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Massier M, Doco-Fenzy M, Egloff M, Le Guillou X, Le Guyader G, Redon S, Benech C, Le Millier K, Uguen K, Ropars J, Sacaze E, Audebert-Bellanger S, Apetrei A, Molin A, Gruchy N, Vincent-Devulder A, Spodenkiewicz M, Jacquin C, Loron G, Thibaud M, Delplancq G, Brisset S, Lesieur-Sebellin M, Malan V, Romana S, Rio M, Marlin S, Amiel J, Marquet V, Dauriat B, Moradkhani K, Mercier S, Isidor B, Arpin S, Pujalte M, Jedraszak G, Pebrel-Richard C, Salaun G, Laffargue F, Boudjarane J, Missirian C, Chelloug N, Toutain A, Chiesa J, Keren B, Mignot C, Gouy E, Jaillard S, Landais E, Poirsier C. 3q29 duplications: A cohort of 46 patients and a literature review. Am J Med Genet A 2024; 194:e63531. [PMID: 38421086 DOI: 10.1002/ajmg.a.63531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 03/02/2024]
Abstract
Duplications of the 3q29 cytoband are rare chromosomal copy number variations (CNVs) (overlapping or recurrent ~1.6 Mb 3q29 duplications). They have been associated with highly variable neurodevelopmental disorders (NDDs) with various associated features or reported as a susceptibility factor to the development of learning disabilities and neuropsychiatric disorders. The smallest region of overlap and the phenotype of 3q29 duplications remain uncertain. We here report a French cohort of 31 families with a 3q29 duplication identified by chromosomal microarray analysis (CMA), including 14 recurrent 1.6 Mb duplications, eight overlapping duplications (>1 Mb), and nine small duplications (<1 Mb). Additional genetic findings that may be involved in the phenotype were identified in 11 patients. Focusing on apparently isolated 3q29 duplications, patients present mainly mild NDD as suggested by a high rate of learning disabilities in contrast to a low proportion of patients with intellectual disabilities. Although some are de novo, most of the 3q29 duplications are inherited from a parent with a similar mild phenotype. Besides, the study of small 3q29 duplications does not provide evidence for any critical region. Our data suggest that the overlapping and recurrent 3q29 duplications seem to lead to mild NDD and that a severe or syndromic clinical presentation should warrant further genetic analyses.
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Affiliation(s)
- Marie Massier
- Department of Genetics, Reims University Hospital, Reims, France
| | - Martine Doco-Fenzy
- Department of Genetics, Reims University Hospital, Reims, France
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Matthieu Egloff
- Department of Genetics, Poitiers University Hospital, Poitiers, France
- University of Poitiers, INSERM, LNEC, Department of Genetics, Poitiers University Hospital, Poitiers, France
| | - Xavier Le Guillou
- Department of Genetics, Poitiers University Hospital, Poitiers, France
- University of Poitiers, CNRS, LMA, Department of Genetics, Poitiers University Hospital, Poitiers, France
| | | | - Sylvia Redon
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Caroline Benech
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | | | - Kevin Uguen
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Juliette Ropars
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Elise Sacaze
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Séverine Audebert-Bellanger
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Andreea Apetrei
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Arnaud Molin
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Nicolas Gruchy
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Aline Vincent-Devulder
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | | | - Clémence Jacquin
- Department of Genetics, Reims University Hospital, Reims, France
| | - Gauthier Loron
- Department of Neonatal Medicine and Pediatric Intensive Care, University of Reims Champagne-Ardenne, CReSTIC, Reims University Hospital, Reims, France
| | - Marie Thibaud
- Department of Pediatrics, American Memorial Hospital, Reims, France
| | | | - Sophie Brisset
- Constitutional Genetics Unit, Versailles Hospital, Le Chesnay, France
| | - Marion Lesieur-Sebellin
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Valérie Malan
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Serge Romana
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Marlène Rio
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Sandrine Marlin
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Jeanne Amiel
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Valentine Marquet
- Department of Cytogenetics, Clinical Genetics and Reproductive Biology, Limoges University Hospital, Limoges, France
| | - Benjamin Dauriat
- Department of Cytogenetics, Clinical Genetics and Reproductive Biology, Limoges University Hospital, Limoges, France
| | | | - Sandra Mercier
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Bertrand Isidor
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Stéphanie Arpin
- Department of Genetics, Tours University Hospital, UMR 1253, iBrain, University of Tours, Inserm, Tours, France
| | | | - Guillaume Jedraszak
- Constitutional Genetic Laboratory, University Hospital of Amiens & UR4666 HEMATIM, University of Picardie Jules Verne, Amiens, France
| | - Céline Pebrel-Richard
- Cytogenetic Medical Department; UIC Cytogenetics of Rare Diseases and Reproduction (GRUIC ADERGEN), Rare Diseases Reference Center (CRMR): Developmental Anomalies and Malformative Syndromes in the Auvergne Region, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Gaëlle Salaun
- Cytogenetic Medical Department; UIC Cytogenetics of Rare Diseases and Reproduction (GRUIC ADERGEN), Rare Diseases Reference Center (CRMR): Developmental Anomalies and Malformative Syndromes in the Auvergne Region, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Fanny Laffargue
- Department of Medical Genetics, UIC ADDIR (GRIUC ADERGEN), Constitutive Reference Center CLAD South-East: Developmental anomalies and malformative syndromes, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - John Boudjarane
- Medical Genetics Department, Timone Enfants University Hospital, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Chantal Missirian
- Medical Genetics Department, Timone Enfants University Hospital, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Nora Chelloug
- Department of Medical Genetics, Toulouse University Hospital, Toulouse, France
| | - Annick Toutain
- Department of Genetics, Tours University Hospital, UMR 1253, iBrain, University of Tours, Inserm, Tours, France
| | - Jean Chiesa
- Department of Genetics, Nimes, University Hospital, Nimes University Hospital, Nimes, France
| | - Boris Keren
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Cyril Mignot
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Evan Gouy
- Department of Genetics, Hospices Civils de Lyon, Lyon, France
| | - Sylvie Jaillard
- Department of Cytogenetics and Cell Biology, Rennes university hospital, Rennes, France
| | - Emilie Landais
- Department of Genetics, Reims University Hospital, Reims, France
| | - Céline Poirsier
- Department of Genetics, Reims University Hospital, Reims, France
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Janzing AM, Eklund E, De Koning TJ, Eggink H. Clinical Characteristics Suggestive of a Genetic Cause in Cerebral Palsy: A Systematic Review. Pediatr Neurol 2024; 153:144-151. [PMID: 38382247 DOI: 10.1016/j.pediatrneurol.2024.01.025] [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: 06/29/2023] [Revised: 01/11/2024] [Accepted: 01/27/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Cerebral palsy (CP) is a clinical diagnosis and was long categorized as an acquired disorder, but more and more genetic etiologies are being identified. This review aims to identify the clinical characteristics that are associated with genetic CP to aid clinicians in selecting candidates for genetic testing. METHODS The PubMed database was systematically searched to identify genes associated with CP. The clinical characteristics accompanying these genetic forms of CP were compared with published data of large CP populations resulting in the identification of potential indicators of genetic CP. RESULLTS Of 1930 articles retrieved, 134 were included. In these, 55 CP genes (described in two or more cases, n = 272) and 79 candidate genes (described in only one case) were reported. The most frequently CP-associated genes were PLP1 (21 cases), ARG1 (17 cases), and CTNNB1 (13 cases). Dyskinesia and the absence of spasticity were identified as strong potential indicators of genetic CP. Presence of intellectual disability, no preterm birth, and no unilateral distribution of symptoms were classified as moderate genetic indicators. CONCLUSIONS Genetic causes of CP are increasingly identified. The clinical characteristics associated with genetic CP can aid clinicians regarding to which individual with CP to offer genetic testing. The identified potential genetic indicators need to be validated in large CP cohorts but can provide the first step toward a diagnostic algorithm for genetic CP.
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Affiliation(s)
- Anna M Janzing
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Expertise Center Movement Disorders Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Erik Eklund
- Faculty of Medicine, Department of Clinical Sciences, Pediatrics, Lund University, Lund, Sweden
| | - Tom J De Koning
- Expertise Center Movement Disorders Groningen, University Medical Center Groningen, Groningen, The Netherlands; Faculty of Medicine, Department of Clinical Sciences, Pediatrics, Lund University, Lund, Sweden; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hendriekje Eggink
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Expertise Center Movement Disorders Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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Yilmaz F, Gurusamy U, Mosley TJ, Hallast P, Kim K, Mostovoy Y, Purcell RH, Shaikh TH, Zwick ME, Kwok PY, Lee C, Mulle JG. High level of complexity and global diversity of the 3q29 locus revealed by optical mapping and long-read sequencing. Genome Med 2023; 15:35. [PMID: 37165454 PMCID: PMC10170684 DOI: 10.1186/s13073-023-01184-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 04/20/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND High sequence identity between segmental duplications (SDs) can facilitate copy number variants (CNVs) via non-allelic homologous recombination (NAHR). These CNVs are one of the fundamental causes of genomic disorders such as the 3q29 deletion syndrome (del3q29S). There are 21 protein-coding genes lost or gained as a result of such recurrent 1.6-Mbp deletions or duplications, respectively, in the 3q29 locus. While NAHR plays a role in CNV occurrence, the factors that increase the risk of NAHR at this particular locus are not well understood. METHODS We employed an optical genome mapping technique to characterize the 3q29 locus in 161 unaffected individuals, 16 probands with del3q29S and their parents, and 2 probands with the 3q29 duplication syndrome (dup3q29S). Long-read sequencing-based haplotype resolved de novo assemblies from 44 unaffected individuals, and 1 trio was used for orthogonal validation of haplotypes and deletion breakpoints. RESULTS In total, we discovered 34 haplotypes, of which 19 were novel haplotypes. Among these 19 novel haplotypes, 18 were detected in unaffected individuals, while 1 novel haplotype was detected on the parent-of-origin chromosome of a proband with the del3q29S. Phased assemblies from 44 unaffected individuals enabled the orthogonal validation of 20 haplotypes. In 89% (16/18) of the probands, breakpoints were confined to paralogous copies of a 20-kbp segment within the 3q29 SDs. In one del3q29S proband, the breakpoint was confined to a 374-bp region using long-read sequencing. Furthermore, we categorized del3q29S cases into three classes and dup3q29S cases into two classes based on breakpoints. Finally, we found no evidence of inversions in parent-of-origin chromosomes. CONCLUSIONS We have generated the most comprehensive haplotype map for the 3q29 locus using unaffected individuals, probands with del3q29S or dup3q29S, and available parents, and also determined the deletion breakpoint to be within a 374-bp region in one proband with del3q29S. These results should provide a better understanding of the underlying genetic architecture that contributes to the etiology of del3q29S and dup3q29S.
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Affiliation(s)
- Feyza Yilmaz
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Umamaheswaran Gurusamy
- Cardiovascular Research Institute and Institute for Human Genetics, UCSF School of Medicine, 513 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Trenell J Mosley
- Graduate Program in Genetics and Molecular Biology, Laney Graduate School, Emory University, 201 Dowman Drive, Atlanta, GA, 30322, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Kwondo Kim
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Yulia Mostovoy
- Cardiovascular Research Institute and Institute for Human Genetics, UCSF School of Medicine, 513 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Ryan H Purcell
- Laboratory of Translational Cell Biology, Department of Cell Biology, Emory University School of Medicine, 100 Woodruff Circle, Atlanta, GA, 30322, USA
| | - Tamim H Shaikh
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, 13123 E 16Th Ave, Aurora, CO, 80045, USA
| | - Michael E Zwick
- Department of Genetics, Rutgers University-New Brunswick, Rutgers University, Piscataway, New Brunswick, NJ, 08901, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute and Institute for Human Genetics, UCSF School of Medicine, 513 Parnassus Ave, San Francisco, CA, 94143, USA
- Department of Dermatology, UCSF School of Medicine, 1701 Divisadero Street, San Francisco, CA, 94115, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
| | - Jennifer G Mulle
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, 671 Hoes Lane, New Brunswick, NJ, 08901, USA.
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4
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Dobrigna M, Poëa-Guyon S, Rousseau V, Vincent A, Toutain A, Barnier JV. The molecular basis of p21-activated kinase-associated neurodevelopmental disorders: From genotype to phenotype. Front Neurosci 2023; 17:1123784. [PMID: 36937657 PMCID: PMC10017488 DOI: 10.3389/fnins.2023.1123784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Although the identification of numerous genes involved in neurodevelopmental disorders (NDDs) has reshaped our understanding of their etiology, there are still major obstacles in the way of developing therapeutic solutions for intellectual disability (ID) and other NDDs. These include extensive clinical and genetic heterogeneity, rarity of recurrent pathogenic variants, and comorbidity with other psychiatric traits. Moreover, a large intragenic mutational landscape is at play in some NDDs, leading to a broad range of clinical symptoms. Such diversity of symptoms is due to the different effects DNA variations have on protein functions and their impacts on downstream biological processes. The type of functional alterations, such as loss or gain of function, and interference with signaling pathways, has yet to be correlated with clinical symptoms for most genes. This review aims at discussing our current understanding of how the molecular changes of group I p21-activated kinases (PAK1, 2 and 3), which are essential actors of brain development and function; contribute to a broad clinical spectrum of NDDs. Identifying differences in PAK structure, regulation and spatio-temporal expression may help understanding the specific functions of each group I PAK. Deciphering how each variation type affects these parameters will help uncover the mechanisms underlying mutation pathogenicity. This is a prerequisite for the development of personalized therapeutic approaches.
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Affiliation(s)
- Manon Dobrigna
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Sandrine Poëa-Guyon
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Véronique Rousseau
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Aline Vincent
- Department of Genetics, EA7450 BioTARGen, University Hospital of Caen, Caen, France
| | - Annick Toutain
- Department of Genetics, University Hospital of Tours, UMR 1253, iBrain, Université de Tours, INSERM, Tours, France
| | - Jean-Vianney Barnier
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
- *Correspondence: Jean-Vianney Barnier,
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Madaan P, Kaushal Y, Srivastava P, Crow YJ, Livingston JH, Ahuja C, Sankhyan N. Delineating the epilepsy phenotype of NRROS-related microgliopathy: A case report and literature review. Seizure 2022; 100:15-20. [PMID: 35716448 DOI: 10.1016/j.seizure.2022.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 10/18/2022] Open
Abstract
BACKGROUND Negative regulator of reactive oxygen species (NRROS) related microgliopathy, a rare and recently recognized neurodegenerative condition, is caused by pathogenic variants in the NRROS gene, which plays a major role in the regulation of transforming growth factor-beta 1. METHODS We report a child presenting with infantile spasms syndrome (ISS) with subsequent progressive neurodegeneration who was identified to harbour a novel likely pathogenic NRROS variant (c.1359del; p.Ser454Alafs*11). The previously published reports of patients with this disorder were also reviewed systematically. RESULTS Including our index patient, 11 children (6 girls) were identified in total. Early development was normal in seven of these eleven children. All had a history of drug-resistant epilepsy, with 3 having epileptic spasms. The median age at seizure onset and developmental regression was 12 months, and the median age at death was 36 months. Intracranial calcifications were described in eight of eleven children. Neuroimaging revealed progressive cerebral atrophy and white matter loss in all children. The most common reported genetic variation was c.1981delC; (p.Leu661Serfs*97) observed in two families (likely due to a founder effect). CONCLUSIONS Pathogenic variants in NRROS should be suspected in children with neuro-regression and drug-resistant epilepsy including ISS with onset in the first two years of life. Punctate or serpiginous calcifications at the grey-white matter junction and acquired microcephaly are further clues towards the diagnosis.
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Affiliation(s)
- Priyanka Madaan
- Pediatric Neurology Unit, Department of Pediatrics, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Yashovardhan Kaushal
- Pediatric Neurology Unit, Department of Pediatrics, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | | | - Yanick J Crow
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK; Laboratory of Neurogenetics and Neuroinflammation, Institut Imagine, Université de Paris, Paris, France
| | - John H Livingston
- Department of Paediatric Neurology, Leeds Teaching Hospitals, Leeds, UK
| | - Chirag Ahuja
- Department of Radiodiagnosis and Imaging (Section of Neuroimaging and Interventional Radiology), PGIMER, Chandigarh, India
| | - Naveen Sankhyan
- Pediatric Neurology Unit, Department of Pediatrics, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India.
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Osei-Owusu IA, Norris AL, Joynt AT, Thorpe J, Cho S, Tierney E, Schmidt J, Hagopian L, Harris J, Pevsner J. Characterization of an unbalanced translocation causing 3q28qter duplication and 10q26.2qter deletion in a patient with global developmental delay and self-injury. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005884. [PMID: 33335013 PMCID: PMC7784495 DOI: 10.1101/mcs.a005884] [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] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/08/2020] [Indexed: 01/17/2023] Open
Abstract
Chromosomal structural variation can cause severe neurodevelopmental and neuropsychiatric phenotypes. Here we present a nonverbal female adolescent with severe stereotypic movement disorder with severe problem behavior (e.g., self-injurious behavior, aggression, and disruptive and destructive behaviors), autism spectrum disorder, severe intellectual disability, attention deficit hyperactivity disorder, and global developmental delay. Previous cytogenetic analysis revealed balanced translocations present in the patient's apparently normal mother. We hypothesized the presence of unbalanced translocations in the patient due to maternal history of spontaneous abortions. Whole-genome sequencing and whole-genome optical mapping, complementary next-generation genomic technologies capable of the accurate and robust detection of structural variants, identified t(3;10), t(10;14), and t(3;14) three-way balanced translocations in the mother and der(10)t(3;14;10) and der(14)t(3;14;10) translocations in the patient. Instead of a t(3;10), she inherited a normal maternal copy of Chromosome 3, resulting in an unbalanced state of a 3q28qter duplication and 10q26.2qter deletion. Copy-imbalanced genes in one or both of these regions, such as DLG1, DOCK1, and EBF3, may contribute to the patient's phenotype that spans neurodevelopmental, musculoskeletal, and psychiatric domains, with the possible contribution of a maternally inherited 15q13.2q13.3 deletion.
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Affiliation(s)
- Ikeoluwa A Osei-Owusu
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Alexis L Norris
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Anya T Joynt
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Jeremy Thorpe
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Soonweng Cho
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Elaine Tierney
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Psychiatry, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Jonathan Schmidt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Behavioral Psychology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Louis Hagopian
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Behavioral Psychology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Jacqueline Harris
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Jonathan Pevsner
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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7
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Pollak RM, Zinsmeister MC, Murphy MM, Zwick ME, Mulle JG. New phenotypes associated with 3q29 duplication syndrome: Results from the 3q29 registry. Am J Med Genet A 2020; 182:1152-1166. [PMID: 32154651 DOI: 10.1002/ajmg.a.61540] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 01/15/2023]
Abstract
3q29 duplication syndrome (3q29dup) is a rare genomic disorder caused by a 1.6 Mb duplication (GRCh38 chr3:195,998,000-197,623,000). Case reports indicate the 3q29dup is likely to be pathogenic, but the full range of manifestations is not well understood. We used the 3q29 registry (https://3q29.com) to ascertain 31 individuals with 3q29dup, the largest cohort ever surveyed in a systematic way. For comparison, we ascertained 117 individuals with the reciprocal 3q29 deletion and 64 typically developing controls. We used a custom medical and demographic questionnaire to assess physical and developmental phenotypes, and two standardized instruments, the Social Responsiveness Scale and Child Behavior Checklist/Adult Behavior Checklist, to assess social disability. Participants with 3q29dup report a high rate of problems in the first year of life (80.6%), including feeding problems (55%), failure to gain weight (42%), hypotonia (39%), and respiratory distress (29%). In early childhood, learning problems (71.0%) and seizures (25.8%) are common. Additionally, the rate of self-reported autism spectrum disorder diagnoses (39%) is substantially elevated compared to the general population, suggesting that the 3q29 duplication may be an autism susceptibility locus. This is the most comprehensive description of 3q29dup to date. Our findings can be used to develop evidence-based strategies for early intervention and management of 3q29dup.
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Affiliation(s)
- Rebecca M Pollak
- Genetics and Molecular Biology, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Michael C Zinsmeister
- Genetic Counseling Training Program, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Melissa M Murphy
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Michael E Zwick
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | | | - Jennifer G Mulle
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia, USA.,Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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8
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Marziali F, Dizanzo MP, Cavatorta AL, Gardiol D. Differential expression of DLG1 as a common trait in different human diseases: an encouraging issue in molecular pathology. Biol Chem 2020; 400:699-710. [PMID: 30517074 DOI: 10.1515/hsz-2018-0350] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022]
Abstract
Human disc large (DLG1) is a scaffolding protein that through the interaction with diverse cell partners participates in the control of key cellular processes such as polarity, proliferation and migration. Experimental data have mainly identified DLG1 as a tumor suppressor. An outstanding point for DLG1 protein is that altered DLG1 expression and DLG1 gene mutations were observed in different pathologies, including cancer and neurological and immunological disorders. Evident changes in DLG1 abundance and/or cell localization were identified in a number of studies suggesting its participation in molecular mechanisms responsible for the development of such illnesses. In this review, we focus on some of the latest findings regarding DLG1 alterations in different diseases as well as its potential use as a biomarker for pathological progression. We further address the current knowledge on the molecular mechanisms regulating DLG1 expression and the posttranslational modifications that may affect DLG1 cell localization and functions. Despite the advances in this field, there are still open questions about the precise molecular link between alterations in DLG1 expression and the development of each specific pathology. The complete understanding of this concern will give us new scenarios for the design of promising diagnosis and therapeutic tools.
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Affiliation(s)
- Federico Marziali
- Instituto de Biología Molecular y Celular de Rosario-CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - María Paula Dizanzo
- Instituto de Biología Molecular y Celular de Rosario-CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Ana Laura Cavatorta
- Instituto de Biología Molecular y Celular de Rosario-CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Daniela Gardiol
- Instituto de Biología Molecular y Celular de Rosario-CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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9
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Entire FGF12 duplication by complex chromosomal rearrangements associated with West syndrome. J Hum Genet 2019; 64:1005-1014. [PMID: 31311986 DOI: 10.1038/s10038-019-0641-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/23/2019] [Accepted: 06/26/2019] [Indexed: 11/09/2022]
Abstract
Complex rearrangements of chromosomes 3 and 9 were found in a patient presenting with severe epilepsy, developmental delay, dysmorphic facial features, and skeletal abnormalities. Molecular cytogenetic analysis revealed 46,XX.ish der(9)(3qter→3q28::9p21.1→9p22.3::9p22.3→9qter)(RP11-368G14+,RP11-299O8-,RP11-905L2++,RP11-775E6++). Her dysmorphic features are consistent with 3q29 microduplication syndrome and inv dup del(9p). Trio-based WES of the patient revealed no pathogenic single nucleotide variants causing epilepsy, but confirmed a 3q28q29 duplication involving FGF12, which encodes fibroblast growth factor 12. FGF12 positively regulates the activity of voltage-gated sodium channels. Recently, only one recurrent gain-of-function variant [NM_021032.4:c.341G>A:p.(Arg114His)] in FGF12 was found in a total of 10 patients with severe early-onset epilepsy. We propose that the patient's entire FGF12 duplication may be analogous to the gain-of-function variant in FGF12 in the epileptic phenotype of this patient.
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10
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Arican P, Olgac Dundar N, Ozyilmaz B, Cavusoglu D, Gencpinar P, Erdogan KM, Saka Guvenc M. Chromosomal Microarray Analysis in Children with Unexplained Developmental Delay/Intellectual Disability. J Pediatr Genet 2019; 8:1-9. [PMID: 30775046 DOI: 10.1055/s-0038-1676583] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 10/30/2018] [Indexed: 10/27/2022]
Abstract
Chromosomal microarray (CMA) analysis for discovery of copy number variants (CNVs) is now recommended as a first-line diagnostic tool in patients with unexplained developmental delay/intellectual disability (DD/ID) and autism spectrum disorders. In this study, we present the results of CMA analysis in patients with DD/ID. Of 210 patients, pathogenic CNVs were detected in 26 (12%) and variants of uncertain clinical significance in 36 (17%) children. The diagnosis of well-recognized genetic syndromes was achieved in 12 patients. CMA analysis revealed pathogenic de novo CNVs, such as 11p13 duplication with new clinical features. Our results support the utility of CMA as a routine diagnostic test for unexplained DD/ID.
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Affiliation(s)
- Pinar Arican
- Department of Pediatric Neurology, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Nihal Olgac Dundar
- Department of Pediatric Neurology, Katip Celebi University, Izmir, Turkey
| | - Berk Ozyilmaz
- Department of Medical Genetics, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Dilek Cavusoglu
- Department of Pediatric Neurology, Katip Celebi University, Izmir, Turkey
| | - Pinar Gencpinar
- Department of Pediatric Neurology, Katip Celebi University, Izmir, Turkey
| | - Kadri Murat Erdogan
- Department of Medical Genetics, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Merve Saka Guvenc
- Department of Medical Genetics, Tepecik Training and Research Hospital, Izmir, Turkey
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11
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Tassano E, Uccella S, Giacomini T, Severino M, Siri L, Gherzi M, Celle ME, Porta S, Gimelli G, Ronchetto P. 3q29 microduplication syndrome: Description of two new cases and delineation of the minimal critical region. Eur J Med Genet 2018; 61:428-433. [PMID: 29501613 DOI: 10.1016/j.ejmg.2018.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 01/31/2018] [Accepted: 02/26/2018] [Indexed: 12/28/2022]
Abstract
Heterogeneous clinical and neuropsychological features, such as intellectual disability, developmental and language delay, hypotonia, and, to a lesser extent, microcephaly that is present in about the half of the reported patients, characterize the 3q29 microduplication syndrome with usually a milder phenotype compared with the corresponding 3q29 microdeletion syndrome. The duplications described so far range from 2.3 Mb to 1.6 Mb, spanning from TFRC to BDH1 genes. Here we report on two patients with overlapping interstitial duplications of the 3q29 region differing in size. Patient 1 harboured a common-seized 3q29 microduplication spanning ∼1.6 Mb, while patient 2 carried a very small 3q29 microduplication of 448.8 Kb encompassing only two genes, DLG1 and BDH1. Both patients presented clinical characteristics similar to those reported in the literature in 3q29 microduplication syndrome. Interestingly, heterotopic gray matter nodules were found along the right lateral ventricle on brain MRI in patient 1, thus expanding the neuroradiological phenotype in 3q29 microduplication syndrome, while patient 2 allowed us to define with more precision the smallest region of overlap (SRO). Gene content analysis of the duplicated region suggests that gain-of-dosage of DLG1 and BDH1 may be a good candidate for the main clinical features of this syndrome.
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Affiliation(s)
- Elisa Tassano
- Laboratory of Cytogenetics, Istituto Giannina Gaslini, Genoa, Italy.
| | - Sara Uccella
- Unit of Child Neuropsychiatry, Istituto Giannina Gaslini, University of Genova, Genoa, Italy
| | - Thea Giacomini
- Unit of Child Neuropsychiatry, Istituto Giannina Gaslini, University of Genova, Genoa, Italy
| | | | - Laura Siri
- "La Nostra Famiglia" Association, Varazze (Sv) - Scientific Institute E. Medea, Lecco, Bosisio Parini, Italy
| | - Marcella Gherzi
- Unit of Child Neuropsychiatry, Istituto Giannina Gaslini, University of Genova, Genoa, Italy
| | - Maria Elena Celle
- Unit of Child Neuropsychiatry, Head Neck and Neuroscience Department, Istituto Giannina Gaslini, Genoa, Italy
| | - Simona Porta
- Laboratory of Cytogenetics, Istituto Giannina Gaslini, Genoa, Italy
| | - Giorgio Gimelli
- Laboratory of Cytogenetics, Istituto Giannina Gaslini, Genoa, Italy
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12
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3q29 Chromosomal duplication in a neonate with associated myelomeningocele and midline cranial defects. Clin Dysmorphol 2017; 26:221-223. [PMID: 28763312 DOI: 10.1097/mcd.0000000000000193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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13
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Dworschak GC, Crétolle C, Hilger A, Engels H, Korsch E, Reutter H, Ludwig M. Comprehensive review of the duplication 3q syndrome and report of a patient with Currarino syndrome and de novo duplication 3q26.32-q27.2. Clin Genet 2016; 91:661-671. [PMID: 27549440 DOI: 10.1111/cge.12848] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/16/2016] [Accepted: 08/17/2016] [Indexed: 12/19/2022]
Abstract
Partial duplications of the long arm of chromosome 3, dup(3q), are a rare but well-described condition, sharing features of Cornelia de Lange syndrome. Around two thirds of cases are derived from unbalanced translocations, whereas pure dup(3q) have rarely been reported. Here, we provide an extensive review of the literature on dup(3q). This search revealed several patients with caudal malformations and anomalies, suggesting that caudal malformations or anomalies represent an inherent phenotypic feature of dup(3q). In this context, we report a patient with a pure de novo duplication 3q26.32-q27.2. The patient had the clinical diagnosis of Currarino syndrome (CS) (characterized by the triad of sacral anomalies, anorectal malformations and a presacral mass) and additional features, frequently detected in patients with a dup(3q). Mutations within the MNX1 gene were found to be causative in CS but no MNX1 mutation could be detected in our patient. Our comprehensive search for candidate genes located in the critical region of the duplication 3q syndrome, 3q26.3-q27, revealed a so far neglected phenotypic overlap of dup(3q) and the Pierpont syndrome, associated with a mutation of the TBL1XR1 gene on 3q26.32.
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Affiliation(s)
- G C Dworschak
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Pediatrics, Children's Hospital, University of Bonn, Bonn, Germany
| | - C Crétolle
- Department of Pediatric Surgery, Paris Descartes University, Paris, France.,National Reference Centre for Rare Diseases on Anorectal Malformations and Rare Pelvic Anomalies, Necker-Enfants Malades Hospital, Paris Descartes University, Paris, France
| | - A Hilger
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - H Engels
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - E Korsch
- Clinic for Pediatric Diseases, Kliniken der Stadt Köln GmbH, Cologne, Germany
| | - H Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - M Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
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14
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Grill B, Murphey RK, Borgen MA. The PHR proteins: intracellular signaling hubs in neuronal development and axon degeneration. Neural Dev 2016; 11:8. [PMID: 27008623 PMCID: PMC4806438 DOI: 10.1186/s13064-016-0063-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/15/2016] [Indexed: 11/10/2022] Open
Abstract
During development, a coordinated and integrated series of events must be accomplished in order to generate functional neural circuits. Axons must navigate toward target cells, build synaptic connections, and terminate outgrowth. The PHR proteins (consisting of mammalian Phr1/MYCBP2, Drosophila Highwire and C. elegans RPM-1) function in each of these events in development. Here, we review PHR function across species, as well as the myriad of signaling pathways PHR proteins regulate. These findings collectively suggest that the PHR proteins are intracellular signaling hubs, a concept we explore in depth. Consistent with prominent developmental functions, genetic links have begun to emerge between PHR signaling networks and neurodevelopmental disorders, such as autism, schizophrenia and intellectual disability. Finally, we discuss the recent and important finding that PHR proteins regulate axon degeneration, which has further heightened interest in this fascinating group of molecules.
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Affiliation(s)
- Brock Grill
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, FL, 33458, USA.
| | - Rodney K Murphey
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL, 33458, USA
| | - Melissa A Borgen
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, FL, 33458, USA
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15
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Yu W, You X, Wang D, Dong K, Su J, Li C, Liu J, Zhang Q, You F, Wang X, Huang J, Qiao B, Duan W. Microarray analysis unmasked two siblings with pure hereditary spastic paraplegia shared a run of homozygosity region on chromosome 3q28-q29. J Neurol Sci 2015; 359:351-5. [PMID: 26671141 DOI: 10.1016/j.jns.2015.10.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 10/21/2015] [Accepted: 10/27/2015] [Indexed: 11/29/2022]
Abstract
Hereditary spastic paraplegia (HSP) is a clinical and genetic heterogeneity group of neurodegenerative disorders which is characterized by progressive weakness and spasticity of the lower limbs. More than 70 genetic types of HSP have been described so far. Here we describe a Chinese non-consanguineous family with two affected siblings manifesting early-onset autosomal recessive HSP in pure forms. To identify genotype and characterize phenotype, CytoScan HD array analysis was performed on the two siblings. A run of homozygosity (ROH) shared by the two patients was detected on chromosome 3q28-q29. The ROH region, about 7.7Mb on the chromosome 3:190172058-197851260 partially overlapped with the ROH region of SPG14 previously reported. Subsequently, microsatellite analysis confirmed this ROH and whole-exome sequencing was carried out while no causative mutations were found in the exons of known HSP genes and 68 candidate genes in that region. In conclusion, our data suggest the ROH in this region may play a pivotal role in SPG14 pathogenesis. This is the first clinical description of a pure form spastic paraplegia in a non-consanguineous family associated with the SPG14 locus.
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Affiliation(s)
- Wenqian Yu
- Institute of Cardiovascular Disease, General Hospital of Jinan Military Region, 8 Lashan Road, Jinan 250022, China
| | - Xiangdong You
- Division of Quality Management, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Dong Wang
- Institute of Cardiovascular Disease, General Hospital of Jinan Military Region, 8 Lashan Road, Jinan 250022, China
| | - Kai Dong
- Institute of Cardiovascular Disease, General Hospital of Jinan Military Region, 8 Lashan Road, Jinan 250022, China
| | - Jing Su
- Department of Neurology, General Hospital of Jinan Military Region, 25 Shifan Road, Jinan 250031, China
| | - Chuanfen Li
- Department of Neurology, General Hospital of Jinan Military Region, 25 Shifan Road, Jinan 250031, China
| | - Jinxiu Liu
- Institute of Cardiovascular Disease, General Hospital of Jinan Military Region, 8 Lashan Road, Jinan 250022, China
| | - Qianqian Zhang
- Institute of Cardiovascular Disease, General Hospital of Jinan Military Region, 8 Lashan Road, Jinan 250022, China
| | - Feng You
- Institute of Cardiovascular Disease, General Hospital of Jinan Military Region, 8 Lashan Road, Jinan 250022, China
| | - Xiangrong Wang
- Institute of Cardiovascular Disease, General Hospital of Jinan Military Region, 8 Lashan Road, Jinan 250022, China
| | - Jing Huang
- Institute of Cardiovascular Disease, General Hospital of Jinan Military Region, 8 Lashan Road, Jinan 250022, China
| | - Bin Qiao
- Institute of Cardiovascular Disease, General Hospital of Jinan Military Region, 8 Lashan Road, Jinan 250022, China.
| | - Wenyuan Duan
- Institute of Cardiovascular Disease, General Hospital of Jinan Military Region, 8 Lashan Road, Jinan 250022, China.
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