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McCoy MD, Sarasua SM, DeLuca JM, Davis S, Rogers RC, Phelan K, Boccuto L. Genetics of kidney disorders in Phelan-McDermid syndrome: evidence from 357 registry participants. Pediatr Nephrol 2024; 39:749-760. [PMID: 37733098 DOI: 10.1007/s00467-023-06146-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/07/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND Phelan-McDermid syndrome (PMS) is a rare genetic disorder caused by SHANK3 pathogenic variants or chromosomal rearrangements affecting the chromosome 22q13 region. Previous research found that kidney disorders, primarily congenital anomalies of the kidney and urinary tract, are common in people with PMS, yet research into candidate genes has been hampered by small study sizes and lack of attention to these problems. METHODS We used a cohort of 357 people from the Phelan-McDermid Syndrome Foundation International Registry to investigate the prevalence of kidney disorders in PMS using a cross-sectional design and to identify 22q13 genes contributing to these disorders. RESULTS Kidney disorders reported included vesicoureteral reflux (n = 37), hydronephrosis (n = 36), dysplastic kidneys (n = 19), increased kidney size (n = 19), polycystic kidneys (15 cases), and kidney stones (n = 4). Out of 315 subjects with a 22q13 deletion, 101 (32%) had at least one kidney disorder, while only one out of 42 (2%) individuals with a SHANK3 pathogenic variant had a kidney disorder (increased kidney size). We identified two genomic regions that were significantly associated with having a kidney disorder with the peak associations observed near positions approximately 5 Mb and 400 Kb from the telomere. CONCLUSIONS The candidate genes for kidney disorders include FBLN1, WNT7B, UPK3A, CELSR1, and PLXNB2. This study demonstrates the utility of patient registries for uncovering genetic contributions to rare diseases. Future work should focus on functional studies for these genes to assess their potential pathogenic contribution to the different subsets of kidney disorders.
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Affiliation(s)
- Megan D McCoy
- School of Nursing, Healthcare Genetics Program, Clemson University, Clemson, SC, 29634, USA
| | - Sara M Sarasua
- School of Nursing, Healthcare Genetics Program, Clemson University, Clemson, SC, 29634, USA.
| | - Jane M DeLuca
- School of Nursing, Healthcare Genetics Program, Clemson University, Clemson, SC, 29634, USA
| | - Stephanie Davis
- School of Nursing, Healthcare Genetics Program, Clemson University, Clemson, SC, 29634, USA
| | | | - Katy Phelan
- Genetics Laboratory, Florida Cancer Specialists and Research Institute, Fort Myers, FL, 33916, USA
| | - Luigi Boccuto
- School of Nursing, Healthcare Genetics Program, Clemson University, Clemson, SC, 29634, USA
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2
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Hasnain A, Thompson LL, Hoppman NL, Hovanes K, Liu J, Hashemi B. Constitutional Chromothripsis on Chromosome 2: A Rare Case with Severe Presentation. Case Rep Genet 2024; 2024:6319030. [PMID: 38322183 PMCID: PMC10846923 DOI: 10.1155/2024/6319030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/08/2024] Open
Abstract
Chromothripsis is characterized by shattering and subsequent reassembly of chromosomes by DNA repair processes, which can give rise to a variety of congenital abnormalities and cancer. Constitutional chromothripsis is a rare occurrence, reported in children presenting with a wide range of birth defects. We present a case of a female child born with multiple major congenital abnormalities including severe microcephaly, ocular dysgenesis, heart defect, and imperforate anus. Chromosomal microarray and mate pair sequencing identified a complex chromosomal rearrangement involving the terminal end of the long arm of chromosome 2, with two duplications (located at 2p25.3-p25.1 and 2q35-q37.2 regions) and two deletions (located at 2q37.2-q37.3 and 2q37.3 regions) along with structural changes including inverted segments. A review of the literature for complex rearrangements on chromosome 2 revealed overlapping features; however, our patient had a significantly more severe phenotype which resulted in early death at the age of 2 years. Breakpoints analysis did not reveal the involvement of any candidate genes. We concluded that the complexity of the genomic rearrangement and the combined dosage/structural effect of these copy number variants are likely explanations for the severe presentation in our patient.
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Affiliation(s)
- Afia Hasnain
- Genomics Laboratory, Diagnostic Services, Shared Health, Winnipeg, MB, Canada
| | - Laura L. Thompson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L. Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Jing Liu
- Genomics Laboratory, Diagnostic Services, Shared Health, Winnipeg, MB, Canada
| | - Bita Hashemi
- Genetics and Metabolism Program, Shared Health, Winnipeg, MB, Canada
- Department of Pediatrics, Division of Genetics and Metabolism, Saskatchewan Health Authority, Saskatoon, SK, Canada
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3
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Koza SA, Tabet AC, Bonaglia MC, Andres S, Anderlid BM, Aten E, Stiefsohn D. Consensus recommendations on counselling in Phelan-McDermid syndrome, with special attention to recurrence risk and to ring chromosome 22. Eur J Med Genet 2023; 66:104773. [PMID: 37120077 DOI: 10.1016/j.ejmg.2023.104773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/10/2023] [Accepted: 04/26/2023] [Indexed: 05/01/2023]
Abstract
This paper focuses on genetic counselling in Phelan-McDermid syndrome (PMS), a rare neurodevelopmental disorder caused by a deletion 22q13.3 or a pathogenic variant in SHANK3. It is one of a series of papers written by the European PMS consortium as a consensus guideline. We reviewed the available literature based on pre-set questions to formulate recommendations on counselling, diagnostic work-up and surveillance for tumours related to ring chromosome 22. All recommendations were approved by the consortium, which consists of professionals and patient representatives, using a voting procedure. PMS can only rarely be diagnosed based solely on clinical features and requires confirmation via genetic testing. In most cases, the family will be referred to a clinical geneticist for counselling after the genetic diagnosis has been made. Family members will be investigated and, if indicated, the chance of recurrence discussed with them. Most individuals with PMS have a de novo deletion or a pathogenic variant of SHANK3. The 22q13.3 deletion can be a simple deletion, a ring chromosome 22, or the result of a parental balanced chromosomal anomaly, influencing the risk of recurrence. Individuals with a ring chromosome 22 have an increased risk of NF2-related schwannomatosis (formerly neurofibromatosis type 2) and atypical teratoid rhabdoid tumours, which are associated with the tumour-suppressor genes NF2 and SMARCB1, respectively, and both genes are located on chromosome 22. The prevalence of PMS due to a ring chromosome 22 is estimated to be 10-20%. The risk of developing a tumour in an individual with a ring chromosome 22 can be calculated as 2-4%. However, those individuals who do develop tumours often have multiple. We recommend referring all individuals with PMS and their parents to a clinical geneticist or a comparably experienced medical specialist for genetic counselling, further genetic testing, follow-up and discussion of prenatal diagnostic testing in subsequent pregnancies. We also recommend karyotyping to diagnose or exclude a ring chromosome 22 in individuals with a deletion 22q13.3 detected by molecular tests. If a ring chromosome 22 is found, we recommend discussing personalised follow-up for NF2-related tumours and specifically cerebral imaging between the age of 14 and 16 years.
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Affiliation(s)
- Sylvia A Koza
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands
| | - Anne C Tabet
- Cytogenetic Unit, Genetic Department, Robert Debré Hospital, Human Genetic and Cognitive Function, Pasteur Institute, Paris, France
| | - Maria C Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | | | - Britt-Marie Anderlid
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Emmelien Aten
- Leiden University Medical Center, Department of Clinical Genetics, Leiden, the Netherlands
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4
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Schön M, Pablo L, Julián N, Mattina T, Gunnarsson C, Hadzsiev K, Verpelli C, Bourgeron T, Sarah J, van Ravenswaaij-Arts CMA, Hennekam RC. Definition and clinical variability of SHANK3-related Phelan-McDermid syndrome. Eur J Med Genet 2023; 66:104754. [PMID: 37003575 DOI: 10.1016/j.ejmg.2023.104754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/14/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023]
Abstract
Phelan-McDermid syndrome (PMS) is an infrequently described syndrome that presents with a disturbed development, neurological and psychiatric characteristics, and sometimes other comorbidities. As part of the development of European medical guidelines we studied the definition, phenotype, genotype-phenotype characteristics, and natural history of the syndrome. The number of confirmed diagnoses of PMS in different European countries was also assessed and it could be concluded that PMS is underdiagnosed. The incidence of PMS in European countries is estimated to be at least 1 in 30,000. Next generation sequencing, including analysis of copy number variations, as first tier in diagnostics of individuals with intellectual disability will likely yield a larger number of individuals with PMS than presently known. A definition of PMS by its phenotype is at the present not possible, and therefore PMS-SHANK3 related is defined by the presence of SHANK3 haploinsufficiency, either by a deletion involving region 22q13.2-33 or a pathogenic/likely pathogenic variant in SHANK3. In summarizing the phenotype, we subdivided it into that of individuals with a 22q13 deletion and that of those with a pathogenic/likely pathogenic SHANK3 variant. The phenotype of individuals with PMS is variable, depending in part on the deletion size or, whether only a variant of SHANK3 is present. The core phenotype in the domains development, neurology, and senses are similar in those with deletions and SHANK3 variants, but individuals with a SHANK3 variant more often are reported to have behavioural disorders and less often urogenital malformations and lymphedema. The behavioural disorders may, however, be a less outstanding feature in individuals with deletions accompanied by more severe intellectual disability. Data available on the natural history are limited. Results of clinical trials using insulin-like growth factor I (IGF-1), intranasal insulin, and oxytocin are available, other trials are in progress. The present guidelines for PMS aim at offering tools to caregivers and families to provide optimal care to individuals with PMS.
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Affiliation(s)
- Michael Schön
- Institute for Anatomy and Cell Biology, Ulm University, Germany.
| | - Lapunzina Pablo
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII; ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Nevado Julián
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII; ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Teresa Mattina
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
| | - Cecilia Gunnarsson
- Department of Clinical Genetics and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Centre for Rare Diseases in South East Region of Sweden, Linköping University, Linköping, Sweden
| | - Kinga Hadzsiev
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary
| | | | - Thomas Bourgeron
- Génétique Humaine et Fonctions Cognitives, Institut Pasteur, UMR3571 CNRS, Université de Paris Cité, IUF, 75015, Paris, France
| | - Jesse Sarah
- Department of Neurology, Ulm University, Germany
| | | | - Raoul C Hennekam
- Department of Pediatrics, Amsterdam University Medical Center, Amsterdam, the Netherlands
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5
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de Coo IF, Jesse S, Le TL, Sala C, Bourgeron T. Consensus recommendations on Epilepsy in Phelan-McDermid syndrome. Eur J Med Genet 2023; 66:104746. [PMID: 36967043 DOI: 10.1016/j.ejmg.2023.104746] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/10/2023] [Accepted: 03/18/2023] [Indexed: 03/28/2023]
Abstract
Phelan-McDermid syndrome (PMS) is a 22q13.3 deletion syndrome that presents with a disturbed development, neurological and psychiatric characteristics, and sometimes other comorbidities like seizures. The epilepsy manifests itself in a variety of seizure semiologies. Further diagnostics using electroencephalogram (EEG) and brain magnetic resonance imaging (MRI) are important in conjunction with the clinical picture of the seizures to decide whether anticonvulsant therapy is necessary. As part of the development of European consensus guidelines we focussed on the prevalence and semiology of epileptic seizures in PMS associated with a pathogenic variant in the SHANK3 gene or the 22q13 deletion involving SHANK3, in order to then be able to make recommendations regarding diagnosis and therapy.
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6
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Burgdorf JS, Yoon S, Dos Santos M, Lammert CR, Moskal JR, Penzes P. An IGFBP2-derived peptide promotes neuroplasticity and rescues deficits in a mouse model of Phelan-McDermid syndrome. Mol Psychiatry 2023; 28:1101-1111. [PMID: 36481930 PMCID: PMC10084719 DOI: 10.1038/s41380-022-01904-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022]
Abstract
We developed an IGFBP2-mimetic peptide fragment, JB2, and showed that it promotes basal synaptic structural and functional plasticity in cultured neurons and mice. We demonstrate that JB2 directly binds to dendrites and synapses, and its biological activity involves NMDA receptor activation, gene transcription and translation, and IGF2 receptors. It is not IGF1 receptor-dependent. In neurons, JB2 induced extensive remodeling of the membrane phosphoproteome. Synapse and cytoskeletal regulation, autism spectrum disorder (ASD) risk factors, and a Shank3-associated protein network were significantly enriched among phosphorylated and dephosphorylated proteins. Haploinsufficiency of the SHANK3 gene on chromosome 22q13.3 often causes Phelan-McDermid Syndrome (PMS), a genetically defined form of autism with profound deficits in motor behavior, sensory processing, language, and cognitive function. We identified multiple disease-relevant phenotypes in a Shank3 heterozygous mouse and showed that JB2 rescued deficits in synaptic function and plasticity, learning and memory, ultrasonic vocalizations, and motor function; it also normalized neuronal excitability and seizure susceptibility. Notably, JB2 rescued deficits in the auditory evoked response latency, alpha peak frequency, and steady-state electroencephalography response, measures with direct translational value to human subjects. These data demonstrate that JB2 is a potent modulator of neuroplasticity with therapeutic potential for the treatment of PMS and ASD.
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Affiliation(s)
- Jeffrey S Burgdorf
- Falk Center for Molecular Therapeutics, Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, 60201, USA
- Gate neurosciences, Inc., Carmel, IN, 46032, USA
| | - Sehyoun Yoon
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Marc Dos Santos
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Catherine R Lammert
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Joseph R Moskal
- Falk Center for Molecular Therapeutics, Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, 60201, USA
- Gate neurosciences, Inc., Carmel, IN, 46032, USA
| | - Peter Penzes
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Northwestern University, Center for Autism and Neurodevelopment, Chicago, IL, 60611, USA.
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7
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Sarasua SM, DeLuca JM, Rogers C, Phelan K, Rennert L, Powder KE, Weisensee K, Boccuto L. Head Size in Phelan-McDermid Syndrome: A Literature Review and Pooled Analysis of 198 Patients Identifies Candidate Genes on 22q13. Genes (Basel) 2023; 14:540. [PMID: 36980813 PMCID: PMC10048319 DOI: 10.3390/genes14030540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 02/24/2023] Open
Abstract
Phelan-McDermid syndrome (PMS) is a multisystem disorder that is associated with deletions of the 22q13 genomic region or pathogenic variants in the SHANK3 gene. Notable features include developmental issues, absent or delayed speech, neonatal hypotonia, seizures, autism or autistic traits, gastrointestinal problems, renal abnormalities, dolichocephaly, and both macro- and microcephaly. Assessment of the genetic factors that are responsible for abnormal head size in PMS has been hampered by small sample sizes as well as a lack of attention to these features. Therefore, this study was conducted to investigate the relationship between head size and genes on chromosome 22q13. A review of the literature was conducted to identify published cases of 22q13 deletions with information on head size to conduct a pooled association analysis. Across 56 studies, we identified 198 cases of PMS with defined deletion sizes and head size information. A total of 33 subjects (17%) had macrocephaly, 26 (13%) had microcephaly, and 139 (70%) were normocephalic. Individuals with macrocephaly had significantly larger genomic deletions than those with microcephaly or normocephaly (p < 0.0001). A genomic region on 22q13.31 was found to be significantly associated with macrocephaly with CELSR1, GRAMD4, and TBCD122 suggested as candidate genes. Investigation of these genes will aid the understanding of head and brain development.
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Affiliation(s)
- Sara M. Sarasua
- Healthcare Genetics and Genomics Program, Clemson University School of Nursing, Clemson, SC 29634, USA
| | - Jane M. DeLuca
- Healthcare Genetics and Genomics Program, Clemson University School of Nursing, Clemson, SC 29634, USA
| | | | - Katy Phelan
- Florida Cancer Specialists & Research Institute, Fort Myers, FL 33908, USA
| | - Lior Rennert
- Department of Public Health Sciences, Clemson University, Clemson, SC 29634, USA
| | - Kara E. Powder
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Katherine Weisensee
- Department of Sociology, Anthropology and Criminal Justice, Clemson University, Clemson, SC 29634, USA
| | - Luigi Boccuto
- Healthcare Genetics and Genomics Program, Clemson University School of Nursing, Clemson, SC 29634, USA
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8
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Li P, Dupont B, Hu Q, Crimi M, Shen Y, Lebedev I, Liehr T. The past, present, and future for constitutional ring chromosomes: A report of the international consortium for human ring chromosomes. Human Genetics and Genomics Advances 2022; 3:100139. [PMID: 36187226 PMCID: PMC9519620 DOI: 10.1016/j.xhgg.2022.100139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Human ring chromosomes (RCs) are rare diseases with an estimated newborn incidence of 1/50,000 and an annual occurrence of 2,800 patients globally. Over the past 60 years, banding cytogenetics, fluorescence in situ hybridization (FISH), chromosome microarray analysis (CMA), and whole-genome sequencing (WGS) has been used to detect an RC and further characterize its genomic alterations. Ring syndrome featuring sever growth retardation and variable intellectual disability has been considered as general clinical presentations for all RCs due to the cellular losses from the dynamic mosaicism of RC instability through mitosis. Cytogenomic heterogeneity ranging from simple complete RCs to complex rearranged RCs and variable RC intolerance with different relative frequencies have been observed. Clinical heterogeneity, including chromosome-specific deletion and duplication syndromes, gene-related organ and tissue defects, cancer predisposition to different types of tumors, and reproductive failure, has been reported in the literature. However, the patients with RCs reported in the literature accounted for less than 1% of its occurrence. Current diagnostic practice lacks laboratory standards for analyzing cellular behavior and genomic imbalances of RCs to evaluate the compound effects on patients. Under-representation of clinical cases and lack of comprehensive diagnostic analysis make it a challenge for evidence-based interpretation of clinico-cytogenomic correlations and recommendation of follow-up clinical management. Given recent advancements in genomic technologies and organized efforts by international collaborations and patient advocacy organizations, the prospective of standardized cytogenomic diagnosis and evidence-based clinical management for all patients with RCs could be achieved at an unprecedented global scale.
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Affiliation(s)
- Peining Li
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Corresponding author
| | - Barbara Dupont
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, SC, USA
- Corresponding author
| | - Qiping Hu
- Department of Cell Biology and Genetics, Institute of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Marco Crimi
- Ring 14 International, Via Santa Maria Alla Porta 2, 20123 Milano, Italy
- Kaleidos SCS, Scientific Office, Via Moretti Andrea 20, 24121 Bergamo, Italy
| | - Yiping Shen
- Division of Genetics and Genomics, Boston Children’s Hospital, Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Igor Lebedev
- Laboratory of Ontogenetics, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk 634050, Russia
- Corresponding author
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, 07747 Jena, Germany
- Corresponding author
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9
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Nevado J, García-Miñaúr S, Palomares-Bralo M, Vallespín E, Guillén-Navarro E, Rosell J, Bel-Fenellós C, Mori MÁ, Milá M, Del Campo M, Barrúz P, Santos-Simarro F, Obregón G, Orellana C, Pachajoa H, Tenorio JA, Galán E, Cigudosa JC, Moresco A, Saleme C, Castillo S, Gabau E, Pérez-Jurado L, Barcia A, Martín MS, Mansilla E, Vallcorba I, García-Murillo P, Cammarata-Scalisi F, Gonçalves Pereira N, Blanco-Lago R, Serrano M, Ortigoza-Escobar JD, Gener B, Seidel VA, Tirado P, Lapunzina P. Variability in Phelan-McDermid Syndrome in a Cohort of 210 Individuals. Front Genet 2022; 13:652454. [PMID: 35495150 PMCID: PMC9044489 DOI: 10.3389/fgene.2022.652454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/16/2022] [Indexed: 12/18/2022] Open
Abstract
Phelan-McDermid syndrome (PMS, OMIM# 606232) results from either different rearrangements at the distal region of the long arm of chromosome 22 (22q13.3) or pathogenic sequence variants in the SHANK3 gene. SHANK3 codes for a structural protein that plays a central role in the formation of the postsynaptic terminals and the maintenance of synaptic structures. Clinically, patients with PMS often present with global developmental delay, absent or severely delayed speech, neonatal hypotonia, minor dysmorphic features, and autism spectrum disorders (ASD), among other findings. Here, we describe a cohort of 210 patients with genetically confirmed PMS. We observed multiple variant types, including a significant number of small deletions (<0.5 Mb, 64/189) and SHANK3 sequence variants (21 cases). We also detected multiple types of rearrangements among microdeletion cases, including a significant number with post-zygotic mosaicism (9.0%, 17/189), ring chromosome 22 (10.6%, 20/189), unbalanced translocations (de novo or inherited, 6.4%), and additional rearrangements at 22q13 (6.3%, 12/189) as well as other copy number variations in other chromosomes, unrelated to 22q deletions (14.8%, 28/189). We compared the clinical and genetic characteristics among patients with different sizes of deletions and with SHANK3 variants. Our findings suggest that SHANK3 plays an important role in this syndrome but is probably not uniquely responsible for all the spectrum features in PMS. We emphasize that only an adequate combination of different molecular and cytogenetic approaches allows an accurate genetic diagnosis in PMS patients. Thus, a diagnostic algorithm is proposed.
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Affiliation(s)
- Julián Nevado
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Sixto García-Miñaúr
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - María Palomares-Bralo
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Elena Vallespín
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | | | | | - Cristina Bel-Fenellós
- Departamento de Investigación y Psicología en Educación, Facultad de Educación, UCM, Madrid, Spain.,CEE Estudio-3, Afanias, Madrid, Spain
| | - María Ángeles Mori
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | | | | | - Pilar Barrúz
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | | | | | | | - Jair Antonio Tenorio
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Enrique Galán
- Hospital Materno-Infantil Infanta Cristina, Badajoz, Spain
| | | | | | - César Saleme
- Maternity Nuestra Señora de la Merced, Tucumán, Argentina
| | - Silvia Castillo
- Sección Genética, Hospital Clínico Universidad de Chile, Santiago, Chile.,Clínica Alemana, Santiago, Chile
| | | | - Luis Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Servicio de Genética, Instituto de Investigaciones Médicas Hospital del Mar (IMIM)/Universitat Pompeu Fabra, Barcelona, Spain
| | - Ana Barcia
- Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - Maria Soledad Martín
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Elena Mansilla
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Isabel Vallcorba
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | | | | | | | - Raquel Blanco-Lago
- Servicio de Neuropediatría, Hospital Universitario Central de Asturias, Oviedo (Asturias), Spain
| | - Mercedes Serrano
- Unidad de Neuropediatría, Hospital San Joan de Deu, Barcelona, Spain
| | | | | | | | - Pilar Tirado
- Servicio de Neuropediatría, Hospital Universitario La Paz, Madrid, Spain
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
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10
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Cammarata-Scalisi F, Callea M, Martinelli D, Willoughby CE, Tadich AC, Araya Castillo M, Lacruz-Rengel MA, Medina M, Grimaldi P, Bertini E, Nevado J. Clinical and Genetic Aspects of Phelan–McDermid Syndrome: An Interdisciplinary Approach to Management. Genes (Basel) 2022; 13:genes13030504. [PMID: 35328058 PMCID: PMC8955098 DOI: 10.3390/genes13030504] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023] Open
Abstract
Phelan–McDermid syndrome (PMS) is a rare, heterogeneous, and complex neurodevelopmental disorder. It is generally caused by a heterozygous microdeletion of contiguous genes located in the distal portion of the long arm of chromosome 22, including the SHANK3 gene. Sequence variants of SHANK3, including frameshift, nonsense mutations, small indels and splice site mutations also result in PMS. Furthermore, haploinsufficiency in SHANK3 has been suggested as the main cause of PMS. SHANK3 is also associated with intellectual disability, autism spectrum disorder and schizophrenia. The phenotype of PMS is variable, and lacks a distinctive phenotypic characteristic, so the clinical diagnosis should be confirmed by genetic analysis. PMS is a multi-system disorder, and clinical care must encompass various specialties and therapists. The role of risperidone, intranasal insulin, insulin growth factor 1, and oxytocin as potential therapeutic options in PMS will be discussed in this review. The diagnosis of PMS is important to provide an appropriate clinical evaluation, treatment, and genetic counseling.
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Affiliation(s)
- Francisco Cammarata-Scalisi
- Pediatric Service, Regional of Antofagasta Hospital, Antofagasta 1240835, Chile; (F.C.-S.); (A.C.T.); (M.M.)
| | - Michele Callea
- Pediatric Dentistry and Special Dental Care Unit, Meyer Children’s University Hospital, 50139 Florence, Italy
- Correspondence: (M.C.); (D.M.)
| | - Diego Martinelli
- Unit of Metabolism, Bambino Gesù Children’s Research Hospital IRCCS, 00165 Rome, Italy
- Correspondence: (M.C.); (D.M.)
| | - Colin Eric Willoughby
- Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, Northern Ireland, UK;
| | - Antonio Cárdenas Tadich
- Pediatric Service, Regional of Antofagasta Hospital, Antofagasta 1240835, Chile; (F.C.-S.); (A.C.T.); (M.M.)
| | | | | | - Marco Medina
- Pediatric Service, Regional of Antofagasta Hospital, Antofagasta 1240835, Chile; (F.C.-S.); (A.C.T.); (M.M.)
| | - Piercesare Grimaldi
- Department of Public Health and Pediatric Sciences, University of Torino, 10126 Torino, Italy;
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Department of Neurosciences, Bambino Gesu’ Children’s Research Hospital IRCCS, 00165 Rome, Italy;
| | - Julián Nevado
- Instituto de Genética Médica y Molecular (INGEMM), Instituto de Investigación del Hospital Universitario La Paz (IdIPaz), 28046 Madrid, Spain; or
- Centro de Investigación Biomédica en RED de Enfermedades Raras (CIBERER), 28046 Madrid, Spain
- ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Hospital La Paz, 28046 Madrid, Spain
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11
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Juchem KW, Gounder AP, Gao JP, Seccareccia E, Yeddula N, Huffmaster NJ, Côté-Martin A, Fogal SE, Souza D, Wang SS, Glynn ERA, Yung I, Ritchie J, Li L, Zheng J, Mbow ML, Li J, Chanda SK. NFAM1 Promotes Pro-Inflammatory Cytokine Production in Mouse and Human Monocytes. Front Immunol 2022; 12:773445. [PMID: 35095847 PMCID: PMC8793151 DOI: 10.3389/fimmu.2021.773445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
NFAT activating protein with ITAM motif 1 (NFAM1) is an ITAM bearing-transmembrane receptor that has been reported to play a role in B cell signaling and development. We performed expression analysis of NFAM1 using publicly available gene expression data sets and found that NFAM1 expression is significantly induced in intestinal biopsies from Crohn’s disease (CD) and ulcerative colitis (UC) patients. At the cellular level, we further observed high expression of NFAM1 in monocytes and neutrophils, and low expression in B and T cells. To explore the role of NFAM1 in multiple immune cells and its potential role in IBD, we generated NFAM1-/- mice. In contrast with previous reports using NFAM1-transgenic mice, NFAM1-/- mice have no obvious defects in immune cell development, or B cell responses. Interestingly, NFAM1-/- monocytes produce reduced levels of TNF-α in response to activation by multiple IBD-relevant stimuli, including CD40L, TLR ligands and MDP. Additional cytokines and chemokines such as IL-6, IL-12, CCL3 and CCL4 are also reduced in CD40L stimulated NFAM1-/- monocytes. Collectively, these findings indicate that NFAM1 promotes monocyte activation, thereby amplifying the response to diverse stimuli. Similarly, we observed that deletion of NFAM1 in human monocytes reduces expression of CD40L-induced CCL4. Lastly, to assess the role of NFAM1 in IBD, we compared development of anti-CD40 induced colitis in NFAM1+/+ and NFAM1-/- mice. We found that although NFAM1 deletion had no impact on development of gut pathology, we did observe a decrease in serum TNF-α, confirming that NFAM1 promotes pro-inflammatory cytokine production in vivo. Taken together, we conclude that NFAM1 functions to amplify cytokine production and should be further evaluated as a therapeutic target for treatment of autoimmune disease.
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Affiliation(s)
- Kathryn W Juchem
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Anshu P Gounder
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Jian Ping Gao
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Elise Seccareccia
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Narayana Yeddula
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Nicholas J Huffmaster
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Alexandra Côté-Martin
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Steven E Fogal
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Donald Souza
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Sarah Sirui Wang
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Elizabeth R A Glynn
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Ivy Yung
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Julie Ritchie
- Department of Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Li Li
- Department of Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Jie Zheng
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - M Lamine Mbow
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Jun Li
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
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12
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Srikanth S, Jain L, Zepeda-Mendoza C, Cascio L, Jones K, Pauly R, DuPont B, Rogers C, Sarasua S, Phelan K, Morton C, Boccuto L. Position effects of 22q13 rearrangements on candidate genes in Phelan-McDermid syndrome. PLoS One 2021; 16:e0253859. [PMID: 34228749 PMCID: PMC8259982 DOI: 10.1371/journal.pone.0253859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/15/2021] [Indexed: 11/19/2022] Open
Abstract
Phelan-McDermid syndrome (PMS) is a multi-system disorder characterized by significant variability in clinical presentation. The genetic etiology is also variable with differing sizes of deletions in the chromosome 22q13 region and types of genetic abnormalities (e.g., terminal or interstitial deletions, translocations, ring chromosomes, or SHANK3 variants). Position effects have been shown to affect gene expression and function and play a role in the clinical presentation of various genetic conditions. This study employed a topologically associating domain (TAD) analysis approach to investigate position effects of chromosomal rearrangements on selected candidate genes mapped to 22q13 in 81 individuals with PMS. Data collected were correlated with clinical information from these individuals and with expression and metabolic profiles of lymphoblastoid cells from selected cases. The data confirmed TAD predictions for genes encompassed in the deletions and the clinical and molecular data indicated clear differences among individuals with different 22q13 deletion sizes. The results of the study indicate a positive correlation between deletion size and phenotype severity in PMS and provide evidence of the contribution of other genes to the clinical variability in this developmental disorder by reduced gene expression and altered metabolomics.
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Affiliation(s)
- Sujata Srikanth
- Greenwood Genetic Center, Greenwood, SC, United States of America
| | - Lavanya Jain
- School of Nursing, Healthcare Genetics Program, Clemson University, Clemson, SC, United States of America
| | - Cinthya Zepeda-Mendoza
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
| | - Lauren Cascio
- Greenwood Genetic Center, Greenwood, SC, United States of America
| | - Kelly Jones
- Greenwood Genetic Center, Greenwood, SC, United States of America
| | - Rini Pauly
- Greenwood Genetic Center, Greenwood, SC, United States of America
| | - Barb DuPont
- Greenwood Genetic Center, Greenwood, SC, United States of America
| | - Curtis Rogers
- Greenwood Genetic Center, Greenwood, SC, United States of America
| | - Sara Sarasua
- School of Nursing, Healthcare Genetics Program, Clemson University, Clemson, SC, United States of America
| | - Katy Phelan
- Genetics Laboratory, Florida Cancer Specialists and Research Institute, Fort Myers, FL, United States of America
| | - Cynthia Morton
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States of America
- Division of Human Communication, Development and Hearing, School of Biological Sciences, Manchester Academic Health Science Center, Manchester, United Kingdom
| | - Luigi Boccuto
- Greenwood Genetic Center, Greenwood, SC, United States of America
- School of Nursing, College of Behavioral, Social and Health Sciences, Clemson University, Clemson, SC, United States of America
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13
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Nikitina TV, Kashevarova AA, Gridina MM, Lopatkina ME, Khabarova AA, Yakovleva YS, Menzorov AG, Minina YA, Pristyazhnyuk IE, Vasilyev SA, Fedotov DA, Serov OL, Lebedev IN. Complex biology of constitutional ring chromosomes structure and (in)stability revealed by somatic cell reprogramming. Sci Rep 2021; 11:4325. [PMID: 33619287 PMCID: PMC7900208 DOI: 10.1038/s41598-021-83399-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/01/2021] [Indexed: 01/07/2023] Open
Abstract
Human ring chromosomes are often unstable during mitosis, and daughter cells can be partially or completely aneuploid. We studied the mitotic stability of four ring chromosomes, 8, 13, 18, and 22, in long-term cultures of skin fibroblasts and induced pluripotent stem cells (iPSCs) by GTG karyotyping and aCGH. Ring chromosome loss and secondary aberrations were observed in all fibroblast cultures except for r(18). We found monosomy, fragmentation, and translocation of indexed chromosomes. In iPSCs, aCGH revealed striking differences in mitotic stability both between iPSC lines with different rings and, in some cases, between cell lines with the same ring chromosome. We registered the spontaneous rescue of karyotype 46,XY,r(8) to 46,XY in all six iPSC lines through ring chromosome loss and intact homologue duplication with isoUPD(8)pat occurrence, as proven by SNP genotype distribution analysis. In iPSCs with other ring chromosomes, karyotype correction was not observed. Our results suggest that spontaneous correction of the karyotype with ring chromosomes in iPSCs is not universal and that pluripotency is compatible with a wide range of derivative karyotypes. We conclude that marked variability in the frequency of secondary rearrangements exists in both fibroblast and iPSC cultures, expanding the clinical significance of the constitutional ring chromosome.
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Affiliation(s)
- T V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Ushaika Street 10, Tomsk, 634050, Russia.
| | - A A Kashevarova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Ushaika Street 10, Tomsk, 634050, Russia
| | - M M Gridina
- Department of Molecular Mechanisms of Development, Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - M E Lopatkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Ushaika Street 10, Tomsk, 634050, Russia
| | - A A Khabarova
- Department of Molecular Mechanisms of Development, Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - Yu S Yakovleva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Ushaika Street 10, Tomsk, 634050, Russia.,Department of Medical Genetics, Siberian State Medical University, Tomsk, 634050, Russia
| | - A G Menzorov
- Department of Molecular Mechanisms of Development, Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yu A Minina
- Department of Molecular Mechanisms of Development, Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - I E Pristyazhnyuk
- Department of Molecular Mechanisms of Development, Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - S A Vasilyev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Ushaika Street 10, Tomsk, 634050, Russia
| | - D A Fedotov
- Department of Medical Genetics, Siberian State Medical University, Tomsk, 634050, Russia
| | - O L Serov
- Department of Molecular Mechanisms of Development, Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
| | - I N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Ushaika Street 10, Tomsk, 634050, Russia.,Department of Medical Genetics, Siberian State Medical University, Tomsk, 634050, Russia
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14
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Feng C, Zhao J, Ji F, Su L, Chen Y, Jiao J. TCF20 dysfunction leads to cortical neurogenesis defects and autistic-like behaviors in mice. EMBO Rep 2020; 21:e49239. [PMID: 32510763 DOI: 10.15252/embr.201949239] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/12/2022] Open
Abstract
Recently, de novo mutations of transcription factor 20 (TCF20) were found in patients with autism by large-scale exome sequencing. However, how TCF20 modulates brain development and whether its dysfunction causes ASD remain unclear. Here, we show that TCF20 deficits impair neurogenesis in mouse. TCF20 deletion significantly reduces the number of neurons, which leads to abnormal brain functions. Furthermore, transcriptome analysis and ChIP-qPCR reveal that the DNA demethylation factor TDG is a downstream target gene of TCF20. As a nonspecific DNA demethylation factor, TDG potentially affects many genes. Combined TDG ChIP-seq and GO analysis of TCF20 RNA-Seq identifies T-cell factor 4 (TCF-4) as a common target. TDG controls the DNA methylation level in the promoter area of TCF-4, affecting TCF-4 expression and modulating neural differentiation. Overexpression of TDG or TCF-4 rescues the deficient neurogenesis of TCF20 knockdown brains. Together, our data reveal that TCF20 is essential for neurogenesis and we suggest that defects in neurogenesis caused by TCF20 loss are associated with ASD.
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Affiliation(s)
- Chao Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Sino-Danish College at University of Chinese Academy of Sciences, Beijing, China
| | - Jinyue Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fen Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Libo Su
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yihui Chen
- Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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15
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Koltsova AS, Pendina AA, Efimova OA, Chiryaeva OG, Kuznetzova TV, Baranov VS. On the Complexity of Mechanisms and Consequences of Chromothripsis: An Update. Front Genet 2019; 10:393. [PMID: 31114609 PMCID: PMC6503150 DOI: 10.3389/fgene.2019.00393] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/11/2019] [Indexed: 12/28/2022] Open
Abstract
In the present review, we focus on the phenomenon of chromothripsis, a new type of complex chromosomal rearrangements. We discuss the challenges of chromothripsis detection and its distinction from other chromoanagenesis events. Along with already known causes and mechanisms, we introduce aberrant epigenetic regulation as a possible pathway to chromothripsis. We address the issue of chromothripsis characteristics in cancers and benign tumours, as well as chromothripsis inheritance in cases of its occurrence in germ cells, zygotes and early embryos. Summarising the presented data on different phenotypic effect of chromothripsis, we assume that its consequences are most likely determined not by the chromosome shattering and reassembly themselves, but by the genome regions involved in the rearrangement.
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Affiliation(s)
- Alla S Koltsova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Anna A Pendina
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Olga A Efimova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Olga G Chiryaeva
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Tatyana V Kuznetzova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Vladislav S Baranov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
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16
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Kurtas NE, Xumerle L, Giussani U, Pansa A, Cardarelli L, Bertini V, Valetto A, Liehr T, Clara Bonaglia M, Errichiello E, Delledonne M, Zuffardi O. Insertional translocation involving an additional nonchromothriptic chromosome in constitutional chromothripsis: Rule or exception? Mol Genet Genomic Med 2018; 7:e00496. [PMID: 30565424 PMCID: PMC6393660 DOI: 10.1002/mgg3.496] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/06/2018] [Accepted: 10/02/2018] [Indexed: 01/17/2023] Open
Abstract
Background Chromothripsis, which is the local massive shattering of one or more chromosomes and their reassembly in a disordered array with frequent loss of some fragments, has been mainly reported in association with abnormal phenotypes. We report three unrelated healthy persons, two of which parenting a child with some degree of intellectual disability, carrying a chromothripsis involving respectively one, two, and three chromosomes, which was detected only after whole‐genome sequencing. Unexpectedly, in all three cases a fragment from one of the chromothripsed chromosomes resulted to be inserted within a nonchromothripsed one. Methods Conventional cytogenetic techniques, paired‐end whole‐genome sequencing, polymerase chain reaction, and Sanger sequencing were used to characterize complex rearrangements, copy‐number variations, and breakpoint sequences in all three families. Results In two families, one parent was carrier of a balanced chromothripsis causing in the index case a deletion and a noncontiguous duplication at 3q in case 1, and a t(6;14) translocation associated with interstitial 14q deletion in case 2. In the third family, an unbalanced chromothripsis involving chromosomes 6, 7, and 15 was inherited to the proband by the mosaic parent. In all three parents, the chromothripsis was concurrent with an insertional translocation of a portion of one of the chromothriptic chromosomes within a further chromosome that was not involved in the chromothripsis event. Conclusion Our findings show that (a) both simple and complex unbalanced rearrangements may result by the recombination of a cryptic parental balanced chromothripsis and that (b) insertional translocations are the spy of more complex rearrangements and not simply a three‐breakpoint event.
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Affiliation(s)
| | - Luciano Xumerle
- Personal Genomics srl, Department of Biotechnologies, University of Verona, Verona, Italy
| | | | | | | | | | | | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Lecco, Italy
| | | | - Massimo Delledonne
- Personal Genomics srl, Department of Biotechnologies, University of Verona, Verona, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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17
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Sheth F, Liehr T, Shah V, Shah H, Tewari S, Solanki D, Trivedi S, Sheth J. A child with intellectual disability and dysmorphism due to complex ring chromosome 6: identification of molecular mechanism with review of literature. Ital J Pediatr 2018; 44:114. [PMID: 30305128 PMCID: PMC6180451 DOI: 10.1186/s13052-018-0571-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 09/21/2018] [Indexed: 11/29/2022] Open
Abstract
Background Ring chromosome 6 (r(6)) is a rare disorder that mainly occurs as a ‘de novo’ event. Nonetheless, a wide phenotypic spectrum has been reported in r(6) cases, depending on breakpoints, size of involved region, copy number alterations and mosaicism of cells with r(6) and/or monosomy 6 due to loss of r(6). Case presentation An 11-year-old male was referred with developmental delay, intellectual disability and microcephaly. Physical examination revealed additionally short stature and multiple facial dysmorphisms. Banding cytogenetic studies revealed a karyotype of mos 46,XY,r(6)(p25.3q27)[54]/45,XY,-6[13]/46,XY,r(6)(::p25.3→q27::p25.3→q27::)[13]/46,XY[6]/47,XY,r(6)(p25.3q27)×2[2]dn. Additionally, molecular karyotyping and molecular cytogenetics confirmed the breakpoints and characterized a 1.3 Mb contiguous duplication at 6p25.3. Conclusion The present study has accurately identified copy number alterations caused by ring chromosome formation. A review of the literature suggests that hemizygous expression of TBP gene in 6q27~qter, is likely to be the underlying cause of the phenotype. The phenotypic correlation and clinical severity in r(6) cases continue to remain widely diverse in spite of numerous reports of genomic variations.
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Affiliation(s)
- Frenny Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380009, India.
| | - Thomas Liehr
- University Clinic Jena, Institute of Human Genetics, Am Klinikum 1, 07747, Jena, Germany
| | - Viraj Shah
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380009, India
| | - Hillary Shah
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380009, India
| | - Stuti Tewari
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380009, India
| | - Dhaval Solanki
- Mantra Child Neurology & Epilepsy Hospital, 3rd floor, Oarnate complex, Kalubha road, Kalanala, Bhavanagar, 364001, India
| | - Sunil Trivedi
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380009, India
| | - Jayesh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380009, India
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Kashevarova AA, Belyaeva EO, Nikonov AM, Plotnikova OV, Skryabin NA, Nikitina TV, Vasilyev SA, Yakovleva YS, Babushkina NP, Tolmacheva EN, Lopatkina ME, Savchenko RR, Nazarenko LP, Lebedev IN. Compound phenotype in a girl with r(22), concomitant microdeletion 22q13.32-q13.33 and mosaic monosomy 22. Mol Cytogenet 2018; 11:26. [PMID: 29736186 PMCID: PMC5923029 DOI: 10.1186/s13039-018-0375-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/12/2018] [Indexed: 02/07/2023] Open
Abstract
Background Ring chromosome instability may influence a patient's phenotype and challenge its interpretation. Results Here, we report a 4-year-old girl with a compound phenotype. Cytogenetic analysis revealed her karyotype to be 46,XX,r(22). aCGH identified a 180 kb 22q13.32 duplication, a de novo 2.024 Mb subtelomeric 22q13.32-q13.33 deletion, which is associated with Phelan-McDermid syndrome, and a maternal single gene 382-kb TUSC7 deletion of uncertain clinical significance located in the region of the 3q13.31 deletion syndrome. All chromosomal aberrations were confirmed by real-time PCR in lymphocytes and detected in skin fibroblasts. The deletions were also found in the buccal epithelium. According to FISH analysis, 8% and 24% of the patient's lymphocytes and skin fibroblasts, respectively, had monosomy 22. Conclusions We believe that a combination of 22q13.32-q13.33 deletion and monosomy 22 in a portion of cells can better define the clinical phenotype of the patient. Importantly, the in vivo presence of monosomic cells indicates ring chromosome instability, which may favor karyotype correction that is significant for the development of chromosomal therapy protocols.
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Affiliation(s)
| | - Elena O Belyaeva
- 1Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | | | | | | | | | | | - Yulia S Yakovleva
- 1Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia.,3Siberian State Medical University, Tomsk, Russia
| | | | | | | | | | - Lyudmila P Nazarenko
- 1Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia.,3Siberian State Medical University, Tomsk, Russia
| | - Igor N Lebedev
- 1Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia.,3Siberian State Medical University, Tomsk, Russia
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