Wiedemann syndrome (BWS), a human genomic imprinting disorder, is characterized by phenotypic variability that might include overgrowth, macroglossia, abdominal wall defects, neonatal hypoglycaemia, lateralized overgrowth and predisposition to embryonal tumours. Delineation of the molecular defects within the imprinted 11p15.5 region can predict familial recurrence risks and the risk (and type) of embryonal tumour. Despite recent advances in knowledge, there is marked heterogeneity in clinical diagnostic criteria and care. As detailed in this Consensus Statement, an international consensus group agreed upon 72 recommendations for the clinical and molecular diagnosis and management of BWS, including comprehensive protocols for the molecular investigation, care and treatment of patients from the prenatal period to adulthood. The consensus recommendations apply to patients with Beckwith-Wiedemann spectrum (BWSp), covering classical BWS without a molecular diagnosis and BWS-related phenotypes with an 11p15.5 molecular anomaly. Although the consensus group recommends a tumour surveillance programme targeted by molecular subgroups, surveillance might differ according to the local health-care system (for example, in the United States), and the results of targeted and universal surveillance should be evaluated prospectively. International collaboration, including a prospective audit of the results of implementing these consensus recommendations, is required to expand the evidence base for the design of optimum care pathways.
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Affiliation(s)
- Frédéric Brioude
- Sorbonne Université, Pierre and Marie Curie-Paris VI University (UPMC) Université Paris 06, INSERM UMR_S938 Centre de Recherche Saint-Antoine (CRSA), APHP Hôpital Trousseau, Explorations Fonctionnelles Endocriniennes, 26 Avenue du Docteur Arnold Netter, F-75012 Paris, France
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia and the Department of Pediatrics at the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandro Mussa
- Department of Public Health and Pediatric Sciences, University of Torino, Piazza Polonia 94, 10126 Torino, Italy
- Neonatal Intensive Care Unit, Department of Gynaecology and Obstetrics, Sant'Anna Hospital, Città della Salute e della Scienza di Torino, Corso Spezia 60, 10126 Torino, Italy
| | - Alison C Foster
- Birmingham Health Partners, West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham B15 2TG, UK
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jet Bliek
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, PO Box 7057 1007 MB Amsterdam, The Netherlands
| | - Giovanni Battista Ferrero
- Department of Public Health and Pediatric Sciences, University of Torino, Piazza Polonia 94, 10126 Torino, Italy
| | - Susanne E Boonen
- Clinical Genetic Unit, Department of Pediatrics, Zealand University Hospital, Sygehusvej 10 4000 Roskilde, Denmark
| | - Trevor Cole
- Birmingham Health Partners, West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham B15 2TG, UK
| | - Robert Baker
- Beckwith-Wiedemann Support Group UK, The Drum and Monkey, Wonston, Hazelbury Bryan, Sturminster Newton, Dorset DT10 2EE, UK
| | - Monica Bertoletti
- Italian Association of Beckwith-Wiedemann syndrome (AIBWS) Piazza Turati, 3, 21029, Vergiate (VA), Italy
| | - Guido Cocchi
- Alma Mater Studiorum, Bologna University, Paediatric Department, Neonatology Unit, Via Massarenti 11, 40138 Bologna BO, Italy
| | - Carole Coze
- Aix-Marseille Univ et Assistance Publique Hôpitaux de Marseille (APHM), Hôpital d'Enfants de La Timone, Service d'Hématologie-Oncologie Pédiatrique, 264 Rue Saint Pierre, 13385 Marseille, France
| | - Maurizio De Pellegrin
- Pediatric Orthopaedic Unit IRCCS Ospedale San Raffaele, Milan, Via Olgettina Milano, 60, 20132 Milano MI, Italy
| | - Khalid Hussain
- Department of Paediatric Medicine, Division of Endocrinology, Sidra Medical and Research Center, Al Gharrafa Street, Ar-Rayyan, Doha, Qatar
| | - Abdulla Ibrahim
- Department of Plastic and Reconstructive Surgery, North Bristol National Health Service (NHS) Trust, Southmead Hospital, Bristol BS10 5NB, UK
| | - Mark D Kilby
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Fetal Medicine Centre, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Edgbaston, Birmingham, B15 2TG, UK
| | | | - Christian P Kratz
- Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Strasse 1 30625, Hannover, Germany
| | - Edmund J Ladusans
- Department of Paediatric Cardiology, Royal Manchester Children's Hospital, Manchester, M13 8WL UK
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM Paseo de La Castellana, 261, 28046, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Yves Le Bouc
- Sorbonne Université, Pierre and Marie Curie-Paris VI University (UPMC) Université Paris 06, INSERM UMR_S938 Centre de Recherche Saint-Antoine (CRSA), APHP Hôpital Trousseau, Explorations Fonctionnelles Endocriniennes, 26 Avenue du Docteur Arnold Netter, F-75012 Paris, France
| | - Saskia M Maas
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, PO Box 7057 1007 MB Amsterdam, The Netherlands
| | - Fiona Macdonald
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, B15 2TG UK
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, L. Puusepa 2, 51014, Tartu, Estonia
| | - Licia Peruzzi
- European Society for Paediatric Nephrology (ESPN), Inherited Kidney Disorders Working Group
- AOU Città della Salute e della Scienza di Torino, Regina Margherita Children's Hospital, Turin, Italy
| | - Sylvie Rossignol
- Service de Pédiatrie, Hôpitaux Universitaires de Strasbourg, Laboratoire de Génétique Médicale, INSERM U1112 Avenue Molière 67098 STRASBOURG Cedex, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 4 Rue Kirschleger, 67000 Strasbourg, France
| | - Silvia Russo
- Medical Cytogenetics and Molecular Genetics Laboratory, Centro di Ricerche e Tecnologie Biomediche IRCCS, Istituto Auxologico Italiano, Via Zucchi 18, 20095 Cusano, Milan, Italy
| | - Caroleen Shipster
- Great Ormond Street Hospital for Children National Health Service (NHS) Foundation Trust, London, WC1N 3JH, UK
| | - Agata Skórka
- Department of Medical Genetics, The Children's Memorial Health Institute, 20, 04-730, Warsaw, Poland
- Department of Pediatrics, The Medical University of Warsaw, Zwirki i Wigury 63a, 02-091 Warszawa, Poland
| | - Katrina Tatton-Brown
- South West Thames Regional Genetics Service and St George's University of London and Institute of Cancer Research, London, SW17 0RE, UK
| | - Jair Tenorio
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM Paseo de La Castellana, 261, 28046, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Chiara Tortora
- Regional Center for CLP, Smile House, San Paolo University Hospital, Via Antonio di Rudinì, 8, 20142, Milan, Italy
| | - Karen Grønskov
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Irène Netchine
- Sorbonne Université, Pierre and Marie Curie-Paris VI University (UPMC) Université Paris 06, INSERM UMR_S938 Centre de Recherche Saint-Antoine (CRSA), APHP Hôpital Trousseau, Explorations Fonctionnelles Endocriniennes, 26 Avenue du Docteur Arnold Netter, F-75012 Paris, France
| | - Raoul C Hennekam
- Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam-Zuidoost, Amsterdam, The Netherlands
| | - Dirk Prawitt
- Center for Pediatrics and Adolescent Medicine, Johannes Gutenberg University Medical Center, Langenbeckstr. 1, D-55101, Mainz, Germany
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Thomas Eggermann
- Institute of Human Genetics, University Hospital, Technical University of Aachen, Templergraben 55, 52062, Aachen, Germany
| | - Deborah J G Mackay
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Andrea Riccio
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania Luigi Vanvitelli, Caserta and Institute of Genetics and Biophysics "A. Buzzati-Traverso" - CNR, Via Pietro Castellino, 111,80131, Naples, Italy
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
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de Sá Machado Araújo G, da Silva Francisco Junior R, Dos Santos Ferreira C, Mozer Rodrigues PT, Terra Machado D, Louvain de Souza T, Teixeira de Souza J, Figueiredo Osorio da Silva C, Alves da Silva AF, Andrade CCF, da Silva AT, Ramos V, Garcia AB, Machado FB, Medina-Acosta E. Maternal 5 mCpG Imprints at the PARD6G-AS1 and GCSAML Differentially Methylated Regions Are Decoupled From Parent-of-Origin Expression Effects in Multiple Human Tissues. Front Genet 2018; 9:36. [PMID: 29545821 PMCID: PMC5838017 DOI: 10.3389/fgene.2018.00036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/29/2018] [Indexed: 11/13/2022] Open
Abstract
A hallmark of imprinted genes in mammals is the occurrence of parent-of-origin-dependent asymmetry of DNA cytosine methylation (5mC) of alleles at CpG islands (CGIs) in their promoter regions. This 5mCpG asymmetry between the parental alleles creates allele-specific imprinted differentially methylated regions (iDMRs). iDMRs are often coupled to the transcriptional repression of the methylated allele and the activation of the unmethylated allele in a tissue-specific, developmental-stage-specific and/or isoform-specific fashion. iDMRs function as regulatory platforms, built through the recruitment of chemical modifications to histones to achieve differential, parent-of-origin-dependent chromatin segmentation states. Here, we used a comparative computational data mining approach to identify 125 novel constitutive candidate iDMRs that integrate the maximal number of allele-specific methylation region records overlapping CGIs in human methylomes. Twenty-nine candidate iDMRs display gametic 5mCpG asymmetry, and another 96 are candidate secondary iDMRs. We established the maternal origin of the 5mCpG imprints of one gametic (PARD6G-AS1) and one secondary (GCSAML) iDMRs. We also found a constitutively hemimethylated, nonimprinted domain at the PWWP2AP1 promoter CGI with oocyte-derived methylation asymmetry. Given that the 5mCpG level at the iDMRs is not a sufficient criterion to predict active or silent locus states and that iDMRs can regulate genes from a distance of more than 1 Mb, we used RNA-Seq experiments from the Genotype-Tissue Expression project and public archives to assess the transcriptional expression profiles of SNPs across 4.6 Mb spans around the novel maternal iDMRs. We showed that PARD6G-AS1 and GCSAML are expressed biallelically in multiple tissues. We found evidence of tissue-specific monoallelic expression of ZNF124 and OR2L13, located 363 kb upstream and 419 kb downstream, respectively, of the GCSAML iDMR. We hypothesize that the GCSAML iDMR regulates the tissue-specific, monoallelic expression of ZNF124 but not of OR2L13. We annotated the non-coding epigenomic marks in the two maternal iDMRs using data from the Roadmap Epigenomics project and showed that the PARD6G-AS1 and GCSAML iDMRs achieve contrasting activation and repression chromatin segmentations. Lastly, we found that the maternal 5mCpG imprints are perturbed in several hematopoietic cancers. We conclude that the maternal 5mCpG imprints at PARD6G-AS1 and GCSAML iDMRs are decoupled from parent-of-origin transcriptional expression effects in multiple tissues.
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Affiliation(s)
- Graziela de Sá Machado Araújo
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Ronaldo da Silva Francisco Junior
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Cristina Dos Santos Ferreira
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Pedro Thyago Mozer Rodrigues
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Douglas Terra Machado
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thais Louvain de Souza
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Faculdade de Medicina de Campos, Campos dos Goytacazes, Brazil
| | - Jozimara Teixeira de Souza
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Cleiton Figueiredo Osorio da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Antônio Francisco Alves da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Claudia Caixeta Franco Andrade
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Faculdade Metropolitana São Carlos, Bom Jesus do Itabapoana, Brazil
| | - Alan Tardin da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Victor Ramos
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Ana Beatriz Garcia
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Filipe Brum Machado
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Enrique Medina-Acosta
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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42
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Mackay DJ, Temple IK. Human imprinting disorders: Principles, practice, problems and progress. Eur J Med Genet 2017; 60:618-626. [DOI: 10.1016/j.ejmg.2017.08.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/02/2017] [Accepted: 08/11/2017] [Indexed: 12/17/2022]
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43
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Mining Novel Candidate Imprinted Genes Using Genome-Wide Methylation Screening and Literature Review. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1020013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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44
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Wu D, Gong C, Su C. Genome-wide analysis of differential DNA methylation in Silver-Russell syndrome. SCIENCE CHINA-LIFE SCIENCES 2017. [PMID: 28624953 DOI: 10.1007/s11427-017-9079-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Silver-Russell Syndrome (SRS) is clinically heterogeneous disorder characterized by low birth weight, postnatal growth restriction, and variable dysmorphic features. Current evidence strongly implicates imprinted genes as an important etiology of SRS. Although almost half of the patients showed DNA hypomethylation at the H19/IGF2 imprinted domain, and approximately 7%-10% of SRS patients have maternal uniparental disomy of chromosome 7 (UPD (7) mat); the rest of the SRS patients shows unknown etiology. In this study, we investigate whether there are further DNA methylation defects in SRS patients. We measured DNA methylation in seven SRS patients and five controls at more than 485,000 CpG sites using DNA methylation microarrays. We analyzed methylation changes genome-wide and identified the differentially methylated regions (DMRs) using bisulfite sequencing and digital PCR. Our analysis identifies epimutations at the previously characterized domains of H19/IGF2, providing proof of principle that our methodology can detect the changes in DNA methylation at imprinted loci. In addition, our results showed a novel SRS associated imprinted gene OSBPL5 located on chromosome 11p14 with the probe cg25963939, which is hypomethylated in 4/7 patients (P=0.023, β=-0.243). We also report DMRs in other genes including TGFβ3, HSF1, GAP43, NOTCH4 and MYH14. These DMRs were found to be associated with SRS using GO pathway analysis. In this study, we identified the probe cg25963939, located at the 5'UTR of imprinted gene OSBPL5, as a novel DMR that is associated with SRS. This finding provides new insights into the mechanism of SRS etiology and aid the further stratification of SRS patients by molecular phenotypes.
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Affiliation(s)
- Di Wu
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, MOE Key Laboratory of Major Diseases in Children, Beijing, 100045, China
| | - Chunxiu Gong
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, MOE Key Laboratory of Major Diseases in Children, Beijing, 100045, China.
| | - Chang Su
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, MOE Key Laboratory of Major Diseases in Children, Beijing, 100045, China
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45
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Wakeling EL, Brioude F, Lokulo-Sodipe O, O'Connell SM, Salem J, Bliek J, Canton APM, Chrzanowska KH, Davies JH, Dias RP, Dubern B, Elbracht M, Giabicani E, Grimberg A, Grønskov K, Hokken-Koelega ACS, Jorge AA, Kagami M, Linglart A, Maghnie M, Mohnike K, Monk D, Moore GE, Murray PG, Ogata T, Petit IO, Russo S, Said E, Toumba M, Tümer Z, Binder G, Eggermann T, Harbison MD, Temple IK, Mackay DJG, Netchine I. Diagnosis and management of Silver-Russell syndrome: first international consensus statement. Nat Rev Endocrinol 2017; 13:105-124. [PMID: 27585961 DOI: 10.1038/nrendo.2016.138] [Citation(s) in RCA: 292] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This Consensus Statement summarizes recommendations for clinical diagnosis, investigation and management of patients with Silver-Russell syndrome (SRS), an imprinting disorder that causes prenatal and postnatal growth retardation. Considerable overlap exists between the care of individuals born small for gestational age and those with SRS. However, many specific management issues exist and evidence from controlled trials remains limited. SRS is primarily a clinical diagnosis; however, molecular testing enables confirmation of the clinical diagnosis and defines the subtype. A 'normal' result from a molecular test does not exclude the diagnosis of SRS. The management of children with SRS requires an experienced, multidisciplinary approach. Specific issues include growth failure, severe feeding difficulties, gastrointestinal problems, hypoglycaemia, body asymmetry, scoliosis, motor and speech delay and psychosocial challenges. An early emphasis on adequate nutritional status is important, with awareness that rapid postnatal weight gain might lead to subsequent increased risk of metabolic disorders. The benefits of treating patients with SRS with growth hormone include improved body composition, motor development and appetite, reduced risk of hypoglycaemia and increased height. Clinicians should be aware of possible premature adrenarche, fairly early and rapid central puberty and insulin resistance. Treatment with gonadotropin-releasing hormone analogues can delay progression of central puberty and preserve adult height potential. Long-term follow up is essential to determine the natural history and optimal management in adulthood.
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Affiliation(s)
- Emma L Wakeling
- North West Thames Regional Genetics Service, London North West Healthcare NHS Trust, Watford Road, Harrow HA1 3UJ, UK
| | - Frédéric Brioude
- AP-HP, Hôpitaux Universitaires Paris Est (AP-HP) Hôpital des Enfants Armand Trousseau, Service d'Explorations Fonctionnelles Endocriniennes, 26 avenue du Dr Arnold Netter, 75012 Paris, France
- Centre de Recherche Saint Antoine, INSERM UMR S938, 34 rue Crozatier, 75012 Paris, France
- Sorbonne Universities, UPMC UNIV Paris 06, 4 place Jussieu, 75005 Paris, France
| | - Oluwakemi Lokulo-Sodipe
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Susan M O'Connell
- Department of Paediatrics and Child Health, Cork University Hospital, Wilton, Cork T12 DC4A, Ireland
| | - Jennifer Salem
- MAGIC Foundation, 6645 W. North Avenue, Oak Park, Illinois 60302, USA
| | - Jet Bliek
- Academic Medical Centre, Department of Clinical Genetics, Laboratory for Genome Diagnostics, Meibergdreef 15, 1105AZ Amsterdam, Netherlands
| | - Ana P M Canton
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo, Av. Dr. Arnaldo, 455 5° andar sala 5340 (LIM25), 01246-000 São Paulo, SP, Brazil
| | - Krystyna H Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Justin H Davies
- Department of Paediatric Endocrinology, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Renuka P Dias
- Institutes of Metabolism and Systems Research, Vincent Drive, University of Birmingham, Birmingham B15 2TT, UK
- Centre for Endocrinology, Diabetes and Metabolism, Vincent Drive, Birmingham Health Partners, Birmingham B15 2TH, UK
- Department of Paediatric Endocrinology and Diabetes, Birmingham Children's Hospital NHS Foundation Trust, Steelhouse Lane, Birmingham B4 6NH, UK
| | - Béatrice Dubern
- AP-HP, Hôpitaux Universitaires Paris Est (AP-HP) Hôpital des Enfants Armand Trousseau, Nutrition and Gastroenterology Department, 26 avenue du Dr Arnold Netter, 75012 Paris, France
- Trousseau Hospital, HUEP, APHP, UPMC, 75012 Paris, France
| | - Miriam Elbracht
- Insitute of Human Genetics, Technical University of Aachen, Pauwelsstr. 30, D-52074 Aachen, Germany
| | - Eloise Giabicani
- AP-HP, Hôpitaux Universitaires Paris Est (AP-HP) Hôpital des Enfants Armand Trousseau, Service d'Explorations Fonctionnelles Endocriniennes, 26 avenue du Dr Arnold Netter, 75012 Paris, France
- Centre de Recherche Saint Antoine, INSERM UMR S938, 34 rue Crozatier, 75012 Paris, France
- Sorbonne Universities, UPMC UNIV Paris 06, 4 place Jussieu, 75005 Paris, France
| | - Adda Grimberg
- Perelman School of Medicine, University of Pennsylvania, The Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Suite 11NW30, Philadelphia, Pennsylvania 19104, USA
| | - Karen Grønskov
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Gl. Landevej 7, 2600 Glostrup, Copenhagen, Denmark
| | - Anita C S Hokken-Koelega
- Erasmus University Medical Center, Pediatrics, Subdivision of Endocrinology, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Alexander A Jorge
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo, Av. Dr. Arnaldo, 455 5° andar sala 5340 (LIM25), 01246-000 São Paulo, SP, Brazil
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Ohkura, Setagayaku, Tokyo 157-8535, Japan
| | - Agnes Linglart
- APHP, Department of Pediatric Endocrinology, Reference Center for Rare Disorders of the Mineral Metabolism and Plateforme d'Expertise Paris Sud Maladies Rares, Hospital Bicêtre Paris Sud, 78 Rue du Général Leclerc, 94270 Le Kremlin-Bicêtre, France
| | - Mohamad Maghnie
- IRCCS Istituto Giannina Gaslini, University of Genova, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Klaus Mohnike
- Otto-von-Guericke University, Department of Pediatrics, Leipziger Street 44, 39120 Magdeburg, Germany
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Bellvitge Biomedical Research Institute, Gran via 199-203, Hospital Duran i Reynals, 08908, Barcelona, Spain
| | - Gudrun E Moore
- Fetal Growth and Development Group, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Philip G Murray
- Centre for Paediatrics and Child Health, Institute of Human Development, Royal Manchester Children's Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Isabelle Oliver Petit
- Pediatric Endocrinology, Genetic, Bone Disease &Gynecology Unit, Children's Hospital, TSA 70034, 31059 Toulouse, France
| | - Silvia Russo
- Instituto Auxologico Italiano, Cytogenetic and Molecular Genetic Laboratory, via Ariosto 13 20145 Milano, Italy
| | - Edith Said
- Department of Anatomy &Cell Biology, Centre for Molecular Medicine &Biobanking, Faculty of Medicine &Surgery, University of Malta, Msida MSD2090, Malta
- Section of Medical Genetics, Department of Pathology, Mater dei Hospital, Msida MSD2090, Malta
| | - Meropi Toumba
- IASIS Hospital, 8 Voriou Ipirou, 8036, Paphos, Cyprus
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Zeynep Tümer
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Gl. Landevej 7, 2600 Glostrup, Copenhagen, Denmark
| | - Gerhard Binder
- University Children's Hospital, Pediatric Endocrinology, Hoppe-Seyler-Strasse 1, 72070 Tuebingen, Germany
| | - Thomas Eggermann
- Insitute of Human Genetics, Technical University of Aachen, Pauwelsstr. 30, D-52074 Aachen, Germany
| | - Madeleine D Harbison
- Mount Sinai School of Medicine, 5 E 98th Street #1192, New York, New York 10029, USA
| | - I Karen Temple
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Deborah J G Mackay
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Irène Netchine
- AP-HP, Hôpitaux Universitaires Paris Est (AP-HP) Hôpital des Enfants Armand Trousseau, Service d'Explorations Fonctionnelles Endocriniennes, 26 avenue du Dr Arnold Netter, 75012 Paris, France
- Centre de Recherche Saint Antoine, INSERM UMR S938, 34 rue Crozatier, 75012 Paris, France
- Sorbonne Universities, UPMC UNIV Paris 06, 4 place Jussieu, 75005 Paris, France
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46
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Peter CJ, Fischer LK, Kundakovic M, Garg P, Jakovcevski M, Dincer A, Amaral AC, Ginns EI, Galdzicka M, Bryce CP, Ratner C, Waber DP, Mokler D, Medford G, Champagne FA, Rosene DL, McGaughy JA, Sharp AJ, Galler JR, Akbarian S. DNA Methylation Signatures of Early Childhood Malnutrition Associated With Impairments in Attention and Cognition. Biol Psychiatry 2016; 80:765-774. [PMID: 27184921 PMCID: PMC5036982 DOI: 10.1016/j.biopsych.2016.03.2100] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 03/10/2016] [Accepted: 03/12/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Early childhood malnutrition affects 113 million children worldwide, impacting health and increasing vulnerability for cognitive and behavioral disorders later in life. Molecular signatures after childhood malnutrition, including the potential for intergenerational transmission, remain unexplored. METHODS We surveyed blood DNA methylomes (~483,000 individual CpG sites) in 168 subjects across two generations, including 50 generation 1 individuals hospitalized during the first year of life for moderate to severe protein-energy malnutrition, then followed up to 48 years in the Barbados Nutrition Study. Attention deficits and cognitive performance were evaluated with the Connors Adult Attention Rating Scale and Wechsler Abbreviated Scale of Intelligence. Expression of nutrition-sensitive genes was explored by quantitative reverse transcriptase polymerase chain reaction in rat prefrontal cortex. RESULTS We identified 134 nutrition-sensitive, differentially methylated genomic regions, with most (87%) specific for generation 1. Multiple neuropsychiatric risk genes, including COMT, IFNG, MIR200B, SYNGAP1, and VIPR2 showed associations of specific methyl-CpGs with attention and IQ. IFNG expression was decreased in prefrontal cortex of rats showing attention deficits after developmental malnutrition. CONCLUSIONS Early childhood malnutrition entails long-lasting epigenetic signatures associated with liability for attention and cognition, and limited potential for intergenerational transmission.
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Affiliation(s)
- Cyril J. Peter
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Laura K. Fischer
- The Chester M. Pierce, MD Division of Global Psychiatry, Massachusetts General Hospital, Harvard Medical School, Charlestown MA 02129
| | - Marija Kundakovic
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Paras Garg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Mira Jakovcevski
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Max-Planck Institute for Psychiatry, D-Munich 80804
| | - Aslihan Dincer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ana C. Amaral
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129
| | - Edward I Ginns
- Departments of Psychiatry, Neurology, and Clinical Pathology, University of Massachusetts Medical School, Shrewsbury, MA 01545
| | - Marzena Galdzicka
- Department of Pathology, University of Massachusetts Medical School, Shrewsbury, MA 01545
| | | | - Chana Ratner
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Deborah P Waber
- Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115
| | - David Mokler
- Department of Biomedical Sciences, College of Osteopathic Medicine, University of New England, Biddeford, ME
| | | | | | - Douglas L. Rosene
- Department of Anatomy & Neurobiology, Boston University School of Medicine, Boston MA 02118
| | - Jill A. McGaughy
- Department of Psychology, University of New Hampshire, Durham, NH 03077
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Janina R. Galler
- The Chester M. Pierce, MD Division of Global Psychiatry, Massachusetts General Hospital, Harvard Medical School, Charlestown MA 02129
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York.
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47
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Grafodatskaya D, Choufani S, Basran R, Weksberg R. An Update on Molecular Diagnostic Testing of Human Imprinting Disorders. J Pediatr Genet 2016; 6:3-17. [PMID: 28180023 DOI: 10.1055/s-0036-1593840] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/16/2016] [Indexed: 01/07/2023]
Abstract
Imprinted genes are expressed in a parent of origin manner. Dysregulation of imprinted genes expression causes various disorders associated with abnormalities of growth, neurodevelopment, and metabolism. Molecular mechanisms leading to imprinting disorders and strategies for their diagnosis are discussed in this review article.
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Affiliation(s)
- Daria Grafodatskaya
- Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Sanaa Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Raveen Basran
- Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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48
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Joshi RS, Garg P, Zaitlen N, Lappalainen T, Watson CT, Azam N, Ho D, Li X, Antonarakis SE, Brunner HG, Buiting K, Cheung SW, Coffee B, Eggermann T, Francis D, Geraedts JP, Gimelli G, Jacobson SG, Le Caignec C, de Leeuw N, Liehr T, Mackay DJ, Montgomery SB, Pagnamenta AT, Papenhausen P, Robinson DO, Ruivenkamp C, Schwartz C, Steiner B, Stevenson DA, Surti U, Wassink T, Sharp AJ. DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome. Am J Hum Genet 2016; 99:555-566. [PMID: 27569549 DOI: 10.1016/j.ajhg.2016.06.032] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/30/2016] [Indexed: 02/07/2023] Open
Abstract
Genomic imprinting is a mechanism in which gene expression varies depending on parental origin. Imprinting occurs through differential epigenetic marks on the two parental alleles, with most imprinted loci marked by the presence of differentially methylated regions (DMRs). To identify sites of parental epigenetic bias, here we have profiled DNA methylation patterns in a cohort of 57 individuals with uniparental disomy (UPD) for 19 different chromosomes, defining imprinted DMRs as sites where the maternal and paternal methylation levels diverge significantly from the biparental mean. Using this approach we identified 77 DMRs, including nearly all those described in previous studies, in addition to 34 DMRs not previously reported. These include a DMR at TUBGCP5 within the recurrent 15q11.2 microdeletion region, suggesting potential parent-of-origin effects associated with this genomic disorder. We also observed a modest parental bias in DNA methylation levels at every CpG analyzed across ∼1.9 Mb of the 15q11-q13 Prader-Willi/Angelman syndrome region, demonstrating that the influence of imprinting is not limited to individual regulatory elements such as CpG islands, but can extend across entire chromosomal domains. Using RNA-seq data, we detected signatures consistent with imprinted expression associated with nine novel DMRs. Finally, using a population sample of 4,004 blood methylomes, we define patterns of epigenetic variation at DMRs, identifying rare individuals with global gain or loss of methylation across multiple imprinted loci. Our data provide a detailed map of parental epigenetic bias in the human genome, providing insights into potential parent-of-origin effects.
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Affiliation(s)
- Ricky S Joshi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paras Garg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noah Zaitlen
- Department of Medicine, UCSF MC2552, 1700 4th Street, Byers Hall Suite 503C, San Francisco, CA 94158, USA
| | - Tuuli Lappalainen
- New York Genome Center, 101 Avenue of the Americas, 7th Floor, New York, NY 10013, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Corey T Watson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nidha Azam
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xin Li
- Departments of Pathology, Genetics and Computer Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 9th Floor, 1 rue Michel-Servet, 1211 Geneva, Switzerland
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Karin Buiting
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, Germany
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bradford Coffee
- Emory Genetics Laboratory, Emory University, Atlanta, GA 30033, USA
| | - Thomas Eggermann
- Institute of Human Genetics, University Hospital, RWTH, 52074 Aachen, Germany
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Joep P Geraedts
- Department of Genetics and Cell Biology, Research Institute GROW, Faculty of Health, Medicine and Life Sciences, Maastricht University, PO Box 5800, Maastricht AZ 6202, the Netherlands
| | - Giorgio Gimelli
- Laboratorio di Citogenetica, Istituto G. Gaslini, 16148 Genova, Italy
| | - Samuel G Jacobson
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA 19104, USA
| | - Cedric Le Caignec
- CHU Nantes, Service de Génétique Médicale, Institut de Biologie, 9 quai Moncousu, 44093 Nantes, France; INSERM, UMR 957, Nantes 44035, France; Université de Nantes, Nantes atlantique universités, Pathophysiology of Bone Resorption and Therapy of Primary Bone Tumours, Nantes 44035, France
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Deborah J Mackay
- Wessex Regional Genetics Laboratory Salisbury District Hospital, Salisbury, Wiltshire SO2 8BJ, UK
| | - Stephen B Montgomery
- Departments of Pathology, Genetics and Computer Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alistair T Pagnamenta
- National Institute for Health Research Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Peter Papenhausen
- Division of Cytogenetics, LabCorp, Center for Molecular Biology and Pathology, Research Triangle Park, NC 27709, USA
| | - David O Robinson
- Wessex Regional Genetics Laboratory Salisbury District Hospital, Salisbury, Wiltshire SO2 8BJ, UK
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Charles Schwartz
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Bernhard Steiner
- Institute of Medical Genetics, University of Zurich, 8603 Schwerzenbach, Switzerland
| | - David A Stevenson
- Division of Medical Genetics, Lucile Salter Packard Children's Hospital, 300 Pasteur Drive, Boswell Building A097, Stanford, CA 94304, USA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Thomas Wassink
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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49
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Sanchez-Delgado M, Riccio A, Eggermann T, Maher ER, Lapunzina P, Mackay D, Monk D. Causes and Consequences of Multi-Locus Imprinting Disturbances in Humans. Trends Genet 2016; 32:444-455. [PMID: 27235113 DOI: 10.1016/j.tig.2016.05.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/20/2022]
Abstract
Eight syndromes are associated with the loss of methylation at specific imprinted loci. There has been increasing evidence that these methylation defects in patients are not isolated events occurring at a given disease-associated locus but that some of these patients may have multi-locus imprinting disturbances (MLID) affecting additional imprinted regions. With the recent advances in technology, methylation profiling has revealed that imprinted loci represent only a small fraction of the methylation differences observed between the gametes. To figure out how imprinting anomalies occur at multiple imprinted domains, we have to understand the interplay between DNA methylation and histone modifications in the process of selective imprint protection during pre-implantation reprogramming, which, if disrupted, leads to these complex imprinting disorders (IDs).
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Affiliation(s)
- Marta Sanchez-Delgado
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Andrea Riccio
- DiSTABiF, Seconda Università degli Studi di Napoli, Caserta; Institute of Genetics and Biophysics - ABT, CNR, Napoli, Italy
| | - Thomas Eggermann
- Institute of Human Genetics University Hospital Aachen, Aachen, Germany
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain; CIBERER, Centro deInvestigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Deborah Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine University of Southampton, Southampton, UK
| | - David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain.
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50
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Genome-Wide DNA Methylation Analysis and Epigenetic Variations Associated with Congenital Aortic Valve Stenosis (AVS). PLoS One 2016; 11:e0154010. [PMID: 27152866 PMCID: PMC4859473 DOI: 10.1371/journal.pone.0154010] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 04/07/2016] [Indexed: 11/19/2022] Open
Abstract
Congenital heart defect (CHD) is the most common cause of death from congenital anomaly. Among several candidate epigenetic mechanisms, DNA methylation may play an important role in the etiology of CHDs. We conducted a genome-wide DNA methylation analysis using an Illumina Infinium 450k human methylation assay in a cohort of 24 newborns who had aortic valve stenosis (AVS), with gestational-age matched controls. The study identified significantly-altered CpG methylation at 59 sites in 52 genes in AVS subjects as compared to controls (either hypermethylated or demethylated). Gene Ontology analysis identified biological processes and functions for these genes including positive regulation of receptor-mediated endocytosis. Consistent with prior clinical data, the molecular function categories as determined using DAVID identified low-density lipoprotein receptor binding, lipoprotein receptor binding and identical protein binding to be over-represented in the AVS group. A significant epigenetic change in the APOA5 and PCSK9 genes known to be involved in AVS was also observed. A large number CpG methylation sites individually demonstrated good to excellent diagnostic accuracy for the prediction of AVS status, thus raising possibility of molecular screening markers for this disorder. Using epigenetic analysis we were able to identify genes significantly involved in the pathogenesis of AVS.
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