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Zreibe K, Kanner CH, Uher D, Beard G, Patterson M, Harris M, Doerger J, Calamia S, Chung WK, Montes J. Characterizing ambulatory function in children with PPP2R5D-related neurodevelopmental disorder. Gait Posture 2024; 110:77-83. [PMID: 38547676 PMCID: PMC11056288 DOI: 10.1016/j.gaitpost.2024.03.012] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/29/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
BACKGROUND Individuals with PPP2R5D-related neurodevelopmental disorder have an atypical gait pattern characterized by ataxia and incoordination. Structured, quantitative assessments are needed to further understand the impact of these impairments on function. RESEARCH QUESTION How do gait parameters and ambulatory function of individuals with PPP2R5D-related neurodevelopmental disorder compare to age and sex matched healthy norms? METHODS Twenty-six individuals with PPP2R5D pathogenic genetic variants participated in this observational, single visit study. Participants completed at least one of the following gait assessments: quantitative gait analysis at three different speeds (preferred pace walking (PPW), fast paced walking (FPW) and running, six-minute walk test (6MWT), 10-meter walk run (10MWR), and timed up and go (TUG). Descriptive statistics were used to summarize gait variables. Percent of predicted values were calculated using published norms. Paired t-tests and regression analyses were used to compare gait variables. RESULTS The median age of the participants was 8 years (range 4-27) and eighteen (69.2 %) were female. Individuals with PPP2R5D-related neurodevelopmental disorder walked slower and with a wider base of support than predicted for their age and sex. Stride velocity ranged from 48.9 % to 70.1 % and stride distance from 58.5 % to 81.9 % of predicted during PPW. Percent of predicted distance walked on the 6MWT ranged from 30.6 % to 71.1 % representing varied walking impairment. Increases in stride distance, not cadence, were associated with changes in stride velocity in FPW (R2 = 0.675, p =< 0.001) and running conditions (R2 = 0.918, p =< 0.001). SIGNIFICANCE We quantitatively assessed the abnormal gait in individuals with PPP2R5D-related neurodevelopmental disorder. These impairments may affect ability to adapt to environmental changes and participation in daily life. Rehabilitative interventions targeting gait speed and balance may improve function and safety for individuals with PPP2R5D-related neurodevelopmental disorder.
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Affiliation(s)
- Kyle Zreibe
- Department of Rehabilitation, UHealth-Jackson Holtz Children's Hospital, Miami, FL, USA; Department of Rehabilitation & Regenerative Medicine, Columbia University Irving Medical Center, New York, NY, USA.
| | - Cara H Kanner
- Department of Rehabilitation & Regenerative Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - David Uher
- Department of Biobehavioral Sciences, Teachers College, Columbia University, New York, NY, USA
| | - Gabriella Beard
- Department of Rehabilitation & Regenerative Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Madison Patterson
- Department of Rehabilitation & Regenerative Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Matthew Harris
- Department of Rehabilitation & Regenerative Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Jerome Doerger
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Sean Calamia
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA USA
| | - Jacqueline Montes
- Department of Rehabilitation & Regenerative Medicine, Columbia University Irving Medical Center, New York, NY, USA
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Sudnawa KK, Garber A, Cohen R, Calamia S, Kanner CH, Montes J, Bain JM, Fee RJ, Chung WK. Clinical phenotypic spectrum of CTNNB1 neurodevelopmental disorder. Clin Genet 2024; 105:523-532. [PMID: 38247296 DOI: 10.1111/cge.14487] [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: 12/16/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
Pathogenic heterozygous loss of function variants in CTNNB1 are associated with CTNNB1 neurodevelopmental disorder. We report the clinical phenotype of individuals with CTNNB1 neurodevelopmental disorder using both caregiver-reported data (medical history, adaptive function, quality of life, and behavior issues) and in-person clinical assessments (neurological, motor, and cognitive function) in 32 individuals with likely pathogenic or pathogenic CTNNB1 variants. Most individuals had truncal hypotonia, muscle weakness, hypertonia, dystonia, microcephaly, and many had a history of tethered cord. Visual problems included strabismus, hyperopia, and familial exudative vitreoretinopathy. Half of individuals walked without an assistive device. The mean Gross Motor Functional Measure-66 score was 56.6 (SD = 14.8). Average time to complete Nine-Hole Peg Test was slower than norms. Mean general conceptual ability composite scores from Differential Ability Scales Second Edition were very low (M = 58.3, SD = 11.3). Fifty-five percent of individuals had low adaptive functioning based on the Vineland Adaptive Behavioral Scales. Based upon the Child Behavior Checklist total problems score, the majority (65%) of individuals had behavioral challenges. The mean overall Quality of Life Inventory-Disability score was 81.7 (SD = 11.9). These data provide a detailed characterization of clinical features in individuals with CTNNB1 neurodevelopmental disorder.
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Affiliation(s)
- Khemika K Sudnawa
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Pramongkutklao Hospital and Pramongkutklao College of Medicine, Bangkok, Thailand
| | - Alison Garber
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Ryan Cohen
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Sean Calamia
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Cara H Kanner
- Department of Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Jacqueline Montes
- Department of Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Jennifer M Bain
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Robert J Fee
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Hospital, New York, New York, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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3
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Layo-Carris DE, Lubin EE, Sangree AK, Clark KJ, Durham EL, Gonzalez EM, Smith S, Angireddy R, Wang XM, Weiss E, Mendoza-Londono R, Dupuis L, Damseh N, Velasco D, Valenzuela I, Codina-Solà M, Ziats C, Have J, Clarkson K, Steel D, Kurian M, Barwick K, Carrasco D, Dagli AI, Nowaczyk MJM, Hančárová M, Bendová Š, Prchalova D, Sedláček Z, Baxová A, Nowak CB, Douglas J, Chung WK, Longo N, Platzer K, Klöckner C, Averdunk L, Wieczorek D, Krey I, Zweier C, Reis A, Balci T, Simon M, Kroes HY, Wiesener A, Vasileiou G, Marinakis NM, Veltra D, Sofocleous C, Kosma K, Traeger Synodinos J, Voudris KA, Vuillaume ML, Gueguen P, Derive N, Colin E, Battault C, Au B, Delatycki M, Wallis M, Gallacher L, Majdoub F, Smal N, Weckhuysen S, Schoonjans AS, Kooy RF, Meuwissen M, Cocanougher BT, Taylor K, Pizoli CE, McDonald MT, James P, Roeder ER, Littlejohn R, Borja NA, Thorson W, King K, Stoeva R, Suerink M, Nibbeling E, Baskin S, L E Guyader G, Kaplan J, Muss C, Carere DA, Bhoj EJK, Bryant LM. Expanded phenotypic spectrum of neurodevelopmental and neurodegenerative disorder Bryant-Li-Bhoj syndrome with 38 additional individuals. Eur J Hum Genet 2024:10.1038/s41431-024-01610-1. [PMID: 38678163 DOI: 10.1038/s41431-024-01610-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
Bryant-Li-Bhoj syndrome (BLBS), which became OMIM-classified in 2022 (OMIM: 619720, 619721), is caused by germline variants in the two genes that encode histone H3.3 (H3-3A/H3F3A and H3-3B/H3F3B) [1-4]. This syndrome is characterized by developmental delay/intellectual disability, craniofacial anomalies, hyper/hypotonia, and abnormal neuroimaging [1, 5]. BLBS was initially categorized as a progressive neurodegenerative syndrome caused by de novo heterozygous variants in either H3-3A or H3-3B [1-4]. Here, we analyze the data of the 58 previously published individuals along 38 unpublished, unrelated individuals. In this larger cohort of 96 people, we identify causative missense, synonymous, and stop-loss variants. We also expand upon the phenotypic characterization by elaborating on the neurodevelopmental component of BLBS. Notably, phenotypic heterogeneity was present even amongst individuals harboring the same variant. To explore the complex phenotypic variation in this expanded cohort, the relationships between syndromic phenotypes with three variables of interest were interrogated: sex, gene containing the causative variant, and variant location in the H3.3 protein. While specific genotype-phenotype correlations have not been conclusively delineated, the results presented here suggest that the location of the variants within the H3.3 protein and the affected gene (H3-3A or H3-3B) contribute more to the severity of distinct phenotypes than sex. Since these variables do not account for all BLBS phenotypic variability, these findings suggest that additional factors may play a role in modifying the phenotypes of affected individuals. Histones are poised at the interface of genetics and epigenetics, highlighting the potential role for gene-environment interactions and the importance of future research.
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Affiliation(s)
- Dana E Layo-Carris
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Emily E Lubin
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Annabel K Sangree
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kelly J Clark
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily L Durham
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth M Gonzalez
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarina Smith
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rajesh Angireddy
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiao Min Wang
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Erin Weiss
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Lucie Dupuis
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Nadirah Damseh
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Danita Velasco
- Children's Nebraska, University of Nebraska Medical Center, Omaha, NE, USA
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics and Rare Disease Unit Hospital Vall d'Hebron, Barcelona, Spain
- Medicine Genetics Group, Vall Hebron Research Institute, Barcelona, Spain
| | - Marta Codina-Solà
- Department of Clinical and Molecular Genetics and Rare Disease Unit Hospital Vall d'Hebron, Barcelona, Spain
- Medicine Genetics Group, Vall Hebron Research Institute, Barcelona, Spain
| | | | - Jaclyn Have
- Shodair Children's Hospital, Helena, MT, USA
| | | | - Dora Steel
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Manju Kurian
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Katy Barwick
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Diana Carrasco
- Department of Clinical Genetics, Cook Children's Hospital, Fort Worth, TX, USA
| | - Aditi I Dagli
- Orlando Health, Arnold Palmer Hospital For Children, Orlando, FL, USA
| | - M J M Nowaczyk
- McMaster University Medical Centre, Hamilton, ON, Canada
| | - Miroslava Hančárová
- Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Šárka Bendová
- Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Darina Prchalova
- Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Zdeněk Sedláček
- Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Alica Baxová
- Charles University First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Catherine Bearce Nowak
- Division of Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, MA, USA
| | | | - Wendy K Chung
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | | | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Luisa Averdunk
- Institute of Human Genetics, Heinrich-Heine-University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Heinrich-Heine-University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - Ilona Krey
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
- Department of Human Genetics, Inselspital Bern, University of Bern, Bern, Switzerland
| | - Andre Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Tugce Balci
- University of Western Ontario, London, ON, Canada
| | - Marleen Simon
- Department of Genetics, University Medical Center, Utrecht, Netherlands
| | - Hester Y Kroes
- Department of Genetics, University Medical Center, Utrecht, Netherlands
| | - Antje Wiesener
- Department of Genetics, University Medical Center, Utrecht, Netherlands
| | - Georgia Vasileiou
- Department of Genetics, University Medical Center, Utrecht, Netherlands
| | - Nikolaos M Marinakis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Danai Veltra
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Christalena Sofocleous
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantina Kosma
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Joanne Traeger Synodinos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos A Voudris
- Second Department of Paediatrics, University of Athens, 'P & A Kyriakou' Children's Hospital, Athens, Greece
| | - Marie-Laure Vuillaume
- Service de Génétique, CHU de Tours, Tours, France
- UMR1253, iBrain, Inserm, University of Tours, Tours, France
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA, Paris, France
| | - Paul Gueguen
- Service de Génétique, CHU de Tours, Tours, France
- UMR1253, iBrain, Inserm, University of Tours, Tours, France
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA, Paris, France
| | - Nicolas Derive
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA, Paris, France
| | - Estelle Colin
- Service de Génétique Médicale, CHU d'Angers, Angers, France
| | | | - Billie Au
- University of Calgary, Calgary, AB, Canada
| | - Martin Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, TAS, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Fatma Majdoub
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Medical Genetics Department, University Hedi Chaker Hospital of Sfax, Sfax, Tunisia
| | - Noor Smal
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sarah Weckhuysen
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Pediatric Neurology, University Hospital Antwerp, Antwerp, Belgium
- Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium
- NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - An-Sofie Schoonjans
- Department of Pediatric Neurology, University Hospital Antwerp, Antwerp, Belgium
- Department of Pediatrics, Duke University Hospital, Durham, NC, USA
| | - R Frank Kooy
- Center of Medical Genetics, Antwerp University Hospital/University of Antwerp, Edegem, Belgium
| | - Marije Meuwissen
- Department of Pediatrics, Duke University Hospital, Durham, NC, USA
- Center of Medical Genetics, Antwerp University Hospital/University of Antwerp, Edegem, Belgium
| | | | - Kathryn Taylor
- Division of Pediatric Neurology, Duke University Hospital, Durham, NC, USA
| | - Carolyn E Pizoli
- Division of Pediatric Neurology, Duke University Hospital, Durham, NC, USA
| | - Marie T McDonald
- Division of Medical Genetics, Duke University Hospital, Durham, NC, USA
| | - Philip James
- DMG Children's Rehabilitative Services, Phoenix, AZ, USA
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA
| | - Rebecca Littlejohn
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA
| | - Nicholas A Borja
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Willa Thorson
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kristine King
- Genetics Department, Mary Bridge Children's Hospital, Multicare Health System, Tacoma, WA, USA
| | - Radka Stoeva
- Medical genetics department, Centre Hospitalier, Le Mans, France
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Esther Nibbeling
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Stephanie Baskin
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Gwenaël L E Guyader
- Service de Génétique médicale, Centre Labellisé Anomalies du Développement-Ouest Site, Poitiers, France
| | | | | | | | - Elizabeth J K Bhoj
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Laura M Bryant
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
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Jutla A, Harvey L, Veenstra-VanderWeele J, Chung WK. Motor difficulties in 16p11.2 copy number variation. Autism Res 2024. [PMID: 38660979 DOI: 10.1002/aur.3132] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/17/2024] [Indexed: 04/26/2024]
Abstract
The rare genetic variants 16p11.2 duplication and 16p11.2 deletion have opposing effects on brain structure and function, yet are associated with broadly similar clinical phenotypes that include autism, intellectual impairment, psychiatric illness, and motor difficulties. In recent years, studies have identified subtle distinctions between the phenotypic effects of 16p11.2 duplication and 16p11.2 deletion with respect to patterns of autism, intellectual impairment, and psychiatric illness. However, although divergent phenotypic findings in some motor domains have been reported, no study has yet made a comprehensive comparison of motor difficulties between 16p11.2 deletion and 16p11.2 duplication carriers to elucidate points of convergence and divergence. We sought to make such a comparison in a group of 133 16p11.2 deletion carriers, 122 duplication carriers, and 388 familial controls, hypothesizing that motor impairment would overall be greater in deletion than duplication carriers. In a series of regression models, we found that 16p11.2 deletion status tended to predict greater impairment along indices of gross motor function, but less impairment along indices of fine motor function. These findings point to a potential pattern of performance difficulties that could be investigated in future studies. Elucidating motor differences between 16p11.2 duplication and 16p11.2 deletion carriers may help in understanding the complex effect of 16p11.2 copy number variation and other rare genetic causes of autism.
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Affiliation(s)
- Amandeep Jutla
- Department of Psychiatry, Columbia University, New York, New York, USA
- New York State Psychiatric Institute, New York, New York, USA
| | - Loraine Harvey
- City University of New York School of Medicine, New York, New York, USA
| | - Jeremy Veenstra-VanderWeele
- Department of Psychiatry, Columbia University, New York, New York, USA
- New York State Psychiatric Institute, New York, New York, USA
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University, New York, New York, USA
- Simons Foundation, New York, New York, USA
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Klitzman R, Bezborodko E, Chung WK, Appelbaum PS. Views of Genetic Testing for Autism Among Autism Self-Advocates: A Qualitative Study. AJOB Empir Bioeth 2024:1-18. [PMID: 38643392 DOI: 10.1080/23294515.2024.2336903] [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] [Indexed: 04/22/2024]
Abstract
BACKGROUND Autism self-advocates' views regarding genetic tests for autism are important, but critical questions about their perspectives arise. METHODS We interviewed 11 autism self-advocates, recruited through autism self-advocacy websites, for 1 h each. RESULTS Interviewees viewed genetic testing and its potential pros and cons through the lens of their own indiviudal perceived challenges, needs and struggles, especially concerning stigma and discrimination, lack of accommodations and misunderstandings from society about autism, their particular needs for services, and being blamed by others and by themselves for autistic traits. Their views of genetic testing tended not to be binary, but rather depended on how the genetic test results would be used. Interviewees perceived pros of genetic testing both in general and with regard to themselves (e.g., by providing "scientific proof" of autism as a diagnosis and possibly increasing availability of services). But they also perceived disadvantages and limitations of testing (e.g., possible eugenic applications). Participants distinguished between what they felt would be best for themselves and for the autistic community as a whole. When asked if they would undergo testing for themselves, if offered, interviewees added several considerations (e.g., undergoing testing because they support science in general). Interviewees were divided whether a genetic diagnosis would or should reduce self-blame, and several were wary of testing unless treatment, prevention or societal attitudes changed. Weighing these competing pros and cons could be difficult. CONCLUSIONS This study, the first to use in-depth qualitative interviews to assess views of autism self-advocates regarding genetic testing, highlights key complexities. Respondents felt that such testing is neither wholly good or bad in itself, but rather may be acceptable depending on how it is used, and should be employed in beneficial, not harmful ways. These findings have important implications for practice, education of multiple stakeholders, research, and policy.
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Affiliation(s)
- Robert Klitzman
- Department of Psychiatry, Columbia University, New York, NY, USA
| | | | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul S Appelbaum
- Department of Law Ethics and Psychiatry, NYP Columbia University Irving Medical, New York Presbyterian Hospital, New York, NY, USA
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Chung WK, Kanne SM, Hu Z. An Opportunity to Fill a Gap for Newborn Screening of Neurodevelopmental Disorders. Int J Neonatal Screen 2024; 10:33. [PMID: 38651398 PMCID: PMC11036277 DOI: 10.3390/ijns10020033] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
Screening newborns using genome sequencing is being explored due to its potential to expand the list of conditions that can be screened. Previously, we proposed the need for large-scale pilot studies to assess the feasibility of screening highly penetrant genetic neurodevelopmental disorders. Here, we discuss the initial experience from the GUARDIAN study and the systemic gaps in clinical services that were identified in the early stages of the pilot study.
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Affiliation(s)
- Wendy K. Chung
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Stephen M. Kanne
- Department of Psychiatry, Weill Cornell Medical College, New York, NY 10065, USA;
| | - Zhanzhi Hu
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
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Trivedi MS, Manley H, Yi H, Silverman T, Chung WK, Appelbaum PS, Starck R, Schecter I, Kukafka R, Crew KD. Pilot study of a decision aid on BRCA1/2 genetic testing among Orthodox Jewish women. Fam Cancer 2024:10.1007/s10689-024-00371-6. [PMID: 38609522 DOI: 10.1007/s10689-024-00371-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/05/2024] [Indexed: 04/14/2024]
Abstract
INTRODUCTION Orthodox Jewish women face unique social, cultural, and religious factors that may influence uptake of BRCA1/2 genetic testing. We examined the impact of a web-based decision aid (DA) on BRCA1/2 genetic testing intention/completion among Orthodox Jewish women. We conducted a single-arm pilot study among 50 Orthodox Jewish women who were given access to a web-based DA entitled RealRisks and administered serial surveys at baseline and 1 and 6 months after exposure to the DA. Descriptive statistics were conducted for baseline characteristics and study measures. Comparisons were made to assess changes in study measures over time. Fifty Orthodox Jewish women enrolled in the study with a mean age of 43.9 years (standard deviation [SD] 14.6), 70% Modern Orthodox, 2% with personal history of breast cancer, and 68% and 16% with a family history of breast or ovarian cancer, respectively. At baseline, 27 (54%) participants intended to complete genetic testing. Forty-three participants (86%) completed RealRisks and the 1-month survey and 38 (76%) completed the 6-month survey. There was a significant improvement in BRCA1/2 genetic testing knowledge and decrease in decisional conflict after exposure to the DA. At 1 month, only 20 (46.5%) completed or intended to complete genetic testing (p = 0.473 compared to baseline). While the DA improved genetic testing knowledge and reduced decisional conflict, genetic testing intention/completion did not increase over time. Future interventions should directly address barriers to BRCA1/2 genetic testing uptake and include input from leaders in the Orthodox Jewish community. CLINICALTRIALS GOV ID NCT03624088 (8/7/18).
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Affiliation(s)
- Meghna S Trivedi
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, 161 Fort Washington Avenue HIP 10, New York, NY, 10032, USA.
| | - Haley Manley
- College of Law, DePaul University, Chicago, IL, USA
| | - Haeseung Yi
- Department of Health and Behavior Studies, Teachers College, Columbia University, New York, NY, USA
| | - Thomas Silverman
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Rebecca Starck
- Institute for Applied Research and Community Collaboration (ARCC), Spring Valley, NY, USA
| | - Isaac Schecter
- Institute for Applied Research and Community Collaboration (ARCC), Spring Valley, NY, USA
- Achieve Behavioral Health, Monsey, NY, USA
| | - Rita Kukafka
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Katherine D Crew
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, 161 Fort Washington Avenue HIP 10, New York, NY, 10032, USA
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8
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Sabatello M, Bakken S, Chung WK, Cohn E, Crew KD, Kiryluk K, Kukafka R, Weng C, Appelbaum PS. Return of polygenic risk scores in research: Stakeholders' views on the eMERGE-IV study. HGG Adv 2024; 5:100281. [PMID: 38414240 PMCID: PMC10950748 DOI: 10.1016/j.xhgg.2024.100281] [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: 08/24/2023] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
Research on polygenic risk scores (PRSs) for common, genetically complex chronic diseases aims to improve health-related predictions, tailor risk-reducing interventions, and improve health outcomes. Yet, the study and use of PRSs in clinical settings raise equity, clinical, and regulatory challenges that can be greater for individuals from historically marginalized racial, ethnic, and other minoritized communities. As part of the National Human Genome Research Institute-funded Electronic Medical Records and Genomics IV Network, we conducted online focus groups with patients/community members, clinicians, and members of institutional review boards to explore their views on key issues, including PRS research, return of PRS results, clinical translation, and barriers and facilitators to health behavioral changes in response to PRS results. Across stakeholder groups, our findings indicate support for PRS development and a strong interest in having PRS results returned to research participants. However, we also found multi-level barriers and significant differences in stakeholders' views about what is needed and possible for successful implementation. These include researcher-participant interaction formats, health and genomic literacy, and a range of structural barriers, such as financial instability, insurance coverage, and the absence of health-supporting infrastructure and affordable healthy food options in poorer neighborhoods. Our findings highlight the need to revisit and implement measures in PRS studies (e.g., incentives and resources for follow-up care), as well as system-level policies to promote equity in genomic research and health outcomes.
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Affiliation(s)
- Maya Sabatello
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York, NY, USA; Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, New York, NY, USA.
| | - Suzanne Bakken
- School of Nursing and Department of Biomedical Informatic, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth Cohn
- Northwell Health 600 Community Drive, Manhasset, NY, USA
| | - Katherine D Crew
- Department of Medicine and Epidemiology, Columbia University, New York, NY 10032, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Rita Kukafka
- Departments of Biomedical Informatics and Sociomedical Sciences, Columbia University, New York, NY 10032, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
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9
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Hui D, Dudek S, Kiryluk K, Walunas TL, Kullo IJ, Wei WQ, Tiwari HK, Peterson JF, Chung WK, Davis B, Khan A, Kottyan L, Limdi NA, Feng Q, Puckelwartz MJ, Weng C, Smith JL, Karlson EW, Center RG, Jarvik GP, Ritchie MD. Risk factors affecting polygenic score performance across diverse cohorts. medRxiv 2024:2023.05.10.23289777. [PMID: 38645167 PMCID: PMC11030495 DOI: 10.1101/2023.05.10.23289777] [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] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Apart from ancestry, personal or environmental covariates may contribute to differences in polygenic score (PGS) performance. We analyzed effects of covariate stratification and interaction on body mass index (BMI) PGS (PGS BMI ) across four cohorts of European (N=491,111) and African (N=21,612) ancestry. Stratifying on binary covariates and quintiles for continuous covariates, 18/62 covariates had significant and replicable R 2 differences among strata. Covariates with the largest differences included age, sex, blood lipids, physical activity, and alcohol consumption, with R 2 being nearly double between best and worst performing quintiles for certain covariates. 28 covariates had significant PGS BMI -covariate interaction effects, modifying PGS BMI effects by nearly 20% per standard deviation change. We observed overlap between covariates that had significant R 2 differences among strata and interaction effects - across all covariates, their main effects on BMI were correlated with their maximum R 2 differences and interaction effects (0.56 and 0.58, respectively), suggesting high-PGS BMI individuals have highest R 2 and increase in PGS effect. Using quantile regression, we show the effect of PGS BMI increases as BMI itself increases, and that these differences in effects are directly related to differences in R 2 when stratifying by different covariates. Given significant and replicable evidence for context-specific PGS BMI performance and effects, we investigated ways to increase model performance taking into account non-linear effects. Machine learning models (neural networks) increased relative model R 2 (mean 23%) across datasets. Finally, creating PGS BMI directly from GxAge GWAS effects increased relative R 2 by 7.8%. These results demonstrate that certain covariates, especially those most associated with BMI, significantly affect both PGS BMI performance and effects across diverse cohorts and ancestries, and we provide avenues to improve model performance that consider these effects.
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10
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Wynn J, Karlsen A, Huber B, Levine A, Salem A, White LC, Luby M, Bezborodko E, Xiao S, Chung WK, Klitzman RL, Appelbaum PS. Impact of a Genetic Diagnosis for a Child's Autism on Parental Perceptions. J Autism Dev Disord 2024:10.1007/s10803-024-06273-x. [PMID: 38578549 DOI: 10.1007/s10803-024-06273-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2024] [Indexed: 04/06/2024]
Abstract
Genetic testing is recommended as part of an autism assessment, and most parents support genetic testing for their minor children. However, the impact on parents of receiving a monogenetic/ copy number variant diagnosis for autism in their child is not well understood. To explore this, we surveyed and interviewed parents of children in the SPARK study, a study of autism that includes genetic testing. Surveys were administered one month before and one and 12 months after parents received their child's genetic result. Interviews were conducted approximately one month after results disclosure. A genetic diagnosis (GD) for their child appeared to reduce parents' sense of self-blame and feelings of guilt, and this impact was relatively stable. The data also indicate a modest impact on parents' actions related to the condition, perceptions of themselves, and some aspects of life planning for their child, as measured by quantitative instruments at one month and 12 months after receipt of results. Other measures of parental identity and expectations for their child, in contrast, showed little change following receipt of genetic findings. Overall, parents who were told that no GD was identified showed minimal changes in their responses over time. These results suggest a discernable but relatively limited impact of genetic test results on parents of children with autism. These results should be reassuring to clinicians caring for children with autism and are consistent with studies in other areas of medicine that have suggested that genetic results tend to have fewer effects-negative or positive-than were anticipated.
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Affiliation(s)
- Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.
| | - Anna Karlsen
- Columbia University Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Benjamin Huber
- Department of Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alina Levine
- Department of Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Amanie Salem
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | | | | | - Ekaterina Bezborodko
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Simons Foundation, New York, NY, USA
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert L Klitzman
- Department of Psychiatry and Masters of Bioethics Program, and New York State Psychiatric Institute, Columbia University, New York, NY, USA
| | - Paul S Appelbaum
- Department of Psychiatry, and New York State Psychiatric Institute, Columbia University Irving Medical Center, New York, NY, USA
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11
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Kaiyrzhanov R, Rad A, Lin SJ, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Karimiani EG, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Tayfun GA, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Monajemi GB, Mohammadi P, Samie S, Banu SH, Pinto Basto J, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Issa AH, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain 2024; 147:1436-1456. [PMID: 37951597 PMCID: PMC10994533 DOI: 10.1093/brain/awad380] [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: 05/18/2022] [Revised: 09/13/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Using exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with myristic acid alkyne (YnMyr) chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), aged 1-50 years, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%) and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%) and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%) and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each) as well as hypertrophy of the clava (24%) were common neuroimaging findings. Acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localization and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-myristoylation was similarly affected in acbd6-deficient zebrafish and X. tropicalis models, including Fus, Marcks and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders.
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Affiliation(s)
- Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Aboulfazl Rad
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar 009851, Iran
- Tübingen Hearing Research Centre, Department of Otolaryngology, Head and Neck Surgery, Eberhard Karls University, 72076 Tübingen, Germany
| | - Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | | | - Wouter W Kallemeijn
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London W12 0BZ, UK
- Chemical Biology and Therapeutic Discovery Lab, The Francis Crick Institute, London NW1 1AT, UK
| | - Annie Godwin
- European Xenopus Resource Centre—XenMD, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, 12622 Cairo, Egypt
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Tracy Lau
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Cassidy Petree
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Ehsan Ghayoor Karimiani
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George’s University of London, London SW17 0RE, UK
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad 1696700, Iran
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg 69120, Germany
| | | | | | - Ulrich A Schatz
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck 6020, Austria
- Institute of Human Genetics, Technical University of Munich, Munich, 81675, Germany
| | - Marc P Baggelaar
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London W12 0BZ, UK
- Biomolecular Mass Spectrometry & Proteomics Group, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Muhammad Ilyas
- Department of BioEngineering, University of Engineering and Applied Sciences, 19130 Swat, Pakistan
- Centre for Omic Sciences, Islamia College University, 25000 Peshawar, Pakistan
| | - Tipu Sultan
- Department of Pediatric Neurology, Institute of Child Health, Children Hospital, Lahore 54600, Pakistan
| | - Javeria Raza Alvi
- Department of Pediatric Neurology, Institute of Child Health, Children Hospital, Lahore 54600, Pakistan
| | - Manizha Ganieva
- Department of Neurology, Avicenna Tajik State Medical University, 734063 Dushanbe, Tajikistan
| | - Ben Fowler
- Imaging Core, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Ruxandra Aanicai
- Department of Medical Genetics, CENTOGENE GmbH, 18055 Rostock, Germany
| | - Gulsen Akay Tayfun
- Department of Pediatric Genetics, Marmara University Medical School, 34722 Istanbul, Turkey
| | - Abdulaziz Al Saman
- Pediatric Neurology Department, National Neuroscience Institute, King Fahad Medical City, 49046 Riyadh, Saudi Arabia
| | - Abdulrahman Alswaid
- King Saud Bin Abdulaziz University for Health Sciences, Department of Pediatrics, King Abdullah Specialized Children’s Hospital, Riyadh 11461, Saudi Arabia
| | - Nafise Amiri
- International Collaboration on Repair Discoveries (ICORD), University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Nilufar Asilova
- Department of Neurology, Avicenna Tajik State Medical University, 734063 Dushanbe, Tajikistan
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Patra Yeetong
- Division of Human Genetics, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Matloob Azam
- Pediatrics and Child Neurology, Wah Medical College, 47000 Wah Cantt, Pakistan
| | - Meisam Babaei
- Department of Pediatrics, North Khorasan University of Medical Sciences, Bojnurd 94149-74877, Iran
| | | | - Pouria Mohammadi
- Children’s Medical Center, Pediatrics Center of Excellence, Ataxia Clinic, Tehran University of Medical Sciences, Tehran 1416634793, Iran
- Faculty of Medical Sciences, Department of Medical Genetics, Tarbiat Modares University, Tehran 1411944961, Iran
| | - Saeed Samie
- Pars Advanced and Minimally Invasive Medical Manners Research Center, Pars Hospital, Tehran, Iran
| | - Selina Husna Banu
- Department of Paediatric Neurology and Development, Dr. M.R. Khan Shishu (Children) Hospital and Institute of Child Health, Dhaka 1216, Bangladesh
| | - Jorge Pinto Basto
- Department of Medical Genetics, CENTOGENE GmbH, 18055 Rostock, Germany
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Mislen Bauer
- Division of Clinical Genetics and Metabolism, Nicklas Children's Hospital, Miami, FL 33155, USA
| | - Peter Bauer
- Department of Medical Genetics, CENTOGENE GmbH, 18055 Rostock, Germany
| | - Christian Beetz
- Department of Medical Genetics, CENTOGENE GmbH, 18055 Rostock, Germany
| | - Masoud Garshasbi
- Faculty of Medical Sciences, Department of Medical Genetics, Tarbiat Modares University, Tehran 1411944961, Iran
| | | | - Wafaa Eyaid
- Department of Genetics and Precision Medicine, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh 11426, Saudi Arabia
| | - Hind Ahmed
- Department of Genetics and Precision Medicine, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh 11426, Saudi Arabia
| | - Narges Hashemi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, 13131–99137 Mashhad, Iran
| | - Kazem Hassanpour
- Non-Communicable Diseases Research Center, Sabzevar University of Medical Sciences, 319 Sabzevar, Iran
| | - Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 68010, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neurology, Texas Children’s Hospital, Houston, TX 77030, USA
- Pediatric Neurology, Neurogenetics and Rare Diseases, Boys Town National Research Hospital, Boys Town, NE 68131, USA
| | - Sherozjon Ibrohimov
- Department of Neurology, Avicenna Tajik State Medical University, 734063 Dushanbe, Tajikistan
| | - Ban A Abdul-Majeed
- Molecular Pathology and Genetics, The Pioneer Molecular Pathology Lab, Baghdad 10044, Iraq
| | - Maria Imdad
- Centre for Human Genetics, Hazara University, 21300 Mansehra, Pakistan
| | - Maksudjon Isrofilov
- Department of Neurology, Avicenna Tajik State Medical University, 734063 Dushanbe, Tajikistan
| | - Qassem Kaiyal
- Department of Pediatric Neurology, Clalit Health Care, 2510500 Haifa, Israel
| | - Suliman Khan
- Department of Medical Genetics, CENTOGENE GmbH, 18055 Rostock, Germany
| | - Brian Kirmse
- SOM-Peds-Genetics, University of Mississippi Medical Center, Jackson MS, 39216, USA
| | - Janet Koster
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers location AMC, 1100 DD Amsterdam, The Netherlands
| | - Charles Marques Lourenço
- Faculdade de Medicina, Centro Universitario Estácio de Ribeirão Preto, 14096-160 São Paulo, Brazil
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Oana Moldovan
- Serviço de Genética Médica, Departamento de Pediatria, Hospital de Santa Maria, Centro Hospitalar Universitário de Lisboa Norte, 1649-035 Lisboa, Portugal
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Maryam Najafi
- Pediatrics Genetics Division, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine, Freiburg University, 79106 Freiburg, Germany
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 68010, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Vincenzo Salpietro
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Miriam Schmidts
- Pediatrics Genetics Division, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine, Freiburg University, 79106 Freiburg, Germany
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Adel Shalata
- Pediatrics and Medical Genetics, the Simon Winter Institute for Human Genetics, Bnai Zion Medical Center, 31048 Haifa, Israel
- Bruce Rappaport Faculty of Medicine, the Technion institution of Technology, 3200003 Haifa, Israel
| | - Mohammad Mahroum
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Jawabreh Kassem Talbeya
- Pediatrics and Medical Genetics, the Simon Winter Institute for Human Genetics, Bnai Zion Medical Center, 31048 Haifa, Israel
- Department of Radiology, The Bnai Zion Medical Center, Haifa 31048, Israel
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Dayana Vazquez
- Division of Clinical Genetics and Metabolism, Nicklas Children's Hospital, Miami, FL 33155, USA
| | - Annalisa Vetro
- Neuroscience Department, Meyer Children's Hospital IRCCS, 50139 Florence, Italy
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers location AMC, 1100 DD Amsterdam, The Netherlands
| | - Mashaya Zaman
- Department of Paediatric Neurology and Development, Dr. M.R. Khan Shishu (Children) Hospital and Institute of Child Health, Dhaka 1216, Bangladesh
| | - Tina A Schrader
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Renzo Guerrini
- Neuroscience Department, Meyer Children's Hospital IRCCS, 50139 Florence, Italy
- Neuroscience, Pharmacology and Child Health Department, University of Florence, 50139 Florence, Italy
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neurology, Texas Children’s Hospital, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph Gleeson
- Department of Neurosciences, University of California, San Diego, CA 92093, USA
- Department of Neurosciences, Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Mohnish Suri
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham NG5 1PB, UK
| | - Yalda Jamshidi
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George’s University of London, London SW17 0RE, UK
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, OX3 7FZ, UK
| | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Barbara Vona
- Tübingen Hearing Research Centre, Department of Otolaryngology, Head and Neck Surgery, Eberhard Karls University, 72076 Tübingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
- Institute for Auditory Neuroscience and Inner Ear Lab, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Michael Schrader
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | | | - Matthew Guille
- European Xenopus Resource Centre—XenMD, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London W12 0BZ, UK
- Chemical Biology and Therapeutic Discovery Lab, The Francis Crick Institute, London NW1 1AT, UK
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK
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Pan X, Tao AM, Lu S, Ma M, Hannan SB, Slaugh R, Drewes Williams S, O'Grady L, Kanca O, Person R, Carter MT, Platzer K, Schnabel F, Abou Jamra R, Roberts AE, Newburger JW, Revah-Politi A, Granadillo JL, Stegmann APA, Sinnema M, Accogli A, Salpietro V, Capra V, Ghaloul-Gonzalez L, Brueckner M, Simon MEH, Sweetser DA, Glinton KE, Kirk SE, Wangler MF, Yamamoto S, Chung WK, Bellen HJ. De novo variants in FRYL are associated with developmental delay, intellectual disability, and dysmorphic features. Am J Hum Genet 2024; 111:742-760. [PMID: 38479391 PMCID: PMC11023917 DOI: 10.1016/j.ajhg.2024.02.007] [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: 08/23/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 04/07/2024] Open
Abstract
FRY-like transcription coactivator (FRYL) belongs to a Furry protein family that is evolutionarily conserved from yeast to humans. The functions of FRYL in mammals are largely unknown, and variants in FRYL have not previously been associated with a Mendelian disease. Here, we report fourteen individuals with heterozygous variants in FRYL who present with developmental delay, intellectual disability, dysmorphic features, and other congenital anomalies in multiple systems. The variants are confirmed de novo in all individuals except one. Human genetic data suggest that FRYL is intolerant to loss of function (LoF). We find that the fly FRYL ortholog, furry (fry), is expressed in multiple tissues, including the central nervous system where it is present in neurons but not in glia. Homozygous fry LoF mutation is lethal at various developmental stages, and loss of fry in mutant clones causes defects in wings and compound eyes. We next modeled four out of the five missense variants found in affected individuals using fry knockin alleles. One variant behaves as a severe LoF variant, whereas two others behave as partial LoF variants. One variant does not cause any observable defect in flies, and the corresponding human variant is not confirmed to be de novo, suggesting that this is a variant of uncertain significance. In summary, our findings support that fry is required for proper development in flies and that the LoF variants in FRYL cause a dominant disorder with developmental and neurological symptoms due to haploinsufficiency.
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Affiliation(s)
- Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Alice M Tao
- Vagelos School of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Shabab B Hannan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Sarah Drewes Williams
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Lauren O'Grady
- Division of Medical Genetics & Metabolism, Massachusetts General for Children, Boston, MA, USA; MGH Institute of Health Professions, Charlestown, MA, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | | | - Melissa T Carter
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Franziska Schnabel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Amy E Roberts
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Medicine, Division of Genetics, Boston Children's Hospital, Boston, MA, USA
| | - Jane W Newburger
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Anya Revah-Politi
- Institute for Genomic Medicine and Precision Genomics Laboratory, Columbia University Irving Medical Center, New York, NY, USA
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Margje Sinnema
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Andrea Accogli
- Division of Medical Genetics, Department of Medicine, McGill University Health Center, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, University College London Institute of Neurology, Queen Square, London, UK
| | - Valeria Capra
- Unit of Medical Genetics and Genomics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Lina Ghaloul-Gonzalez
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Martina Brueckner
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Marleen E H Simon
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - David A Sweetser
- Division of Medical Genetics & Metabolism, Massachusetts General for Children, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kevin E Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Genetics, Texas Children's Hospital, Houston, TX, USA
| | - Susan E Kirk
- Section of Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Cancer and Hematology Center, Houston, TX, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Wendy K Chung
- Departments of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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Goin-Kochel RP, Lozano I, Duhon G, Marzano G, Daniels A, Law JK, Diehl K, Green Snyder L, Feliciano P, Chung WK. Evidence-based recruitment strategies for clinical research: Study personnel's and research participants' perceptions about successful methods of outreach for a U.S. Autism-Research Cohort. J Clin Transl Sci 2024; 8:e65. [PMID: 38690223 PMCID: PMC11058577 DOI: 10.1017/cts.2024.512] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 02/15/2024] [Accepted: 03/25/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction Under enrollment of participants in clinical research is costly and delays study completion to impact public health. Given that research personnel make decisions about which strategies to pursue and participants are the recipients of these efforts, we surveyed research staff (n = 52) and participants (n = 4,144) affiliated with SPARK (Simons Foundation Powering Autism for Knowledge) - the largest study of autism in the U.S. - to understand their perceptions of effective recruitment strategies. Methods In Study 1, research personnel were asked to report recruitment strategies that they tried for SPARK and to indicate which ones they would and would not repeat/recommend. In Study 2, SPARK participants were asked to indicate all the ways they heard about the study prior to enrollment and which one was most influential in their decisions to enroll. Results Staff rated speaking with a SPARK-study-team member (36.5%), speaking with a medical provider (19.2%), word of mouth (11.5%), and a live TV news story (11.5%) as the most successful strategies. Participants most often heard about SPARK via social media (47.0%), speaking with a medical provider (23.1%), and an online search (20.1%). Research personnel's and participants' views on effective recruitment strategies often differed, with the exception of speaking with a medical provider. Conclusion Results suggest that a combination of strategies is likely to be most effective in reaching diverse audiences. Findings have implications for the selection of strategies that meet a study's specific needs, as well as recruitment-strategy "combinations" that may enhance the influence of outreach efforts.
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Affiliation(s)
- Robin P. Goin-Kochel
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Ivana Lozano
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Gabrielle Duhon
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Gabriela Marzano
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Amy Daniels
- Simons Foundation, New York, NY, USA
- Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - J. Kiely Law
- Simons Foundation, New York, NY, USA
- Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Katharine Diehl
- Simons Foundation, New York, NY, USA
- Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Pamela Feliciano
- Simons Foundation, New York, NY, USA
- Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Wendy K. Chung
- Simons Foundation, New York, NY, USA
- Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
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14
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Ma M, Ganapathi M, Zheng Y, Tan KL, Kanca O, Bove KE, Quintanilla N, Sag SO, Temel SG, LeDuc CA, McPartland AJ, Pereira EM, Shen Y, Hagen J, Thomas CP, Galván NTN, Pan X, Lu S, Rosenfeld JA, Calame DG, Wangler MF, Lupski JR, Pehlivan D, Hertel PM, Chung WK, Bellen HJ. Homozygous missense variants in YKT6 result in loss of function and are associated with developmental delay, with or without severe infantile liver disease and risk for hepatocellular carcinoma. Genet Med 2024:101125. [PMID: 38522068 DOI: 10.1016/j.gim.2024.101125] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
PURPOSE YKT6 plays important roles in multiple intracellular vesicle trafficking events but has not been associated with Mendelian diseases. METHODS We report three unrelated individuals with rare homozygous missense variants in YKT6 who exhibited neurological disease with or without a progressive infantile liver disease. We modeled the variants in Drosophila. We generated wild-type and variant genomic rescue constructs (GRs) of the fly ortholog dYkt6 and compared their ability in rescuing the loss-of-function phenotypes in mutant flies. We also generated a dYkt6KozakGAL4 allele to assess the expression pattern of dYkt6. RESULTS Two individuals are homozygous for YKT6 [NM_006555.3:c.554A>G p.(Tyr185Cys)] and exhibited normal prenatal course followed by failure to thrive, developmental delay and progressive liver disease. Haplotype analysis identified a shared homozygous region flanking the variant, suggesting a common ancestry. The third individual is homozygous for YKT6 [NM_006555.3:c.191A>G p.(Tyr64Cys)] and exhibited neurodevelopmental disorders and optic atrophy. Fly dYkt6 is essential and is expressed in the fat body (analogous to liver) and central nervous system. Wild-type GR can rescue the lethality and autophagic flux defects whereas the variants are less efficient in rescuing the phenotypes. CONCLUSION The YKT6 variants are partial loss-of-function alleles and the p.(Tyr185Cys) is more severe than p.(Tyr64Cys).
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Affiliation(s)
- Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Irving Medical center, New York, NY 10032, USA
| | - Yiming Zheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Present affiliation: School of Life Science, Xiamen University, Xiamen, Fujian Province 361102, China
| | - Kai-Li Tan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Present affiliation: Emergent Biosolutions, 5901 E Lombard St, Baltimore, MD 21202, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Kevin E Bove
- Department of Pathology & Laboratory Medicine, Cincinnati Childrens hospital Medical center, Cincinnati, OH 45229, USA
| | - Norma Quintanilla
- Department of Pathology and Immunology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sebnem O Sag
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa 16220, Turkey
| | - Sehime G Temel
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa 16220, Turkey
| | - Charles A LeDuc
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | | | - Elaine M Pereira
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Jacob Hagen
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Christie P Thomas
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Nhu Thao Nguyen Galván
- Division of Abdominal Transplantation, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Paula M Hertel
- Texas Children's Hospital, Houston, TX 77030, USA; Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.
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15
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Shadrina M, Kalay Ö, Demirkaya-Budak S, LeDuc CA, Chung WK, Turgut D, Budak G, Arslan E, Semenyuk V, Davis-Dusenbery B, Seidman CE, Yost HJ, Jain A, Gelb BD. Automated Identification of Germline de novo Mutations in Family Trios: A Consensus-Based Informatic Approach. bioRxiv 2024:2024.03.08.584100. [PMID: 38559260 PMCID: PMC10979888 DOI: 10.1101/2024.03.08.584100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Accurate identification of germline de novo variants (DNVs) remains a challenging problem despite rapid advances in sequencing technologies as well as methods for the analysis of the data they generate, with putative solutions often involving ad hoc filters and visual inspection of identified variants. Here, we present a purely informatic method for the identification of DNVs by analyzing short-read genome sequencing data from proband-parent trios. Our method evaluates variant calls generated by three genome sequence analysis pipelines utilizing different algorithms-GATK HaplotypeCaller, DeepTrio and Velsera GRAF-exploring the assumption that a requirement of consensus can serve as an effective filter for high-quality DNVs. We assessed the efficacy of our method by testing DNVs identified using a previously established, highly accurate classification procedure that partially relied on manual inspection and used Sanger sequencing to validate a DNV subset comprising less confident calls. The results show that our method is highly precise and that applying a force-calling procedure to putative variants further removes false-positive calls, increasing precision of the workflow to 99.6%. Our method also identified novel DNVs, 87% of which were validated, indicating it offers a higher recall rate without compromising accuracy. We have implemented this method as an automated bioinformatics workflow suitable for large-scale analyses without need for manual intervention.
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Affiliation(s)
- Mariya Shadrina
- Mindich Child Health and Development Institute and the Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York, NY, USA
| | - Özem Kalay
- Velsera Inc, 529 Main St, Suite 6610, Charlestown, MA, USA
| | | | - Charles A. LeDuc
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Wendy K. Chung
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Deniz Turgut
- Velsera Inc, 529 Main St, Suite 6610, Charlestown, MA, USA
| | - Gungor Budak
- Velsera Inc, 529 Main St, Suite 6610, Charlestown, MA, USA
| | - Elif Arslan
- Velsera Inc, 529 Main St, Suite 6610, Charlestown, MA, USA
| | | | | | - Christine E. Seidman
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - H. Joseph Yost
- Molecular Medicine Program, University of Utah, Salt Lake City, UT, USA
| | - Amit Jain
- Velsera Inc, 529 Main St, Suite 6610, Charlestown, MA, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine, New York, NY, USA
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16
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Chung WK, Dasgupta S, Regier DS, Solomon BD. The clinical geneticist workforce: Community forums to address challenges and opportunities. Genet Med 2024; 26:101121. [PMID: 38469792 DOI: 10.1016/j.gim.2024.101121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024] Open
Affiliation(s)
- Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Shoumita Dasgupta
- Department of Medicine, Biomedical Genetics Section, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA
| | - Debra S Regier
- Children's National Rare Disease Institute, Children's National Hospital, Washington, DC
| | - Benjamin D Solomon
- Office of the Clinical Director and Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MA.
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17
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Maroofian R, Zamani M, Kaiyrzhanov R, Liebmann L, Karimiani EG, Vona B, Huebner AK, Calame DG, Misra VK, Sadeghian S, Azizimalamiri R, Mohammadi MH, Zeighami J, Heydaran S, Toosi MB, Akhondian J, Babaei M, Hashemi N, Schnur RE, Suri M, Setzke J, Wagner M, Brunet T, Grochowski CM, Emrick L, Chung WK, Hellmich UA, Schmidts M, Lupski JR, Galehdari H, Severino M, Houlden H, Hübner CA. Biallelic variants in SLC4A10 encoding a sodium-dependent bicarbonate transporter lead to a neurodevelopmental disorder. Genet Med 2024; 26:101034. [PMID: 38054405 DOI: 10.1016/j.gim.2023.101034] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/07/2023] Open
Abstract
PURPOSE SLC4A10 encodes a plasma membrane-bound transporter, which mediates Na+-dependent HCO3- import, thus mediating net acid extrusion. Slc4a10 knockout mice show collapsed brain ventricles, an increased seizure threshold, mild behavioral abnormalities, impaired vision, and deafness. METHODS Utilizing exome/genome sequencing in families with undiagnosed neurodevelopmental disorders and international data sharing, 11 patients from 6 independent families with biallelic variants in SLC4A10 were identified. Clinico-radiological and dysmorphology assessments were conducted. A minigene assay, localization studies, intracellular pH recordings, and protein modeling were performed to study the possible functional consequences of the variant alleles. RESULTS The families harbor 8 segregating ultra-rare biallelic SLC4A10 variants (7 missense and 1 splicing). Phenotypically, patients present with global developmental delay/intellectual disability and central hypotonia, accompanied by variable speech delay, microcephaly, cerebellar ataxia, facial dysmorphism, and infrequently, epilepsy. Neuroimaging features range from some non-specific to distinct neuroradiological findings, including slit ventricles and a peculiar form of bilateral curvilinear nodular heterotopia. In silico analyses showed 6 of 7 missense variants affect evolutionarily conserved residues. Functional analyses supported the pathogenicity of 4 of 7 missense variants. CONCLUSION We provide evidence that pathogenic biallelic SLC4A10 variants can lead to neurodevelopmental disorders characterized by variable abnormalities of the central nervous system, including altered brain ventricles, thus resembling several features observed in knockout mice.
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Affiliation(s)
- Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom.
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran; Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Lutz Liebmann
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller Universität, Am Klinikum 1, Jena, Germany
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, United Kingdom
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany; Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Antje K Huebner
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller Universität, Am Klinikum 1, Jena, Germany
| | - Daniel G Calame
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Vinod K Misra
- Division of Genetic, Genomic & Metabolic Disorders, Discipline of Pediatrics, College of Medicine, Central Michigan University, Mount Pleasant, MI
| | - Saeid Sadeghian
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Reza Azizimalamiri
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Jawaher Zeighami
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
| | - Sogand Heydaran
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mehran Beiraghi Toosi
- Pediatric Neurology Department, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran; Neuroscience Research Center, Mashhad University of Medical Science, Mashhad, Iran
| | - Javad Akhondian
- Pediatric Neurology Department, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meisam Babaei
- Department of Pediatrics, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Narges Hashemi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Mohnish Suri
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Jonas Setzke
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany; Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany; Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, LMU Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Lisa Emrick
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ute A Hellmich
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Jena, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Miriam Schmidts
- Pediatrics Genetics Division, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine, Freiburg University, Freiburg, Germany; Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - James R Lupski
- Texas Children's Hospital, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Christian A Hübner
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller Universität, Am Klinikum 1, Jena, Germany; Center for Rare Diseases, Jena University Hospital, Jena, Germany
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18
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Barzak FM, Lu A, Geltzeiler AR, Ledgerwood EC, Chung WK, Day CL. A novel RNF125 variant associated with Tenorio syndrome alters ubiquitin chain binding. Clin Genet 2024; 105:254-261. [PMID: 37986019 DOI: 10.1111/cge.14457] [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: 09/17/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023]
Abstract
A key signalling pathway required for clearance of viruses from host cells relies on the receptor protein, retinoic acid-inducible gene I (RIG-I). The activity of RIG-I is tightly controlled, and once bound to viral dsRNA, addition of lysine 63-linked ubiquitin chains activates signalling. Meanwhile, the addition of lysine 48-linked ubiquitin chains to RIG-I is required to terminate signalling when the infection has been resolved. Really interesting new gene (RING) finger protein 125 (RNF125) is the E3 ligase responsible for addition of the ubiquitin chains that terminate signalling, with disruption of its function associated with Tenorio syndrome. Here we describe a novel RNF125 gene variant in an individual with clinical symptoms including intellectual disability, macrocephaly and congenital heart disease, consistent with Tenorio syndrome. The newly identified Tenorio syndrome-associated variant [(NM_017831.4):c.670G>C p.Glu224Gln] is the first to be found in the ubiquitin interaction motif (UIM) of RNF125. While the E3 ligase activity of this RNF125 variant is retained, it has an impaired ability to interact with lysine 63-linked ubiquitin chains. The function of the UIM in RNF125 is uncertain; however, this study suggests that the UIM binds lysine 63-linked ubiquitin chains, and that this interaction is required for the normal function of RNF125.
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Affiliation(s)
- Fareeda M Barzak
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Anita Lu
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Alexa R Geltzeiler
- Department of Pediatrics, Boston Children's Hospital Harvard Medical School Boston, Boston, Massachusetts, USA
| | - Elizabeth C Ledgerwood
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital Harvard Medical School Boston, Boston, Massachusetts, USA
| | - Catherine L Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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19
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Sudnawa KK, Chung WK. SPARKing New Insight Into Autism Across the Lifespan. Am J Intellect Dev Disabil 2024; 129:91-95. [PMID: 38411241 DOI: 10.1352/1944-7558-129.2.91] [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] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Autism is heterogeneous at many levels, including clinical symptoms and etiology. A key strategy in studying heterogeneous conditions is having large enough sample sizes to stratify into smaller groups that are more homogeneous. SPARK and Simons Searchlight are large and growing research cohorts of individuals with autism in the United States and individuals with genetically defined neurodevelopmental conditions around the world, respectively. They both provide freely available phenotypic and genotypic data with the ability to re-contact participants through the research match program. Deep dives into each gene in Searchlight provide comprehensive natural history data to understand the differing clinical courses to inform proper clinical care, and work toward treatment for each condition. Moreover, pilots of genetically based newborn screening programs for neurogenetic disorders can provide opportunities for equitable and early diagnosis to try to improve outcomes with earlier interventions.
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Affiliation(s)
- Khemika K Sudnawa
- Khemika K. Sudnawa, Boston Children's Hospital, Harvard Medical School and Department of Pediatrics and Pramongkutklao Hospital and Pramongkutklao College of Medicine, Bangkok, Thailand
| | - Wendy K Chung
- Wendy K. Chung, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School
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20
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Sudnawa KK, Calamia S, Geltzeiler A, Chung WK. Clinical phenotypes of individuals with Chung-Jansen syndrome across age groups. Am J Med Genet A 2024; 194:e63471. [PMID: 37961033 DOI: 10.1002/ajmg.a.63471] [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: 04/18/2023] [Revised: 09/06/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]
Abstract
Pathogenic variants in pleckstrin homology domain interacting protein (PHIP) are associated with Chung-Jansen syndrome characterized by developmental delay, intellectual disability, behavioral challenges, hypotonia, obesity, and dysmorphic features. We report phenotypes and genotypes of 47 individuals with likely pathogenic/pathogenic PHIP variants. Variants were de novo in 61.7%, unknown inheritance in 29.8%, and inherited in 8.5%. The median age of the individuals was 10.9 years, approximately equally divided by sex. Individuals in this cohort frequently had a history of developmental delay (85.1%), attention-deficit/hyperactivity disorder (51.1%), anxiety (46.8%), depression (27.7%), and sleep difficulties (42.6%). Depression was significantly higher in the older age group (>12 years old). Most individuals had moderately low adaptive functioning based on the Vineland-3 (mean = 76.8, standard deviation = 12.0). Overall, 55.8% of individuals were obese/overweight. The percentage of obese individuals was greater in the older age group (>12 years old) and evolves over time. Other common symptoms were hypotonia (78.7%), constipation (48.9%), visual problems (66%), and cryptorchidism (39.1% of males). Our findings provide additional natural history data for Chung-Jansen syndrome and provide opportunities for early intervention of healthy eating habits and awareness of developing mood and behavioral challenges over the life course.
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Affiliation(s)
- Khemika K Sudnawa
- Department of Pediatrics, Columbia University, New York, New York, USA
- Department of Pediatrics, Pramongkutklao Hospital and Pramongkutklao College of Medicine, Bangkok, Thailand
| | - Sean Calamia
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Alexa Geltzeiler
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York, USA
- Department of Medicine, Columbia University, New York, New York, USA
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21
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Ming NR, Noble D, Chussid S, Ziegler A, Chung WK. Caregiver-reported dental manifestations in individuals with genetic neurodevelopmental disorders. Int J Paediatr Dent 2024; 34:145-152. [PMID: 37655712 DOI: 10.1111/ipd.13116] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 07/04/2023] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Children with neurodevelopmental disorders (NDDs) often have poor oral health and dental abnormalities. An increasing number of genes have been associated with neurodevelopmental conditions affecting the oral cavity, but the specific dental features associated with many genes remain unknown. AIM To report the types and frequencies of dental manifestations in children with neurodevelopmental conditions of known genetic cause. DESIGN A 30-question survey assesing ectodermal and dental features was administered through Simons Searchlight, with which formed a recontactable cohort of individuals with genetic NDDs often associated with autism spectrum disorder (ASD). RESULTS Data were collected from a largely paediatric population with 620 affected individuals across 39 genetic conditions and 145 unaffected siblings without NDDs for comparison. Drooling, difficulty accessing dental care, late primary teeth eruption, abnormal primary and permanent teeth formation, misshapen nails, and hair loss were more frequent in individuals with NDDs. Additionally, we evidenced an association between three new pathogenic gene variant/oral manifestation pairs: CSNK2A1/unusual primary teeth, DYRK1A/late primary teeth eruption, and PPP2R5D/sialorrhea. CONCLUSION Our results demonstrate that genetic NDDs caused by mutations in CSNK2A1, DYRK1A, and PP2R5D are associated with unique dental manifestations, and knowledge of these features can be helpful to personalize dental care.
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Affiliation(s)
- Neil R Ming
- College of Dental Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Deanna Noble
- College of Dental Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Steven Chussid
- Department of Paediatric Dentistry, Columbia University Irving Medical Center, New York, New York, USA
| | - Alban Ziegler
- Department of Paediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Wendy K Chung
- Department of Paediatrics, Columbia University Irving Medical Center, New York, New York, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
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22
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Pendleton KE, Hernandez-Garcia A, Lyu JM, Campbell IM, Shaw CA, Vogt J, High FA, Donahoe PK, Chung WK, Scott DA. FOXP1 Haploinsufficiency Contributes to the Development of Congenital Diaphragmatic Hernia. J Pediatr Genet 2024; 13:29-34. [PMID: 38567173 PMCID: PMC10984716 DOI: 10.1055/s-0043-1767731] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 04/11/2022] [Indexed: 03/30/2023]
Abstract
FOXP1 encodes a transcription factor involved in tissue regulation and cell-type-specific functions. Haploinsufficiency of FOXP1 is associated with a neurodevelopmental disorder: autosomal dominant mental retardation with language impairment with or without autistic features. More recently, heterozygous FOXP1 variants have also been shown to cause a variety of structural birth defects including central nervous system (CNS) anomalies, congenital heart defects, congenital anomalies of the kidney and urinary tract, cryptorchidism, and hypospadias. In this report, we present a previously unpublished case of an individual with congenital diaphragmatic hernia (CDH) who carries an approximately 3.8 Mb deletion. Based on this deletion, and deletions previously reported in two other individuals with CDH, we define a CDH critical region on chromosome 3p13 that includes FOXP1 and four other protein-coding genes. We also provide detailed clinical descriptions of two previously reported individuals with CDH who carry de novo, pathogenic variants in FOXP1 that are predicted to trigger nonsense-mediated mRNA decay. A subset of individuals with putatively deleterious FOXP4 variants has also been shown to develop CDH. Since FOXP proteins function as homo- or heterodimers and the homologs of FOXP1 and FOXP4 are expressed at the same time points in the embryonic mouse diaphragm, they may function together as a dimer, or in parallel as homodimers, to regulate gene expression during diaphragm development. Not all individuals with heterozygous, loss-of-function changes in FOXP1 develop CDH. Hence, we conclude that FOXP1 acts as a susceptibility factor that contributes to the development of CDH in conjunction with other genetic, epigenetic, environmental, and/or stochastic factors.
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Affiliation(s)
- Katherine E. Pendleton
- Genetics and Genomics Program, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Andres Hernandez-Garcia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Jennifer M. Lyu
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, United States
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Ian M. Campbell
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham, United Kingdom
| | - Frances A. High
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, United States
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Patricia K. Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States
| | - Wendy K. Chung
- Departments of Pediatrics, Columbia University, New York, New York, United States
- Department of Medicine, Columbia University, New York, New York, United States
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States
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23
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Garber A, Weingarten LS, Abreu NJ, Elloumi HZ, Haack T, Hildebrant C, Martínez-Gil N, Mathews J, Müller AJ, Valenzuela Palafoll I, Steigerwald C, Chung WK. Rare predicted deleterious FEZF2 variants are associated with a neurodevelopmental phenotype. Am J Med Genet A 2024:e63578. [PMID: 38425142 DOI: 10.1002/ajmg.a.63578] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/07/2024] [Accepted: 02/17/2024] [Indexed: 03/02/2024]
Abstract
FEZF2 encodes a transcription factor critical to neurodevelopment that regulates other neurodevelopment genes. Rare variants in FEZF2 have previously been suggested to play a role in autism, and cases of 3p14 microdeletions that include FEZF2 share a neurodevelopmental phenotype including mild dysmorphic features and intellectual disability. We identified seven heterozygous predicted deleterious variants in FEZF2 (three frameshifts, one recurrent missense in two independent cases, one nonsense, and one complete gene deletion) in unrelated individuals with neurodevelopmental disorders including developmental delay/intellectual disability, autism, and/or attention-deficit/hyperactivity. Variants were confirmed to be de novo in five of seven cases and paternally inherited from an affected father in one. Predicted deleterious variants in FEZF2 may affect the expression of genes that are involved in fate choice pathways in developing neurons, and thus contribute to the neurodevelopmental phenotype. Future studies are needed to clarify the mechanism by which FEZF2 leads to this neurodevelopmental disorder.
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Affiliation(s)
- Alison Garber
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Lisa S Weingarten
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Nicolas J Abreu
- Department of Neurology, NYU Grossman School of Medicine, New York, New York, USA
| | | | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Clara Hildebrant
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Núria Martínez-Gil
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, Barcelona, Spain
- Medical Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Jennifer Mathews
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Amelie Johanna Müller
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Irene Valenzuela Palafoll
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, Barcelona, Spain
- Medical Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Connolly Steigerwald
- Department of Neurology, NYU Grossman School of Medicine, New York, New York, USA
| | - Wendy K Chung
- Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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24
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Yi H, Trivedi MS, Crew KD, Schechter I, Appelbaum P, Chung WK, Allegrante JP, Kukafka R. Understanding Social, Cultural, and Religious Factors Influencing Medical Decision-Making on BRCA1/2 Genetic Testing in the Orthodox Jewish Community. Public Health Genomics 2024; 27:57-67. [PMID: 38402864 DOI: 10.1159/000536391] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/10/2024] [Indexed: 02/27/2024] Open
Abstract
INTRODUCTION Although the prevalence of a pathogenic variant in the BRCA1 and BRCA2 genes is about 1:400 (0.25%) in the general population, the prevalence is as high as 1:40 (2.5%) among the Ashkenazi Jewish population. Despite cost-effective preventive measures for mutation carriers, Orthodox Jews constitute a cultural and religious group that requires different approaches to BRCA1 and BRCA2 genetic testing relative to other groups. This study analyzed a dialog of key stakeholders and community members to explore factors that influence decision-making about BRCA1 and BRCA2 genetic testing in the New York Orthodox Jewish community. METHODS Qualitative research methods, based on Grounded Theory and Narrative Research, were utilized to analyze the narrative data collected from 49 key stakeholders and community members. A content analysis was conducted to identify themes; inter-rater reliability was 71%. RESULTS Facilitators of genetic testing were a desire for preventive interventions and education, while barriers to genetic testing included negative emotions, feared impact on family/romantic relationships, cost, and stigma. Views differed on the role of religious leaders and healthcare professionals in medical decision-making. Education, health, and community were discussed as influential factors, and concerns were expressed about disclosure, implementation, and information needs. CONCLUSION This study elicited the opinions of Orthodox Jewish women (decision-makers) and key stakeholders (influencers) who play critical roles in the medical decision-making process. The findings have broad implications for engaging community stakeholders within faith-based or culturally distinct groups to ensure better utilization of healthcare services for cancer screening and prevention designed to improve population health.
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Affiliation(s)
- Haeseung Yi
- Department of Health Studies and Applied Educational Psychology, Teachers College, Columbia University, New York, New York, USA,
| | - Meghna S Trivedi
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA
| | - Katherine D Crew
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Isaac Schechter
- Achieve Behavioral Health, Monsey, New York, USA
- Institute for Applied Research and Community Collaboration (ARCC), Spring Valley, New York, USA
| | - Paul Appelbaum
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Center for Law, Ethics and Psychiatry, New York State Psychiatric Institute, New York, New York, USA
| | - Wendy K Chung
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - John P Allegrante
- Department of Health Studies and Applied Educational Psychology, Teachers College, Columbia University, New York, New York, USA
- Department of Sociomedical Sciences, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Rita Kukafka
- Department of Sociomedical Sciences, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
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25
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Yiangou K, Mavaddat N, Dennis J, Zanti M, Wang Q, Bolla MK, Abubakar M, Ahearn TU, Andrulis IL, Anton-Culver H, Antonenkova NN, Arndt V, Aronson KJ, Augustinsson A, Baten A, Behrens S, Bermisheva M, de Gonzalez AB, Białkowska K, Boddicker N, Bodelon C, Bogdanova NV, Bojesen SE, Brantley KD, Brauch H, Brenner H, Camp NJ, Canzian F, Castelao JE, Cessna MH, Chang-Claude J, Chenevix-Trench G, Chung WK, Colonna SV, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Devilee P, Dörk T, Dunning AM, Eccles DM, Eliassen AH, Engel C, Eriksson M, Evans DG, Fasching PA, Fletcher O, Flyger H, Fritschi L, Gago-Dominguez M, Gentry-Maharaj A, González-Neira A, Guénel P, Hahnen E, Haiman CA, Hamann U, Hartikainen JM, Ho V, Hodge J, Hollestelle A, Honisch E, Hooning MJ, Hoppe R, Hopper JL, Howell S, Howell A, Jakovchevska S, Jakubowska A, Jernström H, Johnson N, Kaaks R, Khusnutdinova EK, Kitahara CM, Koutros S, Kristensen VN, Lacey JV, Lambrechts D, Lejbkowicz F, Lindblom A, Lush M, Mannermaa A, Mavroudis D, Menon U, Murphy RA, Nevanlinna H, Obi N, Offit K, Park-Simon TW, Patel AV, Peng C, Peterlongo P, Pita G, Plaseska-Karanfilska D, Pylkäs K, Radice P, Rashid MU, Rennert G, Roberts E, Rodriguez J, Romero A, Rosenberg EH, Saloustros E, Sandler DP, Sawyer EJ, Schmutzler RK, Scott CG, Shu XO, Southey MC, Stone J, Taylor JA, Teras LR, van de Beek I, Willett W, Winqvist R, Zheng W, Vachon CM, Schmidt MK, Hall P, MacInnis RJ, Milne RL, Pharoah PD, Simard J, Antoniou AC, Easton DF, Michailidou K. Differences in polygenic score distributions in European ancestry populations: implications for breast cancer risk prediction. medRxiv 2024:2024.02.12.24302043. [PMID: 38410445 PMCID: PMC10896416 DOI: 10.1101/2024.02.12.24302043] [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] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The 313-variant polygenic risk score (PRS313) provides a promising tool for breast cancer risk prediction. However, evaluation of the PRS313 across different European populations which could influence risk estimation has not been performed. Here, we explored the distribution of PRS313 across European populations using genotype data from 94,072 females without breast cancer, of European-ancestry from 21 countries participating in the Breast Cancer Association Consortium (BCAC) and 225,105 female participants from the UK Biobank. The mean PRS313 differed markedly across European countries, being highest in south-eastern Europe and lowest in north-western Europe. Using the overall European PRS313 distribution to categorise individuals leads to overestimation and underestimation of risk in some individuals from south-eastern and north-western countries, respectively. Adjustment for principal components explained most of the observed heterogeneity in mean PRS. Country-specific PRS distributions may be used to calibrate risk categories in individuals from different countries.
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Affiliation(s)
- Kristia Yiangou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus, 2371
| | - Nasim Mavaddat
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Maria Zanti
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus, 2371
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA, 20850
| | - Thomas U. Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA, 20850
| | - Irene L. Andrulis
- Fred A, Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA, 92617
| | - Natalia N. Antonenkova
- NN Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus, 223040
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
| | - Kristan J. Aronson
- Department of Public Health Sciences, and Cancer Research Institute, Queen’s University, Kingston, ON, Canada, K7L 3N6
| | | | - Adinda Baten
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium, 3000
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia, 450054
- St Petersburg State University, St, Petersburg, Russia, 199034
| | | | - Katarzyna Białkowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland, 71-252
| | - Nicholas Boddicker
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA, 55905
| | - Clara Bodelon
- Department of Population Science, American Cancer Society, Atlanta, GA, USA, 30303
| | - Natalia V. Bogdanova
- NN Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus, 223040
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany, 30625
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany, 30625
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark, 2730
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark, 2730
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, 2200
| | - Kristen D. Brantley
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA, 02115
| | - Hiltrud Brauch
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany, 70376
- iFIT-Cluster of Excellence, University of Tübingen, Tübingen, Germany, 72074
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany, 72074
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany, 69120
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
| | - Nicola J. Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA, 84112
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
| | - Jose E. Castelao
- Oncology and Genetics Unit, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS) Foundation, Complejo Hospitalario Universitario de Santiago, SERGAS, Vigo, Spain, 36312
| | - Melissa H. Cessna
- Department of Pathology, Intermountain Healthcare, Salt Lake City, UT, USA, 84143
- Intermountain Biorepository, Intermountain Healthcare, Salt Lake City, UT, USA, 84143
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, 20246
| | - Georgia Chenevix-Trench
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia, 4006
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA, 10032
| | - NBCS Collaborators
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway, 0379
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway, 0450
- Department of Research, Vestre Viken Hospital, Drammen, Norway, 3019
- Section for Breast- and Endocrine Surgery, Department of Cancer, Division of Surgery, Cancer and Transplantation Medicine, Oslo University Hospital-Ullevål, Oslo, Norway, 0450
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway, 0379
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway, 1478
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway, 0379
- Department of Oncology, Division of Surgery, Cancer and Transplantation Medicine, Oslo University Hospital-Radiumhospitalet, Oslo, Norway, 0379
- National Advisory Unit on Late Effects after Cancer Treatment, Oslo University Hospital, Oslo, Norway, 0379
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway, 1478
- Oslo Breast Cancer Research Consortium, Oslo University Hospital, Oslo, Norway, 0379
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway, 0379
| | - Sarah V. Colonna
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA, 84112
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA, 55905
| | - Angela Cox
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK, S10 2TN
| | - Simon S. Cross
- Division of Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, UK, S10 2TN
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 171 65
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA, 19111
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands, 2333 ZA
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands, 2333 ZA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany, 30625
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Diana M. Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK, SO17 1BJ
| | - A. Heather Eliassen
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA, 02115
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA, 02115
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA, 02115
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany, 04107
- LIFE - Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany, 04103
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 171 65
| | - D. Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK, M13 9WL
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK, M13 9WL
| | - Peter A. Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany, 91054
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK, SW7 3RP
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark, 2730
| | - Lin Fritschi
- School of Population Health, Curtin University, Perth, Western Australia, Australia, 6102
| | - Manuela Gago-Dominguez
- Cancer Genetics and Epidemiology Group, Genomic Medicine Group, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain, 15706
| | - Aleksandra Gentry-Maharaj
- MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK, WC1V 6LJ
- Department of Women’s Cancer, Elizabeth Garrett Anderson Institute for Women’s Health, University College London, London, UK
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain, 28029
- Spanish Network on Rare Diseases (CIBERER)
| | - Pascal Guénel
- Team ‘Exposome and Heredity’, CESP, Gustave Roussy, INSERM, University Paris-Saclay, UVSQ, Villejuif, France, 94805
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany, 50937
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany, 50937
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA, 90033
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
| | - Jaana M. Hartikainen
- Cancer RC, University of Eastern Finland, Kuopio, Finland, 70210
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland, 70210
| | - Vikki Ho
- Health Innovation and Evaluation Hub, Université de Montréal Hospital Research Centre (CRCHUM), Montréal, Québec, Canada
| | - James Hodge
- Department of Population Science, American Cancer Society, Atlanta, GA, USA, 30303
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands, 3015 GD
| | - Ellen Honisch
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany, 40225
| | - Maartje J. Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands, 3015 GD
| | - Reiner Hoppe
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany, 70376
- University of Tübingen, Tübingen, Germany, 72074
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia, 3010
| | - Sacha Howell
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Nightingale/Prevent Breast Cancer Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Manchester Breast Centre, Manchester Cancer Research Centre, The Christie Hospital, Manchester, UK
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK, M13 9PL
| | - ABCTB Investigators
- Australian Breast Cancer Tissue Bank, Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia, 2145
| | - kConFab Investigators
- Research Department, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia, 3000
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia, 3000
| | - Simona Jakovchevska
- Research Centre for Genetic Engineering and Biotechnology ‘Georgi D, Efremov’, MASA, Skopje, Republic of North Macedonia, 1000
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland, 71-252
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland, 171-252
| | - Helena Jernström
- Oncology, Clinical Sciences in Lund, Lund University, Lund, Sweden, 221 85
| | - Nichola Johnson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK, SW7 3RP
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
| | - Elza K. Khusnutdinova
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia, 450054
- Department of Genetics and Fundamental Medicine, Ufa University of Science and Technology, Ufa, Russia, 450076
| | - Cari M. Kitahara
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA, 20892
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA, 20850
| | - Vessela N. Kristensen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway, 0450
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway, 0379
| | - James V. Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA, 91010
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA, 91010
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, 3000
- VIB Center for Cancer Biology, VIB, Leuven, Belgium, 3001
| | | | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden, 171 76
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden, 171 76
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Arto Mannermaa
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland, 70210
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland, 70210
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece, 711 10
| | - Usha Menon
- MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK, WC1V 6LJ
| | - Rachel A. Murphy
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada, V5Z 1L3
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland, 00290
| | - Nadia Obi
- Institute for Occupational and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, 20246
- Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, 20246
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10065
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10065
| | | | - Alpa V. Patel
- Department of Population Science, American Cancer Society, Atlanta, GA, USA, 30303
| | - Cheng Peng
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA, 02115
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy, 20139
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain, 28029
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology ‘Georgi D, Efremov’, MASA, Skopje, Republic of North Macedonia, 1000
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland, 90220
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland, 90220
| | - Paolo Radice
- Unit of Predictice Medicine, Molecular Bases of Genetic Risk, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy, 20133
| | - Muhammad U. Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan, 54000
| | - Gad Rennert
- Technion, Faculty of Medicine and Association for Promotion of Research in Precision Medicine, Haifa, Israel
| | - Eleanor Roberts
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Juan Rodriguez
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 171 65
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain, 28222
| | - Efraim H. Rosenberg
- Department of Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, the Netherlands, 1066 CX
| | | | - Dale P. Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA, 27709
| | - Elinor J. Sawyer
- School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy’s Campus, King’s College London, London, UK
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany, 50937
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany, 50937
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany, 50931
| | - Christopher G. Scott
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA, 55905
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA, 37232
| | - Melissa C. Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia, 3168
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia, 3010
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia, 3004
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia, 3010
- Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia, Perth, Western Australia, Australia, 6000
| | - Jack A. Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA, 27709
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA, 27709
| | - Lauren R. Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA, 30303
| | - Irma van de Beek
- Department of Clinical Genetics, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, the Netherlands, 1066 CX
| | - Walter Willett
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA, 02115
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA, 02115
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA, 02115
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland, 90220
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland, 90220
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA, 37232
| | - Celine M. Vachon
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA, 55905
| | - Marjanka K. Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands, 1066 CX
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, the Netherlands, 1066 CX
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands, 2333 ZA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 171 65
- Department of Oncology, Södersjukhuset, Stockholm, Sweden, 118 83
| | - Robert J. MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia, 3010
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia, 3004
| | - Roger L. Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia, 3010
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia, 3168
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia, 3004
| | - Paul D.P. Pharoah
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, USA, 90069
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec – Université Laval Research Center, Québec City, Québec, Canada, G1V 4G2
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus, 2371
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
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Kanner CH, Uher D, Zreibe K, Beard G, Patterson M, Harris M, Doerger J, Calamia S, Chung WK, Montes J. Validation of a modified version of the gross motor function measure in PPPR5D related neurodevelopmental disorder. Orphanet J Rare Dis 2024; 19:45. [PMID: 38326877 PMCID: PMC10848481 DOI: 10.1186/s13023-024-03067-3] [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: 09/19/2023] [Accepted: 02/03/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Protein phosphatase 2 regulatory subunit B' Delta (PPP2R5D)-related neurodevelopmental disorder is a rare genetic condition caused by pathogenic variants in the PPP2R5D gene. Clinical signs include hypotonia, gross motor delay, intellectual disability (ID), epilepsy, speech delays, and abnormal gait among other impairments. As this disorder was recognized within the last decade, there are only 103 people published diagnoses to date. A thorough understanding of the motor manifestations of this disorder has not yet been established. Knowledge of the natural history of PPP2R5D related neurodevelopmental disorder will lead to improved standard of care treatments as well as serve as a baseline foundation for future clinical trials. Appropriate outcome measures are necessary for use in clinical trials to uniformly measure function and monitor potential for change. The aim of this study was to validate the gross motor function measure (GMFM) in children and adults with PPP2R5D-related neurodevelopmental disorder in order to better characterize the disorder. RESULTS Thirty-eight individuals with PPP2R5D pathogenic variants, median age 8.0 years (range 1-27) were evaluated. Gross motor, upper limb and ambulatory function were assessed using the GMFM-66, six-minute walk test (6MWT), 10-meter walk run (10MWR), timed up and go (TUG), and revised upper limb module (RULM). The pediatric disability inventory computer adapted test (PEDI-CAT) captured caregiver reported assessment. Median GMFM-66 score was 60.6 (SD = 17.3, range 21.1-96.0). There were strong associations between the GMFM-66 and related mobility measures, 10MWR (rs = -0.733; p < 0.001), TUG (rs= -0.747; p = 0.003), 6MWT (r = 0.633; p = 0.006), RULM (r = 0.763; p < 0.001), PEDICAT-mobility (r = 0.855; p < 0.001), and daily activities (r = 0.822; p < 0.001) domains. CONCLUSIONS The GMFM is a valid measure for characterizing motor function in individuals with PPP2R5D related neurodevelopmental disorder. The GMFM-66 had strong associations with the RULM and timed function tests which characterized gross motor, upper limb and ambulatory function demonstrating concurrent validity. The GMFM-66 was also able to differentiate between functional levels in PPP2R5D related neurodevelopmental disorder demonstrating discriminant validity. Future studies should examine its sensitivity to change over time, ability to identify sub-phenotypes, and suitability as an outcome measure in future clinical trials in individuals with PPP2R5D variants.
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Affiliation(s)
- Cara H Kanner
- Department of Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, 617 West 168th Street, New York, NY, 10032, USA.
| | - David Uher
- Department of Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, 617 West 168th Street, New York, NY, 10032, USA
- Department of Biobehavioral Sciences, Teachers College, Columbia University, New York, NY, USA
| | - Kyle Zreibe
- Department of Rehabilitation, UHealth-Jackson Holtz Children's Hospital, Miami, FL, USA
| | - Gabriella Beard
- Department of Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, 617 West 168th Street, New York, NY, 10032, USA
| | - Madison Patterson
- Department of Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, 617 West 168th Street, New York, NY, 10032, USA
| | - Matthew Harris
- Department of Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, 617 West 168th Street, New York, NY, 10032, USA
| | - Jerome Doerger
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Sean Calamia
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jacqueline Montes
- Department of Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, 617 West 168th Street, New York, NY, 10032, USA
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27
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Kehm RD, Knight JA, Houghton LC, McDonald JA, Schwartz LA, Goldberg M, Chung WK, Frost CJ, Wei Y, Bradbury AR, Keegan THM, Daly MB, Buys SS, Andrulis IL, John EM, Terry MB. Childhood physical activity and pubertal timing: findings from the LEGACY girls study. Int J Epidemiol 2024; 53:dyad193. [PMID: 38205889 PMCID: PMC10859159 DOI: 10.1093/ije/dyad193] [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: 02/24/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND There is limited research on whether physical activity (PA) in early childhood is associated with the timing of pubertal events in girls. METHODS We used data collected over 2011-16 from the LEGACY Girls Study (n = 984; primarily aged 6-13 years at study enrolment), a multicentre North American cohort enriched for girls with a breast cancer family history (BCFH), to evaluate if PA is associated with age at thelarche, pubarche and menarche. Maternal-reported questionnaire data measured puberty outcomes, PA in early childhood (ages 3-5 years) and total metabolic equivalents of organized PA in middle childhood (ages 7-9 years). We used interval-censored Weibull parametric survival regression models with age as the time scale and adjusted for sociodemographic factors, and we tested for effect modification by BCFH. We used inverse odds weighting to test for mediation by body mass index-for-age z-score (BMIZ) measured at study enrolment. RESULTS Being highly active vs inactive in early childhood was associated with later thelarche in girls with a BCFH [adjusted hazard ratio (aHR) = 0.39, 95% CI = 0.26-0.59), but not in girls without a BCFH. In all girls, irrespective of BCFH, being in the highest vs lowest quartile of organized PA in middle childhood was associated with later menarche (aHR = 0.70, 95% CI = 0.50-0.97). These associations remained after accounting for potential mediation by BMIZ. CONCLUSION This study provides new data that PA in early childhood may be associated with later thelarche in girls with a BCFH, also further supporting an overall association between PA in middle childhood and later menarche.
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Affiliation(s)
- Rebecca D Kehm
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Julia A Knight
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Lauren C Houghton
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Jasmine A McDonald
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Lisa A Schwartz
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mandy Goldberg
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Departments of Pediatrics and Medicine, Columbia University Irving Medical centre, New York, NY, USA
| | - Caren J Frost
- College of Social Work, University of Utah, Salt Lake City, UT, USA
| | - Ying Wei
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Angela R Bradbury
- Departments of Medicine and Hematology/Oncology and of Medical Ethics and Health Policy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Theresa H M Keegan
- Department of Internal Medicine, Center for Oncology Hematology Outcomes Research and Training (COHORT), University of California, Davis, Sacramento, CA, USA
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer centre, Philadelphia, PA, USA
| | - Saundra S Buys
- Department of Medicine, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, UT, USA
| | - Irene L Andrulis
- Fred A. Litwin centre for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Esther M John
- Departments of Epidemiology & Population Health and Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
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28
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Klitzman R, Bezborodko E, Chung WK, Appelbaum PS. Receiving de novo genetic diagnoses for autism with intellectual disability: parents' views of impacts on families' reproductive decisions. J Community Genet 2024; 15:85-96. [PMID: 37843780 PMCID: PMC10857994 DOI: 10.1007/s12687-023-00679-3] [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: 07/25/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Parents of children with autism who receive genetic diagnoses of de novo variants face challenges in understanding the implications for reproductive decision-making. We interviewed 28 parents who received de novo genetic diagnoses for their child's autism and intellectual disability (ID). These genetic variants proved to have reproductive implications for not only the child's parents, but the child and his/her neurotypical siblings, aunts, uncles, and cousins. Parents had often already finished building their families but varied, overall, in whether the results had affected, or might have influenced, their reproductive decisions. Parents' views were shaped by factors related to not only genetics, but also parental age, financial considerations, competing hopes and visions for their family's future, perceived abilities to care for an additional child with similar symptoms, and the extent of the child's symptoms. Members of a couple sometimes disagreed about whether to have more children. Parents pondered, too, the possibility of preimplantation genetic testing, though misunderstandings about it arose. Children with autism vary widely in their abilities to understand the reproductive implications of genetic diagnoses for themselves. Neurotypical offspring were much relieved to understand that their own children would not be affected. While some autism self-advocates have been concerned that genetic testing related to autism could lead to eugenics, the present data, concerning de novo genetic findings, raise other perspectives. These data, the first to explore several key aspects of the reproductive implications of genetic diagnoses for this group, have important implications for future practice, education, and research-e.g., concerning various family members.
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Affiliation(s)
- Robert Klitzman
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Joseph L. Mailman School of Public Health, Columbia University, 1051 Riverside Drive, Mail Unit #15, New York, NY, 10032, USA.
| | - Ekaterina Bezborodko
- Department of Law, Ethics and Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul S Appelbaum
- Medicine and Law, Center for Law, Ethics and Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
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29
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Lennon NJ, Kottyan LC, Kachulis C, Abul-Husn NS, Arias J, Belbin G, Below JE, Berndt SI, Chung WK, Cimino JJ, Clayton EW, Connolly JJ, Crosslin DR, Dikilitas O, Velez Edwards DR, Feng Q, Fisher M, Freimuth RR, Ge T, Glessner JT, Gordon AS, Patterson C, Hakonarson H, Harden M, Harr M, Hirschhorn JN, Hoggart C, Hsu L, Irvin MR, Jarvik GP, Karlson EW, Khan A, Khera A, Kiryluk K, Kullo I, Larkin K, Limdi N, Linder JE, Loos RJF, Luo Y, Malolepsza E, Manolio TA, Martin LJ, McCarthy L, McNally EM, Meigs JB, Mersha TB, Mosley JD, Musick A, Namjou B, Pai N, Pesce LL, Peters U, Peterson JF, Prows CA, Puckelwartz MJ, Rehm HL, Roden DM, Rosenthal EA, Rowley R, Sawicki KT, Schaid DJ, Smit RAJ, Smith JL, Smoller JW, Thomas M, Tiwari H, Toledo DM, Vaitinadin NS, Veenstra D, Walunas TL, Wang Z, Wei WQ, Weng C, Wiesner GL, Yin X, Kenny EE. Selection, optimization and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse US populations. Nat Med 2024; 30:480-487. [PMID: 38374346 PMCID: PMC10878968 DOI: 10.1038/s41591-024-02796-z] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
Polygenic risk scores (PRSs) have improved in predictive performance, but several challenges remain to be addressed before PRSs can be implemented in the clinic, including reduced predictive performance of PRSs in diverse populations, and the interpretation and communication of genetic results to both providers and patients. To address these challenges, the National Human Genome Research Institute-funded Electronic Medical Records and Genomics (eMERGE) Network has developed a framework and pipeline for return of a PRS-based genome-informed risk assessment to 25,000 diverse adults and children as part of a clinical study. From an initial list of 23 conditions, ten were selected for implementation based on PRS performance, medical actionability and potential clinical utility, including cardiometabolic diseases and cancer. Standardized metrics were considered in the selection process, with additional consideration given to strength of evidence in African and Hispanic populations. We then developed a pipeline for clinical PRS implementation (score transfer to a clinical laboratory, validation and verification of score performance), and used genetic ancestry to calibrate PRS mean and variance, utilizing genetically diverse data from 13,475 participants of the All of Us Research Program cohort to train and test model parameters. Finally, we created a framework for regulatory compliance and developed a PRS clinical report for return to providers and for inclusion in an additional genome-informed risk assessment. The initial experience from eMERGE can inform the approach needed to implement PRS-based testing in diverse clinical settings.
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Affiliation(s)
| | - Leah C Kottyan
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Josh Arias
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gillian Belbin
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Sonja I Berndt
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - James J Cimino
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - David R Crosslin
- Tulane University, New Orleans, LA, USA
- University of Washington, Seattle, WA, USA
| | | | | | - QiPing Feng
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Tian Ge
- Mass General Brigham, Boston, MA, USA
| | | | | | | | | | - Maegan Harden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Margaret Harr
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joel N Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Clive Hoggart
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Hsu
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | | | | | | | - Amit Khera
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Katie Larkin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nita Limdi
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Ruth J F Loos
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuan Luo
- Northwestern University, Evanston, IL, USA
| | | | - Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa J Martin
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Li McCarthy
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tesfaye B Mersha
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Bahram Namjou
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Nihal Pai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Cynthia A Prows
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dan M Roden
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | - Hemant Tiwari
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | | | - Zhe Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wei-Qi Wei
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | - Eimear E Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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30
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Maleyeff L, Newburger JW, Wypij D, Thomas NH, Anagnoustou E, Brueckner M, Chung WK, Cleveland J, Cunningham S, Gelb BD, Goldmuntz E, Hagler DJ, Huang H, King E, McQuillen P, Miller TA, Norris‐Brilliant A, Porter GA, Roberts AE, Grant PE, Im K, Morton SU. Association of genetic and sulcal traits with executive function in congenital heart disease. Ann Clin Transl Neurol 2024; 11:278-290. [PMID: 38009418 PMCID: PMC10863927 DOI: 10.1002/acn3.51950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 11/28/2023] Open
Abstract
OBJECTIVE Persons with congenital heart disease (CHD) are at increased risk of neurodevelopmental disabilities, including impairments to executive function. Sulcal pattern features correlate with executive function in adolescents with single-ventricle heart disease and tetralogy of Fallot. However, the interaction of sulcal pattern features with genetic and participant factors in predicting executive dysfunction is unknown. METHODS We studied sulcal pattern features, participant factors, and genetic risk for executive function impairment in a cohort with multiple CHD types using stepwise linear regression and machine learning. RESULTS Genetic factors, including predicted damaging de novo or rare inherited variants in neurodevelopmental disabilities risk genes, apolipoprotein E genotype, and principal components of sulcal pattern features were associated with executive function measures after adjusting for age at testing, sex, mother's education, and biventricular versus single-ventricle CHD in a linear regression model. Using regression trees and bootstrap validation, younger participant age and larger alterations in sulcal pattern features were consistently identified as important predictors of decreased cognitive flexibility with left hemisphere graph topology often selected as the most important predictor. Inclusion of both sulcal pattern and genetic factors improved model fit compared to either alone. INTERPRETATION We conclude that sulcal measures remain important predictors of cognitive flexibility, and the model predicting executive outcomes is improved by inclusion of potential genetic sources of neurodevelopmental risk. If confirmed, measures of sulcal patterning may serve as early imaging biomarkers to identify those at heightened risk for future neurodevelopmental disabilities.
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Affiliation(s)
- Lara Maleyeff
- Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMassachusettsUSA
| | - Jane W. Newburger
- Department of PediatricsHarvard Medical SchoolBostonMassachusettsUSA
- Department of CardiologyBoston Children's HospitalBostonMassachusettsUSA
| | - David Wypij
- Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMassachusettsUSA
- Department of PediatricsHarvard Medical SchoolBostonMassachusettsUSA
- Department of CardiologyBoston Children's HospitalBostonMassachusettsUSA
| | - Nina H. Thomas
- Department of Child and Adolescent Psychiatry and Behavioral Sciences and Center for Human Phenomic ScienceChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
- Department of PsychiatryUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Evdokia Anagnoustou
- Department of PediatricsHolland Bloorview Kids Rehabilitation Hospital, University of TorontoTorontoOntarioCanada
| | - Martina Brueckner
- Department of GeneticsYale University School of MedicineNew HavenConnecticutUSA
- Department of PediatricsYale University School of MedicineNew HavenConnecticutUSA
| | - Wendy K. Chung
- Department of PediatricsColumbia University Medical CenterNew YorkNew YorkUSA
- Department of MedicineColumbia University Medical CenterNew YorkNew YorkUSA
| | - John Cleveland
- Department of Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Department of Pediatrics, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Sean Cunningham
- Division of General Pediatrics, Department of PediatricsUniversity of UtahSalt Lake CityUtahUSA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and Department of PediatricsIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Elizabeth Goldmuntz
- Division of Cardiology, Department of PediatricsChildren's Hospital of Philadelphia, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Donald J Hagler
- Center for Multimodal Imaging and GeneticsUniversity of California San DiegoSan DiegoCaliforniaUSA
- Department of Radiology, School of MedicineUniversity of California San DiegoSan DiegoCaliforniaUSA
| | - Hao Huang
- Department of RadiologyChildren's Hospital of Philadelphia, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Eileen King
- Department of PediatricsUniversity of CincinnatiCincinnatiOhioUSA
- Division of Biostatistics and EpidemiologyCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Patrick McQuillen
- Department of PediatricsUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of NeurologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Thomas A. Miller
- Department of PediatricsPrimary Children's Hospital, University of UtahSalt Lake CityUtahUSA
- Division of Pediatric CardiologyMaine Medical CenterPortlandMaineUSA
| | - Ami Norris‐Brilliant
- Department of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - George A. Porter
- Department of PediatricsUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Amy E. Roberts
- Department of PediatricsHarvard Medical SchoolBostonMassachusettsUSA
- Department of CardiologyBoston Children's HospitalBostonMassachusettsUSA
- Division of Genetics and GenomicsBoston Children's HospitalBostonMassachusettsUSA
| | - P. Ellen Grant
- Department of PediatricsHarvard Medical SchoolBostonMassachusettsUSA
- Division of Newborn Medicine, Department of PediatricsBoston Children's HospitalBostonMassachusettsUSA
- Fetal Neonatal Neuroimaging and Developmental Science CenterBoston Children's HospitalBostonMassachusettsUSA
- Department of RadiologyBoston Children's HospitalBostonMassachusettsUSA
| | - Kiho Im
- Department of PediatricsHarvard Medical SchoolBostonMassachusettsUSA
- Division of Newborn Medicine, Department of PediatricsBoston Children's HospitalBostonMassachusettsUSA
- Fetal Neonatal Neuroimaging and Developmental Science CenterBoston Children's HospitalBostonMassachusettsUSA
| | - Sarah U. Morton
- Department of PediatricsHarvard Medical SchoolBostonMassachusettsUSA
- Division of Newborn Medicine, Department of PediatricsBoston Children's HospitalBostonMassachusettsUSA
- Fetal Neonatal Neuroimaging and Developmental Science CenterBoston Children's HospitalBostonMassachusettsUSA
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31
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Stokes G, Li Z, Talaba N, Genthe W, Brix MB, Pham B, Wienhold MD, Sandok G, Hernan R, Wynn J, Tang H, Tabima DM, Rodgers A, Hacker TA, Chesler NC, Zhang P, Murad R, Yuan JXJ, Shen Y, Chung WK, McCulley DJ. Rescuing lung development through embryonic inhibition of histone acetylation. Sci Transl Med 2024; 16:eadc8930. [PMID: 38295182 DOI: 10.1126/scitranslmed.adc8930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
A major barrier to the impact of genomic diagnosis in patients with congenital malformations is the lack of understanding regarding how sequence variants contribute to disease pathogenesis and whether this information could be used to generate patient-specific therapies. Congenital diaphragmatic hernia (CDH) is among the most common and severe of all structural malformations; however, its underlying mechanisms are unclear. We identified loss-of-function sequence variants in the epigenomic regulator gene SIN3A in two patients with complex CDH. Tissue-specific deletion of Sin3a in mice resulted in defects in diaphragm development, lung hypoplasia, and pulmonary hypertension, the cardinal features of CDH and major causes of CDH-associated mortality. Loss of SIN3A in the lung mesenchyme resulted in reduced cellular differentiation, impaired cell proliferation, and increased DNA damage. Treatment of embryonic Sin3a mutant mice with anacardic acid, an inhibitor of histone acetyltransferase, reduced DNA damage, increased cell proliferation and differentiation, improved lung and pulmonary vascular development, and reduced pulmonary hypertension. These findings demonstrate that restoring the balance of histone acetylation can improve lung development in the Sin3a mouse model of CDH.
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Affiliation(s)
- Giangela Stokes
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | - Zhuowei Li
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | - Nicole Talaba
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | - William Genthe
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Maria B Brix
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Betty Pham
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | | | - Gracia Sandok
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Rebecca Hernan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Haiyang Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Diana M Tabima
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Allison Rodgers
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Timothy A Hacker
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Naomi C Chesler
- Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center and Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Pan Zhang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Rabi Murad
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jason X-J Yuan
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yufeng Shen
- Department of Systems Biology, Department of Biomedical Informatics, and JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David J McCulley
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
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32
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Casillan A, Florido ME, Galarza-Cornejo J, Bakken S, Lynch JA, Chung WK, Mittendorf KF, Berner ES, Connolly JJ, Weng C, Holm IA, Khan A, Kiryluk K, Limdi NA, Petukhova L, Sabatello M, Wynn J. Participant-guided development of bilingual genomic educational infographics for Electronic Medical Records and Genomics Phase IV study. J Am Med Inform Assoc 2024; 31:306-316. [PMID: 37860921 PMCID: PMC10797276 DOI: 10.1093/jamia/ocad207] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/11/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
OBJECTIVE Developing targeted, culturally competent educational materials is critical for participant understanding of engagement in a large genomic study that uses computational pipelines to produce genome-informed risk assessments. MATERIALS AND METHODS Guided by the Smerecnik framework that theorizes understanding of multifactorial genetic disease through 3 knowledge types, we developed English and Spanish infographics for individuals enrolled in the Electronic Medical Records and Genomics Network. Infographics were developed to explain concepts in lay language and visualizations. We conducted iterative sessions using a modified "think-aloud" process with 10 participants (6 English, 4 Spanish-speaking) to explore comprehension of and attitudes towards the infographics. RESULTS We found that all but one participant had "awareness knowledge" of genetic disease risk factors upon viewing the infographics. Many participants had difficulty with "how-to" knowledge of applying genetic risk factors to specific monogenic and polygenic risks. Participant attitudes towards the iteratively-refined infographics indicated that design saturation was reached. DISCUSSION There were several elements that contributed to the participants' comprehension (or misunderstanding) of the infographics. Visualization and iconography techniques best resonated with those who could draw on prior experiences or knowledge and were absent in those without. Limited graphicacy interfered with the understanding of absolute and relative risks when presented in graph format. Notably, narrative and storytelling theory that informed the creation of a vignette infographic was most accessible to all participants. CONCLUSION Engagement with the intended audience who can identify strengths and points for improvement of the intervention is necessary to the development of effective infographics.
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Affiliation(s)
- Aimiel Casillan
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, United States
| | - Michelle E Florido
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, United States
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, United States
| | - Jamie Galarza-Cornejo
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Suzanne Bakken
- Department of Nursing Scholarship and Research, School of Nursing, Columbia University Irving Medical Center, New York, NY 10032, United States
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - John A Lynch
- Department of Communication, School of Communication, Film, and Media Studies, University of Cincinnati, Cincinnati, OH 45221, United States
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Eta S Berner
- Department of Health Services Administration, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - John J Connolly
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Ingrid A Holm
- Division of Genetics and Genomics and Manton Center for Orphan Diseases Research, Boston Children’s Hospital, Boston, MA 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, United States
- Department of Medicine, Division of Nephrology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, United States
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, United States
| | - Nita A Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, United States
| | - Lynn Petukhova
- Department of Epidemiology, Columbia Mailman School of Public Health, New York, NY 10032, United States
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Maya Sabatello
- Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Irving Medical Center, New York, NY 10032, United States
- Department of Medical Humanities and Ethics, Division of Ethics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Julia Wynn
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, United States
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, United States
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33
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Scott SN, Siguencia M, Stanczyk FZ, Hartmann MF, Wudy SA, White M, Chung WK, Santella RM, Terry MB, Houghton LC. Urinary Androgens Provide Additional Evidence Related to Metabolism and Are Correlated With Serum Androgens in Girls. J Endocr Soc 2024; 8:bvad161. [PMID: 38234314 PMCID: PMC10790961 DOI: 10.1210/jendso/bvad161] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Indexed: 01/19/2024] Open
Abstract
Context Androgen levels are generally measured in serum samples, but urine may be a more feasible option, especially in children, as it is a noninvasive alternative. Objective To assess the correlations of 10 urinary androgen metabolites with 4 serum androgens [dehydroepiandrosterone-sulfate (DHEA-S), androstenedione, and total and free testosterone] and assess if their correlations differ by participant characteristics. Methods Our study consisted of 44 girls, ages 6-13, who participated in the New York site of the LEGACY Girls Study and had both serum and urine samples collected at the same visit. We performed Pearson's correlation coefficient tests between 4 serum and 10 individual urinary metabolite measures and their sum. We examined the influence of participant characteristics on the magnitude and direction of the correlations. Results The summed urinary metabolite measures had the highest correlation with free testosterone in serum (global sum, r = 0.83) and correlated least with DHEA-S in serum (global sum, r = 0.64). The correlation between individual urinary metabolites and serum androgens ranged from 0.08 to 0.84.Two 11-oxygenated urinary metabolites (5α-androstane-3α-ol-11,17-dione5β-androstane-3α,11β-diol-17-one) were weakly correlated with all serum androgens. Participant age, weight, height, waist:hip ratio, and pubic hair growth stage changed the correlations between urinary and serum androgens measures between 10% and 213%. Conclusion The sum of urinary androgen metabolites was a good marker of circulating androstenedione, testosterone, and free testosterone. Individual urinary metabolites provide additional information about the metabolic processes of disease development compared to the antecedent serum androgens.
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Affiliation(s)
- Sasinya N Scott
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Marvin Siguencia
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Frank Z Stanczyk
- Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Michaela F Hartmann
- Steroid Research and Mass Spectrometry Unit, Laboratory of Translational Hormone Analytics in Pediatric Endocrinology, Division of Pediatric Endocrinology & Diabetology, Center of Child and Adolescent Medicine, Justus Liebig University, 35392, Giessen, Germany
| | - Stefan A Wudy
- Steroid Research and Mass Spectrometry Unit, Laboratory of Translational Hormone Analytics in Pediatric Endocrinology, Division of Pediatric Endocrinology & Diabetology, Center of Child and Adolescent Medicine, Justus Liebig University, 35392, Giessen, Germany
| | - Melissa White
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Wendy K Chung
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Regina M Santella
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Lauren C Houghton
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
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Salpietro V, Maroofian R, Zaki MS, Wangen J, Ciolfi A, Barresi S, Efthymiou S, Lamaze A, Aughey GN, Al Mutairi F, Rad A, Rocca C, Calì E, Accogli A, Zara F, Striano P, Mojarrad M, Tariq H, Giacopuzzi E, Taylor JC, Oprea G, Skrahina V, Rehman KU, Abd Elmaksoud M, Bassiony M, El Said HG, Abdel-Hamid MS, Al Shalan M, Seo G, Kim S, Lee H, Khang R, Issa MY, Elbendary HM, Rafat K, Marinakis NM, Traeger-Synodinos J, Ververi A, Sourmpi M, Eslahi A, Khadivi Zand F, Beiraghi Toosi M, Babaei M, Jackson A, Bertoli-Avella A, Pagnamenta AT, Niceta M, Battini R, Corsello A, Leoni C, Chiarelli F, Dallapiccola B, Faqeih EA, Tallur KK, Alfadhel M, Alobeid E, Maddirevula S, Mankad K, Banka S, Ghayoor-Karimiani E, Tartaglia M, Chung WK, Green R, Alkuraya FS, Jepson JEC, Houlden H. Bi-allelic genetic variants in the translational GTPases GTPBP1 and GTPBP2 cause a distinct identical neurodevelopmental syndrome. Am J Hum Genet 2024; 111:200-210. [PMID: 38118446 PMCID: PMC10806450 DOI: 10.1016/j.ajhg.2023.11.012] [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: 05/15/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023] Open
Abstract
The homologous genes GTPBP1 and GTPBP2 encode GTP-binding proteins 1 and 2, which are involved in ribosomal homeostasis. Pathogenic variants in GTPBP2 were recently shown to be an ultra-rare cause of neurodegenerative or neurodevelopmental disorders (NDDs). Until now, no human phenotype has been linked to GTPBP1. Here, we describe individuals carrying bi-allelic GTPBP1 variants that display an identical phenotype with GTPBP2 and characterize the overall spectrum of GTP-binding protein (1/2)-related disorders. In this study, 20 individuals from 16 families with distinct NDDs and syndromic facial features were investigated by whole-exome (WES) or whole-genome (WGS) sequencing. To assess the functional impact of the identified genetic variants, semi-quantitative PCR, western blot, and ribosome profiling assays were performed in fibroblasts from affected individuals. We also investigated the effect of reducing expression of CG2017, an ortholog of human GTPBP1/2, in the fruit fly Drosophila melanogaster. Individuals with bi-allelic GTPBP1 or GTPBP2 variants presented with microcephaly, profound neurodevelopmental impairment, pathognomonic craniofacial features, and ectodermal defects. Abnormal vision and/or hearing, progressive spasticity, choreoathetoid movements, refractory epilepsy, and brain atrophy were part of the core phenotype of this syndrome. Cell line studies identified a loss-of-function (LoF) impact of the disease-associated variants but no significant abnormalities on ribosome profiling. Reduced expression of CG2017 isoforms was associated with locomotor impairment in Drosophila. In conclusion, bi-allelic GTPBP1 and GTPBP2 LoF variants cause an identical, distinct neurodevelopmental syndrome. Mutant CG2017 knockout flies display motor impairment, highlighting the conserved role for GTP-binding proteins in CNS development across species.
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Affiliation(s)
- Vincenzo Salpietro
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Jamie Wangen
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Sabina Barresi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Angelique Lamaze
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK; Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany
| | - Gabriel N Aughey
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
| | - Fuad Al Mutairi
- Genetic and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | | | - Clarissa Rocca
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Elisa Calì
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Andrea Accogli
- Division of Medical Genetics, Department of Pediatrics, McGill University, Montreal, Canada
| | - Federico Zara
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Unit of Pediatric Neurology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Huma Tariq
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Edoardo Giacopuzzi
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK; Genomics Research Centre, Human Technopole, Milan, Italy; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | | | - Marwa Abd Elmaksoud
- Neurology Unit, Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Mahmoud Bassiony
- Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Huda G El Said
- Department of Family Health, High Institute of Public Health, University of Alexandria, Alexandria, Egypt
| | - Mohamed S Abdel-Hamid
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Maha Al Shalan
- Genetic and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | | | | | - Hane Lee
- 3billion, Inc, Seoul, South Korea
| | | | - Mahmoud Y Issa
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Hasnaa M Elbendary
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Karima Rafat
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Nikolaos M Marinakis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Joanne Traeger-Synodinos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Athina Ververi
- Genetics Unit, Department of Obstetrics & Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital, Thessaloniki, Greece
| | | | - Atieh Eslahi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Masshad, Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Masshad, Iran
| | | | - Mehran Beiraghi Toosi
- Pediatric Neurology Department, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meisam Babaei
- Department of Pediatrics, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | | | | | - Marcello Niceta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Antonio Corsello
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Chiara Leoni
- Center for Rare Diseases and Birth Defects, Department of Women and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | | | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Eissa Ali Faqeih
- Unit of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Majid Alfadhel
- Genetic and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia; College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Eman Alobeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Kshitij Mankad
- Department of Neuroradiology, Great Ormond Street Hospital, London, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Ehsan Ghayoor-Karimiani
- Genetics Research Centre, Molecular and Clinical Sciences Institute, University of London, St George's, Cranmer Terrace, London SW17 0RE, UK
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital Harvard Medical School, Boston, MA 02115, USA
| | - Rachel Green
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - James E C Jepson
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
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Wu CG, Balakrishnan VK, Merrill RA, Parihar PS, Konovolov K, Chen YC, Xu Z, Wei H, Sundaresan R, Cui Q, Wadzinski BE, Swingle MR, Musiyenko A, Chung WK, Honkanen RE, Suzuki A, Huang X, Strack S, Xing Y. B56δ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan's syndrome mutations. Proc Natl Acad Sci U S A 2024; 121:e2310727120. [PMID: 38150499 PMCID: PMC10769853 DOI: 10.1073/pnas.2310727120] [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: 07/01/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023] Open
Abstract
Intrinsically disordered regions (IDR) and short linear motifs (SLiMs) play pivotal roles in the intricate signaling networks governed by phosphatases and kinases. B56δ (encoded by PPP2R5D) is a regulatory subunit of protein phosphatase 2A (PP2A) with long IDRs that harbor a substrate-mimicking SLiM and multiple phosphorylation sites. De novo missense mutations in PPP2R5D cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Our single-particle cryo-EM structures of the PP2A-B56δ holoenzyme reveal that the long, disordered arms at the B56δ termini fold against each other and the holoenzyme core. This architecture suppresses both the phosphatase active site and the substrate-binding protein groove, thereby stabilizing the enzyme in a closed latent form with dual autoinhibition. The resulting interface spans over 190 Å and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is coupled to an allosteric network responsive to phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations increase the holoenzyme activity and perturb the phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the normal variant.
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Affiliation(s)
- Cheng-Guo Wu
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
- Biophysics Program, University of Wisconsin at Madison, Madison, WI53706
| | - Vijaya K. Balakrishnan
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
| | - Ronald A. Merrill
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA52242
| | - Pankaj S. Parihar
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
| | - Kirill Konovolov
- Chemistry Department, University of Wisconsin at Madison, Madison, WI53706
| | - Yu-Chia Chen
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
- Molecular and Cellular Pharmacology Program, University of Wisconsin at Madison, Madison, WI53706
| | - Zhen Xu
- Protein and Crystallography Facility, University of Iowa, Iowa City, IA52242
| | - Hui Wei
- The Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY10027
| | - Ramya Sundaresan
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, MA02215
| | | | - Mark R. Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL36688
| | - Alla Musiyenko
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL36688
| | - Wendy K. Chung
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA02215
| | - Richard E. Honkanen
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL36688
| | - Aussie Suzuki
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
- Biophysics Program, University of Wisconsin at Madison, Madison, WI53706
- Molecular and Cellular Pharmacology Program, University of Wisconsin at Madison, Madison, WI53706
| | - Xuhui Huang
- Biophysics Program, University of Wisconsin at Madison, Madison, WI53706
- Chemistry Department, University of Wisconsin at Madison, Madison, WI53706
| | - Stefan Strack
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA52242
| | - Yongna Xing
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
- Biophysics Program, University of Wisconsin at Madison, Madison, WI53706
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Klitzman R, Bezborodko E, Chung WK, Appelbaum PS. Parents' views of benefits and limitations of receiving genetic diagnoses for their offspring. Child Care Health Dev 2024; 50:e13212. [PMID: 38097387 PMCID: PMC10841588 DOI: 10.1111/cch.13212] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/16/2023] [Accepted: 11/18/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Individuals with autism with intellectual disabilities (ID) are increasingly undergoing genetic testing, posing questions of how parents view/respond to such results. METHODS Twenty-eight parents whose offspring had received genetic diagnoses of de novo pathogenic variants associated with autism were interviewed. RESULTS Genetic diagnoses parents receive concerning their offspring's autism/intellectual disabilities can be 'double-edged' in several ways, having advantages, but also certain disadvantages and limitations. Benefits were medical/scientific (e.g., ending diagnostic odysseys and potentially contributing to research), emotional (e.g., relief, peace of mind and less self-blame), cognitive, social (e.g., validation and confirmation with others - it's 'not just in our head') and financial (e.g., estate planning), now and in the future (e.g., preparing for possible future symptoms, development and availability of treatment and setting realistic expectations). Limitations included a lack of medical treatments related to the genetic diagnosis, a sense of finality and heightened uncertainties which can increase anxieties (e.g., concerning additional symptoms associated with genetic diagnoses and offspring's ability to live independently in the future). Overall, parents were glad to receive the results, seeing the pros outweighing the cons. Parents responded to these tensions in various ways, having mixed feelings, recognizing the trade-offs and/or focusing on their offspring's present needs. Factors such as age of offspring at receipt of genetic diagnosis, parent's scientific background and prior views and degrees of self-blame affected these responses. CONCLUSIONS These data, the first to examine how parents perceive genetic diagnoses received for offspring with autism and ID through whole exome/whole genome sequencing, highlight practical medical and psychological benefits as well as limitations. These findings thus have important implications for future education, engagement of families and research. Providers should be aware of these issues, to inform and assist families, who are considering such testing, about these potential pros and cons and responses.
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Affiliation(s)
- Robert Klitzman
- Professor of Psychiatry and Director of the Masters of Bioethics Program; Department of Psychiatry; Columbia University; New York, NY, USA
| | - Ekaterina Bezborodko
- Research Associate; Department of Law Ethics and Psychiatry; Columbia University; New York, NY, USA
| | - Wendy K. Chung
- Chief, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School Boston, MA, USA
| | - Paul S. Appelbaum
- Elizabeth K. Dollard Professor of Psychiatry, Medicine and Law; Center for Law, Ethics and Psychiatry, Columbia University Irving Medical Center, New York, NY USA
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Levy AM, Ganapathi M, Chung WK, Tümer Z. A deep intronic DLG4 variant resulting in DLG4-related synaptopathy. Clin Genet 2024; 105:77-80. [PMID: 37525972 DOI: 10.1111/cge.14411] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/02/2023]
Abstract
The rare autosomal dominant brain disorder DLG4-related synaptopathy is caused by de novo variants in DLG4 (encoding PSD-95), the majority of which are predicted to be protein-truncating. In addition to splice site variants, a number of synonymous and missense DLG4 variants are predicted to exert their effect through altered RNA splicing, although the pathogenicity of these variants is uncertain without functional RNA studies. Here, we describe a young boy with a deep intronic DLG4 variant (c.2105+235C>T) identified using whole genome sequencing. By using reverse-transcription PCR on RNA derived from peripheral blood, we demonstrate that DLG4 mRNA expression is detectable in blood and the deep intronic variant gives rise to two alternative DLG4 transcripts, one of which includes a pseudoexon. Both alternative transcripts are out-of-frame and predicted to result in protein-truncation, thereby establishing the genetic diagnosis for the proband. This adds to the evidence concerning the pathogenic potential of deep intronic variants and underlines the importance of functional studies, even in cases where reported tissue-specific gene expression might suggest otherwise.
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Affiliation(s)
- Amanda M Levy
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Mythily Ganapathi
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York City, New York, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York City, New York, USA
| | - Zeynep Tümer
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Al-Qazazi R, Emon IM, Potus F, Martin AY, Lima PDA, Vlasschaert C, Chen KH, Wu D, Gupta AD, Noordhof C, Jefferson L, McNaughton AJM, Bick AG, Pauciulo MW, Nichols WC, Chung WK, Hassoun PM, Damico RL, Rauh MJ, Archer SL. Germline and Somatic Mutations in DNA Methyltransferase 3A (DNMT3A) Predispose to Pulmonary Arterial Hypertension (PAH) in Humans and Mice: Implications for Associated PAH. medRxiv 2023:2023.12.30.23300391. [PMID: 38234783 PMCID: PMC10793539 DOI: 10.1101/2023.12.30.23300391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Background Mutations are found in 10-20% of idiopathic PAH (IPAH) patients, but none are consistently identified in connective tissue disease-associated PAH (APAH), which accounts for ∼45% of PAH cases. TET2 mutations, a cause of clonal hematopoiesis of indeterminant potential (CHIP), predispose to an inflammatory type of PAH. We now examine mutations in another CHIP gene, DNMT3A , in PAH. Methods We assessed DNMT3A mutation prevalence in PAH Biobank subjects as compared with controls, first using whole exome sequencing (WES)-derived CHIP calls in 1832 PAH Biobank patients versus 7509 age-and sex-matched gnomAD controls. We then performed deep, targeted panel sequencing of CHIP genes on a subset of 710 PAH Biobank patients and compared the prevalence of DNMT3A mutations therein to an independent pooled control cohort (N = 3645). In another cohort of 80 PAH patients and 41 controls, DNMT3A mRNA expression was studied in peripheral blood mononuclear cells (PBMCs). Finally, we evaluated the development of PAH in a conditional, hematopoietic, Dnmt3a knockout mouse model. Results DNMT3A mutations were more frequent in PAH cases versus control subjects in the WES dataset (OR 2.60, 95% CI: 1.71-4.27). Among PAH patients, 33 had DNMT3A variants, most of whom had APAH (21/33). While 21/33 had somatic mutations (female:male 17:4), germline variants occurred in 12/33 (female:male 11:1). Hemodynamics were comparable with and without DNMT3A mutations (mPAP=58±21 vs. 52±18 mmHg); however, patients with DNMT3A mutations were unresponsive to acute vasodilator testing. Targeted panel sequencing identified that 14.6% of PAH patients had CHIP mutations (104/710), with DNMT3A accounting for 49/104. There was a significant association between all CHIP mutations and PAH in analyses adjusted for age and sex (OR 1.40, 95% CI: 1.09-1.80), though DNMT3A CHIP alone was not significantly enriched (OR:1.15, 0.82-1.61). DNMT3A expression was reduced in patient-derived versus control PAH-PBMCs. Spontaneous PAH developed in Dnmt3a -/- mice, and it was exacerbated by 3 weeks of hypoxia. Dnmt3a -/- mice had increased lung macrophages and elevated plasma IL-13. The IL-1β antibody canakinumab attenuated PAH in Dnmt3a -/- mice. Conclusions Germline and acquired DNMT3A variants predispose to PAH in humans. DNMT3A mRNA expression is reduced in human PAH PBMCs. Hematopoietic depletion of Dnmt3a causes inflammatory PAH in mice. DNMT3A is a novel APAH gene and may be a biomarker and therapeutic target.
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39
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Klitzman R, Bezborodko E, Chung WK, Appelbaum PS. Impact of Receiving Genetic Diagnoses on Parents' Perceptions of Their Children with Autism and Intellectual Disability. J Autism Dev Disord 2023:10.1007/s10803-023-06195-0. [PMID: 38158539 DOI: 10.1007/s10803-023-06195-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2023] [Indexed: 01/03/2024]
Abstract
To assess whether genetic test results identifying the cause of a child's autism, when accompanied by other neurodevelopmental disorders (NDD), including intellectual disability, alter how parents perceive and treat their child. 28 parents of 22 individuals with autism (mean age: 15 years), usually with other NDDs, were interviewed after receiving genetic diagnoses indicating a de novo mutation through the Simons Foundation Powering Autism Research for Knowledge study. Diagnosis of a de novo genetic variant can alter parental perceptions of offspring with autism and other NDDs. Parents often blamed their child less, saw their child as less in control of symptoms, and developed more patience, framing expectations accordingly. Parents had mixed feelings about receiving genetic diagnoses, with sadness sometimes accompanying reframed expectations. Genetic diagnoses could change views of the child among extended family members, teachers, social service agencies, insurers, and broader communities and society. Genetic testing might also reduce delays in diagnoses of autism among African American, Latino and other children. These data, the first to examine several critical aspects of how parents and others view children with autism and other NDDs after receiving genetic diagnoses, highlight vital needs for education of multiple stakeholders (including geneticists, other physicians, genetic counselors, parents, individuals with autism, social service agencies, insurers, policymakers, and the broader public), research (to include perspectives of extended family members, insurers, social service agencies and teachers) and practice (to increase recognition and awareness of the potential benefits and effects of genetic testing for such children).
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Affiliation(s)
- Robert Klitzman
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Joseph L. Mailman School of Public Health, Columbia University, 1051 Riverside Drive; Mail Unit #15, New York, NY, 10032, USA.
| | | | - Wendy K Chung
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul S Appelbaum
- Department of Law Ethics and Psychiatry, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY, USA
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Zhao Y, Zhong G, Hagen J, Pan H, Chung WK, Shen Y. A probabilistic graphical model for estimating selection coefficient of missense variants from human population sequence data. medRxiv 2023:2023.12.11.23299809. [PMID: 38168397 PMCID: PMC10760286 DOI: 10.1101/2023.12.11.23299809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Accurately predicting the effect of missense variants is a central problem in interpretation of genomic variation. Commonly used computational methods does not capture the quantitative impact on fitness in populations. We developed MisFit to estimate missense fitness effect using biobank-scale human population genome data. MisFit jointly models the effect at molecular level ( d ) and population level (selection coefficient, s ), assuming that in the same gene, missense variants with similar d have similar s . MisFit is a probabilistic graphical model that integrates deep neural network components and population genetics models efficiently with inductive bias based on biological causality of variant effect. We trained it by maximizing probability of observed allele counts in 236,017 European individuals. We show that s is informative in predicting frequency across ancestries and consistent with the fraction of de novo mutations given s . Finally, MisFit outperforms previous methods in prioritizing missense variants in individuals with neurodevelopmental disorders.
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Affiliation(s)
- Yige Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
- The Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032
| | - Guojie Zhong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
- The Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032
| | - Jake Hagen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032
| | - Hongbing Pan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032
| | - Wendy K. Chung
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032
- JP Sulzberger Columbia Genome Center, Columbia University, New York, NY 10032
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Daniels AM, Law JK, Green Snyder L, Diehl K, Goin-Kochel RP, Feliciano P, Chung WK. Effectiveness of multimodal participant recruitment in SPARK, a large, online longitudinal research study of autism. J Clin Transl Sci 2023; 8:e64. [PMID: 38655455 PMCID: PMC11036434 DOI: 10.1017/cts.2023.697] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 04/26/2024] Open
Abstract
Background SPARK launched in 2016 to build a US cohort of autistic individuals and their family members. Enrollment includes online consent to share data and optional consent to provide saliva for genomic analysis. SPARK's recruitment strategies include social media and support of a nation-wide network of clinical sites. This study evaluates SPARK's recruitment strategies to enroll a core study population. Methods Individuals who joined between January 31, 2018, and May 29, 2019 were included in the analysis. Data include sociodemographic characteristics, clinical site referral, the website URL used to join, how the participant heard about SPARK, enrollment completion (online registration, study consents, and returning saliva sample), and completion of the baseline questionnaire. Logistic regressions were performed to evaluate the odds of core participant status (completing enrollment and baseline questionnaire) by recruitment strategy. Results In total, 31,715 individuals joined during the study period, including 40% through a clinical site. Overall, 88% completed online registration, 46% returned saliva, and 38% were core participants. Those referred by a clinical site were almost twice as likely to be core participants. Those who directly visited the SPARK website or performed a Google search were more likely to be core participants than those who joined through social media. Discussion Being a core participant may be associated with the "personal" connection and support provided by a clinical site and/or site staff, as well as greater motivation to seek research opportunities. Findings from this study underscore the value of adopting a multimodal recruitment approach that combines social media and a physical presence.
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Affiliation(s)
| | - J. Kiely Law
- Simons Foundation, New York, NY,
USA
- Kennedy Krieger Institute, Baltimore,
MD, USA
| | | | | | | | | | - Wendy K. Chung
- Department of Pediatrics, Boston Children’s Hospital, Harvard
Medical School, Boston, MA,
USA
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Maroofian R, Kaiyrzhanov R, Cali E, Zamani M, Zaki MS, Ferla M, Tortora D, Sadeghian S, Saadi SM, Abdullah U, Karimiani EG, Efthymiou S, Yeşil G, Alavi S, Al Shamsi AM, Tajsharghi H, Abdel-Hamid MS, Saadi NW, Al Mutairi F, Alabdi L, Beetz C, Ali Z, Toosi MB, Rudnik-Schöneborn S, Babaei M, Isohanni P, Muhammad J, Khan S, Al Shalan M, Hickey SE, Marom D, Elhanan E, Kurian MA, Marafi D, Saberi A, Hamid M, Spaull R, Meng L, Lalani S, Maqbool S, Rahman F, Seeger J, Palculict TB, Lau T, Murphy D, Mencacci NE, Steindl K, Begemann A, Rauch A, Akbas S, Aslanger AD, Salpietro V, Yousaf H, Ben-Shachar S, Ejeskär K, Al Aqeel AI, High FA, Armstrong-Javors AE, Zahraei SM, Seifi T, Zeighami J, Shariati G, Sedaghat A, Asl SN, Shahrooei M, Zifarelli G, Burglen L, Ravelli C, Zschocke J, Schatz UA, Ghavideldarestani M, Kamel WA, Van Esch H, Hackenberg A, Taylor JC, Al-Gazali L, Bauer P, Gleeson JJ, Alkuraya FS, Lupski JR, Galehdari H, Azizimalamiri R, Chung WK, Baig SM, Houlden H, Severino M. Biallelic MED27 variants lead to variable ponto-cerebello-lental degeneration with movement disorders. Brain 2023; 146:5031-5043. [PMID: 37517035 PMCID: PMC10690011 DOI: 10.1093/brain/awad257] [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: 01/27/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
MED27 is a subunit of the Mediator multiprotein complex, which is involved in transcriptional regulation. Biallelic MED27 variants have recently been suggested to be responsible for an autosomal recessive neurodevelopmental disorder with spasticity, cataracts and cerebellar hypoplasia. We further delineate the clinical phenotype of MED27-related disease by characterizing the clinical and radiological features of 57 affected individuals from 30 unrelated families with biallelic MED27 variants. Using exome sequencing and extensive international genetic data sharing, 39 unpublished affected individuals from 18 independent families with biallelic missense variants in MED27 have been identified (29 females, mean age at last follow-up 17 ± 12.4 years, range 0.1-45). Follow-up and hitherto unreported clinical features were obtained from the published 12 families. Brain MRI scans from 34 cases were reviewed. MED27-related disease manifests as a broad phenotypic continuum ranging from developmental and epileptic-dyskinetic encephalopathy to variable neurodevelopmental disorder with movement abnormalities. It is characterized by mild to profound global developmental delay/intellectual disability (100%), bilateral cataracts (89%), infantile hypotonia (74%), microcephaly (62%), gait ataxia (63%), dystonia (61%), variably combined with epilepsy (50%), limb spasticity (51%), facial dysmorphism (38%) and death before reaching adulthood (16%). Brain MRI revealed cerebellar atrophy (100%), white matter volume loss (76.4%), pontine hypoplasia (47.2%) and basal ganglia atrophy with signal alterations (44.4%). Previously unreported 39 affected individuals had seven homozygous pathogenic missense MED27 variants, five of which were recurrent. An emerging genotype-phenotype correlation was observed. This study provides a comprehensive clinical-radiological description of MED27-related disease, establishes genotype-phenotype and clinical-radiological correlations and suggests a differential diagnosis with syndromes of cerebello-lental neurodegeneration and other subtypes of 'neuro-MEDopathies'.
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Affiliation(s)
- Reza Maroofian
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Elisa Cali
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
- Ati Mehr Kasra Genetics Institute, Kianpars, Ahvaz, Iran
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo 12622, Egypt
| | - Matteo Ferla
- Wellcome Centre for Human Genetics, University of Oxford and Oxford NIHR Biomedical Research Centre, Oxford, OX3 7BN UK
| | - Domenico Tortora
- Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Saeid Sadeghian
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saadia Maryam Saadi
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, 44000 Faisalabad, Pakistan
| | - Uzma Abdullah
- University Institute of Biochemistry and Biotechnology, PMAS Arid Agriculture University, 46300 Rawalpindi, Pakistan
| | - Ehsan Ghayoor Karimiani
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
- Molecular and Clinical Sciences Institute, St. George’s, University of London, London SW17 0RE, UK
- Innovative Medical Research Center, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Gözde Yeşil
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Turkey
| | - Shahryar Alavi
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Aisha M Al Shamsi
- Genetic Division, Pediatrics Department, Tawam Hospital, Al Ain, UAE
| | - Homa Tajsharghi
- School of Health Science, Division Biomedicine and Translational Medicine, University of Skovde, SE-541 28 Skovde, Sweden
| | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, 12622 Cairo, Egypt
| | - Nebal Waill Saadi
- College of Medicine, University of Baghdad, 10071 Baghdad, Iraq
- Children Welfare Teaching Hospital, 10071 Baghdad, Iraq
| | - Fuad Al Mutairi
- Genetics and Precision Medicine department, King Abdullah Specialized Children’s Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, 22384 Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, 22384 Riyadh, Saudi Arabia
| | - Lama Alabdi
- Department of Zoology, College of Science, King Saud University, 11421 Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, 12713 Riyadh, Saudi Arabia
| | | | - Zafar Ali
- Department of Cellular and Molecular Medicine, WJC PANUM, University of Copenhagen, DK-1165 Copenhagen, Denmark
- Centre for Biotechnology and Microbiology, University of Swat, Swat 19120, Pakistan
| | - Mehran Beiraghi Toosi
- Pediatric Neurology Department Pediatric Ward Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Meisam Babaei
- Department of Pediatrics, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Pirjo Isohanni
- Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Department of Child Neurology, Children’s Hospital, Paediatric Research Center, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
| | - Jameel Muhammad
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, 44000 Faisalabad, Pakistan
- Centre for Regenerative Medicine and Stem Cell Research, Juma Building, Aga Khan University, Karachi 74800, Pakistan
| | - Sheraz Khan
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, 44000 Faisalabad, Pakistan
| | - Maha Al Shalan
- Genetics and Precision Medicine department, King Abdullah Specialized Children’s Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, 22384 Riyadh, Saudi Arabia
| | - Scott E Hickey
- Division of Genetic & Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Daphna Marom
- Genetics Institute and Genomic Center, Tel Aviv Sourasky Medical Center, and Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Emil Elhanan
- Nephro-Genetic Clinic, Nephrology Department and Genetics Institute, Tel Aviv Medical Center, Tel Aviv 64239, Israel
| | - Manju A Kurian
- Molecular Neurosciences, Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Department of Neurology, Great Ormond Street Hospital, London WC1N 1EH, UK
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
| | - Alihossein Saberi
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Hamid
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Robert Spaull
- Nephro-Genetic Clinic, Nephrology Department and Genetics Institute, Tel Aviv Medical Center, Tel Aviv 64239, Israel
- Molecular Neurosciences, Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Linyan Meng
- Department of Neurology, Great Ormond Street Hospital, London WC1N 1EH, UK
| | - Seema Lalani
- Department of Neurology, Great Ormond Street Hospital, London WC1N 1EH, UK
| | - Shazia Maqbool
- Developmental-Behavioural Paediatrics Department, University of Child Health Sciences & The Children’s Hospital, 54000 Lahore, Pakistan
| | - Fatima Rahman
- Developmental-Behavioural Paediatrics Department, University of Child Health Sciences & The Children’s Hospital, 54000 Lahore, Pakistan
| | - Jürgen Seeger
- Center for Social Pediatrics and Epilepsy Outpatient Clinic Frankfurt Mitte, 60316 Frankfurt am Main, Germany
| | | | - Tracy Lau
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - David Murphy
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Niccolo Emanuele Mencacci
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Anais Begemann
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Sinan Akbas
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Turkey
| | - Ayça Dilruba Aslanger
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Turkey
| | - Vincenzo Salpietro
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
- Department of Biotechnological and Applied Clinical Sciences (DISCAB), University of L’Aquila, 67100 L’Aquila, Italy
| | - Hammad Yousaf
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, 44000 Faisalabad, Pakistan
| | - Shay Ben-Shachar
- Clalit Research Institute, Clalit Health Services, 6578898 Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katarina Ejeskär
- School of Health Science, Division Biomedicine and Translational Medicine, University of Skovde, SE-541 28 Skovde, Sweden
| | - Aida I Al Aqeel
- Department of Pediatrics, Prince Sultan Military Medical City, 12233 Riyadh, Saudi Arabia
- American University of Beirut, 1107 2020 Beirut, Lebanon
- Alfaisal University, 11533 Riyadh, Saudi Arabia
| | - Frances A High
- Division of Medical Genetics, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Amy E Armstrong-Javors
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Tahereh Seifi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
| | - Jawaher Zeighami
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
- Ati Mehr Kasra Genetics Institute, Kianpars, Ahvaz, Iran
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Alireza Sedaghat
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
- Diabetes Research center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Samaneh Noroozi Asl
- Department of Pediatrics Endocrinology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohmmad Shahrooei
- Specialized Immunology Laboratory of Dr Shahrooei, Sina Medical Complex, Ahvaz, Iran
- Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, 3000 Leuven, Belgium
| | | | - Lydie Burglen
- Cerebellar Malformations and Congenital diseases Reference Center and Neurogenetics Lab, Department of Genetics, Armand Trousseau Hospital, AP-HP Sorbonne Université, 75006 Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, 75015 Paris, France
| | - Claudia Ravelli
- Pediatric Neurology Department, Movement Disorders Center, Armand Trousseau Hospital, AP-HP Sorbonne Université, 75006 Paris, France
| | - Johannes Zschocke
- Institute of Human Genetics, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Ulrich A Schatz
- Institute of Human Genetics, Medical University Innsbruck, 6020 Innsbruck, Austria
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität Munich, 81675 Munich, Germany
| | | | - Walaa A Kamel
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Neurology, Faculty of Medicine, Beni-Suef University, 62521 Beni Suef, Egypt
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
- Laboratory for the Genetics of Cognition, Department of Human Genetics, KU Leuven–University of Leuven, 3000 Leuven, Belgium
| | - Annette Hackenberg
- Department of Pediatric Neurology, University Children's Hospital Zürich, University of Zürich, 8032 Zürich, Switzerland
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, University of Oxford and Oxford NIHR Biomedical Research Centre, Oxford, OX3 7BN UK
| | - Lihadh Al-Gazali
- Departments of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE
| | | | - Joseph J Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Fowzan Sami Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Ati Mehr Kasra Genetics Institute, Kianpars, Ahvaz, Iran
| | - Reza Azizimalamiri
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Wendy K Chung
- Boston Children’s Hospital and Harvard Medical School Boston, MA 02115, USA
| | - Shahid Mahmood Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, 44000 Faisalabad, Pakistan
- Department of Biological and Biomedical Sciences, Aga Khan University, 74800 Karachi, Pakistan
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
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Tambi R, Zehra B, Nandkishore S, Sharafat S, Kader F, Nassir N, Mohamed N, Ahmed A, Abdel Hameid R, Alasrawi S, Brueckner M, Kuebler WM, Chung WK, Alsheikh-Ali A, Di Donato RM, Uddin M, Berdiev BK. Single-cell reconstruction and mutation enrichment analysis identifies dysregulated cardiomyocyte and endothelial cells in congenital heart disease. Physiol Genomics 2023; 55:634-646. [PMID: 37811720 DOI: 10.1152/physiolgenomics.00070.2023] [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: 07/13/2023] [Revised: 09/19/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023] Open
Abstract
Congenital heart disease (CHD) is one of the most prevalent neonatal congenital anomalies. To catalog the putative candidate CHD risk genes, we collected 16,349 variants [single-nucleotide variants (SNVs) and Indels] impacting 8,308 genes in 3,166 CHD cases for a comprehensive meta-analysis. Using American College of Medical Genetics (ACMG) guidelines, we excluded the 0.1% of benign/likely benign variants and the resulting dataset consisted of 83% predicted loss of function variants and 17% missense variants. Seventeen percent were de novo variants. A stepwise analysis identified 90 variant-enriched CHD genes, of which six (GPATCH1, NYNRIN, TCLD2, CEP95, MAP3K19, and TTC36) were novel candidate CHD genes. Single-cell transcriptome cluster reconstruction analysis on six CHD tissues and four controls revealed upregulation of the top 10 frequently mutated genes primarily in cardiomyocytes. NOTCH1 (highest number of variants) and MYH6 (highest number of recurrent variants) expression was elevated in endocardial cells and cardiomyocytes, respectively, and 60% of these gene variants were associated with tetralogy of Fallot and coarctation of the aorta, respectively. Pseudobulk analysis using the single-cell transcriptome revealed significant (P < 0.05) upregulation of both NOTCH1 (endocardial cells) and MYH6 (cardiomyocytes) in the control heart data. We observed nine different subpopulations of CHD heart cardiomyocytes of which only four were observed in the control heart. This is the first comprehensive meta-analysis combining genomics and CHD single-cell transcriptomics, identifying the most frequently mutated CHD genes, and demonstrating CHD gene heterogeneity, suggesting that multiple genes contribute to the phenotypic heterogeneity of CHD. Cardiomyocytes and endocardial cells are identified as major CHD-related cell types.NEW & NOTEWORTHY Congential heart disease (CHD) is one of the most prevalent neonatal congenital anomalies. We present a comprehensive analysis combining genomics and CHD single-cell transcriptome. Our study identifies 90 potential candidate CHD risk genes of which 6 are novel. The risk genes have heterogenous expression suggestive of multiple genes contributing to the phenotypic heterogeneity of CHD. Cardiomyocytes and endocardial cells are identified as major CHD-related cell types.
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Affiliation(s)
- Richa Tambi
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Binte Zehra
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Sharon Nandkishore
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Shermin Sharafat
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Faiza Kader
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Nasna Nassir
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Nesrin Mohamed
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Awab Ahmed
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Reem Abdel Hameid
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Samah Alasrawi
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Al Jalila Children's Hospital, Dubai, United Arab Emirates
| | - Martina Brueckner
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States
- Department of Pediatrics, Yale University, New Haven, Connecticut, United States
| | - Wolfgang M Kuebler
- Institute of Physiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Wendy K Chung
- Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - Alawi Alsheikh-Ali
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Mohammed Uddin
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Cellular Intelligence Lab, GenomeArc Incorporated, Toronto, Ontario, Canada
| | - Bakhrom K Berdiev
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Cellular Intelligence Lab, GenomeArc Incorporated, Toronto, Ontario, Canada
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Chung WK, Herrera FF. Health supervision for children and adolescents with 16p11.2 deletion syndrome. Cold Spring Harb Mol Case Stud 2023; 9:a006316. [PMID: 38050025 PMCID: PMC10815286 DOI: 10.1101/mcs.a006316] [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] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
Rare genetic conditions are challenging for the primary care provider to manage without proper guidelines. This clinical review is designed to assist the pediatrician, family physician, or internist in the primary care setting to manage the complexities of 16p11.2 deletion syndrome. A multidisciplinary medical home with the primary care provider leading the care and armed with up-to-date guidelines will prove most helpful to the rare genetic patient population. A special focus on technology to fill gaps in deficits, review of case studies on novel medical treatments, and involvement with the educational system for advocacy with an emphasis on celebrating diversity will serve the rare genetic syndrome population well.
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Affiliation(s)
- Wendy K Chung
- Harvard Medical School and Boston Children's Hospital, Boston, Massachusetts 02115, USA
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Shain J, Michel A, May MS, Qunaj L, El-Sadr W, Chung WK, Appelbaum PS, Jacobson JS, Justman J, Neugut AI. Cancer genetic mutation prevalence in sub-Saharan Africa: A review of existing data. Semin Oncol 2023; 50:123-130. [PMID: 38171987 DOI: 10.1053/j.seminoncol.2023.12.001] [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: 11/20/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Cancer represents a leading cause of death worldwide. Germline mutations in several genes increase the risk of developing several cancers, including cancers of the breast, ovary, pancreas, colorectum, and melanoma. An understanding of the population prevalence of pathogenic germline variants can be helpful in the design of public health interventions, such as genetic testing, which has downstream implications for cancer screening, prevention, and treatment. While population-based studies of pathogenic germline variants exist, most such studies have been conducted in White populations. Limited data exist regarding the prevalence of germline mutations within sub-Saharan African populations. MATERIALS AND METHODS We identified countries defined as sub-Saharan Africa by the World Bank and conducted a scoping literature review using PubMed. For each country, we identified and summarized studies that focused on the prevalence of germline genetic mutations with sample sizes >10 and in a population directly from sub-Saharan Africa, either with or without diseases associated with the relevant genetic mutations. Studies that evaluated the prevalence of somatic or likely benign variants were excluded. RESULTS Within the 48 countries in sub-Saharan Africa, we identified 34 studies which meet the inclusion criteria. Twenty studies were conducted in South Africa, Nigeria, or Burkina Faso; four countries had more than two published papers. We found that 33 of 48 countries in sub-Saharan Africa lacked any genetic studies. Notably, there has been an increase in relevant studies starting in 2020. Importantly, of the 34 studies identified, 29 included data on BRCA1 or BRCA2. Data on the prevalence of mutations contributing to familial cancer syndromes other than BRCA1 and BRCA2 was limited. CONCLUSIONS While some progress has been made towards understanding the prevalence of germline mutations in cancer susceptibility genes, the characterization of genetic mutations among sub-Saharan African populations remains strikingly incomplete. Given the genetic diversity in the region, there remains a great need for large-scale, population-based studies to understand the prevalence of germline pathogenic variants and adequately capture all the subpopulations in this part of the world.
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Affiliation(s)
- Joshua Shain
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Alissa Michel
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Michael S May
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Lindor Qunaj
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Wafaa El-Sadr
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Wendy K Chung
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Psychiatry, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Paul S Appelbaum
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Judith S Jacobson
- Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Jessica Justman
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Alfred I Neugut
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY.
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O'Shea D, Schmoke N, Porigow C, Murray LP, Chung WK, Kattan M, Jang M, Antosy A, Middlesworth W, Khlevner J. Recent Advances in the Genetic Pathogenesis, Diagnosis, and Management of Esophageal Atresia and Tracheoesophageal Fistula: A Review. J Pediatr Gastroenterol Nutr 2023; 77:703-712. [PMID: 37771007 DOI: 10.1097/mpg.0000000000003952] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 09/30/2023]
Abstract
Infants born with esophageal atresia and tracheoesophageal fistula, a complex congenital malformation occurring in 1/2500-4000 live births, may suffer threats to their cardiac, respiratory, and digestive health in addition to anomalies that may exist in the genitourinary and musculoskeletal systems. Optimal care for these patients throughout their lives is best achieved through a coordinated, multidisciplinary approach that our health care system is not always well-equipped to provide. This review, though not exhaustive, highlights the components of care that pertain to initial surgical reconstruction and subsequent diagnosis and management of the complications that are most frequently encountered. Authors from among the many specialties involved in the care of these patients summarize the current best practice with attention to the most recent advances. Assessment and improvement of quality of life and transition to adult specialists as children grow to adulthood is also reviewed.
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Affiliation(s)
- Delia O'Shea
- From the Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Nicholas Schmoke
- the Division of Pediatric Surgery, Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Chloe Porigow
- the Division of Pediatric Surgery, Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Laurie P Murray
- the Division of Pediatric Pulmonology, Department of Pediatrics, Columbia University Irving Medical Center/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Wendy K Chung
- the Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY
| | - Meyer Kattan
- the Division of Pediatric Pulmonology, Department of Pediatrics, Columbia University Irving Medical Center/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Minyoung Jang
- the Department of Otolaryngology Head and Neck Surgery, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Alexandra Antosy
- From the Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - William Middlesworth
- the Division of Pediatric Surgery, Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Julie Khlevner
- From the Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
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47
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Gupta Y, Friedman DJ, McNulty MT, Khan A, Lane B, Wang C, Ke J, Jin G, Wooden B, Knob AL, Lim TY, Appel GB, Huggins K, Liu L, Mitrotti A, Stangl MC, Bomback A, Westland R, Bodria M, Marasa M, Shang N, Cohen DJ, Crew RJ, Morello W, Canetta P, Radhakrishnan J, Martino J, Liu Q, Chung WK, Espinoza A, Luo Y, Wei WQ, Feng Q, Weng C, Fang Y, Kullo IJ, Naderian M, Limdi N, Irvin MR, Tiwari H, Mohan S, Rao M, Dube GK, Chaudhary NS, Gutiérrez OM, Judd SE, Cushman M, Lange LA, Lange EM, Bivona DL, Verbitsky M, Winkler CA, Kopp JB, Santoriello D, Batal I, Pinheiro SVB, Oliveira EA, Simoes E Silva AC, Pisani I, Fiaccadori E, Lin F, Gesualdo L, Amoroso A, Ghiggeri GM, D'Agati VD, Magistroni R, Kenny EE, Loos RJF, Montini G, Hildebrandt F, Paul DS, Petrovski S, Goldstein DB, Kretzler M, Gbadegesin R, Gharavi AG, Kiryluk K, Sampson MG, Pollak MR, Sanna-Cherchi S. Strong protective effect of the APOL1 p.N264K variant against G2-associated focal segmental glomerulosclerosis and kidney disease. Nat Commun 2023; 14:7836. [PMID: 38036523 PMCID: PMC10689833 DOI: 10.1038/s41467-023-43020-9] [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: 08/25/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
African Americans have a significantly higher risk of developing chronic kidney disease, especially focal segmental glomerulosclerosis -, than European Americans. Two coding variants (G1 and G2) in the APOL1 gene play a major role in this disparity. While 13% of African Americans carry the high-risk recessive genotypes, only a fraction of these individuals develops FSGS or kidney failure, indicating the involvement of additional disease modifiers. Here, we show that the presence of the APOL1 p.N264K missense variant, when co-inherited with the G2 APOL1 risk allele, substantially reduces the penetrance of the G1G2 and G2G2 high-risk genotypes by rendering these genotypes low-risk. These results align with prior functional evidence showing that the p.N264K variant reduces the toxicity of the APOL1 high-risk alleles. These findings have important implications for our understanding of the mechanisms of APOL1-associated nephropathy, as well as for the clinical management of individuals with high-risk genotypes that include the G2 allele.
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Affiliation(s)
- Yask Gupta
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Institute for Inflammation Medicine, University of Lubeck, Lübeck, Germany
| | - David J Friedman
- Nephrology Division, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michelle T McNulty
- Division of Pediatric Nephrology, Boston Children's Hospital, Boston, MA, USA
- Kidney Disease Initiative and Medical and Population Genetics Program, Broad Institute, Boston, MA, USA
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Brandon Lane
- Division of Nephrology, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Chen Wang
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Juntao Ke
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Gina Jin
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Benjamin Wooden
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Andrea L Knob
- Nephrology Division, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Tze Y Lim
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Unit of Genomic Variability and Complex Diseases, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Gerald B Appel
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Kinsie Huggins
- Division of Nephrology, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Lili Liu
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Adele Mitrotti
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePre-J) Nephrology, Dialysis and Transplantation Unit, University of Bari Aldo Moro, Bari, Italy
| | - Megan C Stangl
- Division of Nephrology, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Andrew Bomback
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Rik Westland
- Department of Pediatric Nephrology, Emma Children's Hospital, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Monica Bodria
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Laboratory on Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Maddalena Marasa
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Ning Shang
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - David J Cohen
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Russell J Crew
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - William Morello
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milano, Italy
| | - Pietro Canetta
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Jai Radhakrishnan
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Jeremiah Martino
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Qingxue Liu
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Angelica Espinoza
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yuan Luo
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Wei-Qi Wei
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiping Feng
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Yilu Fang
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Iftikhar J Kullo
- Atherosclerosis and Lipid Genomics Laboratory, Mayo Clinic, Rochester, MN, USA
| | | | - Nita Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sumit Mohan
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Maya Rao
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Geoffrey K Dube
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Ninad S Chaudhary
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Orlando M Gutiérrez
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Nephrology, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Suzanne E Judd
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mary Cushman
- Department of Medicine and Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, USA
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ethan M Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Daniel L Bivona
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Miguel Verbitsky
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Cheryl A Winkler
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health and Basic Research Program, Frederick National Laboratory, Frederick, MD, USA
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Dominick Santoriello
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ibrahim Batal
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sérgio Veloso Brant Pinheiro
- Universidade Federal de Minas Gerais (UFMG), Faculdade de Medicina, Laboratório Interdisciplinar de Investigação Médica, Departamento de Pediatria, Unidade de Nefrologia Pediátrica, Belo Horizonte, MG, Brazil
| | - Eduardo Araújo Oliveira
- Universidade Federal de Minas Gerais (UFMG), Faculdade de Medicina, Laboratório Interdisciplinar de Investigação Médica, Departamento de Pediatria, Unidade de Nefrologia Pediátrica, Belo Horizonte, MG, Brazil
| | - Ana Cristina Simoes E Silva
- Universidade Federal de Minas Gerais (UFMG), Faculdade de Medicina, Laboratório Interdisciplinar de Investigação Médica, Departamento de Pediatria, Unidade de Nefrologia Pediátrica, Belo Horizonte, MG, Brazil
| | - Isabella Pisani
- Nephrology Unit, Parma University Hospital, and Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Enrico Fiaccadori
- Nephrology Unit, Parma University Hospital, and Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Loreto Gesualdo
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePre-J) Nephrology, Dialysis and Transplantation Unit, University of Bari Aldo Moro, Bari, Italy
| | - Antonio Amoroso
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Department of Medical Sciences, University of Turin, Turin, Italy
| | - Gian Marco Ghiggeri
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Laboratory on Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Vivette D D'Agati
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Riccardo Magistroni
- Surgical, Medical and Dental Department of Morphological Sciences, Section of Nephrology, University of Modena and Reggio Emilia, Modena, Italy
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Translational Genomics, Icahn School of Medicine, New York, NY, 10027, USA
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine, New York, NY, 10027, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Giovanni Montini
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milano, Italy
- Department of Clinical Sciences and Community Health, Giuliana and Bernardo Caprotti Chair of Pediatrics, University of Milano, Milano, Italy
| | - Friedhelm Hildebrandt
- Harvard Medical School, Boston, MA, USA
- Division of Pediatric Nephrology, Boston Children's Hospital, Boston, MA, USA
| | - Dirk S Paul
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Rasheed Gbadegesin
- Division of Nephrology, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Ali G Gharavi
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Matthew G Sampson
- Harvard Medical School, Boston, MA, USA
- Division of Pediatric Nephrology, Boston Children's Hospital, Boston, MA, USA
- Kidney Disease Initiative and Medical and Population Genetics Program, Broad Institute, Boston, MA, USA
| | - Martin R Pollak
- Nephrology Division, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Simone Sanna-Cherchi
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
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48
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Lin SJ, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C, Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A, Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T, Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney GK. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Med 2023; 15:102. [PMID: 38031187 PMCID: PMC10688095 DOI: 10.1186/s13073-023-01258-4] [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: 09/19/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship. METHODS Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity. RESULTS A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy. CONCLUSIONS Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as "OGDHL-related disorders".
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Affiliation(s)
- Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Barbara Vona
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
- Department of Otolaryngology-Head and Neck Surgery, Tübingen Hearing Research Center, Eberhard Karls University, Tübingen, 72076, Germany
| | - Tracy Lau
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Huda Shujaa Aldeen
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace London, London, UK
| | - Clarissa Rocca
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Mahmoud M Noureldeen
- Department of Pediatrics, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Ahmed K Saad
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Cassidy Petree
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | | | | | | | - Emalyn Elise Cork
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pratishtha Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Narges Hashemi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Aboulfazl Rad
- Department of Otolaryngology-Head and Neck Surgery, Tübingen Hearing Research Center, Eberhard Karls University, Tübingen, 72076, Germany
| | - Juanita Neira
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Mehran Beiraghi Toosi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Cordula Knopp
- Institute for Human Genetics and Genomic Medicine, RWTH Aachen University, Pauwelsstr. 30, Aachen, 52074, Germany
| | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, RWTH Aachen University, Pauwelsstr. 30, Aachen, 52074, Germany
| | - Thomas D Challman
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Rebecca Smith
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Asmahan Abdalla
- Department of Pediatric Endocrinology, Gaafar Ibn Auf Children's Tertiary Hospital, Khartoum, Sudan
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Manali Joshi
- Bioinformatics Centre, S. P. Pune University, Pune, India
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospitaland, Harvard Medical School , Boston, MA, USA
| | - Andres Moreno-De-Luca
- Department of Diagnostic Radiology, Kingston Health Sciences Centre, Queen's University, Kingston, ON, Canada
| | - Henry Houlden
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK.
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA.
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49
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Chen F, Ahimaz P, Wang K, Chung WK, Ta C, Weng C, Liu C. Phenotype-Driven Molecular Genetic Test Recommendation for Diagnosing Pediatric Rare Disorders. Res Sq 2023:rs.3.rs-3593490. [PMID: 38045411 PMCID: PMC10690317 DOI: 10.21203/rs.3.rs-3593490/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Rare disease patients often endure prolonged diagnostic odysseys and may still remain undiagnosed for years. Selecting the appropriate genetic tests is crucial to lead to timely diagnosis. Phenotypic features offer great potential for aiding genomic diagnosis in rare disease cases. We see great promise in effective integration of phenotypic information into genetic test selection workflow. In this study, we present a phenotype-driven molecular genetic test recommendation (Phen2Test) for pediatric rare disease diagnosis. Phen2Test was constructed using frequency matrix of phecodes and demographic data from the EHR before ordering genetic tests, with the objective to streamline the selection of molecular genetic tests (whole-exome / whole-genome sequencing, or gene panels) for clinicians with minimum genetic training expertise. We developed and evaluated binary classifiers based on 1,005 individuals referred to genetic counselors for potential genetic evaluation. In the evaluation using the gold standard cohort, the model achieved strong performance with an AUROC of 0.82 and an AUPRC of 0.92. Furthermore, we tested the model on another silver standard cohort (n=6,458), achieving an overall AUROC of 0.72 and an AUPRC of 0.671. Phen2Test was adjusted to align with current clinical guidelines, showing superior performance with more recent data, demonstrating its potential for use within a learning healthcare system as a genomic medicine intervention that adapts to guideline updates. This study showcases the practical utility of phenotypic features in recommending molecular genetic tests with performance comparable to clinical geneticists. Phen2Test could assist clinicians with limited genetic training and knowledge to order appropriate genetic tests.
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Affiliation(s)
- Fangyi Chen
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University, New York, NY, USA
- Institute of Genomic Medicine, Columbia University, New York, NY, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wendy K. Chung
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Casey Ta
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
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Edwards NA, Kashyap A, Warren A, Agricola ZN, Kenny AP, Shen Y, Chung WK, Zorn AM. Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in trachea-esophageal morphogenesis. bioRxiv 2023:2023.10.11.561909. [PMID: 37873300 PMCID: PMC10592723 DOI: 10.1101/2023.10.11.561909] [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] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Disruptions in foregut morphogenesis can result in life-threatening conditions where the trachea and esophagus fail to separate properly, such as esophageal atresia (EA) and tracheoesophageal fistulas (TEF). The developmental basis of these congenital anomalies is poorly understood, but recent genome sequencing reveals that de novo variants in intracellular trafficking genes are enriched in EA/TEF patients. Here we show that mutation of orthologous genes in Xenopus disrupts trachea-esophageal separation similar to EA/TEF patients. We show that the Rab11a recycling endosome pathway is required to localize Vangl-Celsr polarity complexes at the cell surface where opposite sides of the common foregut tube fuse. Partial loss of endosome trafficking or the Vangl/Celsr complex disrupts epithelial polarity and cell division orientation. Mutant cells accumulate at the fusion point, fail to downregulate cadherin, and do not separate into distinct trachea and esophagus. These data provide new insights into the mechanisms of congenital anomalies and general paradigms of tissue fusion during organogenesis.
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