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Luo Y, Zhou T, Liu D, Wang F, Zhao Q. AIMER: A SNP-independent software for identifying imprinting-like allelic methylated regions from DNA methylome. Comput Struct Biotechnol J 2024; 23:566-576. [PMID: 38274999 PMCID: PMC10809074 DOI: 10.1016/j.csbj.2023.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/27/2024] Open
Abstract
Genomic imprinting is essential for mammalian growth and embryogenesis. High-throughput bisulfite sequencing accompanied with parental haplotype-specific information allows analysis of imprinted genes and imprinting control regions (ICRs) on a large scale. Currently, although several allelic methylated regions (AMRs) detection software were developed, methods for detecting imprinted AMRs is still limited. Here, we developed a SNP-independent statistical approach, AIMER, to detect imprinting-like AMRs. By using the mouse frontal cortex methylome as input, we demonstrated that AIMER performs very well in detecting known germline ICRs compared with other methods. Furthermore, we found the putative parental AMRs AIMER detected could be distinguished from sequence-dependent AMRs. Finally, we found a novel germline imprinting-like AMR using WGBS data from 17 distinct mouse tissue samples. The results indicate that AIMER is a good choice for detecting imprinting-like (parent-of-origin-dependent) AMRs. We hope this method will be helpful for future genomic imprinting studies. The Python source code for our project is now publicly available on both GitHub (https://github.com/ZhaoLab-TMU/AIMER) and Gitee (https://gitee.com/zhaolab_tmu/AIMER).
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Affiliation(s)
| | | | - Deng Liu
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Fan Wang
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qian Zhao
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
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2
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van Bever Y, Boers RG, Brüggenwirth HT, van IJcken WF, Magielsen FJ, de Klein A, Boers JB, Looijenga LH, Brosens E, Gribnau J, Hannema SE. Genome-wide methylation analysis in patients with proximal hypospadias - a pilot study and review of the literature. Epigenetics 2024; 19:2392048. [PMID: 39151125 DOI: 10.1080/15592294.2024.2392048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/03/2024] [Accepted: 08/06/2024] [Indexed: 08/18/2024] Open
Abstract
In patients with proximal hypospadias, often no genetic cause is identified despite extensive genetic testing. Many genes involved in sex development encode transcription factors with strict timing and dosing of the gene products. We hypothesised that there might be recurrent differences in DNA methylation in boys with hypospadias and that these might differ between patients born small versus appropriate for gestational age. Genome-wide Methylated DNA sequencing (MeD-seq) was performed on 32bp LpnPI restriction enzyme fragments after RE-digestion in leucocytes from 16 XY boys with unexplained proximal hypospadias, one with an unexplained XX testicular disorder/difference of sex development (DSD) and twelve, healthy, sex- and age-matched controls. Five of seven differentially methylated regions (DMRs) between patients and XY controls were in the Long Intergenic Non-Protein Coding RNA 665 (LINC00665; CpG24525). Three patients showed hypermethylation of MAP3K1. Finally, no DMRs in XX testicular DSD associated genes were identified in the XX boy versus XX controls. In conclusion, we observed no recognizable epigenetic signature in 16 boys with XY proximal hypospadias and no difference between children born small versus appropriate for gestational age. Comparison to previous methylation studies in individuals with hypospadias did not show consistent findings, possibly due to the use of different inclusion criteria, tissues and methods.
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Affiliation(s)
- Yolande van Bever
- Department of Clinical Genetics, Erasmus MC, Sophia Children's Hospital, Rotterdam, The Netherlands
- Erasmus MC Center of Expertise for DSD, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Hennie T Brüggenwirth
- Department of Clinical Genetics, Erasmus MC, Sophia Children's Hospital, Rotterdam, The Netherlands
- Erasmus MC Center of Expertise for DSD, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Wilfred Fj van IJcken
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
- Department of Cell biology, Erasmus MC, Rotterdam, Netherlands
| | - Frank J Magielsen
- Department of Clinical Genetics, Erasmus MC, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Joachim B Boers
- Department of Developmental Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Leendert Hj Looijenga
- Princess Máxima Center for Pediatric Oncology, Utrecht, and Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Sabine E Hannema
- Erasmus MC Center of Expertise for DSD, Sophia Children's Hospital, Rotterdam, The Netherlands
- Department of Paediatric Endocrinology, Amsterdam University Medical Centers, Location Vrije Universiteit, Amsterdam, The Netherlands
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3
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Lin HY, Lee CL, Tu YR, Chang YH, Niu DM, Chang CY, Chiu PC, Chou YY, Hsiao HP, Tsai MC, Chao MC, Tsai LP, Yang CF, Su PH, Pan YW, Lee CH, Chu TH, Chuang CK, Lin SP. Quantitative DNA Methylation Analysis and Epigenotype-Phenotype Correlations in Taiwanese Patients with Silver-Russell Syndrome. Int J Med Sci 2024; 21:8-18. [PMID: 38164354 PMCID: PMC10750329 DOI: 10.7150/ijms.84154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 10/18/2023] [Indexed: 01/03/2024] Open
Abstract
Background: Silver-Russell syndrome (SRS; OMIM #180860) is a clinically and genetically heterogeneous imprinting disorder characterized by prenatal and postnatal growth failure. The aim of this study was to identify the epigenotype-phenotype correlations in these patients using quantitative DNA methylation analysis. Methods: One hundred and eighty-three subjects clinically suspected of having SRS were referred for diagnostic testing by the methylation profiling of H19-associated imprinting center (IC) 1 and imprinted PEG1/MEST regions using methylation-specific high-resolution melting analysis and methylation quantification with the MassARRAY assay. Correlations between quantitative DNA methylation status and clinical manifestations of the subjects according to the Netchine-Harbison (N-H) clinical scoring system for SRS were analyzed. Results: Among the 183 subjects, 90 had a clinical diagnosis of SRS [N-H score ≥ 4 (maximum = 6)] and 93 had an SRS score < 4. Molecular lesions were detected in 41% (37/90) of the subjects with a clinical diagnosis of SRS, compared with 3% (3/93) of those with an N-H score < 4. The IC1 methylation level was negatively correlated with the N-H score. The molecular diagnosis rate was positively correlated with the N-H score. Thirty-one subjects had IC1 hypomethylation (IC1 methylation level <35% by the MassARRAY assay), seven had maternal uniparental disomy 7, and two had pathogenic copy number variants. Among the 90 subjects with an N-H score ≥ 4, the IC1 methylation level was significantly different between those with or without some clinical SRS features, including birth length ≤ 10th centile, relative macrocephaly at birth, normal cognitive development, body asymmetry, clinodactyly of the fifth finger, and genital abnormalities. Conclusions: This study confirmed the suitability of the N-H clinical scoring system as clinical diagnostic criteria for SRS. Quantitative DNA methylation analysis using the MassARRAY assay can improve the detection of epigenotype-phenotype correlations, further promoting better genetic counseling and multidisciplinary management for these patients.
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Affiliation(s)
- Hsiang-Yu Lin
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- MacKay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chung-Lin Lee
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- MacKay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
| | - Yuan-Rong Tu
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Ya-Hui Chang
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
| | - Dau-Ming Niu
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
- Department of Pediatrics, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chia-Ying Chang
- Department of Pediatrics, MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Pao Chin Chiu
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yen-Yin Chou
- Department of Pediatrics, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Hui-Pin Hsiao
- Department of Pediatrics, Kaohsiung Medical University Chung Ho Memorial Hospital, Kaohsiung, Taiwan
| | - Meng-Che Tsai
- Department of Pediatrics, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Mei-Chyn Chao
- Department of Pediatrics, Changhua Christian Children's Hospital, Changhua, Taiwan
| | - Li-Ping Tsai
- Department of Pediatrics, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
| | - Chia-Feng Yang
- Department of Pediatrics, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Pen-Hua Su
- Department of Pediatrics, Chung Shan Medical University, Taichung, Taiwan
| | - Yu-Wen Pan
- Department of Pediatrics, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Chen-Hao Lee
- Department of Pediatrics, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Tzu-Hung Chu
- Department of Pediatrics, China Medical University Hsinchu Hospital, Taiwan
| | - Chih-Kuang Chuang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- College of Medicine, Fu-Jen Catholic University, Taipei, Taiwan
| | - Shuan-Pei Lin
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
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4
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Vimercati A, Tannorella P, Orlandini E, Calzari L, Moro M, Guzzetti S, Selicorni A, Crippa M, Larizza L, Bonati MT, Russo S. Case report: atypical Silver-Russell syndrome patient with hand dystonia: the valuable support of the consensus statement to the wide syndromic spectrum. Front Genet 2023; 14:1198821. [PMID: 37529781 PMCID: PMC10387531 DOI: 10.3389/fgene.2023.1198821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/19/2023] [Indexed: 08/03/2023] Open
Abstract
The amount of Insulin Growth Factor 2 (IGF2) controls the rate of embryonal and postnatal growth. The IGF2 and adjacent H19 are the imprinted genes of the telomeric cluster in the 11p15 chromosomal region regulated by differentially methylated regions (DMRs) or imprinting centers (ICs): H19/IGF2:IG-DMR (IC1). Dysregulation due to IC1 Loss-of-Methylation (LoM) or Gain-of-Methyaltion (GoM) causes Silver-Russell syndrome (SRS) or Beckwith-Wiedemann syndrome (BWS) disorders associated with growth retardation or overgrowth, respectively. Specific features define each of the two syndromes, but isolated asymmetry is a common cardinal feature, which is considered sufficient for a diagnosis in the BWS spectrum. Here, we report the case of a girl with right body asymmetry, which suggested BWS spectrum. Later, BWS/SRS molecular analysis identified IC1_LoM revealing the discrepant diagnosis of SRS. A clinical re-evaluation identified a relative macrocephaly and previously unidentified growth rate at lower limits of normal at birth, feeding difficulties, and asymmetry. Interestingly, and never previously described in IC1_LoM SRS patients, since the age of 16, she has developed hand-writer's cramps, depression, and bipolar disorder. Trio-WES identified a VPS16 heterozygous variant [NM_022575.4:c.2185C>G:p.Leu729Val] inherited from her healthy mother. VPS16 is involved in the endolysosomal system, and its dysregulation is linked to autosomal dominant dystonia with incomplete penetrance and variable expressivity. IGF2 involvement in the lysosomal pathway led us to speculate that the neurological phenotype of the proband might be triggered by the concurrent IGF2 deficit and VPS16 alteration.
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Affiliation(s)
- Alessandro Vimercati
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Pierpaola Tannorella
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Eleonora Orlandini
- Specialty School of Pediatrics, Alma Mater University of Bologna, Bologna, Italy
| | - Luciano Calzari
- Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Mirella Moro
- Department of Endocrine and Metabolic Diseases and Lab of Endocrine and Metabolic Research, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Sara Guzzetti
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | | | - Milena Crippa
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Lidia Larizza
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Maria Teresa Bonati
- Unit of Medical Genetics, Institute for Maternal and Child Health Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Burlo Garofalo, Trieste, Italy
| | - Silvia Russo
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
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5
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Epigenetics in fetal alcohol spectrum disorder. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:211-239. [PMID: 37019593 DOI: 10.1016/bs.pmbts.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During pregnancy, alcohol abuse and its detrimental effects on developing offspring are major public health, economic and social challenges. The prominent characteristic attributes of alcohol (ethanol) abuse during pregnancy in humans are neurobehavioral impairments in offspring due to damage to the central nervous system (CNS), causing structural and behavioral impairments that are together named fetal alcohol spectrum disorder (FASD). Development-specific alcohol exposure paradigms were established to recapitulate the human FASD phenotypes and establish the underlying mechanisms. These animal studies have offered some critical molecular and cellular underpinnings likely to account for the neurobehavioral impairments associated with prenatal ethanol exposure. Although the pathogenesis of FASD remains unclear, emerging literature proposes that the various genomic and epigenetic components that cause the imbalance in gene expression can significantly contribute to the development of this disease. These studies acknowledged numerous immediate and enduring epigenetic modifications, such as methylation of DNA, post-translational modifications (PTMs) of histone proteins, and regulatory networks related to RNA, using many molecular approaches. Methylated DNA profiles, PTMs of histone proteins, and RNA-regulated expression of genes are essential for synaptic and cognitive behavior. Thus, offering a solution to many neuronal and behavioral impairments reported in FASD. In the current chapter, we review the recent advances in different epigenetic modifications that cause the pathogenesis of FASD. The information discussed can help better explain the pathogenesis of FASD and thereby might provide a basis for finding novel therapeutic targets and innovative treatment strategies.
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6
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Hettmer S, Linardic CM, Kelsey A, Rudzinski ER, Vokuhl C, Selfe J, Ruhen O, Shern JF, Khan J, Kovach AR, Lupo PJ, Gatz SA, Schäfer BW, Volchenboum S, Minard-Colin V, Koscielniak E, Hawkins DS, Bisogno G, Sparber-Sauer M, Venkatramani R, Merks JHM, Shipley J. Molecular testing of rhabdomyosarcoma in clinical trials to improve risk stratification and outcome: A consensus view from European paediatric Soft tissue sarcoma Study Group, Children's Oncology Group and Cooperative Weichteilsarkom-Studiengruppe. Eur J Cancer 2022; 172:367-386. [PMID: 35839732 DOI: 10.1016/j.ejca.2022.05.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/27/2022] [Accepted: 05/22/2022] [Indexed: 02/07/2023]
Abstract
Rhabdomyosarcomas (RMSs) are the most common soft tissue sarcomas in children/adolescents less than 18 years of age with an annual incidence of 1-2/million. Inter/intra-tumour heterogeneity raise challenges in clinical, pathological and biological research studies. Risk stratification in European and North American clinical trials previously relied on clinico-pathological features, but now, incorporates PAX3/7-FOXO1-fusion gene status in the place of alveolar histology. International working groups propose a coordinated approach through the INternational Soft Tissue SaRcoma ConsorTium to evaluate the specific genetic abnormalities and generate and integrate molecular and clinical data related to patients with RMS across different trial settings. We review relevant data and present a consensus view on what molecular features should be assessed. In particular, we recommend the assessment of the MYOD1-LR122R mutation for risk escalation, as it has been associated with poor outcomes in spindle/sclerosing RMS and rare RMS with classic embryonal histopathology. The prospective analyses of rare fusion genes beyond PAX3/7-FOXO1 will generate new data linked to outcomes and assessment of TP53 mutations and CDK4 amplification may confirm their prognostic value. Pathogenic/likely pathogenic germline variants in TP53 and other cancer predisposition genes should also be assessed. DNA/RNA profiling of tumours at diagnosis/relapse and serial analyses of plasma samples is recommended where possible to validate potential molecular biomarkers, identify new biomarkers and assess how liquid biopsy analyses can have the greatest benefit. Together with the development of new molecularly-derived therapeutic strategies that we review, a synchronised international approach is expected to enhance progress towards improved treatment assignment, management and outcomes for patients with RMS.
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Affiliation(s)
- Simone Hettmer
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Germany
| | - Corinne M Linardic
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA; Department of Pharmacology and Cancer Biology; Duke University of Medicine, Durham, NC, USA
| | - Anna Kelsey
- Department of Paediatric Histopathology, Royal Manchester Children's Hospital, Manchester Foundation Trust, Manchester, UK
| | - Erin R Rudzinski
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA
| | - Christian Vokuhl
- Section of Pediatric Pathology, Department of Pathology, University Hospital Bonn, Germany
| | - Joanna Selfe
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Olivia Ruhen
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Jack F Shern
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA; Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Javed Khan
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Alexander R Kovach
- Department of Pharmacology and Cancer Biology; Duke University of Medicine, Durham, NC, USA
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Susanne A Gatz
- Institute of Cancer and Genomic Sciences, Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Birmingham, UK
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | | | | | - Ewa Koscielniak
- Klinikum der Landeshauptstadt Stuttgart GKAöR, Olgahospital, Stuttgart Cancer Center, Zentrum für Kinder-, Jugend- und Frauenmedizin, Pädiatrie 5 (Pädiatrische Onkologie, Hämatologie, Immunologie), Stuttgart, Germany; Medizinische Fakultät, University of Tübingen, Germany
| | - Douglas S Hawkins
- Seattle Children's Hospital, University of Washington, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gianni Bisogno
- Hematology Oncology Division, Department of Women's and Children's Health, University of Padova, Padua, Italy
| | - Monika Sparber-Sauer
- Klinikum der Landeshauptstadt Stuttgart GKAöR, Olgahospital, Stuttgart Cancer Center, Zentrum für Kinder-, Jugend- und Frauenmedizin, Pädiatrie 5 (Pädiatrische Onkologie, Hämatologie, Immunologie), Stuttgart, Germany; Medizinische Fakultät, University of Tübingen, Germany
| | - Rajkumar Venkatramani
- Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | | | - Janet Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK.
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7
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Clinical spectrum of female genital malformations in prenatal diagnosis. Arch Gynecol Obstet 2022; 306:1847-1862. [DOI: 10.1007/s00404-022-06441-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/09/2022] [Indexed: 11/02/2022]
Abstract
Abstract
Introduction
Fetal genital malformations represent a rare and heterogeneous group of congenital malformations of the disorders of sexual development (DSD) spectrum.
Methods
A thorough literature review on the main topics in the prenatal approach towards DSD was conducted.
Results
First, a thorough overview on prenatal characteristics of the most common fetal genital malformations of ovaries, uterus and external genitalia, and second, a standardized approach for differential diagnosis in the presence of direct and indirect prenatal signs of DSDs.
Conclusions
This review is mainly directed towards the aspects of female genital malformations with aspects of male DSD explained as well to aid in the prenatal differential diagnosis.
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Özer E, Geyik F, Alp Ünkar Z, Ercan O, Tüysüz B. The Methylation Status in the Chromosome 11p15.5 Region and Metabolic Disorders in Children with Syndromic and Nonsyndromic Intrauterine Growth Restriction. Mol Syndromol 2022; 13:108-116. [PMID: 35418826 PMCID: PMC8928180 DOI: 10.1159/000518630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/21/2021] [Indexed: 10/03/2023] Open
Abstract
Loss of methylation (LoM) of the imprinting control region 1 (ICR1) in the chromosome 11p15.5 domain is detected in patients with Silver-Russell syndrome (SRS), characterized by asymmetric pre- and postnatal growth restriction, and typical craniofacial features. The patients with intrauterine growth restriction (IUGR) possess a high risk for adult metabolic problems. This study is aimed to investigate the methylation levels of the chromosome 11p15.5 region and metabolic problems in children with syndromic and nonsyndromic IUGR. Methylation analysis was performed for chromosome 11p15.5 in 49 patients (33 with suspected SRS and 16 nonsyndromic IUGR) with Netchine-Harbison clinical scoring (NHCS); uniparental disomy for chromosomes 6, 7, 14, and 20 was evaluated for those who were negative. LoM of ICR1 was detected in 14 of 33 suspected SRS patients with 3 or more criteria of NHCS, 5 had borderline LoM. Maternal uniparental disomy of the chromosomes 7 and 14 was found in 2 patients. The overall detection rate of SRS was 45.5%. While clinical findings were similar in patients with LoM and borderline LoM of ICR1, typical craniofacial findings were significantly less in the patients with normal methylation. Methylation patterns were not found to be impaired in the nonsyndromic IUGR group. Metabolic complications were evaluated in a total of 63 patients including 33 SRS-suspicious, 16 nonsyndromic IUGR, and 14 patients with 3M or SHORT syndrome. Increased rates of hypercalciuria, insulin resistance, and dyslipidemia were detected in patients with both syndromic and nonsyndromic IUGR. We would like to emphasize that detecting typical facial findings is effective in the diagnosis of SRS and paying attention to metabolic problems in the follow-up of patients with IUGR is recommended.
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Affiliation(s)
- Emre Özer
- Department of Pediatric Genetics, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Filiz Geyik
- Department of Genetics, Aziz Sancar Experimental Medicine Research Institute, Istanbul University, Istanbul, Turkey
| | - Zeynep Alp Ünkar
- Department of Neonatology, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Oya Ercan
- Department of Pediatric Endocrinology, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Beyhan Tüysüz
- Department of Pediatric Genetics, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey
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9
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Epigenotype, Genotype, and Phenotype Analysis of Taiwanese Patients with Silver-Russell Syndrome. J Pers Med 2021; 11:jpm11111197. [PMID: 34834549 PMCID: PMC8624617 DOI: 10.3390/jpm11111197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/29/2021] [Accepted: 11/11/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Silver–Russell syndrome (SRS) is a clinically and genetically heterogeneous disorder characterized by severe intrauterine growth retardation, poor postnatal growth, characteristic facial features, and body asymmetry. Hypomethylation of the imprinted genes of the chromosome 11p15.5 imprinting gene cluster and maternal uniparental disomy of chromosome 7 (mUPD7) are the major epigenetic disturbances. The aim of this study was to characterize the epigenotype, genotype, and phenotype of these patients in Taiwan. Methods: Two hundred and six subjects with clinically suspected SRS were referred for diagnostic testing, which was performed by profiling the methylation of H19-associated imprinting center (IC) 1 and the imprinted PEG1/MEST region using methylation-specific multiplex ligation-dependent probe amplification and high-resolution melting analysis with a methylation-specific polymerase chain reaction assay. We also applied a whole genome strategy to detect copy number changes and loss of heterozygosity. Clinical manifestations were recorded and analyzed according to the SRS scoring system proposed by Bartholdi et al. Results: Among the 206 referred subjects, 100 were classified as having a clinical diagnosis of SRS (score ≥ 8, maximum = 15) and 106 had an SRS score ≤ 7. Molecular lesions were detected in 45% (45/100) of the subjects with a clinical diagnosis of SRS, compared to 5% (5/106) of those with an SRS score ≤ 7. Thirty-seven subjects had IC1 hypomethylation, ten subjects had mUPD7, and three subjects had microdeletions. Several clinical features were found to be statistically different (p < 0.05) between the “IC1 hypomethylation” and “mUPD7” groups, including relative macrocephaly at birth (89% vs. 50%), triangular shaped face (89% vs. 50%), clinodactyly of the fifth finger (68% vs. 20%), and SRS score (11.4 ± 2.2 vs. 8.3 ± 2.5). Conclusions: The SRS score was positively correlated with the molecular diagnosis rate (p < 0.001). The SRS subjects with mUPD7 seemed to have fewer typical features and lower SRS scores than those with IC1 hypomethylation. Careful clinical observation and timely molecular confirmation are important to allow for an early diagnosis and multidisciplinary management of these patients.
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10
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Gutherz OR, Deyssenroth M, Li Q, Hao K, Jacobson JL, Chen J, Jacobson SW, Carter RC. Potential roles of imprinted genes in the teratogenic effects of alcohol on the placenta, somatic growth, and the developing brain. Exp Neurol 2021; 347:113919. [PMID: 34752786 DOI: 10.1016/j.expneurol.2021.113919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022]
Abstract
Despite several decades of research and prevention efforts, fetal alcohol spectrum disorders (FASD) remain the most common preventable cause of neurodevelopmental disabilities worldwide. Animal and human studies have implicated fetal alcohol-induced alterations in epigenetic programming as a chief mechanism in FASD. Several studies have demonstrated fetal alcohol-related alterations in methylation and expression of imprinted genes in placental, brain, and embryonic tissue. Imprinted genes are epigenetically regulated in a parent-of-origin-specific manner, in which only the maternal or paternal allele is expressed, and the other allele is silenced. The chief functions of imprinted genes are in placental development, somatic growth, and neurobehavior-three domains characteristically affected in FASD. In this review, we summarize the growing body of literature characterizing prenatal alcohol-related alterations in imprinted gene methylation and/or expression and discuss potential mechanistic roles for these alterations in the teratogenic effects of prenatal alcohol exposure. Future research is needed to examine potential physiologic mechanisms by which alterations in imprinted genes disrupt development in FASD, which may, in turn, elucidate novel targets for intervention. Furthermore, mechanistic alterations in imprinted gene expression and/or methylation in FASD may inform screening assays that identify individuals with FASD neurobehavioral deficits who may benefit from early interventions.
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Affiliation(s)
- Olivia R Gutherz
- Institute of Human Nutrition, Columbia University Medical Center, United States of America
| | - Maya Deyssenroth
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, United States of America
| | - Qian Li
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, United States of America
| | - Ke Hao
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, United States of America
| | - Joseph L Jacobson
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, United States of America; Department of Human Biology, University of Cape Town Faculty of Health Sciences, South Africa
| | - Jia Chen
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, United States of America
| | - Sandra W Jacobson
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, United States of America; Department of Human Biology, University of Cape Town Faculty of Health Sciences, South Africa
| | - R Colin Carter
- Institute of Human Nutrition, Columbia University Medical Center, United States of America; Departments of Emergency Medicine and Pediatrics, Columbia University Medical Center, United States of America.
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11
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Shin CH, Lim C, Kim HY, Yoo WJ, Cho TJ, Choi IH, Ko JM. Prospective study of epigenetic alterations responsible for isolated hemihyperplasia/hemihypoplasia and their association with leg length discrepancy. Orphanet J Rare Dis 2021; 16:418. [PMID: 34627330 PMCID: PMC8501601 DOI: 10.1186/s13023-021-02042-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/19/2021] [Indexed: 11/12/2022] Open
Abstract
Background Hemihyperplasia and hemihypoplasia result in leg length discrepancy (LLD) by causing skeletal asymmetry. Beckwith–Wiedemann syndrome (BWS) and Silver–Russell syndrome (SRS) are opposite growth-affecting disorders caused by opposite epigenetic alterations at the same chromosomal locus, 11p15, to induce hemihyperplasia and hemihypoplasia, respectively. Because of their somatic mosaicism, BWS and SRS show a wide spectrum of clinical phenotypes. We evaluated the underlying epigenetic alterations and potential epigenotype-phenotype correlations, focusing on LLD, in a group of individuals with isolated hemihyperplasia/hemihypoplasia. Results We prospectively collected paired blood-tissue samples from 30 patients with isolated hemihyperplasia/hemihypoplasia who underwent surgery for LLD. Methylation-specific multiplex-ligation-dependent probe amplification assay (MS-MLPA) and bisulfite pyrosequencing for differentially methylated regions 1 and 2 (DMR1 and DMR2) on chromosome 11p15 were performed using the patient samples. Samples from patients showing no abnormalities in MS-MLPA or bisulfite pyrosequencing were analyzed by single nucleotide polymorphism (SNP) microarray and CDKN1C Sanger sequencing. We introduced a metric named as the methylation difference, defined as the difference in DNA methylation levels between DMR1 and DMR2. The correlation between the methylation difference and the predicted LLD at skeletal maturity, calculated using a multiplier method, was evaluated. Predicted LLD was standardized for stature. Ten patients (33%) showed epigenetic alterations in MS-MLPA and bisulfite pyrosequencing. Of these, six and four patients had epigenetic alterations related to BWS and SRS, respectively. The clinical diagnosis of hemihyperplasia/hemihypoplasia was not compatible with the epigenetic alterations in four of these ten patients. No patients showed abnormalities in SNP array or their CDKN1C sequences. The standardized predicted LLD was moderately correlated with the methylation difference using fat tissue (r = 0.53; p = 0.002) and skin tissue (r = 0.50; p = 0.005) in all patients. Conclusions Isolated hemihyperplasia and hemihypoplasia can occur as a spectrum of BWS and SRS. Although the accurate differentiation between isolated hemihyperplasia and isolated hemihypoplasia is important in tumor surveillance planning, it is often difficult to clinically differentiate these two diseases without epigenetic tests. Epigenetic tests may play a role in the prediction of LLD, which would aid in treatment planning. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-02042-6.
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Affiliation(s)
- Chang Ho Shin
- Division of Paediatric Orthopaedics, Seoul National University Children's Hospital, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 03080, Republic of Korea
| | - Chaemoon Lim
- Department of Orthopaedic Surgery, Jeju National University Hospital, 15 Aran 13-gil, Jeju, 63241, Republic of Korea
| | - Hwa Young Kim
- Division of Clinical Genetics, Department of Paediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 03080, Republic of Korea
| | - Won Joon Yoo
- Division of Paediatric Orthopaedics, Seoul National University Children's Hospital, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 03080, Republic of Korea
| | - Tae-Joon Cho
- Division of Paediatric Orthopaedics, Seoul National University Children's Hospital, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 03080, Republic of Korea
| | - In Ho Choi
- Division of Paediatric Orthopaedics, Seoul National University Children's Hospital, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 03080, Republic of Korea
| | - Jung Min Ko
- Division of Clinical Genetics, Department of Paediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 03080, Republic of Korea.
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12
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Isolated Hypomethylation of IGF2 Associated with Severe Hypoglycemia Responsive to Growth Hormone Treatment. Diagnostics (Basel) 2021; 11:diagnostics11050749. [PMID: 33922271 PMCID: PMC8146043 DOI: 10.3390/diagnostics11050749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 11/17/2022] Open
Abstract
Hypomethylation of H19 and IGF2 can cause Silver-Russell syndrome (SRS), a clinically and genetically heterogeneous condition characterized by intrauterine growth restriction, poor postnatal growth, relative macrocephaly, craniofacial abnormalities, body asymmetry, hypoglycemia and feeding difficulties. Isolated hypomethylation of IGF2 has been reported in single cases of SRS as well. Here, we report on a 19-month-old patient who presented with two episodes of hypoglycemic seizures. No intrauterine growth restriction was observed, the patient did not present with SRS-typical facial features, and postnatal growth in the first months of life was along the lower normal percentiles. Exome sequencing did not reveal any likely pathogenic variants explaining the phenotype; however, hypomethylation studies revealed isolated hypomethylation of IGF2, while the methylation of H19 appeared normal. Hypoglycemia responded well to growth hormone therapy, and the boy showed good catch-up growth. Our case demonstrates that SRS and isolated IGF2 hypomethylation should be considered early in the diagnosis of recurrent hypoglycemia in childhood, especially in combination with small gestational age and poor growth.
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13
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Kindsfather AJ, Czekalski MA, Pressimone CA, Erisman MP, Mann MRW. Perturbations in imprinted methylation from assisted reproductive technologies but not advanced maternal age in mouse preimplantation embryos. Clin Epigenetics 2019; 11:162. [PMID: 31767035 PMCID: PMC6878706 DOI: 10.1186/s13148-019-0751-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/23/2019] [Indexed: 12/19/2022] Open
Abstract
Background Over the last several decades, the average age of first-time mothers has risen steadily. With increasing maternal age comes a decrease in fertility, which in turn has led to an increase in the use of assisted reproductive technologies by these women. Assisted reproductive technologies (ARTs), including superovulation and embryo culture, have been shown separately to alter imprinted DNA methylation maintenance in blastocysts. However, there has been little investigation on the effects of advanced maternal age, with or without ARTs, on genomic imprinting. We hypothesized that ARTs and advanced maternal age, separately and together, alter imprinted methylation in mouse preimplantation embryos. For this study, we examined imprinted methylation at three genes, Snrpn, Kcnq1ot1, and H19, which in humans are linked to ART-associated methylation errors that lead to imprinting disorders. Results Our data showed that imprinted methylation acquisition in oocytes was unaffected by increasing maternal age. Furthermore, imprinted methylation was normally acquired when advanced maternal age was combined with superovulation. Analysis of blastocyst-stage embryos revealed that imprinted methylation maintenance was also not affected by increasing maternal age. In a comparison of ARTs, we observed that the frequency of blastocysts with imprinted methylation loss was similar between the superovulation only and the embryo culture only groups, while the combination of superovulation and embryo culture resulted in a higher frequency of mouse blastocysts with maternal imprinted methylation perturbations than superovulation alone. Finally, the combination of increasing maternal age with ARTs had no additional effect on the frequency of imprinted methylation errors. Conclusion Collectively, increasing maternal age with or without superovulation had no effect of imprinted methylation acquisition at Snrpn, Kcnq1ot1, and H19 in oocytes. Furthermore, during preimplantation development, while ARTs generated perturbations in imprinted methylation maintenance in blastocysts, advanced maternal age did not increase the burden of imprinted methylation errors at Snrpn, Kcnq1ot1, and H19 when combined with ARTs. These results provide cautious optimism that advanced maternal age is not a contributing factor to imprinted methylation errors in embryos produced in the clinic. Furthermore, our data on the effects of ARTs strengthen the need to advance clinical methods to reduce imprinted methylation errors in in vitro-produced embryos.
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Affiliation(s)
- Audrey J Kindsfather
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Ave, Pittsburgh, PA, 15213, USA.,Magee-Womens Research Institute, 204 Craft Ave, Pittsburgh, PA, 15213, USA
| | - Megan A Czekalski
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Ave, Pittsburgh, PA, 15213, USA.,Magee-Womens Research Institute, 204 Craft Ave, Pittsburgh, PA, 15213, USA
| | - Catherine A Pressimone
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Ave, Pittsburgh, PA, 15213, USA.,Magee-Womens Research Institute, 204 Craft Ave, Pittsburgh, PA, 15213, USA
| | - Margaret P Erisman
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Ave, Pittsburgh, PA, 15213, USA.,Magee-Womens Research Institute, 204 Craft Ave, Pittsburgh, PA, 15213, USA
| | - Mellissa R W Mann
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Ave, Pittsburgh, PA, 15213, USA. .,Magee-Womens Research Institute, 204 Craft Ave, Pittsburgh, PA, 15213, USA.
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14
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Castillejo-Lopez C, Pjanic M, Pirona AC, Hetty S, Wabitsch M, Wadelius C, Quertermous T, Arner E, Ingelsson E. Detailed Functional Characterization of a Waist-Hip Ratio Locus in 7p15.2 Defines an Enhancer Controlling Adipocyte Differentiation. iScience 2019; 20:42-59. [PMID: 31557715 PMCID: PMC6817687 DOI: 10.1016/j.isci.2019.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/10/2019] [Accepted: 09/05/2019] [Indexed: 12/22/2022] Open
Abstract
We combined CAGE sequencing in human adipocytes during differentiation with data from genome-wide association studies to identify an enhancer in the SNX10 locus on chromosome 7, presumably involved in body fat distribution. Using reporter assays and CRISPR-Cas9 gene editing in human cell lines, we characterized the role of the enhancer in adipogenesis. The enhancer was active during adipogenesis and responded strongly to insulin and isoprenaline. The allele associated with increased waist-hip ratio in human genetic studies was associated with higher enhancer activity. Mutations of the enhancer resulted in less adipocyte differentiation. RNA sequencing of cells with disrupted enhancer showed reduced expression of established adipocyte markers, such as ADIPOQ and LPL, and identified CHI3L1 on chromosome 1 as a potential gene involved in adipocyte differentiation. In conclusion, we identified and characterized an enhancer in the SNX10 locus and outlined its plausible mechanisms of action and downstream targets. An enhancer active during adipogenesis is located in an obesity GWAS locus The enhancer responded strongly to insulin and isoprenaline Mutation of the enhancer by CRISPR-Cas9 decreased adipocyte differentiation Knockout of CHI3L1 decreased adipocyte differentiation
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Affiliation(s)
- Casimiro Castillejo-Lopez
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Milos Pjanic
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anna Chiara Pirona
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Susanne Hetty
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Endocrinology and Diabetes, University of Ulm, Ulm, Germany
| | - Claes Wadelius
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Erik Arner
- Laboratory for Applied Regulatory Genomics Network Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA 94305, USA.
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15
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Goedegebuure WJ, Smeets CCJ, Renes JS, de Rijke YB, Hokken-Koelega ACS. Gonadal function and pubertal development in patients with Silver-Russell syndrome. Hum Reprod 2019; 33:2122-2130. [PMID: 30252068 DOI: 10.1093/humrep/dey286] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/10/2018] [Indexed: 11/12/2022] Open
Abstract
STUDY QUESTION Is gonadal function affected in males and females with Silver-Russell Syndrome (SRS)? SUMMARY ANSWER Sertoli cell dysfunction is more common in males with SRS, with 11p15 LOM, but gonadal function seems to be unaffected in females with SRS. WHAT IS KNOWN ALREADY Males with SRS have an increased risk for genital abnormalities such as cryptorchidism and hypospadias, which could be associated with reproductive problems in later life. In SRS females, an association has been described with Mayer-Rokitansky-Küster-Hauser syndrome, which might compromise their reproductive function. STUDY DESIGN, SIZE, DURATION Longitudinal follow-up study, involving 154 subjects, over a time period of 20 years. PARTICIPANTS/MATERIALS, SETTING, METHODS Thirty-one SRS patients (14 males) and 123 non-SRS patients born at same gestational age (SGA; 65 males). All received growth hormone and 27.3% received additional gonadotropin-releasing hormone analog treatment (GnRHa). MAIN RESULTS AND THE ROLE OF CHANCE Mean age at onset of puberty was 11.5 years in SRS males versus 11.6 years in non-SRS males (P = 0.51), and 10.5 years in SRS females versus 10.7 years in non-SRS females (P = 0.50). Four of the 14 SRS males had a post-pubertal inhibin-B level below the fifth percentile compared to healthy controls, and two of them an FSH above the 95th percentile, indicating Sertoli cell dysfunction. One of them had a history of bilateral cryptorchidism and orchiopexy. All SRS females had AMH, LH and FSH levels within the reference range. Pubertal duration to Tanner stage five was similar in SRS and non-SRS. Pubertal height gain was better in SRS patients who additionally received GnRHa (P < 0.01). Mean age at menarche was 13.1 years in SRS versus 13.3 years in non-SRS (P = 0.62). One SRS female had primary amenorrhea due to Müllerian agenesis. LIMITATIONS, REASONS FOR CAUTION As this is a rare syndrome, the SRS group had a small size. WIDER IMPLICATIONS OF THE FINDINGS As gonadal function is not affected in females with SRS, it is likely that reproductive function is also not affected. Sertoli cell dysfunction in males with SRS could cause impaired reproductive function and should be assessed during pubertal development. STUDY FUNDING/COMPETING INTEREST(S) No external funding was used for the study. The authors have no conflicts of interest.
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Affiliation(s)
- W J Goedegebuure
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus University Medical Centre, Rotterdam, The Netherlands.,Dutch Growth Research Foundation, Rotterdam, The Netherlands
| | - C C J Smeets
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - J S Renes
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Y B de Rijke
- Department of Clinical Chemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - A C S Hokken-Koelega
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus University Medical Centre, Rotterdam, The Netherlands.,Dutch Growth Research Foundation, Rotterdam, The Netherlands
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16
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Adachi M, Fukami M, Kagami M, Sho N, Yamazaki Y, Tanaka Y, Asakura Y, Hanakawa J, Muroya K. Severe in utero under-virilization in a 46,XY patient with Silver-Russell syndrome with 11p15 loss of methylation. J Pediatr Endocrinol Metab 2019; 32:191-196. [PMID: 30676999 DOI: 10.1515/jpem-2018-0464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/16/2018] [Indexed: 11/15/2022]
Abstract
Background Silver-Russell syndrome (SRS) is characterized by growth retardation and variable features including macrocephaly, body asymmetry, and genital manifestations such as cryptorchidism in 46,XY patients. Case presentation The patient was born at 39 weeks with a birth weight of 1344 g. Subtle clitoromegaly warranted a thorough evaluation, which disclosed 46,XY karyotype, bilateral undescended testes, and a rudimentary uterus. Because of severe under-virilization, the patient was assigned as female. Failure to thrive, macrocephaly, and body asymmetry led to the diagnosis of SRS, confirmed by marked hypomethylation of H19/IGF2 intergenic differentially methylated region (IG-DMR). From age 9 years, progressive virilization occurred, which necessitated luteinizing hormone-releasing hormone analog (LHRHa) treatment. Gonadal resection at 15 years revealed immature testes with mostly Sertoli-cell-only tubules. Panel analysis for 46,XY-differences of sex development (DSD) failed to detect any pathogenic variants. Conclusions This is the second reported case of molecularly proven 46,XY SRS accompanied by severe under-virilization. SRS should be included in the differential diagnosis of 46,XY-DSD.
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Affiliation(s)
- Masanori Adachi
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Noriko Sho
- Department of Child and Adolescent Psychiatry, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yuichiro Yamazaki
- Department of Urology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yukichi Tanaka
- Division of Diagnostic Pathology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yumi Asakura
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Junko Hanakawa
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Koji Muroya
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
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17
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Ge S, Zhao P, Liu X, Zhao Z, Liu M. Necessity to Evaluate Epigenetic Quality of the Sperm for Assisted Reproductive Technology. Reprod Sci 2018; 26:315-322. [DOI: 10.1177/1933719118808907] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Shaoqin Ge
- Hebei University Health Science Center, Baoding, China
- The Institute for Reproductive Medicine of Hebei University, Baoding, China
- The Center for Reproductive Medicine of Affiliated Hospital of Hebei University, Baoding, China
| | - Penghui Zhao
- Hebei University Health Science Center, Baoding, China
| | - Xuanchen Liu
- Hebei University Health Science Center, Baoding, China
| | - Zhenghui Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meiyun Liu
- The Center for Reproductive Medicine of Affiliated Hospital of Hebei University, Baoding, China
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18
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Juarez-Carreño S, Morante J, Dominguez M. Systemic signalling and local effectors in developmental stability, body symmetry, and size. Cell Stress 2018; 2:340-361. [PMID: 31225459 PMCID: PMC6551673 DOI: 10.15698/cst2018.12.167] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Symmetric growth and the origins of fluctuating asymmetry are unresolved phenomena of biology. Small, and sometimes noticeable, deviations from perfect bilateral symmetry reflect the vulnerability of development to perturbations. The degree of asymmetry is related to the magnitude of the perturbations and the ability of an individual to cope with them. As the left and right sides of an individual were presumed to be genetically identical, deviations of symmetry were traditionally attributed to non-genetic effects such as environmental and developmental noise. In this review, we draw attention to other possible sources of variability, especially to somatic mutations and transposons. Mutations are a major source of phenotypic variability and recent genomic data have highlighted somatic mutations as ubiquitous, even in phenotypically normal individuals. We discuss the importance of factors that are responsible for buffering and stabilizing the genome and for maintaining size robustness and quality through elimination of less-fit or damaged cells. However, the important question that arises from these studies is whether this self-correcting capacity and intrinsic organ size controls are sufficient to explain how symmetric structures can reach an identical size and shape. Indeed, recent discoveries in the fruit fly have uncovered a conserved hormone of the insulin/IGF/relaxin family, Dilp8, that is responsible for stabilizing body size and symmetry in the face of growth perturbations. Dilp8 alarm signals periphery growth status to the brain, where it acts on its receptor Lgr3. Loss of Dilp8-Lgr3 signaling renders flies incapable of detecting growth perturbations and thus maintaining a stable size and symmetry. These findings help to understand how size and symmetry of somatic tissues remain undeterred in noisy environments, after injury or illnesses, and in the presence of accumulated somatic mutations.
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Affiliation(s)
- Sergio Juarez-Carreño
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas-Universidad Miguel Hernández (CSIC-UMH), Avda Santiago Ramón y Cajal s/n, Campus de Sant Joan, Alicante, Spain
| | - Javier Morante
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas-Universidad Miguel Hernández (CSIC-UMH), Avda Santiago Ramón y Cajal s/n, Campus de Sant Joan, Alicante, Spain
| | - Maria Dominguez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas-Universidad Miguel Hernández (CSIC-UMH), Avda Santiago Ramón y Cajal s/n, Campus de Sant Joan, Alicante, Spain
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19
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Pianka MA, McIntosh AT, Patel SD, Bakhshi PR, Jung M. Close yet so far away: a look into the management strategies of genetic imprinting disorders. AMERICAN JOURNAL OF STEM CELLS 2018; 7:72-81. [PMID: 30510842 PMCID: PMC6261869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 09/26/2018] [Indexed: 06/09/2023]
Abstract
Genetic imprinting is the process of epigenetic labelling or silencing of particular genes, based on the maternal or paternal origin of the gene, in a heritable pattern. The incidence of imprinting disorders has become a growing concern due to the potential association between these congenital syndromes and assisted reproductive technologies (ARTs). This review presents a general summary of the imprinting process as well as the current knowledge surrounding the genetic and epigenetic underpinnings of the most prevalent imprinting disorders: Beckwith-Wiedemann syndrome (BWS), Silver-Russell syndrome (SRS), Prader-Willi syndrome (PWS), and Angelman syndrome (AS). As research continues to elucidate the molecular pathways that characterize genetic imprinting, efforts have been made to establish guidelines that incorporate phenotypic manifestations as well as genetic testing to ensure safe and effective management of symptoms. While these efforts are likely to benefit future clinical management, their efficacy cannot yet be generalized to all patients diagnosed with these syndromes, as many of the genetic abnormalities and the associated phenotypic manifestations have yet to be characterized. Furthermore, future advances in the knowledge of epigenetic processes and genetic loci involved in the development of these syndromes may allow for the development of curative therapies.
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Affiliation(s)
- Mark A Pianka
- Georgetown University School of MedicineWashington, DC, USA
| | | | - Sahaj D Patel
- Georgetown University School of MedicineWashington, DC, USA
| | | | - Mira Jung
- Department of Radiation Medicine/Oncology, MedStar Georgetown University HospitalWashington, DC, USA
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20
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Soellner L, Kraft F, Sauer S, Begemann M, Kurth I, Elbracht M, Eggermann T. Search for cis-acting factors and maternal effect variants in Silver-Russell patients with ICR1 hypomethylation and their mothers. Eur J Hum Genet 2018; 27:42-48. [PMID: 30218098 DOI: 10.1038/s41431-018-0269-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 07/06/2018] [Accepted: 08/09/2018] [Indexed: 11/09/2022] Open
Abstract
Silver-Russell syndrome is an imprinting disorder characterized by severe intrauterine and postnatal growth retardation. The majority of patients show loss of methylation (LOM) of the H19/IGF2 IG-DMR (ICR1) in 11p15.5. In ~10% of these patients aberrant methylation of additional imprinted loci on other chromosomes than 11 can be observed (multilocus imprinting defect - MLID). Recently, genomic variations in the ICR1 have been associated with disturbed methylation of the ICR1. In addition, variants in factors contributing to the life cycle of imprinting are discussed to cause aberrant imprinting, including MLID. These variants can either be identified in the patients with imprinting disorders themselves or in their mothers. We performed comprehensive studies to elucidate the role of both cis-acting variants in 11p15.5 as well as of maternal effect variants in the etiology of ICR1 LOM. Whereas copy number analysis and next generation sequencing in the ICR1 did not provide any evidence for a variant, search for maternal effect variants in 21 mothers of patients with ICR1 LOM identified two carriers of NLRP5 variants. By considering our results as well as those from the literature, we conclude that the causes for epimutations are heterogeneous. MLID might be regarded as an own etiological subgroup, associated with maternal effect variants in NLRP and functionally related genes. In addition, these variants might also contribute to LOM of single imprinted loci. Furthermore, genomic variants in the patients themselves might result in aberrant methylation patterns and need further investigation.
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Affiliation(s)
- Lukas Soellner
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Florian Kraft
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Sabrina Sauer
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany.,Labor Dr. Wisplinghoff, Köln, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany.
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Eggermann T, Ledig S, Begemann M, Elbracht M, Kurth I, Wieacker P. Search for altered imprinting marks in Mayer-Rokitansky-Küster-Hauser patients. Mol Genet Genomic Med 2018; 6:1225-1228. [PMID: 30099855 PMCID: PMC6305658 DOI: 10.1002/mgg3.426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/21/2018] [Accepted: 06/05/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Mayer-Rokitansky-Küster-Hauser syndrome (MRKH) is the second most common cause of primary amenorrhea and characterized by absence of the uterus and the upper part of the vagina. The etiology of MRKH is mainly unknown but a contribution of genomic alterations is probable. A molecular disturbance so far neglected in MRKH research is aberrant methylation at imprinted loci. In fact, MRKH has been reported in patients with the imprinting disorder Silver-Russell syndrome. METHODS We report on a rare patient with MRKH and SRS due to an ICR1 hypomethylation in 11p15.5. On the basis of this observation we screened a large cohort of MRKH patients (n > 100) for aberrant methylation at nine imprinted loci. RESULTS We failed to detect any epimutation, thus we conclude that imprinting defects at least at the currently known disease-relevant imprinted loci do not contribute to the isolated MRKH phenotype. However, it cannot be excluded that altered methylation marks at other loci are involved in the etiology of MRKH. CONCLUSION The molecular basis for MRKH remains unclear in the majority of patients, but future studies on the association between MRKH and ICR1 hypomethylation/SRS will to enlighten the role of epigenetics in the etiology of MRKH.
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Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, Technical University RWTH Aachen, Aachen, Germany
| | - Susanne Ledig
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Technical University RWTH Aachen, Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Technical University RWTH Aachen, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Technical University RWTH Aachen, Aachen, Germany
| | - Peter Wieacker
- Institute of Human Genetics, University of Münster, Münster, Germany
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Gonzalez-Nahm S, Mendez MA, Benjamin-Neelon SE, Murphy SK, Hogan VK, Rowley DL, Hoyo C. DNA methylation of imprinted genes at birth is associated with child weight status at birth, 1 year, and 3 years. Clin Epigenetics 2018; 10:90. [PMID: 29988473 PMCID: PMC6025828 DOI: 10.1186/s13148-018-0521-0] [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: 02/09/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022] Open
Abstract
Background This study assessed the associations between nine differentially methylated regions (DMRs) of imprinted genes in DNA derived from umbilical cord blood leukocytes in males and females and (1) birth weight for gestational age z score, (2) weight-for-length (WFL) z score at 1 year, and (3) body mass index (BMI) z score at 3 years. Methods We conducted multiple linear regression in n = 567 infants at birth, n = 288 children at 1 year, and n = 294 children at 3 years from the Newborn Epigenetics Study (NEST). We stratified by sex and adjusted for race/ethnicity, maternal education, maternal pre-pregnancy BMI, prenatal smoking, maternal age, gestational age, and paternal race. We also conducted analysis restricting to infants not born small for gestational age. Results We found an association between higher methylation of the sequences regulating paternally expressed gene 10 (PEG10) and anthropometric z scores at 1 year (β = 0.84; 95% CI = 0.34, 1.33; p = 0.001) and 3 years (β = 1.03; 95% CI = 0.37, 1.69; p value = 0.003) in males only. Higher methylation of the DMR regulating mesoderm-specific transcript (MEST) was associated with lower anthropometric z scores in females at 1 year (β = - 1.03; 95% CI - 1.60, - 0.45; p value = 0.001) and 3 years (β = - 1.11; 95% CI - 1.98, - 0.24; p value = 0.01). These associations persisted when we restricted to infants not born small for gestational age. Conclusion Our data support a sex-specific association between altered methylation and weight status in early life. These methylation marks can contribute to the compendium of epigenetically regulated regions detectable at birth, influencing obesity in childhood. Larger studies are required to confirm these findings.
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Affiliation(s)
- Sarah Gonzalez-Nahm
- Department of Health, Behavior and Society, Johns Hopkins Bloomberg School of Public Health, 624 N Broadway, Baltimore, MD 21205 USA
| | - Michelle A. Mendez
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Sara E. Benjamin-Neelon
- Department of Health, Behavior and Society, Johns Hopkins Bloomberg School of Public Health, 624 N Broadway, Baltimore, MD 21205 USA
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC USA
| | | | - Diane L. Rowley
- Department of Maternal and Child Health, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC USA
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23
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Assisted Reproductive Technologies and imprinting disorders: Results of a study from a French congenital malformations registry. Eur J Med Genet 2018; 61:518-523. [PMID: 29775803 DOI: 10.1016/j.ejmg.2018.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/10/2018] [Indexed: 01/17/2023]
Abstract
INTRODUCTION Assisted Reproductive Technologies (ART) is increasingly used to help infertile couples to have children around the world. A number of studies have been published reporting an increased risk of major malformations in children born following ART, especially an increased incidence of epigenetic diseases (ED). This study aimed to assess the incidence of epigenetic diseases with affected imprinting genes in infants or children from pregnancies obtained through IVF/ICSI compared to infants or children from pregnancies obtained spontaneously. PATIENT DATA This is a monocentric retrospective epidemiological study based on data from a French congenital malformations registry called REMERA (Registre des Malformations en Rhône-Alpes) which exhaustively monitors all pregnancies in Rhone-Alpes region, whatever their nature of onset (spontaneous pregnancies or pregnancies from ART). This registry collects all malformations, except minor malformations (EUROCAT), and all polymalformative syndromes concerning all fetuses and children born alive or not, from 20 weeks of pregnancy (or 22 weeks of amenorrhea) and all medical termination of pregnancy whatever the term. Inclusion criteria are all diagnoses of epigenetic diseases (ED) related to parental imprinting recorded in the period January 2006 to December 2015. METHODS For each year, the total number of births (including stillbirths) was collected from the annual activity reports of the registry. The exhaustive number of cases of epigenetic diseases was known in the registry. Were collected the number of births resulting from ART pregnancies in the study population. This incidence of ED was compared between births from spontaneous pregnancies and those obtained through ART (IVF/ICSI) with a generalized linear model (GLM: binomial regression). RESULTS In total, 46 cases of epigenetic diseases were analyzed on the REMERA registry files from 2006 to 2015. 4 cases from the 46 analyzed cases were from pregnancies induced by ART. ART was a risk factor for epigenetic disease (OR = 2.9 [1.06-8.22] (p = .039)). In ART-pregnancies there were 2 diagnoses: Beckwith-Wiedemann syndrome (BWS) (3 cases out of 4) and Silver-Russell syndrome (SRS) (1 out of 4). DISCUSSION Infants and children obtained through IVF/ICSI appear to be related to a higher risk of epigenetic diseases compared to naturally conceived children. The perspectives of this study are to raise awareness about the creation of registries of congenital malformations and genetic and epigenetic syndromes with systematic and strict reports of all the cases on all the French territory and thus to widen this study with a bigger cohort.
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Abstract
Silver-Russell syndrome (SRS) is a rare congenital imprinting disorder. The genetic findings in SRS patients are heterogeneous and often sporadic. However, chromosomes 7, 11, and 17 are consistently involved in all individuals who meet the strict diagnostic criteria of SRS. There are many clinical features characteristic of SRS; the most common are low birth weight, short stature, triangular face, clinodactyly, relative macrocephaly, ear anomalies, and skeletal asymmetry.
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Muurinen M, Hannula-Jouppi K, Reinius LE, Söderhäll C, Merid SK, Bergström A, Melén E, Pershagen G, Lipsanen-Nyman M, Greco D, Kere J. Hypomethylation of HOXA4 promoter is common in Silver-Russell syndrome and growth restriction and associates with stature in healthy children. Sci Rep 2017; 7:15693. [PMID: 29146936 PMCID: PMC5691194 DOI: 10.1038/s41598-017-16070-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 11/07/2017] [Indexed: 01/03/2023] Open
Abstract
Silver-Russell syndrome (SRS) is a growth retardation syndrome in which loss of methylation on chromosome 11p15 (11p15 LOM) and maternal uniparental disomy for chromosome 7 [UPD(7)mat] explain 20–60% and 10% of the syndrome, respectively. To search for a molecular cause for the remaining SRS cases, and to find a possible common epigenetic change, we studied DNA methylation pattern of more than 450 000 CpG sites in 44 SRS patients. Common to all three SRS subgroups, we found a hypomethylated region at the promoter region of HOXA4 in 55% of the patients. We then tested 39 patients with severe growth restriction of unknown etiology, and found hypomethylation of HOXA4 in 44% of the patients. Finally, we found that methylation at multiple CpG sites in the HOXA4 promoter region was associated with height in a cohort of 227 healthy children, suggesting that HOXA4 may play a role in regulating human growth by epigenetic mechanisms.
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Affiliation(s)
- Mari Muurinen
- Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Katariina Hannula-Jouppi
- Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Department of Dermatology, Skin and Allergy Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Lovisa E Reinius
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Sachs' Children's Hospital, Södersjukhuset, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Marita Lipsanen-Nyman
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Dario Greco
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Faculty of Medicine and Life Sciences & Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland
| | - Juha Kere
- Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland. .,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden. .,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, UK.
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26
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Velker BAM, Denomme MM, Krafty RT, Mann MRW. Maintenance of Mest imprinted methylation in blastocyst-stage mouse embryos is less stable than other imprinted loci following superovulation or embryo culture. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx015. [PMID: 29492315 PMCID: PMC5804554 DOI: 10.1093/eep/dvx015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/07/2017] [Accepted: 07/19/2017] [Indexed: 06/08/2023]
Abstract
Assisted reproductive technologies are fertility treatments used by subfertile couples to conceive their biological child. Although generally considered safe, these pregnancies have been linked to genomic imprinting disorders, including Beckwith-Wiedemann and Silver-Russell Syndromes. Silver-Russell Syndrome is a growth disorder characterized by pre- and post-natal growth retardation. The Mest imprinted domain is one candidate region on chromosome 7 implicated in Silver-Russell Syndrome. We have previously shown that maintenance of imprinted methylation was disrupted by superovulation or embryo culture during pre-implantation mouse development. For superovulation, this disruption did not originate in oogenesis as a methylation acquisition defect. However, in comparison to other genes, Mest exhibits late methylation acquisition kinetics, possibly making Mest more vulnerable to perturbation by environmental insult. In this study, we present a comprehensive evaluation of the effects of superovulation and in vitro culture on genomic imprinting at the Mest gene. Superovulation resulted in disruption of imprinted methylation at the maternal Mest allele in blastocysts with an equal frequency of embryos having methylation errors following low or high hormone treatment. This disruption was not due to a failure of imprinted methylation acquisition at Mest in oocytes. For cultured embryos, both the Fast and Slow culture groups experienced a significant loss of maternal Mest methylation compared to in vivo-derived controls. This loss of methylation was independent of development rates in culture. These results indicate that Mest is more susceptible to imprinted methylation maintenance errors compared to other imprinted genes.
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Affiliation(s)
- Brenna A. M. Velker
- Department of Obstetrics & Gynecology, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada
- Department of Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada
- Children’s Health Research Institute, London, ON, Canada
| | - Michelle M. Denomme
- Department of Obstetrics & Gynecology, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada
- Department of Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada
- Children’s Health Research Institute, London, ON, Canada
- Fertility Laboratories Of Colorado, 10290 Ridgegate Circle, Lonetree, CO 80124 USA
| | - Robert T. Krafty
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mellissa R. W. Mann
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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27
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Elhamamsy AR. Role of DNA methylation in imprinting disorders: an updated review. J Assist Reprod Genet 2017; 34:549-562. [PMID: 28281142 PMCID: PMC5427654 DOI: 10.1007/s10815-017-0895-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/23/2017] [Indexed: 12/20/2022] Open
Abstract
Genomic imprinting is a complex epigenetic process that contributes substantially to embryogenesis, reproduction, and gametogenesis. Only small fraction of genes within the whole genome undergoes imprinting. Imprinted genes are expressed in a monoallelic parent-of-origin-specific manner, which means that only one of the two inherited alleles is expressed either from the paternal or maternal side. Imprinted genes are typically arranged in clusters controlled by differentially methylated regions or imprinting control regions. Any defect or relaxation in imprinting process can cause loss of imprinting in the key imprinted loci. Loss of imprinting in most cases has a harmful effect on fetal development and can result in neurological, developmental, and metabolic disorders. Since DNA methylation and histone modifications play a key role in the process of imprinting. This review focuses on the role of DNA methylation in imprinting process and describes DNA methylation aberrations in different imprinting disorders.
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Affiliation(s)
- Amr Rafat Elhamamsy
- Department of Clinical Pharmacy, School of Pharmacy, Tanta University, Tanta, 31512, Gharbia, Egypt.
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28
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Dimopoulos A, Sicko RJ, Kay DM, Rigler SL, Fan R, Romitti PA, Browne ML, Druschel CM, Caggana M, Brody LC, Mills JL. Copy number variants in a population-based investigation of Klippel-Trenaunay syndrome. Am J Med Genet A 2017; 173:352-359. [PMID: 27901321 PMCID: PMC6205266 DOI: 10.1002/ajmg.a.37868] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 06/16/2016] [Indexed: 01/19/2023]
Abstract
Klippel-Trenaunay syndrome (KTS) is a rare congenital vascular disorder that is thought to occur sporadically; however, reports of familial occurrence suggest a genetic component. We examined KTS cases to identify novel, potentially causal copy number variants (CNVs). We identified 17 KTS cases from all live-births occurring in New York (1998-2010). Extracted DNA was genotyped using Illumina microarrays and CNVs were called using PennCNV software. CNVs selected for follow-up had ≥10 single nucleotide polymorphisms (SNPs) and minimal overlap with in-house controls or controls from the Database of Genomic Variants. We identified 15 candidate CNVs in seven cases; among them a deletion in two cases within transcripts of HDAC9, a histone deacetylase essential for angiogenic sprouting of endothelial cells. One of them also had a duplication upstream of SALL3, a transcription factor essential for embryonic development that inhibits DNMT3A, a DNA methyltransferase responsible for embryonic de novo DNA methylation. Another case had a duplication spanning ING5, a histone acetylation regulator active during embryogenesis. We identified rare genetic variants related to chromatin modification which may have a key role in regulating vascular development during embryogenesis. Further investigation of their implications in the pathogenesis of KTS is warranted. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Aggeliki Dimopoulos
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Robert J. Sicko
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Denise M. Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Shannon L. Rigler
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Ruzong Fan
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Paul A. Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, Iowa
| | - Marilyn L. Browne
- Congenital Malformations Registry, New York State Department of Health, Albany, New York
- Department of Epidemiology and Biostatistics, University at Albany School of Public Health, Rensselaer, New York
| | - Charlotte M. Druschel
- Congenital Malformations Registry, New York State Department of Health, Albany, New York
- Department of Epidemiology and Biostatistics, University at Albany School of Public Health, Rensselaer, New York
| | - Michele Caggana
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Lawrence C. Brody
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - James L. Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
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29
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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: 296] [Impact Index Per Article: 42.3] [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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30
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Eggermann K, Bliek J, Brioude F, Algar E, Buiting K, Russo S, Tümer Z, Monk D, Moore G, Antoniadi T, Macdonald F, Netchine I, Lombardi P, Soellner L, Begemann M, Prawitt D, Maher ER, Mannens M, Riccio A, Weksberg R, Lapunzina P, Grønskov K, Mackay DJG, Eggermann T. EMQN best practice guidelines for the molecular genetic testing and reporting of chromosome 11p15 imprinting disorders: Silver-Russell and Beckwith-Wiedemann syndrome. Eur J Hum Genet 2016; 24:1377-87. [PMID: 27165005 PMCID: PMC5027690 DOI: 10.1038/ejhg.2016.45] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/23/2016] [Accepted: 03/29/2016] [Indexed: 11/24/2022] Open
Abstract
Molecular genetic testing for the 11p15-associated imprinting disorders Silver-Russell and Beckwith-Wiedemann syndrome (SRS, BWS) is challenging because of the molecular heterogeneity and complexity of the affected imprinted regions. With the growing knowledge on the molecular basis of these disorders and the demand for molecular testing, it turned out that there is an urgent need for a standardized molecular diagnostic testing and reporting strategy. Based on the results from the first external pilot quality assessment schemes organized by the European Molecular Quality Network (EMQN) in 2014 and in context with activities of the European Network of Imprinting Disorders (EUCID.net) towards a consensus in diagnostics and management of SRS and BWS, best practice guidelines have now been developed. Members of institutions working in the field of SRS and BWS diagnostics were invited to comment, and in the light of their feedback amendments were made. The final document was ratified in the course of an EMQN best practice guideline meeting and is in accordance with the general SRS and BWS consensus guidelines, which are in preparation. These guidelines are based on the knowledge acquired from peer-reviewed and published data, as well as observations of the authors in their practice. However, these guidelines can only provide a snapshot of current knowledge at the time of manuscript submission and readers are advised to keep up with the literature.
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Affiliation(s)
- Katja Eggermann
- Institut für Humangenetik, RWTH University Aachen, Aachen, Germany
| | - Jet Bliek
- Department of Clinical Genetics, Academic Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Frédéric Brioude
- INSERM, UMR_S 938, Paris, France
- Sorbonne Universities, UPMC Univ Paris 06; UMR_S 938, Paris, France
- Armand Trousseau Hospital, Pediatric Endocrinology, Paris, France
| | - Elizabeth Algar
- Genetics and Molecular Pathology Laboratory, Monash Health and Hudson Institute, Clayton, VIC, Australia
| | - Karin Buiting
- Institut für Humangenetik, Universität Duisburg-Essen, Essen, Germany
| | - Silvia Russo
- Laboratory of Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano IRCCS, Milano, Italy
| | - Zeynep Tümer
- Clinical Genetic Unit, Kennedy Center, Rigshospitalet, Copenhagen University Hospital, Glostrup, Denmark
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Barcelona, Spain
| | - Gudrun Moore
- Fetal Growth and Developmental Group, Genetics and Genomic Medicine Programme, UCL-ICH, London, UK
| | - Thalia Antoniadi
- West Midlands Regional Genetics Laboratory, Birmingham Women's Hospital, Birmingham, UK
| | - Fiona Macdonald
- West Midlands Regional Genetics Laboratory, Birmingham Women's Hospital, Birmingham, UK
| | - Irène Netchine
- INSERM, UMR_S 938, Paris, France
- Sorbonne Universities, UPMC Univ Paris 06; UMR_S 938, Paris, France
- Armand Trousseau Hospital, Pediatric Endocrinology, Paris, France
| | - Paolo Lombardi
- Department of Clinical Genetics, Academic Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Lukas Soellner
- Institut für Humangenetik, RWTH University Aachen, Aachen, Germany
| | | | - Dirk Prawitt
- Center for Pediatrics and Adolescent Medicine, University Medical Center, Mainz, Germany
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Marcel Mannens
- Department of Clinical Genetics, Academic Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Andrea Riccio
- DiSTABiF, Seconda Università degli Studi di Napoli, Caserta, Italy
- Institute of Genetics and Biophysics – ABT, CNR, Napoli, Italy
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Departments of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Pablo Lapunzina
- INGEMM, Instituto de Genética Médica y Molecular, IdiPAZ, Hospital Universitario la Paz, CIBERER, ISCIII, Madrid, Spain
| | - Karen Grønskov
- Clinical Genetic Unit, Kennedy Center, Rigshospitalet, Copenhagen University Hospital, Glostrup, Denmark
| | - Deborah JG Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Thomas Eggermann
- Institut für Humangenetik, RWTH University Aachen, Aachen, Germany
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Abstract
PURPOSE OF REVIEW The purpose of review is to summarize new outcomes for the clinical characterization, molecular strategies, and therapeutic management of Silver-Russell syndrome (SRS). RECENT FINDINGS Various teams have described the clinical characteristics of SRS patients by genotype. A clinical score for the definition of SRS and for orienting molecular investigations has emerged. Insulin-like growth factor 2 (a major fetal growth factor) has been implicated in the pathophysiology of SRS, as the principle molecular mechanism underlying the disease is loss of methylation of the 11p15 region, including the imprinted insulin-like growth factor 2 gene. Maternal uniparental disomy of chromosome 7 and recently identified rare molecular defects have also been reported in patients with SRS. However, 40% of patients still have no molecular diagnosis. SUMMARY The definition of SRS has remained clinical since the first description of this condition, despite the identification of various molecular causes. The clinical issues faced by these patients are similar to those faced by other patients born small for gestational age (SGA), but patients with SRS require specific multidisciplinary management of their nutrition, growth, and metabolism, as they usually present an extreme form of SGA. Molecular analyses can confirm SRS, and are of particular importance for genetic counseling and prenatal testing.
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32
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Derakhshan-Horeh M, Abolhassani F, Jafarpour F, Moini A, Karbalaie K, Hosseini SM, Ostadhosseini S, Nasr-Esfahani MH. Methylation Status of H19/IGF2 Differentially Methylated Region in in vitro Human Blastocysts Donated by Healthy Couples. IRANIAN BIOMEDICAL JOURNAL 2016; 21:16-23. [PMID: 27432596 PMCID: PMC5141249 DOI: 10.6091/.21.1.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Imprinted genes are a unique subset of few genes that have been differentially methylated region (DMR) in a parental origin-dependent manner during gametogenesis, and these genes are highly protected during pre-implantation epigenetic reprogramming. Several studies have shown that the particular vulnerability of imprinting genes during suboptimal pre- and peri-conception micro-environments often is occurred by assisted reproduction techniques (ART). This study investigated the methylation status of H19/IGF2 DMR at high-quality expanding/expanded human blastocysts donated by healthy individuals to evaluate the risks linked to ART. METHODS Methylation levels of H19/IGF2 DMR were analyzed by bisulfite conversion and sequencing at 18 CpG sites (CpGs) located in this region. RESULTS The overall percentage of methylated CpGs and the proportion of hyper-methylated clones of H19/IGF2 DMR in analyzed blastocysts were 37.85±4.87% and 43.75±5.1%, respectively. For validation of our technique, the corresponding methylation levels of peripheral human lymphocytes were defined (49.52±1.86% and 50%, respectively). CONCLUSIONS Considering the absence of in vivo- produced human embryos, it is not possible to conclude that the methylation found in H19/IGF2 DMR is actually normal or abnormal. Regarding the possible risks associated with ART, the procedures should be optimized in order to at least reduce some of the epigenetic risks.
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Affiliation(s)
| | - Farid Abolhassani
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farnoosh Jafarpour
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, Academic Center for Education, Culture and Research (ACECR), Isfahan, Iran
| | - Ashraf Moini
- Department of Endocrinology and Female Infertility, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Obstetrics and Gynecology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Karbalaie
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran; 6Isfahan Fertility and Infertility Center, Isfahan, Iran
| | - Sayyed Morteza Hosseini
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, Academic Center for Education, Culture and Research (ACECR), Isfahan, Iran
| | - Somayyeh Ostadhosseini
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, Academic Center for Education, Culture and Research (ACECR), Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, Academic Center for Education, Culture and Research (ACECR), Isfahan, Iran.,Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran; 6Isfahan Fertility and Infertility Center, Isfahan, Iran.,Isfahan Fertility and Infertility Center, Isfahan, Iran
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33
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Õunap K. Silver-Russell Syndrome and Beckwith-Wiedemann Syndrome: Opposite Phenotypes with Heterogeneous Molecular Etiology. Mol Syndromol 2016; 7:110-21. [PMID: 27587987 DOI: 10.1159/000447413] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2016] [Indexed: 12/13/2022] Open
Abstract
Silver-Russell syndrome (SRS) and Beckwith-Wiedemann syndrome (BWS) are 2 clinically opposite growth-affecting disorders belonging to the group of congenital imprinting disorders. The expression of both syndromes usually depends on the parental origin of the chromosome in which the imprinted genes reside. SRS is characterized by severe intrauterine and postnatal growth retardation with various additional clinical features such as hemihypertrophy, relative macrocephaly, fifth finger clinodactyly, and triangular facies. BWS is an overgrowth syndrome with many additional clinical features such as macroglossia, organomegaly, and an increased risk of childhood tumors. Both SRS and BWS are clinically and genetically heterogeneous, and for clinical diagnosis, different diagnostic scoring systems have been developed. Six diagnostic scoring systems for SRS and 4 for BWS have been previously published. However, neither syndrome has common consensus diagnostic criteria yet. Most cases of SRS and BWS are associated with opposite epigenetic or genetic abnormalities in the 11p15 chromosomal region leading to opposite imbalances in the expression of imprinted genes. SRS is also caused by maternal uniparental disomy 7, which is usually identified in 5-10% of the cases, and is therefore the first imprinting disorder that affects 2 different chromosomes. In this review, we describe in detail the clinical diagnostic criteria and scoring systems as well as molecular causes in both SRS and BWS.
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Affiliation(s)
- Katrin Õunap
- Department of Genetics, United Laboratories, Tartu University Hospital, and Department of Pediatrics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
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34
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Epigenetic Mechanisms in Developmental Alcohol-Induced Neurobehavioral Deficits. Brain Sci 2016; 6:brainsci6020012. [PMID: 27070644 PMCID: PMC4931489 DOI: 10.3390/brainsci6020012] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/17/2016] [Accepted: 04/05/2016] [Indexed: 12/22/2022] Open
Abstract
Alcohol consumption during pregnancy and its damaging consequences on the developing infant brain are significant public health, social, and economic issues. The major distinctive features of prenatal alcohol exposure in humans are cognitive and behavioral dysfunction due to damage to the central nervous system (CNS), which results in a continuum of disarray that is collectively called fetal alcohol spectrum disorder (FASD). Many rodent models have been developed to understand the mechanisms of and to reproduce the human FASD phenotypes. These animal FASD studies have provided several molecular pathways that are likely responsible for the neurobehavioral abnormalities that are associated with prenatal alcohol exposure of the developing CNS. Recently, many laboratories have identified several immediate, as well as long-lasting, epigenetic modifications of DNA methylation, DNA-associated histone proteins and microRNA (miRNA) biogenesis by using a variety of epigenetic approaches in rodent FASD models. Because DNA methylation patterns, DNA-associated histone protein modifications and miRNA-regulated gene expression are crucial for synaptic plasticity and learning and memory, they can therefore offer an answer to many of the neurobehavioral abnormalities that are found in FASD. In this review, we briefly discuss the current literature of DNA methylation, DNA-associated histone proteins modification and miRNA and review recent developments concerning epigenetic changes in FASD.
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35
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Mackay DJG, Eggermann T, Buiting K, Garin I, Netchine I, Linglart A, de Nanclares GP. Multilocus methylation defects in imprinting disorders. Biomol Concepts 2016; 6:47-57. [PMID: 25581766 DOI: 10.1515/bmc-2014-0037] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/07/2014] [Indexed: 12/17/2022] Open
Abstract
Mammals inherit two complete sets of chromosomes, one from the father and one from the mother, and most autosomal genes are expressed from both maternal and paternal alleles. In imprinted genes, the expression of the allele is dependent upon its parental origin. Appropriate regulation of imprinted genes is important for normal development, with several genetic diseases associated with imprinting defects. A common process for controlling gene activity is methylation. The first steps for understanding the functions of DNA methylation and its regulation in mammalian development have led us to identify common (epi)genetic mechanisms involved in the eight human congenital imprinting disorders.
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36
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White CR, Denomme MM, Tekpetey FR, Feyles V, Power SGA, Mann MRW. High Frequency of Imprinted Methylation Errors in Human Preimplantation Embryos. Sci Rep 2015; 5:17311. [PMID: 26626153 PMCID: PMC4667293 DOI: 10.1038/srep17311] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/28/2015] [Indexed: 12/22/2022] Open
Abstract
Assisted reproductive technologies (ARTs) represent the best chance for infertile couples to conceive, although increased risks for morbidities exist, including imprinting disorders. This increased risk could arise from ARTs disrupting genomic imprints during gametogenesis or preimplantation. The few studies examining ART effects on genomic imprinting primarily assessed poor quality human embryos. Here, we examined day 3 and blastocyst stage, good to high quality, donated human embryos for imprinted SNRPN, KCNQ1OT1 and H19 methylation. Seventy-six percent day 3 embryos and 50% blastocysts exhibited perturbed imprinted methylation, demonstrating that extended culture did not pose greater risk for imprinting errors than short culture. Comparison of embryos with normal and abnormal methylation didn’t reveal any confounding factors. Notably, two embryos from male factor infertility patients using donor sperm harboured aberrant methylation, suggesting errors in these embryos cannot be explained by infertility alone. Overall, these results indicate that ART human preimplantation embryos possess a high frequency of imprinted methylation errors.
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Affiliation(s)
- Carlee R White
- Department of Obstetrics &Gynecology, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,Department of Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,Children's Health Research Institute, London, Ontario, Canada
| | - Michelle M Denomme
- Department of Obstetrics &Gynecology, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,Department of Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,Children's Health Research Institute, London, Ontario, Canada
| | - Francis R Tekpetey
- Department of Obstetrics &Gynecology, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,The Fertility Clinic, London Health Sciences Centre, London, Ontario, Canada
| | - Valter Feyles
- Department of Obstetrics &Gynecology, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,The Fertility Clinic, London Health Sciences Centre, London, Ontario, Canada
| | - Stephen G A Power
- Department of Obstetrics &Gynecology, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,The Fertility Clinic, London Health Sciences Centre, London, Ontario, Canada
| | - Mellissa R W Mann
- Department of Obstetrics &Gynecology, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,Department of Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,Children's Health Research Institute, London, Ontario, Canada
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37
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Taylor DH, Chu ETJ, Spektor R, Soloway PD. Long non-coding RNA regulation of reproduction and development. Mol Reprod Dev 2015; 82:932-56. [PMID: 26517592 PMCID: PMC4762656 DOI: 10.1002/mrd.22581] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022]
Abstract
Noncoding RNAs (ncRNAs) have long been known to play vital roles in eukaryotic gene regulation. Studies conducted over a decade ago revealed that maturation of spliced, polyadenylated coding mRNA occurs by reactions involving small nuclear RNAs and small nucleolar RNAs; mRNA translation depends on activities mediated by transfer RNAs and ribosomal RNAs, subject to negative regulation by micro RNAs; transcriptional competence of sex chromosomes and some imprinted genes is regulated in cis by ncRNAs that vary by species; and both small-interfering RNAs and piwi-interacting RNAs bound to Argonaute-family proteins regulate post-translational modifications on chromatin and local gene expression states. More recently, gene-regulating noncoding RNAs have been identified, such as long intergenic and long noncoding RNAs (collectively referred to as lncRNAs)--a class totaling more than 100,000 transcripts in humans, which include some of the previously mentioned RNAs that regulate dosage compensation and imprinted gene expression. Here, we provide an overview of lncRNA activities, and then review the role of lncRNAs in processes vital to reproduction, such as germ cell specification, sex determination and gonadogenesis, sex hormone responses, meiosis, gametogenesis, placentation, non-genetic inheritance, and pathologies affecting reproductive tissues. Results from many species are presented to illustrate the evolutionarily conserved processes lncRNAs are involved in.
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Affiliation(s)
- David H. Taylor
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
| | - Erin Tsi-Jia Chu
- Field of Comparative Biomedical Sciences, Cornell University, Ithaca, New York
| | - Roman Spektor
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
| | - Paul D. Soloway
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
- Field of Comparative Biomedical Sciences, Cornell University, Ithaca, New York
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
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38
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Searle C, Johnson D. Russel-Silver syndrome: A historical note and comment on an older adult. Am J Med Genet A 2015; 170A:466-470. [DOI: 10.1002/ajmg.a.37442] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/03/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Claire Searle
- Clinical Genetics; Nottingham University Hospital; United Kingdom
| | - Diana Johnson
- Clinical Genetics; Sheffield Children's Hospital; United Kingdom
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39
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Arcos-Machancoses JV, Reina PM, Martinez F, Busselo MJ, Perez-Aytes A. Silver-Rusell syndrome caused by epigenetic alteration in a child conceived by intrauterine insemination from donor sperm. Am J Med Genet A 2015; 167A:2861-4. [PMID: 26238787 DOI: 10.1002/ajmg.a.37265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/13/2015] [Indexed: 01/20/2023]
Affiliation(s)
| | | | - Francisco Martinez
- Unidad de Genetica, Hospital Universitari i Politécnic La Fe, Valencia, Spain
| | | | - Antonio Perez-Aytes
- Dismorfologia y Genetica Reproductiva, Grupo de Investigacion en Perinatologia, Instituto de Investigacion Sanitaria Hospital Universitari i Politécnic La Fe, Valencia, Spain
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40
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Kitamura A, Miyauchi N, Hamada H, Hiura H, Chiba H, Okae H, Sato A, John RM, Arima T. Epigenetic alterations in sperm associated with male infertility. Congenit Anom (Kyoto) 2015. [PMID: 26212350 DOI: 10.1111/cga.12113] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The most common form of male infertility is a low sperm count, known as oligozoospermia. Studies suggest that oligozoospermia is associated with epigenetic alterations. Epigenetic alterations in sperm, which may arise due to the exposure of gametes to environmental factors or those that pre-exist in the sperm of infertile individuals, may contribute to the increased incidence of normally rare imprinting disorders in babies conceived after assisted reproductive technology using the sperm of infertile men. Genomic imprinting is an important developmental process whereby the allelic activity of certain genes is regulated by DNA methylation established during gametogenesis. The aberrant expression of several imprinted genes has been linked to various diseases, malignant tumors, lifestyle and mental disorders in humans. Understanding how infertility and environmental factors such as reproductive toxicants, certain foods, and drug exposures during gametogenesis contribute to the origins of these disorders via defects in sperm is of paramount importance. In this review, we discuss the association of epigenetic alterations with abnormal spermatogenesis and the evidence that epigenetic processes, including those required for genomic imprinting, may be sensitive to environmental exposures during gametogenesis, fertilization and early embryonic development. In addition, we review imprinting diseases and their relationships with environmental factors. While the plasticity of epigenetic marks may make these more susceptible to modification by the environment, this also suggests that aberrant epigenetic marks may be reversible. A greater understanding of this process and the function of epidrugs may lead to the development of new treatment methods for many adult diseases in the future.
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Affiliation(s)
- Akane Kitamura
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Naoko Miyauchi
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hirotaka Hamada
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hitoshi Hiura
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hatsune Chiba
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akiko Sato
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
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41
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Anifandis G, Messini CI, Dafopoulos K, Messinis IE. Genes and Conditions Controlling Mammalian Pre- and Post-implantation Embryo Development. Curr Genomics 2015; 16:32-46. [PMID: 25937812 PMCID: PMC4412963 DOI: 10.2174/1389202916666141224205025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/20/2014] [Accepted: 12/23/2014] [Indexed: 01/06/2023] Open
Abstract
Embryo quality during the in vitro developmental period is of great clinical importance. Experimental genetic studies during this period have demonstrated the association between specific gene expression profiles and the production of healthy blastocysts. Although the quality of the oocyte may play a major role in embryo development, it has been well established that the post - fertilization period also has an important and crucial role in the determination of blastocyst quality. A variety of genes (such as OCT, SOX2, NANOG) and their related signaling pathways as well as transcription molecules (such as TGF-β, BMP) have been implicated in the pre- and post-implantation period. Furthermore, DNA methylation has been lately characterized as an epigenetic mark since it is one of the most important processes involved in the maintenance of genome stability. Physiological embryo development appears to depend upon the correct DNA methylation pattern. Due to the fact that soon after fertilization the zygote undergoes several morphogenetic and developmental events including activation of embryonic genome through the transition of the maternal genome, a diverse gene expression pattern may lead to clinically important conditions, such as apoptosis or the production of a chromosomically abnormal embryo. The present review focused on genes and their role during pre-implantation embryo development, giving emphasis on the various parameters that may alter gene expression or DNA methylation patterns. The pre-implantation embryos derived from in vitro culture systems (in vitro fertilization) and the possible effects on gene expression after the prolonged culture conditions are also discussed.
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Affiliation(s)
- G Anifandis
- Department of Obstetrics and Gynaecology ; Embryology Lab, University of Thessalia, School of Health Sciences, Faculty of Medicine, Larisa, Greece
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Abraham MB, Carpenter K, Baynam GS, Mackay DJ, Price G, Choong CS. Report and review of described associations of Mayer-Rokitansky-Küster-Hauser syndrome and Silver-Russell syndrome. J Paediatr Child Health 2015; 51:555-560. [PMID: 25418154 DOI: 10.1111/jpc.12778] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/18/2014] [Indexed: 01/05/2023]
Abstract
Silver-Russell syndrome (SRS) and Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome are described in isolation. However, their co-occurrence has only been rarely reported. Here, we present a case report of an adolescent with SRS who was diagnosed with MRKH during the evaluation of primary amenorrhoea. Multiplex ligation-dependent probe amplification analysis showed a normal methylation pattern and normal dosage at 11p15.5. A PubMed search for all peer-reviewed publications (original articles and reviews) using the key words Silver-Russell syndrome, Mayer-Rokitansky-Küster-Hauser syndrome, genetics, hypomethylation and reproductive anomalies identified three cases of SRS with MRKH, two of which were associated with significant hypomethylation of the H19 imprinting control region of the 11p15.5 locus. This report highlights the association between SRS and MRKH. The absence of hypomethylation and normal dosage at 11p15.5 suggests these two rare entities share alternative aetiopathogenic mechanisms.
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Affiliation(s)
- Mary B Abraham
- Department of Endocrinology and Diabetes, Princess Margaret Hospital for Children, Perth, Western Australia, Australia
| | - Karen Carpenter
- Department of Diagnostic Genomics, PathWest, QEII Medical Centre, Perth, Western Australia, Australia
| | - Gareth S Baynam
- School of Paediatrics and Child Health, The University of Western Australia, Perth, Western Australia, Australia.,Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia.,Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia, Australia
| | - Deborah Jg Mackay
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Glynis Price
- Department of Endocrinology and Diabetes, Princess Margaret Hospital for Children, Perth, Western Australia, Australia
| | - Catherine S Choong
- Department of Endocrinology and Diabetes, Princess Margaret Hospital for Children, Perth, Western Australia, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, Western Australia, Australia
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Eggermann T, Soellner L, Buiting K, Kotzot D. Mosaicism and uniparental disomy in prenatal diagnosis. Trends Mol Med 2015; 21:77-87. [DOI: 10.1016/j.molmed.2014.11.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/18/2014] [Accepted: 11/26/2014] [Indexed: 01/21/2023]
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Genome-wide methylation analysis in Silver-Russell syndrome patients. Hum Genet 2015; 134:317-332. [PMID: 25563730 DOI: 10.1007/s00439-014-1526-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 12/29/2014] [Indexed: 01/09/2023]
Abstract
Silver-Russell syndrome (SRS) is a clinically heterogeneous disorder characterised by severe in utero growth restriction and poor postnatal growth, body asymmetry, irregular craniofacial features and several additional minor malformations. The aetiology of SRS is complex and current evidence strongly implicates imprinted genes. Approximately, half of all patients exhibit DNA hypomethylation at the H19/IGF2 imprinted domain, and around 10% have maternal uniparental disomy of chromosome 7. We measured DNA methylation in 18 SRS patients at >485,000 CpG sites using DNA methylation microarrays. Using a novel bioinformatics methodology specifically designed to identify subsets of patients with a shared epimutation, we analysed methylation changes genome-wide as well as at known imprinted regions to identify SRS-associated epimutations. Our analysis identifies epimutations at the previously characterised domains of H19/IGF2 and at imprinted regions on chromosome 7, providing proof of principle that our methodology can detect DNA methylation changes at imprinted loci. In addition, we discovered two novel epimutations associated with SRS and located at imprinted loci previously linked to relevant mouse and human phenotypes. We identify RB1 as an additional imprinted locus associated with SRS, with a region near the RB1 differentially methylated region hypermethylated in 13/18 (~70%) patients. We also report 6/18 (~33%) patients were hypermethylated at a CpG island near the ANKRD11 gene. We do not observe consistent co-occurrence of epimutations at multiple imprinted loci in single SRS individuals. SRS is clinically heterogeneous and the absence of multiple imprinted loci epimutations reflects the heterogeneity at the molecular level. Further stratification of SRS patients by molecular phenotypes might aid the identification of disease causes.
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Kagami M, Mizuno S, Matsubara K, Nakabayashi K, Sano S, Fuke T, Fukami M, Ogata T. Epimutations of the IG-DMR and the MEG3-DMR at the 14q32.2 imprinted region in two patients with Silver-Russell Syndrome-compatible phenotype. Eur J Hum Genet 2014; 23:1062-7. [PMID: 25351781 PMCID: PMC4795120 DOI: 10.1038/ejhg.2014.234] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/16/2014] [Accepted: 09/19/2014] [Indexed: 01/05/2023] Open
Abstract
Maternal uniparental disomy 14 (UPD(14)mat) and related (epi)genetic aberrations affecting the 14q32.2 imprinted region result in a clinically recognizable condition which is recently referred to as Temple Syndrome (TS). Phenotypic features in TS include pre- and post-natal growth failure, prominent forehead, and feeding difficulties that are also found in Silver–Russell Syndrome (SRS). Thus, we examined the relevance of UPD(14)mat and related (epi)genetic aberrations to the development of SRS in 85 Japanese patients who satisfied the SRS diagnostic criteria proposed by Netchine et al and had neither epimutation of the H19-DMR nor maternal uniparental disomy 7. Pyrosequencing identified hypomethylation of the DLK1-MEG3 intergenic differentially methylated region (IG-DMR) and the MEG3-DMR in two cases. In both cases, microsatellite analysis showed biparental transmission of the homologs of chromosome 14, with no evidence for somatic mosaicism with full or segmental maternal isodisomy involving the imprinted region. FISH and array comparative genomic hybridization revealed neither deletion of the two DMRs nor discernible copy number alteration in the 14q32.2 imprinted region. Methylation patterns were apparently normal in other six disease-associated DMRs. In addition, a thorough literature review revealed a considerable degree of phenotypic overlap between SRS and TS, although body asymmetry was apparently characteristic of SRS. The results indicate the occurrence of epimutation affecting the IG-DMR and the MEG3-DMR in the two cases, and imply that UPD(14)mat and related (epi)genetic aberrations constitute a rare but important underlying factor for SRS.
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Affiliation(s)
- Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Aichi, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shinichiro Sano
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko Fuke
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- 1] Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan [2] Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
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Shin HS, Seo JH, Jeong SH, Park SW, Park Y, Son SW, Kim JS, Kang HG. Exposure of pregnant mice to chlorpyrifos-methyl alters embryonic H19 gene methylation patterns. ENVIRONMENTAL TOXICOLOGY 2014; 29:926-935. [PMID: 23125134 DOI: 10.1002/tox.21820] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 09/11/2012] [Accepted: 09/23/2012] [Indexed: 06/01/2023]
Abstract
The aim of this study was to identify whether chlorpyrifos methyl (CPM) exposure during pregnancy leads to changes in the methylation patterns of H19 gene. CPM 4, 20, 100 mg/kg bw/day was administered to 4 pregnant mice per group between 7 and 12 days post coitum (d.p.c.). Pregnant mice were killed at 13 d.p.c. The genomic methylation in primordial germ cells (PGCs) and fetal organs (the liver, intestine, and placenta) was examined. Four polymorphism sites in the H19 alleles of maternal (C57BL/6J) and paternal (CAST/Ei) alleles were identified at nucleotide position 1407, 1485, 1566, and 1654. The methylation patterns of 17 CpG sites were analyzed. The methylation level in male and female PGCs was not altered by CPM treatment in the maternal allele H19. The methylation level of the paternal H19 allele was altered in only male PGCs in response to the CPM treatment. The methylation level at a binding site for the transcriptional regulator CTCF2 was higher than that at the CTCF1 binding site in all CPM-treated groups. In the placenta, the aggregate methylation level of H19 was 56.89%in control group. But, those levels were ranged from 47.7% to 49.89% after treatment with increasing doses of CPM. H19 gene from the liver and intestine of 13 d.p.c. fetuses treated with CPM was hypomethylated as compared with controls, although H19 mRNA expression was unaltered. In the placenta, H19 expression was slightly increased in the CPM-treated group, although not significantly. IGF2 expression levels were not significantly changed in the placenta. In conclusion, CPM exposure during pregnancy alters the methylation status of the H19 gene in PGCs and embryonic tissues. We infer that these alterations are likely related to changes in DNA demethylase activity.
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Affiliation(s)
- Hyo-Sook Shin
- Toxicology & Residue Chemistry Division, Animal, Plant and Fisheries Quarantine and Inspection Agency, 175 Anyangro, Anyang-si, Gyeonggi-do 430-757, Republic of Korea
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Hiura H, Okae H, Chiba H, Miyauchi N, Sato F, Sato A, Arima T. Imprinting methylation errors in ART. Reprod Med Biol 2014; 13:193-202. [PMID: 25298744 PMCID: PMC4182590 DOI: 10.1007/s12522-014-0183-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 05/19/2014] [Indexed: 02/04/2023] Open
Abstract
There has been an increase in incidence reports of rare imprinting disorders associated with assisted reproductive technology (ART). ART, including in vitro fertilization and intracytoplasmic sperm injections, is an important treatment for infertile people of reproductive age and increasingly produces children. The identification of epigenetic changes at imprinted loci in ART infants has led to the suggestion that ART techniques themselves may predispose embryos to acquire imprinting errors and diseases. In this review, we note that the particular steps of ART may be prone to induction of imprinting methylation errors during gametogenesis, fertilization and early embryonic development. In addition, we explain imprint-associated diseases and their causes. Moreover, from a Japanese nationwide epidemiological study of imprint-associated diseases, we determine their associations with ART. Epigenetic studies will be required to understand the pathogenesis, ART-related risk factor(s) and what precautions can be taken to prevent the occurrence of input methylation errors. We hope that the constitution of children born after each ART procedure will reveal the safest and most ethical approach to use, which will be invaluable for the future development of standard ART.
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Affiliation(s)
- Hitoshi Hiura
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575 Japan
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575 Japan
| | - Hatsune Chiba
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575 Japan
| | - Naoko Miyauchi
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575 Japan
| | - Fumi Sato
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575 Japan
| | - Akiko Sato
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575 Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575 Japan
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Abstract
Over the past few years, advances in genome analyses have identified an emerging class of noncoding RNAs that play critical roles in the regulation of gene expression and epigenetic reprogramming. Given their transcriptional pervasiveness, the potential for these intriguing macromolecules to integrate a myriad of external cellular cues with nuclear responses has become increasingly apparent. Recent studies have implicated noncoding RNAs in epidermal development and keratinocyte differentiation, but the complexity of multilevel regulation of transcriptional programs involved in these processes remains ill defined. In this review, we discuss the relevance of noncoding RNA in normal skin development, their involvement in cutaneous malignancies, and their role in the regulation of adult stem-cell maintenance in stratified epithelial tissues. Furthermore, we provide additional examples highlighting the ubiquity of noncoding RNAs in diverse human diseases.
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Tragante V, Barnes MR, Ganesh SK, Lanktree MB, Guo W, Franceschini N, Smith EN, Johnson T, Holmes MV, Padmanabhan S, Karczewski KJ, Almoguera B, Barnard J, Baumert J, Chang YPC, Elbers CC, Farrall M, Fischer ME, Gaunt TR, Gho JMIH, Gieger C, Goel A, Gong Y, Isaacs A, Kleber ME, Mateo Leach I, McDonough CW, Meijs MFL, Melander O, Nelson CP, Nolte IM, Pankratz N, Price TS, Shaffer J, Shah S, Tomaszewski M, van der Most PJ, Van Iperen EPA, Vonk JM, Witkowska K, Wong COL, Zhang L, Beitelshees AL, Berenson GS, Bhatt DL, Brown M, Burt A, Cooper-DeHoff RM, Connell JM, Cruickshanks KJ, Curtis SP, Davey-Smith G, Delles C, Gansevoort RT, Guo X, Haiqing S, Hastie CE, Hofker MH, Hovingh GK, Kim DS, Kirkland SA, Klein BE, Klein R, Li YR, Maiwald S, Newton-Cheh C, O'Brien ET, Onland-Moret NC, Palmas W, Parsa A, Penninx BW, Pettinger M, Vasan RS, Ranchalis JE, M Ridker P, Rose LM, Sever P, Shimbo D, Steele L, Stolk RP, Thorand B, Trip MD, van Duijn CM, Verschuren WM, Wijmenga C, Wyatt S, Young JH, Zwinderman AH, Bezzina CR, Boerwinkle E, Casas JP, Caulfield MJ, Chakravarti A, Chasman DI, Davidson KW, Doevendans PA, Dominiczak AF, FitzGerald GA, Gums JG, Fornage M, Hakonarson H, Halder I, Hillege HL, Illig T, Jarvik GP, Johnson JA, Kastelein JJP, Koenig W, Kumari M, März W, Murray SS, O'Connell JR, Oldehinkel AJ, Pankow JS, Rader DJ, Redline S, Reilly MP, Schadt EE, Kottke-Marchant K, Snieder H, Snyder M, Stanton AV, Tobin MD, Uitterlinden AG, van der Harst P, van der Schouw YT, Samani NJ, Watkins H, Johnson AD, Reiner AP, Zhu X, de Bakker PIW, Levy D, Asselbergs FW, Munroe PB, Keating BJ. Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci. Am J Hum Genet 2014; 94:349-60. [PMID: 24560520 DOI: 10.1016/j.ajhg.2013.12.016] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 12/20/2013] [Indexed: 11/29/2022] Open
Abstract
Blood pressure (BP) is a heritable risk factor for cardiovascular disease. To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP), we genotyped ~50,000 SNPs in up to 87,736 individuals of European ancestry and combined these in a meta-analysis. We replicated findings in an independent set of 68,368 individuals of European ancestry. Our analyses identified 11 previously undescribed associations in independent loci containing 31 genes including PDE1A, HLA-DQB1, CDK6, PRKAG2, VCL, H19, NUCB2, RELA, HOXC@ complex, FBN1, and NFAT5 at the Bonferroni-corrected array-wide significance threshold (p < 6 × 10(-7)) and confirmed 27 previously reported associations. Bioinformatic analysis of the 11 loci provided support for a putative role in hypertension of several genes, such as CDK6 and NUCB2. Analysis of potential pharmacological targets in databases of small molecules showed that ten of the genes are predicted to be a target for small molecules. In summary, we identified previously unknown loci associated with BP. Our findings extend our understanding of genes involved in BP regulation, which may provide new targets for therapeutic intervention or drug response stratification.
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Affiliation(s)
- Vinicius Tragante
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Department of Medical Genetics, Biomedical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Michael R Barnes
- William Harvey Research Institute National Institute for Health Biomedical Research Unit, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Santhi K Ganesh
- Division of Cardiovascular Medicine, Departments of Internal Medicine and Human Genetics, University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Matthew B Lanktree
- Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Wei Guo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Erin N Smith
- Department of Pediatrics and Rady's Children's Hospital, University of California at San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Toby Johnson
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Michael V Holmes
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sandosh Padmanabhan
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Konrad J Karczewski
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Berta Almoguera
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John Barnard
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jens Baumert
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Yen-Pei Christy Chang
- Departments of Medicine and Epidemiology & Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Clara C Elbers
- Department of Medical Genetics, Biomedical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Martin Farrall
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Mary E Fischer
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53726, USA
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Johannes M I H Gho
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Anuj Goel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Yan Gong
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Aaron Isaacs
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Marcus E Kleber
- Medical Clinic V, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Irene Mateo Leach
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Caitrin W McDonough
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Matthijs F L Meijs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Olle Melander
- Hypertension and Cardiovascular Disease, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden; Centre of Emergency Medicine, Skåne University Hospital, Malmö 20502, Sweden
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK; NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Groby Road, Leicester LE3 9QP, UK
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Nathan Pankratz
- Institute of Human Genetics, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tom S Price
- MRC SGDP Centre, Institute of Psychiatry, London SE5 8AF, UK
| | - Jonathan Shaffer
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Sonia Shah
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Kathleen Lonsdale Building, Gower Place, London WC1E 6BT, UK
| | - Maciej Tomaszewski
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Erik P A Van Iperen
- Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, 3511 GC Utrecht, the Netherlands; Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Kate Witkowska
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Caroline O L Wong
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Li Zhang
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Amber L Beitelshees
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Gerald S Berenson
- Department of Epidemiology, Tulane University, New Orleans, LA 70118, USA
| | - Deepak L Bhatt
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Morris Brown
- Clinical Pharmacology Unit, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Amber Burt
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA 98195, USA
| | - Rhonda M Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - John M Connell
- University of Dundee, Ninewells Hospital &Medical School, Dundee DD1 9SY, UK
| | - Karen J Cruickshanks
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53726, USA; Department of Population Health Sciences, University of Wisconsin, Madison, WI 53726, USA
| | - Sean P Curtis
- Merck Research Laboratories, P.O. Box 2000, Rahway, NJ 07065, USA
| | - George Davey-Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Ron T Gansevoort
- Division of Nephrology, Department of Medicine, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Xiuqing Guo
- Cedars-Sinai Med Ctr-PEDS, Los Angeles, CA 90048, USA
| | - Shen Haiqing
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Claire E Hastie
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Marten H Hofker
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Department Pathology and Medical Biology, Medical Biology Division, Molecular Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - G Kees Hovingh
- Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Daniel S Kim
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Susan A Kirkland
- Department of Community Health and Epidemiology, Dalhousie University, Halifax, NS B3H 1V7, Canada
| | - Barbara E Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53726, USA
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53726, USA
| | - Yun R Li
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Steffi Maiwald
- Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | | | - Eoin T O'Brien
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - N Charlotte Onland-Moret
- Department of Medical Genetics, Biomedical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Walter Palmas
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Afshin Parsa
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Brenda W Penninx
- Department of Psychiatry/EMGO Institute, VU University Medical Centre, 1081 BT Amsterdam, the Netherlands
| | - Mary Pettinger
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ramachandran S Vasan
- Department of Medicine, Boston University School of Medicine, Framingham, MA 02118, USA
| | - Jane E Ranchalis
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA 98195, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Peter Sever
- International Centre for Circulatory Health, Imperial College London, W2 1LA UK
| | - Daichi Shimbo
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Laura Steele
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronald P Stolk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Barbara Thorand
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Mieke D Trip
- Department of Cardiology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, 3015 GE Rotterdam, the Netherlands
| | - W Monique Verschuren
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Sharon Wyatt
- Schools of Nursing and Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - J Hunter Young
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Connie R Bezzina
- Heart Failure Research Center, Department of Clinical and Experimental Cardiology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands; Molecular and Experimental Cardiology Group, Academic Medical Centre, 1105 AZ Amsterdam, the Netherlands
| | - Eric Boerwinkle
- Human Genetics Center and Institute of Molecular Medicine and Division of Epidemiology, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Juan P Casas
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; Genetic Epidemiology Group, Department of Epidemiology and Public Health, University College London, London WC1E 6BT, UK
| | - Mark J Caulfield
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Karina W Davidson
- Departments of Medicine & Psychiatry, Columbia University, New York, NY 10032, USA
| | - Pieter A Doevendans
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Anna F Dominiczak
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Garret A FitzGerald
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John G Gums
- Departments of Pharmacotherapy and Translational Research and Community Health and Family Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Myriam Fornage
- Institute of Molecular Medicine and School of Public Health Division of Epidemiology Human Genetics and Environmental Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Indrani Halder
- School of Medicine, University of Pittsburgh, PA 15261, USA
| | - Hans L Hillege
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Hannover Unified Biobank, Hannover Medical School, Hannover 30625, Germany
| | - Gail P Jarvik
- International Centre for Circulatory Health, Imperial College London, W2 1LA UK
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - John J P Kastelein
- Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Wolfgang Koenig
- Department of Internal Medicine II - Cardiology, University of Ulm Medical Centre, Ulm 89081, Germany
| | - Meena Kumari
- Department of Epidemiology and Public Health, Division of Population Health, University College London, Torrington Place, London WC1E 7HB, UK
| | - Winfried März
- Medical Clinic V, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany; Synlab Academy, Synlab Services GmbH, Mannheim 69214, Germany; Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz 8036, Austria
| | - Sarah S Murray
- Department of Pathology, University of California San Diego, La Jolla, CA 92037, USA
| | - Jeffery R O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - James S Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN 55454, USA
| | - Daniel J Rader
- Cardiovascular Institute, the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Muredach P Reilly
- Cardiovascular Institute, the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | | | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alice V Stanton
- Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, 123 St Stephens Green, Dublin 2, Ireland
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - André G Uitterlinden
- Departments of Epidemiology and Internal Medicine, Erasmus Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands; Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, 3511 GC Utrecht, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Yvonne T van der Schouw
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK; NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Groby Road, Leicester LE3 9QP, UK
| | - Hugh Watkins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute Framingham Heart Study, Framingham, MA 01702, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Paul I W de Bakker
- Department of Medical Genetics, Biomedical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA and Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Levy
- Center for Population Studies, National Heart, Lung, and Blood Institute, Framingham, MA 01702, USA
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, 3511 GC Utrecht, the Netherlands; Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London WC1E 6BT, UK
| | - Patricia B Munroe
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.
| | - Brendan J Keating
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Girardot M, Feil R, Llères D. Epigenetic deregulation of genomic imprinting in humans: causal mechanisms and clinical implications. Epigenomics 2013; 5:715-28. [DOI: 10.2217/epi.13.66] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mammalian genes controlled by genomic imprinting play important roles in development and diverse postnatal processes. A growing number of congenital disorders have been linked to genomic imprinting. Each of these is caused by perturbed gene expression at one principal imprinted domain. Some imprinting disorders, including the Prader–Willi and Angelman syndromes, are caused almost exclusively by genetic mutations. In several others, including the Beckwith–Wiedemann and Silver–Russell growth syndromes, and transient neonatal diabetes mellitus, imprinted expression is perturbed mostly by epigenetic alterations at ‘imprinting control regions’ and at other specific regulatory sequences. In a minority of these patients, DNA methylation is altered at multiple imprinted loci, suggesting that common trans-acting factors are affected. Here, we review the epimutations involved in congenital imprinting disorders and the associated clinical features. Trans-acting factors known to be causally involved are discussed and other trans-acting factors that are potentially implicated are also presented.
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Affiliation(s)
- Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
- Universities of Montpellier I & II, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
| | - David Llères
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
- Universities of Montpellier I & II, Montpellier, France
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