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Mergener R, Nascimento LPC, Böttcher AK, Nunes MR, Zen PRG. What Can Really Be Considered a Syndrome? An Insight Based on 16p11.2 Microduplication. Cell Biochem Funct 2024; 42:e4121. [PMID: 39264303 DOI: 10.1002/cbf.4121] [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: 06/04/2024] [Revised: 08/23/2024] [Accepted: 08/28/2024] [Indexed: 09/13/2024]
Abstract
What is the definition of Syndrome? Since the beginning of studies in genetics, certain terminologies have been created and used to define groups of diseases or alterations. With the advancement of knowledge and the emergence of new technologies, the use of basic concepts is being done in a mistaken or often confusing way. Because of this, revisiting and readjusting the old terms becomes imminent. Here, we explore these concepts and their use, through a literature compilation of an already well-defined genetic alteration (16q11.2 microduplication). We bring comparisons in clinical and molecular scope of the alteration itself and its diagnostic methods, to improve the report of cases, rescuing terminologies and their applicability nowadays.
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Affiliation(s)
- Rafaella Mergener
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Lívia Polisseni Cotta Nascimento
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Kalise Böttcher
- Undergraduate Program in Biomedical Science, UFCSPA, Porto Alegre, Rio Grande do Sul, Brazil
| | - Marcela Rodrigues Nunes
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
- Medical Genetics Resident, UFCSPA/Irmandade da Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Paulo Ricardo Gazzola Zen
- Department of Clinical Medicine, Medical Genetics, UFCSPA/ISCMPA, Porto Alegre, Rio Grande do Sul, Brazil
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Duarte-Bueno LM, Álvarez-Pabón Y, Contreras-García GA. De novo 16p13.3-p12.3 duplication in a child with syndromic developmental delay. GENE REPORTS 2020; 20:100690. [DOI: 10.1016/j.genrep.2020.100690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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D’Angelo CS, Varela MC, de Castro CIE, Otto PA, Perez ABA, Lourenço CM, Kim CA, Bertola DR, Kok F, Garcia-Alonso L, Koiffmann CP. Chromosomal microarray analysis in the genetic evaluation of 279 patients with syndromic obesity. Mol Cytogenet 2018; 11:14. [PMID: 29441128 PMCID: PMC5800070 DOI: 10.1186/s13039-018-0363-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/22/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Syndromic obesity is an umbrella term used to describe cases where obesity occurs with additional phenotypes. It often arises as part of a distinct genetic syndrome with Prader-Willi syndrome being a classical example. These rare forms of obesity provide a unique source for identifying obesity-related genetic changes. Chromosomal microarray analysis (CMA) has allowed the characterization of new genetic forms of syndromic obesity, which are due to copy number variants (CNVs); however, CMA in large cohorts requires more study. The aim of this study was to characterize the CNVs detected by CMA in 279 patients with a syndromic obesity phenotype. RESULTS Pathogenic CNVs were detected in 61 patients (22%) and, among them, 35 had overlapping/recurrent CNVs. Genomic imbalance disorders known to cause syndromic obesity were found in 8.2% of cases, most commonly deletions of 1p36, 2q37 and 17p11.2 (5.4%), and we also detected deletions at 1p21.3, 2p25.3, 6q16, 9q34, 16p11.2 distal and proximal, as well as an unbalanced translocation resulting in duplication of the GNB3 gene responsible for a syndromic for of childhood obesity. Deletions of 9p terminal and 22q11.2 proximal/distal were found in 1% and 3% of cases, respectively. They thus emerge as being new putative obesity-susceptibility loci. We found additional CNVs in our study that overlapped with CNVs previously reported in cases of syndromic obesity, including a new case of 13q34 deletion (CHAMP1), bringing to 7 the number of patients in whom such defects have been described in association with obesity. Our findings implicate many genes previously associated with obesity (e.g. PTBP2, TMEM18, MYT1L, POU3F2, SIM1, SH2B1), and also identified other potentially relevant candidates including TAS1R3, ALOX5AP, and GAS6. CONCLUSION Understanding the genetics of obesity has proven difficult, and considerable insight has been obtained from the study of genomic disorders with obesity associated as part of the phenotype. In our study, CNVs known to be causal for syndromic obesity were detected in 8.2% of patients, but we provide evidence for a genetic basis of obesity in as many as 14% of cases. Overall, our results underscore the genetic heterogeneity in syndromic forms of obesity, which imposes a substantial challenge for diagnosis.
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Affiliation(s)
- Carla Sustek D’Angelo
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
| | - Monica Castro Varela
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
| | - Claudia Irene Emílio de Castro
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
| | - Paulo Alberto Otto
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
| | - Ana Beatriz Alvarez Perez
- Department of Morphology and Genetics, Paulista School of Medicine, Federal University of Sao Paulo (UNIFESP), Sao Paulo, SP Brazil
| | - Charles Marques Lourenço
- Neurogenetics Unit, Clinics Hospital of Ribeirao Preto, Faculty of Medicine, University of Sao Paulo, FMRP-USP, Ribeirao Preto, SP Brazil
| | - Chong Ae Kim
- Genetic Unit, Children’s Institute, Faculty of Medicine, University of Sao Paulo, FMUSP, Sao Paulo, SP Brazil
| | - Debora Romeo Bertola
- Genetic Unit, Children’s Institute, Faculty of Medicine, University of Sao Paulo, FMUSP, Sao Paulo, SP Brazil
| | - Fernando Kok
- Department of Neurology, Faculty of Medicine, University of Sao Paulo, FMUSP, Sao Paulo, SP Brazil
| | - Luis Garcia-Alonso
- Department of Morphology and Genetics, Paulista School of Medicine, Federal University of Sao Paulo (UNIFESP), Sao Paulo, SP Brazil
| | - Celia Priszkulnik Koiffmann
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
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Mutations of N-Methyl-D-Aspartate Receptor Subunits in Epilepsy. Neurosci Bull 2017; 34:549-565. [PMID: 29124671 DOI: 10.1007/s12264-017-0191-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/19/2017] [Indexed: 01/31/2023] Open
Abstract
Epilepsy is one of the most common neurological diseases. Of all cases, 70%-80% are considered to be due to genetic factors. In recent years, a large number of genes have been identified as being involved in epilepsy. Among them, N-methyl-D-aspartate receptor (NMDAR) subunit-encoding genes represent a large proportion, suggesting an important role for NMDARs in epilepsy. In this review, we summarize and analyze the genotypes, functional alterations, and clinical aspects of NMDAR subunit mutations/variants identified from patients with epilepsy. These data will help to throw light upon the pathogenicity of these NMDAR mutations and advance our understanding of the subtle and complicated role of NMDARs in epilepsy. It will also offer new insights into precision therapy for this disorder.
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Ciaccio C, Tucci A, Scuvera G, Estienne M, Esposito S, Milani D. 16p13 microduplication without CREBBP involvement: Moving toward a phenotype delineation. Eur J Med Genet 2016; 60:159-162. [PMID: 28007608 DOI: 10.1016/j.ejmg.2016.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 12/18/2022]
Abstract
The short arm of chromosome 16 is one of the less stable regions of our genome, as over 10% of the euchromatic region of 16p is composed of highly complex low copy repeats that are known to be predisposed to rearrangements mediated by non-allelic homologous recombination. The 16p13.3p13.13 molecular region has been defined as the 16p duplication hotspot, and duplications of chromosome 16p13 have recently been confirmed to cause a recognizable syndrome, with CREBBP being the main phenotype-causing gene. To date, only one case report is present in the literature with a 16p13 duplication without CREBBP involvement; we describe here a second analogous case with a not previously reported 16p13.2p13.13 microduplication. This paper allows us to better delineate the clinical features of 16p13 microduplications that do not encompass CREBBP and, concurrently, to narrow the molecular region responsible for congenital heart defects in 16p duplications as well as to propose GRIN2A as a candidate gene for epilepsy.
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Affiliation(s)
- Claudia Ciaccio
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy.
| | - Arianna Tucci
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
| | - Giulietta Scuvera
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
| | | | - Susanna Esposito
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
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Milone R, Ferrari AR, Pasquariello R, Bargagna S. Complex Phenotype of a Boy With De Novo 16p13.3-13.2 Interstitial Deletion. Child Neurol Open 2016; 3:2329048X16676153. [PMID: 28503620 PMCID: PMC5417293 DOI: 10.1177/2329048x16676153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 08/11/2016] [Accepted: 09/06/2016] [Indexed: 11/23/2022] Open
Abstract
Interstitial deletions encompassing chromosome 16p13.3-13.2 are rarely described in the literature, whereas terminal deletions or duplications involving this region are slightly more frequently described. The authors describe a boy harboring a de novo 16p13.3-13.2 interstitial deletion, with intellectual disability, verbal dyspraxia, epilepsy, and a distinctive brain magnetic resonance finding, namely a nodular heterotopia. The authors found partial genotype–phenotype correspondences regarding epilepsy and intellectual disability, which have been associated with 16p1 region. Conversely, nodular heterotopia and verbal dyspraxia have not been clearly related to this region. These data are in agreement with the emerging concept that similar copy number variants may be the general risk factors for distinct disorders. Verbal dyspraxia, which has not responded to speech therapy, is the child’s most disabling trait. In view of the above, genetic studies should be appraised in cases of serious speech difficulties, especially if they are associated with intellectual disability and epilepsy.
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Affiliation(s)
- Roberta Milone
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, Via Roma 67, Pisa, Italy
- Roberta Milone, MD, Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Viale del Tirreno 331/A, 56128 Calambrone, Pisa, Italy.
| | - Anna Rita Ferrari
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Rosa Pasquariello
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Stefania Bargagna
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Pisa, Italy
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Bidart M, El Atifi M, Miladi S, Rendu J, Satre V, Ray PF, Bosson C, Devillard F, Lehalle D, Malan V, Amiel J, Mencarelli MA, Baldassarri M, Renieri A, Clayton-Smith J, Vieville G, Thevenon J, Amblard F, Berger F, Jouk PS, Coutton C. Microduplication of the ARID1A gene causes intellectual disability with recognizable syndromic features. Genet Med 2016; 19:701-710. [PMID: 27906199 DOI: 10.1038/gim.2016.180] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/04/2016] [Indexed: 12/13/2022] Open
Abstract
PURPOSE To determine whether duplication of the ARID1A gene is responsible for a new recognizable syndrome. METHODS We describe four patients with a 1p36.11 microduplication involving ARID1A as identified by array-comparative genomic hybridization . We performed comparative transcriptomic analysis of patient-derived fibroblasts using RNA sequencing and evaluated the impact of ARID1A duplication on the cell cycle using fluorescence-activated cell sorting. Functional relationships between differentially expressed genes were investigated with ingenuity pathway analysis (IPA). RESULTS Combining the genomic data, we defined a small (122 kb), minimally critical region that overlaps the full ARID1A gene. The four patients shared a strikingly similar phenotype that included intellectual disability and microcephaly. Transcriptomic analysis revealed the deregulated expression of several genes previously linked to microcephaly and developmental disorders as well as the involvement of signaling pathways relevant to microcephaly, among which the polo-like kinase (PLK) pathway was especially notable. Cell-cycle analysis of patient-derived fibroblasts showed a significant increase in the proportion of cells in G1 phase at the expense of G2-M cells. CONCLUSION Our study reports a new microduplication syndrome involving the ARID1A gene. This work is the first step in clarifying the pathophysiological mechanism that links changes in the gene dosage of ARID1A with intellectual disability and microcephaly.Genet Med advance online publication 01 December 2016.
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Affiliation(s)
- Marie Bidart
- UF Clinatec, Pôle Recherche, INSERM UMR 1205, CHU de Grenoble, Grenoble, France.,Université Grenoble-Alpes, Grenoble, France
| | - Michèle El Atifi
- UF Clinatec, Pôle Recherche, INSERM UMR 1205, CHU de Grenoble, Grenoble, France.,Université Grenoble-Alpes, Grenoble, France
| | - Sarra Miladi
- UF Clinatec, Pôle Recherche, INSERM UMR 1205, CHU de Grenoble, Grenoble, France.,Université Grenoble-Alpes, Grenoble, France
| | - John Rendu
- Université Grenoble-Alpes, Grenoble, France.,Département de Biochimie Toxicologie et Pharmacologie, Département de Biochimie Génétique et Moléculaire, Centre Hospitalier Universitaire de Grenoble, Grenoble, France
| | - Véronique Satre
- Université Grenoble-Alpes, Grenoble, France.,Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France.,Equipe "Genetics Epigenetics and Therapies of Infertility," Institut Albert Bonniot, INSERM U823, La Tronche, France
| | - Pierre F Ray
- Université Grenoble-Alpes, Grenoble, France.,Département de Biochimie Toxicologie et Pharmacologie, Département de Biochimie Génétique et Moléculaire, Centre Hospitalier Universitaire de Grenoble, Grenoble, France.,Equipe "Genetics Epigenetics and Therapies of Infertility," Institut Albert Bonniot, INSERM U823, La Tronche, France
| | - Caroline Bosson
- Département de Biochimie Toxicologie et Pharmacologie, Département de Biochimie Génétique et Moléculaire, Centre Hospitalier Universitaire de Grenoble, Grenoble, France
| | - Françoise Devillard
- Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France
| | - Daphné Lehalle
- Service de Génétique, INSERM U781, Hôpital Necker-Enfants Malades, Institut Imagine, University Sorbonne-Paris-Cité, Paris, France
| | - Valérie Malan
- Service de Cytogénétique et UMR_S1163, IHU Imagine, Hôpital Necker-Enfants Malades, Paris, France
| | - Jeanne Amiel
- Service de Génétique, INSERM U781, Hôpital Necker-Enfants Malades, Institut Imagine, University Sorbonne-Paris-Cité, Paris, France
| | | | - Margherita Baldassarri
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.,Medical Genetics, University of Siena, Siena, Italy
| | - Alessandra Renieri
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.,Medical Genetics, University of Siena, Siena, Italy
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Gaëlle Vieville
- Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence "Anomalies du Développement et Syndromes Malformatifs," Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Florence Amblard
- Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France
| | - François Berger
- UF Clinatec, Pôle Recherche, INSERM UMR 1205, CHU de Grenoble, Grenoble, France.,Université Grenoble-Alpes, Grenoble, France
| | - Pierre-Simon Jouk
- Université Grenoble-Alpes, Grenoble, France.,Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France
| | - Charles Coutton
- Université Grenoble-Alpes, Grenoble, France.,Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France.,Equipe "Genetics Epigenetics and Therapies of Infertility," Institut Albert Bonniot, INSERM U823, La Tronche, France
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