1
|
Eggermann T. Human Reproduction and Disturbed Genomic Imprinting. Genes (Basel) 2024; 15:163. [PMID: 38397153 PMCID: PMC10888310 DOI: 10.3390/genes15020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Genomic imprinting is a specific mode of gene regulation which particularly accounts for the factors involved in development. Its disturbance affects the fetus, the course of pregnancy and even the health of the mother. In children, aberrant imprinting signatures are associated with imprinting disorders (ImpDis). These alterations also affect the function of the placenta, which has consequences for the course of the pregnancy. The molecular causes of ImpDis comprise changes at the DNA level and methylation disturbances (imprinting defects/ImpDefs), and there is an increasing number of reports of both pathogenic fetal and maternal DNA variants causing ImpDefs. These ImpDefs can be inherited, but prediction of the pregnancy complications caused is difficult, as they can cause miscarriages, aneuploidies, health issues for the mother and ImpDis in the child. Due to the complexity of imprinting regulation, each pregnancy or patient with suspected altered genomic imprinting requires a specific workup to identify the precise molecular cause and also careful clinical documentation. This review will cover the current knowledge on the molecular causes of aberrant imprinting signatures and illustrate the need to identify this basis as the prerequisite for personalized genetic and reproductive counselling of families.
Collapse
Affiliation(s)
- Thomas Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH University Aachen, Pauwelsstr. 3, D-52074 Aachen, Germany
| |
Collapse
|
2
|
Trapphoff T, Dieterle S. Cryopreservation of Ovarian and Testicular Tissue and the Influence on Epigenetic Pattern. Int J Mol Sci 2023; 24:11061. [PMID: 37446239 DOI: 10.3390/ijms241311061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/29/2023] [Accepted: 07/02/2023] [Indexed: 07/15/2023] Open
Abstract
Ovarian tissue cryopreservation (OTC) or testicular tissue cryopreservation (TTC) are effective and often the only options for fertility preservation in female or male patients due to oncological, medical, or social aspects. While TTC and resumption of spermatogenesis, either in vivo or in vitro, has still be considered an experimental approach in humans, OTC and autotransplantation has been applied increasingly to preserve fertility, with more than 200 live births worldwide. However, the cryopreservation of reproductive cells followed by the resumption of gametogenesis, either in vivo or in vitro, may interfere with sensitive and highly regulated cellular processes. In particular, the epigenetic profile, which includes not just reversible modifications of the DNA itself but also post-translational histone modifications, small non-coding RNAs, gene expression and availability, and storage of related proteins or transcripts, have to be considered in this context. Due to complex reprogramming and maintenance mechanisms of the epigenome in germ cells, growing embryos, and offspring, OTC and TTC are carried out at very critical moments early in the life cycle. Given this background, the safety of OTC and TTC, taking into account the epigenetic profile, has to be clarified. Cryopreservation of mature germ cells (including metaphase II oocytes and mature spermatozoa collected via ejaculation or more invasively after testicular biopsy) or embryos has been used successfully for many years in medically assisted reproduction (MAR). However, tissue freezing followed by in vitro or in vivo gametogenesis has become more attractive in the past, while few human studies have analysed the epigenetic effects, with most data deriving from animal studies. In this review, we highlight the potential influence of the cryopreservation of immature germ cells and subsequent in vivo or in vitro growth and differentiation on the epigenetic profile (including DNA methylation, post-translational histone modifications, and the abundance and availability of relevant transcripts and proteins) in humans and animals.
Collapse
Affiliation(s)
| | - Stefan Dieterle
- Dortmund Fertility Centre, 44135 Dortmund, Germany
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Witten/Herdecke University, 44135 Dortmund, Germany
| |
Collapse
|
3
|
Abstract
Monogenic diabetes includes several clinical conditions generally characterized by early-onset diabetes, such as neonatal diabetes, maturity-onset diabetes of the young (MODY) and various diabetes-associated syndromes. However, patients with apparent type 2 diabetes mellitus may actually have monogenic diabetes. Indeed, the same monogenic diabetes gene can contribute to different forms of diabetes with early or late onset, depending on the functional impact of the variant, and the same pathogenic variant can produce variable diabetes phenotypes, even in the same family. Monogenic diabetes is mostly caused by impaired function or development of pancreatic islets, with defective insulin secretion in the absence of obesity. The most prevalent form of monogenic diabetes is MODY, which may account for 0.5-5% of patients diagnosed with non-autoimmune diabetes but is probably underdiagnosed owing to insufficient genetic testing. Most patients with neonatal diabetes or MODY have autosomal dominant diabetes. More than 40 subtypes of monogenic diabetes have been identified to date, the most prevalent being deficiencies of GCK and HNF1A. Precision medicine approaches (including specific treatments for hyperglycaemia, monitoring associated extra-pancreatic phenotypes and/or following up clinical trajectories, especially during pregnancy) are available for some forms of monogenic diabetes (including GCK- and HNF1A-diabetes) and increase patients' quality of life. Next-generation sequencing has made genetic diagnosis affordable, enabling effective genomic medicine in monogenic diabetes.
Collapse
|
4
|
Connally NJ, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C, Cassa CA, Sunyaev SR. The missing link between genetic association and regulatory function. eLife 2022; 11:74970. [PMID: 36515579 PMCID: PMC9842386 DOI: 10.7554/elife.74970] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
The genetic basis of most traits is highly polygenic and dominated by non-coding alleles. It is widely assumed that such alleles exert small regulatory effects on the expression of cis-linked genes. However, despite the availability of gene expression and epigenomic datasets, few variant-to-gene links have emerged. It is unclear whether these sparse results are due to limitations in available data and methods, or to deficiencies in the underlying assumed model. To better distinguish between these possibilities, we identified 220 gene-trait pairs in which protein-coding variants influence a complex trait or its Mendelian cognate. Despite the presence of expression quantitative trait loci near most GWAS associations, by applying a gene-based approach we found limited evidence that the baseline expression of trait-related genes explains GWAS associations, whether using colocalization methods (8% of genes implicated), transcription-wide association (2% of genes implicated), or a combination of regulatory annotations and distance (4% of genes implicated). These results contradict the hypothesis that most complex trait-associated variants coincide with homeostatic expression QTLs, suggesting that better models are needed. The field must confront this deficit and pursue this 'missing regulation.'
Collapse
Affiliation(s)
- Noah J Connally
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Sumaiya Nazeen
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Huwenbo Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | | | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s HospitalBostonUnited States
| | - Chris Cotsapas
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Neurology, Yale Medical SchoolNew HavenUnited States
- Department of Genetics, Yale Medical SchoolNew HavenUnited States
| | - Christopher A Cassa
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| |
Collapse
|
5
|
León I, Herrero Roldán S, Rodrigo MJ, López Rodríguez M, Fisher J, Mitchell C, Lage-Castellanos A. The shared mother-child epigenetic signature of neglect is related to maternal adverse events. Front Physiol 2022; 13:966740. [PMID: 36091392 PMCID: PMC9448913 DOI: 10.3389/fphys.2022.966740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Studies of DNA methylation have revealed the biological mechanisms by which life adversity confers risk for later physical and mental health problems. What remains unknown is the “biologically embedding” of maternal adverse experiences resulting in maladaptive parenting and whether these epigenetic effects are transmitted to the next generation. This study focuses on neglectful mothering indexed by a severe disregard for the basic and psychological needs of the child. Using the Illumina Human Methylation EPIC BeadChip in saliva samples, we identified genes with differentially methylated regions (DMRs) in those mothers with (n = 51), versus those without (n = 87), neglectful behavior that present similar DMRs patterns in their children being neglected versus non-neglected (n = 40 vs. 75). Mothers reported the emotional intensity of adverse life events. After covariate adjustment and multiple testing corrections, we identified 69 DMRs in the mother epigenome and 42 DMRs in the child epigenome that were simultaneously above the α = 0.01 threshold. The common set of nine DMRs contained genes related to childhood adversity, neonatal and infant diabetes, child neurobehavioral development and other health problems such as obesity, hypertension, cancer, posttraumatic stress, and the Alzheimer’s disease; four of the genes were associated with maternal life adversity. Identifying a shared epigenetic signature of neglect linked to maternal life adversity is an essential step in breaking the intergenerational transmission of one of the most common forms of childhood maltreatment.
Collapse
Affiliation(s)
- Inmaculada León
- Instituto Universitario de Neurociencia, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
| | - Silvia Herrero Roldán
- Instituto Universitario de Neurociencia, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
- *Correspondence: Silvia Herrero Roldán,
| | - María José Rodrigo
- Instituto Universitario de Neurociencia, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
| | - Maykel López Rodríguez
- Department of Pathology and Experimental Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, United States
| | - Jonah Fisher
- Institute for Social Research, University of Michigan, Ann Abor, MI, United States
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, Ann Abor, MI, United States
| | - Agustín Lage-Castellanos
- Department of NeuroInformatics, Cuban Center for Neuroscience, Havana, Cuba
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
| |
Collapse
|
6
|
Kontbay T, Atar M, Demirbilek H. Long-term follow-up of transient neonatal diabetes mellitus due to a novel homozygous c.7734C>T (p.R228C) mutation in ZFP57 gene: relapse at prepubertal age. J Pediatr Endocrinol Metab 2022; 35:695-698. [PMID: 35218690 DOI: 10.1515/jpem-2021-0538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 01/30/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Neonatal diabetes mellitus (NDM) is a rare form of monogenic diabetes present within the first six months of life. NDM can be transient (TNdM) or permanent (PNDM). About 70% of TNDM cases have abnormalities in the imprinted region of chromosome 6q24. In TNDM, diabetes remits at infancy whilst may relapse later in life. Chromosome 6q24 related TNDM usually relapses at the pubertal period, while in some cases, relapse occurs earlier. It has been reported that these cases can respond to sulfonylurea treatment, while more evidence and experience are needed. CASE PRESENTATION Herein, we reported relapse of diabetes at prepubertal age and its response to sulphonylurea therapy in a case with TNDM due to a homozygous c.7734C>T (p.R228C) variant in the ZFP57 gene. CONCLUSIONS A response to the sulphonylurea monotherapy seems not optimal for relapsed TNDM due to chromosome 6q24 abnormalities.
Collapse
Affiliation(s)
- Tuğba Kontbay
- Şanlıurfa Training and Research Hospital, Şanlıurfa, Turkey
| | - Müge Atar
- Şanlıurfa Training and Research Hospital, Şanlıurfa, Turkey
| | - Hüseyin Demirbilek
- Department of Pediatric Endocrinology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| |
Collapse
|
7
|
Qian J, Guo F. De novo programming: establishment of epigenome in mammalian oocytes. Biol Reprod 2022; 107:40-53. [PMID: 35552602 DOI: 10.1093/biolre/ioac091] [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: 12/20/2021] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 11/14/2022] Open
Abstract
Innovations in ultrasensitive and single-cell measurements enable us to study layers of genome regulation in the view of cellular and regulatory heterogeneity. Genome-scale mapping allows to evaluate epigenetic features and dynamics in different genomic contexts, including genebodies, CGIs, ICRs, promoters, PMDs, and repetitive elements. The epigenome of early embryos, fetal germ cells, and sperm has been extensively studied for the past decade, while oocytes remain less clear. Emerging evidence now supports the notion that transcription and chromatin accessibility precede de novo DNA methylation in both human and mouse oocytes. Recent studies also start to chart correlations among different histone modifications and DNA methylation. We discussed the potential mechanistic hierarchy by which shapes oocyte DNA methylome, also provided insights into the convergent and divergent features between human and mice.
Collapse
Affiliation(s)
- Jingjing Qian
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Fan Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
8
|
Tayeh MK, DeVaul J, LeSueur K, Yang C, Bedoyan JK, Thomas P, Hannibal MC, Innis JW. Novel multilocus imprinting disturbances in a child with expressive language delay and intellectual disability. Am J Med Genet A 2022; 188:2209-2216. [PMID: 35365979 PMCID: PMC9321834 DOI: 10.1002/ajmg.a.62752] [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: 12/10/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022]
Abstract
Multilocus imprinting disturbances (MLID) have been associated with up to 12% of patients with Beckwith‐Wiedemann syndrome, Silver‐Russell syndrome, and pseudohypoparathyroidism type 1B (PHP1B). Single‐gene defects affecting components of the subcortical maternal complex (SCMC) have been reported in cases with multilocus hypomethylation defects. We present a patient with speech and language impairment with mild Angelman syndrome (AS) features who demonstrates maternal hypomethylation at 15q11.2 (SNRPN) as well as 11p15.5 (KCNQ1OT1) imprinted loci, but normal methylation at 6q24.2 (PLAGL1), 7p12.1 (GRB10), 7q32.2 (MEST), 11p15.5 (H19), 14q32.2 (MEG3), 19q13.43 (PEG3), and 20q13.32 (GNAS and GNAS‐AS1). The proband also has no copy number nor sequence variants within the AS imprinting center or in UBE3A. Maternal targeted next generation sequencing did not identify any pathogenic variants in ZPF57, NLRP2, NLRP5, NLRP7, KHDC3L, PADI6, TLE6, OOEP, UHRF1 or ZAR1. The presence of very delayed, yet functional speech, behavioral difficulties, EEG abnormalities but without clinical seizures, and normocephaly are consistent with the 15q11.2 hypomethylation defect observed in this patient. To our knowledge, this is the first report of MLID in a patient with mild, likely mosaic, Angelman syndrome.
Collapse
Affiliation(s)
- Marwan K Tayeh
- Department of Medical and Molecular Genetics, Division of Indiana, University Genetics Testing Laboratories, Indiana University, Indianapolis, Indiana, USA
| | - Janean DeVaul
- Department of Pediatrics, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Kristin LeSueur
- Department of Pediatrics, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Chen Yang
- Department of Pediatrics, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jirair K Bedoyan
- Department of Pediatrics, Division of Genetic and Genomic Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Peedikayil Thomas
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Mark C Hannibal
- Department of Pediatrics, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jeffrey W Innis
- Department of Pediatrics, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
9
|
Eggermann T, Yapici E, Bliek J, Pereda A, Begemann M, Russo S, Tannorella P, Calzari L, de Nanclares GP, Lombardi P, Temple IK, Mackay D, Riccio A, Kagami M, Ogata T, Lapunzina P, Monk D, Maher ER, Tümer Z. Trans-acting genetic variants causing multilocus imprinting disturbance (MLID): common mechanisms and consequences. Clin Epigenetics 2022; 14:41. [PMID: 35296332 PMCID: PMC8928698 DOI: 10.1186/s13148-022-01259-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/28/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Imprinting disorders are a group of congenital diseases which are characterized by molecular alterations affecting differentially methylated regions (DMRs). To date, at least twelve imprinting disorders have been defined with overlapping but variable clinical features including growth and metabolic disturbances, cognitive dysfunction, abdominal wall defects and asymmetry. In general, a single specific DMR is affected in an individual with a given imprinting disorder, but there are a growing number of reports on individuals with so-called multilocus imprinting disturbances (MLID), where aberrant imprinting marks (most commonly loss of methylation) occur at multiple DMRs. However, as the literature is fragmented, we reviewed the molecular and clinical data of 55 previously reported or newly identified MLID families with putative pathogenic variants in maternal effect genes (NLRP2, NLRP5, NLRP7, KHDC3L, OOEP, PADI6) and in other candidate genes (ZFP57, ARID4A, ZAR1, UHRF1, ZNF445). RESULTS In 55 families, a total of 68 different candidate pathogenic variants were identified (7 in NLRP2, 16 in NLRP5, 7 in NLRP7, 17 in PADI6, 15 in ZFP57, and a single variant in each of the genes ARID4A, ZAR1, OOEP, UHRF1, KHDC3L and ZNF445). Clinical diagnoses of affected offspring included Beckwith-Wiedemann syndrome spectrum, Silver-Russell syndrome spectrum, transient neonatal diabetes mellitus, or they were suspected for an imprinting disorder (undiagnosed). Some families had recurrent pregnancy loss. CONCLUSIONS Genomic maternal effect and foetal variants causing MLID allow insights into the mechanisms behind the imprinting cycle of life, and the spatial and temporal function of the different factors involved in oocyte maturation and early development. Further basic research together with identification of new MLID families will enable a better understanding of the link between the different reproductive issues such as recurrent miscarriages and preeclampsia in maternal effect variant carriers/families and aneuploidy and the MLID observed in the offsprings. The current knowledge can already be employed in reproductive and genetic counselling in specific situations.
Collapse
Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.
| | - Elzem Yapici
- grid.1957.a0000 0001 0728 696XInstitute of Human Genetics, Medical Faculty, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Jet Bliek
- grid.509540.d0000 0004 6880 3010Department of Human Genetics, Laboratory for Genome Diagnostics, Amsterdam UMC, Amsterdam, Netherlands
| | - Arrate Pereda
- grid.468902.10000 0004 1773 0974Molecular (Epi)Genetics Laboratory, Bioaraba Health Research Institute, Hospital Universitario Araba-Txagorritxu, Vitoria-Gasteiz, Alava Spain
| | - Matthias Begemann
- grid.1957.a0000 0001 0728 696XInstitute of Human Genetics, Medical Faculty, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Silvia Russo
- grid.418224.90000 0004 1757 9530Research Laboratory of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Pierpaola Tannorella
- grid.418224.90000 0004 1757 9530Research Laboratory of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Luciano Calzari
- grid.418224.90000 0004 1757 9530Research Laboratory of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Guiomar Perez de Nanclares
- grid.468902.10000 0004 1773 0974Molecular (Epi)Genetics Laboratory, Bioaraba Health Research Institute, Hospital Universitario Araba-Txagorritxu, Vitoria-Gasteiz, Alava Spain
| | - Paola Lombardi
- grid.509540.d0000 0004 6880 3010Department of Human Genetics, Laboratory for Genome Diagnostics, Amsterdam UMC, Amsterdam, Netherlands
| | - I. Karen Temple
- grid.123047.30000000103590315Wessex Clinical Genetics Service, University Hospital Southampton, Southampton, UK ,grid.430506.40000 0004 0465 4079Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Deborah Mackay
- grid.430506.40000 0004 0465 4079Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Andrea Riccio
- grid.9841.40000 0001 2200 8888Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania ‘Luigi Vanvitelli’, Caserta, Italy ,grid.419869.b0000 0004 1758 2860Institute of Genetics and Biophysics ‘Adriano Buzzati–Traverso’ CNR, Naples, Italy
| | - Masayo Kagami
- grid.63906.3a0000 0004 0377 2305Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Ohkura, Setagayaku, Tokyo, Japan
| | - Tsutomu Ogata
- grid.413553.50000 0004 1772 534XDepartment of Pediatrics, Hamamatsu Medical Center, Hamamatsu, Japan ,grid.505613.40000 0000 8937 6696Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Pablo Lapunzina
- grid.81821.320000 0000 8970 9163CIBERER-ISCIII and INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain ,ERN-Ithaca, European Reference Networks, Madrid, Spain
| | - David Monk
- grid.8273.e0000 0001 1092 7967School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Eamonn R. Maher
- grid.24029.3d0000 0004 0383 8386Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ UK ,grid.24029.3d0000 0004 0383 8386Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ UK
| | - Zeynep Tümer
- grid.475435.4Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
10
|
Vázquez-Mosquera ME, González-Vioque E, Barbosa-Gouveia S, Bellido-Guerrero D, Tejera-Pérez C, Martinez-Olmos MA, Fernández-Pombo A, Castaño-González LA, Chans-Gerpe R, Couce ML. Transcriptomic analysis of patients with clinical suspicion of maturity-onset diabetes of the young (MODY) with a negative genetic diagnosis. Orphanet J Rare Dis 2022; 17:105. [PMID: 35246208 PMCID: PMC8896342 DOI: 10.1186/s13023-022-02263-3] [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: 09/27/2021] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Background Diagnosis of mature-onset diabetes of the young (MODY), a non-autoimmune monogenic form of diabetes mellitus, is confirmed by genetic testing. However, a positive genetic diagnosis is achieved in only around 50% of patients with clinical characteristics of this disease. Results We evaluated the diagnostic utility of transcriptomic analysis in patients with clinical suspicion of MODY but a negative genetic diagnosis. Using Nanostring nCounter technology, we conducted transcriptomic analysis of 19 MODY-associated genes in peripheral blood samples from 19 patients and 8 healthy controls. Normalized gene expression was compared between patients and controls and correlated with each patient’s biochemical and clinical variables. Z-scores were calculated to identify significant changes in gene expression in patients versus controls. Only 7 of the genes analyzed were detected in peripheral blood. HADH expression was significantly lower in patients versus controls. Among patients with suspected MODY, GLIS3 expression was higher in obese versus normal-weight patients, and in patients aged < 25 versus > 25 years at diabetes onset. Significant alteration with respect to controls of any gene was observed in 57.9% of patients. Conclusions Although blood does not seem to be a suitable sample for transcriptomic analysis of patients with suspected MODY, in our study, we detected expression alterations in some of the genes studied in almost 58% of patients. That opens the door for future studies that can clarify the molecular cause of the clinic of these patients and thus be able to maintain a more specific follow-up and treatment in each case. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02263-3.
Collapse
Affiliation(s)
- María E Vázquez-Mosquera
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,European Reference Network for Hereditary Metabolic Disorders (MetabERN), Padova, Italy
| | - Emiliano González-Vioque
- Division of Clinical Biochemistry, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Sofía Barbosa-Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,European Reference Network for Hereditary Metabolic Disorders (MetabERN), Padova, Italy
| | | | - Cristina Tejera-Pérez
- Division of Endocrinology, Complejo Hospitalario Universitario de Ferrol, Ferrol, Spain
| | - Miguel A Martinez-Olmos
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,Division of Endocrinology and Nutrition, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Antía Fernández-Pombo
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,Division of Endocrinology and Nutrition, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Luis A Castaño-González
- Endocrinology and Diabetes Research Group, Instituto de Investigación Sanitaria BioCruces, Barakaldo, Spain
| | - Roi Chans-Gerpe
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,European Reference Network for Hereditary Metabolic Disorders (MetabERN), Padova, Italy
| | - María L Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain. .,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain. .,Universidad de Santiago de Compostela, Santiago de Compostela, Spain. .,European Reference Network for Hereditary Metabolic Disorders (MetabERN), Padova, Italy.
| |
Collapse
|
11
|
Yahaya TO, Anyebe DA. Genes predisposing to neonatal diabetes mellitus and pathophysiology: Current findings. J Neonatal Perinatal Med 2021; 13:543-553. [PMID: 32333556 DOI: 10.3233/npm-190353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Precision medicine, described as a therapeutic procedure in which complex diseases are treated based on the causal gene and pathophysiology, is being considered for diabetes mellitus (DM). To this end, several monogenetic mutations in the beta cells have been linked with neonatal diabetes mellitus (NDM), however, the list of suspect genes is expansive, necessitating an update. This study, therefore, provides an update on NDM candidate genes and pathophysiology. RESULTS Reputable online academic databases were searched for relevant information, which led to the identification of 43 genes whose mutations are linked to the condition. Of the linked genes, mutations in the KCNJ11, ABCC8, and INS genes as well as the genes on 6q24 chromosomal region are the most frequently implicated. Mutations in these genes can cause pancreatic agenesis and developmental errors, resulting in NDM in the first six to twelve months of birth. The clinical presentations of NDM include frequent urination, rapid breathing, and dehydration, among others. CONCLUSIONS Monogenetic mutations in the beta cells may cause NDM with distinct pathophysiology from other DM. Treatment options that target NDM candidate genes and pathophysiology may lead to an improved treatment compared with the present generalized treatment for all forms of DM.
Collapse
Affiliation(s)
- T O Yahaya
- Department of Biology, Federal University Birnin Kebbi, Nigeria
| | - D A Anyebe
- Department of Biochemistry and Molecular Biology, Federal University Birnin Kebbi, Nigeria
| |
Collapse
|
12
|
Transient Neonatal Diabetes Mellitus with the Rare Association of Nonsuppurative Sialadenitis and Genetic Defects in 6q24. Case Rep Pediatr 2021; 2021:5901898. [PMID: 34422424 PMCID: PMC8376448 DOI: 10.1155/2021/5901898] [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: 05/28/2021] [Accepted: 08/04/2021] [Indexed: 11/17/2022] Open
Abstract
Background Transient neonatal diabetes mellitus (TNDM) is the most common cause of diabetes in the first week of life, with an overall incidence of 1 in 90,000 to 160,000 live births. TNDM occurs soon after birth and undergoes spontaneous remission during infancy; however, it may relapse to a permanent form of diabetes mellitus in childhood or adolescence. We report a case of TNDM due to hypomethylation on chromosome 6q24, associated with a rare clinical finding of nonsuppurative submandibular sialadenitis managed by subcutaneous insulin, and who underwent remission by three months of age. Case Presentation. We report a male neonate of Arab ancestry delivered by caesarean section at 37 weeks of gestation. He had intrauterine growth retardation with a birth weight of 2.099 kg. He presented with hyperglycemia on the first day of life, which was managed with parenteral insulin infusion. Blood glucose control was initially difficult to achieve due to difficulties in preparing such small doses of insulin and the significant variations in blood glucose concentrations, without ketosis. Blood tests revealed low serum insulin and C-peptide levels. Genetic analysis revealed multiple loci hypomethylation of the PLAGL1/HYMAI-DMR in the TNDM region in chromosome 6q24 and two pathogenic heterozygous variants in the ZFP57 gene. Segregation analysis showed that both parents were heterozygous carriers of familial ZFP57 variants. The clinical course was associated with bilateral nonsuppurative sialadenitis, which is extremely rare among newborns. Conclusion Sialadenitis is a well-known phenomenon that is rarely diagnosed in neonates. To the best of our knowledge, this is the first case report to describe the exceedingly rare association of nonsuppurative submandibular sialadenitis in a neonate with TNDM due to multiple loci hypomethylation of the PLAGL1/HYMAI-DMR in the TNDM region in 6q24 and heterozygous pathogenic variants in the ZFP57 gene.
Collapse
|
13
|
Müller JA, Groß R, Conzelmann C, Krüger J, Merle U, Steinhart J, Weil T, Koepke L, Bozzo CP, Read C, Fois G, Eiseler T, Gehrmann J, van Vuuren J, Wessbecher IM, Frick M, Costa IG, Breunig M, Grüner B, Peters L, Schuster M, Liebau S, Seufferlein T, Stenger S, Stenzinger A, MacDonald PE, Kirchhoff F, Sparrer KMJ, Walther P, Lickert H, Barth TFE, Wagner M, Münch J, Heller S, Kleger A. SARS-CoV-2 infects and replicates in cells of the human endocrine and exocrine pancreas. Nat Metab 2021; 3:149-165. [PMID: 33536639 DOI: 10.1038/s42255-021-00347-1] [Citation(s) in RCA: 319] [Impact Index Per Article: 106.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/14/2021] [Indexed: 02/07/2023]
Abstract
Infection-related diabetes can arise as a result of virus-associated β-cell destruction. Clinical data suggest that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the coronavirus disease 2019 (COVID-19), impairs glucose homoeostasis, but experimental evidence that SARS-CoV-2 can infect pancreatic tissue has been lacking. In the present study, we show that SARS-CoV-2 infects cells of the human exocrine and endocrine pancreas ex vivo and in vivo. We demonstrate that human β-cells express viral entry proteins, and SARS-CoV-2 infects and replicates in cultured human islets. Infection is associated with morphological, transcriptional and functional changes, including reduced numbers of insulin-secretory granules in β-cells and impaired glucose-stimulated insulin secretion. In COVID-19 full-body postmortem examinations, we detected SARS-CoV-2 nucleocapsid protein in pancreatic exocrine cells, and in cells that stain positive for the β-cell marker NKX6.1 and are in close proximity to the islets of Langerhans in all four patients investigated. Our data identify the human pancreas as a target of SARS-CoV-2 infection and suggest that β-cell infection could contribute to the metabolic dysregulation observed in patients with COVID-19.
Collapse
Affiliation(s)
- Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Carina Conzelmann
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Jana Krüger
- Department of Internal Medicine 1, Ulm University Hospital, Ulm, Germany
| | - Uta Merle
- Department of Internal Medicine 4, University of Heidelberg, Heidelberg, Germany
| | | | - Tatjana Weil
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Clarissa Read
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Giorgio Fois
- Institute of General Physiology, Ulm University, Ulm, Germany
| | - Tim Eiseler
- Department of Internal Medicine 1, Ulm University Hospital, Ulm, Germany
| | - Julia Gehrmann
- Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Joanne van Vuuren
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich, Munich, Germany
| | - Isabel M Wessbecher
- Tissue Bank of the German Center for Infection Research, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Manfred Frick
- Institute of General Physiology, Ulm University, Ulm, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Markus Breunig
- Department of Internal Medicine 1, Ulm University Hospital, Ulm, Germany
| | - Beate Grüner
- Department of Internal Medicine 3, Ulm University Hospital, Ulm, Germany
| | - Lynn Peters
- Department of Internal Medicine 3, Ulm University Hospital, Ulm, Germany
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefan Liebau
- Institute of Neuroanatomy & Developmental Biology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Thomas Seufferlein
- Department of Internal Medicine 1, Ulm University Hospital, Ulm, Germany
| | - Steffen Stenger
- Institute for Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | | | - Patrick E MacDonald
- Alberta Diabetes Institute and Department of Pharmacology, University of Alberta, Edmonton, Canada
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Martin Wagner
- Department of Internal Medicine 1, Ulm University Hospital, Ulm, Germany.
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany.
| | - Sandra Heller
- Department of Internal Medicine 1, Ulm University Hospital, Ulm, Germany.
| | - Alexander Kleger
- Department of Internal Medicine 1, Ulm University Hospital, Ulm, Germany.
| |
Collapse
|
14
|
Monteagudo-Sánchez A, Hernandez Mora JR, Simon C, Burton A, Tenorio J, Lapunzina P, Clark S, Esteller M, Kelsey G, López-Siguero JP, de Nanclares GP, Torres-Padilla ME, Monk D. The role of ZFP57 and additional KRAB-zinc finger proteins in the maintenance of human imprinted methylation and multi-locus imprinting disturbances. Nucleic Acids Res 2020; 48:11394-11407. [PMID: 33053156 PMCID: PMC7672439 DOI: 10.1093/nar/gkaa837] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/10/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Genomic imprinting is an epigenetic process regulated by germline-derived DNA methylation that is resistant to embryonic reprogramming, resulting in parental origin-specific monoallelic gene expression. A subset of individuals affected by imprinting disorders (IDs) displays multi-locus imprinting disturbances (MLID), which may result from aberrant establishment of imprinted differentially methylated regions (DMRs) in gametes or their maintenance in early embryogenesis. Here we investigated the extent of MLID in a family harbouring a ZFP57 truncating variant and characterize the interactions between human ZFP57 and the KAP1 co-repressor complex. By ectopically targeting ZFP57 to reprogrammed loci in mouse embryos using a dCas9 approach, we confirm that ZFP57 recruitment is sufficient to protect oocyte-derived methylation from reprogramming. Expression profiling in human pre-implantation embryos and oocytes reveals that unlike in mice, ZFP57 is only expressed following embryonic-genome activation, implying that other KRAB-zinc finger proteins (KZNFs) recruit KAP1 prior to blastocyst formation. Furthermore, we uncover ZNF202 and ZNF445 as additional KZNFs likely to recruit KAP1 to imprinted loci during reprogramming in the absence of ZFP57. Together, these data confirm the perplexing link between KZFPs and imprint maintenance and highlight the differences between mouse and humans in this respect.
Collapse
Affiliation(s)
- Ana Monteagudo-Sánchez
- Imprinting and Cancer group, Bellvitge Institute for Biomedical Research, Gran via, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jose Ramon Hernandez Mora
- Imprinting and Cancer group, Bellvitge Institute for Biomedical Research, Gran via, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Carlos Simon
- Department of Obstetrics and Gynecology, Valencia University and INCLIVA, Valencia, Spain.,Department of Obstetrics and Gynecology, BIDMC, Harvard University, Boston, MA, USA
| | - Adam Burton
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - Jair Tenorio
- Medical and Molecular Genetics Institute, University Hospital La Paz, Madrid, Spain.,CIBERER, Centro de Investigacion Biomedica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Pablo Lapunzina
- Medical and Molecular Genetics Institute, University Hospital La Paz, Madrid, Spain.,CIBERER, Centro de Investigacion Biomedica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability
| | - Stephen Clark
- Epigenetics Programme, The Babraham Institute, Babraham, Cambridge, UK
| | - Manel Esteller
- Josep Carreras Leukeamia Research Institute, Can Ruti, Cami de les Escoles, Badalona, Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Babraham, Cambridge, UK.,Centre for Trophoblast Research, University of Cambridge, UK
| | | | - Guiomar Perez de Nanclares
- (Epi)Genetics Laboratory, BioAraba Research Health Institute, Araba University Hospital, Vitoria-Gasteiz, Alava, Spain
| | | | - David Monk
- Imprinting and Cancer group, Bellvitge Institute for Biomedical Research, Gran via, L'Hospitalet de Llobregat, Barcelona, Spain.,Biomedical Research Centre, University of East Anglia, Norwich Research Park, Norwich, UK
| |
Collapse
|
15
|
Chang S, Bartolomei MS. Modeling human epigenetic disorders in mice: Beckwith-Wiedemann syndrome and Silver-Russell syndrome. Dis Model Mech 2020; 13:dmm044123. [PMID: 32424032 PMCID: PMC7272347 DOI: 10.1242/dmm.044123] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Genomic imprinting, a phenomenon in which the two parental alleles are regulated differently, is observed in mammals, marsupials and a few other species, including seed-bearing plants. Dysregulation of genomic imprinting can cause developmental disorders such as Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS). In this Review, we discuss (1) how various (epi)genetic lesions lead to the dysregulation of clinically relevant imprinted loci, and (2) how such perturbations may contribute to the developmental defects in BWS and SRS. Given that the regulatory mechanisms of most imprinted clusters are well conserved between mice and humans, numerous mouse models of BWS and SRS have been generated. These mouse models are key to understanding how mutations at imprinted loci result in pathological phenotypes in humans, although there are some limitations. This Review focuses on how the biological findings obtained from innovative mouse models explain the clinical features of BWS and SRS.
Collapse
Affiliation(s)
- Suhee Chang
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
16
|
Sousa M, Bruges-Armas J. Monogenic Diabetes: Genetics and Relevance on Diabetes Mellitus Personalized Medicine. Curr Diabetes Rev 2020; 16:807-819. [PMID: 31886753 DOI: 10.2174/1573399816666191230114352] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/11/2019] [Accepted: 12/12/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Diabetes mellitus (DM) is a complex disease with significant impression in today's world. Aside from the most common types recognized over the years, such as type 1 diabetes (T1DM) and type 2 diabetes (T2DM), recent studies have emphasized the crucial role of genetics in DM, allowing the distinction of monogenic diabetes. METHODS Authors did a literature search with the purpose of highlighting and clarifying the subtypes of monogenic diabetes, as well as the accredited genetic entities responsible for such phenotypes. RESULTS The following subtypes were included in this literature review: maturity-onset diabetes of the young (MODY), neonatal diabetes mellitus (NDM) and maternally inherited diabetes and deafness (MIDD). So far, 14 subtypes of MODY have been identified, while three subtypes have been identified in NDM - transient, permanent, and syndromic. DISCUSSION Despite being estimated to affect approximately 2% of all the T2DM patients in Europe, the exact prevalence of MODY is still unknown, accentuating the need for research focused on biomarkers. Consequently, due to its impact in the course of treatment, follow-up of associated complications, and genetic implications for siblings and offspring of affected individuals, it is imperative to diagnose the monogenic forms of DM accurately. CONCLUSION Currently, advances in the genetics field allowed the recognition of new DM subtypes, which until now, were considered slight variations of the typical forms. Thus, it is imperative to act in the close interaction between genetics and clinical manifestations, to facilitate diagnosis and individualize treatment.
Collapse
MESH Headings
- Deafness/classification
- Deafness/diagnosis
- Deafness/genetics
- Diabetes Mellitus, Type 1/diagnosis
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 2/classification
- Diabetes Mellitus, Type 2/diagnosis
- Diabetes Mellitus, Type 2/genetics
- Genetic Testing
- Genotype
- Humans
- Infant
- Infant, Newborn
- Infant, Newborn, Diseases/classification
- Infant, Newborn, Diseases/diagnosis
- Infant, Newborn, Diseases/genetics
- Mitochondrial Diseases/classification
- Mitochondrial Diseases/diagnosis
- Mitochondrial Diseases/genetics
- Mutation
- Phenotype
- Precision Medicine
- Syndrome
Collapse
Affiliation(s)
- Madalena Sousa
- Serviço Especializado de Epidemiologia e Biologia Molecular (SEEBMO), Hospital de Santo Espírito da Ilha Terceira (HSEIT), Angra do Heroísmo, Azores, Portugal
| | - Jácome Bruges-Armas
- Serviço Especializado de Epidemiologia e Biologia Molecular (SEEBMO), Hospital de Santo Espírito da Ilha Terceira (HSEIT), Angra do Heroísmo, Azores, Portugal
| |
Collapse
|
17
|
Bruno M, Mahgoub M, Macfarlan TS. The Arms Race Between KRAB–Zinc Finger Proteins and Endogenous Retroelements and Its Impact on Mammals. Annu Rev Genet 2019; 53:393-416. [DOI: 10.1146/annurev-genet-112618-043717] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nearly half of the human genome consists of endogenous retroelements (EREs) and their genetic remnants, a small fraction of which carry the potential to propagate in the host genome, posing a threat to genome integrity and cell/organismal survival. The largest family of transcription factors in tetrapods, the Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs), binds to specific EREs and represses their transcription. Since their first appearance over 400 million years ago, KRAB-ZFPs have undergone dramatic expansion and diversification in mammals, correlating with the invasions of new EREs. In this article we review our current understanding of the structure, function, and evolution of KRAB-ZFPs and discuss growing evidence that the arms race between KRAB-ZFPs and the EREs they target is a major driving force for the evolution of new traits in mammals, often accompanied by domestication of EREs themselves.
Collapse
Affiliation(s)
- Melania Bruno
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mohamed Mahgoub
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Todd S. Macfarlan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| |
Collapse
|
18
|
|
19
|
Hodges AJ, Hudson NO, Buck-Koehntop BA. Cys 2His 2 Zinc Finger Methyl-CpG Binding Proteins: Getting a Handle on Methylated DNA. J Mol Biol 2019:S0022-2836(19)30567-4. [PMID: 31628952 DOI: 10.1016/j.jmb.2019.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022]
Abstract
DNA methylation is an essential epigenetic modification involved in the maintenance of genomic stability, preservation of cellular identity, and regulation of the transcriptional landscape needed to maintain cellular function. In an increasing number of disease conditions, DNA methylation patterns are inappropriately distributed in a manner that supports the disease phenotype. Methyl-CpG binding proteins (MBPs) are specialized transcription factors that read and translate methylated DNA signals into recruitment of protein assemblies that can alter local chromatin architecture and transcription. MBPs thus play a key intermediary role in gene regulation for both normal and diseased cells. Here, we highlight established and potential structure-function relationships for the best characterized members of the zinc finger (ZF) family of MBPs in propagating DNA methylation signals into downstream cellular responses. Current and future investigations aimed toward expanding our understanding of ZF MBP cellular roles will provide needed mechanistic insight into normal and disease state functions, as well as afford evaluation for the potential of these proteins as epigenetic-based therapeutic targets.
Collapse
Affiliation(s)
- Amelia J Hodges
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Nicholas O Hudson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Bethany A Buck-Koehntop
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA.
| |
Collapse
|
20
|
ZFP57 regulation of transposable elements and gene expression within and beyond imprinted domains. Epigenetics Chromatin 2019; 12:49. [PMID: 31399135 PMCID: PMC6688207 DOI: 10.1186/s13072-019-0295-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/18/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND KRAB zinc finger proteins (KZFPs) represent one of the largest families of DNA-binding proteins in vertebrate genomes and appear to have evolved to silence transposable elements (TEs) including endogenous retroviruses through sequence-specific targeting of repressive chromatin states. ZFP57 is required to maintain the post-fertilization DNA methylation memory of parental origin at genomic imprints. Here we conduct RNA-seq and ChIP-seq analyses in normal and ZFP57 mutant mouse ES cells to understand the relative importance of ZFP57 at imprints, unique and repetitive regions of the genome. RESULTS Over 80% of ZFP57 targets are TEs, however, ZFP57 is not essential for their repression. The remaining targets lie within unique imprinted and non-imprinted sequences. Though the loss of ZFP57 influences imprinted genes as expected, the majority of unique gene targets lose H3K9me3 with little effect on DNA methylation and very few exhibit alterations in expression. Comparison of ZFP57 mutants with DNA methyltransferase-deleted ES cells (TKO) identifies a remarkably similar pattern of H3K9me3 loss across the genome. These data define regions where H3K9me3 is secondary to DNA methylation and we propose that ZFP57 is the principal if not sole methylation-sensitive KZFP in mouse ES cells. Finally, we examine dynamics of DNA and H3K9 methylation during pre-implantation development and show that sites bound by ZFP57 in ES cells maintain DNA methylation and H3K9me3 at imprints and at non-imprinted regions on the maternally inherited chromosome throughout preimplantation development. CONCLUSION Our analyses suggest the evolution of a rare DNA methylation-sensitive KZFP that is not essential for repeat silencing, but whose primary function is to maintain DNA methylation and repressive histone marks at germline-derived imprinting control regions.
Collapse
|
21
|
Reimann B, Janssen BG, Alfano R, Ghantous A, Espín-Pérez A, de Kok TM, Saenen ND, Cox B, Robinson O, Chadeau-Hyam M, Penders J, Herceg Z, Vineis P, Nawrot TS, Plusquin M. The Cord Blood Insulin and Mitochondrial DNA Content Related Methylome. Front Genet 2019; 10:325. [PMID: 31031804 PMCID: PMC6474284 DOI: 10.3389/fgene.2019.00325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/25/2019] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial dysfunction seems to play a key role in the etiology of insulin resistance. At birth, a link has already been established between mitochondrial DNA (mtDNA) content and insulin levels in cord blood. In this study, we explore shared epigenetic mechanisms of the association between mtDNA content and insulin levels, supporting the developmental origins of this link. First, the association between cord blood insulin and mtDNA content in 882 newborns of the ENVIRONAGE birth cohort was assessed. Cord blood mtDNA content was established via qPCR, while cord blood levels of insulin were determined using electrochemiluminescence immunoassays. Then the cord blood DNA methylome and transcriptome were determined in 179 newborns, using the human 450K methylation Illumina and Agilent Whole Human Genome 8 × 60 K microarrays, respectively. Subsequently, we performed an epigenome-wide association study (EWAS) adjusted for different maternal and neonatal variables. Afterward, we focused on the 20 strongest associations based on p-values to assign transcriptomic correlates and allocate corresponding pathways employing the R packages ReactomePA and RDAVIDWebService. On the regional level, we examined differential methylation using the DMRcate and Bumphunter packages in R. Cord blood mtDNA content and insulin were significantly correlated (r = 0.074, p = 0.028), still showing a trend after additional adjustment for maternal and neonatal variables (p = 0.062). We found an overlap of 33 pathways which were in common between the association with cord blood mtDNA content and insulin levels, including pathways of neurodevelopment, histone modification, cytochromes P450 (CYP)-metabolism, and biological aging. We further identified a DMR annotated to Repulsive Guidance Molecule BMP Co-Receptor A (RGMA) linked to cord blood insulin as well as mtDNA content. Metabolic variation in early life represented by neonatal insulin levels and mtDNA content might reflect or accommodate alterations in neurodevelopment, histone modification, CYP-metabolism, and aging, indicating etiological origins in epigenetic programming. Variation in metabolic hormones at birth, reflected by molecular changes, might via these alterations predispose children to metabolic diseases later in life. The results of this study may provide important markers for following targeted studies.
Collapse
Affiliation(s)
- Brigitte Reimann
- Centre for Environmental Sciences, University of Hasselt, Hasselt, Belgium
| | - Bram G. Janssen
- Centre for Environmental Sciences, University of Hasselt, Hasselt, Belgium
| | - Rossella Alfano
- Centre for Environmental Sciences, University of Hasselt, Hasselt, Belgium
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Almudena Espín-Pérez
- Department of Biomedical Informatics Research, Stanford University, California, CA, United States
| | - Theo M. de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Nelly D. Saenen
- Centre for Environmental Sciences, University of Hasselt, Hasselt, Belgium
| | - Bianca Cox
- Centre for Environmental Sciences, University of Hasselt, Hasselt, Belgium
| | - Oliver Robinson
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, United Kingdom
- Institute for Risk Assessment Sciences (IRAS), Division of Environmental Epidemiology, Utrecht University, Utrecht, Netherlands
| | - Joris Penders
- Laboratory of Clinical Biology, East-Limburg Hospital, Genk, Belgium
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, United Kingdom
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Tim S. Nawrot
- Centre for Environmental Sciences, University of Hasselt, Hasselt, Belgium
- School of Public Health, Occupational and Environmental Medicine, KU Leuven, Leuven, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, University of Hasselt, Hasselt, Belgium
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, United Kingdom
| |
Collapse
|
22
|
Khamis A, Canouil M, Siddiq A, Crouch H, Falchi M, Bulow MV, Ehehalt F, Marselli L, Distler M, Richter D, Weitz J, Bokvist K, Xenarios I, Thorens B, Schulte AM, Ibberson M, Bonnefond A, Marchetti P, Solimena M, Froguel P. Laser capture microdissection of human pancreatic islets reveals novel eQTLs associated with type 2 diabetes. Mol Metab 2019; 24:98-107. [PMID: 30956117 PMCID: PMC6531807 DOI: 10.1016/j.molmet.2019.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Genome wide association studies (GWAS) for type 2 diabetes (T2D) have identified genetic loci that often localise in non-coding regions of the genome, suggesting gene regulation effects. We combined genetic and transcriptomic analysis from human islets obtained from brain-dead organ donors or surgical patients to detect expression quantitative trait loci (eQTLs) and shed light into the regulatory mechanisms of these genes. METHODS Pancreatic islets were isolated either by laser capture microdissection (LCM) from surgical specimens of 103 metabolically phenotyped pancreatectomized patients (PPP) or by collagenase digestion of pancreas from 100 brain-dead organ donors (OD). Genotyping (> 8.7 million single nucleotide polymorphisms) and expression (> 47,000 transcripts and splice variants) analyses were combined to generate cis-eQTLs. RESULTS After applying genome-wide false discovery rate significance thresholds, we identified 1,173 and 1,021 eQTLs in samples of OD and PPP, respectively. Among the strongest eQTLs shared between OD and PPP were CHURC1 (OD p-value=1.71 × 10-24; PPP p-value = 3.64 × 10-24) and PSPH (OD p-value = 3.92 × 10-26; PPP p-value = 3.64 × 10-24). We identified eQTLs in linkage-disequilibrium with GWAS loci T2D and associated traits, including TTLL6, MLX and KIF9 loci, which do not implicate the nearest gene. We found in the PPP datasets 11 eQTL genes, which were differentially expressed in T2D and two genes (CYP4V2 and TSEN2) associated with HbA1c but none in the OD samples. CONCLUSIONS eQTL analysis of LCM islets from PPP led us to identify novel genes which had not been previously linked to islet biology and T2D. The understanding gained from eQTL approaches, especially using surgical samples of living patients, provides a more accurate 3-dimensional representation than those from genetic studies alone.
Collapse
Affiliation(s)
- Amna Khamis
- Imperial College London, Department of Genomics of Common Disease, London, UK; University of Lille, CNRS, Institute Pasteur de Lille, UMR 8199 - EGID, F-59000, Lille, France
| | - Mickaël Canouil
- University of Lille, CNRS, Institute Pasteur de Lille, UMR 8199 - EGID, F-59000, Lille, France
| | - Afshan Siddiq
- Imperial College London, Department of Genomics of Common Disease, London, UK
| | - Hutokshi Crouch
- Imperial College London, Department of Genomics of Common Disease, London, UK
| | - Mario Falchi
- Imperial College London, Department of Genomics of Common Disease, London, UK
| | - Manon von Bulow
- Sanofi-Aventis Deutschland GmbH, Diabetes Research, Frankfurt, Germany
| | - Florian Ehehalt
- Department of Visceral-Thoracic-Vascular Surgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764, Neuherberg, Germany
| | - Lorella Marselli
- University of Pisa, Department of Clinical and Experimental Medicine, Pisa, Italy
| | - Marius Distler
- Department of Visceral-Thoracic-Vascular Surgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764, Neuherberg, Germany
| | - Daniela Richter
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764, Neuherberg, Germany
| | - Jürgen Weitz
- Department of Visceral-Thoracic-Vascular Surgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764, Neuherberg, Germany
| | - Krister Bokvist
- Lilly Research Laboratories, Eli Lilly, 46285-0001, Indianapolis, IN, USA
| | - Ioannis Xenarios
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Bernard Thorens
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, 1015, Switzerland
| | - Anke M Schulte
- Sanofi-Aventis Deutschland GmbH, Diabetes Research, Frankfurt, Germany
| | - Mark Ibberson
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Amelie Bonnefond
- University of Lille, CNRS, Institute Pasteur de Lille, UMR 8199 - EGID, F-59000, Lille, France
| | - Piero Marchetti
- University of Pisa, Department of Clinical and Experimental Medicine, Pisa, Italy
| | - Michele Solimena
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764, Neuherberg, Germany
| | - Philippe Froguel
- Imperial College London, Department of Genomics of Common Disease, London, UK; University of Lille, CNRS, Institute Pasteur de Lille, UMR 8199 - EGID, F-59000, Lille, France.
| |
Collapse
|
23
|
Touati A, Errea-Dorronsoro J, Nouri S, Halleb Y, Pereda A, Mahdhaoui N, Ghith A, Saad A, Perez de Nanclares G, H'mida Ben Brahim D. Transient neonatal diabetes mellitus and hypomethylation at additional imprinted loci: novel ZFP57 mutation and review on the literature. Acta Diabetol 2019; 56:301-307. [PMID: 30315371 DOI: 10.1007/s00592-018-1239-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 09/29/2018] [Indexed: 11/28/2022]
Abstract
AIM 6q24-related transient neonatal diabetes mellitus (6q24-TNDM) is a rare imprinting disorder characterized by uncontrolled hyperglycemia during the first 6 months of life. The molecular etiology of 6q24-TNDM is attributable to overexpression of the paternally inherited PLAGL1 and HYMAI genes located on the 6q24 locus. One of these major defects is maternal loss of methylation (LOM) at 6q24. In addition, approximately 50% of TNDM patients that present LOM at 6q24 can also display hypomethylation at additional imprinted loci (multilocus imprinting disturbances, MLID). Interestingly, the majority of these patients carry mutations in the ZFP57 gene, a transcription factor required for the adequate maintenance of methylation during early embryonic development. METHODS Methylation analysis of 6q24 and additional imprinted loci was carried out by MS-MLPA in a Tunisian male patient with clinical diagnosis of TNMD. For the same patient, mutation analysis of the ZFP57 gene was conducted by direct Sanger sequencing. RESULTS We report a novel nonsense mutation (c.373C > T; p.R125*; ENST00000376883.1) at the ZFP57 gene causing TNDM-MLID and describe detailed phenotype/epigenotype analysis of TNMD patients carrying ZFP57 mutations. CONCLUSION We provide additional support to the role of ZFP57 as a genetic determinant cause of MLID in patients with TNMD.
Collapse
Affiliation(s)
- Ameni Touati
- Department of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia
- High Institute of Biotechnology, Monastir University, Monastir, Tunisia
| | - Javier Errea-Dorronsoro
- Molecular (Epi)Genetic Lab, BioAraba National Health Institute, OSI Araba University Hospital, 01009, Vitoria-Gasteiz, Alava, Spain
| | - Sonia Nouri
- Department of Neonatology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia
- Faculty of Medicine, Sousse University, Sousse, Tunisia
| | - Yosra Halleb
- Department of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia
- Faculty of Medicine, Sousse University, Sousse, Tunisia
| | - Arrate Pereda
- Molecular (Epi)Genetic Lab, BioAraba National Health Institute, OSI Araba University Hospital, 01009, Vitoria-Gasteiz, Alava, Spain
| | - Nabiha Mahdhaoui
- Department of Neonatology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia
- Faculty of Medicine, Sousse University, Sousse, Tunisia
| | - Aida Ghith
- Department of Neonatology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia
- Faculty of Medicine, Sousse University, Sousse, Tunisia
| | - Ali Saad
- Department of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia
- Faculty of Medicine, Sousse University, Sousse, Tunisia
| | - Guiomar Perez de Nanclares
- Molecular (Epi)Genetic Lab, BioAraba National Health Institute, OSI Araba University Hospital, 01009, Vitoria-Gasteiz, Alava, Spain
| | - Dorra H'mida Ben Brahim
- Department of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat HACHED University Hospital, 4000, Sousse, Tunisia.
- Faculty of Medicine, Sousse University, Sousse, Tunisia.
| |
Collapse
|
24
|
Abstract
In addition to the common types of diabetes mellitus, two major monogenic diabetes forms exist. Maturity-onset diabetes of the young (MODY) represents a heterogenous group of monogenic, autosomal dominant diseases. MODY accounts for 1-2% of all diabetes cases, and it is not just underdiagnosed but often misdiagnosed to type 1 or type 2 diabetes. More than a dozen MODY genes have been identified to date, and their molecular classification is of great importance in the correct treatment decision and in the judgment of the prognosis. The most prevalent subtypes are HNF1A, GCK, and HNF4A. Genetic testing for MODY has changed recently due to the technological advancements, as contrary to the sequential testing performed in the past, nowadays all MODY genes can be tested simultaneously by next-generation sequencing. The other major group of monogenic diabetes is neonatal diabetes mellitus which can be transient or permanent, and often the diabetes is a part of a syndrome. It is a severe monogenic disease appearing in the first 6 months of life. The hyperglycemia usually requires insulin. There are two forms, permanent neonatal diabetes mellitus (PNDM) and transient neonatal diabetes mellitus (TNDM). In TNDM, the diabetes usually reverts within several months but might relapse later in life. The incidence of NDM is 1:100,000-1:400,000 live births, and PNDM accounts for half of the cases. Most commonly, neonatal diabetes is caused by mutations in KCNJ11 and ABCC8 genes encoding the ATP-dependent potassium channel of the β cell. Neonatal diabetes has experienced a quick and successful transition into the clinical practice since the discovery of the molecular background. In case of both genetic diabetes groups, recent guidelines recommend genetic testing.
Collapse
Affiliation(s)
- Zsolt Gaál
- 4th Department of Medicine, Jósa András Teaching Hospital, Nyíregyháza, Hungary
| | - István Balogh
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| |
Collapse
|
25
|
Takahashi N, Coluccio A, Thorball CW, Planet E, Shi H, Offner S, Turelli P, Imbeault M, Ferguson-Smith AC, Trono D. ZNF445 is a primary regulator of genomic imprinting. Genes Dev 2019; 33:49-54. [PMID: 30602440 PMCID: PMC6317318 DOI: 10.1101/gad.320069.118] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/07/2018] [Indexed: 12/29/2022]
Abstract
Genomic imprinting is an epigenetic process regulated by germline-derived DNA methylation, causing parental origin-specific monoallelic gene expression. Zinc finger protein 57 (ZFP57) is critical for maintenance of this epigenetic memory during post-fertilization reprogramming, yet incomplete penetrance of ZFP57 mutations in humans and mice suggests additional effectors. We reveal that ZNF445/ZFP445, which we trace to the origins of imprinting, binds imprinting control regions (ICRs) in mice and humans. In mice, ZFP445 and ZFP57 act together, maintaining all but one ICR in vivo, whereas earlier embryonic expression of ZNF445 and its intolerance to loss-of-function mutations indicate greater importance in the maintenance of human imprints.
Collapse
Affiliation(s)
- Nozomi Takahashi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Andrea Coluccio
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Christian W Thorball
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Hui Shi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Michael Imbeault
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | | | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| |
Collapse
|
26
|
Fontana L, Bedeschi MF, Maitz S, Cereda A, Faré C, Motta S, Seresini A, D'Ursi P, Orro A, Pecile V, Calvello M, Selicorni A, Lalatta F, Milani D, Sirchia SM, Miozzo M, Tabano S. Characterization of multi-locus imprinting disturbances and underlying genetic defects in patients with chromosome 11p15.5 related imprinting disorders. Epigenetics 2018; 13:897-909. [PMID: 30221575 PMCID: PMC6284780 DOI: 10.1080/15592294.2018.1514230] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The identification of multilocus imprinting disturbances (MLID) appears fundamental to uncover molecular pathways underlying imprinting disorders (IDs) and to complete clinical diagnosis of patients. However, MLID genetic associated mechanisms remain largely unknown. To characterize MLID in Beckwith-Wiedemann (BWS) and Silver-Russell (SRS) syndromes, we profiled by MassARRAY the methylation of 12 imprinted differentially methylated regions (iDMRs) in 21 BWS and 7 SRS patients with chromosome 11p15.5 epimutations. MLID was identified in 50% of BWS and 29% of SRS patients as a maternal hypomethylation syndrome. By next-generation sequencing, we searched for putative MLID-causative mutations in genes involved in methylation establishment/maintenance and found two novel missense mutations possibly causative of MLID: one in NLRP2, affecting ADP binding and protein activity, and one in ZFP42, likely leading to loss of DNA binding specificity. Both variants were paternally inherited. In silico protein modelling allowed to define the functional effect of these mutations. We found that MLID is very frequent in BWS/SRS. In addition, since MLID-BWS patients in our cohort show a peculiar pattern of BWS-associated clinical signs, MLID test could be important for a comprehensive clinical assessment. Finally, we highlighted the possible involvement of ZFP42 variants in MLID development and confirmed NLRP2 as causative locus in BWS-MLID.
Collapse
Affiliation(s)
- L Fontana
- a Laboratory of Molecular Pathology, Department of Pathophysiology and Transplantation , Università degli Studi di Milano , Milano , Italy
| | - M F Bedeschi
- b Clinical Genetics Unit , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - S Maitz
- c Clinical Pediatric, Genetics Unit , MBBM Foundation, San Gerardo Monza , Monza , Italy
| | - A Cereda
- d Medical Genetics Unit , Papa Giovanni XXIII Hospital , Bergamo , Italy
| | - C Faré
- e Division of Pathology , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - S Motta
- e Division of Pathology , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - A Seresini
- f Medical Genetics Laboratory , Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico , Milano , Italy.,g Fondazione Grigioni per il Morbo di Parkinson , Milano , Italy
| | - P D'Ursi
- h Department of Biomedical Sciences National Research Council , Institute for Biomedical Technologies , Segrate , Italy
| | - A Orro
- h Department of Biomedical Sciences National Research Council , Institute for Biomedical Technologies , Segrate , Italy
| | - V Pecile
- i Medical Genetics Division , Institute for maternal and child health IRCCS Burlo Garofolo , Trieste , Italy
| | - M Calvello
- e Division of Pathology , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy.,j Division of Cancer Prevention and Genetics, IEO , European Institute of Oncology IRCCS , Milano , Italy
| | - A Selicorni
- k UOC Pediatria , ASST Lariana , Como , Italy
| | - F Lalatta
- b Clinical Genetics Unit , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - D Milani
- l Pediatric Highly Intensive Care Unit , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - S M Sirchia
- m Medical Genetics, Department of Health Sciences , Università degli Studi di Milano , Milano , Italy
| | - M Miozzo
- a Laboratory of Molecular Pathology, Department of Pathophysiology and Transplantation , Università degli Studi di Milano , Milano , Italy.,e Division of Pathology , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - S Tabano
- a Laboratory of Molecular Pathology, Department of Pathophysiology and Transplantation , Università degli Studi di Milano , Milano , Italy
| |
Collapse
|
27
|
Yorifuji T, Higuchi S, Hosokawa Y, Kawakita R. Chromosome 6q24-related diabetes mellitus. Clin Pediatr Endocrinol 2018; 27:59-65. [PMID: 29662264 PMCID: PMC5897580 DOI: 10.1297/cpe.27.59] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 01/18/2018] [Indexed: 12/31/2022] Open
Abstract
Chromosome 6q24-related diabetes mellitus is the most common cause of transient neonatal diabetes (TNDM), accounting for approximately two-thirds of all TNDM cases. Patients with 6q24-TNDM develop insulin-requiring diabetes soon after birth, followed by the gradual improvement and eventual remission of the disorder by 18 mo of age. The most important clinical feature of affected patients is a small-for-gestational age (SGA) birth weight, which reflects the lack of insulin in utero. It is believed that 6q24-TNDM is caused by the overexpression of the paternal allele of the imprinted locus in chromosome 6q24, which contains only two expressed genes, PLAGL1 and HYMAI. Identified mechanisms include: (1) duplication of the paternal allele, (2) paternal uniparental disomy, and (3) hypomethylation of the maternal allele. Many patients with TNDM relapse after puberty. Relapsed 6q24-related diabetes is no longer transient and typically occurs in non-obese patients who are autoantibody negative. Thus, these patients possess features indistinguishable from those of maturity-onset diabetes of the young (MODY). Conversely, it has been shown that not all patients with 6q24-related diabetes have a history of TNDM. 6q24-related diabetes should therefore be considered as one of the differential diagnoses for patients with MODY-like diabetes, especially when they are SGA at birth.
Collapse
Affiliation(s)
- Tohru Yorifuji
- Division of Pediatric Endocrinology and Metabolism, Children's Medical Center, Osaka City General Hospital, Osaka, Japan.,Department of Genetic Medicine, Osaka City General Hospital, Osaka, Japan.,Clinical Research Center, Osaka City General Hospital, Osaka, Japan
| | - Shinji Higuchi
- Division of Pediatric Endocrinology and Metabolism, Children's Medical Center, Osaka City General Hospital, Osaka, Japan
| | - Yuki Hosokawa
- Division of Pediatric Endocrinology and Metabolism, Children's Medical Center, Osaka City General Hospital, Osaka, Japan
| | - Rie Kawakita
- Division of Pediatric Endocrinology and Metabolism, Children's Medical Center, Osaka City General Hospital, Osaka, Japan.,Department of Genetic Medicine, Osaka City General Hospital, Osaka, Japan
| |
Collapse
|
28
|
Is ZFP57 binding to H19/IGF2:IG-DMR affected in Silver-Russell syndrome? Clin Epigenetics 2018; 10:23. [PMID: 29484033 PMCID: PMC5822596 DOI: 10.1186/s13148-018-0454-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/02/2018] [Indexed: 01/21/2023] Open
Abstract
Background Loss of paternal methylation (LOM) of the H19/IGF2 intergenic differentially methylated region (H19/IGF2:IG-DMR) causes alteration of H19/IGF2 imprinting and Silver-Russell syndrome (SRS). Recently, internal deletions of the H19/IGF2:IG-DMR have been associated with LOM and SRS when present on the paternal chromosome. In contrast, previously described deletions, most of which cause gain of methylation (GOM) and Beckwith-Wiedemann syndrome (BWS) on maternal transmission, were consistently associated with normal methylation and phenotype if paternally inherited. Presentation of the hypothesis The presence of several target sites (ZTSs) and three demonstrated binding regions (BRs) for the imprinting factor ZFP57 in the H19/IGF2:IG-DMR suggest the involvement of this factor in the maintenance of methylation of this locus. By comparing the extension of the H19/IGF2:IG-DMR deletions with the binding profile of ZFP57, we propose that the effect of the deletions on DNA methylation and clinical phenotype is dependent on their interference with ZFP57 binding. Indeed, deletions strongly affecting a ZFP57 BR result in LOM and SRS, while deletions preserving a significant number of ZFPs in each BR do not alter methylation and are associated with normal phenotype. Testing the hypothesis The generation of transgenic mouse lines in which the endogenous H19/IGF2:IG-DMR is replaced by the human orthologous locus including the three ZFP57 BRs or their mutant versions will allow to test the role of ZFP57 binding in imprinted methylation and growth phenotype. Implications of the hypothesis Similarly to what is proposed for maternally inherited BWS mutations and CTCF and OCT4/SOX2 binding, we suggest that deletions of the H19/IGF2:IG-DMR result in SRS with LOM if ZFP57 binding on the paternal chromosome is affected. Electronic supplementary material The online version of this article (10.1186/s13148-018-0454-7) contains supplementary material, which is available to authorized users.
Collapse
|
29
|
Takahashi N, Gray D, Strogantsev R, Noon A, Delahaye C, Skarnes WC, Tate PH, Ferguson-Smith AC. ZFP57 and the Targeted Maintenance of Postfertilization Genomic Imprints. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2018; 80:177-87. [PMID: 27325708 DOI: 10.1101/sqb.2015.80.027466] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epigenetic modifications play an important role in modulating genome function. In mammals, inappropriate epigenetic states can cause embryonic lethality and various acquired and inherited diseases; hence, it is important to understand how such states are formed and maintained in particular genomic contexts. Genomic imprinting is a process in which epigenetic states provide a sustained memory of parental origin and cause gene expression/repression from only one of the two parental chromosomes. Genomic imprinting is therefore a valuable model to decipher the principles and processes associated with the targeting and maintenance of epigenetic states in general. Krüppel-associated box zinc finger proteins (KRAB-ZFPs) are proteins that have the potential to mediate this. ZFP57, one of the best characterized proteins in this family, has been shown to target and maintain epigenetic states at imprinting control regions after fertilization. Its role in imprinting through the use of ZFP57 mutants in mouse and the wider implications of KRAB-ZFPs for the targeted maintenance of epigenetic states are discussed here.
Collapse
Affiliation(s)
- Nozomi Takahashi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Dionne Gray
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | | | - Angela Noon
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Celia Delahaye
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - William C Skarnes
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Peri H Tate
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | | |
Collapse
|
30
|
Mackay DJ, Temple IK. Human imprinting disorders: Principles, practice, problems and progress. Eur J Med Genet 2017; 60:618-626. [DOI: 10.1016/j.ejmg.2017.08.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/02/2017] [Accepted: 08/11/2017] [Indexed: 12/17/2022]
|
31
|
Iyigun F, Ozcan B, Kulali F, Celik IH, Cetinkaya S, Bas AY, Demirel N. A Newborn with Transient Diabetes Mellitus Accompanied by Ketoacidosis Attributable to a ZFP57 Mutation. J Trop Pediatr 2017; 63:399-401. [PMID: 28334746 DOI: 10.1093/tropej/fmx005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Hyperglycemia commencing within the first 6 months of life requires exogenous insulin therapy and, if the condition persists for >2 weeks, is termed neonatal diabetes mellitus (NDM). This rare illness is of two types: transient and permanent NDM. Most cases come to medical attention because of nonspecific symptoms, including intrauterine growth retardation, dehydration, difficulties in feeding and inadequate weight gain. In the present article, we describe an infant who smelt of ketones during examination and who was diagnosed with transient NDM caused by a ZFP57 mutation, accompanied by ketoacidosis. This is the first report of such a condition.
Collapse
Affiliation(s)
- Fatma Iyigun
- Department of Neonatology, Etlik Zubeyde Hanim Women's Health Teaching and Research Hospital, Ankara 06010, Turkey
| | - Beyza Ozcan
- Department of Neonatology, Konya Teaching and Research Hospital, Konya 42090, Turkey
| | - Ferit Kulali
- Department of Neonatology, Etlik Zubeyde Hanim Women's Health Teaching and Research Hospital, Ankara 06010, Turkey
| | - Istemi Han Celik
- Department of Neonatology, Etlik Zubeyde Hanim Women's Health Teaching and Research Hospital, Ankara 06010, Turkey
| | - Semra Cetinkaya
- Department of Pediatric Endocrinology, Dr. Sami Ulus Children Health and Disease Training and Research Hospital, Ankara 06080, Turkey
| | - Ahmet Yagmur Bas
- Department of Neonatology, Etlik Zubeyde Hanim Women's Health Teaching and Research Hospital, Ankara 06010, Turkey
| | - Nihal Demirel
- Department of Neonatology, Etlik Zubeyde Hanim Women's Health Teaching and Research Hospital, Ankara 06010, Turkey
| |
Collapse
|
32
|
Liu H, Wei Q, Huang C, Zhang Y, Guo Z. Potential Roles of Intrinsic Disorder in Maternal-Effect Proteins Involved in the Maintenance of DNA Methylation. Int J Mol Sci 2017; 18:E1898. [PMID: 28869544 PMCID: PMC5618547 DOI: 10.3390/ijms18091898] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 01/14/2023] Open
Abstract
DNA methylation is an important epigenetic modification that needs to be carefully controlled as a prerequisite for normal early embryogenesis. Compelling evidence now suggests that four maternal-effect proteins, primordial germ cell 7 (PGC7), zinc finger protein 57 (ZFP57), tripartite motif-containing 28 (TRIM28) and DNA methyltransferase (cytosine-5) 1 (DNMT1) are involved in the maintenance of DNA methylation. However, it is still not fully understood how these maternal-effect proteins maintain the DNA methylation imprint. We noticed that a feature common to these proteins is the presence of significant levels of intrinsic disorder so in this study we started from an intrinsic disorder perspective to try to understand these maternal-effect proteins. To do this, we firstly analysed the intrinsic disorder predispositions of PGC7, ZFP57, TRIM28 and DNMT1 by using a set of currently available computational tools and secondly conducted an intensive literature search to collect information on their interacting partners and structural characterization. Finally, we discuss the potential effect of intrinsic disorder on the function of these proteins in maintaining DNA methylation.
Collapse
Affiliation(s)
- Hongliang Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Qing Wei
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China.
| | - Chenyang Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Zekun Guo
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| |
Collapse
|
33
|
Elhamamsy AR. Role of DNA methylation in imprinting disorders: an updated review. J Assist Reprod Genet 2017; 34:549-562. [PMID: 28281142 PMCID: PMC5427654 DOI: 10.1007/s10815-017-0895-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/23/2017] [Indexed: 12/20/2022] Open
Abstract
Genomic imprinting is a complex epigenetic process that contributes substantially to embryogenesis, reproduction, and gametogenesis. Only small fraction of genes within the whole genome undergoes imprinting. Imprinted genes are expressed in a monoallelic parent-of-origin-specific manner, which means that only one of the two inherited alleles is expressed either from the paternal or maternal side. Imprinted genes are typically arranged in clusters controlled by differentially methylated regions or imprinting control regions. Any defect or relaxation in imprinting process can cause loss of imprinting in the key imprinted loci. Loss of imprinting in most cases has a harmful effect on fetal development and can result in neurological, developmental, and metabolic disorders. Since DNA methylation and histone modifications play a key role in the process of imprinting. This review focuses on the role of DNA methylation in imprinting process and describes DNA methylation aberrations in different imprinting disorders.
Collapse
Affiliation(s)
- Amr Rafat Elhamamsy
- Department of Clinical Pharmacy, School of Pharmacy, Tanta University, Tanta, 31512, Gharbia, Egypt.
| |
Collapse
|
34
|
Grafodatskaya D, Choufani S, Basran R, Weksberg R. An Update on Molecular Diagnostic Testing of Human Imprinting Disorders. J Pediatr Genet 2016; 6:3-17. [PMID: 28180023 DOI: 10.1055/s-0036-1593840] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/16/2016] [Indexed: 01/07/2023]
Abstract
Imprinted genes are expressed in a parent of origin manner. Dysregulation of imprinted genes expression causes various disorders associated with abnormalities of growth, neurodevelopment, and metabolism. Molecular mechanisms leading to imprinting disorders and strategies for their diagnosis are discussed in this review article.
Collapse
Affiliation(s)
- Daria Grafodatskaya
- Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Sanaa Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Raveen Basran
- Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
35
|
Okuno M, Yorifuji T, Kagami M, Ayabe T, Urakami T, Kawamura T, Kikuchi N, Yokota I, Kikuchi T, Amemiya S, Suzuki J, Ogata T, Sugihara S, Fukami M. Chromosome 6q24 methylation defects are uncommon in childhood-onset non-autoimmune diabetes mellitus patients born appropriate- or large-for-gestational age. Clin Pediatr Endocrinol 2016; 25:99-102. [PMID: 27507910 PMCID: PMC4965509 DOI: 10.1297/cpe.25.99] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/08/2016] [Indexed: 11/06/2022] Open
Affiliation(s)
- Misako Okuno
- Departments of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan; Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Tohru Yorifuji
- Department of Pediatric Endocrinology and Metabolism, Children's Medical Center, Osaka City General Hospital, Osaka, Japan
| | - Masayo Kagami
- Departments of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tadayuki Ayabe
- Departments of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tatsuhiko Urakami
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | | | - Nobuyuki Kikuchi
- Department of Pediatrics, Yokohama City Minato Red Cross Hospital, Kanagawa, Japan
| | - Ichiro Yokota
- Department of Pediatrics, Division of Pediatric Endocrinology and Metabolism, Shikoku Medical Center for Children and Adults, Kagawa, Japan
| | - Toru Kikuchi
- Department of Pediatrics, Saitama Medical University, Saitama, Japan
| | - Shin Amemiya
- Department of Pediatrics, Saitama Medical University, Saitama, Japan
| | - Junichi Suzuki
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Tsutomu Ogata
- Departments of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan; Department of Pediatrics, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Shigetaka Sugihara
- Department of Pediatrics, Tokyo Women's Medical University Medical Center East, Tokyo, Japan
| | - Maki Fukami
- Departments of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | | |
Collapse
|
36
|
Do C, Lang C, Lin J, Darbary H, Krupska I, Gaba A, Petukhova L, Vonsattel JP, Gallagher M, Goland R, Clynes R, Dwork A, Kral J, Monk C, Christiano A, Tycko B. Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation. Am J Hum Genet 2016; 98:934-955. [PMID: 27153397 DOI: 10.1016/j.ajhg.2016.03.027] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/25/2016] [Indexed: 10/21/2022] Open
Abstract
Haplotype-dependent allele-specific methylation (hap-ASM) can impact disease susceptibility, but maps of this phenomenon using stringent criteria in disease-relevant tissues remain sparse. Here we apply array-based and Methyl-Seq approaches to multiple human tissues and cell types, including brain, purified neurons and glia, T lymphocytes, and placenta, and identify 795 hap-ASM differentially methylated regions (DMRs) and 3,082 strong methylation quantitative trait loci (mQTLs), most not previously reported. More than half of these DMRs have cell type-restricted ASM, and among them are 188 hap-ASM DMRs and 933 mQTLs located near GWAS signals for immune and neurological disorders. Targeted bis-seq confirmed hap-ASM in 12/13 loci tested, including CCDC155, CD69, FRMD1, IRF1, KBTBD11, and S100A(∗)-ILF2, associated with immune phenotypes, MYT1L, PTPRN2, CMTM8 and CELF2, associated with neurological disorders, NGFR and HLA-DRB6, associated with both immunological and brain disorders, and ZFP57, a trans-acting regulator of genomic imprinting. Polymorphic CTCF and transcription factor (TF) binding sites were over-represented among hap-ASM DMRs and mQTLs, and analysis of the human data, supplemented by cross-species comparisons to macaques, indicated that CTCF and TF binding likelihood predicts the strength and direction of the allelic methylation asymmetry. These results show that hap-ASM is highly tissue specific; an important trans-acting regulator of genomic imprinting is regulated by this phenomenon; and variation in CTCF and TF binding sites is an underlying mechanism, and maps of hap-ASM and mQTLs reveal regulatory sequences underlying supra- and sub-threshold GWAS peaks in immunological and neurological disorders.
Collapse
|
37
|
Bak M, Boonen SE, Dahl C, Hahnemann JMD, Mackay DJDG, Tümer Z, Grønskov K, Temple IK, Guldberg P, Tommerup N. Genome-wide DNA methylation analysis of transient neonatal diabetes type 1 patients with mutations in ZFP57. BMC MEDICAL GENETICS 2016; 17:29. [PMID: 27075368 PMCID: PMC4831126 DOI: 10.1186/s12881-016-0292-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 04/08/2016] [Indexed: 12/21/2022]
Abstract
Background Transient neonatal diabetes mellitus 1 (TNDM1) is a rare imprinting disorder characterized by intrautering growth retardation and diabetes mellitus usually presenting within the first six weeks of life and resolves by the age of 18 months. However, patients have an increased risk of developing diabetes mellitus type 2 later in life. Transient neonatal diabetes mellitus 1 is caused by overexpression of the maternally imprinted genes PLAGL1 and HYMAI on chromosome 6q24. One of the mechanisms leading to overexpression of the locus is hypomethylation of the maternal allele of PLAGL1 and HYMAI. A subset of patients with maternal hypomethylation at PLAGL1 have hypomethylation at additional imprinted loci throughout the genome, including GRB10, ZIM2 (PEG3), MEST (PEG1), KCNQ1OT1 and NESPAS (GNAS-AS1). About half of the TNDM1 patients carry mutations in ZFP57, a transcription factor involved in establishment and maintenance of methylation of imprinted loci. Our objective was to investigate whether additional regions are aberrantly methylated in ZFP57 mutation carriers. Methods Genome-wide DNA methylation analysis was performed on four individuals with homozygous or compound heterozygous ZFP57 mutations, three relatives with heterozygous ZFP57 mutations and five controls. Methylation status of selected regions showing aberrant methylation in the patients was verified using bisulfite-sequencing. Results We found large variability among the patients concerning the number and identity of the differentially methylated regions, but more than 60 regions were aberrantly methylated in two or more patients and a novel region within PPP1R13L was found to be hypomethylated in all the patients. The hypomethylated regions in common between the patients are enriched for the ZFP57 DNA binding motif. Conclusions We have expanded the epimutational spectrum of TNDM1 associated with ZFP57 mutations and found one novel region within PPP1R13L which is hypomethylated in all TNDM1 patients included in this study. Functional studies of the locus might provide further insight into the etiology of the disease. Electronic supplementary material The online version of this article (doi:10.1186/s12881-016-0292-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mads Bak
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200, Copenhagen N, Denmark.
| | - Susanne E Boonen
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200, Copenhagen N, Denmark.,Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark
| | - Christina Dahl
- Institute of Cancer Biology, Danish Cancer Society, DK-2100, Copenhagen Ø, Denmark
| | - Johanne M D Hahnemann
- Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark
| | - Deborah J D G Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.,Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury NHS Foundation Trust, SP2 8BJ, Salisbury, UK
| | - Zeynep Tümer
- Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark.,Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200N, Copenhagen, Denmark
| | - Karen Grønskov
- Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark
| | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.,Wessex Clinical Genetics Service, Southampton University Hospitals Trust, Southampton, SO16 5YA, UK
| | - Per Guldberg
- Institute of Cancer Biology, Danish Cancer Society, DK-2100, Copenhagen Ø, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200, Copenhagen N, Denmark
| |
Collapse
|
38
|
Mackay DJG, Eggermann T, Buiting K, Garin I, Netchine I, Linglart A, de Nanclares GP. Multilocus methylation defects in imprinting disorders. Biomol Concepts 2016; 6:47-57. [PMID: 25581766 DOI: 10.1515/bmc-2014-0037] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/07/2014] [Indexed: 12/17/2022] Open
Abstract
Mammals inherit two complete sets of chromosomes, one from the father and one from the mother, and most autosomal genes are expressed from both maternal and paternal alleles. In imprinted genes, the expression of the allele is dependent upon its parental origin. Appropriate regulation of imprinted genes is important for normal development, with several genetic diseases associated with imprinting defects. A common process for controlling gene activity is methylation. The first steps for understanding the functions of DNA methylation and its regulation in mammalian development have led us to identify common (epi)genetic mechanisms involved in the eight human congenital imprinting disorders.
Collapse
|
39
|
Eggermann T, Perez de Nanclares G, Maher ER, Temple IK, Tümer Z, Monk D, Mackay DJG, Grønskov K, Riccio A, Linglart A, Netchine I. Imprinting disorders: a group of congenital disorders with overlapping patterns of molecular changes affecting imprinted loci. Clin Epigenetics 2015; 7:123. [PMID: 26583054 PMCID: PMC4650860 DOI: 10.1186/s13148-015-0143-8] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/29/2015] [Indexed: 12/17/2022] Open
Abstract
Congenital imprinting disorders (IDs) are characterised by molecular changes affecting imprinted chromosomal regions and genes, i.e. genes that are expressed in a parent-of-origin specific manner. Recent years have seen a great expansion in the range of alterations in regulation, dosage or DNA sequence shown to disturb imprinted gene expression, and the correspondingly broad range of resultant clinical syndromes. At the same time, however, it has become clear that this diversity of IDs has common underlying principles, not only in shared molecular mechanisms, but also in interrelated clinical impacts upon growth, development and metabolism. Thus, detailed and systematic analysis of IDs can not only identify unifying principles of molecular epigenetics in health and disease, but also support personalisation of diagnosis and management for individual patients and families.
Collapse
Affiliation(s)
- Thomas Eggermann
- Department of Human Genetics, RWTH Aachen, Pauwelsstr. 30, Aachen, Germany ; Sorbonne Universites, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France ; 3APHP, Pediatric Endocrinology, Armand Trousseau Hospital, Paris, France
| | - Guiomar Perez de Nanclares
- Molecular (Epi)Genetics Laboratory, BioAraba National Health Institute, Hospital Universitario Araba, Vitoria-Gasteiz, Spain
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine University of Southampton, Southampton, UK ; Wessex Clinical Genetics Service, Princess Anne Hospital, Coxford Road, Southampton, UK
| | - Zeynep Tümer
- Clinical Genetic Clinic, Kennedy Center, Rigshospitalet, Copenhagen University Hospital, Glostrup, Denmark
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Hospital Duran i Reynals, Barcelona, Spain
| | - Deborah J G Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine University of Southampton, Southampton, UK ; Wessex Clinical Genetics Service, Princess Anne Hospital, Coxford Road, Southampton, UK
| | - Karen Grønskov
- Clinical Genetic Clinic, Kennedy Center, Rigshospitalet, Copenhagen University Hospital, Glostrup, Denmark
| | - Andrea Riccio
- DiSTABiF, Seconda Università degli Studi di Napoli, Caserta, Italy
| | - Agnès Linglart
- Institute of Genetics and Biophysics-ABT, CNR, Napoli, Italy
| | - Irène Netchine
- Endocrinology and diabetology for children and reference center for rare disorders of calcium and phosphorus metabolism, Bicêtre Paris Sud, APHP, Le Kremlin-Bicêtre, France ; INSERM U986, INSERM, Le Kremlin-Bicêtre, France ; INSERM, UMR_S 938, CDR Saint-Antoine, Paris, F-75012 France
| |
Collapse
|
40
|
Vals MA, Yakoreva M, Kahre T, Mee P, Muru K, Joost K, Teek R, Soellner L, Eggermann T, Õunap K. The Frequency of Methylation Abnormalities Among Estonian Patients Selected by Clinical Diagnostic Scoring Systems for Silver-Russell Syndrome and Beckwith-Wiedemann Syndrome. Genet Test Mol Biomarkers 2015; 19:684-91. [PMID: 26505556 DOI: 10.1089/gtmb.2015.0163] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
AIMS To study the frequency of methylation abnormalities among Estonian patients selected according to published clinical diagnostic scoring systems for Silver-Russell syndrome (SRS) and Beckwith-Wiedemann syndrome (BWS). MATERIALS AND METHODS Forty-eight patients with clinical suspicion of SRS (n = 20) or BWS (n = 28) were included in the study group, to whom methylation-specific multiplex ligation-dependant probe amplification analysis of 11p15 region was made. In addition, to patients with minimal diagnostic score for either SRS or BWS, multilocus methylation-specific single nucleotide primer extension assay was performed. RESULTS Five (38%) SRS patients with positive clinical scoring had abnormal methylation pattern at chromosome 11p15, whereas in the BWS group, only one patient was diagnosed with imprinting control region 2 (ICR2) hypomethylation (8%). An unexpected hypomethylation of the PLAGL1 (6q24) and IGF2R (6q25) genes in the patient with the highest BWS scoring was found. CONCLUSIONS Compared to BWS, diagnostic criteria used for selecting SRS patients gave us a similar detection rate of 11p15 imprinting disorders as seen in other studies. A more careful selection of patients with possible BWS should be considered to improve the detection of molecularly confirmed cases. Genome-wide multilocus methylation tests could be used in routine clinical practice as it increases the detection rates of imprinting disorders.
Collapse
Affiliation(s)
- Mari-Anne Vals
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia .,2 Department of Pediatrics, University of Tartu , Tartu, Estonia .,3 Children's Clinic, Tartu University Hospital , Tartu, Estonia
| | - Maria Yakoreva
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia .,2 Department of Pediatrics, University of Tartu , Tartu, Estonia
| | - Tiina Kahre
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia .,2 Department of Pediatrics, University of Tartu , Tartu, Estonia
| | - Pille Mee
- 4 United Laboratories, Tartu University Hospital , Tartu, Estonia
| | - Kai Muru
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia .,2 Department of Pediatrics, University of Tartu , Tartu, Estonia
| | - Kairit Joost
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia
| | - Rita Teek
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia .,2 Department of Pediatrics, University of Tartu , Tartu, Estonia
| | - Lukas Soellner
- 5 Institute of Human Genetics , RWTH Aachen, Aachen, Germany
| | | | - Katrin Õunap
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia .,2 Department of Pediatrics, University of Tartu , Tartu, Estonia
| |
Collapse
|
41
|
Yorifuji T, Matsubara K, Sakakibara A, Hashimoto Y, Kawakita R, Hosokawa Y, Fujimaru R, Murakami A, Tamagawa N, Hatake K, Nagasaka H, Suzuki J, Urakami T, Izawa M, Kagami M. Abnormalities in chromosome 6q24 as a cause of early-onset, non-obese, non-autoimmune diabetes mellitus without history of neonatal diabetes. Diabet Med 2015; 32:963-7. [PMID: 25809823 DOI: 10.1111/dme.12758] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2015] [Indexed: 01/30/2023]
Abstract
AIMS Abnormalities in the imprinted locus on chromosome 6q24 are the most common causes of transient neonatal diabetes mellitus (6q24-related transient neonatal diabetes). 6q24-Related transient neonatal diabetes is characterized by the patient being small-for-gestational age, diabetes mellitus at birth, spontaneous remission within the first few months and frequent recurrence of diabetes after childhood. However, it is not clear whether individuals with 6q24 abnormalities invariably develop transient neonatal diabetes. This study explored the possibility that 6q24 abnormalities might cause early-onset, non-autoimmune diabetes without transient neonatal diabetes. METHODS The 6q24 imprinted locus was screened for abnormalities in 113 Japanese patients with early-onset, non-obese, non-autoimmune diabetes mellitus who tested negative for mutations in the common maturation-onset diabetes of the young (MODY) genes and without a history of transient neonatal diabetes. Positive patients were further analysed by combined loss of heterozygosity / comparative genomic hybridization analysis and by microsatellite analysis. Detailed clinical data were collected through the medical records of the treating hospitals. RESULTS Three patients with paternal uniparental isodisomy of chromosome 6q24 were identified. None presented with hyperglycaemia in the neonatal period. Characteristically, these patients were born small-for-gestational age, representing 27.2% of the 11 patients whose birth weight standard deviation score (SDS) for gestational age was below -2.0. CONCLUSIONS Abnormalities in the imprinted locus on chromosome 6q24 do not necessarily cause transient neonatal diabetes. Non-penetrant 6q24-related diabetes could be an underestimated cause of early-onset, non-autoimmune diabetes in patients who are not obese and born small-for-gestational age.
Collapse
Affiliation(s)
- T Yorifuji
- Department of Pediatric Endocrinology and Metabolism, Children's Medical Center, Osaka City General Hospital, Osaka, Japan
- Department of Genetic Medicine, Osaka City General Hospital, Osaka, Japan
- Clinical Research Center, Osaka City General Hospital, Osaka, Japan
| | - K Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - A Sakakibara
- Department of Pediatric Endocrinology and Metabolism, Children's Medical Center, Osaka City General Hospital, Osaka, Japan
| | - Y Hashimoto
- Department of Pediatric Endocrinology and Metabolism, Children's Medical Center, Osaka City General Hospital, Osaka, Japan
| | - R Kawakita
- Department of Pediatric Endocrinology and Metabolism, Children's Medical Center, Osaka City General Hospital, Osaka, Japan
| | - Y Hosokawa
- Department of Pediatric Endocrinology and Metabolism, Children's Medical Center, Osaka City General Hospital, Osaka, Japan
| | - R Fujimaru
- Department of Pediatric Endocrinology and Metabolism, Children's Medical Center, Osaka City General Hospital, Osaka, Japan
| | - A Murakami
- Department of Genetic Medicine, Osaka City General Hospital, Osaka, Japan
| | - N Tamagawa
- Department of Genetic Medicine, Osaka City General Hospital, Osaka, Japan
| | - K Hatake
- Clinical Research Center, Osaka City General Hospital, Osaka, Japan
| | - H Nagasaka
- Department of Pediatrics, Takarazuka City Hospital, Japan
| | - J Suzuki
- Department of Pediatrics, Nihon University School of Medicine, Japan
| | - T Urakami
- Department of Pediatrics, Nihon University School of Medicine, Japan
| | - M Izawa
- Department of Endocrinology and Metabolism, Aichi Children's Health and Medical Center, Japan
| | - M Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| |
Collapse
|
42
|
Fang P, Zhang D, Cheng Z, Yan C, Jiang X, Kruger WD, Meng S, Arning E, Bottiglieri T, Choi ET, Han Y, Yang XF, Wang H. Hyperhomocysteinemia potentiates hyperglycemia-induced inflammatory monocyte differentiation and atherosclerosis. Diabetes 2014; 63:4275-90. [PMID: 25008174 PMCID: PMC4237991 DOI: 10.2337/db14-0809] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Hyperhomocysteinemia (HHcy) is associated with increased diabetic cardiovascular diseases. However, the role of HHcy in atherogenesis associated with hyperglycemia (HG) remains unknown. To examine the role and mechanisms by which HHcy accelerates HG-induced atherosclerosis, we established an atherosclerosis-susceptible HHcy and HG mouse model. HHcy was established in mice deficient in cystathionine β-synthase (Cbs) in which the homocysteine (Hcy) level could be lowered by inducing transgenic human CBS (Tg-hCBS) using Zn supplementation. HG was induced by streptozotocin injection. Atherosclerosis was induced by crossing Tg-hCBS Cbs mice with apolipoprotein E-deficient (ApoE(-/-)) mice and feeding them a high-fat diet for 2 weeks. We demonstrated that HHcy and HG accelerated atherosclerosis and increased lesion monocytes (MCs) and macrophages (MØs) and further increased inflammatory MC and MØ levels in peripheral tissues. Furthermore, Hcy-lowering reversed circulating mononuclear cells, MC, and inflammatory MC and MC-derived MØ levels. In addition, inflammatory MC correlated positively with plasma Hcy levels and negatively with plasma s-adenosylmethionine-to-s-adenosylhomocysteine ratios. Finally, l-Hcy and d-glucose promoted inflammatory MC differentiation in primary mouse splenocytes, which was reversed by adenoviral DNA methyltransferase-1. HHcy and HG, individually and synergistically, accelerated atherosclerosis and inflammatory MC and MØ differentiation, at least in part, via DNA hypomethylation.
Collapse
Affiliation(s)
- Pu Fang
- Center for Metabolic Disease Research, School of Medicine, Temple University, Philadelphia, PA Department of Pharmacology, School of Medicine, Temple University, Philadelphia, PA
| | - Daqing Zhang
- Center for Metabolic Disease Research, School of Medicine, Temple University, Philadelphia, PA Department of Pharmacology, School of Medicine, Temple University, Philadelphia, PA
| | - Zhongjian Cheng
- Center for Metabolic Disease Research, School of Medicine, Temple University, Philadelphia, PA Department of Pharmacology, School of Medicine, Temple University, Philadelphia, PA
| | - Chenghui Yan
- Cardiovascular Research Institute and Key Laboratory of Cardiology, Shenyang Northern Hospital, Shenyang, Liaoning, P.R. China
| | - Xiaohua Jiang
- Center for Metabolic Disease Research, School of Medicine, Temple University, Philadelphia, PA Department of Pharmacology, School of Medicine, Temple University, Philadelphia, PA
| | | | - Shu Meng
- Center for Metabolic Disease Research, School of Medicine, Temple University, Philadelphia, PA Department of Pharmacology, School of Medicine, Temple University, Philadelphia, PA
| | - Erland Arning
- Institute of Metabolic Disease, Baylor Research Institute, Dallas, TX
| | | | - Eric T Choi
- Center for Metabolic Disease Research, School of Medicine, Temple University, Philadelphia, PA Department of Surgery, School of Medicine, Temple University, Philadelphia, PA
| | - Yaling Han
- Cardiovascular Research Institute and Key Laboratory of Cardiology, Shenyang Northern Hospital, Shenyang, Liaoning, P.R. China
| | - Xiao-Feng Yang
- Center for Metabolic Disease Research, School of Medicine, Temple University, Philadelphia, PA Department of Pharmacology, School of Medicine, Temple University, Philadelphia, PA Cardiovascular Research Center, School of Medicine, Temple University, Philadelphia, PA Sol Sherry Thrombosis Research Center, School of Medicine, Temple University, Philadelphia, PA
| | - Hong Wang
- Center for Metabolic Disease Research, School of Medicine, Temple University, Philadelphia, PA Department of Pharmacology, School of Medicine, Temple University, Philadelphia, PA Cardiovascular Research Center, School of Medicine, Temple University, Philadelphia, PA Sol Sherry Thrombosis Research Center, School of Medicine, Temple University, Philadelphia, PA
| |
Collapse
|
43
|
Singh P, Rao SC, Parikh R. Neonatal diabetes with intractable epilepsy: DEND syndrome. Indian J Pediatr 2014; 81:1387-8. [PMID: 24912436 DOI: 10.1007/s12098-014-1486-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 05/02/2014] [Indexed: 01/07/2023]
Abstract
Permanent Neonatal Diabetes Mellitus (PNDM), is a rare monogenic disorder, caused by activating mutations of the KATP channel. The most severe clinical form of PNDM presents as Developmental delay, Epilepsy and Neonatal Diabetes (DEND) syndrome. Diagnosis is confirmed by genetic mutation testing. Oral sulfonylurea therapy improves neurological outcome.
Collapse
Affiliation(s)
- Poonam Singh
- Department of Pediatrics, Division of Pediatric Endocrinology, B. J. Wadia Hospital for Children, Parel, Mumbai, India,
| | | | | |
Collapse
|
44
|
Mackay D, Bens S, Perez de Nanclares G, Siebert R, Temple IK. Clinical utility gene card for: Transient Neonatal Diabetes Mellitus, 6q24-related. Eur J Hum Genet 2014; 22:ejhg201427. [PMID: 24569603 PMCID: PMC4135418 DOI: 10.1038/ejhg.2014.27] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Deborah Mackay
- Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Regional Genetics Laboratory, Salisbury Health Care Trust, Salisbury, UK
| | - Susanne Bens
- Institute of Human Genetics, Christian-Albrechts-University Kiel, University Hospital Schleswig-Holstein, Campus Kiel, Schwanenweg 24, Kiel, Germany
| | - Guiomar Perez de Nanclares
- Molecular (Epi)Genetics Laboratory, Research Unit, Hospital Universitario Araba, Vitoria-Gasteiz, Alava, Spain
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel, University Hospital Schleswig-Holstein, Campus Kiel, Schwanenweg 24, Kiel, Germany
| | - I Karen Temple
- Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Coxford Road, Southampton, UK
| |
Collapse
|
45
|
The specification of imprints in mammals. Heredity (Edinb) 2014; 113:176-83. [PMID: 24939713 PMCID: PMC4105455 DOI: 10.1038/hdy.2014.54] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/27/2014] [Accepted: 03/31/2014] [Indexed: 02/01/2023] Open
Abstract
At the heart of genomic imprinting in mammals are imprinting control regions (ICRs), which are the discrete genetic elements that confer imprinted monoallelic expression to several genes in imprinted gene clusters. A characteristic of the known ICRs is that they acquire different epigenetic states, exemplified by differences in DNA methylation, in the sperm and egg, and these imprint marks remain on the sperm- and oocyte-derived alleles into the next generation as a lifelong memory of parental origin. Although there has been much focus on gametic marking of ICRs as the point of imprint specification, recent mechanistic studies and genome-wide DNA methylation profiling do not support the existence of a specific imprinting machinery in germ cells. Rather, ICRs are part of more widespread methylation events that occur during gametogenesis. Instead, a decisive component in the specification of imprints is the choice of which sites of gamete-derived methylation to maintain in the zygote and preimplantation embryo at a time when much of the remainder of the genome is being demethylated. Among the factors involved in this selection, the zinc-finger protein Zfp57 can be regarded as an imprint-specific, sequence-specific DNA binding factor responsible for maintaining methylation at most ICRs. The recent insights into the balance of gametic and zygotic contributions to imprint specification should help understand mechanistic opportunities and constraints on the evolution of imprinting in mammals.
Collapse
|
46
|
Hoyo C, Daltveit AK, Iversen E, Benjamin-Neelon SE, Fuemmeler B, Schildkraut J, Murtha AP, Overcash F, Vidal AC, Wang F, Huang Z, Kurtzberg J, Seewaldt V, Forman M, Jirtle RL, Murphy SK. Erythrocyte folate concentrations, CpG methylation at genomically imprinted domains, and birth weight in a multiethnic newborn cohort. Epigenetics 2014; 9:1120-30. [PMID: 24874916 DOI: 10.4161/epi.29332] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Epigenetic mechanisms are proposed to link maternal concentrations of methyl group donor nutrients with the risk of low birth weight. However, empirical data are lacking. We have examined the association between maternal folate and birth weight and assessed the mediating role of DNA methylation at nine differentially methylated regions (DMRs) of genomically imprinted genes in these associations. Compared with newborns of women with folate levels in the lowest quartile, birth weight was higher in newborns of mothers in the second (β = 143.2, se = 63.2, P = 0.02), third (β = 117.3, se = 64.0, P = 0.07), and fourth (β = 133.9, se = 65.2, P = 0.04) quartiles, consistent with a threshold effect. This pattern of association did not vary by race/ethnicity but was more apparent in newborns of non-obese women. DNA methylation at the PLAGL1, SGCE, DLK1/MEG3 and IGF2/H19 DMRs was associated with maternal folate levels and also birth weight, suggestive of threshold effects. MEG3 DMR methylation mediated the association between maternal folate levels and birth weight (P =0.06). While the small sample size and partial scope of examined DMRs limit our conclusions, our data suggest that, with respect to birth weight, no additional benefits may be derived from increased maternal folate concentrations, especially in non-obese women. These data also support epigenetic plasticity as a key mechanistic response to folate availability during early fetal development.
Collapse
Affiliation(s)
- Cathrine Hoyo
- Department of Biological Sciences; North Carolina State University; Raleigh, NC USA; Department of Obstetrics and Gynecology; Division of Clinical Epidemiology; School of Medicine; Duke University; Durham, NC USA
| | - Anne Kjersti Daltveit
- Department of Global Public Health and Primary Care; University of Bergen; Bergen, Norway
| | - Edwin Iversen
- Department of Statistics; Duke University; Durham, NC USA
| | - Sara E Benjamin-Neelon
- Department of Community and Family Medicine; Duke University School of Medicine and Duke Global Health Institute; Durham, NC USA
| | - Bernard Fuemmeler
- Department of Community and Family Medicine; Duke University; Durham, NC USA
| | - Joellen Schildkraut
- Department of Community and Family Medicine; Duke Cancer Institute; Duke University; Durham, NC USA
| | - Amy P Murtha
- Department of Obstetrics and Gynecology; Division of Maternal-Fetal Medicine; School of Medicine; Duke University; Durham, NC USA
| | - Francine Overcash
- Department of Obstetrics and Gynecology; Division of Clinical Epidemiology; School of Medicine; Duke University; Durham, NC USA
| | - Adriana C Vidal
- Department of Obstetrics and Gynecology; Division of Clinical Epidemiology; School of Medicine; Duke University; Durham, NC USA
| | - Frances Wang
- Department of Community and Family Medicine; Duke Cancer Institute; Duke University; Durham, NC USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology; Division of Gynecologic Oncology; School of Medicine; Duke University; Durham, NC USA
| | - Joanne Kurtzberg
- Duke University Department of Pediatrics; Duke Cancer Institute; School of Medicine; Duke University; Durham, NC USA
| | - Victoria Seewaldt
- Department of Medicine; Division of Oncology; School of Medicine; Duke University; Durham, NC USA
| | - Michele Forman
- Department of Nutritional Sciences; University of Texas; Austin, TX USA
| | - Randy L Jirtle
- Department of Oncology; McArdle Laboratory for Cancer Research; University of Wisconsin-Madison; Madison, WI USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology; Division of Gynecologic Oncology; School of Medicine; Duke University; Durham, NC USA
| |
Collapse
|
47
|
Docherty LE, Rezwan FI, Poole RL, Jagoe H, Lake H, Lockett GA, Arshad H, Wilson DI, Holloway JW, Temple IK, Mackay DJG. Genome-wide DNA methylation analysis of patients with imprinting disorders identifies differentially methylated regions associated with novel candidate imprinted genes. J Med Genet 2014; 51:229-38. [PMID: 24501229 PMCID: PMC3963529 DOI: 10.1136/jmedgenet-2013-102116] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/04/2013] [Accepted: 12/09/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Genomic imprinting is allelic restriction of gene expression potential depending on parent of origin, maintained by epigenetic mechanisms including parent of origin-specific DNA methylation. Among approximately 70 known imprinted genes are some causing disorders affecting growth, metabolism and cancer predisposition. Some imprinting disorder patients have hypomethylation of several imprinted loci (HIL) throughout the genome and may have atypically severe clinical features. Here we used array analysis in HIL patients to define patterns of aberrant methylation throughout the genome. DESIGN We developed a novel informatic pipeline capable of small sample number analysis, and profiled 10 HIL patients with two clinical presentations (Beckwith-Wiedemann syndrome and neonatal diabetes) using the Illumina Infinium Human Methylation450 BeadChip array to identify candidate imprinted regions. We used robust statistical criteria to quantify DNA methylation. RESULTS We detected hypomethylation at known imprinted loci, and 25 further candidate imprinted regions (nine shared between patient groups) including one in the Down syndrome critical region (WRB) and another previously associated with bipolar disorder (PPIEL). Targeted analysis of three candidate regions (NHP2L1, WRB and PPIEL) showed allelic expression, methylation patterns consistent with allelic maternal methylation and frequent hypomethylation among an additional cohort of HIL patients, including six with Silver-Russell syndrome presentations and one with pseudohypoparathyroidism 1B. CONCLUSIONS This study identified novel candidate imprinted genes, revealed remarkable epigenetic convergence among clinically divergent patients, and highlights the potential of epigenomic profiling to expand our understanding of the normal methylome and its disruption in human disease.
Collapse
|
48
|
Takikawa S, Wang X, Ray C, Vakulenko M, Bell FT, Li X. Human and mouse ZFP57 proteins are functionally interchangeable in maintaining genomic imprinting at multiple imprinted regions in mouse ES cells. Epigenetics 2013; 8:1268-79. [PMID: 24135613 DOI: 10.4161/epi.26544] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Genomic imprinting is a common epigenetic phenomenon in mammals. Dysregulation of genomic imprinting has been implicated in a variety of human diseases. ZFP57 is a master regulator in genomic imprinting. Loss of ZFP57 causes loss of DNA methylation imprint at multiple imprinted regions in mouse embryos, as well as in embryonic stem (ES) cells. Similarly, mutations in human ZFP57 result in hypomethylation at many imprinted regions and are associated with transient neonatal diabetes and other human diseases. Mouse and human Zfp57 genes are located in the same syntenic block. However, mouse and human ZFP57 proteins only display about 50% sequence identity with different number of zinc fingers. It is not clear if they share similar mechanisms in maintaining genomic imprinting. Here we report that mouse and human ZFP57 proteins are functionally interchangeable. Expression of exogenous wild-type human ZFP57 could maintain DNA methylation imprint at three imprinted regions in mouse ES cells in the absence of endogenous mouse ZFP57. However, mutant human ZFP57 proteins containing the mutations found in human patients could not substitute for endogenous mouse ZFP57 in maintaining genomic imprinting in ES cells. Like mouse ZFP57, human ZFP57 and its mutant proteins could bind to mouse KAP1, the universal cofactor for KRAB zinc finger proteins, in mouse ES cells. Thus, we conclude that mouse and human ZFP57 are orthologs despite relatively low sequence identity and mouse ES cell system that we had established before is a valuable system for functional analyses of wild-type and mutant human ZFP57 proteins.
Collapse
Affiliation(s)
- Sachiko Takikawa
- Black Family Stem Cell Institute; Department of Developmental and Regenerative Biology; Department of Oncological Sciences; Graduate School of Biological Sciences; Icahn School of Medicine at Mount Sinai; New York, NY USA
| | - Xin Wang
- Black Family Stem Cell Institute; Department of Developmental and Regenerative Biology; Department of Oncological Sciences; Graduate School of Biological Sciences; Icahn School of Medicine at Mount Sinai; New York, NY USA
| | - Chelsea Ray
- Black Family Stem Cell Institute; Department of Developmental and Regenerative Biology; Department of Oncological Sciences; Graduate School of Biological Sciences; Icahn School of Medicine at Mount Sinai; New York, NY USA
| | - Max Vakulenko
- Black Family Stem Cell Institute; Department of Developmental and Regenerative Biology; Department of Oncological Sciences; Graduate School of Biological Sciences; Icahn School of Medicine at Mount Sinai; New York, NY USA
| | - Fong T Bell
- Black Family Stem Cell Institute; Department of Developmental and Regenerative Biology; Department of Oncological Sciences; Graduate School of Biological Sciences; Icahn School of Medicine at Mount Sinai; New York, NY USA
| | - Xiajun Li
- Black Family Stem Cell Institute; Department of Developmental and Regenerative Biology; Department of Oncological Sciences; Graduate School of Biological Sciences; Icahn School of Medicine at Mount Sinai; New York, NY USA
| |
Collapse
|
49
|
Boyraz M, Ulucan K, Taşkın N, Akçay T, Flanagan SE, Mackay DJ. Transient neonatal diabetes mellitus in a Turkish patient with three novel homozygous variants in the ZFP57 gene. J Clin Res Pediatr Endocrinol 2013; 5:125-8. [PMID: 23748067 PMCID: PMC3701919 DOI: 10.4274/jcrpe.928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Neonatal diabetes mellitus (NDM) is a rare form of diabetes that presents within the first six months of life. Nearly 70% of these cases have loss of methylation at the differentially methylated region on chromosome 6q24. To describe the findings in a Turkish male patient with NDM caused by a loss of methylation at chromosome 6q24 and three novel homozygous mutations in the ZFP57 gene, methylation-specific PCR was carried out at 6q24 and mutation analysis of ZFP57 gene was maintained by direct sequencing. Sequencing of ZFP57 gene revealed the hypomethylation of chromosome 6q24 and three novel mutations (chr6:29.641.413 A>T, 29.641.073 C>T, and 29.640.855 G>C), respectively. The latter mutation seems to display the patient's condition due to a highly conservative amino acid substitution in the protein. We suggest the ZFP57 gene as a causative factor for NDM and it should be considered in genetic testing. Further studies including functional analysis of the detected mutations will provide precise information regarding the effect of the mutations.
Collapse
Affiliation(s)
- Mehmet Boyraz
- Şişli Etfal Education and Research Hospital, Division of Pediatric Endocrinology, İstanbul, Turkey
| | - Korkut Ulucan
- Üsküdar University, Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics, İstanbul, Turkey
,* Address for Correspondence: Üsküdar University, Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics, İstanbul, Turkey Phone: +90 216 400 22 22/2409 E-mail:
| | - Necati Taşkın
- Kanuni Sultan Süleyman Education and Research Hospital, Division of Pediatrics, İstanbul, Turkey
| | - Teoman Akçay
- Sadi Konuk Education of Research Hospital, Division of Pediatric Endocrinology, İstanbul, Turkey
| | - Sarah E. Flanagan
- Peninsula College of Medicine and Dentistry, Division of Molecular Genetics, Exeter, UK
| | - Deborah J.G. Mackay
- University of Southampton, School of Medicine, Human Genetics Research Division, Salisbury, UK
| |
Collapse
|