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Placental Mesenchymal Dysplasia and Beckwith-Wiedemann Syndrome. Cancers (Basel) 2022; 14:cancers14225563. [PMID: 36428656 PMCID: PMC9688415 DOI: 10.3390/cancers14225563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Placental mesenchymal dysplasia (PMD) is characterized by placentomegaly, aneurysmally dilated chorionic plate vessels, thrombosis of the dilated vessels, and large grapelike vesicles, and is often mistaken for partial or complete hydatidiform mole with a coexisting normal fetus. Androgenetic/biparental mosaicism (ABM) has been found in many PMD cases. Beckwith-Wiedemann syndrome (BWS) is an imprinting disorder with complex and diverse phenotypes and an increased risk of developing embryonal tumors. There are five major causative alterations: loss of methylation of imprinting control region 2 (KCNQ1OT1:TSS-DMR) (ICR2-LOM), gain of methylation at ICR1 (H19/IGF2:IG-DMR) (ICR1-GOM), paternal uniparental disomy of 11 (pUPD11), loss-of-function variants of the CDKN1C gene, and paternal duplication of 11p15. Additional minor alterations include genetic variants within ICR1, paternal uniparental diploidy/biparental diploidy mosaicism (PUDM, also called ABM), and genetic variants of KCNQ1. ABM (PUDM) is found in both conditions, and approximately 20% of fetuses from PMD cases are BWS and vice versa, suggesting a molecular link. PMD and BWS share some molecular characteristics in some cases, but not in others. These findings raise questions concerning the timing of the occurrence of the molecularly abnormal cells during the postfertilization period and the effects of these abnormalities on cell fates after implantation.
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Yao Y, Hu Y, Yang J, Zhang C, He Y, Qi H, Zeng Y, Zhang A, Liu X, Zhu X. Inhibition of neuronal nitric oxide synthase protects against hippocampal neuronal injuries by increasing neuropeptide Y expression in temporal lobe epilepsy mice. Free Radic Biol Med 2022; 188:45-61. [PMID: 35714846 DOI: 10.1016/j.freeradbiomed.2022.06.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/23/2022] [Accepted: 06/11/2022] [Indexed: 10/18/2022]
Abstract
Neuronal nitric oxide synthase (nNOS) plays a pivotal role in the pathological process of neuronal injury in the development of epilepsy. Our previous study has demonstrated that nitric oxide (NO) derived from nNOS in the epileptic brain is neurotoxic due to its reaction with the superoxide radical with the formation of peroxynitrite. Neuropeptide Y (NPY) is widely expressed in the mammalian brain, which has been implicated in energy homeostasis and neuroprotection. Recent studies suggest that nNOS may act as a mediator of NPY signaling. Here in this study, we sought to determine whether NPY expression is regulated by nNOS, and if so, whether the regulation of NPY by nNOS is associated with the neuronal injuries in the hippocampus of epileptic brain. Our results showed that pilocarpine-induced temporal lobe epilepsy (TLE) mice exhibited an increased level of nNOS expression and a decreased level of NPY expression along with hippocampal neuronal injuries and cognition deficit. Genetic deletion of nNOS gene, however, significantly upregulated hippocampal NPY expression and reduced TLE-induced hippocampal neuronal injuries and cognition decline. Knockdown of NPY abolished nNOS depletion-induced neuroprotection and cognitive improvement in the TLE mice, suggesting that inhibition of nNOS protects against hippocampal neuronal injuries by increasing neuropeptide Y expression in TLE mice. Targeting nNOS-NPY signaling pathway in the epileptic brain might provide clinical benefit by attenuating neuronal injuries and preventing cognitive deficits in epilepsy patients.
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Affiliation(s)
- Yuanyuan Yao
- Department of Pharmacology, Medical School of Southeast University, Nanjing, China
| | - Yang Hu
- Department of Pharmacology, Medical School of Southeast University, Nanjing, China
| | - Jiurong Yang
- Department of Pharmacology, Medical School of Southeast University, Nanjing, China
| | - Canyu Zhang
- Department of Pharmacology, Medical School of Southeast University, Nanjing, China
| | - Yuqi He
- Department of Pharmacology, Medical School of Southeast University, Nanjing, China
| | - Honggang Qi
- Department of Pharmacology, Medical School of Southeast University, Nanjing, China
| | - Yu Zeng
- National Residents Clinical Skills Training Center, Medical School of Southeast University, Nanjing, China
| | - Aifeng Zhang
- Department of Pathology, Medical School of Southeast University, Nanjing, China
| | - Xiufang Liu
- Department of Pathogenic Biology and Immunology, Medical School of Southeast University, Nanjing, China
| | - Xinjian Zhu
- Department of Pharmacology, Medical School of Southeast University, Nanjing, China.
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Freschi A, Del Prete R, Pignata L, Cecere F, Manfrevola F, Mattia M, Cobellis G, Sparago A, Bartolomei MS, Riccio A, Cerrato F. The number of the CTCF binding sites of the H19/IGF2:IG-DMR correlates with DNA methylation and expression imprinting in a humanized mouse model. Hum Mol Genet 2021; 30:1509-1520. [PMID: 34132339 PMCID: PMC8330897 DOI: 10.1093/hmg/ddab132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 01/05/2023] Open
Abstract
The reciprocal parent of origin-specific expression of H19 and IGF2 is controlled by the H19/IGF2:IG-DMR (IC1), whose maternal allele is unmethylated and acts as a CTCF-dependent insulator. In humans, internal IC1 deletions are associated with Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS), depending on their parental origin. These genetic mutations result in aberrant DNA methylation, deregulation of IGF2/H19 and disease with incomplete penetrance. However, the mechanism linking the microdeletions to altered molecular and clinical phenotypes remains unclear. To address this issue, we have previously generated and characterized two knock-in mouse lines with the human wild-type (hIC1wt) or mutant (hIC1∆2.2) IC1 allele replacing the endogenous mouse IC1 (mIC1). Here, we report an additional knock-in line carrying a mutant hIC1 allele with an internal 1.8 kb deletion (hIC1∆1.8). The phenotype of these mice is different from that of the hIC1∆2.2-carrying mice, partially resembling hIC1wt animals. Indeed, proper H19 and Igf2 imprinting and normal growth phenotype were evident in the mice with maternal transmission of hIC1Δ1.8, while low DNA methylation and non-viable phenotype characterize its paternal transmission. In contrast to hIC1wt, E15.5 embryos that paternally inherit hIC1Δ1.8 displayed variegated hIC1 methylation. In addition, increased Igf2 expression, correlating with increased body weight, was found in one third of these mice. Chromatin immunoprecipitation experiments in mouse embryonic stem cells carrying the three different hIC1 alleles demonstrate that the number of CTCF target sites influences its binding to hIC1, indicating that in the mouse, CTCF binding is key to determining hIC1 methylation and Igf2 expression.
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Affiliation(s)
- Andrea Freschi
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Caserta 81100, Italy.,Genetics and Epigenetics of Behaviour (GEB), Istituto Italiano di Tecnologia (IIT), Genova 16163, Italy
| | - Rosita Del Prete
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Caserta 81100, Italy
| | - Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Caserta 81100, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Caserta 81100, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale delle Ricerche (CNR), Naples 80131, Italy
| | - Francesco Manfrevola
- Department of Experimental Medicine, Università degli Studi della Campania "Luigi Vanvitelli", Naples 80138, Italy
| | - Monica Mattia
- Department of Experimental Medicine, Università degli Studi della Campania "Luigi Vanvitelli", Naples 80138, Italy
| | - Gilda Cobellis
- Department of Experimental Medicine, Università degli Studi della Campania "Luigi Vanvitelli", Naples 80138, Italy
| | - Angela Sparago
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Caserta 81100, Italy
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Caserta 81100, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale delle Ricerche (CNR), Naples 80131, Italy
| | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Caserta 81100, Italy
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Pal A, Oakes J, Elnagheeb M, Ideraabdullah FY. Maternal Microdeletion at the H19/Igf2 ICR in Mice Increases Offspring Susceptibility to In Utero Environmental Perturbation. Epigenet Insights 2020; 13:2516865720970575. [PMID: 33313480 PMCID: PMC7716063 DOI: 10.1177/2516865720970575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/09/2020] [Indexed: 12/01/2022] Open
Abstract
Deficiency of methyl donor nutrients folate, choline, and methionine (methyl deficiency) during gestation can impair fetal development and perturb DNA methylation. Here, we assessed genetic susceptibility to methyl deficiency by comparing effects in wildtype C57BL/6J (B6) mice to mutant mice carrying a 1.3 kb deletion at the H19/Igf2 Imprinting Control Region (ICR) (H19 ICRΔ2,3). The H19 ICRΔ2,3 mutation mimics microdeletions observed in Beckwith-Wiedemann syndrome (BWS) patients, who exhibit epimutations in cis that cause loss of imprinting and fetal overgrowth. Dams were treated during pregnancy with 1 of 4 methyl sufficient (MS) or methyl deficient (MD) diets, with or without the antibiotic commonly used to deplete folate producing gut microbes. As expected, after ~9 weeks of treatment, dams in MD and MD + antibiotic groups exhibited substantially reduced plasma folate concentrations. H19 ICRΔ2,3 mutant lines were more susceptible to adverse pregnancy outcomes caused by methyl deficiency (reduced birth rate and increased pup lethality) and antibiotic (decreased litter size and litter survival). Surprisingly, pup growth/development was only minimally affected by methyl deficiency, while antibiotic treatment caused inverse effects on B6 and H19 ICRΔ2,3 lines. B6 pups treated with antibiotic exhibited increased neonatal and weanling bodyweight, while both wildtype and mutant pups of heterozygous H19 ICRΔ2,3/+ dams exhibited decreased neonatal bodyweight that persisted into adulthood. Interestingly, only antibiotic-treated pups carrying the H19 ICRΔ2,3 mutation exhibited altered DNA methylation at the H19/Igf2 ICR, suggesting ICR epimutation was not sufficient to explain the altered phenotypes. These findings demonstrate that genetic mutation of the H19/Igf2 ICR increases offspring susceptibility to developmental perturbation in the methyl deficiency model, maternal and pup genotype play an essential role, and antibiotic treatment in the model also plays a key independent role.
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Affiliation(s)
- Anandita Pal
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Judy Oakes
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Marwa Elnagheeb
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Folami Y Ideraabdullah
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Pignata L, Palumbo O, Cerrato F, Acurzio B, de Álava E, Roma J, Gallego S, Mora J, Carella M, Riccio A, Verde G. Both Epimutations and Chromosome Aberrations Affect Multiple Imprinted Loci in Aggressive Wilms Tumors. Cancers (Basel) 2020; 12:cancers12113411. [PMID: 33217932 PMCID: PMC7698742 DOI: 10.3390/cancers12113411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 12/21/2022] Open
Abstract
The embryonal renal cancer Wilms tumor (WT) accounts for 7% of all children's malignancies. Its most frequent molecular defect is represented by DNA methylation abnormalities at the imprinted 11p15.5 region. Multiple imprinted methylation alterations dictated by chromosome copy-number variations have been recently demonstrated in adult cancers, raising the question of whether multiple imprinted loci were also affected in WT. To address this issue, we analyzed DNA methylation and chromosome profiles of 7 imprinted loci in 48 WT samples. The results demonstrated that methylation abnormalities of multiple imprinted loci occurred in 35% of the cases, but that they were associated with either chromosome aberrations or normal chromosome profiles. Multiple imprinted methylation changes were correlated with tumor stage and presence of metastasis, indicating that these epimutations were more frequent in highly aggressive tumors. When chromosome profiles were affected, these alterations were extended to flanking cancer driver genes. Overall, this study demonstrates the presence of multiple imprinted methylation defects in aggressive WTs and suggests that the mechanism by which they arise in embryonal and adult cancers is different.
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Affiliation(s)
- Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy; (L.P.); (F.C.)
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’ CNR, 80131-Napoli, Italy;
| | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), Italy; (O.P.); (M.C.)
| | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy; (L.P.); (F.C.)
| | - Basilia Acurzio
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’ CNR, 80131-Napoli, Italy;
| | - Enrique de Álava
- Department of Pathology, Institute of Biomedicine of Sevilla (IBiS), Virgen del Rocio University Hospital/CSIC/University of Sevilla/CIBERONC, 41013 Seville, Spain;
- Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, 08035 Seville, Spain
| | - Josep Roma
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute-Universitat Autònoma de Barcelona, 08193 Barcelona, Spain; (J.R.); (S.G.)
| | - Soledad Gallego
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute-Universitat Autònoma de Barcelona, 08193 Barcelona, Spain; (J.R.); (S.G.)
| | - Jaume Mora
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain;
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), Italy; (O.P.); (M.C.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy; (L.P.); (F.C.)
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’ CNR, 80131-Napoli, Italy;
- Correspondence: (A.R.); (G.V.)
| | - Gaetano Verde
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy; (L.P.); (F.C.)
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’ CNR, 80131-Napoli, Italy;
- Correspondence: (A.R.); (G.V.)
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Abstract
Tall stature is usually defined as a height beyond 97th percentile or more than 2 SD above the mean height for age and sex in a defined population. Familiar tall stature, also known as constitutional tall stature, is the most common cause of tall stature. Overnutrition, obesity, also usually causes overgrowth. Tall stature by itself is not a pathological condition, however, there are a number of disorders associated with tall stature. Some genetic disorders and syndromes may be associated with mental retardation and various complications. Therefore, recognition of tall stature and revealing the underlying pathogenic causes and making the diagnosis are important not to miss the serious conditions and to provide adequate medical care and genetic counseling. Pathological causes for tall statute include endocrine disorders, such as excessive growth hormone secretion, hyperthyroidism, precocious puberty and lipodystrophy, chromosome disorders, such as Trisomy X (47, XXX female), Klinefelter Syndrome (47, XXY), XYY syndrome (47, XYY male) and fragile X syndrome, and syndromes and metabolic disorders, such as Marfan Syndrome, Beckwith-Wiedemann Syndrome, Simpson-Golabi-Behmel Syndrome, Sotos Syndrome and homocystinuria. Children may require growth-reductive treatment if the predicted adult height would be excessive and unacceptable. Some hormonal, high doses of sex steroids, or surgical, bilateral percutaneous epiphysiodesis of the distal femur and proximal tibia and fibula, treatment is currently available to reduce adult height.
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Affiliation(s)
- Tatsuhiko Urakami
- Department of Pediatrics, Nihon University School of Medicine, Tokyo, Japan -
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The effectiveness of Wilms tumor screening in Beckwith-Wiedemann spectrum. J Cancer Res Clin Oncol 2019; 145:3115-3123. [PMID: 31583434 DOI: 10.1007/s00432-019-03038-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/25/2019] [Indexed: 10/25/2022]
Abstract
PURPOSE It is well documented that patients with Beckwith-Wiedemann spectrum (BWS) have a significantly higher risk of developing Wilms tumor (WT) than the general population. There has been little research on the timing of WT diagnosis in BWS in regard to optimizing suggested screening protocols. METHODS A literature search was performed to identify all reports of patients with BWS and WT. These data were combined with unpublished data from patients in the authors' cohorts. Age at WT diagnosis was compared against data collected through the NIH Surveillance, Epidemiology, and End Results Program (SEER) registry. RESULTS Patients with BWS had a significantly higher incidence of WT diagnoses between age 12 and 84 months compared to patients in the SEER registry. Patients with BWS and WT diagnosed through screening had significantly lower stages at diagnosis compared to patients with BWS that were not screened. CONCLUSIONS Screening until age 7 years is effective in detecting close to 95% of all WT in patients with BWS.
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The extent of DNA methylation anticipation due to a genetic defect in ICR1 in Beckwith-Wiedemann syndrome. J Hum Genet 2019; 64:937-943. [DOI: 10.1038/s10038-019-0634-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/02/2019] [Accepted: 06/09/2019] [Indexed: 11/08/2022]
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Anvar Z, Acurzio B, Roma J, Cerrato F, Verde G. Origins of DNA methylation defects in Wilms tumors. Cancer Lett 2019; 457:119-128. [PMID: 31103718 DOI: 10.1016/j.canlet.2019.05.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/14/2022]
Abstract
Wilms tumor is an embryonic renal cancer that typically presents in early childhood and accounts for 7% of all paediatric cancers. Different genetic alterations have been described in this malignancy, however, only a few of them are associated with a majority of Wilms tumors. Alterations in DNA methylation, in contrast, are frequent molecular defects observed in most cases of Wilms tumors. How these epimutations are established in this tumor is not yet completely clear. The recent identification of the molecular actors required for the epigenetic reprogramming during embryogenesis suggests novel possible mechanisms responsible for the DNA methylation defects in Wilms tumor. Here, we provide an overview of the DNA methylation alterations observed in this malignancy and discuss the distinct molecular mechanisms by which these epimutations can arise.
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Affiliation(s)
- Zahra Anvar
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, Naples, Italy
| | - Basilia Acurzio
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania 'Luigi Vanvitelli', Caserta, Italy
| | - Josep Roma
- Vall d'Hebron Research Institute-Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Flavia Cerrato
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania 'Luigi Vanvitelli', Caserta, Italy
| | - Gaetano Verde
- Faculty of Medicine and Health Sciences, International University of Catalonia, Sant Cugat del Vallès, Barcelona, Spain.
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Transcription alterations of KCNQ1 associated with imprinted methylation defects in the Beckwith-Wiedemann locus. Genet Med 2019; 21:1808-1820. [PMID: 30635621 PMCID: PMC6687501 DOI: 10.1038/s41436-018-0416-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/10/2018] [Indexed: 11/18/2022] Open
Abstract
Purpose Beckwith–Wiedemann syndrome (BWS) is a developmental disorder caused by dysregulation of the imprinted gene cluster of chromosome 11p15.5 and often associated with loss of methylation (LOM) of the imprinting center 2 (IC2) located in KCNQ1 intron 10. To unravel the etiological mechanisms underlying these epimutations, we searched for genetic variants associated with IC2 LOM. Methods We looked for cases showing the clinical features of both BWS and long QT syndrome (LQTS), which is often associated with KCNQ1 variants. Pathogenic variants were identified by genomic analysis and targeted sequencing. Functional experiments were performed to link these pathogenic variants to the imprinting defect. Results We found three rare cases in which complete IC2 LOM is associated with maternal transmission of KCNQ1 variants, two of which were demonstrated to affect KCNQ1 transcription upstream of IC2. As a consequence of KCNQ1 haploinsufficiency, these variants also cause LQTS on both maternal and paternal transmission. Conclusion These results are consistent with the hypothesis that, similar to what has been demonstrated in mouse, lack of transcription across IC2 results in failure of methylation establishment in the female germline and BWS later in development, and also suggest a new link between LQTS and BWS that is important for genetic counseling.
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Wang KH, Kupa J, Duffy KA, Kalish JM. Diagnosis and Management of Beckwith-Wiedemann Syndrome. Front Pediatr 2019; 7:562. [PMID: 32039119 PMCID: PMC6990127 DOI: 10.3389/fped.2019.00562] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/23/2019] [Indexed: 01/10/2023] Open
Abstract
Beckwith-Wiedemann syndrome (BWS) is a human genomic imprinting disorder that presents with a wide spectrum of clinical features including overgrowth, abdominal wall defects, macroglossia, neonatal hypoglycemia, and predisposition to embryonal tumors. It is associated with genetic and epigenetic changes on the chromosome 11p15 region, which includes two imprinting control regions. Here we review strategies for diagnosing and managing BWS and delineate commonly used genetic tests to establish a molecular diagnosis of BWS. Recommended first-line testing assesses DNA methylation and copy number variation of the BWS region. Tissue mosaicism can occur in patients with BWS, posing a challenge for genetic testing, and a negative test result does not exclude a diagnosis of BWS. Further testing should analyze additional tissue samples or employ techniques with higher diagnostic yield. Identifying the BWS molecular subtype is valuable for coordinating patient care because of the (epi)genotype-phenotype correlations, including different risks and types of embryonal tumors.
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Affiliation(s)
- Kathleen H Wang
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jonida Kupa
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kelly A Duffy
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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12
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Brioude F, Kalish JM, Mussa A, Foster AC, Bliek J, Ferrero GB, Boonen SE, Cole T, Baker R, Bertoletti M, Cocchi G, Coze C, De Pellegrin M, Hussain K, Ibrahim A, Kilby MD, Krajewska-Walasek M, Kratz CP, Ladusans EJ, Lapunzina P, Le Bouc Y, Maas SM, Macdonald F, Õunap K, Peruzzi L, Rossignol S, Russo S, Shipster C, Skórka A, Tatton-Brown K, Tenorio J, Tortora C, Grønskov K, Netchine I, Hennekam RC, Prawitt D, Tümer Z, Eggermann T, Mackay DJG, Riccio A, Maher ER. Expert consensus document: Clinical and molecular diagnosis, screening and management of Beckwith-Wiedemann syndrome: an international consensus statement. Nat Rev Endocrinol 2018; 14:229-249. [PMID: 29377879 PMCID: PMC6022848 DOI: 10.1038/nrendo.2017.166] [Citation(s) in RCA: 314] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Beckwith-Wiedemann syndrome (BWS), a human genomic imprinting disorder, is characterized by phenotypic variability that might include overgrowth, macroglossia, abdominal wall defects, neonatal hypoglycaemia, lateralized overgrowth and predisposition to embryonal tumours. Delineation of the molecular defects within the imprinted 11p15.5 region can predict familial recurrence risks and the risk (and type) of embryonal tumour. Despite recent advances in knowledge, there is marked heterogeneity in clinical diagnostic criteria and care. As detailed in this Consensus Statement, an international consensus group agreed upon 72 recommendations for the clinical and molecular diagnosis and management of BWS, including comprehensive protocols for the molecular investigation, care and treatment of patients from the prenatal period to adulthood. The consensus recommendations apply to patients with Beckwith-Wiedemann spectrum (BWSp), covering classical BWS without a molecular diagnosis and BWS-related phenotypes with an 11p15.5 molecular anomaly. Although the consensus group recommends a tumour surveillance programme targeted by molecular subgroups, surveillance might differ according to the local health-care system (for example, in the United States), and the results of targeted and universal surveillance should be evaluated prospectively. International collaboration, including a prospective audit of the results of implementing these consensus recommendations, is required to expand the evidence base for the design of optimum care pathways.
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Affiliation(s)
- Frédéric Brioude
- Sorbonne Université, Pierre and Marie Curie-Paris VI University (UPMC) Université Paris 06, INSERM UMR_S938 Centre de Recherche Saint-Antoine (CRSA), APHP Hôpital Trousseau, Explorations Fonctionnelles Endocriniennes, 26 Avenue du Docteur Arnold Netter, F-75012 Paris, France
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia and the Department of Pediatrics at the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandro Mussa
- Department of Public Health and Pediatric Sciences, University of Torino, Piazza Polonia 94, 10126 Torino, Italy
- Neonatal Intensive Care Unit, Department of Gynaecology and Obstetrics, Sant'Anna Hospital, Città della Salute e della Scienza di Torino, Corso Spezia 60, 10126 Torino, Italy
| | - Alison C Foster
- Birmingham Health Partners, West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham B15 2TG, UK
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jet Bliek
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, PO Box 7057 1007 MB Amsterdam, The Netherlands
| | - Giovanni Battista Ferrero
- Department of Public Health and Pediatric Sciences, University of Torino, Piazza Polonia 94, 10126 Torino, Italy
| | - Susanne E Boonen
- Clinical Genetic Unit, Department of Pediatrics, Zealand University Hospital, Sygehusvej 10 4000 Roskilde, Denmark
| | - Trevor Cole
- Birmingham Health Partners, West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham B15 2TG, UK
| | - Robert Baker
- Beckwith-Wiedemann Support Group UK, The Drum and Monkey, Wonston, Hazelbury Bryan, Sturminster Newton, Dorset DT10 2EE, UK
| | - Monica Bertoletti
- Italian Association of Beckwith-Wiedemann syndrome (AIBWS) Piazza Turati, 3, 21029, Vergiate (VA), Italy
| | - Guido Cocchi
- Alma Mater Studiorum, Bologna University, Paediatric Department, Neonatology Unit, Via Massarenti 11, 40138 Bologna BO, Italy
| | - Carole Coze
- Aix-Marseille Univ et Assistance Publique Hôpitaux de Marseille (APHM), Hôpital d'Enfants de La Timone, Service d'Hématologie-Oncologie Pédiatrique, 264 Rue Saint Pierre, 13385 Marseille, France
| | - Maurizio De Pellegrin
- Pediatric Orthopaedic Unit IRCCS Ospedale San Raffaele, Milan, Via Olgettina Milano, 60, 20132 Milano MI, Italy
| | - Khalid Hussain
- Department of Paediatric Medicine, Division of Endocrinology, Sidra Medical and Research Center, Al Gharrafa Street, Ar-Rayyan, Doha, Qatar
| | - Abdulla Ibrahim
- Department of Plastic and Reconstructive Surgery, North Bristol National Health Service (NHS) Trust, Southmead Hospital, Bristol BS10 5NB, UK
| | - Mark D Kilby
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Fetal Medicine Centre, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Edgbaston, Birmingham, B15 2TG, UK
| | | | - Christian P Kratz
- Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Strasse 1 30625, Hannover, Germany
| | - Edmund J Ladusans
- Department of Paediatric Cardiology, Royal Manchester Children's Hospital, Manchester, M13 8WL UK
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM Paseo de La Castellana, 261, 28046, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Yves Le Bouc
- Sorbonne Université, Pierre and Marie Curie-Paris VI University (UPMC) Université Paris 06, INSERM UMR_S938 Centre de Recherche Saint-Antoine (CRSA), APHP Hôpital Trousseau, Explorations Fonctionnelles Endocriniennes, 26 Avenue du Docteur Arnold Netter, F-75012 Paris, France
| | - Saskia M Maas
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, PO Box 7057 1007 MB Amsterdam, The Netherlands
| | - Fiona Macdonald
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, B15 2TG UK
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, L. Puusepa 2, 51014, Tartu, Estonia
| | - Licia Peruzzi
- European Society for Paediatric Nephrology (ESPN), Inherited Kidney Disorders Working Group
- AOU Città della Salute e della Scienza di Torino, Regina Margherita Children's Hospital, Turin, Italy
| | - Sylvie Rossignol
- Service de Pédiatrie, Hôpitaux Universitaires de Strasbourg, Laboratoire de Génétique Médicale, INSERM U1112 Avenue Molière 67098 STRASBOURG Cedex, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 4 Rue Kirschleger, 67000 Strasbourg, France
| | - Silvia Russo
- Medical Cytogenetics and Molecular Genetics Laboratory, Centro di Ricerche e Tecnologie Biomediche IRCCS, Istituto Auxologico Italiano, Via Zucchi 18, 20095 Cusano, Milan, Italy
| | - Caroleen Shipster
- Great Ormond Street Hospital for Children National Health Service (NHS) Foundation Trust, London, WC1N 3JH, UK
| | - Agata Skórka
- Department of Medical Genetics, The Children's Memorial Health Institute, 20, 04-730, Warsaw, Poland
- Department of Pediatrics, The Medical University of Warsaw, Zwirki i Wigury 63a, 02-091 Warszawa, Poland
| | - Katrina Tatton-Brown
- South West Thames Regional Genetics Service and St George's University of London and Institute of Cancer Research, London, SW17 0RE, UK
| | - Jair Tenorio
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM Paseo de La Castellana, 261, 28046, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Chiara Tortora
- Regional Center for CLP, Smile House, San Paolo University Hospital, Via Antonio di Rudinì, 8, 20142, Milan, Italy
| | - Karen Grønskov
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Irène Netchine
- Sorbonne Université, Pierre and Marie Curie-Paris VI University (UPMC) Université Paris 06, INSERM UMR_S938 Centre de Recherche Saint-Antoine (CRSA), APHP Hôpital Trousseau, Explorations Fonctionnelles Endocriniennes, 26 Avenue du Docteur Arnold Netter, F-75012 Paris, France
| | - Raoul C Hennekam
- Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam-Zuidoost, Amsterdam, The Netherlands
| | - Dirk Prawitt
- Center for Pediatrics and Adolescent Medicine, Johannes Gutenberg University Medical Center, Langenbeckstr. 1, D-55101, Mainz, Germany
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Thomas Eggermann
- Institute of Human Genetics, University Hospital, Technical University of Aachen, Templergraben 55, 52062, Aachen, Germany
| | - Deborah J G Mackay
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Andrea Riccio
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania Luigi Vanvitelli, Caserta and Institute of Genetics and Biophysics "A. Buzzati-Traverso" - CNR, Via Pietro Castellino, 111,80131, Naples, Italy
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
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13
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Mai Q, Mai X, Huang X, Zhang D, Huang K, Zhou C. Imprinting Status in Two Human Parthenogenetic Embryonic Stem Cell Lines: Analysis of 63 Imprinted Gene Expression Levels in Undifferentiated and Early Differentiated Stages. Stem Cells Dev 2018; 27:430-439. [PMID: 29402175 DOI: 10.1089/scd.2017.0247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human parthenogenetic embryonic stem cells (hPESCs) represent a source of histocompatible tissues for transplantation and carry two copies of the maternal genome, but lack the paternal genome. In this study, we selected 63 known human imprinted genes to investigate the imprinting status of hPESC. The expression level of these genes, including 27 maternally and 36 paternally imprinted were illustrated in hPESC and human embryonic stem cells (hESCs) derived from fertilized embryo lines. The expression activity changes of these genes were analyzed in undifferentiated and early differentiated hPESC lines. In addition, the methylation status of four differentially methylated regions (DMRs) of the imprinted genes was analyzed in undifferentiated and early differentiated hPESC and hESC lines. As a result, we found that all the maternally imprinted genes were expressed at similar levels in the undifferentiated hPESC lines and the hESC lines, except ZNF264 and ATP10A. Twenty-one analyzed paternal imprinted genes were expressed at the same level in two separated hPESC lines as well as compared with the hESC lines, whereas 15 other paternal imprinted genes were significantly downregulated or inactivated in hPESC lines as compared with the hESC line. During prolonged passage, the expression levels of the majority of imprinted genes remained stable in two hPESC lines. The four DMRs, including PEG3/ZIM2 (DMRs), SNURF/SNRPN DMRs, and KVDMR1 DMRs are highly methylated in the genes of two undifferentiated hPESCs and its embryonic bodies (EBs), whereas the genes of the undifferentiated hESCs and its EBs are half methylated. During the early differentiation stage, the imprinted genes showed the same expression trend and the expression levels of H19, IGF2, SLC22A2, SLC22A3/SLC22A18, and CPA4 were significantly upregulated in both hPESC lines. As conclusion, hPESCs show a substantial degree of epigenetic stability with respect to some imprinted genes.
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Affiliation(s)
- Qingyun Mai
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Xiuyun Mai
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China .,2 Reproductive Medical Center , Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xin Huang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Dan Zhang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Kejun Huang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Canquan Zhou
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
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14
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Freschi A, Hur SK, Valente FM, Ideraabdullah FY, Sparago A, Gentile MT, Oneglia A, Di Nucci D, Colucci-D'Amato L, Thorvaldsen JL, Bartolomei MS, Riccio A, Cerrato F. Tissue-specific and mosaic imprinting defects underlie opposite congenital growth disorders in mice. PLoS Genet 2018; 14:e1007243. [PMID: 29470501 PMCID: PMC5839592 DOI: 10.1371/journal.pgen.1007243] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/06/2018] [Accepted: 02/05/2018] [Indexed: 11/18/2022] Open
Abstract
Differential DNA methylation defects of H19/IGF2 are associated with congenital growth disorders characterized by opposite clinical pictures. Due to structural differences between human and mouse, the mechanisms by which mutations of the H19/IGF2 Imprinting Control region (IC1) result in these diseases are undefined. To address this issue, we previously generated a mouse line carrying a humanized IC1 (hIC1) and now replaced the wildtype with a mutant IC1 identified in the overgrowth-associated Beckwith-Wiedemann syndrome. The new humanized mouse line shows pre/post-natal overgrowth on maternal transmission and pre/post-natal undergrowth on paternal transmission of the mutation. The mutant hIC1 acquires abnormal methylation during development causing opposite H19/Igf2 imprinting defects on maternal and paternal chromosomes. Differential and possibly mosaic Igf2 expression and imprinting is associated with asymmetric growth of bilateral organs. Furthermore, tissue-specific imprinting defects result in deficient liver- and placenta-derived Igf2 on paternal transmission and excessive Igf2 in peripheral tissues on maternal transmission, providing a possible molecular explanation for imprinting-associated and phenotypically contrasting growth disorders.
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Affiliation(s)
- Andrea Freschi
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy
| | - Stella K Hur
- Epigenetics Institute, Department of Cell & Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Federica Maria Valente
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy
| | - Folami Y Ideraabdullah
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America.,Department of Nutrition, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Angela Sparago
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy
| | - Maria Teresa Gentile
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy
| | - Andrea Oneglia
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy.,Institute of Genetics and Biophysics, "Adriano Buzzati Traverso" - CNR, Naples, Italy
| | - Diego Di Nucci
- Department of Experimental Medicine, University of Campania, "Luigi Vanvitelli", Naples, Italy
| | - Luca Colucci-D'Amato
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy
| | - Joanne L Thorvaldsen
- Epigenetics Institute, Department of Cell & Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell & Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrea Riccio
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy.,Institute of Genetics and Biophysics, "Adriano Buzzati Traverso" - CNR, Naples, Italy
| | - Flavia Cerrato
- Department of Environmental Technologies, Biological and Pharmaceutical Sciences, University of Campania, "Luigi Vanvitelli", Naples, Italy
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15
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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.
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16
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Carmona JJ, Accomando WP, Binder AM, Hutchinson JN, Pantano L, Izzi B, Just AC, Lin X, Schwartz J, Vokonas PS, Amr SS, Baccarelli AA, Michels KB. Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans. NPJ Genom Med 2017; 2:13. [PMID: 29263828 PMCID: PMC5642382 DOI: 10.1038/s41525-017-0012-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 01/04/2017] [Accepted: 01/12/2017] [Indexed: 12/13/2022] Open
Abstract
We empirically examined the strengths and weaknesses of two human genome-wide DNA methylation platforms: rapid multiplexed reduced representation bisulfite sequencing and Illumina’s Infinium BeadChip. Rapid multiplexed reduced representation bisulfite sequencing required less input DNA, offered more flexibility in coverage, and interrogated more CpG loci at a higher regional density. The Infinium covered slightly more protein coding, cancer-associated and mitochondrial-related genes, both platforms covered all known imprinting clusters, and rapid multiplexed reduced representation bisulfite sequencing covered more microRNA genes than the HumanMethylation450, but fewer than the MethylationEPIC. Rapid multiplexed reduced representation bisulfite sequencing did not always interrogate exactly the same CpG loci, but genomic tiling improved overlap between different libraries. Reproducibility of rapid multiplexed reduced representation bisulfite sequencing and concordance between the platforms increased with CpG density. Only rapid multiplexed reduced representation bisulfite sequencing could genotype samples and measure allele-specific methylation, and we confirmed that Infinium measurements are influenced by nearby single-nucleotide polymorphisms. The respective strengths and weaknesses of these two genome-wide DNA methylation platforms need to be considered when conducting human epigenetic studies. Researchers who study human epigenetics need to carefully consider the platform used to measure genome-wide patterns of DNA methylation. A team led by Karin Michels and Andrea Baccarelli from Harvard University in Boston, Massachusetts, USA, empirically examined the strengths and weaknesses of two methylation profiling tools: Illumina’s Infinium BeadChip, which uses a microarray system to interrogate hundreds of thousands of methylation sites across the genome at single-nucleotide resolution; and a high-throughput sequencing-based approach known as rapid multiplexed reduced representation bisulfite sequencing, or rmRRBS. The former did a better job at reading methylation in protein-coding and mitochondrial-related genes, while the latter required less input DNA and covered more methylation sites across the genome. The authors conclude that a scientist’s platform preference should depend on the nature of his or her investigation.
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Affiliation(s)
- Juan J Carmona
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA.,Program in Quantitative Genomics, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA.,Center for Bioethics, Harvard Medical School, Boston, MA 02115 USA
| | - William P Accomando
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA.,Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Alexandra M Binder
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA.,Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - John N Hutchinson
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115 USA
| | - Lorena Pantano
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115 USA
| | - Benedetta Izzi
- Institute for Prevention and Cancer Epidemiology, Freiburg Medical Center, University of Freiburg, Freiburg, Germany
| | - Allan C Just
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115 USA
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Pantel S Vokonas
- Veterans Affairs Normative Aging Study, Veterans Affairs Boston Healthcare System, Department of Medicine, Boston University School of Medicine, Boston, MA 02118 USA
| | - Sami S Amr
- Department of Pathology, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115 USA.,Translational Genomics Core, Partners Healthcare Personalized Medicine, Cambridge, MA 02139 USA
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Karin B Michels
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA.,Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 USA
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17
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Bachmann N, Crazzolara R, Bohne F, Kotzot D, Maurer K, Enklaar T, Prawitt D, Bergmann C. Novel deletion in 11p15.5 imprinting center region 1 in a patient with Beckwith-Wiedemann syndrome provides insight into distal enhancer regulation and tumorigenesis. Pediatr Blood Cancer 2017; 64. [PMID: 27650505 DOI: 10.1002/pbc.26241] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/23/2016] [Accepted: 08/01/2016] [Indexed: 11/07/2022]
Abstract
BACKGROUND Beckwith-Wiedemann syndrome (BWS) is an early-onset overgrowth disorder with a high risk for embryonal tumors. It is mainly caused by dysregulation of imprinted genes on chromosome 11p15.5; however, the driving forces in the development of tumors are not fully understood. PROCEDURE We report on a female patient presenting with macrosomia, macroglossia, organomegaly and extensive bilateral nephroblastomatosis. Adjuvant chemotherapy was initiated; however, the patient developed hepatoblastoma and Wilms tumor at 5 and 12 months of age, respectively. Subsequent radiofrequency ablation of the liver tumor and partial nephrectomy followed by consolidation therapy achieved complete remission. RESULTS Molecular genetic analysis revealed a maternally derived large deletion of the complete H19-differentially methylated region (H19-DMR; imprinting control region-1 [ICR1]), the whole H19 gene itself as well as large parts of the distal enhancer region within the imprinting cluster-1 (IC1). Extended analysis showed highly elevated insulin-like growth factor 2 (IGF2) expression, possibly explaining at least in part the distinct BWS features and tumor manifestations. CONCLUSIONS This study of a large maternal deletion encompassing the H19 gene and complete ICR1 is the first to demonstrate transcriptional consequences on IGF2 in addition to methylation effects resulting in severe overgrowth and occurrence of multiple tumors in a BWS patient. Studying this deletion helps to clarify the complex molecular processes involved in BWS and provides further insight into tumorigenesis.
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Affiliation(s)
| | - Roman Crazzolara
- Department for Pediatrics, Medical University Innsbruck, Innsbruck, Austria.,Tyrolean Cancer Research Institute, Innsbruck, Austria
| | - Florian Bohne
- Center for Pediatrics and Adolescent Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Dieter Kotzot
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Kathrin Maurer
- Department for Pediatrics, Medical University Innsbruck, Innsbruck, Austria
| | - Thorsten Enklaar
- Center for Pediatrics and Adolescent Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Dirk Prawitt
- Center for Pediatrics and Adolescent Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Carsten Bergmann
- Center for Human Genetics, Bioscientia, Ingelheim, Germany.,Department of Medicine, University Hospital Freiburg, Freiburg, Germany
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18
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Boonen SE, Freschi A, Christensen R, Valente FM, Lildballe DL, Perone L, Palumbo O, Carella M, Uldbjerg N, Sparago A, Riccio A, Cerrato F. Two maternal duplications involving the CDKN1C gene are associated with contrasting growth phenotypes. Clin Epigenetics 2016; 8:69. [PMID: 27313795 PMCID: PMC4910218 DOI: 10.1186/s13148-016-0236-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/08/2016] [Indexed: 01/20/2023] Open
Abstract
Background The overgrowth-associated Beckwith-Wiedemann syndrome (BWS) and the undergrowth-associated Silver-Russell syndrome (SRS) are characterized by heterogeneous molecular defects affecting a large imprinted gene cluster at chromosome 11p15.5-p15.4. While maternal and paternal duplications of the entire cluster consistently result in SRS and BWS, respectively, the phenotypes associated with smaller duplications are difficult to predict due to the complexity of imprinting regulation. Here, we describe two cases with novel inherited partial duplications of the centromeric domain on chromosome 11p15 associated with contrasting growth phenotypes. Findings In a male patient affected by intrauterine growth restriction and postnatal short stature, we identified an in cis maternally inherited duplication of 0.88 Mb including the CDKN1C gene that was significantly up-regulated. The duplication did not include the long non-coding RNA KCNQ1OT1 nor the imprinting control region of the centromeric domain (KCNQ1OT1:TSS-DMR or ICR2) in which methylation was normal. In the mother, also referring a growth restriction phenotype in her infancy, the duplication was de novo and present on her paternal chromosome. A different in cis maternal duplication, 1.13 Mb long and including the abovementioned duplication, was observed in a child affected by Tetralogy of Fallot but with normal growth. In this case, the rearrangement also included most of the KCNQ1OT1 gene and resulted in ICR2 loss of methylation (LOM). In this second family, the mother carried the duplication on her paternal chromosome and showed a normal growth phenotype as well. Conclusions We report two novel in cis microduplications encompassing part of the centromeric domain of the 11p15.5-p15.4 imprinted gene cluster and both including the growth inhibitor CDKN1C gene. Likely, as a consequence of the differential involvement of the regulatory KCNQ1OT1 RNA and ICR2, the smaller duplication is associated with growth restriction on both maternal and paternal transmissions, while the larger duplication, although it includes the smaller one, does not result in any growth anomaly. Our study provides further insights into the phenotypes associated with imprinted gene alterations and highlights the importance of carefully evaluating the affected genes and regulatory elements for accurate genetic counselling of the 11p15 chromosomal rearrangements. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0236-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Andrea Freschi
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Seconda Università degli Studi di Napoli, Caserta, Italy
| | - Rikke Christensen
- Department of Clinical Genetics, Aarhus University Hospital, 8200 Aarhus N, Denmark
| | - Federica Maria Valente
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Seconda Università degli Studi di Napoli, Caserta, Italy
| | | | | | - Orazio Palumbo
- Unità di Genetica Medica, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG Italy
| | - Massimo Carella
- Unità di Genetica Medica, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG Italy
| | - Niels Uldbjerg
- Department of Obstetrics and Gynecology, Aarhus University Hospital, 8200 Aarhus N, Denmark
| | - Angela Sparago
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Seconda Università degli Studi di Napoli, Caserta, Italy
| | - Andrea Riccio
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Seconda Università degli Studi di Napoli, Caserta, Italy.,Istituto di Genetica e Biofisica "Adriano Buzzati-Traverso", Consiglio Nazionale delle Ricerche CNR, Napoli, Italy
| | - Flavia Cerrato
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Seconda Università degli Studi di Napoli, Caserta, Italy
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Mussa A, Russo S, de Crescenzo A, Freschi A, Calzari L, Maitz S, Macchiaiolo M, Molinatto C, Baldassarre G, Mariani M, Tarani L, Bedeschi MF, Milani D, Melis D, Bartuli A, Cubellis MV, Selicorni A, Silengo MC, Larizza L, Riccio A, Ferrero GB. Fetal growth patterns in Beckwith-Wiedemann syndrome. Clin Genet 2016; 90:21-7. [PMID: 26857110 DOI: 10.1111/cge.12759] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/23/2016] [Accepted: 02/03/2016] [Indexed: 01/04/2023]
Abstract
We provide data on fetal growth pattern on the molecular subtypes of Beckwith-Wiedemann syndrome (BWS): IC1 gain of methylation (IC1-GoM), IC2 loss of methylation (IC2-LoM), 11p15.5 paternal uniparental disomy (UPD), and CDKN1C mutation. In this observational study, gestational ages and neonatal growth parameters of 247 BWS patients were compared by calculating gestational age-corrected standard deviation scores (SDS) and proportionality indexes to search for differences among IC1-GoM (n = 21), UPD (n = 87), IC2-LoM (n = 147), and CDKN1C mutation (n = 11) patients. In IC1-GoM subgroup, weight and length are higher than in other subgroups. Body proportionality indexes display the following pattern: highest in IC1-GoM patients, lowest in IC2-LoM/CDKN1C patients, intermediate in UPD ones. Prematurity was significantly more prevalent in the CDKN1C (64%) and IC2-LoM subgroups (37%). Fetal growth patterns are different in the four molecular subtypes of BWS and remarkably consistent with altered gene expression primed by the respective molecular mechanisms. IC1-GoM cases show extreme macrosomia and severe disproportion between weight and length excess. In IC2-LoM/CDKN1C patients, macrosomia is less common and associated with more proportionate weight/length ratios with excess of preterm birth. UPD patients show growth patterns closer to those of IC2-LoM, but manifest a body mass disproportion rather similar to that seen in IC1-GoM cases.
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Affiliation(s)
- A Mussa
- Department of Pediatric and Public Health Sciences, University of Turin, Turin, Italy
| | - S Russo
- Laboratory of Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, Milan, Italy
| | | | - A Freschi
- DiSTABiF, Second University of Naples, Naples, Italy
| | - L Calzari
- Laboratory of Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, Milan, Italy
| | - S Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, S. Gerardo Hospital, Monza, Italia
| | - M Macchiaiolo
- Rare Disease and Medical Genetics Unit, Bambino Gesù Children Hospital, Rome, Italy
| | - C Molinatto
- Department of Pediatric and Public Health Sciences, University of Turin, Turin, Italy
| | - G Baldassarre
- Department of Pediatric and Public Health Sciences, University of Turin, Turin, Italy
| | - M Mariani
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, S. Gerardo Hospital, Monza, Italia
| | - L Tarani
- Department of Pediatric and Pediatric Neuropsychiatry, Sapienza University, Rome, Italy
| | - M F Bedeschi
- Medical Genetics Unit, IRCCS Ca' Granda Foundation, Ospedale Maggiore Policlinico, Milan, Italy
| | - D Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - D Melis
- Clinical Pediatric Genetics, Department of Pediatrics, University "Federico II", Naples, Italy
| | - A Bartuli
- Rare Disease and Medical Genetics Unit, Bambino Gesù Children Hospital, Rome, Italy
| | - M V Cubellis
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - A Selicorni
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, S. Gerardo Hospital, Monza, Italia
| | - M C Silengo
- Department of Pediatric and Public Health Sciences, University of Turin, Turin, Italy
| | - L Larizza
- Laboratory of Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, Milan, Italy
| | - A Riccio
- DiSTABiF, Second University of Naples, Naples, Italy.,Institute of Genetics and Biophysics "A. Buzzati-Traverso" - CNR, Naples, Italy
| | - G B Ferrero
- Department of Pediatric and Public Health Sciences, University of Turin, Turin, Italy
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20
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Russo S, Calzari L, Mussa A, Mainini E, Cassina M, Di Candia S, Clementi M, Guzzetti S, Tabano S, Miozzo M, Sirchia S, Finelli P, Prontera P, Maitz S, Sorge G, Calcagno A, Maghnie M, Divizia MT, Melis D, Manfredini E, Ferrero GB, Pecile V, Larizza L. A multi-method approach to the molecular diagnosis of overt and borderline 11p15.5 defects underlying Silver-Russell and Beckwith-Wiedemann syndromes. Clin Epigenetics 2016; 8:23. [PMID: 26933465 PMCID: PMC4772365 DOI: 10.1186/s13148-016-0183-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 02/08/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Multiple (epi)genetic defects affecting the expression of the imprinted genes within the 11p15.5 chromosomal region underlie Silver-Russell (SRS) and Beckwith-Wiedemann (BWS) syndromes. The molecular diagnosis of these opposite growth disorders requires a multi-approach flowchart to disclose known primary and secondary (epi)genetic alterations; however, up to 20 and 30 % of clinically diagnosed BWS and SRS cases remain without molecular diagnosis. The complex structure of the 11p15 region with variable CpG methylation and low-rate mosaicism may account for missed diagnoses. Here, we demonstrate the relevance of complementary techniques for the assessment of different CpGs and the importance of testing multiple tissues to increase the SRS and BWS detection rate. RESULTS Molecular testing of 147 and 450 clinically diagnosed SRS and BWS cases provided diagnosis in 34 SRS and 185 BWS patients, with 9 SRS and 21 BWS cases remaining undiagnosed and herein referred to as "borderline." A flowchart including complementary techniques and, when applicable, the analysis of buccal swabs, allowed confirmation of the molecular diagnosis in all borderline cases. Comparison of methylation levels by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) in borderline and control cases defined an interval of H19/IGF2:IG-DMR loss of methylation that was distinct between "easy to diagnose" and "borderline" cases, which were characterized by values ≤mean -3 standard deviations (SDs) compared to controls. Values ≥mean +1 SD at H19/IGF2: IG-DMR were assigned to borderline hypermethylated BWS cases and those ≤mean -2 SD at KCNQ1OT1: TSS-DMR to hypomethylated BWS cases; these were supported by quantitative pyrosequencing or Southern blot analysis. Six BWS cases suspected to carry mosaic paternal uniparental disomy of chromosome 11 were confirmed by SNP array, which detected mosaicism till 10 %. Regarding the clinical presentation, borderline SRS were representative of the syndromic phenotype, with exception of one patient, whereas BWS cases showed low frequency of the most common features except hemihyperplasia. CONCLUSIONS A conclusive molecular diagnosis was reached in borderline methylation cases, increasing the detection rate by 6 % for SRS and 5 % for BWS cases. The introduction of complementary techniques and additional tissue analyses into routine diagnostic work-up should facilitate the identification of cases undiagnosed because of mosaicism, a distinctive feature of epigenetic disorders.
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Affiliation(s)
- Silvia Russo
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Luciano Calzari
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Alessandro Mussa
- Department of Pediatric and Public Health Sciences, University of Turin, Torino, Italy
| | - Ester Mainini
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Matteo Cassina
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padua, Padova, Italy
| | - Stefania Di Candia
- Department of Pediatrics, San Raffaele Scientific Institute, Milano, Italy
| | - Maurizio Clementi
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padua, Padova, Italy
| | - Sara Guzzetti
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Silvia Tabano
- Division of Pathology - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Pathophysiology and Transplantation, University of Milan, Milano, Italy
| | - Monica Miozzo
- Division of Pathology - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Pathophysiology and Transplantation, University of Milan, Milano, Italy
| | - Silvia Sirchia
- Department of Health Sciences, University of Milan, Milano, Italy
| | - Palma Finelli
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Paolo Prontera
- Medical Genetics Unit, Department of Surgical and Biomedical Sciences, University of Perugia, Hospital "S. M. della Misericordia", Perugia, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, S. Gerardo Hospital, Monza, Italy
| | - Giovanni Sorge
- Department of Pediatrics and Medical Sciences, AO "Policlinico Vittorio Emanuele", Catania, Italy
| | - Annalisa Calcagno
- Pediatric Endocrine Unit, Department of Pediatrics, IRCCS, Children's Hospital Giannina Gaslini, Genova, Italy
| | - Mohamad Maghnie
- Pediatric Endocrine Unit, Department of Pediatrics, IRCCS, Children's Hospital Giannina Gaslini, Genova, Italy
| | - Maria Teresa Divizia
- Department of Medical Genetics, IRCCS, Children's Hospital Giannina Gaslini, Genova, Italy
| | - Daniela Melis
- Clinical Pediatric Genetics, Department of Pediatrics, University "Federico II", Napoli, Italy
| | - Emanuela Manfredini
- Medical Genetics Unit, Department of Laboratory Medicine, Niguarda Ca' Granda Hospital, Milano, Italy
| | | | - Vanna Pecile
- Institute for Maternal and Child Health, Foundation IRCCS Burlo Garofolo Institute, Trieste, Italy
| | - Lidia Larizza
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
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A novel large deletion of the ICR1 region including H19 and putative enhancer elements. BMC MEDICAL GENETICS 2015; 16:30. [PMID: 25943194 PMCID: PMC4630834 DOI: 10.1186/s12881-015-0173-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 04/22/2015] [Indexed: 02/01/2023]
Abstract
Background Beckwith-Wiedemann syndrome (BWS) is a rare pediatric overgrowth disorder with a variable clinical phenotype caused by deregulation affecting imprinted genes in the chromosomal region 11p15. Alterations of the imprinting control region 1 (ICR1) at the IGF2/H19 locus resulting in biallelic expression of IGF2 and biallelic silencing of H19 account for approximately 10% of patients with BWS. The majority of these patients have epimutations of the ICR1 without detectable DNA sequence changes. Only a few patients were found to have deletions. Most of these deletions are small affecting different parts of the ICR1 differentially methylated region (ICR1-DMR) removing target sequences for CTCF. Only a very few deletions reported so far include the H19 gene in addition to the CTCF binding sites. None of these deletions include IGF2. Case presentation A male patient was born with hypotonia, facial dysmorphisms and hypoglycemia suggestive of Beckwith-Wiedemann syndrome. Using methylation-specific (MS)-MLPA (Multiplex ligation-dependent probe amplification) we have identified a maternally inherited large deletion of the ICR1 region in a patient and his mother. The deletion results in a variable clinical expression with a classical BWS in the mother and a more severe presentation of BWS in her son. By genome-wide SNP array analysis the deletion was found to span ~100 kb genomic DNA including the ICR1DMR, H19, two adjacent non-imprinted genes and two of three predicted enhancer elements downstream to H19. Methylation analysis by deep bisulfite next generation sequencing revealed hypermethylation of the maternal allele at the IGF2 locus in both, mother and child, although IGF2 is not affected by the deletion. Conclusions We here report on a novel large familial deletion of the ICR1 region in a BWS family. Due to the deletion of the ICR1-DMR CTCF binding cannot take place and the residual enhancer elements have access to the IGF2 promoters. The aberrant methylation (hypermethylation) of the maternal IGF2 allele in both affected family members may reflect the active state of the normally silenced maternal IGF2 copy and can be a consequence of the deletion. The deletion results in a variable clinical phenotype and expression. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0173-2) contains supplementary material, which is available to authorized users.
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22
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(Epi)genotype-phenotype correlations in Beckwith-Wiedemann syndrome. Eur J Hum Genet 2015; 24:183-90. [PMID: 25898929 DOI: 10.1038/ejhg.2015.88] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 12/22/2022] Open
Abstract
Beckwith-Wiedemann syndrome (BWS) is characterized by cancer predisposition, overgrowth and highly variable association of macroglossia, abdominal wall defects, nephrourological anomalies, nevus flammeus, ear malformations, hypoglycemia, hemihyperplasia, and organomegaly. BWS molecular defects, causing alteration of expression or activity of the genes regulated by two imprinting centres (IC) in the 11p15 chromosomal region, are also heterogeneous. In this paper we define (epi)genotype-phenotype correlations in molecularly confirmed BWS patients. The characteristics of 318 BWS patients with proven molecular defect were compared among the main four molecular subclasses: IC2 loss of methylation (IC2-LoM, n=190), IC1 gain of methylation (IC1-GoM, n=31), chromosome 11p15 paternal uniparental disomy (UPD, n=87), and cyclin-dependent kinase inhibitor 1C gene (CDKN1C) variants (n=10). A characteristic growth pattern was found in each group; neonatal macrosomia was almost constant in IC1-GoM, postnatal overgrowth in IC2-LoM, and hemihyperplasia more common in UPD (P<0.001). Exomphalos was more common in IC2/CDKN1C patients (P<0.001). Renal defects were typical of UPD/IC1 patients, uretheral malformations of IC1-GoM cases (P<0.001). Ear anomalies and nevus flammeus were associated with IC2/CDKN1C genotype (P<0.001). Macroglossia was less common among UPD patients (P<0.001). Wilms' tumor was associated with IC1-GoM or UPD and never observed in IC2-LoM patients (P<0.001). Hepatoblastoma occurred only in UPD cases. Cancer risk was lower in IC2/CDKN1C, intermediate in UPD, and very high in IC1 cases (P=0.009). In conclusion, (epi)genotype-phenotype correlations define four different phenotypic BWS profiles with some degree of clinical overlap. These observations impact clinical care allowing to move toward (epi) genotype-based follow-up and cancer screening.
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23
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Ideraabdullah FY, Thorvaldsen JL, Myers JA, Bartolomei MS. Tissue-specific insulator function at H19/Igf2 revealed by deletions at the imprinting control region. Hum Mol Genet 2014; 23:6246-59. [PMID: 24990148 DOI: 10.1093/hmg/ddu344] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Parent-of-origin-specific expression at imprinted genes is regulated by allele-specific DNA methylation at imprinting control regions (ICRs). This mechanism of gene regulation, where one element controls allelic expression of multiple genes, is not fully understood. Furthermore, the mechanism of gene dysregulation through ICR epimutations, such as loss or gain of DNA methylation, remains a mystery. We have used genetic mouse models to dissect ICR-mediated genetic and epigenetic regulation of imprinted gene expression. The H19/insulin-like growth factor 2 (Igf2) ICR has a multifunctional role including insulation, activation and repression. Microdeletions at the human H19/IGF2 ICR (IC1) are proposed to be responsible for IC1 epimutations associated with imprinting disorders such as Beckwith-Wiedemann syndrome (BWS). Here, we have generated and characterized a mouse model that mimics BWS microdeletions to define the role of the deleted sequence in establishing and maintaining epigenetic marks and imprinted expression at the H19/IGF2 locus. These mice carry a 1.3 kb deletion at the H19/Igf2 ICR [Δ2,3] removing two of four CCCTC-binding factor (CTCF) sites and the intervening sequence, ∼75% of the ICR. Surprisingly, the Δ2,3 deletion does not perturb DNA methylation at the ICR; however, it does disrupt imprinted expression. While repressive functions of the ICR are compromised by the deletion regardless of tissue type, insulator function is only disrupted in tissues of mesodermal origin where a significant amount of CTCF is poly(ADP-ribosyl)ated. These findings suggest that insulator activity of the H19/Igf2 ICR varies by cell type and may depend on cell-specific enhancers as well as posttranslational modifications of the insulator protein CTCF.
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Affiliation(s)
- Folami Y Ideraabdullah
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 SCTR, 3400 Civic Center Boulevard, Philadelphia PA 19104, USA and Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - Joanne L Thorvaldsen
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 SCTR, 3400 Civic Center Boulevard, Philadelphia PA 19104, USA and
| | - Jennifer A Myers
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 SCTR, 3400 Civic Center Boulevard, Philadelphia PA 19104, USA and
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 SCTR, 3400 Civic Center Boulevard, Philadelphia PA 19104, USA and
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24
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Abi Habib W, Azzi S, Brioude F, Steunou V, Thibaud N, Das Neves C, Le Jule M, Chantot-Bastaraud S, Keren B, Lyonnet S, Michot C, Rossi M, Pasquier L, Gicquel C, Rossignol S, Le Bouc Y, Netchine I. Extensive investigation of the IGF2/H19 imprinting control region reveals novel OCT4/SOX2 binding site defects associated with specific methylation patterns in Beckwith-Wiedemann syndrome. Hum Mol Genet 2014; 23:5763-73. [PMID: 24916376 DOI: 10.1093/hmg/ddu290] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Isolated gain of methylation (GOM) at the IGF2/H19 imprinting control region 1 (ICR1) accounts for about 10% of patients with BWS. A subset of these patients have genetic defects within ICR1, but the frequency of these defects has not yet been established in a large cohort of BWS patients with isolated ICR1 GOM. Here, we carried out a genetic analysis in a large cohort of 57 BWS patients with isolated ICR1 GOM and analyzed the methylation status of the entire domain. We found a new point mutation in two unrelated families and a 21 bp deletion in another unrelated child, both of which were maternally inherited and affected the OCT4/SOX2 binding site in the A2 repeat of ICR1. Based on data from this and previous studies, we estimate that cis genetic defects account for about 20% of BWS patients with isolated ICR1 GOM. Methylation analysis at eight loci of the IGF2/H19 domain revealed that sites surrounding OCT4/SOX2 binding site mutations were fully methylated and methylation indexes declined as a function of distance from these sites. This was not the case in BWS patients without genetic defects identified. Thus, GOM does not spread uniformly across the IGF2/H19 domain, suggesting that OCT4/SOX2 protects against methylation at local sites. These findings add new insights to the mechanism of the regulation of the ICR1 domain. Our data show that mutations and deletions within ICR1 are relatively common. Systematic identification is therefore necessary to establish appropriate genetic counseling for BWS patients with isolated ICR1 GOM.
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Affiliation(s)
- Walid Abi Habib
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris F-75012, France, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris F-75012, France, Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France
| | - Salah Azzi
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris F-75012, France, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris F-75012, France, Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France
| | - Frédéric Brioude
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris F-75012, France, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris F-75012, France, Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France
| | | | - Nathalie Thibaud
- Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France
| | | | - Marilyne Le Jule
- Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France
| | - Sandra Chantot-Bastaraud
- INSERM U933, Service de Génétique et D'Embryologie Médicales, Paris 75571, France, AP-HP, Hôpital Trousseau, Service de Génétique et D'Embryologie Médicales, Paris 75571, France
| | - Boris Keren
- Département de Génétique, CRICM UPMC INSERM UMR_S975/CNRS UMR 7225, GH Pitié-Salpêtrière, APHP, Paris, France
| | - Stanislas Lyonnet
- University Paris Descartes-Sorbonne, Paris Cité, Institut Imagine, INSERM U1163, Hôpital Necker-Enfants Malades, Paris, France
| | - Caroline Michot
- University Paris Descartes-Sorbonne, Paris Cité, Institut Imagine, INSERM U1163, Hôpital Necker-Enfants Malades, Paris, France
| | - Massimiliano Rossi
- Service de Génétique, Centre de Référence des Anomalies du Développement Centre-Est, Hospices Civils de Lyon, Bron, France, INSERM U1028 UMR CNRS 5292, UCBL, CRNL TIGER Team, Lyon, France
| | - Laurent Pasquier
- Service de Génétique Médicale-CLAD Ouest, Hôpital Sud, CHU Rennes, Rennes, France and
| | - Christine Gicquel
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Sylvie Rossignol
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris F-75012, France, Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France
| | - Yves Le Bouc
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris F-75012, France, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris F-75012, France, Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France
| | - Irène Netchine
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris F-75012, France, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris F-75012, France, Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France,
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25
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Maeda T, Higashimoto K, Jozaki K, Yatsuki H, Nakabayashi K, Makita Y, Tonoki H, Okamoto N, Takada F, Ohashi H, Migita M, Kosaki R, Matsubara K, Ogata T, Matsuo M, Hamasaki Y, Ohtsuka Y, Nishioka K, Joh K, Mukai T, Hata K, Soejima H. Comprehensive and quantitative multilocus methylation analysis reveals the susceptibility of specific imprinted differentially methylated regions to aberrant methylation in Beckwith-Wiedemann syndrome with epimutations. Genet Med 2014; 16:903-12. [PMID: 24810686 PMCID: PMC4262761 DOI: 10.1038/gim.2014.46] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 04/07/2014] [Indexed: 01/20/2023] Open
Abstract
Purpose: Expression of imprinted genes is regulated by DNA methylation of differentially methylated regions (DMRs). Beckwith–Wiedemann syndrome is an imprinting disorder caused by epimutations of DMRs at 11p15.5. To date, multiple methylation defects have been reported in Beckwith–Wiedemann syndrome patients with epimutations; however, limited numbers of DMRs have been analyzed. The susceptibility of DMRs to aberrant methylation, alteration of gene expression due to aberrant methylation, and causative factors for multiple methylation defects remain undetermined. Methods: Comprehensive methylation analysis with two quantitative methods, matrix-assisted laser desorption/ionization mass spectrometry and bisulfite pyrosequencing, was conducted across 29 DMRs in 54 Beckwith–Wiedemann syndrome patients with epimutations. Allelic expressions of three genes with aberrant methylation were analyzed. All DMRs with aberrant methylation were sequenced. Results: Thirty-four percent of KvDMR1–loss of methylation patients and 30% of H19DMR–gain of methylation patients showed multiple methylation defects. Maternally methylated DMRs were susceptible to aberrant hypomethylation in KvDMR1–loss of methylation patients. Biallelic expression of the genes was associated with aberrant methylation. Cis-acting pathological variations were not found in any aberrantly methylated DMR. Conclusion: Maternally methylated DMRs may be vulnerable to DNA demethylation during the preimplantation stage, when hypomethylation of KvDMR1 occurs, and aberrant methylation of DMRs affects imprinted gene expression. Cis-acting variations of the DMRs are not involved in the multiple methylation defects.
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Affiliation(s)
- Toshiyuki Maeda
- 1] Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan [2] Department of Pediatrics, Faculty of Medicine, Saga University, Saga, Japan
| | - Ken Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Kosuke Jozaki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Hitomi Yatsuki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yoshio Makita
- Education Center, Asahikawa Medical University, Asahikawa, Japan
| | - Hidefumi Tonoki
- Department of Pediatrics, Maternal, Perinatal, and Child Medical Center, Tenshi Hospital, Sapporo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Izumi, Japan
| | - Fumio Takada
- Department of Medical Genetics, Kitasato University Graduate School of Medical Sciences, Kanagawa, Japan
| | - Hirofumi Ohashi
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Japan
| | - Makoto Migita
- Department of Pediatrics, Nippon Medical School, Tokyo, Japan
| | - Rika Kosaki
- Division of Medical Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Muneaki Matsuo
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuhei Hamasaki
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga, Japan
| | - Yasufumi Ohtsuka
- 1] Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan [2] Department of Pediatrics, Faculty of Medicine, Saga University, Saga, Japan
| | - Kenichi Nishioka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Keiichiro Joh
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | | | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
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Azzi S, Abi Habib W, Netchine I. Beckwith-Wiedemann and Russell-Silver Syndromes: from new molecular insights to the comprehension of imprinting regulation. Curr Opin Endocrinol Diabetes Obes 2014; 21:30-8. [PMID: 24322424 DOI: 10.1097/med.0000000000000037] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW The imprinted human 11p15.5 region encompasses two imprinted domains important for the control of fetal growth: the H19/IGF2 domain in the telomeric region and the KCNQ1OT1/CDKN1C domain in the centromeric region. These two domains are differentially methylated and each is regulated by its own imprinting control region (ICR): ICR1 in the telomeric region and ICR2 in the centromeric region. Aberrant methylation of the 11p15.5 imprinted region, through genetic or epigenetic mechanisms, leads to two clinical syndromes, with opposite growth phenotypes: Russell-Silver Syndrome (RSS; with severe fetal and postnatal growth retardation) and Beckwith-Wiedemann Syndrome (BWS; an overgrowth syndrome). RECENT FINDINGS In this review, we discuss the recently identified molecular abnormalities at 11p15.5 involved in RSS and BWS, which have led to the identification of cis-acting elements and trans-acting regulatory factors involved in the regulation of imprinting in this region. We also discuss the multilocus imprinting disorders identified in various human syndromes, their clinical outcomes and their impact on commonly identified metabolism disorders. SUMMARY These new findings and progress in this field will have direct consequence for diagnostic and predictive tools, risk assessment and genetic counseling for these syndromes.
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Affiliation(s)
- Salah Azzi
- aAP-HP, Hôpital Armand Trousseau, Explorations Fonctionnelles Endocriniennes bUPMC Paris 6, UMR_S938, Centre de Recherche de Saint-Antoine cINSERM, UMR_S938, Centre de Recherche de Saint-Antoine, Paris, France
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Marshall AD, Bailey CG, Rasko JEJ. CTCF and BORIS in genome regulation and cancer. Curr Opin Genet Dev 2013; 24:8-15. [PMID: 24657531 DOI: 10.1016/j.gde.2013.10.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/18/2013] [Accepted: 10/19/2013] [Indexed: 10/25/2022]
Abstract
CTCF plays a vital role in chromatin structure and function. CTCF is ubiquitously expressed and plays diverse roles in gene regulation, imprinting, insulation, intra/interchromosomal interactions, nuclear compartmentalisation, and alternative splicing. CTCF has a single paralogue, the testes-specific CTCF-like gene (CTCFL)/BORIS. CTCF and BORIS can be deregulated in cancer. The tumour suppressor gene CTCF can be mutated or deleted in cancer, or CTCF DNA binding can be altered by epigenetic changes. BORIS is aberrantly expressed frequently in cancer, leading some to propose a pro-tumourigenic role for BORIS. However, BORIS can inhibit cell proliferation, and is mutated in cancer similarly to CTCF suggesting BORIS activation in cancer may be due to global genetic or epigenetic changes typical of malignant transformation.
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Affiliation(s)
- Amy D Marshall
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia; Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, NSW, Australia.
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Higashimoto K, Jozaki K, Kosho T, Matsubara K, Fuke T, Yamada D, Yatsuki H, Maeda T, Ohtsuka Y, Nishioka K, Joh K, Koseki H, Ogata T, Soejima H. A novel de novo point mutation of the OCT-binding site in the IGF2/H19-imprinting control region in a Beckwith-Wiedemann syndrome patient. Clin Genet 2013; 86:539-44. [PMID: 24299031 DOI: 10.1111/cge.12318] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/21/2013] [Accepted: 11/06/2013] [Indexed: 11/29/2022]
Abstract
The IGF2/H19-imprinting control region (ICR1) functions as an insulator to methylation-sensitive binding of CTCF protein, and regulates imprinted expression of IGF2 and H19 in a parental origin-specific manner. ICR1 methylation defects cause abnormal expression of imprinted genes, leading to Beckwith-Wiedemann syndrome (BWS) or Silver-Russell syndrome (SRS). Not only ICR1 microdeletions involving the CTCF-binding site, but also point mutations and a small deletion of the OCT-binding site have been shown to trigger methylation defects in BWS. Here, mutational analysis of ICR1 in 11 BWS and 12 SRS patients with ICR1 methylation defects revealed a novel de novo point mutation of the OCT-binding site on the maternal allele in one BWS patient. In BWS, all reported mutations and the small deletion of the OCT-binding site, including our case, have occurred within repeat A2. These findings indicate that the OCT-binding site is important for maintaining an unmethylated status of maternal ICR1 in early embryogenesis.
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Affiliation(s)
- K Higashimoto
- Division of Molecular Genetics & Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
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Baskin B, Choufani S, Chen YA, Shuman C, Parkinson N, Lemyre E, Micheil Innes A, Stavropoulos DJ, Ray PN, Weksberg R. High frequency of copy number variations (CNVs) in the chromosome 11p15 region in patients with Beckwith-Wiedemann syndrome. Hum Genet 2013; 133:321-30. [PMID: 24154661 DOI: 10.1007/s00439-013-1379-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/05/2013] [Indexed: 01/20/2023]
Abstract
Beckwith-Wiedemann syndrome (BWS), an overgrowth and tumor predisposition syndrome is clinically heterogeneous. Its variable presentation makes molecular diagnosis particularly important for appropriate counseling of patients with respect to embyronal tumor risk and recurrence risk. BWS is characterized by macrosomia, omphalocele, and macroglossia. Additional clinical features can include hemihyperplasia, embryonal tumors, umbilical hernia, and ear anomalies. BWS is etiologically heterogeneous arising from dysregulation of one or both of the chromosome 11p15.5 imprinting centers (IC) and/or imprinted growth regulatory genes on chromosome 11p15.5. Most BWS cases are sporadic and result from loss of maternal methylation at imprinting center 2 (IC2), gain of maternal methylation at imprinting center 1 (IC1) or paternal uniparental disomy (UPD). Heritable forms of BWS (15 %) have been attributed mainly to mutations in the growth suppressor gene CDKN1C, but have also infrequently been identified in patients with copy number variations (CNVs) in the chromosome 11p15.5 region. Four hundred and thirty-four unrelated BWS patients referred to the molecular diagnostic laboratory were tested by methylation-specific multiplex ligation-dependent probe amplification. Molecular alterations were detected in 167 patients, where 103 (62 %) showed loss of methylation at IC2, 23 (14 %) had gain of methylation at IC1, and 41 (25 %) showed changes at both ICs usually associated with paternal UPD. In each of the three groups, we identified patients in whom the abnormalities in the chromosome 11p15.5 region were due to CNVs. Surprisingly, 14 patients (9 %) demonstrated either deletions or duplications of the BWS critical region that were confirmed using comparative genomic hybridization array analysis. The majority of these CNVs were associated with a methylation change at IC1. Our results suggest that CNVs in the 11p15.5 region contribute significantly to the etiology of BWS. We highlight the importance of performing deletion/duplication testing in addition to methylation analysis in the molecular investigation of BWS to improve our understanding of the molecular basis of this disorder, and to provide accurate genetic counseling.
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Affiliation(s)
- Berivan Baskin
- The Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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30
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Epigenetic and genetic alterations of the imprinting disorder Beckwith–Wiedemann syndrome and related disorders. J Hum Genet 2013; 58:402-9. [DOI: 10.1038/jhg.2013.51] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 04/23/2013] [Accepted: 04/26/2013] [Indexed: 12/13/2022]
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31
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Hu J, Sathanoori M, Kochmar S, Madan-Khetarpal S, McGuire M, Surti U. Co-existence of 9p deletion and Silver-Russell syndromes in a patient with maternally inherited cryptic complex chromosome rearrangement involving chromosomes 4, 9, and 11. Am J Med Genet A 2012; 161A:179-84. [DOI: 10.1002/ajmg.a.35658] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 08/20/2012] [Indexed: 11/09/2022]
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Robbins KM, Chen Z, Wells KD, Rivera RM. Expression of KCNQ1OT1, CDKN1C, H19, and PLAGL1 and the methylation patterns at the KvDMR1 and H19/IGF2 imprinting control regions is conserved between human and bovine. J Biomed Sci 2012; 19:95. [PMID: 23153226 PMCID: PMC3533950 DOI: 10.1186/1423-0127-19-95] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/06/2012] [Indexed: 01/22/2023] Open
Abstract
Background Beckwith-Wiedemann syndrome (BWS) is a loss-of-imprinting pediatric overgrowth syndrome. The primary features of BWS include macrosomia, macroglossia, and abdominal wall defects. Secondary features that are frequently observed in BWS patients are hypoglycemia, nevus flammeus, polyhydramnios, visceromegaly, hemihyperplasia, cardiac malformations, and difficulty breathing. BWS is speculated to occur primarily as the result of the misregulation of imprinted genes associated with two clusters on chromosome 11p15.5, namely the KvDMR1 and H19/IGF2. A similar overgrowth phenotype is observed in bovine and ovine as a result of embryo culture. In ruminants this syndrome is known as large offspring syndrome (LOS). The phenotypes associated with LOS are increased birth weight, visceromegaly, skeletal defects, hypoglycemia, polyhydramnios, and breathing difficulties. Even though phenotypic similarities exist between the two syndromes, whether the two syndromes are epigenetically similar is unknown. In this study we use control Bos taurus indicus X Bos taurus taurus F1 hybrid bovine concepti to characterize baseline imprinted gene expression and DNA methylation status of imprinted domains known to be misregulated in BWS. This work is intended to be the first step in a series of experiments aimed at determining if LOS will serve as an appropriate animal model to study BWS. Results The use of F1 B. t. indicus x B. t. taurus tissues provided us with a tool to unequivocally determine imprinted status of the regions of interest in our study. We found that imprinting is conserved between the bovine and human in imprinted genes known to be associated with BWS. KCNQ1OT1 and PLAGL1 were paternally-expressed while CDKN1C and H19 were maternally-expressed in B. t. indicus x B. t. taurus F1 concepti. We also show that in bovids, differential methylation exists at the KvDMR1 and H19/IGF2 ICRs. Conclusions Based on these findings we conclude that the imprinted gene expression of KCNQ1OT1, CDKN1C, H19, and PLAGL1 and the methylation patterns at the KvDMR1 and H19/IGF2 ICRs are conserved between human and bovine. Future work will determine if LOS is associated with misregulation at these imprinted loci, similarly to what has been observed for BWS.
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Spector LG, Birch J. The epidemiology of hepatoblastoma. Pediatr Blood Cancer 2012; 59:776-9. [PMID: 22692949 DOI: 10.1002/pbc.24215] [Citation(s) in RCA: 197] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 05/08/2012] [Indexed: 01/12/2023]
Abstract
Few causes of hepatoblastoma have been conclusively identified, mainly due to the extreme rarity of the disease. Inherited conditions including Familial Adenomatous Polyposis and Beckwith-Wiedemann Syndrome dramatically raise risk of hepatoblastoma but account for few cases overall. A small number of case-control studies investigating risk factors for sporadic hepatoblastoma have been conducted to date. Although most of these studies feature fewer than 200 cases, several clues have emerged. Most notably there is a roughly 20-fold increased risk of hepatoblastoma among children with very low birth weight (<1,500 g) and a doubling of risk among those with moderately low birth weight (1,500-2,500 g). A modicum of evidence points to a possible role of parental tobacco use prior to or during pregnancy in the causation of hepatoblastoma as well.
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Affiliation(s)
- Logan G Spector
- Division of Epidemiology/Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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34
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Beygo J, Citro V, Sparago A, De Crescenzo A, Cerrato F, Heitmann M, Rademacher K, Guala A, Enklaar T, Anichini C, Cirillo Silengo M, Graf N, Prawitt D, Cubellis MV, Horsthemke B, Buiting K, Riccio A. The molecular function and clinical phenotype of partial deletions of the IGF2/H19 imprinting control region depends on the spatial arrangement of the remaining CTCF-binding sites. Hum Mol Genet 2012; 22:544-57. [PMID: 23118352 PMCID: PMC3542864 DOI: 10.1093/hmg/dds465] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
At chromosome 11p15.5, the imprinting centre 1 (IC1) controls the parent of origin-specific expression of the IGF2 and H19 genes. The 5 kb IC1 region contains multiple target sites (CTS) for the zinc-finger protein CTCF, whose binding on the maternal chromosome prevents the activation of IGF2 and allows that of H19 by common enhancers. CTCF binding helps maintaining the maternal IC1 methylation-free, whereas on the paternal chromosome gamete-inherited DNA methylation inhibits CTCF interaction and enhancer-blocking activity resulting in IGF2 activation and H19 silencing. Maternally inherited 1.4–2.2 kb deletions are associated with methylation of the residual CTSs and Beckwith–Wiedemann syndrome, although with different penetrance and expressivity. We explored the relationship between IC1 microdeletions and phenotype by analysing a number of previously described and novel mutant alleles. We used a highly quantitative assay based on next generation sequencing to measure DNA methylation in affected families and analysed enhancer-blocking activity and CTCF binding in cultured cells. We demonstrate that the microdeletions mostly affect IC1 function and CTCF binding by changing CTS spacing. Thus, the extent of IC1 inactivation and the clinical phenotype are influenced by the arrangement of the residual CTSs. A CTS spacing similar to the wild-type allele results in moderate IC1 inactivation and is associated with stochastic DNA methylation of the maternal IC1 and incomplete penetrance. Microdeletions with different CTS spacing display severe IC1 inactivation and are associated with IC1 hypermethylation and complete penetrance. Careful characterization of the IC1 microdeletions is therefore needed to predict recurrence risks and phenotypical outcomes.
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Affiliation(s)
- Jasmin Beygo
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
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35
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Higashimoto K, Nakabayashi K, Yatsuki H, Yoshinaga H, Jozaki K, Okada J, Watanabe Y, Aoki A, Shiozaki A, Saito S, Koide K, Mukai T, Hata K, Soejima H. Aberrant methylation of H19-DMR acquired after implantation was dissimilar in soma versus placenta of patients with Beckwith-Wiedemann syndrome. Am J Med Genet A 2012; 158A:1670-5. [PMID: 22577095 DOI: 10.1002/ajmg.a.35335] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 01/19/2012] [Indexed: 01/15/2023]
Abstract
Gain of methylation (GOM) at the H19-differentially methylated region (H19-DMR) is one of several causative alterations in Beckwith-Wiedemann syndrome (BWS), an imprinting-related disorder. In most patients with epigenetic changes at H19-DMR, the timing of and mechanism mediating GOM is unknown. To clarify this, we analyzed methylation at the imprinting control regions of somatic tissues and the placenta from two unrelated, naturally conceived patients with sporadic BWS. Maternal H19-DMR was abnormally and variably hypermethylated in both patients, indicating epigenetic mosaicism. Aberrant methylation levels were consistently lower in placenta than in blood and skin. Mosaic and discordant methylation strongly suggested that aberrant hypermethylation occurred after implantation, when genome-wide de novo methylation normally occurs. We expect aberrant de novo hypermethylation of H19-DMR happens to a greater extent in embryos than in placentas, as this is normally the case for de novo methylation. In addition, of 16 primary imprinted DMRs analyzed, only H19-DMR was aberrantly methylated, except for NNAT DMR in the placental chorangioma of Patient 2. To our knowledge, these are the first data suggesting when GOM of H19-DMR occurs.
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Affiliation(s)
- Ken Higashimoto
- Division of Molecular Genetics & Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
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Demars J, Gicquel C. Epigenetic and genetic disturbance of the imprinted 11p15 region in Beckwith-Wiedemann and Silver-Russell syndromes. Clin Genet 2012; 81:350-61. [PMID: 22150955 DOI: 10.1111/j.1399-0004.2011.01822.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Genomic imprinting is a particularly attractive example of epigenetic regulation leading to the parental-origin-specific expression of genes. In several ways, the 11p15 imprinted region is an exemplary model for regulation of genomic imprinting. The two imprinted domains are controlled by imprinting control regions (ICRs) which carry opposite germ line imprints and they are regulated by two major mechanisms of imprinting control. Dysregulation of 11p15 genomic imprinting results in two fetal growth disorders [Silver-Russell (SRS) and Beckwith-Wiedemann (BWS) syndromes], with opposite growth phenotypes. BWS and SRS result from abnormal imprinting involving either, both domains or only one of them, with ICR1 and ICR2 more often involved in SRS and BWS respectively. DNA methylation defects affecting ICR1 or ICR2 account for approximately 60% of SRS and BWS patients. Recent studies have identified new cis-acting regulatory elements, as well as new trans-acting factors involved in the regulation of 11p15 imprinting, therefore establishing new mechanisms of BWS and SRS. Those studies also showed that, apart of CTCF, other transcription factors, including factors of the pluripotency network, play a crucial role in the regulation of 11p15 genomic imprinting. Those new findings have direct consequences in molecular testing, risk assessment and genetic counseling of BWS and SRS patients.
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Affiliation(s)
- J Demars
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
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Algar E, Dagar V, Sebaj M, Pachter N. An 11p15 imprinting centre region 2 deletion in a family with Beckwith Wiedemann syndrome provides insights into imprinting control at CDKN1C. PLoS One 2011; 6:e29034. [PMID: 22205991 PMCID: PMC3242768 DOI: 10.1371/journal.pone.0029034] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 11/19/2011] [Indexed: 12/03/2022] Open
Abstract
We report a three generation family with Beckwith Wiedemann syndrome (BWS) in whom we have identified a 330 kb deletion within the KCNQ1 locus, encompassing the 11p15.5 Imprinting Centre II (IC2). The deletion arose on the paternal chromosome in the first generation and was only associated with BWS when transmitted maternally to subsequent generations. The deletion on the maternal chromosome was associated with a lower median level of CDKN1C expression in the peripheral blood of affected individuals when compared to a cohort of unaffected controls (p<0.05), however was not significantly different to the expression levels in BWS cases with loss of methylation (LOM) within IC2 (p<0.78). Moreover the individual with a deletion on the paternal chromosome did not show evidence of elevated CDKN1C expression or features of Russell Silver syndrome. These observations support a model invoking the deletion of enhancer elements required for CDKN1C expression lying within or close to the imprinting centre and importantly extend and validate a single observation from an earlier study. Analysis of 94 cases with IC2 loss of methylation revealed that KCNQ1 deletion is a rare cause of loss of maternal methylation, occurring in only 3% of cases, or in 1.5% of BWS overall.
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Affiliation(s)
- Elizabeth Algar
- Molecular Oncology Laboratory, Murdoch Children's Research Institute, Melbourne, Australia.
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Garavelli L, Rosato S, Wischmeijer A, Gelmini C, Esposito A, Mazzanti L, Franchi F, De Crescenzo A, Palumbo O, Carella M, Riccio A. 22q11.2 Distal Deletion Syndrome: Description of a New Case with Truncus Arteriosus Type 2 and Review. Mol Syndromol 2011; 2:35-44. [PMID: 22582037 DOI: 10.1159/000334262] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2011] [Indexed: 01/06/2023] Open
Abstract
22q11.2 deletion syndrome is mainly characterized by conotruncal congenital heart defects, velopharyngeal insufficiency, hypocalcemia and a characteristic craniofacial appearance. The etiology in the majority of patients is a 3-Mb recurrent deletion in region 22q11.2. Nevertheless, recently some cases of infrequent deletions with various sizes have been reported with a different phenotype. We report on a patient with congenital heart disease (truncus arteriosus type 2) in whom a de novo 1.3-Mb 22q11.2 deletion was detected by array comparative genomic hybridization. The deletion described corresponds to an atypical and distal deletion which spans low copy repeat (LCR) 4 and is associated with breakpoint sites that do not correspond to known LCRs of 22q11.2. We examine the clinical phenotype of our case and compare our findings with those published in the literature. The most prevalent clinical features in this type of deletion are a history of prematurity, pre-natal and post-natal growth retardation, slight facial dysmorphic features, microcephaly and developmental delay, with a speech defect in particular. These are clearly different from those found in the classic 22q11.2 deletion syndrome, and we believe that the main differential diagnosis should be with Silver-Russel syndrome. In our case we observe the cardiac phenotype with truncus arteriosus communis usually seen in the classic 22q11.2 deletion syndrome, and so far associated with the TBX1 gene. Significantly, however, TBX1 is not included in our patient's deletion. The possible roles of a position effect or other genes are discussed.
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Affiliation(s)
- L Garavelli
- Clinical Genetics Unit, Obstetric and Paediatric Department, Reggio Emilia, Italy
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Argente J, Sotos JF. [Overgrowth with and without obesity: clinical and molecular principles]. An Pediatr (Barc) 2011; 76:161.e1-28. [PMID: 22098786 DOI: 10.1016/j.anpedi.2011.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 09/15/2011] [Indexed: 12/26/2022] Open
Abstract
Somatic overgrowth is a complex and heterogeneous pathology that is only partially understood, although developments in molecular biology have allowed the discovery of the aetiological basis of some of these conditions. The differential diagnosis of a patient with a possible variant of normality, a chromosomopathy, a dysmorphic syndrome, a metabolic or an endocrine disease is essential. The initial clinical evaluation should include a correct anamnesis and physical examination, as well as complementary laboratory and image analyses that will help to orient the diagnosis. This should include a full blood counts and complete biochemical analysis, determinations of IGF-I, IGFBP-3, free T4, TSH and homocystinuria, as well as a karyotype and an X-ray of the left hand and wrist. These results should be very beneficial in orienting the diagnosis. Additional molecular studies should be performed when a monogenic disease is suspected. Cardiological, ophthalmological, skeletal, psychological and psychiatric studies should be performed if the clinical information and previously mentioned complementary studies so indicate. In this review, the aetiological basis and the diagnostic-therapeutic principles in the most common causes of overgrowth, will be analysed.
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Affiliation(s)
- J Argente
- Servicios de Pediatría y Endocrinología, Hospital Infantil Universitario Niño Jesús, Instituto de Investigación La Princesa, Departamento de Pediatría, Universidad Autónoma de Madrid, CIBER de fisiopatología de la Obesidad y Nutrición, España.
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40
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Neonatal hepatoblastoma in a newborn with severe phenotype of Beckwith-Wiedemann syndrome. Eur J Pediatr 2011; 170:1407-11. [PMID: 21448630 DOI: 10.1007/s00431-011-1455-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 03/14/2011] [Indexed: 10/18/2022]
Abstract
Beckwith-Wiedemann syndrome is an overgrowth disorder characterized by neonatal macrosomia, abdominal wall defects, macroglossia, renal anomalies, organomegaly, hypoglycemia, and cancer predisposition. Hepatoblastoma is the second most frequent tumor and periodic serum alpha-fetoprotein (αFP) dosage is the cornerstone of the tumor surveillance for its early detection. In this report, we describe the outstanding case of a Beckwith-Wiedemann syndrome (BWS) newborn with severe phenotype and paternal chromosome 11 uniparental disomy (UPD11) associated with a high tumor risk. Based on the clinical picture and previous reports, a close monitoring of αFP was commenced. The marker was normal immediately after birth, but rapidly raised in 20 days, leading to the diagnosis of an extremely aggressive hepatoblastoma. The latter was successfully treated with pre-surgical reductive chemotherapy, gross total mass resection, and subsequent chemotherapy. Based on this observation, the tumor surveillance routinely suggested every 3 months should be more intense and with closer time intervals in newborns with severe BWS phenotype. We suggest monitoring neonatal αFP every 20 days in such cases.
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Chiesa N, De Crescenzo A, Mishra K, Perone L, Carella M, Palumbo O, Mussa A, Sparago A, Cerrato F, Russo S, Lapi E, Cubellis MV, Kanduri C, Cirillo Silengo M, Riccio A, Ferrero GB. The KCNQ1OT1 imprinting control region and non-coding RNA: new properties derived from the study of Beckwith-Wiedemann syndrome and Silver-Russell syndrome cases. Hum Mol Genet 2011; 21:10-25. [PMID: 21920939 PMCID: PMC3235007 DOI: 10.1093/hmg/ddr419] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A cluster of imprinted genes at chromosome 11p15.5 is associated with the growth disorders, Silver–Russell syndrome (SRS) and Beckwith–Wiedemann syndrome (BWS). The cluster is divided into two domains with independent imprinting control regions (ICRs). We describe two maternal 11p15.5 microduplications with contrasting phenotypes. The first is an inverted and in cis duplication of the entire 11p15.5 cluster associated with the maintenance of genomic imprinting and with the SRS phenotype. The second is a 160 kb duplication also inverted and in cis, but resulting in the imprinting alteration of the centromeric domain. It includes the centromeric ICR (ICR2) and the most 5′ 20 kb of the non-coding KCNQ1OT1 gene. Its maternal transmission is associated with ICR2 hypomethylation and the BWS phenotype. By excluding epigenetic mosaicism, cell clones analysis indicated that the two closely located ICR2 sequences resulting from the 160 kb duplication carried discordant DNA methylation on the maternal chromosome and supported the hypothesis that the ICR2 sequence is not sufficient for establishing imprinted methylation and some other property, possibly orientation-dependent, is needed. Furthermore, the 1.2 Mb duplication demonstrated that all features are present for correct imprinting at ICR2 when this is duplicated and inverted within the entire cluster. In the individuals maternally inheriting the 160 kb duplication, ICR2 hypomethylation led to the expression of a truncated KCNQ1OT1 transcript and to down-regulation of CDKN1C. We demonstrated by chromatin RNA immunopurification that the KCNQ1OT1 RNA interacts with chromatin through its most 5′ 20 kb sequence, providing a mechanism likely mediating the silencing activity of this long non-coding RNA.
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Affiliation(s)
- Nicoletta Chiesa
- Dipartimento di Scienze Pediatriche e dell’Adolescenza, Università di Torino, Torino, Italy
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42
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Demars J, Rossignol S, Netchine I, Lee KS, Shmela M, Faivre L, Weill J, Odent S, Azzi S, Callier P, Lucas J, Dubourg C, Andrieux J, Le Bouc Y, El-Osta A, Gicquel C. New insights into the pathogenesis of Beckwith-Wiedemann and Silver-Russell syndromes: contribution of small copy number variations to 11p15 imprinting defects. Hum Mutat 2011; 32:1171-82. [PMID: 21780245 DOI: 10.1002/humu.21558] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 06/12/2011] [Indexed: 01/28/2023]
Abstract
The imprinted 11p15 region is organized in two domains, each of them under the control of its own imprinting control region (ICR1 for the IGF2/H19 domain and ICR2 for the KCNQ1OT1/CDKN1C domain). Disruption of 11p15 imprinting results in two fetal growth disorders with opposite phenotypes: the Beckwith-Wiedemann (BWS) and the Silver-Russell (SRS) syndromes. Various 11p15 genetic and epigenetic defects have been demonstrated in BWS and SRS. Among them, isolated DNA methylation defects account for approximately 60% of patients. To investigate whether cryptic copy number variations (CNVs) involving only part of one of the two imprinted domains account for 11p15 isolated DNA methylation defects, we designed a single nucleotide polymorphism array covering the whole 11p15 imprinted region and genotyped 185 SRS or BWS cases with loss or gain of DNA methylation at either ICR1 or ICR2. We describe herein novel small gain and loss CNVs in six BWS or SRS patients, including maternally inherited cis-duplications involving only part of one of the two imprinted domains. We also show that ICR2 deletions do not account for BWS with ICR2 loss of methylation and that uniparental isodisomy involving only one of the two imprinted domains is not a mechanism for SRS or BWS.
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Affiliation(s)
- Julie Demars
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
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43
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Ideraabdullah FY, Abramowitz LK, Thorvaldsen JL, Krapp C, Wen SC, Engel N, Bartolomei MS. Novel cis-regulatory function in ICR-mediated imprinted repression of H19. Dev Biol 2011; 355:349-57. [PMID: 21600199 DOI: 10.1016/j.ydbio.2011.04.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 04/25/2011] [Accepted: 04/30/2011] [Indexed: 11/27/2022]
Abstract
Expression of coregulated imprinted genes, H19 and Igf2, is monoallelic and parent-of-origin-dependent. Like most imprinted genes, H19 and Igf2 are regulated by a differentially methylated imprinting control region (ICR). CTCF binding sites and DNA methylation at the ICR have previously been identified as key cis-acting elements required for proper H19/Igf2 imprinting. Here, we use mouse models to elucidate further the mechanism of ICR-mediated gene regulation. We specifically address the question of whether sequences outside of CTCF sites at the ICR are required for paternal H19 repression. To this end, we generated two types of mutant ICRs in the mouse: (i) deletion of intervening sequence between CTCF sites (H19(ICR∆IVS)), which changes size and CpG content at the ICR; and (ii) CpG depletion outside of CTCF sites (H19(ICR-8nrCG)), which only changes CpG content at the ICR. Individually, both mutant alleles (H19(ICR∆IVS) and H19(ICR-8nrCG)) show loss of imprinted repression of paternal H19. Interestingly, this loss of repression does not coincide with a detectable change in methylation at the H19 ICR or promoter. Thus, neither intact CTCF sites nor hypermethylation at the ICR is sufficient for maintaining the fully repressed state of the paternal H19 allele. Our findings demonstrate, for the first time in vivo, that sequence outside of CTCF sites at the ICR is required in cis for ICR-mediated imprinted repression at the H19/Igf2 locus. In addition, these results strongly implicate a novel role of ICR size and CpG density in paternal H19 repression.
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Affiliation(s)
- Folami Y Ideraabdullah
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, 415 Curie Boulevard, Philadelphia, PA 19104, USA
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44
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De Crescenzo A, Coppola F, Falco P, Bernardo I, Ausanio G, Cerrato F, Falco L, Riccio A. A novel microdeletion in the IGF2/H19 imprinting centre region defines a recurrent mutation mechanism in familial Beckwith-Wiedemann syndrome. Eur J Med Genet 2011; 54:e451-4. [PMID: 21571108 PMCID: PMC3133689 DOI: 10.1016/j.ejmg.2011.04.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Accepted: 04/25/2011] [Indexed: 11/30/2022]
Abstract
The overgrowth disorder Beckwith–Wiedemann syndrome (BWS) is associated with dysregulation of imprinted genes at chromosome 11p15.5. The molecular defects are heterogeneous but most of the cases are associated with defective DNA methylation at either one of two Imprinting Control Regions (IC1 and IC2) or Uniparental paternal Disomy (UPD) at 11p15.5. In rare cases, the BWS phenotype has been found associated with maternal transmission of IC1 microdeletions. We describe a family with a novel 1.8 kb deletion that is associated with hypermethylation at IC1. The mutation results from recombination between highly homologous sequences containing target sites for the zinc-finger protein CTCF (CTSs). This finding supports the hypothesis that the function of IC1 and the penetrance of the clinical phenotype depend on the spacing of the CTSs resulting from recombination in the mutant allele.
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45
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Nativio R, Sparago A, Ito Y, Weksberg R, Riccio A, Murrell A. Disruption of genomic neighbourhood at the imprinted IGF2-H19 locus in Beckwith-Wiedemann syndrome and Silver-Russell syndrome. Hum Mol Genet 2011; 20:1363-74. [PMID: 21282187 PMCID: PMC3049359 DOI: 10.1093/hmg/ddr018] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 01/12/2011] [Indexed: 12/19/2022] Open
Abstract
Hyper- and hypomethylation at the IGF2-H19 imprinting control region (ICR) result in reciprocal changes in IGF2-H19 expression and the two contrasting growth disorders, Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS). DNA methylation of the ICR controls the reciprocal imprinting of IGF2 and H19 by preventing the binding of the insulator protein, CTCF. We here show that local changes in histone modifications and CTCF--cohesin binding at the ICR in BWS and SRS together with DNA methylation correlate with the higher order chromatin structure at the locus. In lymphoblastoid cells from control individuals, we found the repressive histone H3K9me3 and H4K20me3 marks associated with the methylated paternal ICR allele and the bivalent H3K4me2/H3K27me3 mark together with H3K9ac and CTCF--cohesin associated with the non-methylated maternal allele. In patient-derived cell lines, the mat/pat asymmetric distribution of these epigenetic marks was lost with H3K9me3 and H4K20me3 becoming biallelic in the BWS and H3K4me2, H3K27me3 and H3K9ac together with CTCF-cohesin becoming biallelic in the SRS. We further show that in BWS and SRS cells, there is opposing chromatin looping conformation mediated by CTCF--cohesin binding sites surrounding the locus. In normal cells, lack of CTCF--cohesin binding at the paternal ICR is associated with monoallelic interaction between two CTCF sites flanking the locus. CTCF--cohesin binding at the maternal ICR blocks this interaction by associating with the CTCF site downstream of the enhancers. The two alternative chromatin conformations are differently favoured in BWS and SRS likely predisposing the locus to the activation of IGF2 or H19, respectively.
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Affiliation(s)
- Raffaella Nativio
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, LiKaShing Centre, Cambridge, UK
| | - Angela Sparago
- Institute of Genetics and Biophysics A. Buzzati-Traverso, CNR, Naples, Italy
| | - Yoko Ito
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, LiKaShing Centre, Cambridge, UK
| | - Rosanna Weksberg
- Program in Genetic and Genomic Biology and
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada and
| | - Andrea Riccio
- Institute of Genetics and Biophysics A. Buzzati-Traverso, CNR, Naples, Italy
- Department of Environmental Science, University of Naples 2, Caserta, Italy
| | - Adele Murrell
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, LiKaShing Centre, Cambridge, UK
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Abstract
hsa-mir-483 is located within intron 2 of the IGF2 gene. We have previously shown oncogenic features of miR-483-3p through cooperation with IGF2 or by independently targeting the proapoptotic gene BBC3/PUMA. Here we demonstrate that expression of miR-483 can be induced independently of IGF2 by the oncoprotein β-catenin through an interaction with the basic helix-loop-helix protein upstream stimulatory transcription factor 1. We also show that β-catenin itself is a target of miR-483-3p, triggering a negative regulatory loop that becomes ineffective in cells harboring an activating mutation of β-catenin. These results provide insights into the complex regulation of the IGF2/miR-483 locus, revealing players in the β-catenin pathway.
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Abstract
Genomic imprinting represents a form of epigenetic control of gene expression in which one allele of a gene is preferentially expressed according to the parent-of-origin of the allele. Genomic imprinting plays an important role in normal growth and development. Disruption of imprinting can result in a number of human imprinting syndromes and predispose to cancer. In this chapter, we describe a number of human imprinting syndromes to illustrate the concepts of genomic imprinting and how loss of imprinting of imprinted genes their relationship to human neoplasia.
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Affiliation(s)
- Derek Hock Kiat Lim
- Department of Medical & Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, UK
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48
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Ollikainen M, Smith KR, Joo EJH, Ng HK, Andronikos R, Novakovic B, Abdul Aziz NK, Carlin JB, Morley R, Saffery R, Craig JM. DNA methylation analysis of multiple tissues from newborn twins reveals both genetic and intrauterine components to variation in the human neonatal epigenome. Hum Mol Genet 2010; 19:4176-88. [PMID: 20699328 DOI: 10.1093/hmg/ddq336] [Citation(s) in RCA: 267] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mounting evidence from both animal and human studies suggests that the epigenome is in constant drift over the life course in response to stochastic and environmental factors. In humans, this has been highlighted by a small number of studies that have demonstrated discordant DNA methylation patterns in adolescent or adult monozygotic (MZ) twin pairs. However, to date, it remains unclear when such differences emerge, and how prevalent they are across different tissues. To address this, we examined the methylation of four differentially methylated regions associated with the IGF2/H19 locus in multiple birth tissues derived from 91 twin pairs: 56 MZ and 35 dizygotic (DZ). Tissues included cord blood-derived mononuclear cells and granulocytes, human umbilical vein endothelial cells, buccal epithelial cells and placental tissue. Considerable variation in DNA methylation was observed between tissues and between unrelated individuals. Most interestingly, methylation discordance was also present within twin pairs, with DZ pairs showing greater discordance than MZ pairs. These data highlight the variable contribution of both intrauterine environmental exposures and underlying genetic factors to the establishment of the neonatal epigenome of different tissues and confirm the intrauterine period as a sensitive time for the establishment of epigenetic variability in humans. This has implications for the effects of maternal environment on the development of the newborn epigenome and supports an epigenetic mechanism for the previously described phenomenon of 'fetal programming' of disease risk.
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Affiliation(s)
- Miina Ollikainen
- Developmental Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
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Carella M, Spreafico F, Palumbo O, Storlazzi CT, Tabano S, Miozzo M, Miglionico L, Calvano S, Sindici G, Gamba B, Impera L, Collini P, Zelante L, Radice P, Perotti D. Constitutional ring chromosome 11 mosaicism in a Wilms tumor patient: Cytogenetic, molecular and clinico-pathological studies. Am J Med Genet A 2010; 152A:1756-63. [DOI: 10.1002/ajmg.a.33420] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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50
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Veronese A, Lupini L, Consiglio J, Visone R, Ferracin M, Fornari F, Zanesi N, Alder H, D'Elia G, Gramantieri L, Bolondi L, Lanza G, Querzoli P, Angioni A, Croce CM, Negrini M. Oncogenic role of miR-483-3p at the IGF2/483 locus. Cancer Res 2010; 70:3140-9. [PMID: 20388800 DOI: 10.1158/0008-5472.can-09-4456] [Citation(s) in RCA: 175] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
hsa-mir-483 is located within intron 2 of the IGF2 locus. We found that the mature microRNA (miRNA) miR-483-3p is overexpressed in 100% of Wilms' tumors. In addition, colon, breast, and liver cancers exhibit high or even extremely high levels of miR-483-3p in approximately 30% of the cases. A coregulation with IGF2 mRNA was detected, although some tumors exhibited high expression of miR-483-3p without a concomitant increase of IGF2. These findings suggested that miR-483-3p could cooperate with IGF2 or act as an autonomous oncogene. Indeed, here we prove that an anti-miRNA oligonucleotide against miR-483-3p could inhibit the miRNAs without affecting IGF2 mRNA and it could suppress tumorigenicity of HepG2 cells, a cell line that overexpresses miR-483-3p and IGF2. Conversely, no antitumor effect was elicited by inhibition of IGF2. The oncogenic mechanism of miR-483-3p was at least partially clarified by the finding that it could modulate the proapoptotic protein BBC3/PUMA and miR-483-3p enforced expression could protect cells from apoptosis. Our results indicate that miR-483-3p could function as an antiapoptotic oncogene in various human cancers and reveal a new, potentially important target for anticancer therapy.
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Affiliation(s)
- Angelo Veronese
- Dipartimento di Medicina Sperimentale e Diagnostica, Università di Ferrara, Ferrara, Italy
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