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Mangiavacchi PM, Caldas-Bussiere MC, Mendonça MDS, Rumpf R, Lemos Júnior PES, Alves CS, Carneiro WDS, Dias AJB, Rios ÁFL. Multi-locus DNA methylation analysis of imprinted genes in cattle from somatic cell nuclear transfer. Theriogenology 2022; 186:95-107. [DOI: 10.1016/j.theriogenology.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 10/18/2022]
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Shen Z, Tang Y, Song Y, Shen W, Zou C. Differences of DNA methylation patterns in the placenta of large for gestational age infant. Medicine (Baltimore) 2020; 99:e22389. [PMID: 32991460 PMCID: PMC7523834 DOI: 10.1097/md.0000000000022389] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
To investigate the molecular mechanisms of later metabolic health changes in large for gestational age (LGA) newborns by analyzing deoxyribonucleic acid (DNA) methylation patterns in the placenta of LGA and appropriate for gestational age (AGA) newborns.A total of 6 placentas of LGA and 6 placentas of AGA newborns were enrolled as LGA group and AGA group. DNA methylation was analyzed using the Illumina Infinium Human MethylationEPIC BeadChip microarrays and verified via pyrosequencing and reverse transcription-quantitative real-time polymerase chain reaction. Functional enrichment analysis were constructed by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis based on the differentially methylated regions between LGA and AGA groups.Clinical investigation showed that LGA newborns had significantly lower hemoglobin and blood glucose compared to AGA newborns. Birth weight was negatively correlated to hemoglobin and blood glucose. Genome-wide DNA methylation analysis identified 17 244 methylation variable positions achieving genome-wide significance (adjusted P < .05). 34% methylation variable positions were located in the gene promoter region. A total of 117 differentially methylated regions were revealed by bump hunting analysis, which mapped to 107 genes. Function analysis showed 13 genes enriched in "adhesion and infection process, endocrine and other factor-regulated calcium reabsorption, calcium signaling pathway and transmembrane transport". Four genes linked to type II diabetes mellitus. Among the 13 genes, we selected GNAS and calcium voltage-gated channel subunit alpha1 G for independent verification of pyrosequencing, and the messenger ribonucleic acid levels of guanine nucleotide binding protein, calcium voltage-gated channel subunit alpha1 G, DECR1, and FK506 binding protein 11 were verified by reverse transcription-quantitative real-time polymerase chain reaction.DNA methylation variation and gene expression differences in placental samples were associated with LGA newborns, which linking the effect of intrauterine environment to regulation of the offspring's gene expression. Furthermore, pathway analysis suggested that intrauterine environment affecting fetal growth might had a functional impact on multiple signaling pathways involved in fetal growth, metabolism, and inflammation. Further studies were required to understand the differences of methylation patterns.
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Affiliation(s)
- Zheng Shen
- Department of Clinical laboratory, Zhejiang University School of Medicine Children's Hospital
- National Clinical Research Center for Child Health
| | - Yanfei Tang
- Department of Endocrinology, Zhejiang University School of Medicine Children's Hospital
- Second Hospital of Jiaxing
| | - Yemei Song
- Department of Endocrinology, Zhejiang University School of Medicine Children's Hospital
- Huzhou Central Hospital
| | - Wenxia Shen
- Department of Endocrinology, Zhejiang University School of Medicine Children's Hospital
- Women and Children's Hospital of Shaoxin
| | - Chaochun Zou
- National Clinical Research Center for Child Health
- Department of Endocrinology, Zhejiang University School of Medicine Children's Hospital
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Miranda Furtado CL, Salomão KB, Verruma CG, Paulino Leite SB, Lopes Rios ÁF, Bialecka M, Moustakas I, Mei H, de Paz CCP, Duarte G, Chuva de Sousa Lopes SM, Ramos ES. Variation in DNA methylation in the KvDMR1 (ICR2) region in first-trimester human pregnancies. Fertil Steril 2019; 111:1186-1193. [PMID: 30922639 DOI: 10.1016/j.fertnstert.2019.01.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To investigate the levels of DNA methylation in the KvDMR1 (KvLQT1 differentially methylated region 1) in embryonic and extra-embryonic tissues. DESIGN Cross-sectional study. SETTING University medical center and clinical hospital. PATIENT(S) Embryonic and/or extraembryonic tissues (umbilical cord, chorionic villus, chorion, decidua, and/or amnion) collected from 27 first-trimester pregnancies (up to 12 weeks of gestation, single embryos) from elective abortions, extravillous trophoblasts (EVTs) from the top of individual chorionic villi, and chorionic villi from 10 normal full-term placentas collected after birth. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) DNA methylation of the KvDMR1 region evaluated using quantitative analysis of DNA methylation followed by real-time polymerase chain reaction (qAMP) and bisulfite sequencing (bis-seq) analysis. RESULT(S) The results showed variability in KvDMR1 DNA methylation in different tissues from the same pregnancy. The average of DNA methylation was not different between the embryo, umbilical cord, amnion, and chorionic villi, despite the relatively low level of methylation observed in the amnion (33.50% ± 14.48%). Chorionic villi from term placentas showed a normal methylation pattern at KvDMR1 (42.60% ± 6.08%). The normal methylation pattern at KvDMR1 in chorionic villi (as well as in EVTs) from first-trimester placentas was confirmed by bis-seq. CONCLUSION(S) Our results highlight an existing heterogeneity in DNA methylation of the KvDMR1 region during first trimester and a consistent hypomethylation in the amnion in this period of gestation.
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Affiliation(s)
- Cristiana Libardi Miranda Furtado
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil; Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands; Department of Gynecology and Obstetrics, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - Karina Bezerra Salomão
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Carolina Gennari Verruma
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Álvaro Fabrício Lopes Rios
- Biotechnology Laboratory, Center of Bioscience and Biotechnology, State University of North Fluminense Darcy Ribeiro, Campos dos Goitacazes, Rio de Janeiro, Brazil
| | - Monika Bialecka
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ioannis Moustakas
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands; Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Claudia Cristina Paro de Paz
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil; Instituto de Zootecnia, Centro APTA de Bovinos de Corte, São Paulo, Brazil
| | - Geraldo Duarte
- Department of Gynecology and Obstetrics, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Ester Silveira Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil.
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Mackay DJ, Bliek J, Lombardi MP, Russo S, Calzari L, Guzzetti S, Izzi C, Selicorni A, Melis D, Temple K, Maher E, Brioude F, Netchine I, Eggermann T. Discrepant molecular and clinical diagnoses in Beckwith-Wiedemann and Silver-Russell syndromes. Genet Res (Camb) 2019; 101:e3. [PMID: 30829192 PMCID: PMC7044970 DOI: 10.1017/s001667231900003x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/22/2019] [Indexed: 12/19/2022] Open
Abstract
Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS) are two imprinting disorders associated with opposite molecular alterations in the 11p15.5 imprinting centres. Their clinical diagnosis is confirmed by molecular testing in 50-70% of patients. The authors from different reference centres for BWS and SRS have identified single patients with unexpected and even contradictory molecular findings in respect to the clinical diagnosis. These patients clinically do not fit the characteristic phenotypes of SRS or BWS, but illustrate their clinical heterogeneity. Thus, comprehensive molecular testing is essential for accurate diagnosis and appropriate management, to avoid premature clinical diagnosis and anxiety for the families.
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Affiliation(s)
- Deborah J.G. Mackay
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK and Wessex Regional Genetics Laboratory, Salisbury SP2 8BJ, UK
| | - Jet Bliek
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Maria Paola Lombardi
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Silvia Russo
- Medical Cytogenetics and Molecular Genetics Laboratory, Centro di Ricerche e Tecnologie Biomediche IRCCS, Istituto Auxologico Italiano, Milan, Italy
| | - Luciano Calzari
- Medical Cytogenetics and Molecular Genetics Laboratory, Centro di Ricerche e Tecnologie Biomediche IRCCS, Istituto Auxologico Italiano, Milan, Italy
| | - Sara Guzzetti
- Medical Cytogenetics and Molecular Genetics Laboratory, Centro di Ricerche e Tecnologie Biomediche IRCCS, Istituto Auxologico Italiano, Milan, Italy
| | - Claudia Izzi
- Prenatal Diagnosis Unit, Department of Obstetrics and Gynecology, ASST Spedali Civili of Brescia, Brescia, Italy
| | | | - Daniela Melis
- Department of Pediatrics, University “Federico II”, Napoli, Italy
| | - Karen Temple
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK and Wessex Regional Genetics Laboratory, Salisbury SP2 8BJ, UK
| | - Eamonn Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Frédéric Brioude
- Sorbonne Université, INSERM, UMR 938, Centre de Recherche Saint-Antoine (CRSA), APHP Hôpital Trousseau, 75012 Paris, France
| | - Irène Netchine
- Sorbonne Université, INSERM, UMR 938, Centre de Recherche Saint-Antoine (CRSA), APHP Hôpital Trousseau, 75012 Paris, France
| | - Thomas Eggermann
- Institute of Human Genetics, University Hospital, Technical University of Aachen, Aachen, Germany
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Beaufrère A, Bonnière M, Tantau J, Roth P, Schaerer E, Brioude F, Netchine I, Bessières B, Gelot A, Vekemans M, Razavi F, Heron D, Attié-Bitach T. Corpus Callosum Abnormalities and Short Femurs in Beckwith-Wiedemann Syndrome: A Report of Two Fetal Cases. Fetal Pediatr Pathol 2018; 37:411-417. [PMID: 30595068 DOI: 10.1080/15513815.2018.1520942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Beckwith-Wiedemann syndrome (BWS) is the most common overgrowth syndrome. Clinical features are highly variable, including occasional posterior fossa malformations but no femoral shortening. CASE REPORT We report two fetuses with BWS associated with short femurs and corpus callosum hypoplasia. Case 2 was growth restricted. BWS was confirmed by molecular studies showing a loss of methylation at ICR2 at 11p15 chromosomic region in case 1 and a gain of methylation at ICR1 and a loss of methylation at ICR2 locus in case 2. CONCLUSION Although the phenotype and the genotype of BWS is now well-known, the presence of corpus callosum abnormalities and short femurs expand the phenotypic spectrum of the disorder.
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Affiliation(s)
- Aurélie Beaufrère
- a Unité d'Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP , Paris , France
| | - Maryse Bonnière
- a Unité d'Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP , Paris , France
| | - Julia Tantau
- b Département de Génétique Médicale , Hôpital Trousseau, APHP , Paris , France
| | - Philippe Roth
- c Service de Gynécologie-Obstétrique , Hôpital Necker-Enfants Malades, APHP , Paris , France
| | - Elodie Schaerer
- b Département de Génétique Médicale , Hôpital Trousseau, APHP , Paris , France
| | - Fréderic Brioude
- d Service d'Explorations Fonctionnelles Endocriniennes , Hôpital Trousseau, APHP , Paris , France
| | - Irène Netchine
- d Service d'Explorations Fonctionnelles Endocriniennes , Hôpital Trousseau, APHP , Paris , France
| | - Bettina Bessières
- a Unité d'Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP , Paris , France
| | - Antoinette Gelot
- e Service d'Anatomie et Cytologie Pathologiques , Hôpital Trousseau, APHP , Paris , France
| | - Michel Vekemans
- a Unité d'Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP , Paris , France
| | - Ferechté Razavi
- a Unité d'Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP , Paris , France
| | - Delphine Heron
- b Département de Génétique Médicale , Hôpital Trousseau, APHP , Paris , France
| | - Tania Attié-Bitach
- a Unité d'Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP , Paris , France.,f INSERM U1163, Institut Imagine , Université Paris Descartes , Paris , France
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Ishida M. New developments in Silver-Russell syndrome and implications for clinical practice. Epigenomics 2016; 8:563-80. [PMID: 27066913 DOI: 10.2217/epi-2015-0010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Silver-Russell syndrome is a clinically and genetically heterogeneous disorder, characterized by prenatal and postnatal growth restriction, relative macrocephaly, body asymmetry and characteristic facial features. It is one of the imprinting disorders, which results as a consequence of aberrant imprinted gene expressions. Currently, maternal uniparental disomy of chromosome 7 accounts for approximately 10% of Silver-Russell syndrome cases, while ~50% of patients have hypomethylation at imprinting control region 1 at chromosome 11p15.5 locus, leaving ~40% of cases with unknown etiologies. This review aims to provide a comprehensive list of molecular defects in Silver-Russell syndrome reported to date and to highlight the importance of multiple-loci/tissue testing and trio (both parents and proband) screening. The epigenetic and phenotypic overlaps with other imprinting disorders will also be discussed.
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Affiliation(s)
- Miho Ishida
- University College London, Institute of Child Health, Genetics & Genomic Medicine programme, Genetics & Epigenetics in Health & Diseases Section, 30 Guilford Street, London, WC1N 1EH, UK
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Murphy R, Thompson JM, Tost J, Mitchell EA. No evidence for copy number and methylation variation in H19 and KCNQ10T1 imprinting control regions in children born small for gestational age. BMC MEDICAL GENETICS 2014; 15:67. [PMID: 24934635 PMCID: PMC4089969 DOI: 10.1186/1471-2350-15-67] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/11/2014] [Indexed: 11/24/2022]
Abstract
Background There is a substantial genetic component for birthweight variation, and although there are known associations between fetal genotype and birthweight, the role of common epigenetic variation in influencing the risk for small for gestational age (SGA) is unknown. The two imprinting control regions (ICRs) located on chromosome 11p15.5, involved in the overgrowth disorder Beckwith-Wiedemann syndrome (BWS) and the growth restriction disorder Silver-Russell syndrome (SRS), are prime epigenetic candidates for regulating fetal growth. We investigated whether common variation in copy number in the BWS/SRS 11p15 region or altered methylation levels at IGF2/H19 ICR or KCNQ10T1 ICR was associated with SGA. Methods We used a methylation-specific multiplex-ligation-dependent probe amplification assay to analyse copy number variation in the 11p15 region and methylation of IGF2/H19 and KCNQ10T1 ICRs in blood samples from 153 children (including 80 SGA), as well as bisulfite pyrosequencing to measure methylation at IGF2 differentially methylated region (DMR)0 and H19 DMR. Results No copy number variants were detected in the analyzed cohort. Children born SGA had 2.7% lower methylation at the IGF2 DMR0. No methylation differences were detected at the H19 or KCNQ10T1 DMRs. Conclusions We confirm that a small hypomethylation of the IGF2 DMR0 is detected in peripheral blood leucocytes of children born SGA at term. Copy number variation within the 11p15 BWS/SRS region is not an important cause of non-syndromic SGA at term.
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Affiliation(s)
- Rinki Murphy
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
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Poole RL, Docherty LE, Al Sayegh A, Caliebe A, Turner C, Baple E, Wakeling E, Harrison L, Lehmann A, Temple IK, Mackay DJG. Targeted methylation testing of a patient cohort broadens the epigenetic and clinical description of imprinting disorders. Am J Med Genet A 2013; 161A:2174-82. [PMID: 23913548 DOI: 10.1002/ajmg.a.36049] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 03/13/2013] [Indexed: 11/11/2022]
Abstract
Imprinting disorders are associated with mutations and epimutations affecting imprinted genes, that is those whose expression is restricted by parent of origin. Their diagnosis is challenging for two reasons: firstly, their clinical features, particularly prenatal and postnatal growth disturbance, are heterogeneous and partially overlapping; secondly, their underlying molecular defects include mutation, epimutation, copy number variation, and chromosomal errors, and can be further complicated by somatic mosaicism and multi-locus methylation defects. It is currently unclear to what extent the observed phenotypic heterogeneity reflects the underlying molecular pathophysiology; in particular, the molecular and clinical diversity of multilocus methylation defects remains uncertain. To address these issues we performed comprehensive methylation analysis of imprinted genes in a research cohort of 285 patients with clinical features of imprinting disorders, with or without a positive molecular diagnosis. 20 of 91 patients (22%) with diagnosed epimutations had methylation defects of additional imprinted loci, and the frequency of developmental delay and congenital anomalies was higher among these patients than those with isolated epimutations, indicating that hypomethylation of multiple imprinted loci is associated with increased diversity of clinical presentation. Among 194 patients with clinical features of an imprinting disorder but no molecular diagnosis, we found 15 (8%) with methylation anomalies, including missed and unexpected molecular diagnoses. These observations broaden the phenotypic and epigenetic definitions of imprinting disorders, and show the importance of comprehensive molecular testing for patient diagnosis and management.
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Affiliation(s)
- Rebecca L Poole
- Faculty of Medicine, University of Southampton, Southampton, UK
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