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Sala-Gaston J, Pérez-Villegas EM, Armengol JA, Rawlins LE, Baple EL, Crosby AH, Ventura F, Rosa JL. Autophagy dysregulation via the USP20-ULK1 axis in the HERC2-related neurodevelopmental disorder. Cell Death Discov 2024; 10:163. [PMID: 38570483 PMCID: PMC10991529 DOI: 10.1038/s41420-024-01931-6] [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: 01/09/2024] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
Sequence variants in the HERC2 gene are associated with a significant reduction in HERC2 protein levels and cause a neurodevelopmental disorder known as the HERC2-related disorder, which shares clinical features with Angelman syndrome, including global developmental delay, intellectual disability, autism, and movement disorders. Remarkably, the HERC2 gene is commonly deleted in individuals with Angelman syndrome, suggesting a potential contribution of HERC2 to the pathophysiology of this disease. Given the known critical role of autophagy in brain development and its implication in neurodevelopmental diseases, we undertook different experimental approaches to monitor autophagy in fibroblasts derived from individuals affected by the HERC2-related disorder. Our findings reveal alterations in the levels of the autophagy-related protein LC3. Furthermore, experiments with lysosomal inhibitors provide confirmation of an upregulation of the autophagy pathway in these patient-derived cells. Mechanistically, we corroborate an interaction between HERC2 and the deubiquitylating enzyme USP20; and demonstrate that HERC2 deficiency leads to increased USP20 protein levels. Notably, USP20 upregulation correlates with enhanced stability of the autophagy initiating kinase ULK1, highlighting the role of HERC2 as an autophagy regulator factor through the USP20-ULK1 axis. Moreover, we show that p38 acts as a modulator of this pathway, since p38 activation disrupts HERC2-USP20 interaction, leading to increased USP20 and LC3-II protein levels. Together, these findings uncover a previously unknown role for HERC2 in autophagy regulation and provide insights into the pathomolecular mechanisms underlying the HERC2-related disorder and Angelman syndrome.
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Affiliation(s)
- Joan Sala-Gaston
- Department of Physiological Sciences, University of Barcelona (UB), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Spain
| | - Eva M Pérez-Villegas
- Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, 41013, Seville, Spain
| | - José A Armengol
- Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, 41013, Seville, Spain
| | - Lettie E Rawlins
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Emma L Baple
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Andrew H Crosby
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Francesc Ventura
- Department of Physiological Sciences, University of Barcelona (UB), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Spain
| | - Jose Luis Rosa
- Department of Physiological Sciences, University of Barcelona (UB), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Spain.
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2
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McInnes-Dean H, Mellis R, Daniel M, Walton H, Baple EL, Bertoli M, Fisher J, Gajewska-Knapik K, Holder-Espinasse M, Lafarge C, Leeson-Beevers K, McEwan A, Pandya P, Parker M, Peet S, Roberts L, Sankaran S, Smith A, Tapon D, Wu WH, Wynn SL, Chitty LS, Hill M, Peter M. 'Something that helped the whole picture': Experiences of parents offered rapid prenatal exome sequencing in routine clinical care in the English National Health Service. Prenat Diagn 2024; 44:465-479. [PMID: 38441167 DOI: 10.1002/pd.6537] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 04/11/2024]
Abstract
OBJECTIVES In October 2020, rapid prenatal exome sequencing (pES) was introduced into routine National Health Service (NHS) care in England. This study aimed to explore parent experiences and their information and support needs from the perspective of parents offered pES and of health professionals involved in its delivery. METHODS In this qualitative study, semi-structured interviews were conducted with 42 women and 6 male partners and 63 fetal medicine and genetic health professionals. Interviews were transcribed verbatim and analysed using thematic analysis. RESULTS Overall views about pES were positive and parents were grateful to be offered the test. Highlighted benefits of pES included the value of the additional information for pregnancy management and planning for future pregnancies. An anxious wait for results was common, often associated with the need to make decisions near to 24 weeks in pregnancy when there are legal restrictions for late termination. Descriptions of dealing with uncertainty were also common, even when results had been returned. Many parents described pES results as informing decision-making around whether or not to terminate pregnancy. Some professionals were concerned that a non-informative result could be overly reassuring and highlighted that careful counselling was needed to ensure parents have a good understanding of what the result means for their pregnancy. Emotional support from professionals was valued; however, some parents felt that post-test support was lacking. CONCLUSION Parents and professionals welcomed the introduction of pES. Results inform parents' decision-making around the termination of pregnancy. When there are no diagnostic findings or uncertain findings from pES, personalised counselling that considers scans and other tests are crucial. Directing parents to reliable online sources of information and providing emotional support throughout could improve their experiences of care.
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Affiliation(s)
- Hannah McInnes-Dean
- Antenatal Results and Choices, London, UK
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Rhiannon Mellis
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Morgan Daniel
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Holly Walton
- Department of Applied Health Research, University College London, London, UK
| | - Emma L Baple
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Peninsula Clinical Genetics Service, School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | | | | | - Katarzyna Gajewska-Knapik
- Department of Obstetrics and Gynaecology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Muriel Holder-Espinasse
- Clinical Genetics Department, Guy's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Caroline Lafarge
- School of Human and Social Sciences, University of West London, London, UK
| | | | - Alec McEwan
- Department of Obstetrics and Gynaecology, Nottingham University Hospitals, Nottingham, UK
| | - Pranav Pandya
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
- Fetal Medicine Unit, University College London Hospitals, London, UK
| | - Michael Parker
- The Ethox Centre, Nuffield Department of Population Health and Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, UK
| | | | | | - Srividhya Sankaran
- School of Life Course and Population Sciences, Kings College London, St Thomas' Hospital, London, UK
- Department of Women and Children Health, Evelina Women & Children's Hospital Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Audrey Smith
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Dagmar Tapon
- Queen Charlotte's & Chelsea Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Wing Han Wu
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sarah L Wynn
- Unique - Rare Chromosome Disorder Support Group, Oxted, UK
| | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Melissa Hill
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Michelle Peter
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
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3
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Khalaf-Nazzal R, Dweikat I, Ubeyratna N, Fasham J, Alawneh M, Leslie J, Maree M, Gunning A, Zayed DZ, Voutsina N, McGavin L, Sawafta R, Owens M, Baker W, Turnpenny P, Al-Hijawi F, Baple EL, Crosby AH, Rawlins LE. TECPR2-related hereditary sensory and autonomic neuropathy in two siblings from Palestine. Am J Med Genet A 2024:e63579. [PMID: 38436550 DOI: 10.1002/ajmg.a.63579] [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: 10/11/2023] [Revised: 01/05/2024] [Accepted: 02/17/2024] [Indexed: 03/05/2024]
Abstract
Due to the majority of currently available genome data deriving from individuals of European ancestry, the clinical interpretation of genomic variants in individuals from diverse ethnic backgrounds remains a major diagnostic challenge. Here, we investigated the genetic cause of a complex neurodevelopmental phenotype in two Palestinian siblings. Whole exome sequencing identified a homozygous missense TECPR2 variant (Chr14(GRCh38):g.102425085G>A; NM_014844.5:c.745G>A, p.(Gly249Arg)) absent in gnomAD, segregating appropriately with the inheritance pattern in the family. Variant assessment with in silico pathogenicity prediction and protein modeling tools alongside population database frequencies led to classification as a variant of uncertain significance. As pathogenic TECPR2 variants are associated with hereditary sensory and autonomic neuropathy with intellectual disability, we reviewed previously published candidate TECPR2 missense variants to clarify clinical outcomes and variant classification using current approved guidelines, classifying a number of published variants as of uncertain significance. This work highlights genomic healthcare inequalities and the challenges in interpreting rare genetic variants in populations underrepresented in genomic databases. It also improves understanding of the clinical and genetic spectrum of TECPR2-related neuropathy and contributes to addressing genomic data disparity and inequalities of the genomic architecture in Palestinian populations.
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Affiliation(s)
- Reham Khalaf-Nazzal
- Faculty of Medicine, Arab American University of Palestine, Jenin, Palestine
| | - Imad Dweikat
- Faculty of Medicine, Arab American University of Palestine, Jenin, Palestine
| | - Nishanka Ubeyratna
- RILD Wellcome Wolfson Medical Research Centre, Royal Devon University Hospitals NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
| | - James Fasham
- RILD Wellcome Wolfson Medical Research Centre, Royal Devon University Hospitals NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Maysa Alawneh
- Department of Medicine, College of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
- Paediatric Department, An-Najah National University Hospital, Nablus, Palestine
| | - Joseph Leslie
- RILD Wellcome Wolfson Medical Research Centre, Royal Devon University Hospitals NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
| | - Mosab Maree
- Department of Medicine, College of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Adam Gunning
- RILD Wellcome Wolfson Medical Research Centre, Royal Devon University Hospitals NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
| | - Deyala Z Zayed
- Paediatric Department, An-Najah National University Hospital, Nablus, Palestine
| | - Nikol Voutsina
- RILD Wellcome Wolfson Medical Research Centre, Royal Devon University Hospitals NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
| | - Lucy McGavin
- University Hospitals Plymouth NHS Trust, Plymouth, UK
- University of Plymouth, Plymouth, UK
| | - Reem Sawafta
- Paediatric Department, An-Najah National University Hospital, Nablus, Palestine
| | - Martina Owens
- RILD Wellcome Wolfson Medical Research Centre, Royal Devon University Hospitals NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
| | - Wisam Baker
- Paediatric Department, Dr. Khalil Suleiman Government Hospital, Jenin, Palestine
| | - Peter Turnpenny
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Fida' Al-Hijawi
- Paediatric Community Outpatient Clinics, Palestinian Ministry of Health, Jenin, Palestine
| | - Emma L Baple
- RILD Wellcome Wolfson Medical Research Centre, Royal Devon University Hospitals NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Andrew H Crosby
- RILD Wellcome Wolfson Medical Research Centre, Royal Devon University Hospitals NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
| | - Lettie E Rawlins
- RILD Wellcome Wolfson Medical Research Centre, Royal Devon University Hospitals NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
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4
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Robinson HK, Stals K, Hill S, Parrish A, Baple EL. Rapid genome sequencing for infantile-onset epilepsy within a national health-care setting. Lancet Neurol 2024; 23:139-140. [PMID: 38267181 DOI: 10.1016/s1474-4422(23)00429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/02/2023] [Indexed: 01/26/2024]
Affiliation(s)
- Hannah K Robinson
- Exeter Genomics Laboratory (NHS South West Genomic Laboratory Hub), Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Karen Stals
- Exeter Genomics Laboratory (NHS South West Genomic Laboratory Hub), Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
| | | | - Andrew Parrish
- Exeter Genomics Laboratory (NHS South West Genomic Laboratory Hub), Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Emma L Baple
- Exeter Genomics Laboratory (NHS South West Genomic Laboratory Hub), Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK; Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK; RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK.
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5
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Fasham J, Huebner AK, Liebmann L, Khalaf-Nazzal R, Maroofian R, Kryeziu N, Wortmann SB, Leslie JS, Ubeyratna N, Mancini GMS, van Slegtenhorst M, Wilke M, Haack TB, Shamseldin HE, Gleeson JG, Almuhaizea M, Dweikat I, Abu-Libdeh B, Daana M, Zaki MS, Wakeling MN, McGavin L, Turnpenny PD, Alkuraya FS, Houlden H, Schlattmann P, Kaila K, Crosby AH, Baple EL, Hübner CA. SLC4A10 mutation causes a neurological disorder associated with impaired GABAergic transmission. Brain 2023; 146:4547-4561. [PMID: 37459438 PMCID: PMC10629776 DOI: 10.1093/brain/awad235] [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: 04/08/2022] [Revised: 05/19/2023] [Accepted: 06/06/2023] [Indexed: 11/09/2023] Open
Abstract
SLC4A10 is a plasma-membrane bound transporter that utilizes the Na+ gradient to drive cellular HCO3- uptake, thus mediating acid extrusion. In the mammalian brain, SLC4A10 is expressed in principal neurons and interneurons, as well as in epithelial cells of the choroid plexus, the organ regulating the production of CSF. Using next generation sequencing on samples from five unrelated families encompassing nine affected individuals, we show that biallelic SLC4A10 loss-of-function variants cause a clinically recognizable neurodevelopmental disorder in humans. The cardinal clinical features of the condition include hypotonia in infancy, delayed psychomotor development across all domains and intellectual impairment. Affected individuals commonly display traits associated with autistic spectrum disorder including anxiety, hyperactivity and stereotyped movements. In two cases isolated episodes of seizures were reported in the first few years of life, and a further affected child displayed bitemporal epileptogenic discharges on EEG without overt clinical seizures. While occipitofrontal circumference was reported to be normal at birth, progressive postnatal microcephaly evolved in 7 out of 10 affected individuals. Neuroradiological features included a relative preservation of brain volume compared to occipitofrontal circumference, characteristic narrow sometimes 'slit-like' lateral ventricles and corpus callosum abnormalities. Slc4a10 -/- mice, deficient for SLC4A10, also display small lateral brain ventricles and mild behavioural abnormalities including delayed habituation and alterations in the two-object novel object recognition task. Collapsed brain ventricles in both Slc4a10-/- mice and affected individuals suggest an important role of SLC4A10 in the production of the CSF. However, it is notable that despite diverse roles of the CSF in the developing and adult brain, the cortex of Slc4a10-/- mice appears grossly intact. Co-staining with synaptic markers revealed that in neurons, SLC4A10 localizes to inhibitory, but not excitatory, presynapses. These findings are supported by our functional studies, which show the release of the inhibitory neurotransmitter GABA is compromised in Slc4a10-/- mice, while the release of the excitatory neurotransmitter glutamate is preserved. Manipulation of intracellular pH partially rescues GABA release. Together our studies define a novel neurodevelopmental disorder associated with biallelic pathogenic variants in SLC4A10 and highlight the importance of further analyses of the consequences of SLC4A10 loss-of-function for brain development, synaptic transmission and network properties.
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Affiliation(s)
- James Fasham
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Antje K Huebner
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller Universität, 07747 Jena, Germany
| | - Lutz Liebmann
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller Universität, 07747 Jena, Germany
| | - Reham Khalaf-Nazzal
- Department of Biomedical Sciences, Faculty of Medicine, Arab American University of Palestine, Jenin, P227, Palestine
| | - Reza Maroofian
- Molecular and Clinical Sciences Institute, St. George’s University of London, London SW17 0RE, UK
| | - Nderim Kryeziu
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller Universität, 07747 Jena, Germany
| | - Saskia B Wortmann
- University Children’s Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), 5020 Salzburg, Austria
- Amalia Children’s Hospital, Radboudumc, 6525 GA Nijmegen, The Netherlands
- Institute of Human Genetics, Technische Universität München, 80333 Munich, Germany
| | - Joseph S Leslie
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Nishanka Ubeyratna
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | | | - Martina Wilke
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Joseph G Gleeson
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mohamed Almuhaizea
- Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Imad Dweikat
- Department of Biomedical Sciences, Faculty of Medicine, Arab American University of Palestine, Jenin, P227, Palestine
| | - Bassam Abu-Libdeh
- Department of Pediatrics and Genetics, Makassed Hospital and Al-Quds University, East Jerusalem, 95908, Palestine
| | - Muhannad Daana
- Department of Pediatrics, Arab Women’s Union Hospital, Nablus, P400, Palestine
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Matthew N Wakeling
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Lucy McGavin
- Department of Radiology, Derriford Hospital, Plymouth PL6 8DH, UK
| | - Peter D Turnpenny
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Henry Houlden
- Molecular and Clinical Sciences Institute, St. George’s University of London, London SW17 0RE, UK
| | - Peter Schlattmann
- Institute for Medical Statistics, Computer Science and Data Science, Jena University Hospital, 07747 Jena, Germany
| | - Kai Kaila
- Molecular and Integrative Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Emma L Baple
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Christian A Hübner
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller Universität, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, Friedrich Schiller Universität, 07747 Jena, Germany
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6
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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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7
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Marwan M, Dawood M, Ullah M, Shah IU, Khan N, Hassan MT, Karam M, Rawlins LE, Baple EL, Crosby AH, Saleha S. Unravelling the genetic basis of retinal dystrophies in Pakistani consanguineous families. BMC Ophthalmol 2023; 23:205. [PMID: 37165311 PMCID: PMC10170854 DOI: 10.1186/s12886-023-02948-8] [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: 10/19/2022] [Accepted: 04/26/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Retinitis Pigmentosa (RP) is a clinically and genetically progressive retinal dystrophy associated with severe visual impairments and sometimes blindness, the most common syndromic form of which is Usher syndrome (USH). This study aimed to further increase understanding of the spectrum of RP in the Khyber Pakhtunkhwa region of Pakistan. METHODOLOGY Four consanguineous families of Pashtun ethnic group were investigated which were referred by the local collaborating ophthalmologists. In total 42 individuals in four families were recruited and investigated using whole exome and dideoxy sequencing. Among them, 20 were affected individuals including 6 in both family 1 and 2, 5 in family 3 and 3 in family 4. RESULT Pathogenic gene variants were identified in all four families, including two in cone dystrophy and RP genes in the same family (PDE6C; c.480delG, p.Asn161ThrfsTer33 and TULP1; c.238 C > T, p.Gln80Ter) with double-homozygous individuals presenting with more severe disease. Other pathogenic variants were identified in MERTK (c.2194C > T, p.Arg732Ter), RHO (c.448G > A, p.Glu150Lys) associated with non-syndromic RP, and MYO7A (c.487G > A, p.Gly163Arg) associated with USH. In addition, the reported variants were of clinical significance as the PDE6C variant was detected novel, whereas TULP1, MERTK, and MYO7A variants were detected rare and first time found segregating with retinal dystrophies in Pakistani consanguineous families. CONCLUSIONS This study increases knowledge of the genetic basis of retinal dystrophies in families from Pakistan providing information important for genetic testing and diagnostic provision particularly from the Khyber Pakhtunkhwa region.
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Affiliation(s)
- Muhammad Marwan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Muhammad Dawood
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Mukhtar Ullah
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, 4031, Switzerland
- Department of Ophthalmology, University of Basel, Basel, 4056, Switzerland
| | - Irfan Ullah Shah
- Department of Ophthalmology, KMU Institute of Medical Sciences KIMS, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Niamat Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Muhammad Taimur Hassan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Muhammad Karam
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Lettie E Rawlins
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Emma L Baple
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Andrew H Crosby
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan.
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8
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Kammermeier J, Lamb CA, Jones KDJ, Anderson CA, Baple EL, Bolton C, Braggins H, Coulter TI, Gilmour KC, Gregory V, Hambleton S, Hartley D, Hawthorne AB, Hearn S, Laurence A, Parkes M, Russell RK, Speight RA, Travis S, Wilson DC, Uhlig HH. Genomic diagnosis and care co-ordination for monogenic inflammatory bowel disease in children and adults: consensus guideline on behalf of the British Society of Gastroenterology and British Society of Paediatric Gastroenterology, Hepatology and Nutrition. Lancet Gastroenterol Hepatol 2023; 8:271-286. [PMID: 36634696 DOI: 10.1016/s2468-1253(22)00337-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 01/11/2023]
Abstract
Genomic medicine enables the identification of patients with rare or ultra-rare monogenic forms of inflammatory bowel disease (IBD) and supports clinical decision making. Patients with monogenic IBD frequently experience extremely early onset of treatment-refractory disease, with complex extraintestinal disease typical of immunodeficiency. Since more than 100 monogenic disorders can present with IBD, new genetic disorders and variants are being discovered every year, and as phenotypic expression of the gene defects is variable, adaptive genomic technologies are required. Monogenic IBD has become a key area to establish the concept of precision medicine. Clear guidance and standardised, affordable applications of genomic technologies are needed to implement exome or genome sequencing in clinical practice. This joint British Society of Gastroenterology and British Society of Paediatric Gastroenterology, Hepatology and Nutrition guideline aims to ensure that testing resources are appropriately applied to maximise the benefit to patients on a national scale, minimise health-care disparities in accessing genomic technologies, and optimise resource use. We set out the structural requirements for genomic medicine as part of a multidisciplinary team approach. Initiation of genomic diagnostics should be guided by diagnostic criteria for the individual patient, in particular the age of IBD onset and the patient's history, and potential implications for future therapies. We outline the diagnostic care pathway for paediatric and adult patients. This guideline considers how to handle clinically actionable findings in research studies and the impact of consumer-based genomics for monogenic IBD. This document was developed by multiple stakeholders, including UK paediatric and adult gastroenterology physicians, immunologists, transplant specialists, clinical geneticists, scientists, and research leads of UK genetic programmes, in partnership with patient representatives of several IBD and rare disease charities.
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Affiliation(s)
- Jochen Kammermeier
- Department of Paediatric Gastroenterology, Evelina London Children's Hospital, London, UK
| | - Christopher A Lamb
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; Department of Gastroenterology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Kelsey D J Jones
- Department of Gastroenterology, Great Ormond Street Hospital for Children, London, UK; Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, University of Oxford, Oxford, UK
| | | | - Emma L Baple
- University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Chrissy Bolton
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Helen Braggins
- Department of Immunology, Great Ormond Street Hospital of Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK; Chronic Granulomatous Disorder Society, Dartford, UK
| | - Tanya I Coulter
- Regional Immunology Service for Northern Ireland, Belfast, UK
| | - Kimberly C Gilmour
- Clinical Immunology Laboratory, Great Ormond Street Hospital of Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | | | - Sophie Hambleton
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; Department of Paediatric Immunology, Great North Children's Hospital, Newcastle upon Tyne, UK
| | | | - A Barney Hawthorne
- Department of Gastroenterology, University Hospital of Wales, Cardiff, UK
| | - Sarah Hearn
- Translational Gastroenterology Unit and Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Arian Laurence
- Department of Clinical Immunology, Royal Free Hospital, London, UK; Department of Haematology and Bone Marrow Transplantation, University College Hospital, London, UK
| | - Miles Parkes
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge, UK
| | - Richard K Russell
- Child Life and Health, University of Edinburgh, The Royal Hospital for Children & Young People, Edinburgh, UK; Department of Paediatric Gastroenterology, The Royal Hospital for Children & Young People, Edinburgh, UK; Department of Paediatric Gastroenterology, The Royal Hospital for Children & Young People, Edinburgh, UK
| | - R Alexander Speight
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; Department of Gastroenterology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Simon Travis
- Translational Gastroenterology Unit and Biomedical Research Centre, University of Oxford, Oxford, UK
| | - David C Wilson
- Child Life and Health, University of Edinburgh, The Royal Hospital for Children & Young People, Edinburgh, UK; Department of Paediatric Gastroenterology, The Royal Hospital for Children & Young People, Edinburgh, UK; Department of Paediatric Gastroenterology, The Royal Hospital for Children & Young People, Edinburgh, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit and Biomedical Research Centre, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK.
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9
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Khalaf-Nazzal R, Fasham J, Inskeep KA, Blizzard LE, Leslie JS, Wakeling MN, Ubeyratna N, Mitani T, Griffith JL, Baker W, Al-Hijawi F, Keough KC, Gezdirici A, Pena L, Spaeth CG, Turnpenny PD, Walsh JR, Ray R, Neilson A, Kouranova E, Cui X, Curiel DT, Pehlivan D, Akdemir ZC, Posey JE, Lupski JR, Dobyns WB, Stottmann RW, Crosby AH, Baple EL. Bi-allelic CAMSAP1 variants cause a clinically recognizable neuronal migration disorder. Am J Hum Genet 2022; 109:2068-2079. [PMID: 36283405 PMCID: PMC9674946 DOI: 10.1016/j.ajhg.2022.09.012] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/27/2022] [Indexed: 01/26/2023] Open
Abstract
Non-centrosomal microtubules are essential cytoskeletal filaments that are important for neurite formation, axonal transport, and neuronal migration. They require stabilization by microtubule minus-end-targeting proteins including the CAMSAP family of molecules. Using exome sequencing on samples from five unrelated families, we show that bi-allelic CAMSAP1 loss-of-function variants cause a clinically recognizable, syndromic neuronal migration disorder. The cardinal clinical features of the syndrome include a characteristic craniofacial appearance, primary microcephaly, severe neurodevelopmental delay, cortical visual impairment, and seizures. The neuroradiological phenotype comprises a highly recognizable combination of classic lissencephaly with a posterior more severe than anterior gradient similar to PAFAH1B1(LIS1)-related lissencephaly and severe hypoplasia or absence of the corpus callosum; dysplasia of the basal ganglia, hippocampus, and midbrain; and cerebellar hypodysplasia, similar to the tubulinopathies, a group of monogenic tubulin-associated disorders of cortical dysgenesis. Neural cell rosette lineages derived from affected individuals displayed findings consistent with these phenotypes, including abnormal morphology, decreased cell proliferation, and neuronal differentiation. Camsap1-null mice displayed increased perinatal mortality, and RNAScope studies identified high expression levels in the brain throughout neurogenesis and in facial structures, consistent with the mouse and human neurodevelopmental and craniofacial phenotypes. Together our findings confirm a fundamental role of CAMSAP1 in neuronal migration and brain development and define bi-allelic variants as a cause of a clinically distinct neurodevelopmental disorder in humans and mice.
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Affiliation(s)
- Reham Khalaf-Nazzal
- Biomedical Sciences Department, Faculty of Medicine, Arab American University of Palestine, Jenin P227, Palestine
| | - James Fasham
- Department of Clinical and Biomedical Science, University of Exeter Faculty of Health and Life Science, RILD building, Barrack Road, Exeter EX2 5DW, UK; Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust (Heavitree Hospital), Gladstone Road, Exeter EX1 2ED, UK
| | - Katherine A Inskeep
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH 45229, USA; Institute for Genomic Medicine at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH 43205, USA
| | - Lauren E Blizzard
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH 45229, USA
| | - Joseph S Leslie
- Department of Clinical and Biomedical Science, University of Exeter Faculty of Health and Life Science, RILD building, Barrack Road, Exeter EX2 5DW, UK
| | - Matthew N Wakeling
- Department of Clinical and Biomedical Science, University of Exeter Faculty of Health and Life Science, RILD building, Barrack Road, Exeter EX2 5DW, UK
| | - Nishanka Ubeyratna
- Department of Clinical and Biomedical Science, University of Exeter Faculty of Health and Life Science, RILD building, Barrack Road, Exeter EX2 5DW, UK
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer L Griffith
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wisam Baker
- Paediatrics Department, Dr. Khalil Suleiman Government Hospital, Jenin, Palestine
| | - Fida' Al-Hijawi
- Paediatrics Community Outpatient Clinics, Palestinian Ministry of Health, Jenin, Palestine
| | - Karen C Keough
- Department of Pediatrics, Dell Medical School, 1400 Barbara Jordan Boulevard, Austin, TX 78723, USA; Child Neurology Consultants of Austin, 7940 Shoal Creek Boulevard, Suite 100, Austin, TX 78757, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Başakşehir Çam and Sakura City Hospital, 34480 Istanbul, Turkey
| | - Loren Pena
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Christine G Spaeth
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Peter D Turnpenny
- Department of Clinical and Biomedical Science, University of Exeter Faculty of Health and Life Science, RILD building, Barrack Road, Exeter EX2 5DW, UK; Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust (Heavitree Hospital), Gladstone Road, Exeter EX1 2ED, UK
| | - Joseph R Walsh
- Department of Neurological Surgery, School of Medicine, Washington University in Saint Louis, St. Louis, MO 63110, USA
| | - Randall Ray
- Departments of Pediatrics and Medical Genetics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Amber Neilson
- Genome Engineering & Stem Cell Center, Department of Genetics, School of Medicine, Washington University in Saint Louis, St. Louis, MO 63110, USA
| | - Evguenia Kouranova
- Genome Engineering & Stem Cell Center, Department of Genetics, School of Medicine, Washington University in Saint Louis, St. Louis, MO 63110, USA
| | - Xiaoxia Cui
- Genome Engineering & Stem Cell Center, Department of Genetics, School of Medicine, Washington University in Saint Louis, St. Louis, MO 63110, USA
| | - David T Curiel
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in Saint Louis, St. Louis, MO 63130, USA; Division of Cancer Biology, Department of Radiation Oncology, School of Medicine, Washington University in Saint Louis, St. Louis, MO 63110, USA; Biologic Therapeutics Center, Department of Radiation Oncology, School of Medicine, Washington University in Saint Louis, St. Louis, MO 63110, USA
| | - Davut Pehlivan
- 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
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - William B Dobyns
- Departments of Pediatrics and Genetics, University of Minnesota, Minneapolis, MN, USA
| | - Rolf W Stottmann
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH 45229, USA; Institute for Genomic Medicine at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH 43205, USA; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Andrew H Crosby
- Department of Clinical and Biomedical Science, University of Exeter Faculty of Health and Life Science, RILD building, Barrack Road, Exeter EX2 5DW, UK
| | - Emma L Baple
- Department of Clinical and Biomedical Science, University of Exeter Faculty of Health and Life Science, RILD building, Barrack Road, Exeter EX2 5DW, UK; Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust (Heavitree Hospital), Gladstone Road, Exeter EX1 2ED, UK.
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10
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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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11
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Sala-Gaston J, Pedrazza L, Ramirez J, Martinez-Martinez A, Rawlins LE, Baple EL, Crosby AH, Mayor U, Ventura F, Rosa JL. HERC2 deficiency activates C-RAF/MKK3/p38 signalling pathway altering the cellular response to oxidative stress. Cell Mol Life Sci 2022; 79:548. [PMID: 36241744 PMCID: PMC9568463 DOI: 10.1007/s00018-022-04586-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 10/03/2022] [Accepted: 10/03/2022] [Indexed: 11/03/2022]
Abstract
HERC2 gene encodes an E3 ubiquitin ligase involved in several cellular processes by regulating the ubiquitylation of different protein substrates. Biallelic pathogenic sequence variants in the HERC2 gene are associated with HERC2 Angelman-like syndrome. In pathogenic HERC2 variants, complete absence or marked reduction in HERC2 protein levels are observed. The most common pathological variant, c.1781C > T (p.Pro594Leu), encodes an unstable HERC2 protein. A better understanding of how pathologic HERC2 variants affect intracellular signalling may aid definition of potential new therapies for these disorders. For this purpose, we studied patient-derived cells with the HERC2 Pro594Leu variant. We observed alteration of mitogen-activated protein kinase signalling pathways, reflected by increased levels of C-RAF protein and p38 phosphorylation. HERC2 knockdown experiments reproduced the same effects in other human and mouse cells. Moreover, we demonstrated that HERC2 and RAF proteins form molecular complexes, pull-down and proteomic experiments showed that HERC2 regulates C-RAF ubiquitylation and we found out that the p38 activation due to HERC2 depletion occurs in a RAF/MKK3-dependent manner. The displayed cellular response was that patient-derived and other human cells with HERC2 deficiency showed higher resistance to oxidative stress with an increase in the master regulator of the antioxidant response NRF2 and its target genes. This resistance was independent of p53 and abolished by RAF or p38 inhibitors. Altogether, these findings identify the activation of C-RAF/MKK3/p38 signalling pathway in HERC2 Angelman-like syndrome and highlight the inhibition of RAF activity as a potential therapeutic option for individuals affected with these rare diseases.
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Affiliation(s)
- Joan Sala-Gaston
- Department of Physiological Sciences, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona (UB), C/ Feixa Llarga s/n, 08907, L'Hospitalet de Llobregat, Spain
| | - Leonardo Pedrazza
- Department of Physiological Sciences, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona (UB), C/ Feixa Llarga s/n, 08907, L'Hospitalet de Llobregat, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, UPV/EHU, Leioa, Bizkaia, Spain
| | - Arturo Martinez-Martinez
- Department of Physiological Sciences, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona (UB), C/ Feixa Llarga s/n, 08907, L'Hospitalet de Llobregat, Spain
| | - Lettie E Rawlins
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, UK.,Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Emma L Baple
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, UK.,Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Andrew H Crosby
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, UPV/EHU, Leioa, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain
| | - Francesc Ventura
- Department of Physiological Sciences, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona (UB), C/ Feixa Llarga s/n, 08907, L'Hospitalet de Llobregat, Spain
| | - Jose Luis Rosa
- Department of Physiological Sciences, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona (UB), C/ Feixa Llarga s/n, 08907, L'Hospitalet de Llobregat, Spain.
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12
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Tábara LC, Al-Salmi F, Maroofian R, Al-Futaisi AM, Al-Murshedi F, Kennedy J, Day JO, Courtin T, Al-Khayat A, Galedari H, Mazaheri N, Protasoni M, Johnson M, Leslie JS, Salter CG, Rawlins LE, Fasham J, Al-Maawali A, Voutsina N, Charles P, Harrold L, Keren B, Kunji ERS, Vona B, Jelodar G, Sedaghat A, Shariati G, Houlden H, Crosby AH, Prudent J, Baple EL. TMEM63C mutations cause mitochondrial morphology defects and underlie hereditary spastic paraplegia. Brain 2022; 145:3095-3107. [PMID: 35718349 PMCID: PMC9473353 DOI: 10.1093/brain/awac123] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 07/07/2021] [Revised: 02/10/2022] [Accepted: 03/13/2022] [Indexed: 02/02/2023] Open
Abstract
The hereditary spastic paraplegias (HSP) are among the most genetically diverse of all Mendelian disorders. They comprise a large group of neurodegenerative diseases that may be divided into 'pure HSP' in forms of the disease primarily entailing progressive lower-limb weakness and spasticity, and 'complex HSP' when these features are accompanied by other neurological (or non-neurological) clinical signs. Here, we identified biallelic variants in the transmembrane protein 63C (TMEM63C) gene, encoding a predicted osmosensitive calcium-permeable cation channel, in individuals with hereditary spastic paraplegias associated with mild intellectual disability in some, but not all cases. Biochemical and microscopy analyses revealed that TMEM63C is an endoplasmic reticulum-localized protein, which is particularly enriched at mitochondria-endoplasmic reticulum contact sites. Functional in cellula studies indicate a role for TMEM63C in regulating both endoplasmic reticulum and mitochondrial morphologies. Together, these findings identify autosomal recessive TMEM63C variants as a cause of pure and complex HSP and add to the growing evidence of a fundamental pathomolecular role of perturbed mitochondrial-endoplasmic reticulum dynamics in motor neurone degenerative diseases.
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Affiliation(s)
- Luis Carlos Tábara
- Medical Research Council Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, UK
| | - Fatema Al-Salmi
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
| | - Reza Maroofian
- UCL Queen Square Institute of Neurology, University College
London, London WC1E 6BT, UK
| | - Amna Mohammed Al-Futaisi
- Genetic and Developmental Medicine Clinic, Department of Genetics, College
of Medicine and Health Sciences, Sultan Qaboos University Hospital,
Muscat 123, Oman
| | - Fathiya Al-Murshedi
- Genetic and Developmental Medicine Clinic, Department of Genetics, College
of Medicine and Health Sciences, Sultan Qaboos University Hospital,
Muscat 123, Oman
| | - Joanna Kennedy
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
- Clinical Genetics, University Hospitals Bristol,
Bristol BS2 8EG, UK
| | - Jacob O Day
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
- Faculty of Health, University of Plymouth,
Plymouth PL4 8AA, UK
| | - Thomas Courtin
- Département de génétique, Hôpital Pitié-Salpêtrière, Assistance
Publique-Hôpitaux de Paris, 75019 Paris, Sorbonne
Université, France
| | - Aisha Al-Khayat
- Department of Biology, College of Science, Sultan Qaboos
University, Muscat, Oman
| | - Hamid Galedari
- Department of Genetics, Faculty of Science, Shahid Chamran University of
Ahvaz, Ahvaz, Iran
| | - Neda Mazaheri
- Department of Genetics, Faculty of Science, Shahid Chamran University of
Ahvaz, Ahvaz, Iran
| | - Margherita Protasoni
- Medical Research Council Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, UK
| | - Mark Johnson
- Medical Research Council Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, UK
| | - Joseph S Leslie
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
| | - Claire G Salter
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
| | - Lettie E Rawlins
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital
(Heavitree), Exeter EX1 2ED, UK
| | - James Fasham
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital
(Heavitree), Exeter EX1 2ED, UK
| | - Almundher Al-Maawali
- Genetic and Developmental Medicine Clinic, Department of Genetics, College
of Medicine and Health Sciences, Sultan Qaboos University Hospital,
Muscat 123, Oman
| | - Nikol Voutsina
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
| | - Perrine Charles
- Département de génétique, Hôpital Pitié-Salpêtrière, Assistance
Publique-Hôpitaux de Paris, 75019 Paris, Sorbonne
Université, France
| | - Laura Harrold
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
| | - Boris Keren
- Département de génétique, Hôpital Pitié-Salpêtrière, Assistance
Publique-Hôpitaux de Paris, 75019 Paris, Sorbonne
Université, France
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, UK
| | - Barbara Vona
- Department of Otolaryngology-Head and Neck Surgery, Tübingen Hearing
Research Centre, Eberhard Karls University Tübingen,
Tübingen, Germany
| | - Gholamreza Jelodar
- Pediatric Neurology, Ahvaz Jundishapur University of Medical
Sciences, Ahvaz, Iran
| | - Alireza Sedaghat
- Health Research Institute, Diabetes Research Center, Ahvaz Jundishapur
University of Medical Sciences, Ahvaz, Iran
| | - Gholamreza Shariati
- Department of Medical Genetic, Faculty of Medicine, Ahvaz Jundishapur,
University of Medical Sciences, Ahvaz, Iran
| | - Henry Houlden
- UCL Queen Square Institute of Neurology, University College
London, London WC1E 6BT, UK
| | - Andrew H Crosby
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
| | - Julien Prudent
- Medical Research Council Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, UK
| | - Emma L Baple
- Level 4, RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford)
NHS Foundation Trust, University of Exeter Medical School,
Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital
(Heavitree), Exeter EX1 2ED, UK
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13
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Ma Y, Wang X, Shoshany N, Jiao X, Lee A, Ku G, Baple EL, Fasham J, Nadeem R, Naeem MA, Riazuddin S, Riazuddin SA, Crosby AH, Hejtmancik JF. CLCC1 c. 75C>A Mutation in Pakistani Derived Retinitis Pigmentosa Families Likely Originated With a Single Founder Mutation 2,000-5,000 Years Ago. Front Genet 2022; 13:804924. [PMID: 35391798 PMCID: PMC8980549 DOI: 10.3389/fgene.2022.804924] [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: 10/29/2021] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background: A CLCC1 c. 75C > A (p.D25E) mutation has been associated with autosomal recessive pigmentosa in patients in and from Pakistan. CLCC1 is ubiquitously expressed, and knockout models of this gene in zebrafish and mice are lethal in the embryonic period, suggesting that possible retinitis pigmentosa mutations in this gene might be limited to those leaving partial activity. In agreement with this hypothesis, the mutation is the only CLCC1 mutation associated with retinitis pigmentosa to date, and all identified patients with this mutation share a common SNP haplotype surrounding the mutation, suggesting a common founder. Methods: SNPs were genotyped by a combination of WGS and Sanger sequencing. The original founder haplotype, and recombination pathways were delineated by examination to minimize recombination events. Mutation age was estimated by four methods including an explicit solution, an iterative approach, a Bayesian approach and an approach based solely on ancestral segment lengths using high density SNP data. Results: All members of each of the nine families studied shared a single autozygous SNP haplotype for the CLCC1 region ranging from approximately 1–3.5 Mb in size. The haplotypes shared by the families could be derived from a single putative ancestral haplotype with at most two recombination events. Based on the haplotype and Gamma analysis, the estimated age of the founding mutation varied from 79 to 196 generations, or approximately 2,000–5,000 years, depending on the markers used in the estimate. The DMLE (Bayesian) estimates ranged from 2,160 generations assuming a population growth rate of 0–309 generations assuming a population growth rate of 2% with broad 95% confidence intervals. Conclusion: These results provide insight into the origin of the CLCC1 mutation in the Pakistan population. This mutation is estimated to have occurred 2000–5,000 years ago and has been transmitted to affected families of Pakistani origin in geographically dispersed locations around the world. This is the only mutation in CLCC1 identified to date, suggesting that the CLCC1 gene is under a high degree of constraint, probably imposed by functional requirements for this gene during embryonic development.
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Affiliation(s)
- Yan Ma
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, United States
| | - Xun Wang
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, United States.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Nadav Shoshany
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, United States.,Matlow's Ophthalmo-genetic Laboratory, Shamir Medical Center, Zeriffin, Israel
| | - Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, United States
| | - Adrian Lee
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, United States
| | - Gregory Ku
- Diabetes Center, University of California, San Francisco, San Francisco, CA, United States
| | - Emma L Baple
- Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, 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), Gladstone Road, Exeter, United Kingdom
| | - James Fasham
- Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, 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), Gladstone Road, Exeter, United Kingdom
| | - Raheela Nadeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Andrew H Crosby
- Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - J Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, United States
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14
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Rawlins LE, Almousa H, Khan S, Collins SC, Milev MP, Leslie J, Saint-Dic D, Khan V, Hincapie AM, Day JO, McGavin L, Rowley C, Harlalka GV, Vancollie VE, Ahmad W, Lelliott CJ, Gul A, Yalcin B, Crosby AH, Sacher M, Baple EL. Biallelic variants in TRAPPC10 cause a microcephalic TRAPPopathy disorder in humans and mice. PLoS Genet 2022; 18:e1010114. [PMID: 35298461 PMCID: PMC8963566 DOI: 10.1371/journal.pgen.1010114] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 03/29/2022] [Accepted: 02/20/2022] [Indexed: 11/25/2022] Open
Abstract
The highly evolutionarily conserved transport protein particle (TRAPP) complexes (TRAPP II and III) perform fundamental roles in subcellular trafficking pathways. Here we identified biallelic variants in TRAPPC10, a component of the TRAPP II complex, in individuals with a severe microcephalic neurodevelopmental disorder. Molecular studies revealed a weakened interaction between mutant TRAPPC10 and its putative adaptor protein TRAPPC2L. Studies of patient lymphoblastoid cells revealed an absence of TRAPPC10 alongside a concomitant absence of TRAPPC9, another key TRAPP II complex component associated with a clinically overlapping neurodevelopmental disorder. The TRAPPC9/10 reduction phenotype was recapitulated in TRAPPC10-/- knockout cells, which also displayed a membrane trafficking defect. Notably, both the reduction in TRAPPC9 levels and the trafficking defect in these cells could be rescued by wild type but not mutant TRAPPC10 gene constructs. Moreover, studies of Trappc10-/- knockout mice revealed neuroanatomical brain defects and microcephaly, paralleling findings seen in the human condition as well as in a Trappc9-/- mouse model. Together these studies confirm autosomal recessive TRAPPC10 variants as a cause of human disease and define TRAPP-mediated pathomolecular outcomes of importance to TRAPPC9 and TRAPPC10 mediated neurodevelopmental disorders in humans and mice. Microcephalic neurodevelopmental disorders are a group of conditions that are often inherited in families, involving small head size and abnormal brain development and function. This often results in delayed development of an affected child, affecting their movement, language and/or non-verbal communication and learning, as well as seizures and neuropsychiatric problems. A group of proteins called the transport protein particles (TRAPPs) are important for the transport of cargos inside cells. Alterations within a number of the TRAPP proteins have previously been associated with human inherited diseases called the ‘TRAPPopathies’, which involve neurodevelopmental and skeletal abnormalities. Here we show that TRAPPC10 gene alterations cause a new TRAPPopathy microcephalic neurodevelopmental disorder, and we provide a detailed clinical description of the condition termed ‘TRAPPC10-related disorder’. Our studies in mice lacking the TRAPPC10 gene identified similar features to those of affected humans, including small brain size and skeletal abnormalities. Our molecular studies showed that an affected individual with an alteration in the TRAPPC10 gene has no functional TRAPPC10 protein in their cells, which in turn causes a reduction in levels of another important TRAPP molecule, TRAPPC9. Cells lacking TRAPPC10 also display abnormalities in cellular transport processes. Together our data confirm alterations in TRAPPC10 as a cause of a microcephalic neurodevelopmental disorder in both humans and mice.
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Affiliation(s)
- Lettie E. Rawlins
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, United Kingdom
| | - Hashem Almousa
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Shazia Khan
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Stephan C. Collins
- Institute of Genetics and Molecular and Cellular Biology, Inserm, Illkirch, France
- Inserm, University of Bourgogne Franche-Comté, Dijon, France
| | - Miroslav P. Milev
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Joseph Leslie
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
| | - Djenann Saint-Dic
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Valeed Khan
- Department of Molecular Diagnostics, Rehman Medical Institute, Peshawar, Pakistan
| | | | - Jacob O. Day
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Faculty of Health, University of Plymouth, Plymouth, United Kingdom
| | - Lucy McGavin
- University Hospitals Plymouth NHS Trust, Plymouth, United Kingdom
| | | | - Gaurav V. Harlalka
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Department of Pharmacology, Rajarshi Shahu College of Pharmacy, Malvihir, Buldana, India
| | | | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Asma Gul
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Binnaz Yalcin
- Institute of Genetics and Molecular and Cellular Biology, Inserm, Illkirch, France
- Inserm, University of Bourgogne Franche-Comté, Dijon, France
| | - Andrew H. Crosby
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Emma L. Baple
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, United Kingdom
- * E-mail:
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15
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Fasham J, Lin S, Ghosh P, Radio FC, Farrow EG, Thiffault I, Kussman J, Zhou D, Hemming R, Zahka K, Chioza BA, Rawlins LE, Wenger OK, Gunning AC, Pizzi S, Onesimo R, Zampino G, Barker E, Osawa N, Rodriguez MC, Neuhann TM, Zackai EH, Keena B, Capasso J, Levin AV, Bhoj E, Li D, Hakonarson H, Wentzensen IM, Jackson A, Chandler KE, Coban-Akdemir ZH, Posey JE, Banka S, Lupski JR, Sheppard SE, Tartaglia M, Triggs-Raine B, Crosby AH, Baple EL. Elucidating the clinical spectrum and molecular basis of HYAL2 deficiency. Genet Med 2022; 24:631-644. [PMID: 34906488 PMCID: PMC9933146 DOI: 10.1016/j.gim.2021.10.014] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/03/2021] [Accepted: 10/21/2021] [Indexed: 11/25/2022] Open
Abstract
PURPOSE We previously defined biallelic HYAL2 variants causing a novel disorder in 2 families, involving orofacial clefting, facial dysmorphism, congenital heart disease, and ocular abnormalities, with Hyal2 knockout mice displaying similar phenotypes. In this study, we better define the phenotype and pathologic disease mechanism. METHODS Clinical and genomic investigations were undertaken alongside molecular studies, including immunoblotting and immunofluorescence analyses of variant/wild-type human HYAL2 expressed in mouse fibroblasts, and in silico modeling of putative pathogenic variants. RESULTS Ten newly identified individuals with this condition were investigated, and they were associated with 9 novel pathogenic variants. Clinical studies defined genotype-phenotype correlations and confirmed a recognizable craniofacial phenotype in addition to myopia, cleft lip/palate, and congenital cardiac anomalies as the most consistent manifestations of the condition. In silico modeling of missense variants identified likely deleterious effects on protein folding. Consistent with this, functional studies indicated that these variants cause protein instability and a concomitant cell surface absence of HYAL2 protein. CONCLUSION These studies confirm an association between HYAL2 alterations and syndromic cleft lip/palate, provide experimental evidence for the pathogenicity of missense alleles, enable further insights into the pathomolecular basis of the disease, and delineate the core and variable clinical outcomes of the condition.
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Affiliation(s)
- James Fasham
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom; Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Siying Lin
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Promita Ghosh
- Department of Biochemistry and Medical Genetics, Rax Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù (Bambino Gesù Pediatric Hospital), IRCCS, Rome, Italy
| | - Emily G Farrow
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO
| | | | - Jennifer Kussman
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO
| | - Dihong Zhou
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO
| | - Rick Hemming
- Department of Biochemistry and Medical Genetics, Rax Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kenneth Zahka
- Pediatric Cardiology, Cleveland Clinic, Cleveland, OH
| | - Barry A Chioza
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Lettie E Rawlins
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom; Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Olivia K Wenger
- New Leaf Center, Clinic for Special Children, Mount Eaton, OH
| | - Adam C Gunning
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù (Bambino Gesù Pediatric Hospital), IRCCS, Rome, Italy
| | - Roberta Onesimo
- Center for Rare Disease and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli (Gemelli University Hospital), IRCCS, Rome, Italy
| | - Giuseppe Zampino
- Center for Rare Disease and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli (Gemelli University Hospital), IRCCS, Rome, Italy
| | - Emily Barker
- Department of Biochemistry and Medical Genetics, Rax Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Natasha Osawa
- Department of Biochemistry and Medical Genetics, Rax Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Megan Christine Rodriguez
- Department of Biochemistry and Medical Genetics, Rax Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Beth Keena
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jenina Capasso
- Golisano Children's Hospital and Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY
| | - Alex V Levin
- Golisano Children's Hospital and Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY
| | - Elizabeth Bhoj
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Dong Li
- Golisano Children's Hospital and Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY
| | - Hakon Hakonarson
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | | | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Sarah E Sheppard
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù (Bambino Gesù Pediatric Hospital), IRCCS, Rome, Italy.
| | - Barbara Triggs-Raine
- Department of Biochemistry and Medical Genetics, Rax Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Andrew H Crosby
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom.
| | - Emma L Baple
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom; Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom.
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16
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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: 8] [Impact Index Per Article: 4.0] [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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17
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Dawood M, Lin S, Din TU, Shah IU, Khan N, Jan A, Marwan M, Sultan K, Nowshid M, Tahir R, Ahmed AN, Yasin M, Baple EL, Crosby AH, Saleha S. Novel mutations in PDE6A and CDHR1 cause retinitis pigmentosa in Pakistani families. Int J Ophthalmol 2021; 14:1843-1851. [PMID: 34926197 PMCID: PMC8640774 DOI: 10.18240/ijo.2021.12.06] [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: 02/10/2021] [Accepted: 08/11/2021] [Indexed: 11/23/2022] Open
Abstract
AIM To investigate the genetic basis of autosomal recessive retinitis pigmentosa (arRP) in two consanguineous/ endogamous Pakistani families. METHODS Whole exome sequencing (WES) was performed on genomic DNA samples of patients with arRP to identify disease causing mutations. Sanger sequencing was performed to confirm familial segregation of identified mutations, and potential pathogenicity was determined by predictions of the mutations' functions. RESULTS A novel homozygous frameshift mutation [NM_000440.2:c.1054delG, p. (Gln352Argfs*4); Chr5:g.149286886del (GRCh37)] in the PDE6A gene in an endogamous family and a novel homozygous splice site mutation [NM_033100.3:c.1168-1G>A, Chr10:g.85968484G>A (GRCh37)] in the CDHR1 gene in a consanguineous family were identified. The PDE6A variant p. (Gln352Argfs*4) was predicted to be deleterious or pathogenic, whilst the CDHR1 variant c.1168-1G>A was predicted to result in potential alteration of splicing. CONCLUSION This study expands the spectrum of genetic variants for arRP in Pakistani families.
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Affiliation(s)
- Muhammad Dawood
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Siying Lin
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon EX2 5DW, UK
| | - Taj Ud Din
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Irfan Ullah Shah
- Department of Ophthalmology, KMU Institute of Medical Sciences (KIMS) Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Niamat Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Abid Jan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Marwan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Komal Sultan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Maha Nowshid
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Raheel Tahir
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Asif Naveed Ahmed
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Yasin
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Emma L. Baple
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon EX2 5DW, UK
| | - Andrew H. Crosby
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon EX2 5DW, UK
| | - Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
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18
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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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19
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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: 18] [Impact Index Per Article: 6.0] [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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20
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Khalaf-Nazzal R, Fasham J, Ubeyratna N, Evans DJ, Leslie JS, Warner TT, Al-Hijawi F, Alshaer S, Baker W, Turnpenny PD, Baple EL, Crosby AH. Final Exon Frameshift Biallelic PTPN23 Variants Are Associated with Microcephalic Complex Hereditary Spastic Paraplegia. Brain Sci 2021; 11:614. [PMID: 34064836 PMCID: PMC8151426 DOI: 10.3390/brainsci11050614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022] Open
Abstract
The hereditary spastic paraplegias (HSPs) are a large clinically heterogeneous group of genetic disorders classified as 'pure' when the cardinal feature of progressive lower limb spasticity and weakness occurs in isolation and 'complex' when associated with other clinical signs. Here, we identify a homozygous frameshift alteration occurring in the last coding exon of the protein tyrosine phosphatase type 23 (PTPN23) gene in an extended Palestinian family associated with autosomal recessive complex HSP. PTPN23 encodes a catalytically inert non-receptor protein tyrosine phosphatase that has been proposed to interact with the endosomal sorting complex required for transport (ESCRT) complex, involved in the sorting of ubiquitinated cargos for fusion with lysosomes. In view of our data, we reviewed previously published candidate pathogenic PTPN23 variants to clarify clinical outcomes associated with pathogenic gene variants. This determined that a number of previously proposed candidate PTPN23 alterations are likely benign and revealed that pathogenic biallelic PTPN23 alterations cause a varied clinical spectrum comprising of complex HSP associated with microcephaly, which may occur without intellectual impairment or involve more severe neurological disease. Together, these findings highlight the importance of the inclusion of the PTPN23 gene on HSP gene testing panels globally.
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Affiliation(s)
- Reham Khalaf-Nazzal
- Biomedical Sciences Department, Faculty of Medicine, Arab American University of Palestine, Jenin P227, Palestine
| | - James Fasham
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter EX1 2ED, UK
| | - Nishanka Ubeyratna
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
| | - David J. Evans
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK;
| | - Joseph S. Leslie
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
| | - Thomas T. Warner
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK;
| | - Fida’ Al-Hijawi
- Paediatrics’ Community Outpatient Clinics, Palestinian Ministry of Health, Jenin P200, Palestine;
| | - Shurouq Alshaer
- Faculty of Graduate Studies, Arab American University, Ramallah P622, Palestine;
| | - Wisam Baker
- Paediatrics Department, Dr. Khalil Suleiman Government Hospital, Jenin P200, Palestine;
| | - Peter D. Turnpenny
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter EX1 2ED, UK
| | - Emma L. Baple
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter EX1 2ED, UK
| | - Andrew H. Crosby
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
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21
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Cif L, Demailly D, Lin JP, Barwick KE, Sa M, Abela L, Malhotra S, Chong WK, Steel D, Sanchis-Juan A, Ngoh A, Trump N, Meyer E, Vasques X, Rankin J, Allain MW, Applegate CD, Attaripour Isfahani S, Baleine J, Balint B, Bassetti JA, Baple EL, Bhatia KP, Blanchet C, Burglen L, Cambonie G, Seng EC, Bastaraud SC, Cyprien F, Coubes C, d'Hardemare V, Doja A, Dorison N, Doummar D, Dy-Hollins ME, Farrelly E, Fitzpatrick DR, Fearon C, Fieg EL, Fogel BL, Forman EB, Fox RG, Gahl WA, Galosi S, Gonzalez V, Graves TD, Gregory A, Hallett M, Hasegawa H, Hayflick SJ, Hamosh A, Hully M, Jansen S, Jeong SY, Krier JB, Krystal S, Kumar KR, Laurencin C, Lee H, Lesca G, François LL, Lynch T, Mahant N, Martinez-Agosto JA, Milesi C, Mills KA, Mondain M, Morales-Briceno H, Ostergaard JR, Pal S, Pallais JC, Pavillard F, Perrigault PF, Petersen AK, Polo G, Poulen G, Rinne T, Roujeau T, Rogers C, Roubertie A, Sahagian M, Schaefer E, Selim L, Selway R, Sharma N, Signer R, Soldatos AG, Stevenson DA, Stewart F, Tchan M, Verma IC, de Vries BBA, Wilson JL, Wong DA, Zaitoun R, Zhen D, Znaczko A, Dale RC, de Gusmão CM, Friedman J, Fung VSC, King MD, Mohammad SS, Rohena L, Waugh JL, Toro C, Raymond FL, Topf M, Coubes P, Gorman KM, Kurian MA. KMT2B-related disorders: expansion of the phenotypic spectrum and long-term efficacy of deep brain stimulation. Brain 2021; 143:3242-3261. [PMID: 33150406 DOI: 10.1093/brain/awaa304] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [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: 05/15/2020] [Revised: 06/28/2020] [Accepted: 07/13/2020] [Indexed: 12/31/2022] Open
Abstract
Heterozygous mutations in KMT2B are associated with an early-onset, progressive and often complex dystonia (DYT28). Key characteristics of typical disease include focal motor features at disease presentation, evolving through a caudocranial pattern into generalized dystonia, with prominent oromandibular, laryngeal and cervical involvement. Although KMT2B-related disease is emerging as one of the most common causes of early-onset genetic dystonia, much remains to be understood about the full spectrum of the disease. We describe a cohort of 53 patients with KMT2B mutations, with detailed delineation of their clinical phenotype and molecular genetic features. We report new disease presentations, including atypical patterns of dystonia evolution and a subgroup of patients with a non-dystonic neurodevelopmental phenotype. In addition to the previously reported systemic features, our study has identified co-morbidities, including the risk of status dystonicus, intrauterine growth retardation, and endocrinopathies. Analysis of this study cohort (n = 53) in tandem with published cases (n = 80) revealed that patients with chromosomal deletions and protein truncating variants had a significantly higher burden of systemic disease (with earlier onset of dystonia) than those with missense variants. Eighteen individuals had detailed longitudinal data available after insertion of deep brain stimulation for medically refractory dystonia. Median age at deep brain stimulation was 11.5 years (range: 4.5-37.0 years). Follow-up after deep brain stimulation ranged from 0.25 to 22 years. Significant improvement of motor function and disability (as assessed by the Burke Fahn Marsden's Dystonia Rating Scales, BFMDRS-M and BFMDRS-D) was evident at 6 months, 1 year and last follow-up (motor, P = 0.001, P = 0.004, and P = 0.012; disability, P = 0.009, P = 0.002 and P = 0.012). At 1 year post-deep brain stimulation, >50% of subjects showed BFMDRS-M and BFMDRS-D improvements of >30%. In the long-term deep brain stimulation cohort (deep brain stimulation inserted for >5 years, n = 8), improvement of >30% was maintained in 5/8 and 3/8 subjects for the BFMDRS-M and BFMDRS-D, respectively. The greatest BFMDRS-M improvements were observed for trunk (53.2%) and cervical (50.5%) dystonia, with less clinical impact on laryngeal dystonia. Improvements in gait dystonia decreased from 20.9% at 1 year to 16.2% at last assessment; no patient maintained a fully independent gait. Reduction of BFMDRS-D was maintained for swallowing (52.9%). Five patients developed mild parkinsonism following deep brain stimulation. KMT2B-related disease comprises an expanding continuum from infancy to adulthood, with early evidence of genotype-phenotype correlations. Except for laryngeal dysphonia, deep brain stimulation provides a significant improvement in quality of life and function with sustained clinical benefit depending on symptoms distribution.
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Affiliation(s)
- Laura Cif
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Diane Demailly
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Jean-Pierre Lin
- Complex Motor Disorder Service, Children's Neurosciences Department, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK.,Children's Neuromodulation Group, Women and Children's Health Institute, Faculty of life Sciences and Medicine (FOLSM), King's Health Partners, London, UK
| | - Katy E Barwick
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Mario Sa
- Complex Motor Disorder Service, Children's Neurosciences Department, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Lucia Abela
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sony Malhotra
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK
| | - Wui K Chong
- Developmental Imaging and Biophysics, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Dora Steel
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Neurology, Great Ormond Street Hospital, London, UK
| | - Alba Sanchis-Juan
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge, UK
| | - Adeline Ngoh
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Neurology, Great Ormond Street Hospital, London, UK
| | - Natalie Trump
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Esther Meyer
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK
| | | | - Julia Rankin
- Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Meredith W Allain
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Carolyn D Applegate
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sanaz Attaripour Isfahani
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Julien Baleine
- Unité de Soins Intensifs et Réanimation Pédiatrique et Néonatale, Hôpital Universitaire de Montpellier, Montpellier, France
| | - Bettina Balint
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jennifer A Bassetti
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medical College, New York, NY, USA
| | - Emma L Baple
- Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical and Clinical Science RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Catherine Blanchet
- Département d'Oto-Rhino-Laryngologie et Chirurgie Cervico-Faciale, Hôpital Universitaire de Montpellier, Montpellier, France
| | - Lydie Burglen
- Département de génétique médicale, APHP Hôpital Armand Trousseau, Paris, France
| | - Gilles Cambonie
- Unité de Soins Intensifs et Réanimation Pédiatrique et Néonatale, Hôpital Universitaire de Montpellier, Montpellier, France
| | - Emilie Chan Seng
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | | | - Fabienne Cyprien
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Christine Coubes
- Département de Génétique médicale, Maladies rares et médecine personnalisée, CHU Montpellier, Montpellier, France
| | - Vincent d'Hardemare
- Unité Dyspa, Neurochirurgie Pédiatrique, Hôpital Fondation Rothschild, Paris, France
| | | | - Asif Doja
- Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nathalie Dorison
- Unité Dyspa, Neurochirurgie Pédiatrique, Hôpital Fondation Rothschild, Paris, France
| | - Diane Doummar
- Neuropédiatrie, Centre de référence neurogénétique mouvement anormaux de l'enfant, Hôpital Armand Trousseau, AP-HP, Sorbonne Université, France
| | - Marisela E Dy-Hollins
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ellyn Farrelly
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Palo Alto, CA, USA.,Department of Pediatrics, Lucile Packard Children's Hospital at Stanford, CA, USA
| | - David R Fitzpatrick
- Human Genetics Unit, Medical and Developmental Genetics, University of Edinburgh Western General Hospital, Edinburgh, Scotland, UK
| | - Conor Fearon
- Department of Neurology, The Dublin Neurological Institute at the Mater Misericordiae University Hospital, Dublin, Ireland
| | - Elizabeth L Fieg
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brent L Fogel
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Eva B Forman
- Department of Paediatric Neurology and Clinical Neurophysiology, Children's Health Ireland at Temple Street, Dublin, Ireland
| | - Rachel G Fox
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | | | - William A Gahl
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Serena Galosi
- Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Victoria Gonzalez
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Tracey D Graves
- Department of Neurology, Hinchingbrooke Hospital, North West Anglia NHS Foundation Trust, Huntingdon, UK
| | - Allison Gregory
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Mark Hallett
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Harutomo Hasegawa
- Complex Motor Disorder Service, Children's Neurosciences Department, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK.,Children's Neuromodulation Group, Women and Children's Health Institute, Faculty of life Sciences and Medicine (FOLSM), King's Health Partners, London, UK
| | - Susan J Hayflick
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.,Department of Paediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marie Hully
- Département de Neurologie, APHP-Necker-Enfants Malades, Paris, France
| | - Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Suh Young Jeong
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Joel B Krier
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sidney Krystal
- Département de Neuroradiologie, Hôpital Fondation Rothschild, Paris
| | - Kishore R Kumar
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, NSW, Australia.,Molecular Medicine Laboratory, Concord Hospital, Sydney, NSW, Australia
| | - Chloé Laurencin
- Département de Neurologie, Hôpital Neurologique Pierre Wertheimer, Lyon, France
| | - Hane Lee
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Gaetan Lesca
- Département de Génétique, Hôpital Universitaire de Lyon, Lyon, France
| | | | - Timothy Lynch
- Department of Neurology, The Dublin Neurological Institute at the Mater Misericordiae University Hospital, Dublin, Ireland.,UCD School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Neil Mahant
- Movement Disorders Unit, Department of Neurology, Westmead Hospital, Westmead, NSW, Australia
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Christophe Milesi
- Unité de Soins Intensifs et Réanimation Pédiatrique et Néonatale, Hôpital Universitaire de Montpellier, Montpellier, France
| | - Kelly A Mills
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michel Mondain
- Département d'Oto-Rhino-Laryngologie et Chirurgie Cervico-Faciale, Hôpital Universitaire de Montpellier, Montpellier, France
| | - Hugo Morales-Briceno
- Movement Disorders Unit, Department of Neurology, Westmead Hospital, Westmead, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | | | - John R Ostergaard
- Centre for Rare Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Swasti Pal
- Institute of Genetics and Genomics, Sir Ganga Ram Hospital, Rajender Nagar, New Delhi, India
| | - Juan C Pallais
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Frédérique Pavillard
- Département d'Anesthésie-Réanimation Gui de Chauliac, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Pierre-Francois Perrigault
- Département d'Anesthésie-Réanimation Gui de Chauliac, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | | | - Gustavo Polo
- Département de Neurochirurgie Fonctionnelle, Hôpital Neurologique et Neurochirurgical, Pierre Wertheimer, Lyon, France
| | - Gaetan Poulen
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Tuula Rinne
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Roujeau
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France
| | - Caleb Rogers
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Agathe Roubertie
- Département de Neuropédiatrie, Hôpital Universitaire de Montpellier, Montpellier, France.,INSERM U1051, Institut des Neurosciences de Montpellier, Montpellier, France
| | - Michelle Sahagian
- Division of Neurology, Rady Children's Hospital San Diego, CA, USA.,Department of Neuroscience, University of California San Diego, CA, USA
| | - Elise Schaefer
- Medical Genetics, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Laila Selim
- Cairo University Children Hospital, Pediatric Neurology and Metabolic division, Cairo, Egypt
| | - Richard Selway
- Department of Neurosurgery, King's College Hospital, London, UK
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA.,Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Rebecca Signer
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Ariane G Soldatos
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David A Stevenson
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Fiona Stewart
- Department of Genetic Medicine, Belfast Health and Social Care Trust, Belfast, UK
| | - Michel Tchan
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Department of Genetics, Westmead Hospital, Westmead, NSW, Australia
| | | | - Ishwar C Verma
- Institute of Genetics and Genomics, Sir Ganga Ram Hospital, Rajender Nagar, New Delhi, India
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jenny L Wilson
- Division of Pediatric Neurology, Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Derek A Wong
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Raghda Zaitoun
- Department of Paediatrics, Neurology Division, Ain Shams University Hospital, Cairo, Egypt
| | - Dolly Zhen
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Anna Znaczko
- Department of Genetic Medicine, Belfast Health and Social Care Trust, Belfast, UK
| | - Russell C Dale
- Department of Paediatric Neurology, The Children's Hospital at Westmead, NSW, Australia.,Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Claudio M de Gusmão
- Department of Neurology, Harvard Medical School, Boston, MA, USA.,Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Jennifer Friedman
- Division of Neurology, Rady Children's Hospital San Diego, CA, USA.,Department of Neuroscience, University of California San Diego, CA, USA.,Departments of Paediatrics, University of California, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Victor S C Fung
- Movement Disorders Unit, Department of Neurology, Westmead Hospital, Westmead, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Mary D King
- Department of Paediatric Neurology and Clinical Neurophysiology, Children's Health Ireland at Temple Street, Dublin, Ireland.,UCD School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Shekeeb S Mohammad
- Department of Paediatric Neurology, The Children's Hospital at Westmead, NSW, Australia.,Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Luis Rohena
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, TX, USA.,Department of Pediatrics, Long School of Medicine, UT Health, San Antonio, TX, USA
| | - Jeff L Waugh
- Division of Pediatric Neurology, Department of Pediatrics, University of Texas Southwestern, Dallas, TX, USA
| | - Camilo Toro
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK
| | - Philippe Coubes
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Kathleen M Gorman
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Neurology, Great Ormond Street Hospital, London, UK
| | - Manju A Kurian
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Neurology, Great Ormond Street Hospital, London, UK
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22
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Rickman OJ, Salter CG, Gunning AC, Fasham J, Voutsina N, Leslie JS, McGavin L, Cross HE, Posey JE, Akdemir ZC, Jhangiani SN, Lupski JR, Baple EL, Crosby AH. Dominant mitochondrial membrane protein-associated neurodegeneration (MPAN) variants cluster within a specific C19orf12 isoform. Parkinsonism Relat Disord 2020; 82:84-86. [PMID: 33260061 DOI: 10.1016/j.parkreldis.2020.10.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/15/2020] [Accepted: 10/28/2020] [Indexed: 11/30/2022]
Abstract
Mitochondria membrane protein-associated neurodegeneration (MPAN) neurodegenerative disorder is typically associated with biallelic C19orf12 variants. Here we describe a new and review candidate previous monoallelic de novo C19orf12 variants to define loss of function mutations located in the putative non-membrane spanning C19orf12 isoform as the potential basis of monoallelic MPAN.
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Affiliation(s)
- Olivia J Rickman
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Claire G Salter
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, EX2 5DW, UK; Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, SO16 5YA, UK
| | - Adam C Gunning
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - James Fasham
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, EX2 5DW, UK; Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, EX1 2ED, UK
| | - Nikol Voutsina
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Joseph S Leslie
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Lucy McGavin
- Department of Radiology, Derriford Hospital, Plymouth, UK
| | - Harold E Cross
- University of Arizona College of Medicine, Tucson, AZ, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA, 77030; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA, 77030; Texas Children's Hospital, Houston, TX, USA, 77030
| | - Emma L Baple
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, EX2 5DW, UK; Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, EX1 2ED, UK.
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, EX2 5DW, UK.
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23
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Borah K, Rickman OJ, Voutsina N, Baple EL, Dias IH, Crosby AH, Griffiths HR. Datasets of whole cell and mitochondrial oxysterols derived from THP-1, SH-SY5Y and human peripheral blood mononuclear cells using targeted metabolomics. Data Brief 2020; 33:106382. [PMID: 33134439 PMCID: PMC7586070 DOI: 10.1016/j.dib.2020.106382] [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: 06/04/2020] [Revised: 09/13/2020] [Accepted: 10/01/2020] [Indexed: 11/28/2022] Open
Abstract
The raw datasets of oxysterol quantifications from whole cell and mitochondrial fractions of THP-1 monocytes and macrophages, neuronal-like SH-SH5Y cells and human peripheral blood mononuclear cells are presented. Oxysterols were quantified using a new liquid chromatography-mass spectrometry (LC-MS) and multiple reaction monitoring analysis published in the article "A quantitative LC-MS/MS method for analysis of mitochondrial-specific oxysterol metabolism" in Redox Biology [1]. This method showed improved extraction efficiency and recovery of mono and dihydroxycholesterols from cellular matrix. The datasets derived from the three cell lines are included in the appendix. These datasets provide new information about the oxysterol distribution in THP-1 monocytes and macrophages, SH-SY5Y cells and peripheral blood mononuclear cells. These datasets can be used as a guide for oxysterol distribution in the three cell lines for future studies, and can used for future method optimization, and for comparison of oxysterol recovery with other analytical techniques.
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Affiliation(s)
- Khushboo Borah
- Department of Nutrition, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Olivia J Rickman
- RD&E Hospital Wonford, University of Exeter Medical School, RILD Building, Barrack Road, Exeter EX2 5DW, United Kingdom
| | - Nikol Voutsina
- RD&E Hospital Wonford, University of Exeter Medical School, RILD Building, Barrack Road, Exeter EX2 5DW, United Kingdom
| | - Emma L Baple
- RD&E Hospital Wonford, University of Exeter Medical School, RILD Building, Barrack Road, Exeter EX2 5DW, United Kingdom
| | - Irundika Hk Dias
- Aston Medical School, Aston University, Birmingham B4 7ET, United Kingdom
| | - Andrew H Crosby
- RD&E Hospital Wonford, University of Exeter Medical School, RILD Building, Barrack Road, Exeter EX2 5DW, United Kingdom
| | - Helen R Griffiths
- Department of Nutrition, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom
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24
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Sullivan JM, Motley WW, Johnson JO, Aisenberg WH, Marshall KL, Barwick KE, Kong L, Huh JS, Saavedra-Rivera PC, McEntagart MM, Marion MH, Hicklin LA, Modarres H, Baple EL, Farah MH, Zuberi AR, Lutz CM, Gaudet R, Traynor BJ, Crosby AH, Sumner CJ. Dominant mutations of the Notch ligand Jagged1 cause peripheral neuropathy. J Clin Invest 2020; 130:1506-1512. [PMID: 32065591 DOI: 10.1172/jci128152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 02/13/2019] [Accepted: 12/12/2019] [Indexed: 12/23/2022] Open
Abstract
Notch signaling is a highly conserved intercellular pathway with tightly regulated and pleiotropic roles in normal tissue development and homeostasis. Dysregulated Notch signaling has also been implicated in human disease, including multiple forms of cancer, and represents an emerging therapeutic target. Successful development of such therapeutics requires a detailed understanding of potential on-target toxicities. Here, we identify autosomal dominant mutations of the canonical Notch ligand Jagged1 (or JAG1) as a cause of peripheral nerve disease in 2 unrelated families with the hereditary axonal neuropathy Charcot-Marie-Tooth disease type 2 (CMT2). Affected individuals in both families exhibited severe vocal fold paresis, a rare feature of peripheral nerve disease that can be life-threatening. Our studies of mutant protein posttranslational modification and localization indicated that the mutations (p.Ser577Arg, p.Ser650Pro) impair protein glycosylation and reduce JAG1 cell surface expression. Mice harboring heterozygous CMT2-associated mutations exhibited mild peripheral neuropathy, and homozygous expression resulted in embryonic lethality by midgestation. Together, our findings highlight a critical role for JAG1 in maintaining peripheral nerve integrity, particularly in the recurrent laryngeal nerve, and provide a basis for the evaluation of peripheral neuropathy as part of the clinical development of Notch pathway-modulating therapeutics.
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Affiliation(s)
- Jeremy M Sullivan
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - William W Motley
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Janel O Johnson
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, Maryland, USA
| | - William H Aisenberg
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katherine L Marshall
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katy Es Barwick
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, United Kingdom
| | - Lingling Kong
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer S Huh
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Meriel M McEntagart
- Medical Genetics, Clinical Developmental Sciences, St. George's University of London, London, United Kingdom
| | | | - Lucy A Hicklin
- Department of Ears, Nose and Throat (ENT), St. George's Hospital, London, United Kingdom
| | | | - Emma L Baple
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, United Kingdom
| | - Mohamed H Farah
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Aamir R Zuberi
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Cathleen M Lutz
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, Maryland, USA.,Brain Sciences Institute, Department of Neurology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, United Kingdom
| | - Charlotte J Sumner
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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25
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Fasham J, Leslie JS, Harrison JW, Deline J, Williams KB, Kuhl A, Scott Schwoerer J, Cross HE, Crosby AH, Baple EL. No association between SCN9A and monogenic human epilepsy disorders. PLoS Genet 2020; 16:e1009161. [PMID: 33216760 PMCID: PMC7717534 DOI: 10.1371/journal.pgen.1009161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 07/10/2020] [Revised: 12/04/2020] [Accepted: 09/28/2020] [Indexed: 11/27/2022] Open
Abstract
Many studies have demonstrated the clinical utility and importance of epilepsy gene panel testing to confirm the specific aetiology of disease, enable appropriate therapeutic interventions, and inform accurate family counselling. Previously, SCN9A gene variants, in particular a c.1921A>T p.(Asn641Tyr) substitution, have been identified as a likely autosomal dominant cause of febrile seizures/febrile seizures plus and other monogenic seizure phenotypes indistinguishable from those associated with SCN1A, leading to inclusion of SCN9A on epilepsy gene testing panels. Here we present serendipitous findings of genetic studies that identify the SCN9A c.1921A>T p.(Asn641Tyr) variant at high frequency in the Amish community in the absence of such seizure phenotypes. Together with findings in UK Biobank these data refute an association of SCN9A with epilepsy, which has important clinical diagnostic implications.
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Affiliation(s)
- James Fasham
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Gladstone Road, Exeter, United Kingdom
| | - Joseph S. Leslie
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, United Kingdom
| | - Jamie W. Harrison
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, United Kingdom
- University of Exeter, Department of Biosciences, Exeter, United Kingdom
| | - James Deline
- Center for Special Children, La Farge Medical Clinic-VMH, La Farge, Wisconsin, United States of America
| | - Katie B. Williams
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Ashley Kuhl
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jessica Scott Schwoerer
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Harold E. Cross
- Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, United States of America
| | - Andrew H. Crosby
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, United Kingdom
| | - Emma L. Baple
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Gladstone Road, Exeter, United Kingdom
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26
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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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27
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Borah K, Rickman OJ, Voutsina N, Ampong I, Gao D, Baple EL, Dias IH, Crosby AH, Griffiths HR. A quantitative LC-MS/MS method for analysis of mitochondrial -specific oxysterol metabolism. Redox Biol 2020; 36:101595. [PMID: 32574926 PMCID: PMC7317222 DOI: 10.1016/j.redox.2020.101595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 04/11/2020] [Revised: 05/15/2020] [Accepted: 05/22/2020] [Indexed: 02/07/2023] Open
Abstract
Oxysterols are critical regulators of inflammation and cholesterol metabolism in cells. They are oxidation products of cholesterol and may be differentially metabolised in subcellular compartments and in biological fluids. New analytical methods are needed to improve our understanding of oxysterol trafficking and the molecular interplay between the cellular compartments required to maintain cholesterol/oxysterol homeostasis. Here we describe a method for isolation of oxysterols using solid phase extraction and quantification by liquid chromatography-mass spectrometry, applied to tissue, cells and mitochondria. We analysed five monohydroxysterols; 24(S)-hydroxycholesterol, 25-hydroxycholesterol, 27-hydroxycholesterol, 7α-hydroxycholesterol, 7 ketocholesterol and three dihydroxysterols 7α-24(S)dihydroxycholesterol, 7α-25dihydroxycholesterol, 7α-27dihydroxycholesterol by LC-MS/MS following reverse phase chromatography. Our new method, using Triton and DMSO extraction, shows improved extraction efficiency and recovery of oxysterols from cellular matrix. We validated our method by reproducibly measuring oxysterols in mouse brain tissue and showed that mice fed a high fat diet had significantly lower levels of 24S/25diOHC, 27diOHC and 7ketoOHC. We measured oxysterols in mitochondria from peripheral blood mononuclear cells and highlight the importance of rapid cell isolation to minimise effects of handling and storage conditions on oxysterol composition in clinical samples. In addition, in vitro cell culture systems, of THP-1 monocytes and neuronal-like SH-SH5Y cells, showed mitochondrial-specific oxysterol metabolism and profiles were lineage specific. In summary, we describe a robust and reproducible method validated for improved recovery, quantitative linearity and detection, reproducibility and selectivity for cellular oxysterol analysis. This method enables subcellular oxysterol metabolism to be monitored and is versatile in its application to various biological and clinical samples.
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Affiliation(s)
- Khushboo Borah
- Department of Nutrition, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Olivia J Rickman
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Nikol Voutsina
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Isaac Ampong
- Department of Nutrition, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Dan Gao
- Department of Human Anatomy,Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Emma L Baple
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | | | - Andrew H Crosby
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Helen R Griffiths
- Department of Nutrition, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK.
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28
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Gunning AC, Fryer V, Fasham J, Crosby AH, Ellard S, Baple EL, Wright CF. Assessing performance of pathogenicity predictors using clinically relevant variant datasets. J Med Genet 2020; 58:547-555. [PMID: 32843488 PMCID: PMC8327323 DOI: 10.1136/jmedgenet-2020-107003] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [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: 03/26/2020] [Revised: 05/29/2020] [Accepted: 06/20/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND Pathogenicity predictors are integral to genomic variant interpretation but, despite their widespread usage, an independent validation of performance using a clinically relevant dataset has not been undertaken. METHODS We derive two validation datasets: an 'open' dataset containing variants extracted from publicly available databases, similar to those commonly applied in previous benchmarking exercises, and a 'clinically representative' dataset containing variants identified through research/diagnostic exome and panel sequencing. Using these datasets, we evaluate the performance of three recent meta-predictors, REVEL, GAVIN and ClinPred, and compare their performance against two commonly used in silico tools, SIFT and PolyPhen-2. RESULTS Although the newer meta-predictors outperform the older tools, the performance of all pathogenicity predictors is substantially lower in the clinically representative dataset. Using our clinically relevant dataset, REVEL performed best with an area under the receiver operating characteristic curve of 0.82. Using a concordance-based approach based on a consensus of multiple tools reduces the performance due to both discordance between tools and false concordance where tools make common misclassification. Analysis of tool feature usage may give an insight into the tool performance and misclassification. CONCLUSION Our results support the adoption of meta-predictors over traditional in silico tools, but do not support a consensus-based approach as in current practice.
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Affiliation(s)
- Adam C Gunning
- College of Medicine and Health, University of Exeter Medical School Institute of Biomedical and Clinical Science, Exeter, Devon, UK.,Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Verity Fryer
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - James Fasham
- College of Medicine and Health, University of Exeter Medical School Institute of Biomedical and Clinical Science, Exeter, Devon, UK
| | - Andrew H Crosby
- College of Medicine and Health, University of Exeter Medical School Institute of Biomedical and Clinical Science, Exeter, Devon, UK
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Emma L Baple
- College of Medicine and Health, University of Exeter Medical School Institute of Biomedical and Clinical Science, Exeter, Devon, UK
| | - Caroline F Wright
- College of Medicine and Health, University of Exeter Medical School Institute of Biomedical and Clinical Science, Exeter, Devon, UK
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29
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Rickman OJ, Baple EL, Crosby AH. Lipid metabolic pathways converge in motor neuron degenerative diseases. Brain 2020; 143:1073-1087. [PMID: 31848577 PMCID: PMC7174042 DOI: 10.1093/brain/awz382] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/11/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022] Open
Abstract
Motor neuron diseases (MNDs) encompass an extensive and heterogeneous group of upper and/or lower motor neuron degenerative disorders, in which the particular clinical outcomes stem from the specific neuronal component involved in each condition. While mutations in a large number of molecules associated with lipid metabolism are known to be implicated in MNDs, there remains a lack of clarity regarding the key functional pathways involved, and their inter-relationships. This review highlights evidence that defines defects within two specific lipid (cholesterol/oxysterol and phosphatidylethanolamine) biosynthetic cascades as being centrally involved in MND, particularly hereditary spastic paraplegia. We also identify how other MND-associated molecules may impact these cascades, in particular through impaired organellar interfacing, to propose ‘subcellular lipidome imbalance’ as a likely common pathomolecular theme in MND. Further exploration of this mechanism has the potential to identify new therapeutic targets and management strategies for modulation of disease progression in hereditary spastic paraplegias and other MNDs.
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Affiliation(s)
- Olivia J Rickman
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Emma L Baple
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Andrew H Crosby
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
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30
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Khan S, Rawlins LE, Harlalka GV, Umair M, Ullah A, Shahzad S, Javed M, Baple EL, Crosby AH, Ahmad W, Gul A. Homozygous variants in the HEXB and MBOAT7 genes underlie neurological diseases in consanguineous families. BMC Med Genet 2019; 20:199. [PMID: 31852446 PMCID: PMC6921424 DOI: 10.1186/s12881-019-0907-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/15/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Neurological disorders are a common cause of morbidity and mortality within Pakistani populations. It is one of the most important challenges in healthcare, with significant life-long socio-economic burden. METHODS We investigated the cause of disease in three Pakistani families in individuals with unexplained autosomal recessive neurological conditions, using both genome-wide SNP mapping and whole exome sequencing (WES) of affected individuals. RESULTS We identified a homozygous splice site variant (NM_000521:c.445 + 1G > T) in the hexosaminidase B (HEXB) gene confirming a diagnosis of Sandhoff disease (SD; type II GM2-gangliosidosis), an autosomal recessive lysosomal storage disorder caused by deficiency of hexosaminidases in a single family. In two further unrelated families, we identified a homozygous frameshift variant (NM_024298.3:c.758_778del; p.Glu253_Ala259del) in membrane-bound O-acyltransferase family member 7 (MBOAT7) as the likely cause of disease. MBOAT7 gene variants have recently been identified as a cause of intellectual disability (ID), seizures and autistic features. CONCLUSIONS We identified two metabolic disorders of lipid biosynthesis within three Pakistani families presenting with undiagnosed neurodevelopmental conditions. These findings enabled an accurate neurological disease diagnosis to be provided for these families, facilitating disease management and genetic counselling within this population. This study consolidates variation within MBOAT7 as a cause of neurodevelopmental disorder, broadens knowledge of the clinical outcomes associated with MBOAT7-related disorder, and confirms the likely presence of a regionally prevalent founder variant (c.758_778del; p.Glu253_Ala259del) in Pakistan.
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Affiliation(s)
- Shazia Khan
- Department of Biological Sciences, International Islamic University Islamabad, H-10, Islamabad, 44000, Pakistan.,Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK.,Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Lettie E Rawlins
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK.,Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter, EX1 2ED, UK
| | - Gaurav V Harlalka
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK.,Rajarshi Shahu College of Pharmacy, Malvihir Buldana, Maharashtra, Buldana, 443001, India
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (MNGHA), P.O. Box 3660, Riyadh, 11481, Kingdom of Saudi Arabia
| | - Asmat Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Shaheen Shahzad
- Department of Biological Sciences, International Islamic University Islamabad, H-10, Islamabad, 44000, Pakistan
| | - Muhammad Javed
- National Institute for Genomics & Advanced Biotechnology, NARC, Islamabad, 45500, Pakistan
| | - Emma L Baple
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK.,Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter, EX1 2ED, UK
| | - Andrew H Crosby
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Asma Gul
- Department of Biological Sciences, International Islamic University Islamabad, H-10, Islamabad, 44000, Pakistan.
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31
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Abstract
Multiple Nucleotide Variants (MNVs) are miscalled by the most widely utilised next generation sequencing analysis (NGS) pipelines, presenting the potential for missing diagnoses that would previously have been made by standard Sanger (dideoxy) sequencing. These variants, which should be treated as a single insertion-deletion mutation event, are commonly called as separate single nucleotide variants. This can result in misannotation, incorrect amino acid predictions and potentially false positive and false negative diagnostic results. This risk will be increased as confirmatory Sanger sequencing of Single Nucleotide variants (SNVs) ceases to be standard practice. Using simulated data and re-analysis of sequencing data from a diagnostic targeted gene panel, we demonstrate that the widely adopted pipeline, GATK best practices, results in miscalling of MNVs and that alternative tools can call these variants correctly. The adoption of calling methods that annotate MNVs correctly would present a solution for individual laboratories, however GATK best practices are the basis for important public resources such as the gnomAD database. We suggest integrating a solution into these guidelines would be the optimal approach.
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Affiliation(s)
- Matthew N Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Kevin Colclough
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Andrew Parish
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK.,Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Emma L Baple
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK.,Clinical Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
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32
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Wakeling MN, Laver TW, Colclough K, Parish A, Ellard S, Baple EL. Misannotation of multiple-nucleotide variants risks misdiagnosis. Wellcome Open Res 2019; 4:145. [PMID: 31976378 PMCID: PMC6957021 DOI: 10.12688/wellcomeopenres.15420.2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2019] [Indexed: 11/20/2022] Open
Abstract
Multiple Nucleotide Variants (MNVs) are miscalled by the most widely utilised next generation sequencing analysis (NGS) pipelines, presenting the potential for missing diagnoses that would previously have been made by standard Sanger (dideoxy) sequencing. These variants, which should be treated as a single insertion-deletion mutation event, are commonly called as separate single nucleotide variants. This can result in misannotation, incorrect amino acid predictions and potentially false positive and false negative diagnostic results. This risk will be increased as confirmatory Sanger sequencing of Single Nucleotide variants (SNVs) ceases to be standard practice. Using simulated data and re-analysis of sequencing data from a diagnostic targeted gene panel, we demonstrate that the widely adopted pipeline, GATK best practices, results in miscalling of MNVs and that alternative tools can call these variants correctly. The adoption of calling methods that annotate MNVs correctly would present a solution for individual laboratories, however GATK best practices are the basis for important public resources such as the gnomAD database. We suggest integrating a solution into these guidelines would be the optimal approach.
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Affiliation(s)
- Matthew N. Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Thomas W. Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Kevin Colclough
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Andrew Parish
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Emma L. Baple
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
- Clinical Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
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33
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Mehmood S, Harlalka GV, Dad R, Chioza BA, Ullah MI, Ahmad A, Crosby AH, Baple EL, Hassan MJ. In Silico analysis of SIGMAR1 gene causing distal hereditary motor neuropathy in a Pakistani family. Gene Reports 2019. [DOI: 10.1016/j.genrep.2019.100445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Akbar A, Prince C, Payne C, Fasham J, Ahmad W, Baple EL, Crosby AH, Harlalka GV, Gul A. Novel nonsense variants in SLURP1 and DSG1 cause palmoplantar keratoderma in Pakistani families. BMC Med Genet 2019; 20:145. [PMID: 31443639 PMCID: PMC6708247 DOI: 10.1186/s12881-019-0872-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/02/2019] [Indexed: 12/31/2022]
Abstract
Background Inherited palmoplantar keratodermas (PPKs) are clinically and genetically heterogeneous and phenotypically diverse group of genodermatoses characterized by hyperkeratosis of the palms and soles. More than 20 genes have been reported to be associated with PPKs including desmoglein 1 (DSG1) a key molecular component for epidermal adhesion and differentiation. Mal de Meleda (MDM) is a rare inherited autosomal recessive genodermatosis characterized by transgrediens PPK, associated with mutations in the secreted LY6/PLAUR domain containing 1 (SLURP1) gene. Methods This study describes clinical as well as genetic whole exome sequencing (WES) and di-deoxy sequencing investigations in two Pakistani families with a total of 12 individuals affected by PPK. Results WES identified a novel homozygous nonsense variant in SLURP1, and a novel heterozygous nonsense variant in DSG1, as likely causes of the conditions in each family. Conclusions This study expands knowledge regarding the molecular basis of PPK, providing important information to aid clinical management in families with PPK from Pakistan. Electronic supplementary material The online version of this article (10.1186/s12881-019-0872-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abida Akbar
- Department of Biological Sciences, International Islamic University, H-10, Islamabad, 44000, Pakistan.,College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Claire Prince
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Chloe Payne
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - James Fasham
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-e-Azam University (QAU), Islamabad, Pakistan
| | - Emma L Baple
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Andrew H Crosby
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Gaurav V Harlalka
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK.,Rajarshi Shahu College of Pharmacy, Malvihir Buldana, Maharashtra, Post code 443001, India
| | - Asma Gul
- Department of Biological Sciences, International Islamic University, H-10, Islamabad, 44000, Pakistan.
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Shakil M, Harlalka GV, Ali S, Lin S, D'Atri I, Hussain S, Nasir A, Shahzad MA, Ullah MI, Self JE, Baple EL, Crosby AH, Mahmood S. Tyrosinase (TYR) gene sequencing and literature review reveals recurrent mutations and multiple population founder gene mutations as causative of oculocutaneous albinism (OCA) in Pakistani families. Eye (Lond) 2019; 33:1339-1346. [PMID: 30996339 PMCID: PMC7005860 DOI: 10.1038/s41433-019-0436-9] [Citation(s) in RCA: 5] [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: 08/18/2018] [Revised: 01/21/2019] [Accepted: 03/25/2019] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To investigate eight previously unreported Pakistani families with genetically undefined OCA for mutations in TYR. METHODS Sanger sequencing of TYR has been performed in eight families with OCA phenotype. Mutation analysis was performed to establish the pathogenic role of novel mutation. Bioinformatics analysis was performed to predict the structural and functional impacts on protein due to the mutation. RESULTS In this study, we identified six likely pathogenic variants of TYR (c.272 G>A, c.308 G>A, c.346C>T, c.715 C>T, c.832 C>T and c.1255 G>A), including one novel variant (c.308 G>A; p.Cys103Tyr), segregating as appropriate in each family. Cys103 lies in the highly conserved region of the tyrosinase enzyme, and p.Cys103Tyr is predicted to disturb enzymatic function via alteration of the configurational orientation of TYR leading to a more rigid polypeptide structure. We have also reviewed the mutation spectrum of TYR in Pakistani ethnicity. Published data on OCA families proposed that ~40% have been associated with genetic variations in the TYR gene. The mutations reported in this study have now been described with varying frequencies in Pakistani families, including very rare/unique mutations. CONCLUSION A literature review of TYR gene mutations in Pakistani populations, combined with our genetic data, identified a number of gene mutations likely to represent regional ancestral founder mutations of relevance to Pakistani populations, in addition to sporadic and recurrent 'hotspot' mutations present repeatedly in other regions worldwide.
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Affiliation(s)
- Muhammad Shakil
- Department of Biochemistry, University of Health Sciences (UHS), Lahore, Pakistan
- RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, Devon, EX2 5DW, UK
- Department of Biochemistry, Services Institute of Medical Sciences, Services Hospital, Lahore, Pakistan
| | - Gaurav V Harlalka
- RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Shamshad Ali
- Department of Ophthalmology, Services Institute of Medical Sciences, Services Hospital, Lahore, Pakistan
| | - Siying Lin
- RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Ilaria D'Atri
- RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Shabbir Hussain
- Department of Biochemistry, University of Health Sciences (UHS), Lahore, Pakistan
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, South Korea
| | - Muhammad Aiman Shahzad
- Department of Human Genetics and Molecular Biology, University of Health Sciences (UHS), Lahore, Pakistan
| | - Muhammad Ikram Ullah
- Department of Biochemistry, University of Health Sciences (UHS), Lahore, Pakistan
- Department of Clinical Laboratory Sciences, Jouf University, Sakaka-2014, Saudi Arabia
| | - Jay E Self
- Clinical and Experimental Sciences, University of Southampton, Southampton, UK
| | - Emma L Baple
- RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Andrew H Crosby
- RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Saqib Mahmood
- Department of Human Genetics and Molecular Biology, University of Health Sciences (UHS), Lahore, Pakistan.
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences (UHS), Lahore, Pakistan.
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36
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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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Khan S, Lin S, Harlalka GV, Ullah A, Shah K, Khalid S, Mehmood S, Hassan MJ, Ahmad W, Self JE, Crosby AH, Baple EL, Gul A. BBS5 and INPP5E mutations associated with ciliopathy disorders in families from Pakistan. Ann Hum Genet 2019; 83:477-482. [PMID: 31173343 DOI: 10.1111/ahg.12336] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 04/17/2019] [Accepted: 05/18/2019] [Indexed: 11/28/2022]
Abstract
Ciliopathies are a clinically and genetically heterogeneous group of disorders often exhibiting phenotypic overlap and caused by abnormalities in the structure or function of cellular cilia. As such, a precise molecular diagnosis is important for guiding clinical management and genetic counseling. In the present study, two Pakistani families comprising individuals with overlapping clinical features suggestive of a ciliopathy syndrome, including intellectual disability, obesity, congenital retinal dystrophy, and hypogonadism (in males), were investigated clinically and genetically. Whole-exome sequencing identified the likely causes of disease as a novel homozygous frameshift mutation (NM_152384.2: c.196delA; p.(Arg66Glufs*12); family 1) in BBS5, and a nonsense mutation (NM_019892.5:c.1879C>T; p.Gln627*; family 2) in INPP5E, previously reported in an extended Pakistani family with MORM syndrome. Our findings expand the molecular spectrum associated with BBS5 mutations in Pakistan and provide further supportive evidence that the INPP5E mutation is a common cause of ciliopathy in Northern Pakistan, likely representing a regional founder mutation. This study also highlights the value of genomic studies in Pakistan for families affected by rare heterogeneous developmental disorders and where clinical phenotyping may be limited by geographical and financial constraints. The identification of the spectrum and frequency of disease-causing variants within this setting enables the development of population-specific genetic testing strategies targeting variants common to the local population and improving health care outcomes.
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Affiliation(s)
- Shazia Khan
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, Pakistan.,RILD Wellcome Wolfson Centre, Royal Devon and Exeter Hospital, Exeter, UK
| | - Siying Lin
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter Hospital, Exeter, UK
| | - Gaurav V Harlalka
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter Hospital, Exeter, UK
| | - Asmat Ullah
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan.,Department of Molecualr Biology, Shaheed Zulfiqar Ali Bhutto Medical University, PIMS, Islamabad, Pakistan
| | - Khadim Shah
- Department of Biotechnology, COMSATS University Islamabad, Abbotabad Campus, Pakistan
| | - Sumbul Khalid
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, Pakistan
| | - Sarmad Mehmood
- Atta ur Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Muhammad Jawad Hassan
- Atta ur Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jay E Self
- Clinical and Experimental Sciences, University of Southampton, Southampton, UK
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter Hospital, Exeter, UK
| | - Emma L Baple
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter Hospital, Exeter, UK.,Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Exeter, UK
| | - Asma Gul
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, Pakistan
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Jeffries AR, Maroofian R, Salter CG, Chioza BA, Cross HE, Patton MA, Dempster E, Temple IK, Mackay DJG, Rezwan FI, Aksglaede L, Baralle D, Dabir T, Hunter MF, Kamath A, Kumar A, Newbury-Ecob R, Selicorni A, Springer A, Van Maldergem L, Varghese V, Yachelevich N, Tatton-Brown K, Mill J, Crosby AH, Baple EL. Growth disrupting mutations in epigenetic regulatory molecules are associated with abnormalities of epigenetic aging. Genome Res 2019; 29:1057-1066. [PMID: 31160375 PMCID: PMC6633263 DOI: 10.1101/gr.243584.118] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 05/24/2019] [Indexed: 11/24/2022]
Abstract
Germline mutations in fundamental epigenetic regulatory molecules including DNA methyltransferase 3 alpha (DNMT3A) are commonly associated with growth disorders, whereas somatic mutations are often associated with malignancy. We profiled genome-wide DNA methylation patterns in DNMT3A c.2312G > A; p.(Arg771Gln) carriers in a large Amish sibship with Tatton-Brown–Rahman syndrome (TBRS), their mosaic father, and 15 TBRS patients with distinct pathogenic de novo DNMT3A variants. This defined widespread DNA hypomethylation at specific genomic sites enriched at locations annotated as genes involved in morphogenesis, development, differentiation, and malignancy predisposition pathways. TBRS patients also displayed highly accelerated DNA methylation aging. These findings were most marked in a carrier of the AML-associated driver mutation p.Arg882Cys. Our studies additionally defined phenotype-related accelerated and decelerated epigenetic aging in two histone methyltransferase disorders: NSD1 Sotos syndrome overgrowth disorder and KMT2D Kabuki syndrome growth impairment. Together, our findings provide fundamental new insights into aberrant epigenetic mechanisms, the role of epigenetic machinery maintenance, and determinants of biological aging in these growth disorders.
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Affiliation(s)
- Aaron R Jeffries
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom
| | - Reza Maroofian
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's University of London, London SW17 0RE, United Kingdom
| | - Claire G Salter
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom.,Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.,Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, SO16 5YA, United Kingdom
| | - Barry A Chioza
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom
| | - Harold E Cross
- Department of Ophthalmology and Vision Science, University of Arizona School of Medicine, Tucson, Arizona 85711, USA
| | - Michael A Patton
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom.,Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's University of London, London SW17 0RE, United Kingdom
| | - Emma Dempster
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom
| | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.,Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, SO16 5YA, United Kingdom
| | - Deborah J G Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Faisal I Rezwan
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Lise Aksglaede
- Department of Clinical Genetics, Copenhagen University Hospital, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Diana Baralle
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.,Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, SO16 5YA, United Kingdom
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Clinical Genetics Service, Belfast City Hospital, Belfast, BT9 7AB, United Kingdom
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Clayton, Victoria, VIC 3168, Australia.,Department of Paediatrics, Monash University, Clayton, Victoria, VIC 3168, Australia
| | - Arveen Kamath
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, CF14 4XN, United Kingdom
| | - Ajith Kumar
- North East Thames Regional Genetics Service and Department of Clinical Genetics, Great Ormond Street Hospital, London, WC1N 3JH, United Kingdom
| | - Ruth Newbury-Ecob
- University Hospitals Bristol, Department of Clinical Genetics, St Michael's Hospital, Bristol, BS2 8EG, United Kingdom
| | | | - Amanda Springer
- Monash Genetics, Monash Health, Clayton, Victoria, VIC 3168, Australia.,Department of Paediatrics, Monash University, Clayton, Victoria, VIC 3168, Australia
| | - Lionel Van Maldergem
- Centre de génétique humaine and Clinical Investigation Center 1431 (INSERM), Université de Franche-Comté, 25000, Besançon, France
| | - Vinod Varghese
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, CF14 4XN, United Kingdom
| | - Naomi Yachelevich
- Clinical Genetics Services, New York University Hospitals Center, New York University, New York, New York 10016, USA
| | - Katrina Tatton-Brown
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's University of London, London SW17 0RE, United Kingdom.,Division of Genetics and Epidemiology, Institute of Cancer Research, London SM2 5NG, United Kingdom.,South West Thames Regional Genetics Service, St. George's University Hospitals NHS Foundation Trust, London SW17 0QT, United Kingdom
| | - Jonathan Mill
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom
| | - Andrew H Crosby
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom
| | - Emma L Baple
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom.,Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, EX1 2ED, United Kingdom
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39
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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: 43] [Impact Index Per Article: 8.6] [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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Alakbarzade V, Iype T, Chioza BA, Singh R, Harlalka GV, Hardy H, Sreekantan-Nair A, Proukakis C, Peall K, Clark LN, Caswell R, Lango Allen H, Wakeling M, Chilton JK, Baple EL, Louis ED, Warner TT, Crosby AH. Copy number variation of LINGO1 in familial dystonic tremor. Neurol Genet 2019; 5:e307. [PMID: 30842974 PMCID: PMC6384021 DOI: 10.1212/nxg.0000000000000307] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 11/14/2018] [Indexed: 01/18/2023]
Abstract
Objective To elucidate the genetic cause of a large 5 generation South Indian family with multiple individuals with predominantly an upper limb postural tremor and posturing in keeping with another form of tremor, namely, dystonic tremor. Methods Whole-genome single nucleotide polymorphism (SNP) microarray analysis was undertaken to look for copy number variants in the affected individuals. Results Whole-genome SNP microarray studies identified a tandem duplicated genomic segment of chromosome 15q24 present in all affected family members. Whole-genome sequencing demonstrated that it comprised a ∼550-kb tandem duplication encompassing the entire LINGO1 gene. Conclusions The identification of a genomic duplication as the likely molecular cause of this condition, resulting in an additional LINGO1 gene copy in affected cases, adds further support for a causal role of this gene in tremor disorders and implicates increased expression levels of LINGO1 as a potential pathogenic mechanism.
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Affiliation(s)
- Vafa Alakbarzade
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Thomas Iype
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Barry A Chioza
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Royana Singh
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Gaurav V Harlalka
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Holly Hardy
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Ajith Sreekantan-Nair
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Christos Proukakis
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Kathryn Peall
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Lorraine N Clark
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Richard Caswell
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Hana Lango Allen
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Matthew Wakeling
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - John K Chilton
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Emma L Baple
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Elan D Louis
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Thomas T Warner
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
| | - Andrew H Crosby
- Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT
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Lin S, Harlalka GV, Hameed A, Reham HM, Yasin M, Muhammad N, Khan S, Baple EL, Crosby AH, Saleha S. Novel mutations in ALDH1A3 associated with autosomal recessive anophthalmia/microphthalmia, and review of the literature. BMC Med Genet 2018; 19:160. [PMID: 30200890 PMCID: PMC6131798 DOI: 10.1186/s12881-018-0678-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/02/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND Autosomal recessive anophthalmia and microphthalmia are rare developmental eye defects occurring during early fetal development. Syndromic and non-syndromic forms of anophthalmia and microphthalmia demonstrate extensive genetic and allelic heterogeneity. To date, disease mutations have been identified in 29 causative genes associated with anophthalmia and microphthalmia, with autosomal dominant, autosomal recessive and X-linked inheritance patterns described. Biallelic ALDH1A3 gene variants are the leading genetic causes of autosomal recessive anophthalmia and microphthalmia in countries with frequent parental consanguinity. METHODS This study describes genetic investigations in two consanguineous Pakistani families with a total of seven affected individuals with bilateral non-syndromic clinical anophthalmia. RESULTS Using whole exome and Sanger sequencing, we identified two novel homozygous ALDH1A3 sequence variants as likely responsible for the condition in each family; missense mutation [NM_000693.3:c.1240G > C, p.Gly414Arg; Chr15:101447332G > C (GRCh37)] in exon 11 (family 1), and, a frameshift mutation [NM_000693.3:c.172dup, p.Glu58Glyfs*5; Chr15:101425544dup (GRCh37)] in exon 2 predicted to result in protein truncation (family 2). CONCLUSIONS This study expands the molecular spectrum of pathogenic ALDH1A3 variants associated with anophthalmia and microphthalmia, and provides further insight of the key role of the ALDH1A3 in human eye development.
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Affiliation(s)
- Siying Lin
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Gaurav V Harlalka
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Abdul Hameed
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, 44000, Pakistan
| | - Hadia Moattar Reham
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Muhammad Yasin
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Emma L Baple
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Andrew H Crosby
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, 26000, Pakistan.
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Arshad MW, Harlalka GV, Lin S, D'Atri I, Mehmood S, Shakil M, Hassan MJ, Chioza BA, Self JE, Ennis S, O'Gorman L, Norman C, Aman T, Ali SS, Kaul H, Baple EL, Crosby AH, Ullah MI, Shabbir MI. Mutations in TYR and OCA2 associated with oculocutaneous albinism in Pakistani families. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Li L, Jiao X, D’Atri I, Ono F, Nelson R, Chan CC, Nakaya N, Ma Z, Ma Y, Cai X, Zhang L, Lin S, Hameed A, Chioza BA, Hardy H, Arno G, Hull S, Khan MI, Fasham J, Harlalka GV, Michaelides M, Moore AT, Coban Akdemir ZH, Jhangiani S, Lupski JR, Cremers FPM, Qamar R, Salman A, Chilton J, Self J, Ayyagari R, Kabir F, Naeem MA, Ali M, Akram J, Sieving PA, Riazuddin S, Baple EL, Riazuddin SA, Crosby AH, Hejtmancik JF. Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa. PLoS Genet 2018; 14:e1007504. [PMID: 30157172 PMCID: PMC6133373 DOI: 10.1371/journal.pgen.1007504] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 02/06/2018] [Revised: 09/11/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023] Open
Abstract
We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent. The p.D25E alteration decreased CLCC1 channel function accompanied by accumulation of mutant protein in granules within the ER lumen, while siRNA knockdown of CLCC1 mRNA induced apoptosis in cultured ARPE-19 cells. TALEN KO in zebrafish was lethal 11 days post fertilization. The depressed electroretinogram (ERG) cone response and cone spectral sensitivity of 5 dpf KO zebrafish and reduced eye size, retinal thickness, and expression of rod and cone opsins could be rescued by injection of wild type CLCC1 mRNA. Clcc1+/- KO mice showed decreased ERGs and photoreceptor number. Together these results strongly suggest that intracellular chloride transport by CLCC1 is a critical process in maintaining retinal integrity, and CLCC1 is crucial for survival and function of retinal cells.
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Affiliation(s)
- Lin Li
- Department of Ophthalmology, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ilaria D’Atri
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Fumihito Ono
- Section on Model Synaptic Systems, Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Physiology, Osaka Medical College, Takatsuki, Japan
| | - Ralph Nelson
- Unit on Neural Circuits, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chi-Chao Chan
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Naoki Nakaya
- Section of Molecular Mechanisms of Glaucoma, Laboratory of Molecular and Developmental Biology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Zhiwei Ma
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yan Ma
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xiaoying Cai
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P.R. China
| | - Longhua Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P.R. China
| | - Siying Lin
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Abdul Hameed
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
| | - Barry A. Chioza
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Holly Hardy
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Gavin Arno
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Biosciences, Moorfields Eye Hospital, London, United Kingdom
| | - Sarah Hull
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Biosciences, Moorfields Eye Hospital, London, United Kingdom
| | - Muhammad Imran Khan
- Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - James Fasham
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Department of Clinical Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Gaurav V. Harlalka
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Michel Michaelides
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Biosciences, Moorfields Eye Hospital, London, United Kingdom
| | - Anthony T. Moore
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Biosciences, Moorfields Eye Hospital, London, United Kingdom
- Ophthalmology Department, UCSF School of Medicine, San Francisco, California, United States of America
| | - Zeynep Hande Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
| | - Frans P. M. Cremers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Raheel Qamar
- Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Ahmed Salman
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - John Chilton
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Jay Self
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Firoz Kabir
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Ali
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Javed Akram
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
- National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Paul A. Sieving
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
- National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Emma L. Baple
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Department of Clinical Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - S. Amer Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Andrew H. Crosby
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Thomas N, Glod J, Derse-Anthony C, Baple EL, Obsborne N, Sturley R, Vaidya B, Newbold K, Brooke A. Pregnancy on vandetanib in metastatic medullary thyroid carcinoma associated with multiple endocrine neoplasia type 2B. Clin Endocrinol (Oxf) 2018; 88:754-756. [PMID: 29457255 PMCID: PMC5903939 DOI: 10.1111/cen.13577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicholas Thomas
- Department of Endocrinology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - John Glod
- Paediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Claudia Derse-Anthony
- Clinical Research Directorate/Clinical Monitoring Research Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Emma L Baple
- Department of Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- University of Exeter Medical School, Exeter, UK
| | - Nigel Obsborne
- Department of Neonatology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Rachel Sturley
- Department of Obstetrics, Royal Devon and Exeter NHS Foundation Trust Exeter, UK
| | - Bijay Vaidya
- Department of Endocrinology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Kate Newbold
- Head and Neck Oncology Unit, the Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Antonia Brooke
- Department of Endocrinology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
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45
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Salter CG, Beijer D, Hardy H, Barwick KES, Bower M, Mademan I, De Jonghe P, Deconinck T, Russell MA, McEntagart MM, Chioza BA, Blakely RD, Chilton JK, De Bleecker J, Baets J, Baple EL, Walk D, Crosby AH. Truncating SLC5A7 mutations underlie a spectrum of dominant hereditary motor neuropathies. Neurol Genet 2018; 4:e222. [PMID: 29582019 PMCID: PMC5866402 DOI: 10.1212/nxg.0000000000000222] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/15/2017] [Indexed: 11/29/2022]
Abstract
Objective To identify the genetic cause of disease in 2 previously unreported families with forms of distal hereditary motor neuropathies (dHMNs). Methods The first family comprises individuals affected by dHMN type V, which lacks the cardinal clinical feature of vocal cord paralysis characteristic of dHMN-VII observed in the second family. Next-generation sequencing was performed on the proband of each family. Variants were annotated and filtered, initially focusing on genes associated with neuropathy. Candidate variants were further investigated and confirmed by dideoxy sequence analysis and cosegregation studies. Thorough patient phenotyping was completed, comprising clinical history, examination, and neurologic investigation. Results dHMNs are a heterogeneous group of peripheral motor neuron disorders characterized by length-dependent neuropathy and progressive distal limb muscle weakness and wasting. We previously reported a dominant-negative frameshift mutation located in the concluding exon of the SLC5A7 gene encoding the choline transporter (CHT), leading to protein truncation, as the likely cause of dominantly-inherited dHMN-VII in an extended UK family. In this study, our genetic studies identified distinct heterozygous frameshift mutations located in the last coding exon of SLC5A7, predicted to result in the truncation of the CHT C-terminus, as the likely cause of the condition in each family. Conclusions This study corroborates C-terminal CHT truncation as a cause of autosomal dominant dHMN, confirming upper limb predominating over lower limb involvement, and broadening the clinical spectrum arising from CHT malfunction.
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Affiliation(s)
- Claire G Salter
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Danique Beijer
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Holly Hardy
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Katy E S Barwick
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Matthew Bower
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Ines Mademan
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Peter De Jonghe
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Tine Deconinck
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Mark A Russell
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Meriel M McEntagart
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Barry A Chioza
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Randy D Blakely
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - John K Chilton
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Jan De Bleecker
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Jonathan Baets
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Emma L Baple
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - David Walk
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre (C.G.S., H.H., K.E.S.B., M.A.R., B.A.C., J.K.C., E.L.B., A.H.C.), Royal Devon & Exeter NHS Foundation Trust, Exeter; Wessex Clinical Genetics Service (C.G.S.), Princess Anne Hospital, Southampton, United Kingdom; Neurogenetics Group (D.B., I.M., P.D.J., T.D., J.B.), Center for Molecular Neurology, VIB; Laboratory of Neuromuscular Pathology (D.B., I.M., P.D.J., T.D., J.B.), Institute Born-Bunge, University of Antwerp; Department of Neurology (M.B., D.W.), University of Minnesota, Minneapolis, MN; Department of Neurology (P.D.J., J.B.), Neuromuscular Reference Centre, Antwerp University Hospital, Antwerpen, Belgium; Clinical Genetics (M.M.M.), St. George's University of London, London, United Kingdom; Biomedical Science (R.D.B.), Florida Atlantic University, Jupiter Campus, FL; and Department of Neurology (J.D.B.), University Hospital Ghent, Ghent, Belgium; Peninsula Clinical Genetics Service (E.L.B.), Royal Devon and Exeter Hospital, Exeter, United Kingdom
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46
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Ullah MI, Nasir A, Ahmad A, Harlalka GV, Ahmad W, Hassan MJ, Baple EL, Crosby AH, Chioza BA. Identification of novel L2HGDH mutation in a large consanguineous Pakistani family- a case report. BMC Med Genet 2018; 19:25. [PMID: 29458334 PMCID: PMC5819255 DOI: 10.1186/s12881-018-0532-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/24/2018] [Indexed: 11/27/2022]
Abstract
Background L-2-hydroxyglutaric aciduria (L2HGA) is a progressive neurometabolic disease of brain caused by mutations of in L-2-hydroxyglutarate dehydrogenase (L2HGDH) gene. Cardinal clinical features include cerebellar ataxia, epilepsy, neurodevelopmental delay, intellectual disability, and other clinical neurological deficits. Case presentation We describe an index case of the family presented with generalised tonic-clonic seizure, developmental delay, intellectual disability, and ataxia. Initially, the differential diagnosis was difficult to be established and a SNP genome wide scan identified the candidate region on chromosome 14q22.1. DNA sequencing showed a novel homozygous mutation in the candidate gene L2HGDH (NM_024884.2: c.178G > A; p.Gly60Arg). The mutation p.Gly60Arg lies in the highly conserved FAD/NAD(P)-binding domain of this mitochondrial enzyme, predicted to disturb enzymatic function. Conclusions The combination of homozygosity mapping and DNA sequencing identified a novel mutation in Pakistani family with variable clinical features. This is second report of a mutation in L2HGDH gene from Pakistan and the largest family with L2HGA reported to date.
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Affiliation(s)
- Muhammad Ikram Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,RILD Wellcome Wolfson Centre - Level 4, Royal Devon and Exeter NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Abdul Nasir
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Computational Medicinal Chemistry Laboratory, Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Arsalan Ahmad
- Division of Neurology, Shifa International Hospital, Shifa Tameer e Millat University, Islamabad, Pakistan
| | - Gaurav Vijay Harlalka
- RILD Wellcome Wolfson Centre - Level 4, Royal Devon and Exeter NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Jawad Hassan
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan
| | - Emma L Baple
- RILD Wellcome Wolfson Centre - Level 4, Royal Devon and Exeter NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre - Level 4, Royal Devon and Exeter NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Barry A Chioza
- RILD Wellcome Wolfson Centre - Level 4, Royal Devon and Exeter NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK.
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47
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Stals KL, Wakeling M, Baptista J, Caswell R, Parrish A, Rankin J, Tysoe C, Jones G, Gunning AC, Lango Allen H, Bradley L, Brady AF, Carley H, Carmichael J, Castle B, Cilliers D, Cox H, Deshpande C, Dixit A, Eason J, Elmslie F, Fry AE, Fryer A, Holder M, Homfray T, Kivuva E, McKay V, Newbury‐Ecob R, Parker M, Savarirayan R, Searle C, Shannon N, Shears D, Smithson S, Thomas E, Turnpenny PD, Varghese V, Vasudevan P, Wakeling E, Baple EL, Ellard S. Diagnosis of lethal or prenatal-onset autosomal recessive disorders by parental exome sequencing. Prenat Diagn 2018; 38:33-43. [PMID: 29096039 PMCID: PMC5836855 DOI: 10.1002/pd.5175] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 10/10/2017] [Accepted: 10/23/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Rare genetic disorders resulting in prenatal or neonatal death are genetically heterogeneous, but testing is often limited by the availability of fetal DNA, leaving couples without a potential prenatal test for future pregnancies. We describe our novel strategy of exome sequencing parental DNA samples to diagnose recessive monogenic disorders in an audit of the first 50 couples referred. METHOD Exome sequencing was carried out in a consecutive series of 50 couples who had 1 or more pregnancies affected with a lethal or prenatal-onset disorder. In all cases, there was insufficient DNA for exome sequencing of the affected fetus. Heterozygous rare variants (MAF < 0.001) in the same gene in both parents were selected for analysis. Likely, disease-causing variants were tested in fetal DNA to confirm co-segregation. RESULTS Parental exome analysis identified heterozygous pathogenic (or likely pathogenic) variants in 24 different genes in 26/50 couples (52%). Where 2 or more fetuses were affected, a genetic diagnosis was obtained in 18/29 cases (62%). In most cases, the clinical features were typical of the disorder, but in others, they result from a hypomorphic variant or represent the most severe form of a variable phenotypic spectrum. CONCLUSION We conclude that exome sequencing of parental samples is a powerful strategy with high clinical utility for the genetic diagnosis of lethal or prenatal-onset recessive disorders. © 2017 The Authors Prenatal Diagnosis published by John Wiley & Sons Ltd.
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Wang H, Salter CG, Refai O, Hardy H, Barwick KES, Akpulat U, Kvarnung M, Chioza BA, Harlalka G, Taylan F, Sejersen T, Wright J, Zimmerman HH, Karakaya M, Stüve B, Weis J, Schara U, Russell MA, Abdul-Rahman OA, Chilton J, Blakely RD, Baple EL, Cirak S, Crosby AH. Choline transporter mutations in severe congenital myasthenic syndrome disrupt transporter localization. Brain 2017; 140:2838-2850. [PMID: 29088354 DOI: 10.1093/brain/awx249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 04/21/2017] [Accepted: 08/05/2017] [Indexed: 11/12/2022] Open
Abstract
The presynaptic, high-affinity choline transporter is a critical determinant of signalling by the neurotransmitter acetylcholine at both central and peripheral cholinergic synapses, including the neuromuscular junction. Here we describe an autosomal recessive presynaptic congenital myasthenic syndrome presenting with a broad clinical phenotype due to homozygous choline transporter missense mutations. The clinical phenotype ranges from the classical presentation of a congenital myasthenic syndrome in one patient (p.Pro210Leu), to severe neurodevelopmental delay with brain atrophy (p.Ser94Arg) and extend the clinical outcomes to a more severe spectrum with infantile lethality (p.Val112Glu). Cells transfected with mutant transporter construct revealed a virtually complete loss of transport activity that was paralleled by a reduction in transporter cell surface expression. Consistent with these findings, studies to determine the impact of gene mutations on the trafficking of the Caenorhabditis elegans choline transporter orthologue revealed deficits in transporter export to axons and nerve terminals. These findings contrast with our previous findings in autosomal dominant distal hereditary motor neuropathy of a dominant-negative frameshift mutation at the C-terminus of choline transporter that was associated with significantly reduced, but not completely abrogated choline transporter function. Together our findings define divergent neuropathological outcomes arising from different classes of choline transporter mutation with distinct disease processes and modes of inheritance. These findings underscore the essential role played by the choline transporter in sustaining acetylcholine neurotransmission at both central and neuromuscular synapses, with important implications for treatment and drug selection.
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Affiliation(s)
- Haicui Wang
- University Hospital Cologne, Department of Pediatrics, Kerpener Str. 62, 50937 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany
| | - Claire G Salter
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK.,Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Osama Refai
- Department of Biomedical Science, Charles E. Schmidt College of Medicine and Brain Institute, Florida Atlantic University, Jupiter, FL, USA
| | - Holly Hardy
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Katy E S Barwick
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Ugur Akpulat
- University Hospital Cologne, Department of Pediatrics, Kerpener Str. 62, 50937 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany.,Kastamonu University, 37150 Kastamonu, Turkey
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, 17176 Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Barry A Chioza
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Gaurav Harlalka
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, 17176 Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, 17121 Stockholm, Sweden
| | - Thomas Sejersen
- Science for Life Laboratory, Karolinska Institutet Science Park, 17121 Stockholm, Sweden.,Department of Women's and Children's Health, Division of Pediatric Neurology, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Jane Wright
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Holly H Zimmerman
- Division of Medical Genetics, University of Mississippi Medical Center, Jackson, Mississippi 39216, USA
| | - Mert Karakaya
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany
| | - Burkhardt Stüve
- Children's Hospital Social Pediatric Center, 50735 Cologne, Germany
| | - Joachim Weis
- Institute of Neuropathology and Jülich Aachen Research Alliance (JARA) Brain Translational Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Ulrike Schara
- University Children's Hospital Essen, Essen, Germany
| | - Mark A Russell
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Omar A Abdul-Rahman
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, Mississippi 39216, USA
| | - John Chilton
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Randy D Blakely
- Department of Biomedical Science, Charles E. Schmidt College of Medicine and Brain Institute, Florida Atlantic University, Jupiter, FL, USA
| | - Emma L Baple
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Sebahattin Cirak
- University Hospital Cologne, Department of Pediatrics, Kerpener Str. 62, 50937 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
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49
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Baple EL, Houlden H, Zollo M, Crosby AH. Reply: PRUNE1: a disease-causing gene for secondary microcephaly. Brain 2017; 140:e62. [PMID: 28969377 DOI: 10.1093/brain/awx199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Emma L Baple
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Massimo Zollo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche DMMBM, Università di Napoli Federico II, Via Sergio Pansini 5, Naples, 80131, Italy.,CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, Naples, Italy.,European School of Molecular Medicine, SEMM, University of Milan, Italy
| | - Andrew H Crosby
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
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50
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Ahmed MY, Al-Khayat A, Al-Murshedi F, Al-Futaisi A, Chioza BA, Pedro Fernandez-Murray J, Self JE, Salter CG, Harlalka GV, Rawlins LE, Al-Zuhaibi S, Al-Azri F, Al-Rashdi F, Cazenave-Gassiot A, Wenk MR, Al-Salmi F, Patton MA, Silver DL, Baple EL, McMaster CR, Crosby AH. A mutation of EPT1 (SELENOI) underlies a new disorder of Kennedy pathway phospholipid biosynthesis. Brain 2017; 140:547-554. [PMID: 28052917 PMCID: PMC5382949 DOI: 10.1093/brain/aww318] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [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: 06/29/2016] [Accepted: 10/19/2016] [Indexed: 12/20/2022] Open
Abstract
Mutations in genes involved in lipid metabolism have increasingly been associated with various subtypes of hereditary spastic paraplegia, a highly heterogeneous group of neurodegenerative motor neuron disorders characterized by spastic paraparesis. Here, we report an unusual autosomal recessive neurodegenerative condition, best classified as a complicated form of hereditary spastic paraplegia, associated with mutation in the ethanolaminephosphotransferase 1 (EPT1) gene (now known as SELENOI), responsible for the final step in Kennedy pathway forming phosphatidylethanolamine from CDP-ethanolamine. Phosphatidylethanolamine is a glycerophospholipid that, together with phosphatidylcholine, constitutes more than half of the total phospholipids in eukaryotic cell membranes. We determined that the mutation defined dramatically reduces the enzymatic activity of EPT1, thereby hindering the final step in phosphatidylethanolamine synthesis. Additionally, due to central nervous system inaccessibility we undertook quantification of phosphatidylethanolamine levels and species in patient and control blood samples as an indication of liver phosphatidylethanolamine biosynthesis. Although this revealed alteration to levels of specific phosphatidylethanolamine fatty acyl species in patients, overall phosphatidylethanolamine levels were broadly unaffected indicating that in blood EPT1 inactivity may be compensated for, in part, via alternate biochemical pathways. These studies define the first human disorder arising due to defective CDP-ethanolamine biosynthesis and provide new insight into the role of Kennedy pathway components in human neurological function.
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Affiliation(s)
- Mustafa Y Ahmed
- Medical Research (Level 4), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Aisha Al-Khayat
- Department of Biology, College of Science, Sultan Qaboos University, Sultanate of Oman
| | - Fathiya Al-Murshedi
- Department of Genetics, College of Medicine, Sultan Qaboos University, Sultanate of Oman
| | - Amna Al-Futaisi
- Department of Paediatrics, Sultan Qaboos University Hospital, Sultanate of Oman
| | - Barry A Chioza
- Medical Research (Level 4), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | | | - Jay E Self
- Faculty of Medicine, University of Southampton, UK
| | - Claire G Salter
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Mindelsohn Way, Birmingham, B15 2TG, UK
| | - Gaurav V Harlalka
- Medical Research (Level 4), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Lettie E Rawlins
- Medical Research (Level 4), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Sana Al-Zuhaibi
- Department of Ophthalmology, Sultan Qaboos University Hospital, Sultanate of Oman
| | - Faisal Al-Azri
- Department of Radiology and Molecular Imaging, Sultan Qaboos University Hospital, Sultanate of Oman
| | - Fatma Al-Rashdi
- Department of Paediatrics, Sameal Hospital, Ministry of Health, Sultanate of Oman
| | - Amaury Cazenave-Gassiot
- SLING, Life Sciences Institute, National University of Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore
| | - Markus R Wenk
- SLING, Life Sciences Institute, National University of Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore
| | - Fatema Al-Salmi
- Department of Biology, College of Science, Sultan Qaboos University, Sultanate of Oman
| | - Michael A Patton
- Medical Research (Level 4), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK.,Department of Biology, College of Science, Sultan Qaboos University, Sultanate of Oman
| | - David L Silver
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Emma L Baple
- Medical Research (Level 4), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | | | - Andrew H Crosby
- Medical Research (Level 4), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
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