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Levitin MO, Rawlins LE, Sanchez-Andrade G, Arshad OA, Collins SC, Sawiak SJ, Iffland PH, Andersson MHL, Bupp C, Cambridge EL, Coomber EL, Ellis I, Herkert JC, Ironfield H, Jory L, Kretz PF, Kant SG, Neaverson A, Nibbeling E, Rowley C, Relton E, Sanderson M, Scott EM, Stewart H, Shuen AY, Schreiber J, Tuck L, Tonks J, Terkelsen T, van Ravenswaaij-Arts C, Vasudevan P, Wenger O, Wright M, Day A, Hunter A, Patel M, Lelliott CJ, Crino PB, Yalcin B, Crosby AH, Baple EL, Logan DW, Hurles ME, Gerety SS. Models of KPTN-related disorder implicate mTOR signalling in cognitive and overgrowth phenotypes. Brain 2023; 146:4766-4783. [PMID: 37437211 PMCID: PMC10629792 DOI: 10.1093/brain/awad231] [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: 11/02/2022] [Revised: 05/31/2023] [Accepted: 06/18/2023] [Indexed: 07/14/2023] Open
Abstract
KPTN-related disorder is an autosomal recessive disorder associated with germline variants in KPTN (previously known as kaptin), a component of the mTOR regulatory complex KICSTOR. To gain further insights into the pathogenesis of KPTN-related disorder, we analysed mouse knockout and human stem cell KPTN loss-of-function models. Kptn -/- mice display many of the key KPTN-related disorder phenotypes, including brain overgrowth, behavioural abnormalities, and cognitive deficits. By assessment of affected individuals, we have identified widespread cognitive deficits (n = 6) and postnatal onset of brain overgrowth (n = 19). By analysing head size data from their parents (n = 24), we have identified a previously unrecognized KPTN dosage-sensitivity, resulting in increased head circumference in heterozygous carriers of pathogenic KPTN variants. Molecular and structural analysis of Kptn-/- mice revealed pathological changes, including differences in brain size, shape and cell numbers primarily due to abnormal postnatal brain development. Both the mouse and differentiated induced pluripotent stem cell models of the disorder display transcriptional and biochemical evidence for altered mTOR pathway signalling, supporting the role of KPTN in regulating mTORC1. By treatment in our KPTN mouse model, we found that the increased mTOR signalling downstream of KPTN is rapamycin sensitive, highlighting possible therapeutic avenues with currently available mTOR inhibitors. These findings place KPTN-related disorder in the broader group of mTORC1-related disorders affecting brain structure, cognitive function and network integrity.
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Affiliation(s)
- Maria O Levitin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Evox Therapeutics Limited, Oxford OX4 4HG, UK
| | - Lettie E Rawlins
- RILD Wellcome Wolfson Medical Research Centre, University of Exeter, Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX1 2ED, UK
| | | | - Osama A Arshad
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Stephan C Collins
- INSERM Unit 1231, Université de Bourgogne Franche-Comté, Dijon 21078, France
| | - Stephen J Sawiak
- Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge CB2 3EB, UK
- Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Phillip H Iffland
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Malin H L Andersson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Caleb Bupp
- Spectrum Health, Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA
| | - Emma L Cambridge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Eve L Coomber
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Ian Ellis
- Department of Clinical Genetics, Alder Hey Children’s Hospital, Liverpool L14 5AB, UK
| | - Johanna C Herkert
- Department of Genetics, University Medical Centre, University of Groningen, Groningen 9713 GZ, The Netherlands
| | - Holly Ironfield
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Logan Jory
- Haven Clinical Psychology Practice Ltd, Bude, Cornwall EX23 9HP, UK
| | | | - Sarina G Kant
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3015 GD, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Alexandra Neaverson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Esther Nibbeling
- Laboratory for Diagnostic Genome Analysis, Department of Clinical Genetics, Leiden University Medical Center, Leiden 3015 GD, The Netherlands
| | - Christine Rowley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Institute of Metabolic Science, Cambridge University, Cambridge CB2 0QQ, UK
| | - Emily Relton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Faculty of Health and Medical Science, University of Surrey, Guildford GU2 7YH, UK
| | - Mark Sanderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Ethan M Scott
- New Leaf Center, Clinic for Special Children, Mount Eaton, OH 44659, USA
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Trust, Oxford OX3 7HE, UK
| | - Andrew Y Shuen
- London Health Sciences Centre, London, ON N6A 5W9, Canada
- Division of Medical Genetics, Department of Pediatrics, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5W9, Canada
| | - John Schreiber
- Department of Neurology, Children’s National Medical Center, Washington DC 20007, USA
| | - Liz Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - James Tonks
- Haven Clinical Psychology Practice Ltd, Bude, Cornwall EX23 9HP, UK
| | - Thorkild Terkelsen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus DK-8200, Denmark
| | - Conny van Ravenswaaij-Arts
- Department of Genetics, University Medical Centre, University of Groningen, Groningen 9713 GZ, The Netherlands
| | - Pradeep Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester LE1 7RH, UK
| | - Olivia Wenger
- New Leaf Center, Clinic for Special Children, Mount Eaton, OH 44659, USA
| | - Michael Wright
- Institute of Human Genetics, International Centre for Life, Newcastle upon Tyne NE1 7RU, UK
| | - Andrew Day
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Qkine Ltd., Cambridge CB5 8HW, UK
| | - Adam Hunter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Christopher J Lelliott
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Institute of Metabolic Science, Cambridge University, Cambridge CB2 0QQ, UK
| | - Peter B Crino
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Binnaz Yalcin
- INSERM Unit 1231, Université de Bourgogne Franche-Comté, Dijon 21078, France
| | - Andrew H Crosby
- RILD Wellcome Wolfson Medical Research Centre, University of Exeter, Exeter EX2 5DW, UK
| | - Emma L Baple
- RILD Wellcome Wolfson Medical Research Centre, University of Exeter, Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX1 2ED, UK
| | - Darren W Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Waltham Petcare Science Institute, Waltham on the Wolds LE14 4RT, UK
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sebastian S Gerety
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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2
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Ehrenberg S, Walsh Vockley C, Heiman P, Ammous Z, Wenger O, Vockley J, Ghaloul-Gonzalez L. Natural history of propionic acidemia in the Amish population. Mol Genet Metab Rep 2022; 33:100936. [PMID: 36393899 PMCID: PMC9647228 DOI: 10.1016/j.ymgmr.2022.100936] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/25/2022] [Accepted: 10/30/2022] [Indexed: 11/07/2022] Open
Abstract
Propionic acidemia (PA) in the Amish is caused by a homozygous pathogenic variant (c.1606A>G; p.Asn536Asp) in the PCCB gene. Amish patients can have borderline or normal newborn screening (NBS) results and symptoms can present at any time from early childhood to mid-adulthood. Early diagnosis and initiation of treatment for PA in the non-Amish population improves patient outcomes. Here, we present data from a retrospective chart review of Amish patients diagnosed with PA from three different medical centers in order to document its natural history in the Amish and determine the influence of treatment on outcomes in this population. A total of 38 patients with average current age 19.9 years (range 4y-45y), 57.9% males, were enrolled in the study. Fourteen patients (36.8%) were diagnosed with a positive newborn screening (NBS) while 24 patients (63.2%) had negative or inconclusive NBS or had no record of NBS in their charts. These 24 patients were diagnosed by screening after a family member was diagnosed with PA (14; 58.3%), following a hospitalization for metabolic acidosis (5; 20.8%), hospitalization for seizures (3; 12.5%) or via cord blood (2; 8.3%). The majority of patients were prescribed a protein restricted diet (32; 84.2%), including metabolic formula (29; 76.3%). Most were treated with carnitine (35; 92.1%), biotin (2; 76.3%) and/or Coenzyme Q10 (16; 42.1%). However, treatment adherence varied widely among patients, with 7 (24.1%) of the patients prescribed metabolic formula reportedly nonadherent. Cardiomyopathy was the most prevalent finding (22; 63.2%), followed by developmental delay/intellectual disability (15; 39.5%), long QT (14; 36.8%), seizures (12; 31.6%), failure to thrive (4; 10.5%), and basal ganglia strokes (3; 7.9%). No difference in outcome was obvious for those diagnosed by NBS and treated early with dietary and supplement management, especially for cardiomyopathy. However, this is a limited retrospective observational study. A prospective study with strict documentation of treatment adherence and universal screening for cardiomyopathy and long QT should be conducted to better study the impact of early detection and treatment. Additional treatment options such as liver transplantation and future therapies such as mRNA or gene therapy should be explored in this population.
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Affiliation(s)
- Sarah Ehrenberg
- University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA,Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, PA, USA
| | - Catherine Walsh Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, PA, USA,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA
| | - Paige Heiman
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, PA, USA
| | | | - Olivia Wenger
- New Leaf Center, Mount Eaton, OH, USA,Department of Pediatrics, Akron Children's Hospital, 214 West Bowery Street, Akron, OH 44308, USA
| | - Jerry Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, PA, USA,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA
| | - Lina Ghaloul-Gonzalez
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, PA, USA,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA,Corresponding author at: Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Rangos Research Building, Pittsburgh, PA 15224, USA.
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Leslie JS, Hjeij R, Vivante A, Bearce EA, Dyer L, Wang J, Rawlins L, Kennedy J, Ubeyratna N, Fasham J, Irons ZH, Craig SB, Koenig J, George S, Pode-Shakked B, Bolkier Y, Barel O, Mane S, Frederiksen KK, Wenger O, Scott E, Cross HE, Lorentzen E, Norris DP, Anikster Y, Omran H, Grimes DT, Crosby AH, Baple EL. Biallelic DAW1 variants cause a motile ciliopathy characterized by laterality defects and subtle ciliary beating abnormalities. Genet Med 2022; 24:2249-2261. [PMID: 36074124 PMCID: PMC10584193 DOI: 10.1016/j.gim.2022.07.019] [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: 11/23/2021] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
PURPOSE The clinical spectrum of motile ciliopathies includes laterality defects, hydrocephalus, and infertility as well as primary ciliary dyskinesia when impaired mucociliary clearance results in otosinopulmonary disease. Importantly, approximately 30% of patients with primary ciliary dyskinesia lack a genetic diagnosis. METHODS Clinical, genomic, biochemical, and functional studies were performed alongside in vivo modeling of DAW1 variants. RESULTS In this study, we identified biallelic DAW1 variants associated with laterality defects and respiratory symptoms compatible with motile cilia dysfunction. In early mouse embryos, we showed that Daw1 expression is limited to distal, motile ciliated cells of the node, consistent with a role in left-right patterning. daw1 mutant zebrafish exhibited reduced cilia motility and left-right patterning defects, including cardiac looping abnormalities. Importantly, these defects were rescued by wild-type, but not mutant daw1, gene expression. In addition, pathogenic DAW1 missense variants displayed reduced protein stability, whereas DAW1 loss-of-function was associated with distal type 2 outer dynein arm assembly defects involving axonemal respiratory cilia proteins, explaining the reduced cilia-induced fluid flow in particle tracking velocimetry experiments. CONCLUSION Our data define biallelic DAW1 variants as a cause of human motile ciliopathy and determine that the disease mechanism involves motile cilia dysfunction, explaining the ciliary beating defects observed in affected individuals.
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Affiliation(s)
- Joseph S Leslie
- Institute of Biomedical and Clinical Science, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Rim Hjeij
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Asaf Vivante
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Pediatrics B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | | | - Laura Dyer
- MRC Harwell Institute, Harwell Campus, Oxfordshire, Oxford, United Kingdom
| | - Jiaolong Wang
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Lettie Rawlins
- Institute of Biomedical and Clinical Science, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom; Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Joanna Kennedy
- Institute of Biomedical and Clinical Science, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Nishanka Ubeyratna
- Institute of Biomedical and Clinical Science, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - James Fasham
- Institute of Biomedical and Clinical Science, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom; Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Zoe H Irons
- Institute of Molecular Biology, University of Oregon, Eugene, OR
| | - Samuel B Craig
- Institute of Molecular Biology, University of Oregon, Eugene, OR
| | - Julia Koenig
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Sebastian George
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Yoav Bolkier
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Heart Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Ortal Barel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel; Wohl Institute for Translational Medicine, Sheba Medical Center, Ramat Gan, Israel
| | - Shrikant Mane
- Department of Genetics, Yale School of Medicine, New Haven, CT
| | | | - Olivia Wenger
- New Leaf Center Clinic for Special Children, Mt Eaton, OH
| | - Ethan Scott
- New Leaf Center Clinic for Special Children, Mt Eaton, OH
| | - Harold E Cross
- Department of Ophthalmology and Vision Science, University of Arizona College of Medicine, University of Arizona, Tucson, AZ
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Dominic P Norris
- MRC Harwell Institute, Harwell Campus, Oxfordshire, Oxford, United Kingdom
| | - Yair Anikster
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel; Wohl Institute for Translational Medicine, Sheba Medical Center, Ramat Gan, Israel
| | - Heymut Omran
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Daniel T Grimes
- Institute of Molecular Biology, University of Oregon, Eugene, OR.
| | - Andrew H Crosby
- Institute of Biomedical and Clinical Science, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom.
| | - Emma L Baple
- Institute of Biomedical and Clinical Science, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom; Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom.
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4
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Lin S, Sanchez-Bretaño A, Leslie JS, Williams KB, Lee H, Thomas NS, Callaway J, Deline J, Ratnayaka JA, Baralle D, Schmitt MA, Norman CS, Hammond S, Harlalka GV, Ennis S, Cross HE, Wenger O, Crosby AH, Baple EL, Self JE. Evidence that the Ser192Tyr/Arg402Gln in cis Tyrosinase gene haplotype is a disease-causing allele in oculocutaneous albinism type 1B (OCA1B). NPJ Genom Med 2022; 7:2. [PMID: 35027574 PMCID: PMC8758782 DOI: 10.1038/s41525-021-00275-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/19/2021] [Indexed: 01/09/2023] Open
Abstract
Oculocutaneous albinism type 1 (OCA1) is caused by pathogenic variants in the TYR (tyrosinase) gene which encodes the critical and rate-limiting enzyme in melanin synthesis. It is the most common OCA subtype found in Caucasians, accounting for ~50% of cases worldwide. The apparent 'missing heritability' in OCA is well described, with ~25-30% of clinically diagnosed individuals lacking two clearly pathogenic variants. Here we undertook empowered genetic studies in an extensive multigenerational Amish family, alongside a review of previously published literature, a retrospective analysis of in-house datasets, and tyrosinase activity studies. Together this provides irrefutable evidence of the pathogenicity of two common TYR variants, p.(Ser192Tyr) and p.(Arg402Gln) when inherited in cis alongside a pathogenic TYR variant in trans. We also show that homozygosity for the p.(Ser192Tyr)/p.(Arg402Gln) TYR haplotype results in a very mild, but fully penetrant, albinism phenotype. Together these data underscore the importance of including the TYR p.(Ser192Tyr)/p.(Arg402Gln) in cis haplotype as a pathogenic allele causative of OCA, which would likely increase molecular diagnoses in this missing heritability albinism cohort by 25-50%.
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Affiliation(s)
- Siying Lin
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK
| | - Aida Sanchez-Bretaño
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Joseph S Leslie
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK
| | - Katie B Williams
- Center for Special Children, Vernon Memorial Healthcare, La Farge, WI, USA
| | - Helena Lee
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Southampton Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - N Simon Thomas
- Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
| | - Jonathan Callaway
- Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
| | - James Deline
- Center for Special Children, Vernon Memorial Healthcare, La Farge, WI, USA
| | - J Arjuna Ratnayaka
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Melanie A Schmitt
- University of Wisconsin School of Medicine and Public Health, Department of Ophthalmology & Visual Sciences, Madison, WI, USA
| | - Chelsea S Norman
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- The Rosalind Franklin Institute, Rutherford Appleton Laboratories, Harwell Science and Innovation Campus, Didcot, UK
| | - Sheri Hammond
- Center for Special Children, Vernon Memorial Healthcare, La Farge, WI, USA
| | - Gaurav V Harlalka
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK
- Rajarshi Shahu College of Pharmacy, Malvihir, Buldana, India
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Harold E Cross
- Department of Ophthalmology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Olivia Wenger
- New Leaf Clinic, PO Box 336, 16014 East Chestnut Street, Mount Eaton, OH, 44691, USA
- Department of Pediatrics, Akron Children's Hospital, 214 West Bowery Street, Akron, OH, 44308, USA
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK.
| | - Emma L Baple
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK.
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter, UK.
| | - Jay E Self
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
- Southampton Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton, UK.
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5
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Ammous Z, Rawlins LE, Jones H, Leslie JS, Wenger O, Scott E, Deline J, Herr T, Evans R, Scheid A, Kennedy J, Chioza BA, Ames RM, Cross HE, Puffenberger EG, Harries L, Baple EL, Crosby AH. A biallelic SNIP1 Amish founder variant causes a recognizable neurodevelopmental disorder. PLoS Genet 2021; 17:e1009803. [PMID: 34570759 PMCID: PMC8496849 DOI: 10.1371/journal.pgen.1009803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/07/2021] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
SNIP1 (Smad nuclear interacting protein 1) is a widely expressed transcriptional suppressor of the TGF-β signal-transduction pathway which plays a key role in human spliceosome function. Here, we describe extensive genetic studies and clinical findings of a complex inherited neurodevelopmental disorder in 35 individuals associated with a SNIP1 NM_024700.4:c.1097A>G, p.(Glu366Gly) variant, present at high frequency in the Amish community. The cardinal clinical features of the condition include hypotonia, global developmental delay, intellectual disability, seizures, and a characteristic craniofacial appearance. Our gene transcript studies in affected individuals define altered gene expression profiles of a number of molecules with well-defined neurodevelopmental and neuropathological roles, potentially explaining clinical outcomes. Together these data confirm this SNIP1 gene variant as a cause of an autosomal recessive complex neurodevelopmental disorder and provide important insight into the molecular roles of SNIP1, which likely explain the cardinal clinical outcomes in affected individuals, defining potential therapeutic avenues for future research.
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Affiliation(s)
- Zineb Ammous
- The Community Health Clinic, Topeka, Indiana, United States of America
| | - Lettie E. Rawlins
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, United Kingdom
| | - Hannah Jones
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Joseph S. Leslie
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Olivia Wenger
- New Leaf Center, Clinic for Special Children, Mount Eaton, Ohio, United States of America
| | - Ethan Scott
- New Leaf Center, Clinic for Special Children, Mount Eaton, Ohio, United States of America
| | - Jim Deline
- Center for Special Children, La Farge Medical Center, La Farge, Wisconsin, United States of America
| | - Tom Herr
- Center for Special Children, La Farge Medical Center, La Farge, Wisconsin, United States of America
| | - Rebecca Evans
- The Community Health Clinic, Topeka, Indiana, United States of America
| | - Angela Scheid
- The Community Health Clinic, Topeka, Indiana, United States of America
| | - Joanna Kennedy
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Barry A. Chioza
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Ryan M. Ames
- Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | - Harold E. Cross
- Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, United States of America
| | | | - Lorna Harries
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Emma L. Baple
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, United Kingdom
| | - Andrew H. Crosby
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
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6
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Salter CG, Cai Y, Lo B, Helman G, Taylor H, McCartney A, Leslie JS, Accogoli A, Zara F, Traverso M, Fasham J, Lees JA, Ferla M, Chioza BA, Wenger O, Scott E, Cross HE, Crawford J, Warshawsky I, Keisling M, Agamanolis D, Melver CW, Cox H, Elawad M, Marton T, Wakeling M, Holzinger D, Tippelt S, Munteanu M, Valcheva D, Deal C, Van Meerbeke S, Vockley CW, Butte MJ, Acar U, van der Knaap MS, Korenke GC, Kotzaeridou U, Balla T, Simons C, Uhlig HH, Crosby AH, De Camilli P, Wolf NI, Baple EL. Biallelic PI4KA variants cause neurological, intestinal and immunological disease. Brain 2021; 144:3597-3610. [PMID: 34415310 PMCID: PMC8719846 DOI: 10.1093/brain/awab313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/14/2021] [Accepted: 08/01/2021] [Indexed: 11/22/2022] Open
Abstract
Phosphatidylinositol 4-kinase IIIα (PI4KIIIα/PI4KA/OMIM:600286) is a lipid kinase generating phosphatidylinositol 4-phosphate (PI4P), a membrane phospholipid with critical roles in the physiology of multiple cell types. PI4KIIIα’s role in PI4P generation requires its assembly into a heterotetrameric complex with EFR3, TTC7 and FAM126. Sequence alterations in two of these molecular partners, TTC7 (encoded by TTC7A or TCC7B) and FAM126, have been associated with a heterogeneous group of either neurological (FAM126A) or intestinal and immunological (TTC7A) conditions. Here we show that biallelic PI4KA sequence alterations in humans are associated with neurological disease, in particular hypomyelinating leukodystrophy. In addition, affected individuals may present with inflammatory bowel disease, multiple intestinal atresia and combined immunodeficiency. Our cellular, biochemical and structural modelling studies indicate that PI4KA-associated phenotypical outcomes probably stem from impairment of PI4KIIIα-TTC7-FAM126's organ-specific functions, due to defective catalytic activity or altered intra-complex functional interactions. Together, these data define PI4KA gene alteration as a cause of a variable phenotypical spectrum and provide fundamental new insight into the combinatorial biology of the PI4KIIIα-FAM126-TTC7-EFR3 molecular complex.
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Affiliation(s)
- Claire G Salter
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK.,Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Yiying Cai
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Bernice Lo
- Research Branch, Sidra Medicine, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Guy Helman
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Henry Taylor
- Department of surgery and Cancer, Imperial College London, London, UK
| | - Amber McCartney
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Joseph S Leslie
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | | | | | | | - James Fasham
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK.,Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, UK
| | - Joshua A Lees
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Matteo Ferla
- Wellcome Centre Human Genetics, University of Oxford, Oxford, UK
| | - Barry A Chioza
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | | | | | - Harold E Cross
- Department of Ophthalmology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Joanna Crawford
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Melbourne, Australia
| | | | | | | | | | - Helen Cox
- West Midlands Clinical Genetics Service, Birmingham Women's Hospital, Birmingham, UK
| | - Mamoun Elawad
- Department of Gastroenterology, Sidra Medicine, Doha, Qatar
| | - Tamas Marton
- West Midlands Perinatal Pathology, Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Matthew Wakeling
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | - Dirk Holzinger
- Department of Pediatric Haematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Stephan Tippelt
- Department of Pediatric Haematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Martin Munteanu
- Institute for Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | - Christin Deal
- Children's Hospital of Pittsburgh, UPMC, Division of Pediatric Allergy and Immunology, Pittsburgh, USA
| | - Sara Van Meerbeke
- Children's Hospital of Pittsburgh, UPMC, Division of Pediatric Allergy and Immunology, Pittsburgh, USA
| | - Catherine Walsh Vockley
- Children's Hospital of Pittsburgh, UPMC, Division of Genetic and Genomic Medicine, Pittsburgh, USA
| | - Manish J Butte
- Department of Paediatrics, Division of Immunology, Allergy, and Rheumatology, UCLA, Los Angeles, CA, USA
| | - Utkucan Acar
- Department of Paediatrics, Division of Immunology, Allergy, and Rheumatology, UCLA, Los Angeles, CA, USA
| | - Marjo S van der Knaap
- Amsterdam Leukodystrophy Center, Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Center, VU University Amsterdam and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands.,Department of Functional Genomics, Centre for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - G Christoph Korenke
- Department of Neuropediatrics, University Children's Hospital, Klinikum Oldenburg, 26133 Oldenburg, Germany
| | - Urania Kotzaeridou
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Cas Simons
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Holm H Uhlig
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxfordshire, UK.,Department of Paediatrics, University of Oxford, Oxfordshire, UK.,Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.,Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Nicole I Wolf
- Amsterdam Leukodystrophy Center, Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Center, VU University Amsterdam and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands.,Department of Functional Genomics, Centre for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Emma L Baple
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK.,Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, UK
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7
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Wenger O, Brown M, Smith B, Chowdhury D, Crosby AH, Baple EL, Yoder M, Laxen W, Tortorelli S, Strauss KA. Biochemical phenotype and its relationship to treatment in 16 individuals with PCCB c.1606A > G (p.Asn536Asp) variant propionic acidemia. Mol Genet Metab 2020; 131:316-324. [PMID: 33127324 DOI: 10.1016/j.ymgme.2020.09.006] [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: 07/27/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
Propionic acidemia (PA) is caused by inherited deficiency of mitochondrial propionyl-CoA carboxylase (PCC) and results in significant neurodevelopmental and cardiac morbidity. However, relationships among therapeutic intervention, biochemical markers, and disease progression are poorly understood. Sixteen individuals homozygous for PCCB c.1606A > G (p.Asn536Asp) variant PA participated in a two-week suspension of therapy. Standard metabolic markers (plasma amino acids, blood spot methylcitrate, plasma/urine acylcarnitines, urine organic acids) were obtained before and after stopping treatment. These same markers were obtained in sixteen unaffected siblings. Echocardiography and electrocardiography were obtained from all subjects. We characterized the baseline biochemical phenotype of untreated PCCB c.1606A > G homozygotes and impact of treatment on PCC deficiency biomarkers. Therapeutic regimens varied widely. Suspension of therapy did not significantly alter branched chain amino acid levels, their alpha-ketoacid derivatives, or urine ketones. Carnitine supplementation significantly increased urine propionylcarnitine and its ratio to total carnitine. Methylcitrate blood spot and urine levels did not correlate with other biochemical measures or cardiac outcomes. Treatment of PCCB c.1606A > G homozygotes with protein restriction, prescription formula, and/or various dietary supplements has a limited effect on core biomarkers of PCC deficiency. These patients require further longitudinal study with standardized approaches to better understand the relationship between biomarkers and disease burden.
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Affiliation(s)
- Olivia Wenger
- New Leaf Clinic, PO Box 336, 16014 East Chestnut Street, Mount Eaton, OH, 44691, USA; Department of Pediatrics, Akron Children's Hospital, 214 West Bowery Street, Akron, OH 44308, USA.
| | - Miraides Brown
- Rebecca Considine Research Institute, Akron Children's Hospital, Akron, OH, USA
| | - Brandon Smith
- Department of Pediatrics, Akron Children's Hospital, 214 West Bowery Street, Akron, OH 44308, USA
| | | | - Andrew H Crosby
- Institute of Biomedical and Clinical Science, Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, United Kingdom
| | - Emma L Baple
- Institute of Biomedical and Clinical Science, Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, United Kingdom
| | - Mark Yoder
- Northeast Ohio Medical University, Rootstown, OH, USA
| | - William Laxen
- Biochemical Genetics Laboratory, Mayo Clinic, Rochester, MN, USA
| | | | - Kevin A Strauss
- Clinic for Special Children, Strasburg, PA, USA; Department of Pediatrics, Penn Medicine-Lancaster General Hospital, Lancaster, PA, USA; Departments of Pediatrics and Molecular, Cell & Cancer Biology, University of Massachusetts School of Medicine, Worcester, MA, USA
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8
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Aikman I, Makowski K, Wenger O, Rossman I, Solomon JD. Microcephaly, Hypotonia, and Intracranial Calcifications in an 11-Week-Old Boy. Pediatrics 2020; 146:peds.2019-2795. [PMID: 32820067 DOI: 10.1542/peds.2019-2795] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2020] [Indexed: 11/24/2022] Open
Abstract
An 11-week-old unvaccinated, term Amish boy initially presented with poor feeding, microcephaly, failure to thrive, and developmental delays. His physical examination was significant for both weight and head circumference being less than the third percentile, and he was noted to have micrognathia, truncal hypotonia, and head lag. He was admitted to the pediatric hospital medicine service for further diagnostic evaluation. Laboratory studies assessing for endocrinological and metabolic etiologies yielded negative results, and imaging studies (including a chest radiograph, echocardiogram, and abdominal ultrasound) were normal. However, intracranial calcifications were noted on a head ultrasound. The etiology of his constellation of symptoms was initially thought to be infectious, but the ultimate diagnosis was not made until after discharge from the pediatric hospital medicine service.
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Affiliation(s)
- Inga Aikman
- Akron Children's Hospital, Akron, Ohio; .,Division of Critical Care and Hospital Medicine, Department of Pediatrics, Brody School of Medicine, East Carolina University, Greenville, North Carolina; and
| | | | - Olivia Wenger
- Akron Children's Hospital, Akron, Ohio.,New Leaf Center, Mount Eaton, Ohio
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9
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Fasham J, Arno G, Lin S, Xu M, Carss KJ, Hull S, Lane A, Robson AG, Wenger O, Self JE, Harlalka GV, Salter CG, Schema L, Moss TJ, Cheetham ME, Moore AT, Raymond FL, Chen R, Baple EL, Webster AR, Crosby AH. Delineating the expanding phenotype associated with SCAPER gene mutation. Am J Med Genet A 2019; 179:1665-1671. [PMID: 31192531 PMCID: PMC6772143 DOI: 10.1002/ajmg.a.61202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/01/2019] [Accepted: 05/05/2019] [Indexed: 11/19/2022]
Affiliation(s)
- James Fasham
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom.,Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital (Heavitree), Exeter, United Kingdom
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Siying Lin
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Mingchu Xu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Keren J Carss
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge, United Kingdom.,NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Sarah Hull
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Amelia Lane
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Anthony G Robson
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Olivia Wenger
- New Leaf Center, Clinic for Special Children, Mount Eaton, Ohio
| | - Jay E Self
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Gaurav V Harlalka
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Claire G Salter
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Lynn Schema
- Division of Genetics and Metabolism, University of Minnesota Medical Center - Fairview, Minneapolis, Minnesota
| | - Timothy J Moss
- Division of Genetics and Metabolism, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Michael E Cheetham
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Anthony T Moore
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom.,Ophthalmology Department, UCSF School of Medicine, Koret Vision Centre, San Francisco, California
| | - F Lucy Raymond
- NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Emma L Baple
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom.,Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital (Heavitree), Exeter, United Kingdom
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Andrew H Crosby
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | -
- NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
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10
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Yuan B, Neira J, Pehlivan D, Santiago-Sim T, Song X, Rosenfeld J, Posey JE, Patel V, Jin W, Adam MP, Baple EL, Dean J, Fong CT, Hickey SE, Hudgins L, Leon E, Madan-Khetarpal S, Rawlins L, Rustad CF, Stray-Pedersen A, Tveten K, Wenger O, Diaz J, Jenkins L, Martin L, McGuire M, Pietryga M, Ramsdell L, Slattery L, Abid F, Bertuch AA, Grange D, Immken L, Schaaf CP, Van Esch H, Bi W, Cheung SW, Breman AM, Smith JL, Shaw C, Crosby AH, Eng C, Yang Y, Lupski JR, Xiao R, Liu P. Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies. Genet Med 2019; 21:663-675. [PMID: 30158690 PMCID: PMC6395558 DOI: 10.1038/s41436-018-0085-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 06/01/2018] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes from a clinical exome perspective. METHODS We retrospectively studied patients referred for clinical exome sequencing (CES, N = 10,698). Patients with causative variants in novel or recently described cohesinopathy genes were enrolled for phenotypic characterization. RESULTS Pathogenic or likely pathogenic single-nucleotide and insertion/deletion variants (SNVs/indels) were identified in established disease genes including NIPBL (N = 5), SMC1A (N = 14), SMC3 (N = 4), RAD21 (N = 2), and HDAC8 (N = 8). The phenotypes in this genetically defined cohort skew towards the mild end of CdLS spectrum as compared with phenotype-driven cohorts. Candidate or recently reported cohesinopathy genes were supported by de novo SNVs/indels in STAG1 (N = 3), STAG2 (N = 5), PDS5A (N = 1), and WAPL (N = 1), and one inherited SNV in PDS5A. We also identified copy-number deletions affecting STAG1 (two de novo, one of unknown inheritance) and STAG2 (one of unknown inheritance). Patients with STAG1 and STAG2 variants presented with overlapping features yet without characteristic facial features of CdLS. CONCLUSION CES effectively identified disease-causing alleles at the mild end of the cohensinopathy spectrum and enabled characterization of candidate disease genes.
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Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Juanita Neira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Teresa Santiago-Sim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | | | - Margaret P Adam
- Seattle Children's Hospital, Seattle, Washington, 98105, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, 98105, USA
| | - Emma L Baple
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Gladstone Road, Exeter, EX1 2ED, UK
| | - John Dean
- Clinical Genetics Service, NHS Grampian, Aberdeen, AB25 2ZA, Scotland
| | - Chin-To Fong
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, 14642, USA
| | - Scott E Hickey
- Department of Pediatrics, Nationwide Children's Hospital, Columbus, Ohio, 43205, USA
| | - Louanne Hudgins
- Division of Medical Genetics, Stanford University, Stanford, California, 94305, USA
| | - Eyby Leon
- Rare Disease Institute, Children's National Health System, Washington, DC, 20010, USA
| | | | - Lettie Rawlins
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Gladstone Road, Exeter, EX1 2ED, UK
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, 0424, Oslo, Norway
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710, Skien, Norway
| | - Olivia Wenger
- New Leaf Center, Clinic for Special Children, Mt. Eaton, Ohio, 44659, USA
| | - Jullianne Diaz
- Rare Disease Institute, Children's National Health System, Washington, DC, 20010, USA
| | - Laura Jenkins
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, 15224, USA
| | - Laura Martin
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, 14642, USA
| | - Marianne McGuire
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Marguerite Pietryga
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Linda Ramsdell
- Seattle Children's Hospital, Seattle, Washington, 98105, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, 98105, USA
| | - Leah Slattery
- Division of Medical Genetics, Stanford University, Stanford, California, 94305, USA
| | - Farida Abid
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Alison A Bertuch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Dorothy Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - LaDonna Immken
- Dell Children's Medical Center of Central Texas, Austin, Texas, 78723, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Institute of Human Genetics, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Center for Rare Diseases, University Hospital Cologne, Cologne, Germany
| | - Hilde Van Esch
- Center for Human Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Andrew H Crosby
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Christine Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA.
- Baylor Genetics, Houston, Texas, 77021, USA.
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11
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Jinks RN, Puffenberger EG, Baple E, Harding B, Crino P, Fogo AB, Wenger O, Xin B, Koehler AE, McGlincy MH, Provencher MM, Smith JD, Tran L, Al Turki S, Chioza BA, Cross H, Harlalka GV, Hurles ME, Maroofian R, Heaps AD, Morton MC, Stempak L, Hildebrandt F, Sadowski CE, Zaritsky J, Campellone K, Morton DH, Wang H, Crosby A, Strauss KA. Recessive nephrocerebellar syndrome on the Galloway-Mowat syndrome spectrum is caused by homozygous protein-truncating mutations of WDR73. Brain 2015; 138:2173-90. [PMID: 26070982 PMCID: PMC4511861 DOI: 10.1093/brain/awv153] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/14/2015] [Indexed: 12/20/2022] Open
Abstract
Galloway-Mowat syndrome (GMS) is a neurodevelopmental disorder characterized by microcephaly, cerebellar hypoplasia, nephrosis, and profound intellectual disability. Jinks et al. extend the GMS spectrum by identifying a novel nephrocerebellar syndrome with selective striatal cholinergic interneuron loss and complete lateral geniculate nucleus delamination, caused by a frameshift mutation in WDR73. We describe a novel nephrocerebellar syndrome on the Galloway-Mowat syndrome spectrum among 30 children (ages 1.0 to 28 years) from diverse Amish demes. Children with nephrocerebellar syndrome had progressive microcephaly, visual impairment, stagnant psychomotor development, abnormal extrapyramidal movements and nephrosis. Fourteen died between ages 2.7 and 28 years, typically from renal failure. Post-mortem studies revealed (i) micrencephaly without polymicrogyria or heterotopia; (ii) atrophic cerebellar hemispheres with stunted folia, profound granule cell depletion, Bergmann gliosis, and signs of Purkinje cell deafferentation; (iii) selective striatal cholinergic interneuron loss; and (iv) optic atrophy with delamination of the lateral geniculate nuclei. Renal tissue showed focal and segmental glomerulosclerosis and extensive effacement and microvillus transformation of podocyte foot processes. Nephrocerebellar syndrome mapped to 700 kb on chromosome 15, which contained a single novel homozygous frameshift variant (WDR73 c.888delT; p.Phe296Leufs*26). WDR73 protein is expressed in human cerebral cortex, hippocampus, and cultured embryonic kidney cells. It is concentrated at mitotic microtubules and interacts with α-, β-, and γ-tubulin, heat shock proteins 70 and 90 (HSP-70; HSP-90), and the carbamoyl phosphate synthetase 2/aspartate transcarbamylase/dihydroorotase multi-enzyme complex. Recombinant WDR73 p.Phe296Leufs*26 and p.Arg256Profs*18 proteins are truncated, unstable, and show increased interaction with α- and β-tubulin and HSP-70/HSP-90. Fibroblasts from patients homozygous for WDR73 p.Phe296Leufs*26 proliferate poorly in primary culture and senesce early. Our data suggest that in humans, WDR73 interacts with mitotic microtubules to regulate cell cycle progression, proliferation and survival in brain and kidney. We extend the Galloway-Mowat syndrome spectrum with the first description of diencephalic and striatal neuropathology.
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Affiliation(s)
- Robert N Jinks
- 1 Department of Biology and Biological Foundations of Behaviour Program, Franklin and Marshall College, Lancaster, PA 17604, USA
| | - Erik G Puffenberger
- 1 Department of Biology and Biological Foundations of Behaviour Program, Franklin and Marshall College, Lancaster, PA 17604, USA 2 Clinic for Special Children, Strasburg, PA 17579, USA
| | - Emma Baple
- 3 RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK 4 Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, UK 5 Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Brian Harding
- 6 Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter Crino
- 7 Shriners Hospital Paediatric Research Centre, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Agnes B Fogo
- 8 Division of Renal Pathology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Olivia Wenger
- 9 New Leaf Clinic for Special Children, Mount Eaton, OH 44659, USA 10 Department of Paediatrics, Akron Children's Hospital, Akron, OH 44302, USA
| | - Baozhong Xin
- 11 DDC Clinic for Special Needs Children, Middlefield, OH 44062, USA
| | - Alanna E Koehler
- 1 Department of Biology and Biological Foundations of Behaviour Program, Franklin and Marshall College, Lancaster, PA 17604, USA
| | - Madeleine H McGlincy
- 1 Department of Biology and Biological Foundations of Behaviour Program, Franklin and Marshall College, Lancaster, PA 17604, USA
| | - Margaret M Provencher
- 1 Department of Biology and Biological Foundations of Behaviour Program, Franklin and Marshall College, Lancaster, PA 17604, USA
| | - Jeffrey D Smith
- 1 Department of Biology and Biological Foundations of Behaviour Program, Franklin and Marshall College, Lancaster, PA 17604, USA
| | - Linh Tran
- 1 Department of Biology and Biological Foundations of Behaviour Program, Franklin and Marshall College, Lancaster, PA 17604, USA
| | - Saeed Al Turki
- 12 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Barry A Chioza
- 13 Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter EX1 2LU, UK
| | - Harold Cross
- 14 Department of Ophthalmology, University of Arizona College of Medicine, Tucson, AZ 85711, USA
| | - Gaurav V Harlalka
- 13 Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter EX1 2LU, UK
| | - Matthew E Hurles
- 12 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Reza Maroofian
- 13 Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter EX1 2LU, UK
| | - Adam D Heaps
- 2 Clinic for Special Children, Strasburg, PA 17579, USA
| | - Mary C Morton
- 2 Clinic for Special Children, Strasburg, PA 17579, USA
| | - Lisa Stempak
- 15 Department of Pathology, University Hospitals Case Medical Centre, Cleveland, OH 44106, USA 16 Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Friedhelm Hildebrandt
- 17 Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA 18 Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Carolin E Sadowski
- 18 Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua Zaritsky
- 19 Department of Paediatrics, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE 19803, USA
| | - Kenneth Campellone
- 20 Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - D Holmes Morton
- 1 Department of Biology and Biological Foundations of Behaviour Program, Franklin and Marshall College, Lancaster, PA 17604, USA 2 Clinic for Special Children, Strasburg, PA 17579, USA 21 Lancaster General Hospital, Lancaster, PA 17602, USA
| | - Heng Wang
- 11 DDC Clinic for Special Needs Children, Middlefield, OH 44062, USA 22 Department of Paediatrics, Rainbow Babies and Children's Hospital and Department of Molecular Cardiology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Andrew Crosby
- 3 RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Kevin A Strauss
- 1 Department of Biology and Biological Foundations of Behaviour Program, Franklin and Marshall College, Lancaster, PA 17604, USA 2 Clinic for Special Children, Strasburg, PA 17579, USA 21 Lancaster General Hospital, Lancaster, PA 17602, USA
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Grünthal E, Wenger O. Ergänzende Untersuchungen und Bemerkungen zu der Arbeit: Nachweis von Erblichkeit bei der Alzheimerschen Krankheit usw. Eur Neurol 2008. [DOI: 10.1159/000148594] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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