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Vos N, Reilly J, Elting MW, Campeau PM, Coman D, Stark Z, Tan TY, Amor DJ, Kaur S, StJohn M, Morgan AT, Kamien BA, Patel C, Tedder ML, Merla G, Prontera P, Castori M, Muru K, Collins F, Christodoulou J, Smith J, Zeev BB, Murgia A, Leonardi E, Esber N, Martinez-Monseny A, Casas-Alba D, Wallis M, Mannens M, Levy MA, Relator R, Alders M, Sadikovic B. DNA methylation episignatures are sensitive and specific biomarkers for detection of patients with KAT6A/ KAT6B variants. Epigenomics 2023. [PMID: 37249002 DOI: 10.2217/epi-2023-0079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
Accurate diagnosis for patients living with neurodevelopmental disorders is often met with numerous challenges, related to the ambiguity of findings and lack of specificity in genetic variants leading to pathology. Genome-wide DNA methylation analysis has been used to develop highly sensitive and specific 'episignatures' as biomarkers capable of differentiating and classifying complex neurodevelopmental disorders. In this study we describe distinct episignatures for KAT6A syndrome, caused by pathogenic variants in the lysine acetyltransferase A gene (KAT6A), and for the two neurodevelopmental disorders associated with lysine acetyl transferase B (KAT6B). We demonstrate the ability of our models to differentiate between highly overlapping episignatures, increasing the ability to effectively identify and diagnose these conditions.
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Affiliation(s)
- Niels Vos
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands
| | - Jack Reilly
- Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 5C1, Canada
| | - Mariet W Elting
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands
| | - Philippe M Campeau
- Department of Pediatrics, Sainte-Justine UHC & University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - David Coman
- Department of Metabolic Medicine, Queensland Children's Hospital, South Brisbane, QLD 4101, Australia
- School of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, 3052, Australia
- Department of Paediatrics, University of Melbourne, Grattan Street, Parkville, Victoria, 3010, Australia
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, 3052, Australia
- Department of Paediatrics, University of Melbourne, Grattan Street, Parkville, Victoria, 3010, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Rd, Parkville VIC, 3052, Australia
- University of Melbourne Department of Pediatrics, Parkville, Victoria, 3010, Australia
| | - Simran Kaur
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Rd, Parkville VIC, 3052, Australia
- University of Melbourne Department of Pediatrics, Parkville, Victoria, 3010, Australia
| | - Miya StJohn
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Rd, Parkville VIC, 3052, Australia
- University of Melbourne Department of Pediatrics, Parkville, Victoria, 3010, Australia
| | - Angela T Morgan
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Rd, Parkville VIC, 3052, Australia
- University of Melbourne Department of Pediatrics, Parkville, Victoria, 3010, Australia
| | - Benjamin A Kamien
- Genetics Services of Western Australia, Perth, 6008, Western Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane & Women's Hospital, Herston, QLD 4006, Australia
| | | | - Giuseppe Merla
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo (Foggia), Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federica II, 5 - 80131, Naples, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Piazza dell'Università, 1, 06123, Perugia PG, Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo (Foggia), Italy
| | - Kai Muru
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Riia 23b, 51010, Tartu, Estonia
| | - Felicity Collins
- Discipline of Child and Adolescent Health and Genomic Medicine, Sydney Medical School, Sydney University, Sydney, Camperdown NSW, 2050, Australia
- Department of Clinical Genetics, Western Sydney Genetics Program, Children's Hospital at Westmead, Randwick NSW, 2031, Australia
| | - John Christodoulou
- Department of Clinical Genetics, Western Sydney Genetics Program, Children's Hospital at Westmead, Randwick NSW, 2031, Australia
| | - Janine Smith
- Sydney Children's Hospitals Network-Westmead, Randwick NSW, 2031, Australia
- University of Sydney, Camperdown NSW, 2006, Australia
| | - Bruria Ben Zeev
- Sackler School of Medicine Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Alessandra Murgia
- Laboratory of Molecular Genetics of Neurodevelopment, Department of Women's and Children's Health, University of Padua, Via Giustiniani 3, 35128, Padua, Italy
| | - Emanuela Leonardi
- Laboratory of Molecular Genetics of Neurodevelopment, Department of Women's and Children's Health, University of Padua, Via Giustiniani 3, 35128, Padua, Italy
| | - Natacha Esber
- KAT6A Foundation, 3 Louise Dr., West Nyack, NY 10994, USA
| | - Antonio Martinez-Monseny
- Genetics and Molecular Medicine Department, Rare Disease Pediatric Unit, Hospital Sant Joan de Déu, 2, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - Didac Casas-Alba
- Genetics and Molecular Medicine Department, Rare Disease Pediatric Unit, Hospital Sant Joan de Déu, 2, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - Matthew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Royal Hobart Hospital, Hobart, TAS 7001, Australia
| | - Marcel Mannens
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Marielle Alders
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada
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Martinez-Cayuelas E, Blanco-Kelly F, Lopez-Grondona F, Swafiri ST, Lopez-Rodriguez R, Losada-Del Pozo R, Mahillo-Fernandez I, Moreno B, Rodrigo-Moreno M, Casas-Alba D, Lopez-Gonzalez A, García-Miñaúr S, Ángeles Mori M, Pacio-Minguez M, Rikeros-Orozco E, Santos-Simarro F, Cruz-Rojo J, Quesada-Espinosa JF, Sanchez-Calvin MT, Sanchez-del Pozo J, Bernado Fonz R, Isidoro-Garcia M, Ruiz-Ayucar I, Alvarez-Mora MI, Blanco-Lago R, De Azua B, Eiris J, Garcia-Peñas JJ, Gil-Fournier B, Gomez-Lado C, Irazabal N, Lopez-Gonzalez V, Madrigal I, Malaga I, Martinez-Menendez B, Ramiro-Leon S, Garcia-Hoyos M, Prieto-Matos P, Lopez-Pison J, Aguilera-Albesa S, Alvarez S, Fernández-Jaén A, Llano-Rivas I, Gener-Querol B, Ayuso C, Arteche-Lopez A, Palomares-Bralo M, Cueto-González A, Valenzuela I, Martinez-Monseny A, Lorda-Sanchez I, Almoguera B. Clinical description, molecular delineation and genotype–phenotype correlation in 340 patients with KBG syndrome: addition of 67 new patients. J Med Genet 2022:jmg-2022-108632. [DOI: 10.1136/jmg-2022-108632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/06/2022] [Indexed: 11/30/2022]
Abstract
BackgroundKBG syndrome is a highly variable neurodevelopmental disorder and clinical diagnostic criteria have changed as new patients have been reported. Both loss-of-function sequence variants and large deletions (copy number variations, CNVs) involvingANKRD11cause KBG syndrome, but no genotype–phenotype correlation has been reported.Methods67 patients with KBG syndrome were assessed using a custom phenotypical questionnaire. Manifestations present in >50% of the patients and a ‘phenotypical score’ were used to perform a genotype–phenotype correlation in 340 patients from our cohort and the literature.ResultsNeurodevelopmental delay, macrodontia, triangular face, characteristic ears, nose and eyebrows were the most prevalentf (eatures. 82.8% of the patients had at least one of seven main comorbidities: hearing loss and/or otitis media, visual problems, cryptorchidism, cardiopathy, feeding difficulties and/or seizures. Associations found included a higher phenotypical score in patients with sequence variants compared with CNVs and a higher frequency of triangular face (71.1% vs 42.5% in CNVs). Short stature was more frequent in patients with exon 9 variants (62.5% inside vs 27.8% outside exon 9), and the prevalence of intellectual disability/attention deficit hyperactivity disorder/autism spectrum disorder was lower in patients with the c.1903_1907del variant (70.4% vs 89.4% other variants). Presence of macrodontia and comorbidities were associated with larger deletion sizes and hand anomalies with smaller deletions.ConclusionWe present a detailed phenotypical description of KBG syndrome in the largest series reported to date of 67 patients, provide evidence of a genotype–phenotype correlation between some KBG features and specificANKRD11variants in 340 patients, and propose updated clinical diagnostic criteria based on our findings.
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Jurkute N, Bertacchi M, Arno G, Tocco C, Kim US, Kruszewski AM, Avery RA, Bedoukian EC, Han J, Ahn SJ, Pontikos N, Acheson J, Davagnanam I, Bowman R, Kaliakatsos M, Gardham A, Wakeling E, Oluonye N, Reddy MA, Clark E, Rosser E, Amati-Bonneau P, Charif M, Lenaers G, Meunier I, Defoort S, Vincent-Delorme C, Robson AG, Holder GE, Jeanjean L, Martinez-Monseny A, Vidal-Santacana M, Dominici C, Gaggioli C, Giordano N, Caleo M, Liu GT, Webster AR, Studer M, Yu-Wai-Man P. Pathogenic NR2F1 variants cause a developmental ocular phenotype recapitulated in a mutant mouse model. Brain Commun 2021; 3:fcab162. [PMID: 34466801 PMCID: PMC8397830 DOI: 10.1093/braincomms/fcab162] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 11/28/2022] Open
Abstract
Pathogenic NR2F1 variants cause a rare autosomal dominant neurodevelopmental disorder referred to as the Bosch-Boonstra-Schaaf Optic Atrophy Syndrome. Although visual loss is a prominent feature seen in affected individuals, the molecular and cellular mechanisms contributing to visual impairment are still poorly characterized. We conducted a deep phenotyping study on a cohort of 22 individuals carrying pathogenic NR2F1 variants to document the neurodevelopmental and ophthalmological manifestations, in particular the structural and functional changes within the retina and the optic nerve, which have not been detailed previously. The visual impairment became apparent in early childhood with small and/or tilted hypoplastic optic nerves observed in 10 cases. High-resolution optical coherence tomography imaging confirmed significant loss of retinal ganglion cells with thinning of the ganglion cell layer, consistent with electrophysiological evidence of retinal ganglion cells dysfunction. Interestingly, for those individuals with available longitudinal ophthalmological data, there was no significant deterioration in visual function during the period of follow-up. Diffusion tensor imaging tractography studies showed defective connections and disorganization of the extracortical visual pathways. To further investigate how pathogenic NR2F1 variants impact on retinal and optic nerve development, we took advantage of an Nr2f1 mutant mouse disease model. Abnormal retinogenesis in early stages of development was observed in Nr2f1 mutant mice with decreased retinal ganglion cell density and disruption of retinal ganglion cell axonal guidance from the neural retina into the optic stalk, accounting for the development of optic nerve hypoplasia. The mutant mice showed significantly reduced visual acuity based on electrophysiological parameters with marked conduction delay and decreased amplitude of the recordings in the superficial layers of the visual cortex. The clinical observations in our study cohort, supported by the mouse data, suggest an early neurodevelopmental origin for the retinal and optic nerve head defects caused by NR2F1 pathogenic variants, resulting in congenital vision loss that seems to be non-progressive. We propose NR2F1 as a major gene that orchestrates early retinal and optic nerve head development, playing a key role in the maturation of the visual system.
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Affiliation(s)
- Neringa Jurkute
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Institute of Ophthalmology, University College London, London, UK
| | | | - Gavin Arno
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Institute of Ophthalmology, University College London, London, UK
| | - Chiara Tocco
- Université Côte d’Azur, CNRS, Inserm, iBV, Nice, France
| | - Ungsoo Samuel Kim
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Kim's Eye Hospital, Seoul, South Korea
| | - Adam M Kruszewski
- Department of Neurology, Hospital of the University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Robert A Avery
- Division of Ophthalmology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Ophthalmology, Perelman School of Medicine, Philadelphia, PA, USA
| | - Emma C Bedoukian
- Roberts Individualized Medical Genetics Center, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jinu Han
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung Jun Ahn
- Department of Radiology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Nikolas Pontikos
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Institute of Ophthalmology, University College London, London, UK
| | - James Acheson
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Trust, London, UK
| | - Indran Davagnanam
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Department of Brain Repair & Rehabilitation, UCL Queen Square Institute of Neurology, London, UK
| | - Richard Bowman
- Department of Ophthalmology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Marios Kaliakatsos
- Paediatric Neurology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Alice Gardham
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Emma Wakeling
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ngozi Oluonye
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Wolfson Neurodisability Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Maddy Ashwin Reddy
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Elaine Clark
- Department of Neuroscience, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Elisabeth Rosser
- Department of Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Patrizia Amati-Bonneau
- MitoLab Team, UMR CNRS 6015 - INSERM U1083, Institut MitoVasc, Angers University and Hospital, Angers, France
- Department of Biochemistry and Genetics, University Hospital Angers, Angers, France
- Genetics and Immuno-cell Therapy Team, Mohammed First University, Oujda, Morocco
| | - Majida Charif
- MitoLab Team, UMR CNRS 6015 - INSERM U1083, Institut MitoVasc, Angers University and Hospital, Angers, France
- National Center for Rare Diseases, Inherited Sensory Disorders, Gui de Chauliac Hospital, Montpellier, France
| | - Guy Lenaers
- MitoLab Team, UMR CNRS 6015 - INSERM U1083, Institut MitoVasc, Angers University and Hospital, Angers, France
| | - Isabelle Meunier
- Institut des Neurosciences de Montpellier, INSERM INSERM U1051, Université de Montpellier, Montpellier, France
| | - Sabine Defoort
- Service d'exploration de la vision et neuro-ophtalmologie, CHRU de Lille, Lille, France
| | | | - Anthony G Robson
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Institute of Ophthalmology, University College London, London, UK
| | - Graham E Holder
- Institute of Ophthalmology, University College London, London, UK
- Yong Loo Lin School of Medicine, Department of Ophthalmology, National University of Singapore, Singapore, Singapore
| | - Luc Jeanjean
- Department of Ophthalmology, University Hospital of Nimes, Nimes, France
| | | | | | - Chloé Dominici
- University Côte d'Azur, CNRS UMR7284, INSERM U1081, Institute for Research on Cancer and Aging, Nice, France
| | - Cedric Gaggioli
- University Côte d'Azur, CNRS UMR7284, INSERM U1081, Institute for Research on Cancer and Aging, Nice, France
| | | | | | - Grant T Liu
- Division of Ophthalmology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Ophthalmology, Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Andrew R Webster
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Institute of Ophthalmology, University College London, London, UK
| | | | - Patrick Yu-Wai-Man
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Institute of Ophthalmology, University College London, London, UK
- Cambridge Eye Unit, Addenbrooke’s Hospital, Cambridge University Hospitals, Cambridge, UK
- John van Geest Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
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Zarate YA, Bosanko KA, Thomas MA, Miller DT, Cusmano-Ozog K, Martinez-Monseny A, Curry CJ, Graham JM, Velsher L, Bekheirnia MR, Seidel V, Dedousis D, Mitchell AL, DiMarino AM, Riess A, Balasubramanian M, Fish JL, Caffrey AR, Fleischer N, Pierson TM, Lacro RV. Growth, development, and phenotypic spectrum of individuals with deletions of 2q33.1 involving SATB2. Clin Genet 2021; 99:547-557. [PMID: 33381861 DOI: 10.1111/cge.13912] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/18/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023]
Abstract
SATB2-Associated syndrome (SAS) is an autosomal dominant, multisystemic, neurodevelopmental disorder due to alterations in SATB2 at 2q33.1. A limited number of individuals with 2q33.1 contiguous deletions encompassing SATB2 (ΔSAS) have been described in the literature. We describe 17 additional individuals with ΔSAS, review the phenotype of 33 previously published individuals with 2q33.1 deletions (n = 50, mean age = 8.5 ± 7.8 years), and provide a comprehensive comparison to individuals with other molecular mechanisms that result in SAS (non-ΔSAS). Individuals in the ΔSAS group were often underweight for age (20/41 = 49%) with a progressive decline in weight (95% CI = -2.3 to -1.1, p < 0.0001) and height (95% CI = -2.3 to -1.0, p < 0.0001) Z-score means from birth to last available measurement. ΔSAS individuals were often noted to have a broad spectrum of facial dysmorphism. A composite image of ΔSAS individuals generated by automated image analysis was distinct as compared to matched controls and non-ΔSAS individuals. We also present additional genotype-phenotype correlations for individuals in the ΔSAS group such as an increased risk for aortic root/ascending aorta dilation and primary pulmonary hypertension for those individuals with contiguous gene deletions that include COL3A1/COL5A2 and BMPR2, respectively. Based on these findings, we provide additional care recommendations for individuals with ΔSAS variants.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Katherine A Bosanko
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Mary Ann Thomas
- Departments of Medical Genetics and Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Kristina Cusmano-Ozog
- Department of Pathology, Stanford University Medical Center, Stanford, California, USA
| | - Antonio Martinez-Monseny
- Department of Clinical Genetics and Rare Disease Paediatric Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Cynthia J Curry
- Genetic Medicine, Department of Pediatrics, University of California, San Francisco/Fresno, Fresno, California, USA
| | - John M Graham
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lea Velsher
- Genetics Division, North York General, Toronto, Ontario, Canada
| | - Mir Reza Bekheirnia
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Veronica Seidel
- Clinical Genetics, Department of Pediatrics, HGU Gregorio Marañón, Madrid, Spain
| | - Demitrios Dedousis
- Department of Genetics and Genome Sciences, University Hospitals Center for Human Genetics, Cleveland, Ohio, USA
| | - Anna L Mitchell
- Department of Genetics and Genome Sciences, University Hospitals Center for Human Genetics, Cleveland, Ohio, USA
| | - Amy M DiMarino
- Division of Pediatric Pulmonology, UH Rainbow Babies and Children's Hospital, Cleveland, Ohio, USA
| | - Angelika Riess
- Institute of Medical Genetics and Applied Genomics, Medical faculty, University of Tuebingen, Tuebingen, Germany
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, United States
| | - Aisling R Caffrey
- Health Outcomes, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | | | - Tyler Mark Pierson
- Departments of Pediatrics and Neurology, The Board of Governors Regenerative Medicine Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Ronald V Lacro
- Department of Cardiology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
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5
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Urreizti R, Lopez-Martin E, Martinez-Monseny A, Pujadas M, Castilla-Vallmanya L, Pérez-Jurado LA, Serrano M, Natera-de Benito D, Martínez-Delgado B, Posada-de-la-Paz M, Alonso J, Marin-Reina P, O'Callaghan M, Grinberg D, Bermejo-Sánchez E, Balcells S. Five new cases of syndromic intellectual disability due to KAT6A mutations: widening the molecular and clinical spectrum. Orphanet J Rare Dis 2020; 15:44. [PMID: 32041641 PMCID: PMC7011274 DOI: 10.1186/s13023-020-1317-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 10/18/2019] [Accepted: 01/28/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Pathogenic variants of the lysine acetyltransferase 6A or KAT6A gene are associated with a newly identified neurodevelopmental disorder characterized mainly by intellectual disability of variable severity and speech delay, hypotonia, and heart and eye malformations. Although loss of function (LoF) mutations were initially reported as causing this disorder, missense mutations, to date always involving serine residues, have recently been associated with a form of the disorder without cardiac involvement. RESULTS In this study we present five new patients, four with truncating mutations and one with a missense change and the only one not presenting with cardiac anomalies. The missense change [p.(Gly359Ser)], also predicted to affect splicing by in silico tools, was functionally tested in the patient's lymphocyte RNA revealing a splicing effect for this allele that would lead to a frameshift and premature truncation. CONCLUSIONS An extensive revision of the clinical features of these five patients revealed high concordance with the 80 cases previously reported, including developmental delay with speech delay, feeding difficulties, hypotonia, a high bulbous nose, and recurrent infections. Other features present in some of these five patients, such as cryptorchidism in males, syndactyly, and trigonocephaly, expand the clinical spectrum of this syndrome.
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Affiliation(s)
- Roser Urreizti
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, Barcelona, Spain. .,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain. .,Present address: Neurometabolic Unit, Hospital Sant Joan de Déu, Barcelona, Spain.
| | - Estrella Lopez-Martin
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institute of Rare Diseases Research (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Antonio Martinez-Monseny
- Department of Genetic and Molecular Medicine and Pediatric Rare Diseases Institute (IPER), Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Déu, Barcelona, Spain
| | - Montse Pujadas
- Genetics Unit, University Pompeu Fabra, Hospital del Mar Research Institute IMIM, Barcelona, Spain
| | - Laura Castilla-Vallmanya
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, Barcelona, Spain.,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Luis Alberto Pérez-Jurado
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Genetics Unit, University Pompeu Fabra, Hospital del Mar Research Institute IMIM, Barcelona, Spain.,Women's and Children's Hospital, South Australian Health and Medical Research Institute and The University of Adelaide, Adelaide, Australia
| | - Mercedes Serrano
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Beatriz Martínez-Delgado
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institute of Rare Diseases Research (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Manuel Posada-de-la-Paz
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institute of Rare Diseases Research (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Javier Alonso
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institute of Rare Diseases Research (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Purificación Marin-Reina
- Dysmorpholgy and Clinical Genetics, Division of Neonatology, Neonatal Research Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Mar O'Callaghan
- Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, Barcelona, Spain.,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Eva Bermejo-Sánchez
- Institute of Rare Diseases Research (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, Barcelona, Spain.,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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6
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Zarate YA, Bosanko KA, Caffrey AR, Bernstein JA, Martin DM, Williams MS, Berry-Kravis EM, Mark PR, Manning MA, Bhambhani V, Vargas M, Seeley AH, Estrada-Veras JI, van Dooren MF, Schwab M, Vanderver A, Melis D, Alsadah A, Sadler L, Van Esch H, Callewaert B, Oostra A, Maclean J, Dentici ML, Orlando V, Lipson M, Sparagana SP, Maarup TJ, Alsters SI, Brautbar A, Kovitch E, Naidu S, Lees M, Smith DM, Turner L, Raggio V, Spangenberg L, Garcia-Miñaúr S, Roeder ER, Littlejohn RO, Grange D, Pfotenhauer J, Jones MC, Balasubramanian M, Martinez-Monseny A, Blok LS, Gavrilova R, Fish JL. Mutation update for the SATB2 gene. Hum Mutat 2019; 40:1013-1029. [PMID: 31021519 DOI: 10.1002/humu.23771] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 02/04/2019] [Revised: 04/10/2019] [Accepted: 04/22/2019] [Indexed: 12/20/2022]
Abstract
SATB2-associated syndrome (SAS) is an autosomal dominant neurodevelopmental disorder caused by alterations in the SATB2 gene. Here we present a review of published pathogenic variants in the SATB2 gene to date and report 38 novel alterations found in 57 additional previously unreported individuals. Overall, we present a compilation of 120 unique variants identified in 155 unrelated families ranging from single nucleotide coding variants to genomic rearrangements distributed throughout the entire coding region of SATB2. Single nucleotide variants predicted to result in the occurrence of a premature stop codon were the most commonly seen (51/120 = 42.5%) followed by missense variants (31/120 = 25.8%). We review the rather limited functional characterization of pathogenic variants and discuss current understanding of the consequences of the different molecular alterations. We present an expansive phenotypic review along with novel genotype-phenotype correlations. Lastly, we discuss current knowledge of animal models and present future prospects. This review should help provide better guidance for the care of individuals diagnosed with SAS.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Katherine A Bosanko
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Aisling R Caffrey
- Health Outcomes, College of Pharmacy, Department of Pharmacy Practice, University of Rhode Island, Kingston, Rhode Island
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Donna M Martin
- Departments of Pediatrics and Human Genetics, The University of Michigan, Ann Arbor, Michigan
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Elizabeth M Berry-Kravis
- Departments of Pediatrics, Neurological Sciences, Biochemistry, Rush University Medical Center, Chicago, Illinois
| | - Paul R Mark
- Division of Medical Genetics, Spectrum Health, Grand Rapids, Michigan
| | - Melanie A Manning
- Departments of Pathology and Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Vikas Bhambhani
- Division of Genetics and Genomic Medicine, Children's Hospital and Clinics of Minnesota, Minneapolis, Minnesota
| | - Marcelo Vargas
- Division of Genetics and Genomic Medicine, Children's Hospital and Clinics of Minnesota, Minneapolis, Minnesota
| | - Andrea H Seeley
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Juvianee I Estrada-Veras
- Murtha Cancer Center Research Program, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland.,Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, Maryland.,Pediatric subspecialty-Medical Genetics Service, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Marieke F van Dooren
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Maria Schwab
- Genetics Division, Joseph Sanzari Children's Hospital, Hackensack University Medical Center, Hackensack, New Jersey
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniela Melis
- Department of Translational Medical Science, Section of Pediatrics, Federico II University, Naples, Italy
| | - Adnan Alsadah
- Center for Personalized Genetic Healthcare, Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Laurie Sadler
- Division of Genetics, Oishei Children's Hospital, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, New York
| | - Hilde Van Esch
- Department of Human Genetics, University Hospitals Leuven, KU, Leuven, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ann Oostra
- Department of Pediatric Neurology, Ghent University Hospital, Ghent, Belgium
| | - Jane Maclean
- Pediatric Neurology, Palo Alto Medical Foundation, San Jose, California
| | - Maria Lisa Dentici
- Medical Genetics, Academic Department of Pediatrics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Valeria Orlando
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Mark Lipson
- Department of Genetics, Kaiser Permanente, Sacramento, California
| | - Steven P Sparagana
- Department of Neurology, Texas Scottish Rite Hospital for Children, Dallas, Texas
| | - Timothy J Maarup
- Department of Genetics, Kaiser Permanente, Los Angeles, California
| | - Suzanne Im Alsters
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ariel Brautbar
- Department of Genetics, Cook Chldren's Medical Center, Fort Worth, Texas
| | | | - Sakkubai Naidu
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland
| | - Melissa Lees
- Department of Clinical Genetics, Great Ormond Street Hospital for Children, London, UK
| | | | - Lesley Turner
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Víctor Raggio
- Departamento de Genética, Facultad de Medicina, Montevideo, Uruguay
| | | | - Sixto Garcia-Miñaúr
- Department of Medical Genetics, Hospital Universitario La Paz, Madrid, Spain
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Rebecca O Littlejohn
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Dorothy Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medcine, St Louis, Missouri
| | - Jean Pfotenhauer
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Marilyn C Jones
- Division of Genetics, Department of Pediatrics, University of California, San Diego and Rady Children's Hospital, San Diego, California
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Western Bank, Sheffield, UK
| | - Antonio Martinez-Monseny
- Genetics and Molecular Medicine Department, Rare Disease Pediatric Unit, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Lot Snijders Blok
- Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands.,Language & Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Ralitza Gavrilova
- Departments of Neurology and Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts
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7
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Martinez-Monseny A, Cuadras D, Bolasell M, Muchart J, Arjona C, Borregan M, Algrabli A, Montero R, Artuch R, Velázquez-Fragua R, Macaya A, Pérez-Cerdá C, Pérez-Dueñas B, Pérez B, Serrano M. From gestalt to gene: early predictive dysmorphic features of PMM2-CDG. J Med Genet 2018; 56:236-245. [DOI: 10.1136/jmedgenet-2018-105588] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 12/13/2022]
Abstract
IntroductionPhosphomannomutase-2 deficiency (PMM2-CDG) is associated with a recognisable facial pattern. There are no early severity predictors for this disorder and no phenotype–genotype correlation. We performed a detailed dysmorphology evaluation to describe facial gestalt and its changes over time, to train digital recognition facial analysis tools and to identify early severity predictors.MethodsPaediatric PMM2-CDG patients were evaluated and compared with controls. A computer-assisted recognition tool was trained. Through the evaluation of dysmorphic features (DFs), a simple categorisation was created and correlated with clinical and neurological scores, and neuroimaging.ResultsDysmorphology analysis of 31 patients (4–19 years of age) identified eight major DFs (strabismus, upslanted eyes, long fingers, lipodystrophy, wide mouth, inverted nipples, long philtrum and joint laxity) with predictive value using receiver operating characteristic (ROC) curveanalysis (p<0.001). Dysmorphology categorisation using lipodystrophy and inverted nipples was employed to divide patients into three groups that are correlated with global clinical and neurological scores, and neuroimaging (p=0.005, 0.003 and 0.002, respectively). After Face2Gene training, PMM2-CDG patients were correctly identified at different ages.ConclusionsPMM2-CDG patients’ DFs are consistent and inform about clinical severity when no clear phenotype–genotype correlation is known. We propose a classification of DFs into major and minor with diagnostic risk implications. At present, Face2Gene is useful to suggest PMM2-CDG. Regarding the prognostic value of DFs, we elaborated a simple severity dysmorphology categorisation with predictive value, and we identified five major DFs associated with clinical severity. Both dysmorphology and digital analysis may help physicians to diagnose PMM2-CDG sooner.
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