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Carvalho LML, Jorge AADL, Bertola DR, Krepischi ACV, Rosenberg C. A Comprehensive Review of Syndromic Forms of Obesity: Genetic Etiology, Clinical Features and Molecular Diagnosis. Curr Obes Rep 2024; 13:313-337. [PMID: 38277088 DOI: 10.1007/s13679-023-00543-y] [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] [Accepted: 11/08/2023] [Indexed: 01/27/2024]
Abstract
Syndromic obesity refers to obesity occurring with additional clinical findings, such as intellectual disability/developmental delay, dysmorphic features, and congenital malformations. PURPOSE OF REVIEW: To present a narrative review regarding the genetic etiology, clinical description, and molecular diagnosis of syndromic obesity, which is a rare condition with high phenotypic variability and genetic heterogeneity. The following syndromes are presented in this review: Prader-Willi, Bardet-Biedl, Pseudohypoparathyroidism, Alström, Smith-Magenis, Cohen, Temple, 1p36 deletion, 16p11.2 microdeletion, Kleefstra, SIM1-related, Börjeson-Forssman-Lehmann, WAGRO, Carpenter, MORM, and MYT1L-related syndromes. RECENT FINDINGS: There are three main groups of mechanisms for syndromic obesity: imprinting, transcriptional activity regulation, and cellular cilia function. For molecular diagnostic, methods of genome-wide investigation should be prioritized over sequencing of panels of syndromic obesity genes. In addition, we present novel syndromic conditions that need further delineation, but evidences suggest they have a higher frequency of obesity. The etiology of syndromic obesity tends to be linked to disrupted neurodevelopment (central) and is associated with a diversity of genes and biological pathways. In the genetic investigation of individuals with syndromic obesity, the possibility that the etiology of the syndromic condition is independent of obesity should be considered. The accurate genetic diagnosis impacts medical management, treatment, and prognosis, and allows proper genetic counseling.
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Affiliation(s)
- Laura Machado Lara Carvalho
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
| | - Alexander Augusto de Lima Jorge
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory (LIM/25), Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Débora Romeo Bertola
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
- Genetics Unit of Instituto da Criança, Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
| | - Carla Rosenberg
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil.
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2
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Eggermann T, Monk D, de Nanclares GP, Kagami M, Giabicani E, Riccio A, Tümer Z, Kalish JM, Tauber M, Duis J, Weksberg R, Maher ER, Begemann M, Elbracht M. Imprinting disorders. Nat Rev Dis Primers 2023; 9:33. [PMID: 37386011 DOI: 10.1038/s41572-023-00443-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 07/01/2023]
Abstract
Imprinting disorders (ImpDis) are congenital conditions that are characterized by disturbances of genomic imprinting. The most common individual ImpDis are Prader-Willi syndrome, Angelman syndrome and Beckwith-Wiedemann syndrome. Individual ImpDis have similar clinical features, such as growth disturbances and developmental delay, but the disorders are heterogeneous and the key clinical manifestations are often non-specific, rendering diagnosis difficult. Four types of genomic and imprinting defect (ImpDef) affecting differentially methylated regions (DMRs) can cause ImpDis. These defects affect the monoallelic and parent-of-origin-specific expression of imprinted genes. The regulation within DMRs as well as their functional consequences are mainly unknown, but functional cross-talk between imprinted genes and functional pathways has been identified, giving insight into the pathophysiology of ImpDefs. Treatment of ImpDis is symptomatic. Targeted therapies are lacking owing to the rarity of these disorders; however, personalized treatments are in development. Understanding the underlying mechanisms of ImpDis, and improving diagnosis and treatment of these disorders, requires a multidisciplinary approach with input from patient representatives.
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Affiliation(s)
- Thomas Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany.
| | - David Monk
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Guiomar Perez de Nanclares
- Rare Diseases Research Group, Molecular (Epi)Genetics Laboratory, Bioaraba Research Health Institute, Araba University Hospital-Txagorritxu, Vitoria-Gasteiz, Spain
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Eloïse Giabicani
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, APHP, Hôpital Armand Trousseau, Endocrinologie Moléculaire et Pathologies d'Empreinte, Paris, France
| | - Andrea Riccio
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università della Campania Luigi Vanvitelli, Caserta, Italy
- Institute of Genetics and Biophysics A. Buzzati-Traverso, CNR, Naples, Italy
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jennifer M Kalish
- Division of Human Genetics and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Departments of Pediatrics and Genetics at the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maithé Tauber
- Centre de Référence Maladies Rares PRADORT (syndrome de PRADer-Willi et autres Obésités Rares avec Troubles du comportement alimentaire), Hôpital des Enfants, CHU Toulouse, Toulouse, France
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 - CNRS UMR5051 - Université Toulouse III, Toulouse, France
| | - Jessica Duis
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, Department of Paediatrics and Genetics and Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Matthias Begemann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
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3
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Breton-Larrivée M, Elder E, Legault LM, Langford-Avelar A, MacFarlane AJ, McGraw S. Mitigating the detrimental developmental impact of early fetal alcohol exposure using a maternal methyl donor-enriched diet. FASEB J 2023; 37:e22829. [PMID: 36856720 DOI: 10.1096/fj.202201564r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/23/2023] [Accepted: 02/03/2023] [Indexed: 03/02/2023]
Abstract
Fetal alcohol exposure at any stage of pregnancy can lead to fetal alcohol spectrum disorder (FASD), a group of life-long conditions characterized by congenital malformations, as well as cognitive, behavioral, and emotional impairments. The teratogenic effects of alcohol have long been publicized; yet fetal alcohol exposure is one of the most common preventable causes of birth defects. Currently, alcohol abstinence during pregnancy is the best and only way to prevent FASD. However, alcohol consumption remains astoundingly prevalent among pregnant women; therefore, additional measures need to be made available to help protect the developing embryo before irreparable damage is done. Maternal nutritional interventions using methyl donors have been investigated as potential preventative measures to mitigate the adverse effects of fetal alcohol exposure. Here, we show that a single acute preimplantation (E2.5; 8-cell stage) fetal alcohol exposure (2 × 2.5 g/kg ethanol with a 2h interval) in mice leads to long-term FASD-like morphological phenotypes (e.g. growth restriction, brain malformations, skeletal delays) in late-gestation embryos (E18.5) and demonstrate that supplementing the maternal diet with a combination of four methyl donor nutrients, folic acid, choline, betaine, and vitamin B12, prior to conception and throughout gestation effectively reduces the incidence and severity of alcohol-induced morphological defects without altering DNA methylation status of imprinting control regions and regulation of associated imprinted genes. This study clearly supports that preimplantation embryos are vulnerable to the teratogenic effects of alcohol, emphasizes the dangers of maternal alcohol consumption during early gestation, and provides a potential proactive maternal nutritional intervention to minimize FASD progression, reinforcing the importance of adequate preconception and prenatal nutrition.
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Affiliation(s)
- Mélanie Breton-Larrivée
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
| | - Elizabeth Elder
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
| | - Lisa-Marie Legault
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
| | - Alexandra Langford-Avelar
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
| | - Amanda J MacFarlane
- Agriculture, Food, and Nutrition Evidence Center, Texas A&M University, Texas, Fort Worth, USA.,Department of Nutrition, Texas A&M University, College Station, Texas, USA
| | - Serge McGraw
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada.,Department of Obstetrics and Gynecology, Université de Montréal, Montreal, Canada
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4
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Bilo L, Ochoa E, Lee S, Dey D, Kurth I, Kraft F, Rodger F, Docquier F, Toribio A, Bottolo L, Binder G, Fekete G, Elbracht M, Maher ER, Begemann M, Eggermann T. Molecular characterisation of 36 multilocus imprinting disturbance (MLID) patients: a comprehensive approach. Clin Epigenetics 2023; 15:35. [PMID: 36859312 PMCID: PMC9979536 DOI: 10.1186/s13148-023-01453-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Imprinting disorders (ImpDis) comprise diseases which are caused by aberrant regulation of monoallelically and parent-of-origin-dependent expressed genes. A characteristic molecular change in ImpDis patients is aberrant methylation signatures at disease-specific loci, without an obvious DNA change at the specific differentially methylated region (DMR). However, there is a growing number of reports on multilocus imprinting disturbances (MLIDs), i.e. aberrant methylation at different DMRs in the same patient. These MLIDs account for a significant number of patients with specific ImpDis, and several reports indicate a central role of pathogenic maternal effect variants in their aetiology by affecting the maturation of the oocyte and the early embryo. Though several studies on the prevalence and the molecular causes of MLID have been conducted, homogeneous datasets comprising both genomic and methylation data are still lacking. RESULTS Based on a cohort of 36 MLID patients, we here present both methylation data obtained from next-generation sequencing (NGS, ImprintSeq) approaches and whole-exome sequencing (WES). The compilation of methylation data did not reveal a disease-specific MLID episignature, and a predisposition for the phenotypic modification was not obvious as well. In fact, this lack of epigenotype-phenotype correlation might be related to the mosaic distribution of imprinting defects and their functional relevance in specific tissues. CONCLUSIONS Due to the higher sensitivity of NGS-based approaches, we suggest that ImprintSeq might be offered at reference centres in case of ImpDis patients with unusual phenotypes but MLID negative by conventional tests. By WES, additional MLID causes than the already known maternal effect variants could not be identified, neither in the patients nor in the maternal exomes. In cases with negative WES results, it is currently unclear to what extent either environmental factors or undetected genetic variants contribute to MLID.
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Affiliation(s)
- Larissa Bilo
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Eguzkine Ochoa
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Sunwoo Lee
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Daniela Dey
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Ingo Kurth
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Florian Kraft
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Fay Rodger
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - France Docquier
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Ana Toribio
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- The Alan Turing Institute, London, UK
| | - Gerhard Binder
- Pediatric Endocrinology, University Children's Hospital, Universiy of Tuebingen, Tuebingen, Germany
| | - György Fekete
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Miriam Elbracht
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Matthias Begemann
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Thomas Eggermann
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.
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5
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Becker J, Sun B, Alammari F, Haerty W, Vance KW, Szele FG. What has single-cell transcriptomics taught us about long non-coding RNAs in the ventricular-subventricular zone? Stem Cell Reports 2022; 18:354-376. [PMID: 36525965 PMCID: PMC9860170 DOI: 10.1016/j.stemcr.2022.11.011] [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: 04/25/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNA (lncRNA) function is mediated by the process of transcription or through transcript-dependent associations with proteins or nucleic acids to control gene regulatory networks. Many lncRNAs are transcribed in the ventricular-subventricular zone (V-SVZ), a postnatal neural stem cell niche. lncRNAs in the V-SVZ are implicated in neurodevelopmental disorders, cancer, and brain disease, but their functions are poorly understood. V-SVZ neurogenesis capacity declines with age due to stem cell depletion and resistance to neural stem cell activation. Here we analyzed V-SVZ transcriptomics by pooling current single-cell RNA-seq data. They showed consistent lncRNA expression during stem cell activation, lineage progression, and aging. In conjunction with epigenetic and genetic data, we predicted V-SVZ lncRNAs that regulate stem cell activation and differentiation. Some of the lncRNAs validate known epigenetic mechanisms, but most remain uninvestigated. Our analysis points to several lncRNAs that likely participate in key aspects of V-SVZ stem cell activation and neurogenesis in health and disease.
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Affiliation(s)
- Jemima Becker
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Bin Sun
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Farah Alammari
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia,Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | - Keith W. Vance
- Department of Life Sciences, University of Bath, Bath, UK
| | - Francis George Szele
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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Vihinen M. Individual Genetic Heterogeneity. Genes (Basel) 2022; 13:genes13091626. [PMID: 36140794 PMCID: PMC9498725 DOI: 10.3390/genes13091626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/25/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic variation has been widely covered in literature, however, not from the perspective of an individual in any species. Here, a synthesis of genetic concepts and variations relevant for individual genetic constitution is provided. All the different levels of genetic information and variation are covered, ranging from whether an organism is unmixed or hybrid, has variations in genome, chromosomes, and more locally in DNA regions, to epigenetic variants or alterations in selfish genetic elements. Genetic constitution and heterogeneity of microbiota are highly relevant for health and wellbeing of an individual. Mutation rates vary widely for variation types, e.g., due to the sequence context. Genetic information guides numerous aspects in organisms. Types of inheritance, whether Mendelian or non-Mendelian, zygosity, sexual reproduction, and sex determination are covered. Functions of DNA and functional effects of variations are introduced, along with mechanism that reduce and modulate functional effects, including TARAR countermeasures and intraindividual genetic conflict. TARAR countermeasures for tolerance, avoidance, repair, attenuation, and resistance are essential for life, integrity of genetic information, and gene expression. The genetic composition, effects of variations, and their expression are considered also in diseases and personalized medicine. The text synthesizes knowledge and insight on individual genetic heterogeneity and organizes and systematizes the central concepts.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22184 Lund, Sweden
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Mannens MMAM, Lombardi MP, Alders M, Henneman P, Bliek J. Further Introduction of DNA Methylation (DNAm) Arrays in Regular Diagnostics. Front Genet 2022; 13:831452. [PMID: 35860466 PMCID: PMC9289263 DOI: 10.3389/fgene.2022.831452] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/08/2022] [Indexed: 12/01/2022] Open
Abstract
Methylation tests have been used for decades in regular DNA diagnostics focusing primarily on Imprinting disorders or specific loci annotated to specific disease associated gene promotors. With the introduction of DNA methylation (DNAm) arrays such as the Illumina Infinium HumanMethylation450 Beadchip array or the Illumina Infinium Methylation EPIC Beadchip array (850 k), it has become feasible to study the epigenome in a timely and cost-effective way. This has led to new insights regarding the complexity of well-studied imprinting disorders such as the Beckwith Wiedemann syndrome, but it has also led to the introduction of tests such as EpiSign, implemented as a diagnostic test in which a single array experiment can be compared to databases with known episignatures of multiple genetic disorders, especially neurodevelopmental disorders. The successful use of such DNAm tests is rapidly expanding. More and more disorders are found to be associated with discrete episignatures which enables fast and definite diagnoses, as we have shown. The first examples of environmentally induced clinical disorders characterized by discrete aberrant DNAm are discussed underlining the broad application of DNAm testing in regular diagnostics. Here we discuss exemplary findings in our laboratory covering this broad range of applications and we discuss further use of DNAm tests in the near future.
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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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9
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Receveur A, Puisney-Dakhli C, Kleinfinger P, Gitz L, Grevoul-Fesquet J, Jouni D, Diot R, Tachdjian G, Petit F. First prenatal case of Kagami-Ogata syndrome associated with a small supernumerary marker chromosome derived from chromosome 15. Taiwan J Obstet Gynecol 2022; 61:382-384. [PMID: 35361407 DOI: 10.1016/j.tjog.2022.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2021] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVE Uniparental disomy (UPD) is one of the common causes of imprinting disorders, which can have an impact on gene expression according to the origin of the parental chromosome. Paternal UPD14 leads to Kagami-Ogata syndrome (KOS), which has a more severe phenotype than maternal UPD14, also called Temple syndrome. Small supernumerary marker chromosomes (SSMCs) are defined as structural chromosomal abnormalities that may be inherited or come from micronucleus-mediated chromothripsis. The association of UPD and SSMC is very rare but not fortuitous and several mechanisms can explain this phenomenon. CASE REPORT We report the first prenatal case of paternal isodisomy for chromosome 14 associated with a de novo SSMC originating from chromosome 15 and revealed by KOS. The mechanism could be a chromothripsis mediated by trisomy rescue. CONCLUSION Regarding this case, in relation to a de novo SSMC, it could be important to extend the research of UPD to other acrocentric chromosomes if ultrasound signs are evocative.
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Affiliation(s)
- Aline Receveur
- Service D'Histologie Embryologie Cytogénétique, APHP.Université Paris Saclay, Antoine Béclère Hospital, 157 Rue de La Porte de Trivaux, 92141, Clamart Cedex, France.
| | - Chloé Puisney-Dakhli
- Service D'Histologie Embryologie Cytogénétique, APHP.Université Paris Saclay, Antoine Béclère Hospital, 157 Rue de La Porte de Trivaux, 92141, Clamart Cedex, France
| | | | - Laurence Gitz
- Service de Gynécologie et Obstétrique, Hôpital Du Sud Francilien, 91 Evry, France
| | | | - Dima Jouni
- Service D'Histologie Embryologie Cytogénétique, APHP.Université Paris Saclay, Antoine Béclère Hospital, 157 Rue de La Porte de Trivaux, 92141, Clamart Cedex, France
| | - Romain Diot
- Service D'Histologie Embryologie Cytogénétique, APHP.Université Paris Saclay, Antoine Béclère Hospital, 157 Rue de La Porte de Trivaux, 92141, Clamart Cedex, France
| | - Gérard Tachdjian
- Service D'Histologie Embryologie Cytogénétique, APHP.Université Paris Saclay, Antoine Béclère Hospital, 157 Rue de La Porte de Trivaux, 92141, Clamart Cedex, France
| | - François Petit
- Laboratoire de Génétique Moléculaire, APHP.Université Paris Saclay, Antoine Béclère Hospital, 157 Rue de La Porte de Trivaux, 92141 Clamart, Cedex, France
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10
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Grosvenor SE, Davies JH, Lever M, Sillibourne J, Mackay DJG, Temple IK. A patient with multilocus imprinting disturbance involving hypomethylation at 11p15 and 14q32, and phenotypic features of Beckwith-Wiedemann and Temple syndromes. Am J Med Genet A 2022; 188:1896-1903. [PMID: 35266280 PMCID: PMC9310769 DOI: 10.1002/ajmg.a.62717] [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: 08/25/2021] [Revised: 11/15/2021] [Accepted: 11/30/2021] [Indexed: 11/26/2022]
Abstract
Beckwith‐Wiedemann syndrome (BWS) and Temple syndrome (TS) are classical imprinting disorders (IDs) with nonconfluent clinical features. We report here on a patient with clinical features of both syndromes, in whom epimutations were found at the BWS and TS imprinted regions, consistent with multilocus imprinting disturbance (MLID). This is the first case report of a patient with clinical features of both conditions who was found to have loss of methylation (LOM) of KCNQ1OT1: TSS‐DMR (ICR2) in the 11p15 imprinted region associated with BWS and LOM of MEG3: TSS‐DMR in the 14q32 imprinted region associated with TS. The report draws attention to the importance of testing for MLID as a cause of atypical clinical presentations of patients with IDs.
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Affiliation(s)
- Sarah E Grosvenor
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, UK
| | - Justin H Davies
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, UK.,Department of Paediatric Endocrinology, University Hospital Southampton NHS Foundation Trusts, Southampton, UK
| | - Margaret Lever
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Julie Sillibourne
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Deborah J G Mackay
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - I Karen Temple
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, UK.,Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trusts, Southampton, UK
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11
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Kaur P, Chaudhry C, Kaur A, Panigrahi I, Srivastava P. Case Studies of Two Classical Imprinting Growth Disorders: Silver–Russell and Beckwith–Wiedemann Syndromes. J Pediatr Genet 2021. [DOI: 10.1055/s-0041-1739388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractThe genetic influences on human growth are being increasingly deciphered. Silver–Russell and Beckwith–Wiedemann syndromes (SRS; BWS) are two relatively common genetic syndromes with under- and overgrowth-related issues being the reason for referral. Aberration in genomic imprinting is the underlying genetic pathomechanism behind these syndromes. Herein, we described a series of children with these two growth disorders and give an orientation to the reader of the concept of imprinting as well as the genetic testing strategy and counseling to be offered in these syndromes.
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Affiliation(s)
- Parminder Kaur
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Chakshu Chaudhry
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anupriya Kaur
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Inusha Panigrahi
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Priyanka Srivastava
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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12
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Prasasya R, Grotheer KV, Siracusa LD, Bartolomei MS. Temple syndrome and Kagami-Ogata syndrome: clinical presentations, genotypes, models and mechanisms. Hum Mol Genet 2021; 29:R107-R116. [PMID: 32592473 DOI: 10.1093/hmg/ddaa133] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022] Open
Abstract
Temple syndrome (TS) and Kagami-Ogata syndrome (KOS) are imprinting disorders caused by absence or overexpression of genes within a single imprinted cluster on human chromosome 14q32. TS most frequently arises from maternal UPD14 or epimutations/deletions on the paternal chromosome, whereas KOS most frequently arises from paternal UPD14 or epimutations/deletions on the maternal chromosome. In this review, we describe the clinical symptoms and genetic/epigenetic features of this imprinted region. The locus encompasses paternally expressed protein-coding genes (DLK1, RTL1 and DIO3) and maternally expressed lncRNAs (MEG3/GTL2, RTL1as and MEG8), as well as numerous miRNAs and snoRNAs. Control of expression is complex, with three differentially methylated regions regulating germline, placental and tissue-specific transcription. The strong conserved synteny between mouse chromosome 12aF1 and human chromosome 14q32 has enabled the use of mouse models to elucidate imprinting mechanisms and decipher the contribution of genes to the symptoms of TS and KOS. In this review, we describe relevant mouse models and highlight their value to better inform treatment options for long-term management of TS and KOS patients.
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Affiliation(s)
- Rexxi Prasasya
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen V Grotheer
- Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, 340 Kingsland Street, Building 123, Nutley, NJ 07110, USA
| | - Linda D Siracusa
- Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, 340 Kingsland Street, Building 123, Nutley, NJ 07110, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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13
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Eggermann T. Maternal Effect Mutations: A Novel Cause for Human Reproductive Failure. Geburtshilfe Frauenheilkd 2021; 81:780-788. [PMID: 34294945 PMCID: PMC8288500 DOI: 10.1055/a-1396-4390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/19/2021] [Indexed: 12/12/2022] Open
Abstract
Genetic alterations significantly contribute to the aetiology of reproductive failure and comprise monogenic, chromosomal and epigenetic disturbances. The implementation of next-generation sequencing (NGS) based approaches in research and diagnostics allows the comprehensive analysis of these genetic causes, and the increasing detection rates of genetic mutations causing reproductive complications confirm the potential of the new techniques. Whereas mutations affecting the fetal genome are well known to affect pregnancies and their outcome, the contribution of alterations of the maternal genome was widely unclear. With the recent mainly NGS-based identification of maternal effect variants, a new cause of human reproductive failure has been identified. Maternal effect mutations affect the expression of subcortical maternal complex (SCMC) proteins from the maternal genome, and thereby disturb oocyte maturation and progression of the early embryo. They cause a broad range of reproductive failures and pregnancy complications, including infertility, miscarriages, hydatidiform moles, aneuploidies and imprinting disturbances in the fetus. The identification of women carrying these molecular alterations in SCMC encoding genes is therefore essential for a personalised reproductive and genetic counselling. The diagnostic application of new NGS-based assays allows the comprehensive analysis of these factors, and helps to further decipher these functional links between the factors and their disturbances. A close interdisciplinary collaboration between different disciplines is definitely required to further decipher the complex regulation of early embryo development, and to translate the basic research results into clinical practice.
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Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, RWTH Aachen University, Aachen, Germany
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14
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Benn P. Uniparental disomy: Origin, frequency, and clinical significance. Prenat Diagn 2021; 41:564-572. [PMID: 33179335 DOI: 10.1002/pd.5837] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/28/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023]
Abstract
Uniparental disomy (UPD) is defined as two copies of a whole chromosome derived from the same parent. There can be multiple mechanisms that lead to UPD; these are reviewed in the context of contemporary views on the mechanism leading to aneuploidy. Recent studies indicate that UPD is rare in an apparently healthy population and also rare in spontaneous abortion tissues. The most common type of UPD is a maternal heterodisomy (both maternal allele sets present). Isodisomy (a duplicated single set of alleles) or segmental loss of heterozygosity is sometimes encountered in SNP-based microarray referrals. Decisions regarding the most appropriate follow-up testing should consider the possibility of consanguinity (that will generally involve multiple regions), an imprinted gene disorder (chromosomes 6, 7, 11, 14, 15, 20), expression of an autosomal recessive disorder, and an occult aneuploid cell line that may be confined to the placenta. Upd(16)mat, per se, does not appear to be associated with an abnormal phenotype. UPD provides an insight into the history of early chromosome segregation error and understanding the rates and fate of these events are of key importance in the provision of fertility management and prenatal healthcare.
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Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA
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15
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Zheng K, Yan J, Deng J, Wu W, Wen Y. Modification of Experimental Design and Statistical Method for Mapping Imprinted QTLs Based on Immortalized F2 Population. Front Genet 2020; 11:589047. [PMID: 33329733 PMCID: PMC7714927 DOI: 10.3389/fgene.2020.589047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/29/2020] [Indexed: 11/20/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon, which plays important roles in the growth and development of animals and plants. Immortalized F2 (imF2) populations generated by random cross between recombinant inbred (RI) or doubled haploid (DH) lines have been proved to have significant advantages for mapping imprinted quantitative trait loci (iQTLs), and statistical methods for this purpose have been proposed. In this paper, we propose a special type of imF2 population (R-imF2) for iQTL mapping, which is developed by random reciprocal cross between RI/DH lines. We also propose two modified iQTL mapping methods: two-step point mapping (PM-2) and two-step composite point mapping (CPM-2). Simulation studies indicated that: (i) R-imF2 cannot improve the results of iQTL mapping, but the experimental design can probably reduce the workload of population construction; (ii) PM-2 can increase the precision of estimating the position and effects of a single iQTL; and (iii) CPM-2 can precisely map not only iQTLs, but also non-imprinted QTLs. The modified experimental design and statistical methods will facilitate and promote the study of iQTL mapping.
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Affiliation(s)
- Kehui Zheng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiqiang Yan
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiacong Deng
- School of Ocean and Biochemical Engineering, Fuqing Branch of Fujian Normal University, Fuzhou, China
| | - Weiren Wu
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Weiren Wu,
| | - Yongxian Wen
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Yongxian Wen,
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16
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Vihinen M. Functional effects of protein variants. Biochimie 2020; 180:104-120. [PMID: 33164889 DOI: 10.1016/j.biochi.2020.10.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
Abstract
Genetic and other variations frequently affect protein functions. Scientific articles can contain confusing descriptions about which function or property is affected, and in many cases the statements are pure speculation without any experimental evidence. To clarify functional effects of protein variations of genetic or non-genetic origin, a systematic conceptualisation and framework are introduced. This framework describes protein functional effects on abundance, activity, specificity and affinity, along with countermeasures, which allow cells, tissues and organisms to tolerate, avoid, repair, attenuate or resist (TARAR) the effects. Effects on abundance discussed include gene dosage, restricted expression, mis-localisation and degradation. Enzymopathies, effects on kinetics, allostery and regulation of protein activity are subtopics for the effects of variants on activity. Variation outcomes on specificity and affinity comprise promiscuity, specificity, affinity and moonlighting. TARAR mechanisms redress variations with active and passive processes including chaperones, redundancy, robustness, canalisation and metabolic and signalling rewiring. A framework for pragmatic protein function analysis and presentation is introduced. All of the mechanisms and effects are described along with representative examples, most often in relation to diseases. In addition, protein function is discussed from evolutionary point of view. Application of the presented framework facilitates unambiguous, detailed and specific description of functional effects and their systematic study.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22 184, Lund, Sweden.
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17
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Hara-Isono K, Matsubara K, Fuke T, Yamazawa K, Satou K, Murakami N, Saitoh S, Nakabayashi K, Hata K, Ogata T, Fukami M, Kagami M. Genome-wide methylation analysis in Silver-Russell syndrome, Temple syndrome, and Prader-Willi syndrome. Clin Epigenetics 2020; 12:159. [PMID: 33092629 PMCID: PMC7583213 DOI: 10.1186/s13148-020-00949-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/13/2020] [Indexed: 12/19/2022] Open
Abstract
Background Imprinting disorders (IDs) show overlapping phenotypes, particularly in Silver–Russell syndrome (SRS), Temple syndrome (TS14), and Prader–Willi syndrome (PWS). These three IDs include fetal and postnatal growth failure, feeding difficulty, and muscular hypotonia as major clinical features. However, the mechanism that causes overlapping phenotypes has not been clarified. To investigate the presence or absence of methylation signatures associated with overlapping phenotypes, we performed genome-wide methylation analysis (GWMA). Results GWMA was carried out on 36 patients with three IDs (SRS [n = 16], TS14 [n = 7], PWS [n = 13]) and 11 child controls using HumanMethylation450 BeadChip including 475,000 CpG sites across the human genome. To reveal an aberrantly methylated region shared by SRS, TS14, and PWS groups, we compared genome-wide methylation data of the three groups with those of control subjects. All the identified regions were known as SRS-, TS14-, and PWS-related imprinting-associated differentially methylated regions (iDMRs), and there was no hypermethylated or hypomethylated region shared by different ID groups. To examine the methylation pattern shared by SRS, TS14, and PWS groups, we performed clustering analysis based on GWMA data. The result focusing on 620 probes at the 62 known iDMRs (except for SRS-, TS14-, and PWS-related iDMRs) classified patients into two categories: (1) category A, grossly normal methylation patterns mainly consisting of SRS group patients; and (2) category B, broad and mild hypermethylation patterns mainly consisting of TS14 and PWS group patients. However, we found no obvious relationship between these methylation patterns and phenotypes of patients. Conclusions GWMA in three IDs found no methylation signatures shared by SRS, TS14, and PWS groups. Although clustering analysis showed similar mild hypermethylation patterns in TS14 and PWS groups, further study is needed to clarify the effect of methylation patterns on the overlapping phenotypes.
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Affiliation(s)
- Kaori Hara-Isono
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.,Department of Pediatrics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Tomoko Fuke
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Kazuki Yamazawa
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.,Medical Genetics Center, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan
| | - Kazuhito Satou
- Department of Genome Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Nobuyuki Murakami
- Department of Pediatrics, Dokkyo Medical University Saitama Medical Center, 2-1-50 Minami Koshigaya, Koshigaya, 343-8555, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Kenichiro Hata
- Department of Maternal Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.,Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
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18
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Cao P, Li H, Zuo Y, Nashun B. Characterization of DNA Methylation Patterns and Mining of Epigenetic Markers During Genomic Reprogramming in SCNT Embryos. Front Cell Dev Biol 2020; 8:570107. [PMID: 32984351 PMCID: PMC7492385 DOI: 10.3389/fcell.2020.570107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT), also known as somatic cell cloning, is a commonly used technique to study epigenetic reprogramming. Although SCNT has the advantages of being safe and able to obtain pluripotent cells, early developmental arrest happens in most SCNT embryos. Overcoming epigenetic barriers is currently the primary strategy for improving reprogramming efficiency and improving developmental rate in SCNT embryos. In this study, we analyzed DNA methylation profiles of in vivo fertilized embryos and SCNT embryos with different developmental fates. Overall DNA methylation level was higher in SCNT embryos during global de-methylation process compared to in vivo fertilized embryos. In addition, promoter region, first intron and 3′UTR were found to be the major genomic regions that were hyper-methylated in SCNT embryos. Surprisingly, we found the length of re-methylated region was directly related to the change of methylation level. Furthermore, a number of genes including Dppa2 and Dppa4 which are important for early zygotic genome activation (ZGA) were not properly activated in SCNT embryos. This study comprehensively analyzed genome-wide DNA methylation patterns in SCNT embryos and provided candidate target genes for improving efficiency of genomic reprogramming in SCNT embryos. Since SCNT technology has been widely used in agricultural and pastoral production, protection of endangered animals, and therapeutic cloning, the findings of this study have significant importance for all these fields.
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Affiliation(s)
- Pengbo Cao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Hanshuang Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Buhe Nashun
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
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19
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Zhao X, Chang S, Liu X, Wang S, Zhang Y, Lu X, Zhang T, Zhang H, Wang L. Imprinting aberrations of SNRPN, ZAC1 and INPP5F genes involved in the pathogenesis of congenital heart disease with extracardiac malformations. J Cell Mol Med 2020; 24:9898-9907. [PMID: 32693431 PMCID: PMC7520315 DOI: 10.1111/jcmm.15584] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Congenital heart disease (CHD) with extracardiac malformations (EM) is the most common multiple malformation, resulting from the interaction between genetic abnormalities and environmental factors. Most studies have attributed the causes of CHD with EM to chromosomal abnormalities. However, multi‐system dysplasia is usually caused by both genetic mutations and epigenetic dysregulation. The epigenetic mechanisms underlying the pathogenesis of CHD with EM remain unclear. In this study, we investigated the mechanisms of imprinting alterations, including those of the Small nuclear ribonucleoprotein polypeptide N (SNRPN), PLAG1 like zinc finger 1 (ZAC1) and inositol polyphosphate‐5‐phosphatase F (INPP5F) genes, in the pathogenesis of CHD with EM. The methylation levels of SNRPN, ZAC1, and INPP5F genes were analysed by the MassARRAY platform in 24 children with CHD with EM and 20 healthy controls. The expression levels of these genes were detected by real‐time polymerase chain reaction (PCR). The correlation between methylation regulation and gene expression was confirmed using 5‐azacytidine (5‐Aza) treated cells. The methylation levels of SNRPN and ZAC1 genes were significantly increased in CHD with EM, while that of INPP5F was decreased. The methylation alterations of these genes were negatively correlated with expression. Risk analysis showed that abnormal hypermethylation of SNRPN and ZAC1 resulted in 5.545 and 7.438 times higher risks of CHD with EM, respectively, and the abnormal hypomethylation of INPP5F was 8.38 times higher than that of the control group. We concluded that abnormally high methylation levels of SNRPN and ZAC1 and decreased levels of INPP5F imply an increased risk of CHD with EM by altering their gene functions. This study provides evidence of imprinted regulation in the pathogenesis of multiple malformations.
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Affiliation(s)
- Xiaolei Zhao
- Department of Cardiac Surgery, The Capital Institute of Pediatrics, Beijing, China
| | - Shaoyan Chang
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Xinli Liu
- Department of Obstetrics and Gynecology, PLA Army General Hospital 263rd Clinical Department, Beijing, China
| | - Shuangxing Wang
- Department of Cardiac Surgery, The Capital Institute of Pediatrics, Beijing, China
| | - Yueran Zhang
- Department of Cardiac Surgery, The Capital Institute of Pediatrics, Beijing, China
| | - Xiaolin Lu
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Ting Zhang
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Hui Zhang
- Department of Cardiac Surgery, The Capital Institute of Pediatrics, Beijing, China
| | - Li Wang
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
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20
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Fontana L, Bedeschi MF, Cagnoli GA, Costanza J, Persico N, Gangi S, Porro M, Ajmone PF, Colapietro P, Santaniello C, Crippa M, Sirchia SM, Miozzo M, Tabano S. (Epi)genetic profiling of extraembryonic and postnatal tissues from female monozygotic twins discordant for Beckwith-Wiedemann syndrome. Mol Genet Genomic Med 2020; 8:e1386. [PMID: 32627967 PMCID: PMC7507324 DOI: 10.1002/mgg3.1386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/26/2020] [Accepted: 06/01/2020] [Indexed: 12/19/2022] Open
Abstract
Background Beckwith–Wiedemann syndrome (BWS) is an overgrowth disorder caused by defects at the 11p15.5 imprinted region. Many cases of female monozygotic (MZ) twins discordant for BWS have been reported, but no definitive conclusions have been drawn regarding the link between epigenetic defects, twinning process, and gender. Here, we report a comprehensive characterization and follow‐up of female MZ twins discordant for BWS. Methods Methylation pattern at 11p15.5 and multilocus methylation disturbance (MLID) profiling were performed by pyrosequencing and MassARRAY in placental/umbilical cord samples and postnatal tissues. Whole‐exome sequencing was carried out to identify MLID causative mutations. X‐chromosome inactivation (XCI) was determined by HUMARA test. Results Both twins share KCNQ1OT1:TSS‐DMR loss of methylation (LOM) and MLID in blood and the epigenetic defect remained stable in the healthy twin over time. KCNQ1OT1:TSS‐DMRLOM was nonhomogeneously distributed in placental samples and the twins showed the same severely skewed XCI pattern. No MLID‐causative mutations were identified. Conclusion This is the first report on BWS‐discordant twins with methylation analyses extended to extraembryonic tissues. The results suggest that caution is required when attempting prenatal diagnosis in similar cases. Although the causative mechanism underlying LOM remains undiscovered, the XCI pattern and mosaic LOM suggest that both twinning and LOM/MLID occurred after XCI commitment.
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Affiliation(s)
- Laura Fontana
- Medical Genetics, Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Milano, Italy.,Research Laboratories Coordination Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Maria F Bedeschi
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Giulia A Cagnoli
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Jole Costanza
- Research Laboratories Coordination Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Nicola Persico
- Obstetrics and Gynecology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy.,Department of ClinicalSciences and Community Health, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Silvana Gangi
- NICU, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Matteo Porro
- Pediatric Physical Medicine & Rehabilitation Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Paola F Ajmone
- Child and AdolescentNeuropsychiatric Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Patrizia Colapietro
- Medical Genetics, Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Milano, Italy.,Research Laboratories Coordination Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Carlo Santaniello
- Research Laboratories Coordination Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Milena Crippa
- Medical Cytogenetics& Human Molecular Genetics, Istituto Auxologico Italiano-IRCCS, Milano, Italy
| | - Silvia M Sirchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | - Monica Miozzo
- Medical Genetics, Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Milano, Italy.,Research Laboratories Coordination Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Silvia Tabano
- Medical Genetics, Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Milano, Italy.,Laboratory of Medical Genetics, Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico, Milan, Italy
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21
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Leitão E, Di Persio S, Laurentino S, Wöste M, Dugas M, Kliesch S, Neuhaus N, Horsthemke B. The sperm epigenome does not display recurrent epimutations in patients with severely impaired spermatogenesis. Clin Epigenetics 2020; 12:61. [PMID: 32375885 PMCID: PMC7204326 DOI: 10.1186/s13148-020-00854-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In the past 15 years, numerous studies have described aberrant DNA methylation of imprinted genes (e.g. MEST and H19) in sperm of oligozoospermic men, but the prevalence and genomic extent of abnormal methylation patterns have remained unknown. RESULTS Using deep bisulfite sequencing (DBS), we screened swim-up sperm samples from 40 normozoospermic and 93 patients diagnosed as oligoasthenoteratozoospermic, oligoteratozoospermic or oligozoospermic, which are termed OATs throughout the manuscript, for H19 and MEST methylation. Based on this screening, we defined three patient groups: normal controls (NC), abnormally methylated oligozoospermic (AMO; n = 7) and normally methylated oligozoospermic (NMO; n = 86). Whole-genome bisulfite sequencing (WGBS) of five NC and five AMO samples revealed abnormal methylation levels of all 50 imprinting control regions in each AMO sample. To investigate whether this finding reflected epigenetic germline mosaicism or the presence of residual somatic DNA, we made a genome-wide inventory of soma-germ cell-specific DNA methylation. We found that > 2000 germ cell-specific genes are promoter-methylated in blood and that AMO samples had abnormal methylation levels at these genes, consistent with the presence of somatic cell DNA. The comparison between the five NC and six NMO samples revealed 19 differentially methylated regions (DMRs), none of which could be validated in an independent cohort of 40 men. Previous studies reported a higher incidence of epimutations at single CpG sites in the CTCF-binding region 6 of H19 in infertile patients. DBS analysis of this locus, however, revealed an association between DNA methylation levels and genotype (rs2071094), but not fertility phenotype. CONCLUSIONS Our results suggest that somatic DNA contamination and genetic variation confound methylation studies in sperm of infertile men. While we cannot exclude the existence of rare patients with slightly abnormal sperm methylation at non-recurrent CpG sites, the prevalence of aberrant methylation in swim-up purified sperm of infertile men has likely been overestimated, which is reassuring for patients undergoing assisted reproduction.
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Affiliation(s)
- Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Sara Di Persio
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany.
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, Essen, Germany.,Institute of Human Genetics, University Hospital Münster, Münster, Germany
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22
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Abstract
In 1993, Denise Barlow proposed that genomic imprinting might have arisen from a host defense mechanism designed to inactivate retrotransposons. Although there were few examples at hand, she suggested that there should be maternal-specific and paternal-specific factors involved, with cognate imprinting boxes that they recognized; furthermore, the system should build on conserved biochemical factors, including DNA methylation, and maternal control should predominate for imprints. Here, we revisit this hypothesis in the light of recent advances in our understanding of host defense and DNA methylation and in particular, the link with Krüppel-associated box–zinc finger (KRAB-ZF) proteins.
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Affiliation(s)
- Miroslava Ondičová
- School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Rebecca J. Oakey
- Department of Medical & Molecular Genetics, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Colum P. Walsh
- School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
- * E-mail:
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23
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Li J, Lin X, Wang M, Hu Y, Xue K, Gu S, Lv L, Huang S, Xie W. Potential role of genomic imprinted genes and brain developmental related genes in autism. BMC Med Genomics 2020; 13:54. [PMID: 32216802 PMCID: PMC7099798 DOI: 10.1186/s12920-020-0693-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 02/11/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Autism is a complex disease involving both environmental and genetic factors. Recent efforts have implicated the correlation of genomic imprinting and brain development in autism, however the pathogenesis of autism is not completely clear. Here, we used bioinformatic tools to provide a comprehensive analysis of the autism-related genes, genomic imprinted genes and the spatially and temporally differentially expressed genes of human brain, aiming to explore the relationship between autism, brain development and genomic imprinting. METHODS This study analyzed the distribution correlation between autism-related genes and imprinted genes on chromosomes using sliding windows and statistical methods. The normal brains' gene expression microarray data were reanalyzed to construct a spatio-temporal coordinate system of gene expression during brain development. Finally, we intersected the autism-related genes, imprinted genes and brain spatio-temporally differentially expressed genes for further analysis to find the major biological processes that these genes involved. RESULTS We found a positive correlation between the autism-related genes' and imprinted genes' distribution on chromosomes. Through the analysis of the normal brain microarray data, we constructed a spatio-temporal coordinate system of gene expression during human brain development, and obtained 13 genes that are differentially expressed in the process of brain development, which are both autism-related genes and imprinted genes. Furthermore, enrichment analysis illustrated that these genes are mainly involved in the biological processes, such as gamma-aminobutyric acid signaling pathway, neuron recognition, learning or memory, and regulation of synaptic transmission. Bioinformatic analysis implied that imprinted genes regulate the development and behavior of the brain. And its own mutation or changes in the epigenetic modification state of the imprinted control region could lead to some diseases, indicating that imprinted genes and brain development play an important role in diagnosis and prognosis of autism. CONCLUSION This study systematically correlates brain development and genomic imprinting with autism, which provides a new perspective for the study of genetic mechanisms of autism, and selected the potential candidate biomarkers for early diagnosis of autism in clinic.
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Affiliation(s)
- Jian Li
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, 210096, China.
| | - Xue Lin
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China
| | - Mingya Wang
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, 210096, China
| | - Yunyun Hu
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, 210096, China
| | - Kaiyu Xue
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, 210096, China
| | - Shuanglin Gu
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, 210096, China
| | - Li Lv
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, 210096, China
| | - Saijun Huang
- Foshan Women and Children Hospital, Foshan, 528000, China
| | - Wei Xie
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, 210096, China.
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24
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Wang X, Pang H, Shah BA, Gu H, Zhang L, Wang H. A Male Case of Kagami-Ogata Syndrome Caused by Paternal Unipaternal Disomy 14 as a Result of a Robertsonian Translocation. Front Pediatr 2020; 8:88. [PMID: 32211354 PMCID: PMC7076151 DOI: 10.3389/fped.2020.00088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
Kagami-Ogata syndrome (KOS) is a rare imprinting disorder characterized by skeletal abnormalities, dysmorphic facial features, growth retardation and developmental delay. The genetic etiology of KOS includes paternal uniparental disomy 14 [upd(14)pat], epimutations and microdeletions affecting the maternally derived imprinted region of chromosome 14q32.2. More than seventy KOS cases have been reported thus far; however, only 10, including two familial, are associated with upd(14)pat harboring Robertsonian translocation (ROB). Here, we reported a male infant with clinical manifestations of facial dysmorphism, bell-shaped small thorax, and omphalocele. Karyotype analyses identify a balanced ROB involving the long arms of chromosomes 13 and 14 both in the patient and his father. We further confirm the pattern of upd(14)pat utilizing DNA polymorphic markers. In conclusion, our case report provides a new male KOS case caused by upd(14)pat with paternally inherited Robertsonian translocation, which represents the second male case officially reported. Notably, a KOS case due to upd(14)pat and ROB is rare. An accurate diagnosis requires not only the identification of the characteristic clinical features but also systemic cytogenetic and molecular studies.
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Affiliation(s)
- Xiaoxue Wang
- Department of Hematology, The First Hospital of China Medical University, Shenyang, China.,Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Hui Pang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Birju A Shah
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Hongcang Gu
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Lijun Zhang
- Department of Hematology, The First Hospital of China Medical University, Shenyang, China
| | - Hua Wang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, United States
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25
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Christesen HT, Christensen LG, Löfgren ÅM, Brøndum-Nielsen K, Svensson J, Brusgaard K, Samuelsson S, Elfving M, Jonson T, Grønskov K, Rasmussen L, Backman T, Hansen LK, Larsen AR, Petersen H, Detlefsen S. Tissue variations of mosaic genome-wide paternal uniparental disomy and phenotype of multi-syndromal congenital hyperinsulinism. Eur J Med Genet 2020; 63:103632. [DOI: 10.1016/j.ejmg.2019.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/11/2019] [Accepted: 02/17/2019] [Indexed: 01/12/2023]
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26
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Vasconcelos S, Ramalho C, Marques CJ, Doria S. Altered expression of epigenetic regulators and imprinted genes in human placenta and fetal tissues from second trimester spontaneous pregnancy losses. Epigenetics 2019; 14:1234-1244. [PMID: 31221015 PMCID: PMC6791697 DOI: 10.1080/15592294.2019.1634988] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 01/01/2023] Open
Abstract
Epigenetic mechanisms such as genomic imprinting have a fundamental role in embryo and fetal development. Hence, we here studied expression levels of epigenetic modifiers and imprinted genes in cases of ididopathic spontaneous abortion (SA). Thirty-five placental samples and 35 matched fetal tissues from second trimester SA were analysed; including 16 controls (placental and fetal infections as the known cause of spontaneous abortion) and 19 idiopathic SA cases. Transcript levels of epigenetic regulators and imprinted genes were measured by qRT-PCR and methylation at imprinted genes was studied by bisulfite genomic sequencing and MS-MLPA. Global DNA hydroxymethylation (5-hmC) levels were measured by an ELISA-based assay. We observed an upregulation of TET2 and TET3 in placental samples from idiopathic SA cases; however, no significant difference in global 5-hmC levels was observed. On the contrary, in fetal tissues, TET3 was markedly downregulated in idiopathic SA, showing an opposite trend to that observed in placental tissue. IGF2 and CDKN1C were upregulated and MEST downregulated in placentas from idiopathic SA cases; concordantly, IGF2 was also upregulated in fetal tissues from idiopathic SA cases. Although not reaching statistical significance, an increase in methylation levels of MEST, KvDMR1 and H19 DMRs was observed in idiopathic SA cases, concordantly with the observed changes in expression. Our study reveals, for the first time, deregulation of epigenetic modifiers and imprinted genes in both placental and fetal tissues from idiopathic SA cases in the second trimester of pregnancy, indicating a critical role during pregnancy.
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Affiliation(s)
- Sara Vasconcelos
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Carla Ramalho
- Department of Obstetrics and Gynecology Hospital São João, Faculty of Medicine, Porto, Portugal
| | - C. Joana Marques
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
- I3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sofia Doria
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
- I3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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27
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Wan JH, He P, Xu LL, Li DZ. Confined placental trisomy detection through non-invasive prenatal testing: benefit for pregnancy management. J OBSTET GYNAECOL 2019; 40:1020-1022. [PMID: 31769707 DOI: 10.1080/01443615.2019.1665631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Jun-Hui Wan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Ping He
- Department of Obstetrics and Gynecology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Li-Li Xu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
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28
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Ben Maamar M, King SE, Nilsson E, Beck D, Skinner MK. Epigenetic transgenerational inheritance of parent-of-origin allelic transmission of outcross pathology and sperm epimutations. Dev Biol 2019; 458:106-119. [PMID: 31682807 PMCID: PMC6987017 DOI: 10.1016/j.ydbio.2019.10.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Epigenetic transgenerational inheritance potentially impacts disease etiology, phenotypic variation, and evolution. An increasing number of environmental factors from nutrition to toxicants have been shown to promote the epigenetic transgenerational inheritance of disease. Previous observations have demonstrated that the agricultural fungicide vinclozolin and pesticide DDT (dichlorodiphenyltrichloroethane) induce transgenerational sperm epimutations involving DNA methylation, ncRNA, and histone modifications or retention. These two environmental toxicants were used to investigate the impacts of parent-of-origin outcross on the epigenetic transgenerational inheritance of disease. Male and female rats were collected from a paternal outcross (POC) or a maternal outcross (MOC) F4 generation control and exposure lineages for pathology and epigenetic analysis. This model allows the parental allelic transmission of disease and epimutations to be investigated. There was increased pathology incidence in the MOC F4 generation male prostate, kidney, obesity, and multiple diseases through a maternal allelic transmission. The POC F4 generation female offspring had increased pathology incidence for kidney, obesity and multiple types of diseases through the paternal allelic transmission. Some disease such as testis or ovarian pathology appear to be transmitted through the combined actions of both male and female alleles. Analysis of the F4 generation sperm epigenomes identified differential DNA methylated regions (DMRs) in a genome-wide analysis. Observations demonstrate that DDT and vinclozolin have the potential to promote the epigenetic transgenerational inheritance of disease and sperm epimutations to the outcross F4 generation in a sex specific and exposure specific manner. The parent-of-origin allelic transmission observed appears similar to the process involved with imprinted-like genes.
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Stephanie E King
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
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29
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Chaves TF, Oliveira LF, Ocampos M, Barbato IT, de Luca GR, Barbato Filho JH, de Camargo Pinto LL, Bernardi P, Maris AF. Long contiguous stretches of homozygosity detected by chromosomal microarrays (CMA) in patients with neurodevelopmental disorders in the South of Brazil. BMC Med Genomics 2019; 12:50. [PMID: 30866944 PMCID: PMC6417136 DOI: 10.1186/s12920-019-0496-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/28/2019] [Indexed: 01/14/2023] Open
Abstract
Background Currently, chromosomal microarrays (CMA) are recommended as first-tier test in the investigation of developmental disorders to examine copy number variations. The modern platforms also include probes for single nucleotide polymorphisms (SNPs) that detect homozygous regions in the genome, such as long contiguous stretches of homozygosity (LCSH) also named runs of homozygosity (ROH). LCHS are chromosomal segments resulting from complete or segmental chromosomal homozygosity, which may be indicative of uniparental disomy (UPD), consanguinity, as well as replicative DNA repair events, however also are common findings in normal populations. Knowing common LCSH of a population, which probably represent ancestral haplotypes of low-recombination regions in the genome, facilitates the interpretation of LCSH found in patients, allowing to prioritize those with possible clinical significance. However, population records of ancestral haplotype derived LCSH by SNP arrays are still scarce, particularly for countries such as Brazil where even for the clinic, microarrays that include SNPs are difficult to request due to their high cost. Methods In this study, we evaluate the frequencies and implications of LCSH detected by Affymetrix CytoScan® HD or 750 K platforms in 430 patients with neurodevelopmental disorders in southern Brazil. LCSH were analyzed in the context of pathogenic significance and also explored to identify ancestral haplotype derived LCSH. The criteria for considering a region as LCSH was homozygosis ≥3 Mbp on an autosome. Results In 95% of the patients, at least one LCSH was detected, a total of 1478 LCSH in 407 patients. In 2.6%, the findings were suggestive of UPD. For about 8.5% LCSH suggest offspring from first to fifth grade, more likely to have a clinical impact. Considering recurrent LCSH found at a frequency of 5% or more, we outline 11 regions as potentially representing ancestral haplotypes in our population. The region most involved with homozygosity was 16p11.2p11.1 (49%), followed by 1q21.2q21.3 (21%), 11p11.2p11.12 (19%), 3p21.31p21.2 (16%), 15q15 1q33p32.3 (12%), 2q11.1q12.1 (9%), 1p33p32.3 (6%), 20q11.21q11.23 (6%), 10q22.1q23.31 (5%), 6p22.2p22 (5%), and 7q11.22q11.23 (5%). Conclusions In this work, we show the importance and usefulness of interpreting LCSH in the results of CMA wich incorporate SNPs.
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Affiliation(s)
- Tiago Fernando Chaves
- Biologist, PhD Student in Cell Biology and Development, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
| | - Luan Freitas Oliveira
- Biomedic, PhD Student in Cell Biology and Development, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Maristela Ocampos
- Biologist, PhD in Biotechnology and Molecular Biology, Laboratory Neurogene, Florianópolis, SC, Brazil
| | - Ingrid Tremel Barbato
- Biologist and MSc in Chemical Engineering, Laboratory Neurogene, Florianópolis, SC, Brazil
| | - Gisele Rozone de Luca
- Medical Neuropediatrist, Children's Hospital Joana de Gusmão, Florianópolis, SC, Brazil
| | | | | | - Pricila Bernardi
- Medical Geneticist, University Hospital Professor Polydoro Ernani de São Thiago, Florianópolis, SC, Brazil
| | - Angelica Francesca Maris
- Biologist, PhD in Molecular Biology and Genetics, University Professor in the Department of Cell Biology, Embryology and Genetics, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
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Uniparental isodisomy as a cause of recessive Mendelian disease: a diagnostic pitfall with a quick and easy solution in medium/large NGS analyses. Eur J Hum Genet 2018; 26:1392-1395. [PMID: 29891879 DOI: 10.1038/s41431-018-0195-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/10/2018] [Accepted: 05/22/2018] [Indexed: 01/08/2023] Open
Abstract
Complete uniparental isodisomy (iUPD)-the presence of two identical chromosomes in an individual that originate from only a single parental homolog-is an underestimated cause of recessive Mendelian disease in humans. Correctly identifying iUPD in an index patient is of enormous consequence to correctly counseling the family/couple, as the recurrence risk for siblings is reduced from 25% to usually <1%. In medium/large-scale NGS analyses, we found that complete iUPD can be rapidly and straightforwardly inferred from a singleton dataset (index patient only) through a simple chromosome- and genotype-filtering step in <1 min. We discuss the opportunities of iUPD detection in medium/large-scale NGS analyses by example of a case of CHRNG-associated multiple pterygium syndrome due to complete maternal iUPD. Using computer simulations for several detection thresholds, we validate and estimate sensitivity, specificity, positive (PPV), and negative predictive values (NPV) of the proposed screening method for reliable detection of complete iUPD. When screening for complete iUPD, our models suggest that a >85% proportion of homozygous calls on a single chromosome with ≥30 sufficiently interspaced called variants results in a sensitivity of 97.9% and specificity of 99.7%. The PPV is 95.1%, the NPV 99.9%. When this threshold is exceeded for a chromosome on which a patient harbors an apparently homozygous disease-associated variant, it should be sufficient cause to discuss iUPD as a plausible or probable mechanism of disease in the genetic analysis report, even when parental segregation has not (yet) been performed.
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31
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The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:306-327. [PMID: 29309830 DOI: 10.1016/j.pnpbp.2017.12.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/19/2017] [Accepted: 12/24/2017] [Indexed: 12/13/2022]
Abstract
The complexity of the human brain emerges from a long and finely tuned developmental process orchestrated by the crosstalk between genome and environment. Vis à vis other species, the human brain displays unique functional and morphological features that result from this extensive developmental process that is, unsurprisingly, highly vulnerable to both genetically and environmentally induced alterations. One of the most striking outcomes of the recent surge of sequencing-based studies on neurodevelopmental disorders (NDDs) is the emergence of chromatin regulation as one of the two domains most affected by causative mutations or Copy Number Variations besides synaptic function, whose involvement had been largely predicted for obvious reasons. These observations place chromatin dysfunction at the top of the molecular pathways hierarchy that ushers in a sizeable proportion of NDDs and that manifest themselves through synaptic dysfunction and recurrent systemic clinical manifestation. Here we undertake a conceptual investigation of chromatin dysfunction in NDDs with the aim of systematizing the available evidence in a new framework: first, we tease out the developmental vulnerabilities in human corticogenesis as a structuring entry point into the causation of NDDs; second, we provide a much needed clarification of the multiple meanings and explanatory frameworks revolving around "epigenetics", highlighting those that are most relevant for the analysis of these disorders; finally we go in-depth into paradigmatic examples of NDD-causing chromatin dysregulation, with a special focus on human experimental models and datasets.
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32
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Tesner P, Vlckova M, Drabova J, Vseticka J, Klimova A, Lastuvkova J, Zidovska J, Kremlikova Pourova R, Hancarova M, Sedlacek Z, Kocarek E. Molecular Cytogenetic Diagnostics of Marker Chromosomes: Analysis in Four Prenatal Cases and Long-Term Clinical Evaluation of Carriers. Cytogenet Genome Res 2018; 154:187-195. [DOI: 10.1159/000488790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2018] [Indexed: 01/15/2023] Open
Abstract
The prenatal finding of a small supernumerary marker chromosome (sSMC) is a challenge for genetic counseling. Our analytic algorithm is based on sSMC frequencies and multicolor FISH to accelerate the procedure. The chromosomal origin, size, and degree of mosaicism of the sSMC then determine the prognosis. We illustrate the effectiveness on 4 prenatally identified de novo mosaic sSMCs derived from chromosomes 13/21, X, 3, and 17. Three sSMC carriers had a good prognosis and apparently healthy children were born, showing no abnormality till the last examination at the age of 4 years. One case had a poor prognosis, and the parents decided to terminate the pregnancy. Our work contributes to the laboratory and clinical management of prenatally detected sSMCs. FISH is a reliable method for fast sSMC evaluation and prognosis assessment; it prevents unnecessary delays and uncertainty, allows informed decision making, and reduces unnecessary pregnancy terminations.
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Vigilin interacts with CTCF and is involved in the maintenance of imprinting of IGF2 through a novel RNA-mediated mechanism. Int J Biol Macromol 2017; 108:515-522. [PMID: 29157910 DOI: 10.1016/j.ijbiomac.2017.11.109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 12/16/2022]
Abstract
Accumulating evidence has revealed the imprinting of insulin-like growth factor-2 gene (IGF2) is maintained by binding of CCCTC binding factor (CTCF) to the unmethylated imprinting control region (ICR) between IGF2 and H19 genes. We have previously reported that high-density lipoprotein binding protein (HDLBP/vigilin), a multiKH-domain protein, interacts with CTCF and coexists with it at several CTCF-binding sites on the ICR to regulate general gene expression of IGF2. However, the impact of the interaction on imprinting of IGF2 remains unclear. Here, we demonstrate that cooperation of vigilin and CTCF protects IGF2 from losing of imprinting. Pull-down experiments show that KH1-7 domains of vigilin interact with zinc-finger domains of CTCF. We also display that some RNAs participate in the vigilin-CTCF interaction, one of which is H19 long noncoding RNA (lncRNA). Furthermore, we confirm that H19 lncRNA-knockdown alters the imprinting of IGF2. These data suggest that vigilin interacts with CTCF, mediated by H19 lncRNA, to keep the imprinting of IGF2.
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