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Schlaich E, Hubens WHG, Eggermann T. First-time application of droplet digital PCR for methylation testing of the 11p15.5 imprinting regions. Mol Genet Genomic Med 2023; 11:e2264. [PMID: 37519217 PMCID: PMC10724498 DOI: 10.1002/mgg3.2264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/20/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND Beckwith-Wiedemann syndrome and Silver-Russel syndrome are two imprinting disorders caused by opposite molecular alterations in 11p15.5. With the current diagnostic tests, their molecular diagnosis is challenging due to molecular heterogeneity and mosaic occurrence of the most frequent alterations. As the determination of precise (epi)genotype of patients is relevant as the basis for a personalized treatment, different approaches are needed to increase the sensitivity of diagnostic testing of imprinting disorders. METHODS We established methylation-specific droplet digital PCR approaches (MS-ddPCR) for the two imprinting centers in 11p15.5, and analyzed patients with paternal uniparental disomy of chromosome 11p15.5 (upd(11)pat) and other imprinting defects in the region. The results were compared to those from MS-MLPA (multiplex ligation-dependent probe amplification) and MS-pyrosequencing. RESULTS MS-ddPCR confirmed the molecular alterations in all patients and the results matched well with MS-MLPA. The results of MS-pyrosequencing varied between different runs, whereas MS-ddPCR results were reproducible. CONCLUSION We show for the first time that MS-ddPCR is a reliable and easy applicable method for determination of MS-associated changes in imprinting disorders. It is therefore an additional tool for multimethod diagnostics of imprinting disorders suitable to improve the diagnostic yield.
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Affiliation(s)
- Elia Schlaich
- Institute for Human Genetics and Genome Medicine, Medical Faculty, RWTH Aachen UniversityAachenGermany
| | - Wouter H. G. Hubens
- Institute for Stem Cell Biology, Medical Faculty, RWTH Aachen UniversityAachenGermany
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen UniversityAachenGermany
| | - Thomas Eggermann
- Institute for Human Genetics and Genome Medicine, Medical Faculty, RWTH Aachen UniversityAachenGermany
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Lü Y, Jiang Y, Zhou X, Hao N, Xu C, Guo R, Chang J, Li M, Zhang H, Zhou J, Zhang W(V, Qi Q. Detection of Mosaic Absence of Heterozygosity (AOH) Using Low-Pass Whole Genome Sequencing in Prenatal Diagnosis: A Preliminary Report. Diagnostics (Basel) 2023; 13:2895. [PMID: 37761262 PMCID: PMC10529865 DOI: 10.3390/diagnostics13182895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Objective: Mosaicism is a common biological phenomenon in organisms and has been reported in many types of chromosome abnormalities, including the absence of heterozygosity (AOH). Due to the detection limitations of the sequencing approach, mosaic AOH events are rarely assessed in clinical cases. Herein, we report the performance of mosaic AOH identification using a low-pass (5~8-fold) WGS method (termed 'CMA-seq', an abbreviation for 'Chromosome Analysis by Sequencing') in fetal genetic diagnosis. Methods: Thirty AOH-negative, eleven constitutional AOH, and three mosaic AOH samples were collected as training data sets to develop the algorithm and evaluate the suitable thresholds for distinguishing mosaic AOH. Twenty-four new chromosomal aberrant cases, along with sixteen constitutional AOH samples, which were previously ascertained via the SNP-array-based method, were used as a validation data set to measure the performance in terms of sensitivity and specificity of this algorithm. Results: A new statistic, 'D-value', was implemented to identify and distinguish constitutional and mosaic AOH events. The reporting thresholds for constitutional and mosaic AOH were also established. In the validation set consisting of 24 new cases, seven constitutional AOH cases and 1 mosaic AOH case were successfully identified, indicating that the results were consistent with those of the SNP-array-based method. The results of all sixteen constitutional AOH validation samples also met the threshold requirements. Conclusions: In this study, we developed a new bioinformatic algorithm to accurately distinguish mosaic AOH from constitutional AOH by low-pass WGS. However, due to the small sample size of the training data set, the algorithm proposed in this manuscript still needs further refinements.
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Affiliation(s)
- Yan Lü
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yulin Jiang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Xiya Zhou
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Na Hao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Chenlu Xu
- AmCare Genomics Lab, Guangzhou 510335, China (W.Z.)
| | - Ruidong Guo
- AmCare Genomics Lab, Guangzhou 510335, China (W.Z.)
| | - Jiazhen Chang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Mengmeng Li
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Hanzhe Zhang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Jing Zhou
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | | | - Qingwei Qi
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
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3
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Eggermann T, Prawitt D. Further understanding of paternal uniparental disomy in Beckwith-Wiedemann syndrome. Expert Rev Endocrinol Metab 2022; 17:513-521. [PMID: 36377076 DOI: 10.1080/17446651.2022.2144228] [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: 06/27/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Paternal uniparental disomy of chromosome 11 (upd(11)pat) accounts for up to 20% of molecularly confirmed Beckwith-Wiedemann spectrum (BWSp) cases. It belongs to the BWSp subgroup with the second highest tumor risk, and therefore needs particular awareness in research, diagnostics and clinical management. AREAS COVERED We overview the contribution of paternal (mosaic) uniparental disomy of chromosome 11 (UPD, upd(11)pat) and mosaic paternal uniparental diploidy in patients with Beckwith-Wiedemann features. The review comprises the current knowledge on their formation and their molecular and clinical consequences. Accordingly, the consequences for diagnostic testing and clinical monitoring are compiled. EXPERT OPINION The necessity to diagnostically identify and thus discriminate genome-wide paternal uniparental disomy, and upd(11)pat becomes obvious, due to the differences in the clinical course, disease prognosis, and treatment. In particular, monitoring of tumor development by liquid biopsy might be a promising option in the future. From the research point of view, it should be addressed why 11p is prone to mitotic recombination and thus also provide to the role of upd(11) as second hit in tumorigenesis.
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Affiliation(s)
- Thomas Eggermann
- Medical Faculty, Institute of Human Genetics, RWTH Aachen, Aachen, Germany
| | - Dirk Prawitt
- Center for Paediatrics and Adolescent Medicine, University Medical Center, Mainz, Germany
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Kim HY, Shin CH, Lee YA, Shin CH, Kim GH, Ko JM. Deciphering Epigenetic Backgrounds in a Korean Cohort with Beckwith-Wiedemann Syndrome. Ann Lab Med 2022; 42:668-677. [PMID: 35765875 PMCID: PMC9277041 DOI: 10.3343/alm.2022.42.6.668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/07/2022] [Accepted: 06/08/2022] [Indexed: 11/22/2022] Open
Abstract
Background Beckwith–Wiedemann syndrome (BWS) is a congenital overgrowth disorder caused by genetic or epigenetic alterations at two imprinting centers (ICs) in the 11p15.5 region. Delineation of the molecular defects is important for prognosis and predicting familial recurrence. We evaluated epigenetic alterations and potential epigenotype–phenotype correlations in Korean children with BWS. Methods Forty children with BWS with proven genetic or epigenetic defects in the 11p15.5 region were included. The phenotype was scored using the BWS consensus scoring system. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), bisulfite pyrosequencing, a single-nucleotide polymorphism microarray, and CDKN1C sequencing were used for confirmative diagnosis. Results Patients met the criteria for genetic testing, with a mean clinical score of 5.4±2.0. Methylation alterations were consistent between MS-MLPA and bisulfite pyrosequencing in all patients. Twenty-six patients (65.0%) had IC2 loss of methylation (IC2-LoM), 11 (27.5%) had paternal uniparental disomy (patUPD), and one (2.5%) had IC1 gain of methylation. Macroglossia and external ear anomalies were more common in IC2-LoM than in patUPD, and lateralized overgrowth was more common in patUPD than in IC2-LoM (all P<0.05). Methylation levels at IC2 were inversely correlated with birth weight standard deviation score (r=–0.476, P=0.014) and clinical score (r=–0.520, P=0.006) in the IC2-LoM group. Conclusions Comprehensive molecular analysis of the 11p15.5 region revealed epigenotype–phenotype correlations in our BWS cohort. Bisulfite pyrosequencing can help clarify epigenotypes. Methylation levels were correlated with fetal growth and clinical severity in patients with BWS.
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Affiliation(s)
- Hwa Young Kim
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Young Ah Lee
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Ho Shin
- Department of Orthopaedic Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Gu-Hwan Kim
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Rare Disease Center, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
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Pignata L, Sparago A, Palumbo O, Andreucci E, Lapi E, Tenconi R, Carella M, Riccio A, Cerrato F. Mosaic Segmental and Whole-Chromosome Upd(11)mat in Silver-Russell Syndrome. Genes (Basel) 2021; 12:genes12040581. [PMID: 33923683 PMCID: PMC8073375 DOI: 10.3390/genes12040581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
Molecular defects altering the expression of the imprinted genes of the 11p15.5 cluster are responsible for the etiology of two congenital disorders characterized by opposite growth disturbances, Silver-Russell syndrome (SRS), associated with growth restriction, and Beckwith-Wiedemann syndrome (BWS), associated with overgrowth. At the molecular level, SRS and BWS are characterized by defects of opposite sign, including loss (LoM) or gain (GoM) of methylation at the H19/IGF2:intergenic differentially methylated region (H19/IGF2:IG-DMR), maternal or paternal duplication (dup) of 11p15.5, maternal (mat) or paternal (pat) uniparental disomy (upd), and gain or loss of function mutations of CDKN1C. However, while upd(11)pat is found in 20% of BWS cases and in the majority of them it is segmental, upd(11)mat is extremely rare, being reported in only two SRS cases to date, and in both of them is extended to the whole chromosome. Here, we report on two novel cases of mosaic upd(11)mat with SRS phenotype. The upd is mosaic and isodisomic in both cases but covers the entire chromosome in one case and is restricted to 11p14.1-pter in the other case. The segmental upd(11)mat adds further to the list of molecular defects of opposite sign in SRS and BWS, making these two imprinting disorders even more specular than previously described.
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Affiliation(s)
- Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (L.P.); (A.S.); (F.C.)
| | - Angela Sparago
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (L.P.); (A.S.); (F.C.)
| | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (O.P.); (M.C.)
| | - Elena Andreucci
- Medical Genetics Unit, Meyer Children’s Hospital, 50139 Firenze, Italy; (E.A.); (E.L.)
| | - Elisabetta Lapi
- Medical Genetics Unit, Meyer Children’s Hospital, 50139 Firenze, Italy; (E.A.); (E.L.)
| | - Romano Tenconi
- Department of Pediatrics, Clinical Genetics, Università di Padova, 35122 Padova, Italy;
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (O.P.); (M.C.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (L.P.); (A.S.); (F.C.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Napoli, Italy
- Correspondence:
| | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (L.P.); (A.S.); (F.C.)
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Zhang M, Sun C, Liu R, Dong C, Cheng R, Zheng Z, Wu B, Luo F, Pei Z, Lu W. Phenotypes and epigenetic errors in patients with Beckwith-Wiedemann syndrome in China. Transl Pediatr 2020; 9:653-661. [PMID: 33209728 PMCID: PMC7658761 DOI: 10.21037/tp-20-243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Beckwith-Wiedemann syndrome (BWS) is primarily caused by epigenetic errors. This study aimed to analyze the relationship between the epigenetic errors and phenotypes of BWS and to evaluate the efficacy of diagnosing BWS using patients' clinical characteristics. METHODS Patients clinically diagnosed with BWS were subjected to methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) for (epi)genotyping. The patients' clinical characteristics were analyzed and compared using regression models. The diagnostic efficacy of previous criteria and scoring systems was compared using area under the receiving operating curve (ROC). RESULTS The most common clinical features observed in BWS patients were macroglossia (83.2%), abdominal wall defects (71.3%), and ear creases/pits (55.3%). Patients with the loss of methylation at imprinting control 2 (IC2-LOM) and gaining of methylation at imprinting control 1 (IC1-GOM) subtypes had significantly higher frequencies of ear creases/pits and facial nevus flammeus, and visceromegaly, respectively. Paternal uniparental isodisomy (pUPD) was characterized by significantly less macroglossia but more hemihypertrophy. The area under the curve (AUC) was comparably good in both recently developed scoring systems (0.87 for Ibrahim and 0.82 for Brioude.) and in the scoring system developed using the current cohort (0.88). CONCLUSIONS This study, which is the largest cohort study of BWS cases in China published to date, confirmed the diagnostic efficacy of a recently developed symptom-based BWS scoring system in a Chinese population. Significant differences exist between the phenotypes of BWS epigenetic subtypes; however, the pattern is similar between Asian and European populations.
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Affiliation(s)
- Miaoying Zhang
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Chengjun Sun
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Renchao Liu
- The Molecular Genetic Diagnosis Center, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Chenbin Dong
- Plastic Surgery Department, Children's Hospital of Fudan University, Shanghai, China
| | - Ruoqian Cheng
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Zhangqian Zheng
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- The Molecular Genetic Diagnosis Center, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Feihong Luo
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Zhou Pei
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Wei Lu
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
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8
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Seelan RS, Pisano M, Greene RM. Nucleic acid methylation and orofacial morphogenesis. Birth Defects Res 2019; 111:1593-1610. [PMID: 31385455 DOI: 10.1002/bdr2.1564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022]
Abstract
In this review, we highlight the current state of knowledge of the diverse roles nucleic acid methylation plays in the embryonic development of the orofacial region and how aberrant methylation may contribute to orofacial clefts. We also consider the role of methylation in the regulation of neural crest cell function as it pertains to orofacial ontogeny. Changes in DNA methylation, as a consequence of environmental effects, have been observed in the regulatory regions of several genes, potentially identifying new candidate genes for orofacial clefting and opening promising new avenues for further research. While the focus of this review is primarily on the nonsyndromic forms of orofacial clefting, syndromic forms are briefly discussed in the context of aberrant nucleic acid methylation.
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Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
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Terino M, Plotkin E, Karagozian R. Pancreatoblastoma: an Atypical Presentation and a Literature Review. J Gastrointest Cancer 2019; 49:361-364. [PMID: 28194556 DOI: 10.1007/s12029-017-9925-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Marisa Terino
- Department of Internal Medicine, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030, USA.
| | - Eileen Plotkin
- Department of Gastroenterology and Hepatology, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030, USA
| | - Raffi Karagozian
- Department of Gastroenterology and Hepatology, St. Francis Hospital and Medical Center, 114 Woodland St, Hartford, CT, 06105, USA
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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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Oseni GO, Jain D, Mossey PA, Busch TD, Gowans LJJ, Eshete MA, Adeyemo WL, Laurie CA, Laurie CC, Owais A, Olaitan PB, Aregbesola BS, Oginni FO, Bello SA, Donkor P, Audu R, Onwuamah C, Obiri-Yeboah S, Plange-Rhule G, Ogunlewe OM, James O, Halilu T, Abate F, Abdur-Rahman LO, Oladugba AV, Marazita ML, Murray JC, Adeyemo AA, Butali A. Identification of paternal uniparental disomy on chromosome 22 and a de novo deletion on chromosome 18 in individuals with orofacial clefts. Mol Genet Genomic Med 2018; 6:924-932. [PMID: 30141273 PMCID: PMC6305633 DOI: 10.1002/mgg3.459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/17/2018] [Accepted: 07/23/2018] [Indexed: 01/07/2023] Open
Abstract
Background Orofacial clefts are the most common malformations of the head and neck region. Genetic and environmental factors have been implicated in the etiology of these traits. Methods We recently conducted genotyping of individuals from the African population using the multiethnic genotyping array (MEGA) to identify common genetic variation associated with nonsyndromic orofacial clefts. The data cleaning of this dataset allowed for screening of annotated sex versus genetic sex, confirmation of identify by descent and identification of large chromosomal anomalies. Results We identified the first reported orofacial cleft case associated with paternal uniparental disomy (patUPD) on chromosome 22. We also identified a de novo deletion on chromosome 18. In addition to chromosomal anomalies, we identified cases with molecular karyotypes suggesting Klinefelter syndrome, Turner syndrome and Triple X syndrome. Conclusion Observations from our study support the need for genetic testing when clinically indicated in order to exclude chromosomal anomalies associated with clefting. The identification of these chromosomal anomalies and sex aneuploidies is important in genetic counseling for families that are at risk. Clinicians should share any identified genetic findings and place them in context for the families during routine clinical visits and evaluations.
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Affiliation(s)
- Ganiyu O Oseni
- Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Nigeria
| | - Deepti Jain
- Department of Biostatistics, Genetic Coordinating Center, University of Washington, Seattle, Washington
| | - Peter A Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - Tamara D Busch
- Department of Pediatrics, University of Iowa, Iowa City, Iowa
| | - Lord J J Gowans
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mekonen A Eshete
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Wasiu L Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Cecelia A Laurie
- Department of Biostatistics, Genetic Coordinating Center, University of Washington, Seattle, Washington
| | - Cathy C Laurie
- Department of Biostatistics, Genetic Coordinating Center, University of Washington, Seattle, Washington
| | - Arwa Owais
- Department of Pediatric Dentistry, University of Iowa, Iowa City, Iowa
| | - Peter B Olaitan
- Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Nigeria
| | - Babatunde S Aregbesola
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile Ife, Nigeria
| | - Fadekemi O Oginni
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile Ife, Nigeria
| | | | - Peter Donkor
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Rosemary Audu
- Department of Virology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Chika Onwuamah
- Department of Virology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | | | | | - Olugbenga M Ogunlewe
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Olutayo James
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Taiye Halilu
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Firke Abate
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lukman O Abdur-Rahman
- Division of Pediatric Surgery, Department of Surgery, University of Ilorin, Ilorin, Nigeria
| | | | - Mary L Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | | | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, Iowa
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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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García-Giménez JL, Seco-Cervera M, Tollefsbol TO, Romá-Mateo C, Peiró-Chova L, Lapunzina P, Pallardó FV. Epigenetic biomarkers: Current strategies and future challenges for their use in the clinical laboratory. Crit Rev Clin Lab Sci 2017; 54:529-550. [PMID: 29226748 DOI: 10.1080/10408363.2017.1410520] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetic modifications and regulators represent potential molecular elements which control relevant physiological and pathological features, thereby contributing to the natural history of human disease. These epigenetic modulators can be employed as disease biomarkers, since they show several advantages and provide information about gene function, thus explaining differences among patient endophenotypes. In addition, epigenetic biomarkers can incorporate information regarding the effects of the environment and lifestyle on health and disease, and monitor the effect of applied therapies. Technologies used to analyze these epigenetic biomarkers are constantly improving, becoming much easier to use. Laboratory professionals can easily acquire experience and techniques are becoming more affordable. A high number of epigenetic biomarker candidates are being continuously proposed, making now the moment to adopt epigenetics in the clinical laboratory and convert epigenetic marks into reliable biomarkers. In this review, we describe some current promising epigenetic biomarkers and technologies being applied in clinical practice. Furthermore, we will discuss some laboratory strategies and kits to accelerate the adoption of epigenetic biomarkers into clinical routine. The likelihood is that over time, better markers will be identified and will likely be incorporated into future multi-target assays that might help to optimize its application in a clinical laboratory. This will improve cost-effectiveness, and consequently encourage the development of theragnosis and the application of precision medicine.
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Affiliation(s)
- José Luis García-Giménez
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain.,d Epigenetics Research Platform (CIBERER/UV/INCLIVA) , Valencia , Spain.,e EpiDisease S.L. Spin-Off of CIBERER (ISCIII) , Valencia , Spain
| | - Marta Seco-Cervera
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain
| | - Trygve O Tollefsbol
- f Department of Biology , University of Alabama at Birmingham , Birmingham , AL , USA
| | - Carlos Romá-Mateo
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain.,d Epigenetics Research Platform (CIBERER/UV/INCLIVA) , Valencia , Spain
| | - Lorena Peiró-Chova
- b INCLIVA Biomedical Research Institute , Valencia , Spain.,g INCLIVA Biobank , Valencia , Spain
| | - Pablo Lapunzina
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,h Institute of Medical and Molecular Genetics (INGEMM) , IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid , Madrid , Spain
| | - Federico V Pallardó
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain.,d Epigenetics Research Platform (CIBERER/UV/INCLIVA) , Valencia , Spain
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14
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Wang H, Bender A, Wang P, Karakose E, Inabnet WB, Libutti SK, Arnold A, Lambertini L, Stang M, Chen H, Kasai Y, Mahajan M, Kinoshita Y, Fernandez-Ranvier G, Becker TC, Takane KK, Walker LA, Saul S, Chen R, Scott DK, Ferrer J, Antipin Y, Donovan M, Uzilov AV, Reva B, Schadt EE, Losic B, Argmann C, Stewart AF. Insights into beta cell regeneration for diabetes via integration of molecular landscapes in human insulinomas. Nat Commun 2017; 8:767. [PMID: 28974674 PMCID: PMC5626682 DOI: 10.1038/s41467-017-00992-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/10/2017] [Indexed: 12/19/2022] Open
Abstract
Although diabetes results in part from a deficiency of normal pancreatic beta cells, inducing human beta cells to regenerate is difficult. Reasoning that insulinomas hold the “genomic recipe” for beta cell expansion, we surveyed 38 human insulinomas to obtain insights into therapeutic pathways for beta cell regeneration. An integrative analysis of whole-exome and RNA-sequencing data was employed to extensively characterize the genomic and molecular landscape of insulinomas relative to normal beta cells. Here, we show at the pathway level that the majority of the insulinomas display mutations, copy number variants and/or dysregulation of epigenetic modifying genes, most prominently in the polycomb and trithorax families. Importantly, these processes are coupled to co-expression network modules associated with cell proliferation, revealing candidates for inducing beta cell regeneration. Validation of key computational predictions supports the concept that understanding the molecular complexity of insulinoma may be a valuable approach to diabetes drug discovery. Diabetes results in part from a deficiency of functional pancreatic beta cells. Here, the authors study the genomic and epigenetic landscapes of human insulinomas to gain insight into possible pathways for therapeutic beta cell regeneration, highlighting epigenetic genes and pathways.
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Affiliation(s)
- Huan Wang
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,The Graduate School, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Aaron Bender
- The Graduate School, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Peng Wang
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esra Karakose
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - William B Inabnet
- The Department of Surgery, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Steven K Libutti
- The Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Andrew Arnold
- Center for Molecular Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Luca Lambertini
- The Departments of Environmental Medicine and Public Health and Obstetrics, Gynecology, and Reproductive Sciences, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Micheal Stang
- The Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Herbert Chen
- The Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Yumi Kasai
- The New York Genome Center, New York, NY, 10013, USA
| | - Milind Mahajan
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yayoi Kinoshita
- The Department of Pathology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Thomas C Becker
- The Sarah W. Stedman Center for Nutrition and Metabolism, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Karen K Takane
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Laura A Walker
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shira Saul
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rong Chen
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Donald K Scott
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jorge Ferrer
- The Department of Genetics in Medicine, Imperial College, London, W12 0NN, UK
| | - Yevgeniy Antipin
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Michael Donovan
- The Department of Pathology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew V Uzilov
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Boris Reva
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric E Schadt
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Bojan Losic
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carmen Argmann
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew F Stewart
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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15
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Wang B, Ji T, Zhou X, Wang J, Wang X, Wang J, Zhu D, Zhang X, Sham PC, Zhang X, Ma X, Jiang Y. CNV analysis in Chinese children of mental retardation highlights a sex differentiation in parental contribution to de novo and inherited mutational burdens. Sci Rep 2016; 6:25954. [PMID: 27257017 PMCID: PMC4891738 DOI: 10.1038/srep25954] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/06/2016] [Indexed: 12/28/2022] Open
Abstract
Rare copy number variations (CNVs) are a known genetic etiology in neurodevelopmental disorders (NDD). Comprehensive CNV analysis was performed in 287 Chinese children with mental retardation and/or development delay (MR/DD) and their unaffected parents. When compared with 5,866 ancestry-matched controls, 11~12% more MR/DD children carried rare and large CNVs. The increased CNV burden in MR/DD was predominantly due to de novo CNVs, the majority of which (62%) arose in the paternal germline. We observed a 2~3 fold increase of large CNV burden in the mothers of affected children. By implementing an evidence-based review approach, pathogenic structural variants were identified in 14.3% patients and 2.4% parents, respectively. Pathogenic CNVs in parents were all carried by mothers. The maternal transmission bias of deleterious CNVs was further replicated in a published dataset. Our study confirms the pathogenic role of rare CNVs in MR/DD, and provides additional evidence to evaluate the dosage sensitivity of some candidate genes. It also supports a population model of MR/DD that spontaneous mutations in males' germline are major contributor to the de novo mutational burden in offspring, with higher penetrance in male than female; unaffected carriers of causative mutations, mostly females, then contribute to the inherited mutational burden.
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Affiliation(s)
- Binbin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,National Research Institute of Family Planning, Beijing, China
| | - Taoyun Ji
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xueya Zhou
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China.,Department of Psychiatry and Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jing Wang
- Department of Medical Genetics, The Capital Medical University, Beijing, China
| | - Xi Wang
- National Research Institute of Family Planning, Beijing, China
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | | | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology at No.1 Hospital, Anhui Medical University, Heifei, Anhui, China
| | - Pak Chung Sham
- Department of Psychiatry and Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China
| | - Xu Ma
- National Research Institute of Family Planning, Beijing, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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16
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Ishida M. New developments in Silver-Russell syndrome and implications for clinical practice. Epigenomics 2016; 8:563-80. [PMID: 27066913 DOI: 10.2217/epi-2015-0010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Silver-Russell syndrome is a clinically and genetically heterogeneous disorder, characterized by prenatal and postnatal growth restriction, relative macrocephaly, body asymmetry and characteristic facial features. It is one of the imprinting disorders, which results as a consequence of aberrant imprinted gene expressions. Currently, maternal uniparental disomy of chromosome 7 accounts for approximately 10% of Silver-Russell syndrome cases, while ~50% of patients have hypomethylation at imprinting control region 1 at chromosome 11p15.5 locus, leaving ~40% of cases with unknown etiologies. This review aims to provide a comprehensive list of molecular defects in Silver-Russell syndrome reported to date and to highlight the importance of multiple-loci/tissue testing and trio (both parents and proband) screening. The epigenetic and phenotypic overlaps with other imprinting disorders will also be discussed.
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Affiliation(s)
- Miho Ishida
- University College London, Institute of Child Health, Genetics & Genomic Medicine programme, Genetics & Epigenetics in Health & Diseases Section, 30 Guilford Street, London, WC1N 1EH, UK
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17
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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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Ohtsuka Y, Higashimoto K, Oka T, Yatsuki H, Jozaki K, Maeda T, Kawahara K, Hamasaki Y, Matsuo M, Nishioka K, Joh K, Mukai T, Soejima H. Identification of consensus motifs associated with mitotic recombination and clinical characteristics in patients with paternal uniparental isodisomy of chromosome 11. Hum Mol Genet 2016; 25:1406-19. [PMID: 26908620 DOI: 10.1093/hmg/ddw023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 01/25/2016] [Indexed: 11/14/2022] Open
Abstract
Uniparental disomy (UPD) is defined as the inheritance of both homologs of a given genomic region from only one parent. The majority of UPD includes an entire chromosome. However, the extent of UPD is sometimes limited to a subchromosomal region (segmental UPD). Mosaic paternal UPD (pUPD) of chromosome 11 is found in approximately 20% of patients with Beckwith-Wiedemann syndrome (BWS) and almost all pUPDs are segmental isodisomic pUPDs resulting from mitotic recombination at an early embryonic stage. A mechanism initiating a DNA double strand break (DSB) within 11p has been predicted to lead to segmental pUPD. However, no consensus motif has yet been found. Here, we analyzed 32 BWS patients with pUPD by SNP array and searched for consensus motifs. We identified four consensus motifs frequently appearing within breakpoint regions of segmental pUPD. These motifs were found in another nine BWS patients with pUPD. In addition, the seven motifs found in meiotic recombination hot spots could not be found within pUPD breakpoint regions. Histone H3 lysine 4 trimethylation, a marker of DSB initiation, could not be found either. These findings suggest that the mechanism(s) of mitotic recombination leading to segmental pUPD are different from that of meiotic recombination. Furthermore, we found seven patients with paternal uniparental diploidy (PUD) mosaicism. Comparison of clinical features between segmental pUPDs and PUDs showed that developmental disability and cardiac abnormalities were additional characteristic features of PUD mosaicism, along with high risk of tumor development. We also found that macroglossia was characteristic of segmental pUPD mosaicism.
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Affiliation(s)
- Yasufumi Ohtsuka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Department of Pediatrics, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Ken Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine
| | - Takehiko Oka
- World Fusion Co., Ltd., Tokyo 103-0013, Japan and
| | - Hitomi Yatsuki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine
| | - Kosuke Jozaki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine
| | - Toshiyuki Maeda
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Department of Pediatrics, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | | | - Yuhei Hamasaki
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Muneaki Matsuo
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Kenichi Nishioka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine
| | - Keiichiro Joh
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine
| | | | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine,
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Mussa A, Russo S, Larizza L, Riccio A, Ferrero GB. (Epi)genotype-phenotype correlations in Beckwith-Wiedemann syndrome: a paradigm for genomic medicine. Clin Genet 2015; 89:403-415. [PMID: 26138266 DOI: 10.1111/cge.12635] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/24/2015] [Accepted: 06/30/2015] [Indexed: 12/23/2022]
Abstract
Beckwith-Wiedemann syndrome (BWS) is the commonest overgrowth cancer predisposition disorder and represents a model for human imprinting dysregulation and tumorigenesis. BWS features can variably combine and present a widely variable range of severity in the phenotypic expression. This wide spectrum is paralleled at molecular level by complex (epi)genetic defects on chromosome 11p15.5 leading to disrupted expression of imprinted genes controlling growth and cellular proliferation. In this review, we outline the spectrum of clinical manifestations of BWS analyzing their (epi)genotype-phenotype correlations. The differences observed in the phenotypic profiles of BWS molecular subtypes allow a composite view of this syndrome with implications on clinical care, diagnosis, follow-up, and management, and provide directions for future disease monitoring.
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Affiliation(s)
- A Mussa
- Department of Pediatrics and Public Health Sciences, University of Torino, Torino, Italy
| | - S Russo
- Laboratory of Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, Milan, Italy
| | - L Larizza
- Laboratory of Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, Milan, Italy.,Department of Health Sciences, University of Milan, Milan, Italy
| | - A Riccio
- DiSTABiF, Second University of Naples, Napoli, Italy.,Institute of Genetics and Biophysics "A. Buzzati-Traverso" - CNR, Naples, Italy
| | - G B Ferrero
- Department of Pediatrics and Public Health Sciences, University of Torino, Torino, Italy
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20
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Abraham MB, Carpenter K, Baynam GS, Mackay DJ, Price G, Choong CS. Report and review of described associations of Mayer-Rokitansky-Küster-Hauser syndrome and Silver-Russell syndrome. J Paediatr Child Health 2015; 51:555-560. [PMID: 25418154 DOI: 10.1111/jpc.12778] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/18/2014] [Indexed: 01/05/2023]
Abstract
Silver-Russell syndrome (SRS) and Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome are described in isolation. However, their co-occurrence has only been rarely reported. Here, we present a case report of an adolescent with SRS who was diagnosed with MRKH during the evaluation of primary amenorrhoea. Multiplex ligation-dependent probe amplification analysis showed a normal methylation pattern and normal dosage at 11p15.5. A PubMed search for all peer-reviewed publications (original articles and reviews) using the key words Silver-Russell syndrome, Mayer-Rokitansky-Küster-Hauser syndrome, genetics, hypomethylation and reproductive anomalies identified three cases of SRS with MRKH, two of which were associated with significant hypomethylation of the H19 imprinting control region of the 11p15.5 locus. This report highlights the association between SRS and MRKH. The absence of hypomethylation and normal dosage at 11p15.5 suggests these two rare entities share alternative aetiopathogenic mechanisms.
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Affiliation(s)
- Mary B Abraham
- Department of Endocrinology and Diabetes, Princess Margaret Hospital for Children, Perth, Western Australia, Australia
| | - Karen Carpenter
- Department of Diagnostic Genomics, PathWest, QEII Medical Centre, Perth, Western Australia, Australia
| | - Gareth S Baynam
- School of Paediatrics and Child Health, The University of Western Australia, Perth, Western Australia, Australia.,Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia.,Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia, Australia
| | - Deborah Jg Mackay
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Glynis Price
- Department of Endocrinology and Diabetes, Princess Margaret Hospital for Children, Perth, Western Australia, Australia
| | - Catherine S Choong
- Department of Endocrinology and Diabetes, Princess Margaret Hospital for Children, Perth, Western Australia, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, Western Australia, Australia
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21
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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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Ohtsuka Y, Higashimoto K, Sasaki K, Jozaki K, Yoshinaga H, Okamoto N, Takama Y, Kubota A, Nakayama M, Yatsuki H, Nishioka K, Joh K, Mukai T, Yoshiura KI, Soejima H. Autosomal recessive cystinuria caused by genome-wide paternal uniparental isodisomy in a patient with Beckwith-Wiedemann syndrome. Clin Genet 2014; 88:261-6. [PMID: 25171146 DOI: 10.1111/cge.12496] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 01/08/2023]
Abstract
Approximately 20% of Beckwith-Wiedemann syndrome (BWS) cases are caused by mosaic paternal uniparental disomy of chromosome 11 (pUPD11). Although pUPD11 is usually limited to the short arm of chromosome 11, a small minority of BWS cases show genome-wide mosaic pUPD (GWpUPD). These patients show variable clinical features depending on mosaic ratio, imprinting status of other chromosomes, and paternally inherited recessive mutations. To date, there have been no reports of a mosaic GWpUPD patient with an autosomal recessive disease caused by a paternally inherited recessive mutation. Here, we describe a patient concurrently showing the clinical features of BWS and autosomal recessive cystinuria. Genetic analyses revealed that the patient has mosaic GWpUPD and an inherited paternal homozygous mutation in SLC7A9. This is the first report indicating that a paternally inherited recessive mutation can cause an autosomal recessive disease in cases of GWpUPD mosaicism. Investigation into recessive mutations and the dysregulation of imprinting domains is critical in understanding precise clinical conditions of patients with mosaic GWpUPD.
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Affiliation(s)
- Y Ohtsuka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - K Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - K Sasaki
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - K Jozaki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - H Yoshinaga
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - N Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Y Takama
- Department of Pediatric Surgery, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - A Kubota
- Department of Pediatric Surgery, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - M Nakayama
- Department of Pathology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - H Yatsuki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - K Nishioka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - K Joh
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - T Mukai
- Nishikyushu University, Saga, Japan
| | - K-i Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - H 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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Abstract
Neonatal or perinatal tumours frequently relate to prenatal or developmental events and have a short exposure window which provides an opportunity to study tumours in a selective sensitive period of development. As a result, they display a number of host-specific features which include occasional spontaneous maturational changes with cells still responding to developmental influences. Neonatal tumours (NNT) are studied for a number of important reasons. Firstly, many of the benign tumours arising from soft tissue appear to result from disturbances in growth and development and some are associated with other congenital anomalies. Study of these aspects may open the door for investigation of genetic and epigenetic changes in genes controlling foetal development as well as environmental and drug effects during pregnancy. Secondly, the clinical behaviour of NNT differs from that of similar tumours occurring later in childhood. In addition, certain apparently malignant NNT can 'change course' in infancy leading to the maturation of apparently highly malignant tumours. Thirdly, NNT underline the genetic associations of most tumours but appear to differ in the effects of proto-oncogenes and other oncogenic factors. In this context, there are also connections between the foetal and neonatal period and some "adult" cancers. Fourthly, they appear to arise in a period in which minimal environmental interference has occurred, thus providing a unique potential window of opportunity to study the pathogenesis of tumour behaviour. This study will seek to review what is currently known in each of these areas of study as they apply to NNT. Further study of the provocative differences in tumour behaviour in neonates provides insights into the natural history of cancer in humans and promotes novel cancer therapies.
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Affiliation(s)
- S W Moore
- Department of Paediatric Surgery, Faculty of Medicine and Health Sciences, University of Stellenbosch, P.O. Box 19063, Tygerberg, 7505, South Africa,
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25
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Calvello M, Tabano S, Colapietro P, Maitz S, Pansa A, Augello C, Lalatta F, Gentilin B, Spreafico F, Calzari L, Perotti D, Larizza L, Russo S, Selicorni A, Sirchia SM, Miozzo M. Quantitative DNA methylation analysis improves epigenotype-phenotype correlations in Beckwith-Wiedemann syndrome. Epigenetics 2013; 8:1053-60. [PMID: 23917791 PMCID: PMC3891686 DOI: 10.4161/epi.25812] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Beckwith-Wiedemann syndrome (BWS) is a rare disorder characterized by overgrowth and predisposition to embryonal tumors. BWS is caused by various epigenetic and/or genetic alterations that dysregulate the imprinted genes on chromosome region 11p15.5. Molecular analysis is required to reinforce the clinical diagnosis of BWS and to identify BWS patients with cancer susceptibility. This is particularly crucial prenatally because most signs of BWS cannot be recognized in utero. We established a reliable molecular assay by pyrosequencing to quantitatively evaluate the methylation profiles of ICR1 and ICR2. We explored epigenotype-phenotype correlations in 19 patients that fulfilled the clinical diagnostic criteria for BWS, 22 patients with suspected BWS, and three fetuses with omphalocele. Abnormal methylation was observed in one prenatal case and 19 postnatal cases, including seven suspected BWS. Seven cases showed ICR1 hypermethylation, five cases showed ICR2 hypomethylation, and eight cases showed abnormal methylation of ICR1 and ICR2 indicating paternal uniparental disomy (UPD). More cases of ICR1 alterations and UPD were found than expected. This is likely due to the sensitivity of this approach, which can detect slight deviations in methylation from normal levels. There was a significant correlation (p < 0.001) between the percentage of ICR1 methylation and BWS features: severe hypermethylation (range: 75–86%) was associated with macroglossia, macrosomia, and visceromegaly, whereas mild hypermethylation (range: 55–59%) was associated with umbilical hernia and diastasis recti. Evaluation of ICR1 and ICR2 methylation by pyrosequencing in BWS can improve epigenotype-phenotype correlations, detection of methylation alterations in suspected cases, and identification of UPD.
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Affiliation(s)
- Mariarosaria Calvello
- Division of Pathology; Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico; Milano, Italy
| | - Silvia Tabano
- Division of Pathology; Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico; Milano, Italy; Department of Pathophysiology and Transplantation; Università degli Studi di Milano; Milano, Italy
| | - Patrizia Colapietro
- Department of Health Sciences; Università degli Studi di Milano; Milano, Italy
| | - Silvia Maitz
- Clinical Genetics; Pediatric Department; S. Gerardo Hospital; Fondazione MBBM; Università di Milano-Bicocca; Monza, Italy
| | - Alessandra Pansa
- Department of Pathophysiology and Transplantation; Università degli Studi di Milano; Milano, Italy
| | - Claudia Augello
- Department of Pathophysiology and Transplantation; Università degli Studi di Milano; Milano, Italy
| | - Faustina Lalatta
- Clinical Genetics Unit; Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico; Milano, Italy
| | - Barbara Gentilin
- Clinical Genetics Unit; Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico; Milano, Italy
| | - Filippo Spreafico
- Pediatric Oncology Unit; Fondazione IRCCS Istituto Nazionale dei Tumori; Milano, Italy
| | - Luciano Calzari
- Molecular Biology Laboratory; Istituto Auxologico Italiano; Milano, Italy
| | - Daniela Perotti
- Molecular Bases of Genetic Risk and Genetic Testing Unit; Department of Preventive and Predictive Medicine; Fondazione IRCCS Istituto Nazionale dei Tumori; Milano, Italy
| | - Lidia Larizza
- Department of Health Sciences; Università degli Studi di Milano; Milano, Italy; Molecular Biology Laboratory; Istituto Auxologico Italiano; Milano, Italy
| | - Silvia Russo
- Molecular Biology Laboratory; Istituto Auxologico Italiano; Milano, Italy
| | - Angelo Selicorni
- Clinical Genetics; Pediatric Department; S. Gerardo Hospital; Fondazione MBBM; Università di Milano-Bicocca; Monza, Italy
| | - Silvia M Sirchia
- Division of Pathology; Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico; Milano, Italy; Department of Health Sciences; Università degli Studi di Milano; Milano, Italy
| | - Monica Miozzo
- Division of Pathology; Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico; Milano, Italy; Department of Pathophysiology and Transplantation; Università degli Studi di Milano; Milano, Italy
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SNP arrays in Beckwith-Wiedemann syndrome: an improved diagnostic strategy. Eur J Med Genet 2013; 56:546-50. [PMID: 23892181 DOI: 10.1016/j.ejmg.2013.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 06/07/2013] [Indexed: 11/21/2022]
Abstract
Beckwith-Wiedemann syndrome is an overgrowth disorder with an increased risk of childhood tumors that results from a dysregulation of imprinted gene expression in the 11p15 region. Since epigenetic defects are the most frequent anomalies, first-line diagnostic methods involve methylation analysis. When paternal isodisomy is suspected, it should be confirmed by a second technique capable of distinguishing true 11p15 paternal disomy (patUPD) from paternal 11p15 duplication or 11p15 trisomy. We sought to evaluate the interest of using SNP arrays in the Beckwith-Wiedemann syndrome diagnostic strategy. We analyzed the SNP profiles of 25 Beckwith Wiedemann patients with previously determined methylation indexes. Among them, 3 had 11p15 trisomies, 13 had patUPD, 8 had an inconclusive methylation index and 1 had a normal result. All known trisomies and known patUPDs were detected. Moreover we found 7 low-rate mosaicisms 11p15 patUPDs among the 8 patients with an inconclusive methylation index. We were able to precisely characterize the sizes and mosaicism rates of the anomalies. We demonstrate that SNP arrays are of real diagnostic interest in Beckwith-Wiedemann syndrome: 1) they help to distinguish patUPDs from trisomies more precisely than karyotyping and FISH, 2) they help determine the size and mosaicism rate of patUPDs, 3) they provide complementary information in inconclusive cases, helping to distinguish low-rate patUPD mosaicism from other BWS-related molecular defects.
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27
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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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Abstract
BACKGROUND The differentiation between a giant fibroadenoma and a phyllodes tumor can be a precarious diagnostic task. However, the distinction between the 2 lesions is important to make, especially since the latter can be malignant and consequently the prognoses differ. PROCEDURE We used various genetic approaches to study a breast tumor showing features of both entities in a 10-year-old girl with a congenital cerebral malformation and diabetes mellitus. RESULTS Cytogenetic analysis of cultured tumor cells from 3 different samples revealed a hyperdiploid karyotype: 50-54,XX,+5,+13,+17,+18,+19,+20,+21. High-resolution single nucleotide polymorphism array analysis not only confirmed the trisomies, but also revealed uniparental disomy (UPD) for chromosomes 10, 11, and 22. A consequence of UPD11 was a homozygous deletion in chromosome band 11p15 affecting the PARVA gene; this gene was hemizygously lost in constitutional DNA. Extended analysis of the family revealed that the deletion was inherited, but it did not segregate with breast tumors or congenital malformations. CONCLUSIONS Combined with the literature data, the findings in the present case strongly suggest that biphasic tumors with high hyperdiploid karyotypes constitute a distinct clinicomorphologic subgroup of benign breast tumors, being particularly common among young children.
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30
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Kantaputra PN, Sittiwangkul R, Sonsuwan N, Romanelli V, Tenorio J, Lapunzina P. A novel mutation inCDKN1Cin sibs with Beckwith-Wiedemann syndrome and cleft palate, sensorineural hearing loss, and supernumerary flexion creases. Am J Med Genet A 2012. [DOI: 10.1002/ajmg.a.35663] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Cardoso LCA, Tenorio Castaño JA, Pereira HS, Lima MADFD, Dos Santos ACE, de Faria PS, Ferman S, Seuánez HN, Nevado JB, de Almeida JCC, Lapunzina P, Vargas FR. Constitutional and somatic methylation status of DMRH19 and KvDMR in Wilms tumor patients. Genet Mol Biol 2012; 35:714-24. [PMID: 23271929 PMCID: PMC3526076 DOI: 10.1590/s1415-47572012005000073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 07/24/2012] [Indexed: 12/18/2022] Open
Abstract
The most frequent epigenetic alterations in Wilms tumor (WT) occur at WT2, assigned to 11p15. WT2 consists of two domains: telomeric domain 1 (DMRH19) that contains the IGF2 gene and an imprinted maternally expressed transcript (H19) and centromeric domain 2 (KvDMR) that contains the genes KCNQ1, KCNQ1OT1 and CDKN1C. In this work, we used pyrosequencing and MS-MLPA to compare the methylation patterns of DMRH19/KvDMR in blood and tumor samples from 40 WT patients. Normal constitutional KvDMR methylation indicated that most of the epigenetic alterations in WT occur at DMRH19. Constitutional DMRH19 hypermethylation (HM DMRH19) was observed in two patients with Beckwith-Wiedemann syndrome. Pyrosequencing and MS-MLPA showed HM DMRH19 in 28/34 tumor samples: 16/34 with isolated HM DMRH19 and 12/34 with concomitant HM DMRH19 and KvDMR hypomethylation, indicating paternal uniparental disomy. With the exception of one blood sample, the MS-MLPA and pyrosequencing findings were concordant. Diffuse or focal anaplasia was present in five tumor samples and was associated with isolated somatic HM DMRH19 in four of them. Constitutional 11p15 methylation abnormalities were present in 5% of the samples and somatic abnormalities in the majority of tumors. Combined analysis of DMRH19/KvDMR by pyrosequencing and MS-MLPA is beneficial for characterizing epigenetic anomalies in WT, and MS-MLPA is useful and reliable for estimation of DNA methylation in a clinical setting.
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Affiliation(s)
- Leila C A Cardoso
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. ; Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
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Different methylation patterns in BWS/SRS cases clarified by MS-MLPA. Mol Biol Rep 2012; 40:263-8. [PMID: 23086270 DOI: 10.1007/s11033-012-2057-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 10/03/2012] [Indexed: 12/26/2022]
Abstract
Molecular abnormalities in the 11p15.5 imprinted gene cluster lead to two different growth diseases: Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS). They are mainly caused by epigenetic alterations in one of the two imprinting 11p15 control regions (ICR1 and ICR2). These CpG-rich regions are differentially methylated on the maternally and paternally derived chromosomes. We report four different methylation patterns along the BWS/SRS critical region, clarified by methylation-specific multiplex ligation-dependent probe amplification. The mathematical processing of the data provides information about alterations in the methylation status: from hypo- to almost complete demethylation of KvDMR, hypo- and hypermethylation of H19DMR and combined results from both regions provide information on paternal uniparental disomy (patUPD). The study concerns two BWS cases with KvDMR hypomethylation and almost complete loss of methylation, respectively; two patUPD11p15 cases with H19DMR hypermethylation/KvDMR hypomethylation, and one SRS case with H19DMR demethylation. In some cases KvDMR hypomethylation in patUPD11p15 can be difficult to assess, which requires combination with STR analysis or alternative method. The STR analysis provides also information on complete or segmental coverage and iso- or heterodisomy. Following this systematic approach, the precise diagnosis can be clarified in a few days and different methylation patterns could be detected.
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Perez-Nanclares G, Romanelli V, Mayo S, Garin I, Zazo Seco C, Fernandez-Rebollo E, Martínez F, Lapunzina P, de Nanclares GP. Detection of hypomethylation syndrome among patients with epigenetic alterations at the GNAS locus. J Clin Endocrinol Metab 2012; 97:E1060-7. [PMID: 22492776 DOI: 10.1210/jc.2012-1081] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CONTEXT Genomic imprinting is the modification of the genome so that genes from only one (rather than two) of the parental alleles are expressed. The mechanism underlying imprinting is epigenetic, occurring via changes in DNA methylation and histone modifications rather than through alterations in the DNA sequence. To date, nine different imprinting disorders have been clinically and genetically identified and a considerable research effort has been focused on determining the cause of the corresponding methylation defects. OBJECTIVE Our objective was to identify multilocus imprinting defects and characterize any mutations in trans-acting genes in patients with pseudohypoparathyroidism (PHP) caused by epigenetic alterations at GNAS locus. DESIGN We have investigated multilocus imprinting defects in 22 PHP patients with aberrant methylation at the GNAS locus not due to previously described deletions or to paternal uniparental disomy (UPD) of chromosome 20. RESULTS We found that, in contrast to what has been described in growth disorders, multilocus hypomethylation is an uncommon event in PHP patients. We were also unable to identify any genetic alteration causative of the epigenetic defects in the currently known methylation regulatory genes. CONCLUSION Our work suggests that a trans-acting gene regulating the establishment or maintenance of imprinting at GNAS locus, if it exists, should be specific to PHP cases caused by epigenetic defects at GNAS.
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Affiliation(s)
- Gustavo Perez-Nanclares
- Molecular (Epi)Genetics Lab Research Unit, Hospital Txagorritxu, E-01009, Vitoria-Gasteiz, Alava, Spain
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Abstract
Orofacial clefts occur with a frequency of 1 to 2 per 1000 live births. Cleft palate, which accounts for 30% of orofacial clefts, is caused by the failure of the secondary palatal processes--medially directed, oral projections of the paired embryonic maxillary processes--to fuse. Both gene mutations and environmental effects contribute to the complex etiology of this disorder. Although much progress has been made in identifying genes whose mutations are associated with cleft palate, little is known about the mechanisms by which the environment adversely influences gene expression during secondary palate development. An increasing body of evidence, however, implicates epigenetic processes as playing a role in adversely influencing orofacial development. Epigenetics refers to inherited changes in phenotype or gene expression caused by processes other than changes in the underlying DNA sequence. Such processes include, but are not limited to, DNA methylation, microRNA effects, and histone modifications that alter chromatin conformation. In this review, we describe our current understanding of the possible role epigenetics may play during development of the secondary palate. Specifically, we present the salient features of the embryonic palatal methylome and profile the expression of numerous microRNAs that regulate protein-encoding genes crucial to normal orofacial ontogeny.
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Affiliation(s)
- Ratnam S Seelan
- Department of Molecular, Cellular and Craniofacial Biology, Birth Defects Center, ULSD, University of Louisville, 501 S. Preston Street, Louisville, KY 40202, USA
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Kearney HM, Kearney JB, Conlin LK. Diagnostic Implications of Excessive Homozygosity Detected by SNP-Based Microarrays: Consanguinity, Uniparental Disomy, and Recessive Single-Gene Mutations. Clin Lab Med 2011; 31:595-613, ix. [DOI: 10.1016/j.cll.2011.08.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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The consequences of uniparental disomy and copy number neutral loss-of-heterozygosity during human development and cancer. Biol Cell 2011; 103:303-17. [PMID: 21651501 DOI: 10.1042/bc20110013] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
UPD (uniparental disomy) describes the inheritance of a pair of chromosomes from only one parent. Mechanisms that lead to UPD include trisomy rescue, gamete complementation, monosomy rescue and somatic recombination. Most of these mechanisms can involve aberrant chromosomes, particularly isochromosomes and Robertsonian translocations. In the last decade, the number of UPD cases reported in the literature has increased exponentially. This is partly due to the advances in genomic technologies that have allowed for high-resolution SNP (single nucleotide polymorphism) studies, which have complemented traditional methods relying on polymorphic microsatellite markers. In this review, we discuss aberrant cellular mechanisms leading to UPD and their impact on gene expression. Special emphasis is placed on the unmasking of mutant recessive alleles and the disruption of imprinted gene dosage, which give rise to specific and recurrent imprinting phenotypes. Finally, we discuss how copy number maps determined from SNP array datasets have helped identify not only deletions and duplications but also recurrent copy number neutral regions of loss-of-heterozygosity, which have been reported in many cancer types and that may constitute an important driving force in cancer. These tiny regions of UPD also alter imprinted gene dosage, which may have cumulative tumourgenic effects in addition to that of unmasking homozygous cancer-associated mutations.
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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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