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Cavusoglu D, Ozturk G, Turkdogan D, Kurul SH, Yis U, Komur M, Incecik F, Kara B, Sahin T, Unver O, Dilber C, Mert GG, Gunay C, Uzan GS, Ersoy O, Oktay Y, Mermer S, Tuncer GO, Gungor O, Ozcora GDK, Gumus U, Sezer O, Cetin GO, Demir F, Yilmaz A, Gurbuz G, Topcu M, Topaloglu H, Ceylan AC, Ceylaner S, Gleeson JG, Icagasioglu DF, Sonmez FM. Evaluation of the Patients with the Diagnosis of Pontocerebellar Hypoplasia: A Multicenter National Study. Cerebellum 2024:10.1007/s12311-024-01690-1. [PMID: 38622473 DOI: 10.1007/s12311-024-01690-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 04/17/2024]
Abstract
Pontocerebellar hypoplasia (PCH) is a heterogeneous group of neurodegenerative disorders characterized by hypoplasia and degeneration of the cerebellum and pons. We aimed to identify the clinical, laboratory, and imaging findings of the patients with diagnosed PCH with confirmed genetic analysis. We collected available clinical data, laboratory, and imaging findings in our retrospective multicenter national study of 64 patients with PCH in Turkey. The genetic analysis included the whole-exome sequencing (WES), targeted next-generation sequencing (NGS), or single gene analysis. Sixty-four patients with PCH were 28 female (43.8%) and 36 (56.3%) male. The patients revealed homozygous mutation in 89.1%, consanguinity in 79.7%, pregnancy at term in 85.2%, microcephaly in 91.3%, psychomotor retardation in 98.4%, abnormal neurological findings in 100%, seizure in 63.8%, normal biochemistry and metabolic investigations in 92.2%, and dysmorphic findings in 51.2%. The missense mutation was found to be the most common variant type in all patients with PCH. It was detected as CLP1 (n = 17) was the most common PCH related gene. The homozygous missense variant c.419G > A (p.Arg140His) was identified in all patients with CLP1. Moreover, all patients showed the same homozygous missense variant c.919G > T (p.A307S) in TSEN54 group (n = 6). In Turkey, CLP1 was identified as the most common causative gene with the identical variant c.419G > A; p.Arg140His. The current study supports that genotype data on PCH leads to phenotypic variability over a wide phenotypic spectrum.
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Affiliation(s)
- Dilek Cavusoglu
- Departments of Pediatric Neurology, Afyonkarahisar Health Sciences University, Afyon, Turkey
| | - Gulten Ozturk
- Departments of Pediatric Neurology, Marmara University, Istanbul, Turkey
| | - Dilsad Turkdogan
- Departments of Pediatric Neurology, Marmara University, Istanbul, Turkey
| | - Semra Hiz Kurul
- Departments of Pediatric Neurology, Dokuz Eylul University, Izmir, Turkey
| | - Uluc Yis
- Departments of Pediatric Neurology, Dokuz Eylul University, Izmir, Turkey
| | - Mustafa Komur
- Departments of Pediatric Neurology, Mersin University, Mersin, Turkey
| | - Faruk Incecik
- Departments of Pediatric Neurology, Cukurova University, Adana, Turkey
| | - Bulent Kara
- Departments of Pediatric Neurology, Kocaeli University, Kocaeli, Turkey
| | - Turkan Sahin
- Departments of Pediatric Neurology, Bezmialem Vakif University, Istanbul, Turkey
| | - Olcay Unver
- Departments of Pediatric Neurology, Marmara University, Istanbul, Turkey
| | - Cengiz Dilber
- Departments of Pediatric Neurology, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey
| | - Gulen Gul Mert
- Departments of Pediatric Neurology, Cukurova University, Adana, Turkey
| | - Cagatay Gunay
- Departments of Pediatric Neurology, Dokuz Eylul University, Izmir, Turkey
| | | | - Ozlem Ersoy
- Departments of Pediatric Neurology, Mersin University, Mersin, Turkey
| | - Yavuz Oktay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Serdar Mermer
- Departments of Medical Genetics, Mersin University, Mersin, Turkey
| | - Gokcen Oz Tuncer
- Departments of Pediatric Neurology, Ondokuz Mayıs University, Samsun, Turkey
| | - Olcay Gungor
- Departments of Pediatric Neurology, Pamukkale University, Denizli, Turkey
| | | | - Ugur Gumus
- Departments of Medical Genetics, Dr Ersin Arslan Training and Research Hospital, Gaziantep, Turkey
| | - Ozlem Sezer
- Departments of Medical Genetics, Samsun Training and Research Hospital, Samsun, Turkey
| | - Gokhan Ozan Cetin
- Departments of Medical Genetics, Pamukkale University, Denizli, Turkey
| | - Fatma Demir
- Departments of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Arzu Yilmaz
- Departments of Pediatric Neurology, Ankara Training and Research Hospital, Ankara, Turkey
| | - Gurkan Gurbuz
- Departments of Pediatric Neurology, Tekirdag Namik Kemal University, Tekirdag, Turkey
| | - Meral Topcu
- Departments of Pediatric Neurology, Hacettepe University,Retired Lecturer, Ankara, Turkey
| | - Haluk Topaloglu
- Departments of Pediatric Neurology, Yeditepe University, Istanbul, Turkey
| | - Ahmet Cevdet Ceylan
- Departments of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
| | | | - Joseph G Gleeson
- Department of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, La Jolla, San Diego, CA, USA
| | | | - F Mujgan Sonmez
- Departments of Pediatric Neurology, Department of Child Neurology, Karadeniz Technical University Medical Faculty, Retired Lecturer, Trabzon, Turkey.
- Yuksek Ihtisas University, Faculty of Medicine, Ankara, Turkey.
- , Aziziye Mah. Cinnah Cad. 102/3, Cankaya, Ankara, Türkiye.
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Wilson LA, Macken WL, Perry LD, Record CJ, Schon KR, Frezatti RSS, Raga S, Naidu K, Köken ÖY, Polat I, Kapapa MM, Dominik N, Efthymiou S, Morsy H, Nel M, Fassad MR, Gao F, Patel K, Schoonen M, Bisschoff M, Vorster A, Jonvik H, Human R, Lubbe E, Nonyane M, Vengalil S, Nashi S, Srivastava K, Lemmers RJLF, Reyaz A, Mishra R, Töpf A, Trainor CI, Steyn EC, Mahungu AC, van der Vliet PJ, Ceylan AC, Hiz AS, Çavdarlı B, Semerci Gündüz CN, Ceylan GG, Nagappa M, Tallapaka KB, Govindaraj P, van der Maarel SM, Narayanappa G, Nandeesh BN, Wa Somwe S, Bearden DR, Kvalsund MP, Ramdharry GM, Oktay Y, Yiş U, Topaloğlu H, Sarkozy A, Bugiardini E, Henning F, Wilmshurst JM, Heckmann JM, McFarland R, Taylor RW, Smuts I, van der Westhuizen FH, Sobreira CFDR, Tomaselli PJ, Marques W, Bhatia R, Dalal A, Srivastava MVP, Yareeda S, Nalini A, Vishnu VY, Thangaraj K, Straub V, Horvath R, Chinnery PF, Pitceathly RDS, Muntoni F, Houlden H, Vandrovcova J, Reilly MM, Hanna MG. Neuromuscular disease genetics in under-represented populations: increasing data diversity. Brain 2023; 146:5098-5109. [PMID: 37516995 PMCID: PMC10690022 DOI: 10.1093/brain/awad254] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/04/2023] [Indexed: 08/01/2023] Open
Abstract
Neuromuscular diseases (NMDs) affect ∼15 million people globally. In high income settings DNA-based diagnosis has transformed care pathways and led to gene-specific therapies. However, most affected families are in low-to-middle income countries (LMICs) with limited access to DNA-based diagnosis. Most (86%) published genetic data is derived from European ancestry. This marked genetic data inequality hampers understanding of genetic diversity and hinders accurate genetic diagnosis in all income settings. We developed a cloud-based transcontinental partnership to build diverse, deeply-phenotyped and genetically characterized cohorts to improve genetic architecture knowledge, and potentially advance diagnosis and clinical management. We connected 18 centres in Brazil, India, South Africa, Turkey, Zambia, Netherlands and the UK. We co-developed a cloud-based data solution and trained 17 international neurology fellows in clinical genomic data interpretation. Single gene and whole exome data were analysed via a bespoke bioinformatics pipeline and reviewed alongside clinical and phenotypic data in global webinars to inform genetic outcome decisions. We recruited 6001 participants in the first 43 months. Initial genetic analyses 'solved' or 'possibly solved' ∼56% probands overall. In-depth genetic data review of the four commonest clinical categories (limb girdle muscular dystrophy, inherited peripheral neuropathies, congenital myopathy/muscular dystrophies and Duchenne/Becker muscular dystrophy) delivered a ∼59% 'solved' and ∼13% 'possibly solved' outcome. Almost 29% of disease causing variants were novel, increasing diverse pathogenic variant knowledge. Unsolved participants represent a new discovery cohort. The dataset provides a large resource from under-represented populations for genetic and translational research. In conclusion, we established a remote transcontinental partnership to assess genetic architecture of NMDs across diverse populations. It supported DNA-based diagnosis, potentially enabling genetic counselling, care pathways and eligibility for gene-specific trials. Similar virtual partnerships could be adopted by other areas of global genomic neurological practice to reduce genetic data inequality and benefit patients globally.
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Affiliation(s)
- Lindsay A Wilson
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Luke D Perry
- Institute of Child Health and Centre for Neuromuscular Diseases, Neurosciences Unit, The Dubowitz Neuromuscular Centre, University College London, UCL Great Ormond Street, Great Ormond Street Hospital, London WC1N 3JH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Christopher J Record
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Katherine R Schon
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rodrigo S S Frezatti
- Department of Neurosciences, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Sharika Raga
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Paediatric Neurology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Kireshnee Naidu
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
- Division of Neurology, Department of Medicine, Stellenbosch University, Cape Town, South Africa
| | - Özlem Yayıcı Köken
- Faculty of Medicine, Department of Pediatric Neurology, Akdeniz University, Antalya, Turkey
| | - Ipek Polat
- Faculty of Medicine, Pediatric Neurology Department, Dokuz Eylül University, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Musambo M Kapapa
- Department of Physiotherapy, University of Zambia School of Health Sciences & University Teaching Hospital Neurology Research Office, Lusaka, Zambia
| | - Natalia Dominik
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Heba Morsy
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Melissa Nel
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Mahmoud R Fassad
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Fei Gao
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Krutik Patel
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Maryke Schoonen
- Focus Area for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Michelle Bisschoff
- Focus Area for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Armand Vorster
- Focus Area for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Hallgeir Jonvik
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Ronel Human
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Elsa Lubbe
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Malebo Nonyane
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Saraswati Nashi
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Kosha Srivastava
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Alisha Reyaz
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Rinkle Mishra
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Christina I Trainor
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elizabeth C Steyn
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Amokelani C Mahungu
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Patrick J van der Vliet
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Ahmet Cevdet Ceylan
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
- Faculty of Medicine, Department of Medical Genetics, Ankara Yıldırım Beyazıt University, Ankara, Turkey
| | - A Semra Hiz
- Faculty of Medicine, Pediatric Neurology Department, Dokuz Eylül University, Izmir, Turkey
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
| | - Büşranur Çavdarlı
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
| | - C Nur Semerci Gündüz
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
- Faculty of Medicine, Department of Medical Genetics, Ankara Yıldırım Beyazıt University, Ankara, Turkey
| | - Gülay Güleç Ceylan
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
- Faculty of Medicine, Department of Medical Genetics, Ankara Yıldırım Beyazıt University, Ankara, Turkey
| | - Madhu Nagappa
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Karthik B Tallapaka
- CSIR—Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana, India
| | - Periyasamy Govindaraj
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | | | - Gayathri Narayanappa
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Bevinahalli N Nandeesh
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Somwe Wa Somwe
- Department of Clinical Sciences, School of Medicine and Health Sciences, University of Lusaka, Lusaka, Zambia
| | - David R Bearden
- University of Zambia Department of Educational Psychology, Lusaka, Zambia
- Department of Neurology, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Michelle P Kvalsund
- Department of Neurology, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Internal Medicine, University of Zambia School of Medicine, Lusaka, Zambia
| | - Gita M Ramdharry
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Yavuz Oktay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
| | - Uluç Yiş
- Faculty of Medicine, Pediatric Neurology Department, Dokuz Eylül University, Izmir, Turkey
| | | | - Anna Sarkozy
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Franclo Henning
- Division of Neurology, Department of Medicine, Stellenbosch University, Cape Town, South Africa
| | - Jo M Wilmshurst
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Paediatric Neurology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Jeannine M Heckmann
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Izelle Smuts
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | | | | | - Pedro J Tomaselli
- Department of Neurosciences, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Wilson Marques
- Department of Neurosciences, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Rohit Bhatia
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - M V Padma Srivastava
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Sireesha Yareeda
- Department of Neurology, Nizam’s Institute of Medical Sciences (NIMS), Hyderabad, Telangana, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Venugopalan Y Vishnu
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Kumarasamy Thangaraj
- CSIR—Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana, India
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Francesco Muntoni
- Institute of Child Health and Centre for Neuromuscular Diseases, Neurosciences Unit, The Dubowitz Neuromuscular Centre, University College London, UCL Great Ormond Street, Great Ormond Street Hospital, London WC1N 3JH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
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Özsoy Ö, Cinleti T, Günay Ç, Sarıkaya Uzan G, Yeşilmen MC, Lochmüller H, Horvath R, Yiş U, Oktay Y, Hiz Kurul S. DPAGT1-CDG: Report of Two New Pediatric Patients and Brief Review of the Literature. Mol Syndromol 2023; 14:322-330. [PMID: 37766827 PMCID: PMC10521235 DOI: 10.1159/000529494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/27/2023] [Indexed: 09/29/2023] Open
Abstract
Introduction Congenital glycosylation disorders are multisystem diseases with heterogeneous clinical manifestations caused by defects in the synthesis of the glycan moiety of glycoproteins or glycolipids or the binding of glycans to proteins and lipids. DPAGT1 (UDP-GlcNAc: dolichol phosphate N-acetylglucosamine-1-phosphotransferase) is an initiating protein in the biosynthetic pathway of dolichol-linked oligosaccharides required for protein N-glycosylation. Pathogenic variants in DPAGT1 (UDP-GlcNAc: dolichol phosphate N-acetylglucosamine-1-phosphotransferase) gene cause a rare type of congenital glycosylation disorder called DPAGT1-CDG (formerly CDG-Ij) (OMIM #608093). It is a rare autosomal recessive disease or a milder version with congenital myasthenic syndrome known as DPAGT1-CMS. A severe disease course with hypotonia, cataracts, skeletal deformities, resistant epilepsy, intellectual disability, global developmental delay, premature death has been described in most patients with DPAGT1-CDG. Patient Presentation We describe two patients with variants in the DPAGT1 gene: an 8-month-old boy with a homozygous, missense DPAGT1:c.339T>G (p.Phe113Leu) novel variant and a 13-year-old female patient with compound heterozygous variants, DPAGT1:c.466C>T (p.Arg156Cys, R156C) and DPAGT1:c.161+5G>A. While the 8-month-old patient was diagnosed with congenital cataract at the age of 1 month, had dysmorphic findings, and epilepsy, clinical symptoms in the other patient appeared later but with more prominent muscle weakness, behavioral disorder, dysmorphic findings, and no epilepsy. Discussion Cholinesterase inhibitor therapy was found to be effective in patients against muscle weakness, supporting DPAGT1 deficiency as the underlying etiology. We started pyridostigmine treatment in our patient with more pronounced muscle weakness, and we saw its benefit. We aimed to present our patients diagnosed with DPAGT1-CDG due to different variants in the same gene and different clinical presentations, treatment and to compare them with other patients in the literature.
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Affiliation(s)
- Özlem Özsoy
- Department of Pediatric Neurology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Tayfun Cinleti
- Department of Pediatric Genetics, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Çağatay Günay
- Department of Pediatric Neurology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Gamze Sarıkaya Uzan
- Department of Pediatric Neurology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Mehmet Can Yeşilmen
- Department of Pediatric Neurology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Hanns Lochmüller
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
- Department of Neuropediatrics and Muscle Disorders, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Division of Neurology, Department of Medicine, The Ottawa Hospital, and Brain and Mind Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Uluç Yiş
- Department of Pediatric Neurology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, İzmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Semra Hiz Kurul
- Department of Pediatric Neurology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, İzmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey
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Harwood AJ, Petrakis S, Oktay Y, Pasterkamp RJ. Editorial: Mental health: cell models to mechanisms. Front Cell Dev Biol 2023; 11:1244425. [PMID: 37560163 PMCID: PMC10407806 DOI: 10.3389/fcell.2023.1244425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023] Open
Affiliation(s)
- Adrian J. Harwood
- Neuroscience and Mental Health Innovation Institute (NMHII), Cardiff University, Cardiff, United Kingdom
| | - Spyros Petrakis
- Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece
| | - Yavuz Oktay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Türkiye
| | - R. Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, UMC Utrecht, Utrecht University, Utrecht, Netherlands
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Ozturk BT, Ozel F, Yaras T, Ekinci B, Oktay Y, Aysevener EO, Alkın T, Direk N. The Relationship Between Cardiovascular Disease Risk and Major Depression. Noro Psikiyatr Ars 2023; 60:124-128. [PMID: 37287563 PMCID: PMC10242288 DOI: 10.29399/npa.28191] [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: 04/04/2022] [Accepted: 07/14/2022] [Indexed: 06/09/2023] Open
Abstract
Introduction Cardiovascular risk in depression has been investigated in small clinical samples and population-based studies revealing inconclusive results. However, cardiovascular risk in drug-naive depressed patients has not been tested extensively. Methods Body mass index-based Framingham Cardiovascular Risk Scores and soluble intercellular adhesion molecule-1 (sICAM-1) levels were used to assess the risk of cardiovascular disease in drug-naive depressed patients and healthy volunteers. Conclusion There were no significant differences in Framingham Cardiovascular Risk Scores and individually assessed risk variables between patients and healthy controls (HC). Both groups were comparable in terms of sICAM-1. Results The widely recognized association between cardiovascular risk and major depression might be more prominent in older depressed patients and patients with recurring episodes.
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Affiliation(s)
- Bilge Targıtay Ozturk
- Department of Psychiatry, Dokuz Eylul University Medical School, Izmir, Turkey
- Department of Psychiatry, Izmir Cesme Alper Cizgenakat State Hospital, Izmir, Turkey
| | - Fatih Ozel
- Department of Psychiatry, Dokuz Eylul University Medical School, Izmir, Turkey
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Tutku Yaras
- ızmir Biomedicine and Genome Center, Izmir, Turkey
| | - Burcu Ekinci
- ızmir Biomedicine and Genome Center, Izmir, Turkey
| | - Yavuz Oktay
- ızmir Biomedicine and Genome Center, Izmir, Turkey
- Department of Medical Biology, Dokuz Eylul University Medical School, Izmir, Turkey
| | - Elif Onur Aysevener
- Department of Psychiatry, Dokuz Eylul University Medical School, Izmir, Turkey
| | - Tunc Alkın
- Department of Psychiatry, Dokuz Eylul University Medical School, Izmir, Turkey
| | - Neşe Direk
- Department of Psychiatry, Dokuz Eylul University Medical School, Izmir, Turkey
- Istanbul Faculty of Medicine, Department of Psychiatry, Istanbul University, Istanbul, Turkey
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6
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Lecca M, Pehlivan D, Suñer DH, Weiss K, Coste T, Zweier M, Oktay Y, Danial-Farran N, Rosti V, Bonasoni MP, Malara A, Contrò G, Zuntini R, Pollazzon M, Pascarella R, Neri A, Fusco C, Marafi D, Mitani T, Posey JE, Bayramoglu SE, Gezdirici A, Hernandez-Rodriguez J, Cladera EA, Miravet E, Roldan-Busto J, Ruiz MA, Bauzá CV, Ben-Sira L, Sigaudy S, Begemann A, Unger S, Güngör S, Hiz S, Sonmezler E, Zehavi Y, Jerdev M, Balduini A, Zuffardi O, Horvath R, Lochmüller H, Rauch A, Garavelli L, Tournier-Lasserve E, Spiegel R, Lupski JR, Errichiello E. Bi-allelic variants in the ESAM tight-junction gene cause a neurodevelopmental disorder associated with fetal intracranial hemorrhage. Am J Hum Genet 2023; 110:681-690. [PMID: 36996813 PMCID: PMC10119151 DOI: 10.1016/j.ajhg.2023.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/07/2023] [Indexed: 03/31/2023] Open
Abstract
The blood-brain barrier (BBB) is an essential gatekeeper for the central nervous system and incidence of neurodevelopmental disorders (NDDs) is higher in infants with a history of intracerebral hemorrhage (ICH). We discovered a rare disease trait in thirteen individuals, including four fetuses, from eight unrelated families associated with homozygous loss-of-function variant alleles of ESAM which encodes an endothelial cell adhesion molecule. The c.115del (p.Arg39Glyfs∗33) variant, identified in six individuals from four independent families of Southeastern Anatolia, severely impaired the in vitro tubulogenic process of endothelial colony-forming cells, recapitulating previous evidence in null mice, and caused lack of ESAM expression in the capillary endothelial cells of damaged brain. Affected individuals with bi-allelic ESAM variants showed profound global developmental delay/unspecified intellectual disability, epilepsy, absent or severely delayed speech, varying degrees of spasticity, ventriculomegaly, and ICH/cerebral calcifications, the latter being also observed in the fetuses. Phenotypic traits observed in individuals with bi-allelic ESAM variants overlap very closely with other known conditions characterized by endothelial dysfunction due to mutation of genes encoding tight junction molecules. Our findings emphasize the role of brain endothelial dysfunction in NDDs and contribute to the expansion of an emerging group of diseases that we propose to rename as "tightjunctionopathies."
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Affiliation(s)
- Mauro Lecca
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Damià Heine Suñer
- Molecular Diagnostics and Clinical Genetics Unit, Hospital Universitari Son Espases, Palma, Illes Balears, Spain; Genomics of Health, Institute of Health Research of the Balearic Islands, Palma, Illes Balears, Spain
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Haifa, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Thibault Coste
- AP-HP, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France; Université de Paris, INSERM UMR-1141 Neurodiderot, Paris, France
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey; Department of Medical Biology, School of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
| | | | - Vittorio Rosti
- Center for the Study of Myelofibrosis, Laboratory of Biochemistry, Biotechnology and Advanced Diagnosis, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | | | - Alessandro Malara
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Laboratory of Biochemistry-Biotechnology and Advanced Diagnostics, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Gianluca Contrò
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Roberta Zuntini
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Marzia Pollazzon
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Rosario Pascarella
- Neuroradiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alberto Neri
- Ophthalmology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Carlo Fusco
- Child Neurology and Psychiatry Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer Ellen Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sadik Etka Bayramoglu
- Tertiary ROP Center, Health Science University Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul 34480, Turkey
| | | | - Emilia Amengual Cladera
- Genomics of Health, Institute of Health Research of the Balearic Islands, Palma, Illes Balears, Spain
| | - Elena Miravet
- Metabolic Pathologies and Pediatric Neurology Unit, Pediatric Service, Hospital Universitari Son Espases, Palma, Illes Balears, Spain
| | - Jorge Roldan-Busto
- Pediatric Radiology Unit, Radiology Service, Hospital Universitari Son Espases, Palma, Illes Balears, Spain
| | - María Angeles Ruiz
- Metabolic Pathologies and Pediatric Neurology Unit, Pediatric Service, Hospital Universitari Son Espases, Palma, Illes Balears, Spain
| | - Cristofol Vives Bauzá
- Neurobiology, Institute of Health Research of the Balearic Islands, Palma, Illes Balears, Spain
| | - Liat Ben-Sira
- Department of Radiology, Division of Pediatric Radiology, Dana Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel; Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Sabine Sigaudy
- AP-HM, Service de Génétique, Hôpital de la Timone, Marseille, France
| | - Anaïs Begemann
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Sheila Unger
- Medical Genetics Service, CHUV, University of Lausanne, Lausanne, Switzerland
| | - Serdal Güngör
- Inonu University, Faculty of Medicine, Turgut Ozal Research Center, Department of Pediatric Neurology, Malatya, Turkey
| | - Semra Hiz
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey; Department of Pediatric Neurology, School of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
| | - Ece Sonmezler
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Yoav Zehavi
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel; Department of Pediatrics B, Emek Medical Center, Afula, Israel
| | - Michael Jerdev
- Poriya Medical Center and the Azrieli Faculty of Medicine, Bar-Ilan University, Ramat-Gan, Israel
| | - Alessandra Balduini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PY, UK; Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0PY, UK
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada; Brain and Mind Research Institute, University of Ottawa, Ottawa ON K1H 8L1, Canada; Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON K1H 8L1, Canada
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland; University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Elisabeth Tournier-Lasserve
- AP-HP, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France; Université de Paris, INSERM UMR-1141 Neurodiderot, Paris, France
| | - Ronen Spiegel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel; Department of Pediatrics B, Emek Medical Center, Afula, Israel
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Edoardo Errichiello
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy.
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7
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Günay Ç, Aykol D, Özsoy Ö, Sönmezler E, Hanci YS, Kara B, Akkoyunlu Sünnetçi D, Cine N, Deniz A, Özer T, Ölçülü CB, Yilmaz Ö, Kanmaz S, Yilmaz S, Tekgül H, Yildiz N, Acar Arslan E, Cansu A, Olgaç Dündar N, Kusgoz F, Didinmez E, Gençpinar P, Aksu Uzunhan T, Ertürk B, Gezdirici A, Ayaz A, Ölmez A, Ayanoğlu M, Tosun A, Topçu Y, Kiliç B, Aydin K, Çağlar E, Ersoy Kosvali Ö, Okuyaz Ç, Besen Ş, Tekin Orgun L, Erol İ, Yüksel D, Sezer A, Atasoy E, Toprak Ü, Güngör S, Ozgor B, Karadağ M, Dilber C, Şahinoğlu B, Uyur Yalçin E, Eldes Hacifazlioglu N, Yaramiş A, Edem P, Gezici Tekin H, Yilmaz Ü, Ünalp A, Turay S, Biçer D, Gül Mert G, Dokurel Çetin İ, Kirik S, Öztürk G, Karal Y, Sanri A, Aksoy A, Polat M, Özgün N, Soydemir D, Sarikaya Uzan G, Ülker Üstebay D, Gök A, Yeşilmen MC, Yiş U, Karakülah G, Bursali A, Oktay Y, Hiz Kurul S. Shared Biological Pathways and Processes in Patients with Intellectual Disability: A Multicenter Study. Neuropediatrics 2023. [PMID: 36787800 DOI: 10.1055/a-2034-8528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
BACKGROUND Although the underlying genetic causes of intellectual disability (ID) continue to be rapidly identified, the biological pathways and processes that could be targets for a potential molecular therapy are not yet known. This study aimed to identify ID-related shared pathways and processes utilizing enrichment analyses. METHOD In this multicenter study, causative genes of patients with ID were used as input for Disease Ontology (DO), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. RESULTS Genetic test results of 720 patients from 27 centers were obtained. Patients with chromosomal deletion/duplication, non-ID genes, novel genes, and results with changes in more than one gene were excluded. A total of 558 patients with 341 different causative genes were included in the study. Pathway-based enrichment analysis of the ID-related genes via ClusterProfiler revealed 18 shared pathways, with lysine degradation and nicotine addiction being the most common. The most common of the 25 overrepresented DO terms was ID. The most frequently overrepresented GO biological process, cellular component, and molecular function terms were regulation of membrane potential, ion channel complex, and voltage-gated ion channel activity/voltage-gated channel activity, respectively. CONCLUSION Lysine degradation, nicotine addiction, and thyroid hormone signaling pathways are well-suited to be research areas for the discovery of new targeted therapies in ID patients.
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Affiliation(s)
- Çağatay Günay
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Duygu Aykol
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Özlem Özsoy
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Ece Sönmezler
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Yaren Sena Hanci
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Bülent Kara
- Department of Pediatric Neurology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | | | - Naci Cine
- Department of Medical Genetics, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Adnan Deniz
- Department of Pediatric Neurology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Tolgahan Özer
- Department of Medical Genetics, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Cemile Büşra Ölçülü
- Department of Child Neurology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Özlem Yilmaz
- Department of Child Neurology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Seda Kanmaz
- Department of Child Neurology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Sanem Yilmaz
- Department of Child Neurology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Hasan Tekgül
- Department of Child Neurology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Nihal Yildiz
- Department of Pediatric Neurology, Karadeniz Technical University, Faculty of Medicine, Farabi Hospital, Trabzon, Turkey
| | - Elif Acar Arslan
- Department of Pediatric Neurology, Karadeniz Technical University, Faculty of Medicine, Farabi Hospital, Trabzon, Turkey
| | - Ali Cansu
- Department of Pediatric Neurology, Karadeniz Technical University, Faculty of Medicine, Farabi Hospital, Trabzon, Turkey
| | - Nihal Olgaç Dündar
- Department of Pediatric Neurology, İzmir Katip Çelebi University, Izmir, Turkey
| | - Fatma Kusgoz
- Department of Pediatric Neurology, Tepecik Research and Training Hospital, Izmir, Turkey
| | - Elif Didinmez
- Department of Pediatric Neurology, Tepecik Research and Training Hospital, Izmir, Turkey
| | - Pınar Gençpinar
- Department of Pediatric Neurology, İzmir Katip Çelebi University, Izmir, Turkey
| | - Tuğçe Aksu Uzunhan
- Department of Pediatric Neurology, Prof Dr Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Biray Ertürk
- Department of Pediatric Neurology, Prof Dr Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Başakşehir Çam and Sakura City Hospital, Istanbul, Turkey
| | - Akif Ayaz
- Department of Medical Genetics, Istanbul Medipol University School of Medicine, Istanbul, Turkey
| | - Akgün Ölmez
- Denizli Pediatric Neurology Clinic, Denizli, Turkey
| | - Müge Ayanoğlu
- Department of Child Neurology, Adnan Menderes University School of Medicine, Aydın, Turkey
| | - Ayşe Tosun
- Department of Child Neurology, Adnan Menderes University School of Medicine, Aydın, Turkey
| | - Yasemin Topçu
- Department of Pediatric Neurology, Istanbul Medipol University Faculty of Medicine, Istanbul, Turkey
| | - Betül Kiliç
- Department of Pediatric Neurology, Istanbul Medipol University Faculty of Medicine, Istanbul, Turkey
| | - Kürşad Aydin
- Department of Pediatric Neurology, Istanbul Medipol University Faculty of Medicine, Istanbul, Turkey
| | - Ezgi Çağlar
- Departments of Pediatric Neurology, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Özlem Ersoy Kosvali
- Departments of Pediatric Neurology, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Çetin Okuyaz
- Departments of Pediatric Neurology, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Şeyda Besen
- Division of Pediatric Neurology, Başkent University Adana Medical and Research Center Faculty of Medicine, Adana, Turkey
| | - Leman Tekin Orgun
- Division of Pediatric Neurology, Başkent University Adana Medical and Research Center Faculty of Medicine, Adana, Turkey
| | - İlknur Erol
- Division of Pediatric Neurology, Başkent University Adana Medical and Research Center Faculty of Medicine, Adana, Turkey
| | - Deniz Yüksel
- Department of Pediatric Neurology, University of Health Sciences Faculty of Medicine, Dr Sami Ulus Maternity Child Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Abdullah Sezer
- Department of Genetics, University of Health Sciences Faculty of Medicine, Dr Sami Ulus Maternity Child Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Ergin Atasoy
- Department of Pediatric Neurology, University of Health Sciences Faculty of Medicine, Dr Sami Ulus Maternity Child Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Ülkühan Toprak
- Department of Pediatric Neurology, University of Health Sciences Faculty of Medicine, Dr Sami Ulus Maternity Child Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Serdal Güngör
- Department of Paediatric Neurology, Inonu University Faculty of Medicine, Turgut Ozal Research Center, Malatya, Turkey
| | - Bilge Ozgor
- Department of Paediatric Neurology, Inonu University Faculty of Medicine, Turgut Ozal Research Center, Malatya, Turkey
| | - Meral Karadağ
- Department of Paediatric Neurology, Inonu University Faculty of Medicine, Turgut Ozal Research Center, Malatya, Turkey
| | - Cengiz Dilber
- Department of Pediatric Neurology, Kahramanmaras Sutcu Imam University Faculty of Medicine, Kahramanmaraş, Turkey
| | - Bahtiyar Şahinoğlu
- Deparment of Genetics, Dr Ersin Arslan Traning and Research Hospital, Gaziantep, Turkey
| | - Emek Uyur Yalçin
- Departments of Pediatrics and Pediatric Neurology, University of Health Sciences, Zeynep Kamil Maternity and Children's Diseases Hospital, Istanbul, Turkey
| | - Nilüfer Eldes Hacifazlioglu
- Departments of Pediatrics and Pediatric Neurology, University of Health Sciences, Zeynep Kamil Maternity and Children's Diseases Hospital, Istanbul, Turkey
| | - Ahmet Yaramiş
- Diyarbakır Pediatric Neurology Clinic, Diyarbakır, Turkey
| | - Pınar Edem
- Department of Pediatric Neurology, Bakırcay University, Cigli District Training Hospital, Izmir, Turkey
| | - Hande Gezici Tekin
- Department of Pediatric Neurology, Bakırcay University, Cigli District Training Hospital, Izmir, Turkey
| | - Ünsal Yilmaz
- Department of Pediatric Neurology, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
| | - Aycan Ünalp
- Department of Pediatric Neurology, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
| | - Sevim Turay
- Department of Pediatric Neurology, Duzce University Faculty of Medicine, Düzce, Turkey
| | - Didem Biçer
- Department of Pediatric Neurology, Çukurova University Faculty of Medicine, Adana, Turkey
| | - Gülen Gül Mert
- Department of Pediatric Neurology, Çukurova University Faculty of Medicine, Adana, Turkey
| | - İpek Dokurel Çetin
- Department of Pediatric Neurology, Balıkesir Atatürk Training and Research Hospital, Balıkesir, Turkey
| | - Serkan Kirik
- Fırat University School of Medicine, Pediatric Neurology, Elazığ, Turkey
| | - Gülten Öztürk
- Department of Pediatric Neurology, Marmara University School of Medicine, Istanbul, Turkey
| | - Yasemin Karal
- Department of Pediatric Neurology, Trakya University, Faculty of Medicine, Edirne, Turkey
| | - Aslıhan Sanri
- Department of Pediatric Genetics, University of Health Sciences, Samsun Training and Research Hospital, Samsun, Turkey
| | - Ayşe Aksoy
- Department of Pediatric Neurology, Ondokuz Mayıs University, Samsun, Turkey
| | - Muzaffer Polat
- Department of Pediatric Neurology, Celal Bayar University School of Medicine, Manisa, Turkey
| | - Nezir Özgün
- Department of Pediatric Neurology, Mardin Artuklu University, Faculty of Health Sciences, Mardin, Turkey
| | - Didem Soydemir
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Gamze Sarikaya Uzan
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Döndü Ülker Üstebay
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Ayşen Gök
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Mehmet Can Yeşilmen
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Uluç Yiş
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Ahmet Bursali
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Semra Hiz Kurul
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
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8
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Özbek M, Toy HI, Oktay Y, Karakülah G, Suner A, Pavlopoulou A. An in silico approach to the identification of diagnostic and prognostic markers in low-grade gliomas. PeerJ 2023; 11:e15096. [PMID: 36945359 PMCID: PMC10024901 DOI: 10.7717/peerj.15096] [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: 10/04/2022] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
Low-grade gliomas (LGG) are central nervous system Grade I tumors, and as they progress they are becoming one of the deadliest brain tumors. There is still great need for timely and accurate diagnosis and prognosis of LGG. Herein, we aimed to identify diagnostic and prognostic biomarkers associated with LGG, by employing diverse computational approaches. For this purpose, differential gene expression analysis on high-throughput transcriptomics data of LGG versus corresponding healthy brain tissue, derived from TCGA and GTEx, respectively, was performed. Weighted gene co-expression network analysis of the detected differentially expressed genes was carried out in order to identify modules of co-expressed genes significantly correlated with LGG clinical traits. The genes comprising these modules were further used to construct gene co-expression and protein-protein interaction networks. Based on the network analyses, we derived a consensus of eighteen hub genes, namely, CD74, CD86, CDC25A, CYBB, HLA-DMA, ITGB2, KIF11, KIFC1, LAPTM5, LMNB1, MKI67, NCKAP1L, NUSAP1, SLC7A7, TBXAS1, TOP2A, TYROBP, and WDFY4. All detected hub genes were up-regulated in LGG, and were also associated with unfavorable prognosis in LGG patients. The findings of this study could be applicable in the clinical setting for diagnosing and monitoring LGG.
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Affiliation(s)
- Melih Özbek
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Halil Ibrahim Toy
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Faculty of Medicine, Department of Medical Biology, Dokuz Eylül University, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Aslı Suner
- Faculty of Medicine, Department of Biostatistics and Medical Informatics, Izmir, Turkey
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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9
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Tetik M, Direk N, Uzgan BÖ, Aykaç C, Ekinci B, Yaraş T, Kuruoğlu A, Özel F, Ermiş Ç, Alkın T, Oktay Y. Associations Between Blood Levels of NLRP3 Inflammasome Components and Obsessive Compulsive Disorder. Noro Psikiyatr Ars 2023; 60:28-36. [PMID: 36911567 PMCID: PMC9999221 DOI: 10.29399/npa.28127] [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: 02/06/2022] [Accepted: 04/14/2022] [Indexed: 11/07/2022] Open
Abstract
Introduction Even though the effect of inflammation on pathogenesis of obsessive compulsive disorder (OCD) is known, information regarding the underlying mechanisms are yet to be revealed. The NLRP3 inflammasome complex is an important component of the innate immune system that initiates and mediates inflammatory response to a variety of stimuli. This study aims to inquire into a possible association between NLRP3 inflammasome complex and OCD. Methods This case-control study included 103 participants (51 cases with OCD and 52 healthy controls). All participants were evaluated with the Yale Brown Obsessive Compulsive Scale, Hamilton Depression Scale, and Hewitt Multidimensional Perfectionism Scale. RNA and proteins were extracted from peripheral blood mononuclear cells. Expression of NLRP3 inflammasome components were determined using quantitative real-time polymerase chain reaction (PCR) and Western blotting. Levels of Serum IL-1beta and IL-18 cytokine were determined by ELISA. Results NEK7 and CASP1 mRNA levels were significantly higher in OCD patients, compared to controls. Pro-caspase-1 protein levels were elevated, as well. Regression analysis showed that NEK7 mRNA and pro-caspase-1 protein levels can differentiate OCD and healthy control groups. Conclusion Our results provide insight into the molecular alterations that could explain the inflammation-OCD association.
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Affiliation(s)
- Melike Tetik
- Department of Neuroscience, Health Sciences Institute, Dokuz Eylül University, İzmir, Turkey
| | - Neşe Direk
- Department of Psychiatry, İstanbul University Faculty of Medicine, İstanbul, Turkey
| | - Betül Önder Uzgan
- Department of Biology, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Cansu Aykaç
- Department of Psychiatry, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Burcu Ekinci
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey.,İzmir Biomedicine and Genome Center, İzmir, Turkey
| | - Tutku Yaraş
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey.,İzmir Biomedicine and Genome Center, İzmir, Turkey
| | - Aykut Kuruoğlu
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey.,İzmir Biomedicine and Genome Center, İzmir, Turkey
| | - Fatih Özel
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Çağatay Ermiş
- Department of Child and Adolescent Psychiatry, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Tunç Alkın
- Department of Neuroscience, Health Sciences Institute, Dokuz Eylül University, İzmir, Turkey.,Department of Psychiatry, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Yavuz Oktay
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey.,İzmir Biomedicine and Genome Center, İzmir, Turkey.,Department of Medical Biology, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
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10
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Hiz Kurul S, Oktay Y, Töpf A, Szabó NZ, Güngör S, Yaramis A, Sonmezler E, Matalonga L, Yis U, Schon K, Paramonov I, Kalafatcilar İP, Gao F, Rieger A, Arslan N, Yilmaz E, Ekinci B, Edem PP, Aslan M, Özgör B, Lochmüller A, Nair A, O'Heir E, Lovgren AK, Maroofian R, Houlden H, Polavarapu K, Roos A, Müller JS, Hathazi D, Chinnery PF, Laurie S, Beltran S, Lochmüller H, Horvath R. High diagnostic rate of trio exome sequencing in consanguineous families with neurogenetic diseases. Brain 2022; 145:1507-1518. [PMID: 34791078 PMCID: PMC9128813 DOI: 10.1093/brain/awab395] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 02/02/2023] Open
Abstract
Consanguineous marriages have a prevalence rate of 24% in Turkey. These carry an increased risk of autosomal recessive genetic conditions, leading to severe disability or premature death, with a significant health and economic burden. A definitive molecular diagnosis could not be achieved in these children previously, as infrastructures and access to sophisticated diagnostic options were limited. We studied the cause of neurogenetic disease in 246 children from 190 consanguineous families recruited in three Turkish hospitals between 2016 and 2020. All patients underwent deep phenotyping and trio whole exome sequencing, and data were integrated in advanced international bioinformatics platforms. We detected causative variants in 119 known disease genes in 72% of families. Due to overlapping phenotypes 52% of the confirmed genetic diagnoses would have been missed on targeted diagnostic gene panels. Likely pathogenic variants in 27 novel genes in 14% of the families increased the diagnostic yield to 86%. Eighty-two per cent of causative variants (141/172) were homozygous, 11 of which were detected in genes previously only associated with autosomal dominant inheritance. Eight families carried two pathogenic variants in different disease genes. De novo (9.3%), X-linked recessive (5.2%) and compound heterozygous (3.5%) variants were less frequent compared to non-consanguineous populations. This cohort provided a unique opportunity to better understand the genetic characteristics of neurogenetic diseases in a consanguineous population. Contrary to what may be expected, causative variants were often not on the longest run of homozygosity and the diagnostic yield was lower in families with the highest degree of consanguinity, due to the high number of homozygous variants in these patients. Pathway analysis highlighted that protein synthesis/degradation defects and metabolic diseases are the most common pathways underlying paediatric neurogenetic disease. In our cohort 164 families (86%) received a diagnosis, enabling prevention of transmission and targeted treatments in 24 patients (10%). We generated an important body of genomic data with lasting impacts on the health and wellbeing of consanguineous families and economic benefit for the healthcare system in Turkey and elsewhere. We demonstrate that an untargeted next generation sequencing approach is far superior to a more targeted gene panel approach, and can be performed without specialized bioinformatics knowledge by clinicians using established pipelines in populations with high rates of consanguinity.
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Affiliation(s)
- Semra Hiz Kurul
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
- Department of Paediatric Neurology, School of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
- Department of Medical Biology, School of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Institute of Translational and Clinical Research, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Nóra Zs Szabó
- Epilepsy-Neurology Polyclinic of Buda Children's Hospital, New Saint John's Hospital and Northern -Buda United Hospitals, Budapest 1023, Hungary
| | - Serdal Güngör
- Department of Paediatric Neurology, Faculty of Medicine, Turgut Ozal Research Center, Inonu University, Malatya 44210, Turkey
| | - Ahmet Yaramis
- Pediatric Neurology Clinic, Diyarbakir 21070, Turkey
| | - Ece Sonmezler
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Uluc Yis
- Department of Paediatric Neurology, School of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
| | - Katherine Schon
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PY, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Ida Paramonov
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - İpek Polat Kalafatcilar
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
- Department of Paediatric Neurology, School of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
| | - Fei Gao
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PY, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Aliz Rieger
- Rehabilitation Centre for the Physically Handicapped, Budapest 1528, Hungary
| | - Nur Arslan
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Department of Paediatric Nutrition and Metabolism, School of Medicine, Dokuz Eylul University, Izmir 1528, Turkey
| | - Elmasnur Yilmaz
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Burcu Ekinci
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Pinar Pulat Edem
- Department of Paediatric Neurology, School of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
| | - Mahmut Aslan
- Department of Paediatric Neurology, Faculty of Medicine, Turgut Ozal Research Center, Inonu University, Malatya 44210, Turkey
| | - Bilge Özgör
- Department of Paediatric Neurology, Faculty of Medicine, Turgut Ozal Research Center, Inonu University, Malatya 44210, Turkey
| | - Angela Lochmüller
- GKT School of Medical Education, King's College London, London SE1 1UL, UK
| | - Ashwati Nair
- GKT School of Medical Education, King's College London, London SE1 1UL, UK
| | - Emily O'Heir
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA SE1 1UL, USA
| | - Alysia K Lovgren
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA SE1 1UL, USA
| | | | - Reza Maroofian
- Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, University College London, London WC1N 3BG, UK
| | - Henry Houlden
- Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, University College London, London WC1N 3BG, UK
| | - Kiran Polavarapu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa ON K1H 8L1, Canada
| | - Andreas Roos
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa ON K1H 8L1, Canada
- Leibniz-Institut für Analytische Wissenschaften, ISAS e.V., Dortmund 44227, Germany
- Department of Pediatric Neurology, University of Duisburg-Essen, Essen 45141, Germany
| | - Juliane S Müller
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PY, UK
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0PY, UK
| | - Denisa Hathazi
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PY, UK
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0PY, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PY, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Steven Laurie
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Hanns Lochmüller
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa ON K1H 8L1, Canada
- Department of Neuropediatrics and Muscle Disorders, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg 79106, Germany
- Division of Neurology, Department of Medicine, The Ottawa Hospital; and Brain and Mind Research Institute, University of Ottawa, Ottawa ON K1Y 4E9, Canada
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PY, UK
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0PY, UK
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11
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Arlt A, Kohlschmidt N, Hentschel A, Bartels E, Groß C, Töpf A, Edem P, Szabo N, Sickmann A, Meyer N, Schara-Schmidt U, Lau J, Lochmüller H, Horvath R, Oktay Y, Roos A, Hiz S. Novel insights into PORCN mutations, associated phenotypes and pathophysiological aspects. Orphanet J Rare Dis 2022; 17:29. [PMID: 35101074 PMCID: PMC8802438 DOI: 10.1186/s13023-021-02068-w] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 09/30/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Goltz syndrome (GS) is a X-linked disorder defined by defects of mesodermal- and ectodermal-derived structures and caused by PORCN mutations. Features include striated skin-pigmentation, ocular and skeletal malformations and supernumerary or hypoplastic nipples. Generally, GS is associated with in utero lethality in males and most of the reported male patients show mosaicism (only three non-mosaic surviving males have been described so far). Also, precise descriptions of neurological deficits in GS are rare and less severe phenotypes might not only be caused by mosaicism but also by less pathogenic mutations suggesting the need of a molecular genetics and functional work-up of these rare variants. RESULTS We report two cases: one girl suffering from typical skin and skeletal abnormalities, developmental delay, microcephaly, thin corpus callosum, periventricular gliosis and drug-resistant epilepsy caused by a PORCN nonsense-mutation (c.283C > T, p.Arg95Ter). Presence of these combined neurological features indicates that CNS-vulnerability might be a guiding symptom in the diagnosis of GS patients. The other patient is a boy with a supernumerary nipple and skeletal anomalies but also, developmental delay, microcephaly, cerebral atrophy with delayed myelination and drug-resistant epilepsy as predominant features. Skin abnormalities were not observed. Genotyping revealed a novel PORCN missense-mutation (c.847G > C, p.Asp283His) absent in the Genome Aggregation Database (gnomAD) but also identified in his asymptomatic mother. Given that non-random X-chromosome inactivation was excluded in the mother, fibroblasts of the index had been analyzed for PORCN protein-abundance and -distribution, vulnerability against additional ER-stress burden as well as for protein secretion revealing changes. CONCLUSIONS Our combined findings may suggest incomplete penetrance for the p.Asp283His variant and provide novel insights into the molecular etiology of GS by adding impaired ER-function and altered protein secretion to the list of pathophysiological processes resulting in the clinical manifestation of GS.
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Affiliation(s)
- Annabelle Arlt
- Institute of Clinical Genetics and Tumor Genetics, Bonn, Germany
| | | | | | - Enrika Bartels
- Institute of Clinical Genetics and Tumor Genetics, Bonn, Germany
| | - Claudia Groß
- Institute of Clinical Genetics and Tumor Genetics, Bonn, Germany
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Pınar Edem
- Department of Medical Biology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Nora Szabo
- Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Albert Sickmann
- Leibniz Institute for Analytical Sciences (ISAS), Dortmund, Germany
| | - Nancy Meyer
- Pediatric Neurology, Faculty of Medicine, University of Duisburg-Essen, University Hospital, Essen, Germany
| | - Ulrike Schara-Schmidt
- Pediatric Neurology, Faculty of Medicine, University of Duisburg-Essen, University Hospital, Essen, Germany
| | - Jarred Lau
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Yavuz Oktay
- Department of Medical Biology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Andreas Roos
- Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.
| | - Semra Hiz
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
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12
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Richard EM, Bakhtiari S, Marsh APL, Kaiyrzhanov R, Wagner M, Shetty S, Pagnozzi A, Nordlie SM, Guida BS, Cornejo P, Magee H, Liu J, Norton BY, Webster RI, Worgan L, Hakonarson H, Li J, Guo Y, Jain M, Blesson A, Rodan LH, Abbott MA, Comi A, Cohen JS, Alhaddad B, Meitinger T, Lenz D, Ziegler A, Kotzaeridou U, Brunet T, Chassevent A, Smith-Hicks C, Ekstein J, Weiden T, Hahn A, Zharkinbekova N, Turnpenny P, Tucci A, Yelton M, Horvath R, Gungor S, Hiz S, Oktay Y, Lochmuller H, Zollino M, Morleo M, Marangi G, Nigro V, Torella A, Pinelli M, Amenta S, Husain RA, Grossmann B, Rapp M, Steen C, Marquardt I, Grimmel M, Grasshoff U, Korenke GC, Owczarek-Lipska M, Neidhardt J, Radio FC, Mancini C, Claps Sepulveda DJ, McWalter K, Begtrup A, Crunk A, Guillen Sacoto MJ, Person R, Schnur RE, Mancardi MM, Kreuder F, Striano P, Zara F, Chung WK, Marks WA, van Eyk CL, Webber DL, Corbett MA, Harper K, Berry JG, MacLennan AH, Gecz J, Tartaglia M, Salpietro V, Christodoulou J, Kaslin J, Padilla-Lopez S, Bilguvar K, Munchau A, Ahmed ZM, Hufnagel RB, Fahey MC, Maroofian R, Houlden H, Sticht H, Mane SM, Rad A, Vona B, Jin SC, Haack TB, Makowski C, Hirsch Y, Riazuddin S, Kruer MC. Bi-allelic variants in SPATA5L1 lead to intellectual disability, spastic-dystonic cerebral palsy, epilepsy, and hearing loss. Am J Hum Genet 2021; 108:2006-2016. [PMID: 34626583 DOI: 10.1016/j.ajhg.2021.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022] Open
Abstract
Spermatogenesis-associated 5 like 1 (SPATA5L1) represents an orphan gene encoding a protein of unknown function. We report 28 bi-allelic variants in SPATA5L1 associated with sensorineural hearing loss in 47 individuals from 28 (26 unrelated) families. In addition, 25/47 affected individuals (53%) presented with microcephaly, developmental delay/intellectual disability, cerebral palsy, and/or epilepsy. Modeling indicated damaging effect of variants on the protein, largely via destabilizing effects on protein domains. Brain imaging revealed diminished cerebral volume, thin corpus callosum, and periventricular leukomalacia, and quantitative volumetry demonstrated significantly diminished white matter volumes in several individuals. Immunofluorescent imaging in rat hippocampal neurons revealed localization of Spata5l1 in neuronal and glial cell nuclei and more prominent expression in neurons. In the rodent inner ear, Spata5l1 is expressed in the neurosensory hair cells and inner ear supporting cells. Transcriptomic analysis performed with fibroblasts from affected individuals was able to distinguish affected from controls by principal components. Analysis of differentially expressed genes and networks suggested a role for SPATA5L1 in cell surface adhesion receptor function, intracellular focal adhesions, and DNA replication and mitosis. Collectively, our results indicate that bi-allelic SPATA5L1 variants lead to a human disease characterized by sensorineural hearing loss (SNHL) with or without a nonprogressive mixed neurodevelopmental phenotype.
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Affiliation(s)
- Elodie M Richard
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Ashley P L Marsh
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, Queen Square, WC1N 3BG London, UK
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Sheetal Shetty
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Alex Pagnozzi
- CSIRO Health and Biosecurity, The Australian e-Health Research Centre, Brisbane, QLD 4029, Australia
| | - Sandra M Nordlie
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Brandon S Guida
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Patricia Cornejo
- Pediatric Neuroradiology Division, Pediatric Radiology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; University of Arizona College of Medicine, Phoenix, AZ 85004, USA; Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Helen Magee
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - James Liu
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Bethany Y Norton
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Richard I Webster
- Neurology Department, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Lisa Worgan
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jiankang Li
- Department of Computer Science, City University of Hong Kong, Kowloon 999077, Hong Kong
| | - Yiran Guo
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Mahim Jain
- Department of Bone and Osteogenesis Imperfecta, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Alyssa Blesson
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, MD 21211, USA
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Mary-Alice Abbott
- University of Massachusetts Medical School - Baystate, Baystate Children's Hospital, Springfield, MA 01107, USA
| | - Anne Comi
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Bader Alhaddad
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Dominic Lenz
- Centre of Child and Adolescent Medicine, Department of Pediatric Neurology and Metabolic Medicine, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Andreas Ziegler
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Urania Kotzaeridou
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Anna Chassevent
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Constance Smith-Hicks
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Joseph Ekstein
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, New York, NY 11211, USA
| | - Tzvi Weiden
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem 9054020, Israel
| | - Andreas Hahn
- Department of Child Neurology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Nazira Zharkinbekova
- Department of Neurology, South Kazakhstan Medical Academy, Shymkent 160001, Kazakhstan
| | - Peter Turnpenny
- Clinical Genetics, Royal Devon & Exeter NHS Foundation Trust, EX1 2ED Exeter, UK
| | - Arianna Tucci
- Clinical Pharmacology, William Harvey Research Institute, Charterhouse Square, School of Medicine and Dentistry Queen Mary University of London, London EC1M 6BQ, UK
| | - Melissa Yelton
- Penn State Health Children's Hospital, Hershey, PA 17033, USA
| | - Rita Horvath
- Department of Clinical Neurosciences, John Van Geest Cambridge Centre for Brain Repair, University of Cambridge School of Clinical Medicine, CB2 0PY Cambridge, UK
| | - Serdal Gungor
- Inonu University, Faculty of Medicine, Turgut Ozal Research Center, Department of Paediatric Neurology, 44280 Malatya, Turkey
| | - Semra Hiz
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, 35340 Izmir, Turkey; Department of Pediatric Neurology, Faculty of Medicine, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, 35340 Izmir, Turkey; Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University, 35220 Izmir, Turkey
| | - Hanns Lochmuller
- Children's Hospital of Eastern Ontario Research Institute; Division of Neurology, Department of Medicine, The Ottawa Hospital, and Brain and Mind Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Marcella Zollino
- Università Cattolica Sacro Cuore, Facoltà di Medicina e Chirurgia, Dipartimento Scienze della Vita e Sanità Pubblica, 00168 Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Sezione di Medicina Genomica, 00168 Roma, Italy
| | - Manuela Morleo
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy
| | - Giuseppe Marangi
- Università Cattolica Sacro Cuore, Facoltà di Medicina e Chirurgia, Dipartimento Scienze della Vita e Sanità Pubblica, 00168 Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Sezione di Medicina Genomica, 00168 Roma, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy
| | - Simona Amenta
- Università Cattolica Sacro Cuore, Facoltà di Medicina e Chirurgia, Dipartimento Scienze della Vita e Sanità Pubblica, 00168 Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Sezione di Medicina Genomica, 00168 Roma, Italy
| | - Ralf A Husain
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
| | - Benita Grossmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tuebingen, Germany
| | - Marion Rapp
- Institute of Systems Motor Science, University of Lübeck, 23538 Lübeck, Germany
| | - Claudia Steen
- Department of Paediatric and Adolescent Medicine, St Joseph Hospital, 12101 Berlin, Germany
| | - Iris Marquardt
- University Children's Hospital Oldenburg, Department of Neuropaediatric and Metabolic Diseases, 26133 Oldenburg, Germany
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tuebingen, Germany
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tuebingen, Germany
| | - G Christoph Korenke
- University Children's Hospital Oldenburg, Department of Neuropaediatric and Metabolic Diseases, 26133 Oldenburg, Germany
| | - Marta Owczarek-Lipska
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, 26129 Oldenburg, Germany; Junior Research Group, Genetics of Childhood Brain Malformations, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, 26129 Oldenburg, Germany
| | - John Neidhardt
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, 26129 Oldenburg, Germany; Research Center Neurosensory Science, University of Oldenburg, 26129 Oldenburg, Germany
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Cecilia Mancini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | | | - Amber Begtrup
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Amy Crunk
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | | | | | | | - Maria Margherita Mancardi
- Unit of Child Neuropsichiatry, Department of Clinical and Surgical Neurosciences and Rehabilitation, IRCCS Giannina Gaslini, Genoa 16147, Italy
| | - Florian Kreuder
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3168, Australia
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRRCS Istituto Giannina Gaslini, 16148 Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16142 Genoa, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16142 Genoa, Italy; Unit of Medical Genetics, IRRCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Warren A Marks
- Department of Neurology, Cook Children's Medical Center, Fort Worth, TX 76104, USA; Department of Pediatrics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Clare L van Eyk
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Dani L Webber
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Mark A Corbett
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Kelly Harper
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Jesia G Berry
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Alastair H MacLennan
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Jozef Gecz
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Vincenzo Salpietro
- Pediatric Neurology and Muscular Diseases Unit, IRRCS Istituto Giannina Gaslini, 16148 Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16142 Genoa, Italy
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia; Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Jan Kaslin
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3168, Australia
| | - Sergio Padilla-Lopez
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Alexander Munchau
- Institute of Systems Motor Science, University of Lübeck, 23538 Lübeck, Germany
| | - Zubair M Ahmed
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael C Fahey
- Department of Paediatrics, Monash University, Melbourne, VIC 3168, Australia
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, Queen Square, WC1N 3BG London, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, Queen Square, WC1N 3BG London, UK
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Shrikant M Mane
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Aboulfazl Rad
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Barbara Vona
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tuebingen, Germany; Centre for Rare Diseases, University of Tübingen, 72074 Tuebingen, Germany
| | - Christine Makowski
- Department of Paediatrics, Adolescent Medicine and Neonatology, Munich Clinic, Schwabing Hospital and Technical University of Munich, School of Medicine, 80804 Munich, Germany
| | - Yoel Hirsch
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, New York, NY 11211, USA
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA.
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA.
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13
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Okay K, Varış PÜ, Miral S, Ekinci B, Yaraş T, Karakülah G, Oktay Y. Alternative splicing and gene co-expression network-based analysis of dizygotic twins with autism-spectrum disorder and their parents. Genomics 2021; 113:2561-2571. [PMID: 34087420 DOI: 10.1016/j.ygeno.2021.05.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/21/2020] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/25/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with high heritability, however, understanding the complexity of the underlying genetic basis has proven to be a challenging task. We hypothesized that dissecting the aberrations in alternative splicing (AS) and their effects on expression networks might provide insight. Therefore, we performed AS and co-expression analyses of total RNA isolated from Peripheral Blood Mononuclear Cells (PBMCs) of two pairs of dizygotic (DZ) twins with non-syndromic autism and their parents. We identified 183 differential AS events in 146 genes, seven of them being Simons Foundation Autism Research Initiative (SFARI) Category 1-3 genes, three of which had previously been reported to be alternatively spliced in ASD post-mortem brains. Gene co-expression analysis identified 7 modules with 513 genes, 5 of which were SFARI Category 1 or Category 2 genes. Among differentially AS genes within the modules, ZNF322 and NR4A1 could be potentially interesting targets for further investigations.
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Affiliation(s)
- Kaan Okay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey
| | - Pelin Ünal Varış
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, Dokuz Eylül University, Balçova, Izmir, Turkey; Barış Psychiatric Hospital, Nicosia, Cyprus
| | - Süha Miral
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, Dokuz Eylül University, Balçova, Izmir, Turkey
| | - Burcu Ekinci
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey
| | - Tutku Yaraş
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey.
| | - Yavuz Oktay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir, Turkey; Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, Balçova, Izmir, Turkey.
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14
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Oktay Y, Güngör S, Zeltner L, Wiethoff S, Schöls L, Sonmezler E, Yilmaz E, Munro B, Bender B, Kernstock C, Kaemereit S, Liepelt I, Töpf A, Yis U, Laurie S, Yaramis A, Zuchner S, Hiz S, Lochmüller H, Schüle R, Horvath R. Confirmation of TACO1 as a Leigh Syndrome Disease Gene in Two Additional Families. J Neuromuscul Dis 2021; 7:301-308. [PMID: 32444556 PMCID: PMC7458500 DOI: 10.3233/jnd-200510] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Background: In 2009, we identified TACO1 as a novel mitochondrial disease gene in a single family, however no second family has been described to confirm the role of TACO1 in mitochondrial disease. Objective: In this report, we describe two independent consanguineous families carrying pathogenic variants in TACO1, confirming the phenotype. Methods: Detailed clinical investigations and whole exome sequencing with haplotype analysis have been performed in several members of the two reported families. Results: Clinical phenotype of the patients confirms the originally reported phenotype of a childhood-onset progressive cerebellar and pyramidal syndrome with optic atrophy and learning difficulties. Brain MRI showed periventricular white matter lesions with multiple cystic defects, suggesting leukoencephalopathy in both patients. One patient carried the previously described homozygous TACO1 variant (p.His158ProfsTer8) and haplotype analysis suggested that this variant is a rare founder mutation. The second patient from another family carried a homozygous novel frame shift variant (p.Cys85PhefsTer15). Conclusions: The identification of two Turkish families with similar characteristic clinical presentation and an additional homozygous nonsense mutation confirms that TACO1 is a human mitochondrial disease gene. Although most patients with this clinical presentation undergo next generation sequencing analysis, screening for selected founder mutations in the Turkish population based on the precise clinical presentation may reduce time and cost of finding the genetic diagnosis even in the era of massively parallel sequencing.
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Affiliation(s)
- Yavuz Oktay
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Serdal Güngör
- Inonu University, Faculty of Medicine, Turgut Ozal Research Center, Department of Paediatric Neurology, Malatya, Turkey
| | - Lena Zeltner
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany
| | - Sarah Wiethoff
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany
| | - Ludger Schöls
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Ece Sonmezler
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Elmasnur Yilmaz
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Benjamin Munro
- Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Benjamin Bender
- Diagnostic and Interventional Neuroradiology, Radiologic Clinics, University of Tübingen, Tübingen, Germany
| | - Christoph Kernstock
- Centre for Ophthalmology, University Eye Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Sofie Kaemereit
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany
| | - Inga Liepelt
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Ana Töpf
- John Waltom Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Uluc Yis
- Dokuz Eylul University, School of Medicine, Department of Paediatric Neurology, Izmir, Turkey
| | - Steven Laurie
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ahmet Yaramis
- Pediatric Neurology Clinic, Private Office, Diyarbakir, Turkey
| | - Stephan Zuchner
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Semra Hiz
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey.,Dokuz Eylul University, School of Medicine, Department of Paediatric Neurology, Izmir, Turkey
| | - Hanns Lochmüller
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Neuropediatrics and Muscle Disorders, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany.,Children's Hospital of Eastern Ontario Research Institute; Division of Neurology, Department of Medicine, The Ottawa Hospital; and Brain and Mind Research Institute, University of Ottawa, Canada
| | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
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15
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Gungor S, Oktay Y, Hiz S, Aranguren-Ibáñez Á, Kalafatcilar I, Yaramis A, Karaca E, Yis U, Sonmezler E, Ekinci B, Aslan M, Yilmaz E, Özgör B, Balaraju S, Szabo N, Laurie S, Beltran S, MacArthur DG, Hathazi D, Töpf A, Roos A, Lochmuller H, Vernos I, Horvath R. Autosomal recessive variants in TUBGCP2 alter the γ-tubulin ring complex leading to neurodevelopmental disease. iScience 2021; 24:101948. [PMID: 33458610 PMCID: PMC7797523 DOI: 10.1016/j.isci.2020.101948] [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: 05/15/2020] [Revised: 09/20/2020] [Accepted: 12/11/2020] [Indexed: 12/23/2022] Open
Abstract
Microtubules help building the cytoskeleton of neurons and other cells. Several components of the gamma-tubulin (γ-tubulin) complex have been previously reported in human neurodevelopmental diseases. We describe two siblings from a consanguineous Turkish family with dysmorphic features, developmental delay, brain malformation, and epilepsy carrying a homozygous mutation (p.Glu311Lys) in TUBGCP2 encoding the γ-tubulin complex 2 (GCP2) protein. This variant is predicted to disrupt the electrostatic interaction of GCP2 with GCP3. In primary fibroblasts carrying the variant, we observed a faint delocalization of γ-tubulin during the cell cycle but normal GCP2 protein levels. Through mass spectrometry, we observed dysregulation of multiple proteins involved in the assembly and organization of the cytoskeleton and the extracellular matrix, controlling cellular adhesion and of proteins crucial for neuronal homeostasis including axon guidance. In summary, our functional and proteomic studies link TUBGCP2 and the γ-tubulin complex to the development of the central nervous system in humans.
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Affiliation(s)
- Serdal Gungor
- Inonu University, Faculty of Medicine, Turgut Ozal Research Center, Department of Paediatric Neurology, Malatya, Turkey
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University and Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Semra Hiz
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Dokuz Eylul University, Faculty of Medicine, Department of Pediatric Neurology Izmir, Turkey
| | - Álvaro Aranguren-Ibáñez
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Ipek Kalafatcilar
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Dokuz Eylul University, Faculty of Medicine, Department of Pediatric Neurology Izmir, Turkey
| | - Ahmet Yaramis
- Pediatric Neurology Clinic, Private Office, Diyarbakir, Turkey
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University and Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Uluc Yis
- Dokuz Eylul University, Faculty of Medicine, Department of Pediatric Neurology Izmir, Turkey
| | - Ece Sonmezler
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Burcu Ekinci
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Mahmut Aslan
- Dokuz Eylul University, Faculty of Medicine, Department of Pediatric Neurology Izmir, Turkey
| | - Elmasnur Yilmaz
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Bilge Özgör
- Inonu University, Faculty of Medicine, Turgut Ozal Research Center, Department of Paediatric Neurology, Malatya, Turkey
| | - Sunitha Balaraju
- John Walton Muscular Dystrophy Research Centre, Institute of Translational and Clinical Research, Newcastle University, Newcastle upon Tyne, UK
- Department of Clinical Neurosciences, John Van Geest Cambridge Centre for Brain Repair, University of Cambridge School of Clinical Medicine, Robinson Way, Cambridge CB2 0PY, UK
| | - Nora Szabo
- Department of Clinical Neurosciences, John Van Geest Cambridge Centre for Brain Repair, University of Cambridge School of Clinical Medicine, Robinson Way, Cambridge CB2 0PY, UK
- Budai Children Hospital, Észak-Közép-budai Centrum, Új Szent János Kórház és Szakrendelő, Budapest, Hungary
| | - Steven Laurie
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Daniel G. MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Denisa Hathazi
- Department of Clinical Neurosciences, John Van Geest Cambridge Centre for Brain Repair, University of Cambridge School of Clinical Medicine, Robinson Way, Cambridge CB2 0PY, UK
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Institute of Translational and Clinical Research, Newcastle University, Newcastle upon Tyne, UK
| | - Andreas Roos
- Leibniz Institut für Analytische Wissenschaften, ISAS, Dortmund, Germany & Pediatric Neurology, University Hospital, University of Duisburg-Essen, Faculty of Medicine, Essen, Germany
| | - Hanns Lochmuller
- Children's Hospital of Eastern Ontario Research Institute; Division of Neurology, Department of Medicine, the Ottawa Hospital; and Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
| | - Isabelle Vernos
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Spain
| | - Rita Horvath
- John Walton Muscular Dystrophy Research Centre, Institute of Translational and Clinical Research, Newcastle University, Newcastle upon Tyne, UK
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16
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Eskier D, Suner A, Oktay Y, Karakülah G. Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load. PeerJ 2020; 8:e10181. [PMID: 33083157 PMCID: PMC7560320 DOI: 10.7717/peerj.10181] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 08/09/2020] [Accepted: 09/23/2020] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2 is a betacoronavirus responsible for COVID-19, a pandemic with global impact that first emerged in late 2019. Since then, the viral genome has shown considerable variance as the disease spread across the world, in part due to the zoonotic origins of the virus and the human host adaptation process. As a virus with an RNA genome that codes for its own genomic replication proteins, mutations in these proteins can significantly impact the variance rate of the genome, affecting both the survival and infection rate of the virus, and attempts at combating the disease. In this study, we analyzed the mutation densities of viral isolates carrying frequently observed mutations for four proteins in the RNA synthesis complex over time in comparison to wildtype isolates. Our observations suggest mutations in nsp14, an error-correcting exonuclease protein, have the strongest association with increased mutation load without selective pressure and across the genome, compared to nsp7, nsp8 and nsp12, which form the core polymerase complex. We propose nsp14 as a priority research target for understanding genomic variance rate in SARS-CoV-2 isolates and nsp14 mutations as potential predictors for high mutability strains.
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Affiliation(s)
- Doğa Eskier
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Aslı Suner
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey.,Faculty of Medicine, Department of Medical Biology, Dokuz Eylül University, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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17
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Eskier D, Suner A, Karakülah G, Oktay Y. Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. PeerJ 2020; 8:e9703. [PMID: 32879797 PMCID: PMC7443079 DOI: 10.7717/peerj.9703] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 06/17/2020] [Accepted: 07/22/2020] [Indexed: 01/20/2023] Open
Abstract
Since its emergence in Wuhan, China in late 2019, the origin and evolution of SARS-CoV-2 have been among the most debated issues related to COVID-19. Throughout its spread around the world, the viral genome continued acquiring new mutations and some of them became widespread. Among them, 14408 C>T and 23403 A>G mutations in RdRp and S, respectively, became dominant in Europe and the US, which led to debates regarding their effects on the mutability and transmissibility of the virus. In this study, we aimed to investigate possible differences between time-dependent variation of mutation densities (MDe) of viral strains that carry these two mutations and those that do not. Our analyses at the genome and gene level led to two important findings: First, time-dependent changes in the average MDe of circulating SARS-CoV-2 genomes showed different characteristics before and after the beginning of April, when daily new case numbers started levelling off. Second, this pattern was much delayed or even non-existent for the "mutant" (MT) strain that harbored both 14408 C>T and 23403 A>G mutations. Although these differences were not limited to a few hotspots, it is intriguing that the MDe increase is most evident in two critical genes, S and Orf1ab, which are also the genes that harbor the defining mutations of the MT genotype. The nature of these unexpected relationships warrants further research.
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Affiliation(s)
- Doğa Eskier
- Izmir International Biomedicine and Genome Institute (iBG-İzmir), Dokuz Eylül University, Izmir, Turkey
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
| | - Aslı Suner
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir International Biomedicine and Genome Institute (iBG-İzmir), Dokuz Eylül University, Izmir, Turkey
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
| | - Yavuz Oktay
- Izmir International Biomedicine and Genome Institute (iBG-İzmir), Dokuz Eylül University, Izmir, Turkey
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
- Faculty of Medicine, Department of Medical Biology, Dokuz Eylül University, Izmir, Turkey
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18
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Abstract
COVID-19, caused by the novel SARS-CoV-2 virus, started in China in late 2019, and soon became a global pandemic. With the help of thousands of viral genome sequences that have been accumulating, it has become possible to track the evolution of the viral genome over time as it spread across the world. An important question that still needs to be answered is whether any of the common mutations affect the viral properties, and therefore the disease characteristics. Therefore, we sought to understand the effects of mutations in RNA-dependent RNA polymerase (RdRp), particularly the common 14408C>T mutation, on mutation rate and viral spread. By focusing on mutations in the slowly evolving M or E genes, we aimed to minimize the effects of selective pressure. Our results indicate that 14408C>T mutation increases the mutation rate, while the third-most common RdRp mutation, 15324C>T, has the opposite effect. It is possible that 14408C>T mutation may have contributed to the dominance of its co-mutations in Europe and elsewhere.
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Affiliation(s)
- Doğa Eskier
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Aslı Suner
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
- Faculty of Medicine, Department of Medical Biology, Dokuz Eylül University, Izmir, Turkey
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Töpf A, Oktay Y, Balaraju S, Yilmaz E, Sonmezler E, Yis U, Laurie S, Thompson R, Roos A, MacArthur DG, Yaramis A, Güngör S, Lochmüller H, Hiz S, Horvath R. Severe neurodevelopmental disease caused by a homozygous TLK2 variant. Eur J Hum Genet 2020; 28:383-387. [PMID: 31558842 PMCID: PMC7028915 DOI: 10.1038/s41431-019-0519-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
A distinct neurodevelopmental phenotype characterised mainly by mild motor and language delay and facial dysmorphism, caused by heterozygous de novo or dominant variants in the TLK2 gene has recently been described. All cases reported carried either truncating variants located throughout the gene, or missense changes principally located at the C-terminal end of the protein mostly resulting in haploinsufficiency of TLK2. Through whole exome sequencing, we identified a homozygous missense variant in TLK2 in a patient showing more severe symptoms than those previously described, including cerebellar vermis hypoplasia and West syndrome. Both parents are heterozygous for the variant and clinically unaffected highlighting that recessive variants in TLK2 can also be disease causing and may act through a different pathomechanism.
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Affiliation(s)
- Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Department of Medical Biology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Sunitha Balaraju
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Elmasnur Yilmaz
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Ece Sonmezler
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Uluc Yis
- Department of Paediatric Neurology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Steven Laurie
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rachel Thompson
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Andreas Roos
- Leibniz Institut für Analytische Wissenschaften, ISAS, Dortmund, Germany
- Pediatric Neurology, University Children's Hospital, University of Duisburg-Essen, Faculty of Medicine, Essen, Germany
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ahmet Yaramis
- Pediatric Neurology Clinic, Diyarbakir Memorial Hospital, Diyarbakir, Turkey
| | - Serdal Güngör
- Department of Paediatric Neurology, Faculty of Medicine, Turgut Ozal Research Center, Inonu University, Malatya, Turkey
| | - Hanns Lochmüller
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
| | - Semra Hiz
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Department of Paediatric Neurology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Rita Horvath
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.
- Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
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20
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Yiş U, Hiz S, Güneş S, Diniz G, Baydan F, Töpf A, Sonmezler E, Lochmüller H, Horvath R, Oktay Y. Dihydropyridine Receptor Congenital Myopathy In A Consangineous Turkish Family. J Neuromuscul Dis 2020; 6:377-384. [PMID: 31227654 DOI: 10.3233/jnd-190383] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Dihydropyridine receptor congenital myopathy is a recently described congenital myopathy caused by dominant or recessive mutations in the CACNA1S gene. To date, only 11 cases from 7 families were described in a single report. Here, we describe a consanguineous family with three affected children, presenting congenital hypotonia, contractures, ophthalmoplegia and respiratory insufficiency, with a novel homozygous mutation in the CACNA1S gene. They also showed cognitive delay, pes equinovarus deformity and neurogenic changes that have not been associated with this myopathy in the previous reports. This report expands the phenotypic spectrum of dihydropyridine receptor congenital myopathy and underscores the importance of whole exome sequencing in early onset neuromuscular disorders.
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Affiliation(s)
- Uluç Yiş
- Department of Pediatrics, Dokuz Eylül University, School of Medicine, Division of Child Neurology, İzmir, Turkey
| | - Semra Hiz
- Department of Pediatrics, Dokuz Eylül University, School of Medicine, Division of Child Neurology, İzmir, Turkey
| | - Sezgin Güneş
- Department of Neonatology, Medical Park Hospital, İzmir, Turkey
| | - Gülden Diniz
- Tepecik Research and Training Hospital, University of Health Sciences, İzmir, Turkey
| | - Figen Baydan
- Tepecik Research and Training Hospital, University of Health Sciences, İzmir, Turkey
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Ece Sonmezler
- Izmir International Biomedicine and Genom Institute, Dokuz Eylul University, Izmir, Turkey
| | - Hanns Lochmüller
- Department of Medicine, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada and Division of Neurology, The Ottawa Hospital, Ottawa, Canada
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge School of Clinical, Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Yavuz Oktay
- Izmir International Biomedicine and Genom Institute, Dokuz Eylul University, Izmir, Turkey.,Department of Medical Biology, Dokuz Eylul University, Faculty of Medicine, Izmir, Turkey.,Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
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21
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Yaramis A, Lochmüller H, Töpf A, Sonmezler E, Yilmaz E, Hiz S, Yis U, Gungor S, Ipek Polat A, Edem P, Beltran S, Laurie S, Yaramis A, Horvath R, Oktay Y. COL4A1-related autosomal recessive encephalopathy in 2 Turkish children. Neurol Genet 2020; 6:e392. [PMID: 32042920 PMCID: PMC6975172 DOI: 10.1212/nxg.0000000000000392] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/08/2019] [Indexed: 12/01/2022]
Abstract
OBJECTIVE This study presents the neurologic phenotypes of 2 brothers with a novel homozygous COL4A1 mutation that was identified in a large Turkish consanguineous cohort of neurogenetic diseases. METHODS Whole-exome sequencing and bioinformatic analysis of consanguineous families with children affected by early-onset, neurogenetic disorders was performed using the RD-Connect Genome-Phenome Analysis Platform. We also performed clinical, EEG, and neuroimaging analyses in unaffected siblings and parents. RESULTS We have identified a homozygous missense mutation in COL4A1 (p.Gly1278Ser, NM_001845.5:c.3832G>T) in 2 siblings affected by small vessel brain disease with periventricular leukoencephalopathy and ocular defects. Presenting symptoms included mild weakness, hemiparetic gait, pyramidal findings, and seizures, whereas their intellectual and behavioral functions were normal. Both parents and 5 of the siblings (3 boys and 2 girls) were heterozygous for the variant. They did not show any clinical or laboratory signs of small vessel disease. CONCLUSIONS COL4A1 has previously been associated with dominant small vessel disease of the brain and other organs, manifesting with high penetrance in heterozygous mutation carriers. Our findings provide evidence that COL4A1-related encephalopathy can be inherited in an autosomal recessive manner, which is important for counseling, prognosis, and treatment. Genotype-phenotype correlations remain to be established.
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Affiliation(s)
- Ahmet Yaramis
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Hanns Lochmüller
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Ana Töpf
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Ece Sonmezler
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Elmasnur Yilmaz
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Semra Hiz
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Uluc Yis
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Serdal Gungor
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Ayse Ipek Polat
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Pinar Edem
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Sergi Beltran
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Steven Laurie
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Aysenur Yaramis
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Rita Horvath
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
| | - Yavuz Oktay
- Pediatric Neurology Clinic (A.Y.), Private Office, Diyarbakir, Turkey; Children's Hospital of Eastern Ontario Research Institute (H.L.), University of Ottawa, Canada; Division of Neurology (H.L.), Department of Medicine, The Ottawa Hospital, Canada; John Walton Muscular Dystrophy Research Centre (A.T.), Institute of Genetic Medicine, Newcastle University, UK; Dokuz Eylul University (S.H., E.S., E.Y., Y.O.), Izmir International Biomedicine and Genome Institute, Turkey; Faculty of Medicine (S.H., U.Y., A.I.P., P.E.), Department of Paediatric Neurology, Dokuz Eylul University, Izmir, Turkey; Faculty of Medicine (S.G.), Turgut Ozal Research Center, Department of Paediatric Neurology, Inonu University, Malatya, Turkey; CNAG-CRG (S.L., H.L., S.B.), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (S.L.), Barcelona, Spain; Koc University (A.Y.), School of Medicine, Medical Student, Istanbul, Turkey; Department of Clinical Neurosciences (R.H.), University of Cambridge School of Clinical Medicine, UK; Izmir Biomedicine and Genome Center (Y.O.), Dokuz Eylul University Health Campus, Turkey; and Faculty of Medicine (Y.O.), Department of Medical Biology, Dokuz Eylul University, Izmir, Turkey
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22
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Ülgen E, Can Ö, Bilguvar K, Oktay Y, Akyerli CB, Danyeli AE, Yakıcıer MC, Sezerman OU, Pamir MN, Özduman K. Whole exome sequencing-based analysis to identify DNA damage repair deficiency as a major contributor to gliomagenesis in adult diffuse gliomas. J Neurosurg 2019; 132:1435-1446. [PMID: 30952131 DOI: 10.3171/2019.1.jns182938] [Citation(s) in RCA: 10] [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: 10/15/2018] [Accepted: 01/10/2019] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Processes that cause or contribute to cancer, such as aging, exposure to carcinogens, or DNA damage repair deficiency (DDRd), create predictable and traceable nucleotide alterations in one's genetic code (termed "mutational signatures"). Large studies have previously identified various such mutational signatures across cancers that can be attributed to the specific causative processes. To gain further insight into the processes in glioma development, the authors analyzed mutational signatures in adult diffuse gliomas (DGs). METHODS Twenty-five DGs and paired blood samples were whole exome sequenced. Somatic mutational signatures were identified using 2 different methods. Associations of the signatures with age at diagnosis, molecular subset, and mutational load were investigated. As DDRd-related signatures were frequently observed, germline and somatic DDR gene mutations as well as microsatellite instability (MSI) status were determined for all samples. For validation of signature prevalence, publicly available data from The Cancer Genome Atlas (TCGA) were used. RESULTS Each tumor had a unique combination of signatures. The most common signatures were signature 1 (88%, aging related), signature 3 (52%, homologous recombination related), and signature 15 (56%, mismatch repair related). Eighty-four percent of the tumors contained at least 1 DDRd signature. The findings were validated using public TCGA data. The weight of signature 1 positively correlated with age (r = 0.43) while cumulative weight of DDRd signatures negatively correlated with age (r = -0.16). Each subject had at least 1 germline/somatic alteration in a DDR gene, the most common being the risk single nucleotide polymorphism rs1800734 in MLH1. The rs1800734-AA genotype had a higher cumulative DDRd weight as well as higher mutational load; TP53 was the most common somatically altered DDR gene. MSI was observed in 24% of the tumors. No significant associations of MSI status with mutational load, rs1800734, or the cumulative weight of DDRd signatures were identified. CONCLUSIONS Current findings suggest that DDRd may act as a fundamental mechanism in gliomagenesis rather than being a random, secondary event.
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Affiliation(s)
- Ege Ülgen
- Departments of1Biostatistics and Medical Informatics
| | - Özge Can
- 2Department of Medical Engineering, Acibadem Mehmet Ali Aydınlar University, School of Engineering, Istanbul, Turkey
| | - Kaya Bilguvar
- 3Department of Genetics, Yale Center for Genome Analysis, Yale University, School of Medicine, New Haven, Connecticut
| | - Yavuz Oktay
- 4Izmir International Biomedicine and Genome Institute (IBG), Dokuz Eylül University, Izmir.,5Department of Medical Biology, Dokuz Eylül University, Izmir; and
| | | | | | - M Cengiz Yakıcıer
- 8Department of Molecular Biology, Acibadem Mehmet Ali Aydınlar University, School of Arts and Sciences, Istanbul, Turkey
| | | | - M Necmettin Pamir
- 9Neurosurgery, Acibadem Mehmet Ali Aydınlar University, School of Medicine, Istanbul
| | - Koray Özduman
- 9Neurosurgery, Acibadem Mehmet Ali Aydınlar University, School of Medicine, Istanbul
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23
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Topf A, Oktay Y, Balaraju S, Yılmaz E, Sönmezler E, Yaramis A, Güngör S, Laurie S, Beltran S, Gut I, Lochmüller H, Hiz S, Horvath R. MITOCHONDRIAL DISEASES (Posters). Neuromuscul Disord 2018. [DOI: 10.1016/j.nmd.2018.06.221] [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: 10/28/2022]
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24
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Akyerli CB, Yüksel Ş, Can Ö, Erson-Omay EZ, Oktay Y, Coşgun E, Ülgen E, Erdemgil Y, Sav A, von Deimling A, Günel M, Yakıcıer MC, Pamir MN, Özduman K. Use of telomerase promoter mutations to mark specific molecular subsets with reciprocal clinical behavior in IDH mutant and IDH wild-type diffuse gliomas. J Neurosurg 2017. [PMID: 28621624 DOI: 10.3171/2016.11.jns16973] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Recent studies have established that hemispheric diffuse gliomas may be grouped into subsets on the basis of molecular markers; these subsets are loosely correlated with the histopathological diagnosis but are strong predictors of clinical tumor behavior. Based on an analysis of molecular and clinical parameters, the authors hypothesized that mutations of the telomerase promoter (TERTp-mut) mark separate oncogenic programs among isocitrate dehydrogenase 1 and/or 2 (IDH) mutant (IDH-mut) and IDH wild-type (IDH-wt) diffuse gliomas independent of histopathology or WHO grade. METHODS Four molecular subsets of the combined statuses of IDH and TERT-promoter mutations (double mutant, IDH only, TERT only, and double negative) were defined. Differences in age, anatomical location, molecular genetics, and survival rates in a surgical cohort of 299 patients with a total of 356 hemispheric diffuse gliomas (WHO Grade II, III, or IV) were analyzed. RESULTS TERTp-mut were present in 38.8% of IDH-mut and 70.2% of IDH-wt gliomas. The mutational status was stable in each patient at 57 recurrence events over a 2645-month cumulative follow-up period. Among patients with IDH-mut gliomas, those in the double-mutant subset had better survival and a lower incidence of malignant degeneration than those in the IDH-only subset. Of patients in the double-mutant subset, 96.3% were also positive for 1p/19q codeletions. All patients with 1p/19q codeletions had TERTp-mut. In patients with IDH-mut glioma, epidermal growth factor receptor or phosphatase and tensin homolog mutations were not observed, and copy-number variations were uncommon. Among IDH-wt gliomas, the TERT-only subset was associated with significantly higher age, higher Ki-67 labeling index, primary glioblastoma-specific oncogenic changes, and poor survival. The double-negative subset was genetically and biologically heterogeneous. Survival analyses (Kaplan-Meier, multivariate, and regression-tree analyses) confirmed that patients in the 4 molecular subsets had distinct prognoses. CONCLUSIONS Molecular subsets result in different tumor biology and clinical behaviors in hemispheric diffuse gliomas.
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Affiliation(s)
| | | | - Özge Can
- 2Department of Medical Engineering, Faculty of Engineering; and
| | - E Zeynep Erson-Omay
- 3Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | | | | | | | | | | | - Andreas von Deimling
- 7Department of Neuropathology, Heidelberg University; and.,8German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Clinical Cooperation Unit (CCU) Neuropathology, Heidelberg, Germany
| | - Murat Günel
- 3Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - M Cengiz Yakıcıer
- 10Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Acıbadem University, Istanbul, Turkey
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25
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Pavlopoulou A, Oktay Y, Vougas K, Louka M, Vorgias CE, Georgakilas AG. Determinants of resistance to chemotherapy and ionizing radiation in breast cancer stem cells. Cancer Lett 2016; 380:485-493. [DOI: 10.1016/j.canlet.2016.07.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 12/13/2022]
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26
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Zhang J, Khvorostov I, Hong JS, Oktay Y, Vergnes L, Nuebel E, Wahjudi PN, Setoguchi K, Wang G, Do A, Jung HJ, McCaffery JM, Kurland IJ, Reue K, Lee WNP, Koehler CM, Teitell MA. UCP2 regulates energy metabolism and differentiation potential of human pluripotent stem cells. EMBO J 2016; 35:899. [PMID: 27084758 DOI: 10.15252/embj.201694054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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27
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Claypool SM, Oktay Y, Boontheung P, Loo JA, Koehler CM. Cardiolipin defines the interactome of the major ADP/ATP carrier protein of the mitochondrial inner membrane. J Biophys Biochem Cytol 2012. [PMCID: PMC3384408 DOI: 10.1083/jcb.2008011521977c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Abstract
Leiomyosarcomas of the breast are rare tumors. Less than 16 such cases have been reported in the literature so far. We present a case of a 44 year female patient who was found to have primary leiomyosarcoma of the breast.
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Affiliation(s)
- Y Oktay
- Göztepe Training and Research Hospital, Istanbul, Turkey
| | - A Fikret
- Göztepe Training and Research Hospital, Istanbul, Turkey
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29
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Zhang JI, Khvorostov I, Hong J, Oktay Y, Vergnes L, Nuebel E, Do A, Jung HJ, McCaffery M, Reue K, Koehler C, Teitell M. Abstract 4360: Distinct energy metabolism in human pluripotent stem cells and differentiated cells regulated by UCP2. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-4360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
It has been assumed, based largely on morphologic evidence, that human pluripotent stem cells (hPSCs) contain underdeveloped, bioenergetically inactive mitochondria. In contrast, differentiated cells harbor a fused, branching mitochondrial network, with oxidative phosphorylation (OXPHOS) as the main energy source. A role for mitochondria in hPSC bioenergetics therefore remains uncertain. Here we show that hPSCs have functional respiratory complexes that consume O2 at maximal capacity. Despite this, ATP generation in hPSCs is mainly by glycolysis. To help maintain hPSC mitochondrial membrane potential, cell proliferation, and viability, glycolytic ATP is hydrolyzed by the mitochondrial F1F0ATP synthase. Uncoupling protein 2 (UCP2) regulates this unique pattern of hPSC energy metabolism while suppressing reactive oxygen species. Upon differentiation, UCP2 is repressed and cells shift from glycolysis and fatty acid oxidation to glucose oxidation dependency. Ectopic UCP2 expression during differentiation blocks this metabolic transition and blocks proper embryoid body formation. Combined, our data show that hPSC have distinct bioenergetics regulated by UCP2 and repression of UCP2 is required for metabolic reprogramming along differentiation
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4360. doi:10.1158/1538-7445.AM2011-4360
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Wang G, Chen HW, Oktay Y, Zhang J, Allen EL, Smith GM, Fan KC, Hong JS, French SW, McCaffery JM, Lightowlers RN, Morse HC, Koehler CM, Teitell MA. PNPASE regulates RNA import into mitochondria. Cell 2010; 142:456-67. [PMID: 20691904 DOI: 10.1016/j.cell.2010.06.035] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [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: 12/22/2009] [Revised: 03/20/2010] [Accepted: 05/13/2010] [Indexed: 02/04/2023]
Abstract
RNA import into mammalian mitochondria is considered essential for replication, transcription, and translation of the mitochondrial genome but the pathway(s) and factors that control this import are poorly understood. Previously, we localized polynucleotide phosphorylase (PNPASE), a 3' --> 5' exoribonuclease and poly-A polymerase, in the mitochondrial intermembrane space, a location lacking resident RNAs. Here, we show a new role for PNPASE in regulating the import of nuclear-encoded RNAs into the mitochondrial matrix. PNPASE reduction impaired mitochondrial RNA processing and polycistronic transcripts accumulated. Augmented import of RNase P, 5S rRNA, and MRP RNAs depended on PNPASE expression and PNPASE-imported RNA interactions were identified. PNPASE RNA processing and import activities were separable and a mitochondrial RNA targeting signal was isolated that enabled RNA import in a PNPASE-dependent manner. Combined, these data strongly support an unanticipated role for PNPASE in mediating the translocation of RNAs into mitochondria.
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Affiliation(s)
- Geng Wang
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
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Claypool SM, Oktay Y, Boontheung P, Loo JA, Koehler CM. Cardiolipin defines the interactome of the major ADP/ATP carrier protein of the mitochondrial inner membrane. ACTA ACUST UNITED AC 2008; 182:937-50. [PMID: 18779372 PMCID: PMC2528576 DOI: 10.1083/jcb.200801152] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Defined mutations in the mitochondrial ADP/ATP carrier (AAC) are associated with certain types of progressive external ophthalmoplegia. AAC is required for oxidative phosphorylation (OXPHOS), and dysregulation of AAC has been implicated in apoptosis. Little is known about the AAC interactome, aside from a known requirement for the phospholipid cardiolipin (CL) and that it is thought to function as a homodimer. Using a newly developed dual affinity tag, we demonstrate that yeast AAC2 physically participates in several protein complexes of distinct size and composition. The respiratory supercomplex and several smaller AAC2-containing complexes, including other members of the mitochondrial carrier family, are identified here. In the absence of CL, most of the defined interactions are destabilized or undetectable. The absence of CL and/or AAC2 results in distinct yet additive alterations in respiratory supercomplex structure and respiratory function. Thus, a single lipid can significantly alter the functional interactome of an individual protein.
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Affiliation(s)
- Steven M Claypool
- Department of Chemistry and Biochemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Oktay Y, Dioum E, Matsuzaki S, Ding K, Yan LJ, Haller RG, Szweda LI, Garcia JA. Hypoxia-inducible factor 2alpha regulates expression of the mitochondrial aconitase chaperone protein frataxin. J Biol Chem 2007; 282:11750-6. [PMID: 17322295 DOI: 10.1074/jbc.m611133200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [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] [Indexed: 11/06/2022] Open
Abstract
Mice lacking Epas1, encoding the transcription factor Hypoxia-inducible Factor 2alpha (HIF-2alpha), exhibit an apparent mitochondrial disease state. Similarities between knock-outs of Epas1 and of Sod2, encoding the mitochondrial antioxidant enzyme manganese superoxide dismutase, led to the identification of Sod2 as a HIF-2alpha target gene. However, Sod2 levels in Epas1(-)(/)(-) liver are intermediate between that of Sod(+)(/)(-) and Sod2(-)(/)(-) mice, which have subtle or severe phenotypes, respectively. This suggests that additional HIF-2alpha target genes besides Sod2 contribute to the Epas1(-)(/)(-) mitochondrial disease state. To define the nature of the mitochondrial defect in Epas1(-)(/)(-) liver, we performed biophysical, biochemical, and molecular studies. In the setting of decreased Sod2 levels and increased oxidative stress, we found reduced respiration, sensitized mitochondrial permeability transition pore opening, intact electron transport chain activities, and impaired mitochondrial aconitase activity. Mitochondrial aconitase protein levels were preserved, whereas mRNA and protein levels for frataxin, the oxidative stress-regulated mitochondrial aconitase chaperone protein, were markedly reduced in Epas1(-)(/)(-) livers. The mouse Fxn promoter was preferentially activated by HIF-2alpha through a consensus HIF-responsive enhancer element. In summary, the studies reveal that Fxn, like Sod2, is a nuclear-encoded, mitochondrial-localized HIF-2alpha target gene required for optimal mitochondrial homeostasis. These findings expand upon the previously defined role of HIF-2alpha in the cellular response to oxidative stress and identify a novel link of HIF-2alpha with mitochondrial homeostasis.
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Affiliation(s)
- Yavuz Oktay
- Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
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Scortegagna M, Ding K, Zhang Q, Oktay Y, Bennett MJ, Bennett M, Shelton JM, Richardson JA, Moe O, Garcia JA. HIF-2α regulates murine hematopoietic development in an erythropoietin-dependent manner. Blood 2005; 105:3133-40. [PMID: 15626745 DOI: 10.1182/blood-2004-05-1695] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.4] [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] [Indexed: 12/18/2022] Open
Abstract
AbstractErythropoiesis in the adult mammal depends critically on erythropoietin, an inducible cytokine with pluripotent effects. Erythropoietin gene expression increases under conditions associated with lowered oxygen content such as anemia and hypoxia. HIF-1α, the founding member of the hypoxia-inducible factor (HIF) alpha class, was identified by its ability to bind and activate the hypoxia-responsive enhancer in the erythropoietin regulatory region in vitro. The existence of multiple HIF alpha members raises the question of which HIF alpha member or members regulates erythropoietin expression in vivo. We previously reported that mice lacking wild-type HIF-2α, encoded by the EPAS1 gene, exhibit pancytopenia. In this study, we have characterized the etiology of this hematopoietic phenotype. Molecular studies of EPAS1-null kidneys reveal dramatically decreased erythropoietin gene expression. EPAS1-null as well as heterozygous mice have impaired renal erythropoietin induction in response to hypoxia. Treatment of EPAS1-null mice with exogenous erythropoietin reverses the hematopoietic and other defects. We propose that HIF-2α is an essential regulator of murine erythropoietin production. Impairments in HIF signaling, involving either HIF-1α or HIF-2α, may play a prominent role in conditions involving altered hematopoietic or erythropoietin homeostasis.
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Affiliation(s)
- Marzia Scortegagna
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-8573, USA
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Scortegagna M, Ding K, Oktay Y, Gaur A, Thurmond F, Yan LJ, Marck BT, Matsumoto AM, Shelton JM, Richardson JA, Bennett MJ, Garcia JA. Multiple organ pathology, metabolic abnormalities and impaired homeostasis of reactive oxygen species in Epas1-/- mice. Nat Genet 2003; 35:331-40. [PMID: 14608355 DOI: 10.1038/ng1266] [Citation(s) in RCA: 381] [Impact Index Per Article: 18.1] [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: 07/11/2003] [Accepted: 10/22/2003] [Indexed: 12/14/2022]
Abstract
Hypoxia-inducible factor (HIF) transcription factors respond to multiple environmental stressors, including hypoxia and hypoglycemia. We report that mice lacking the HIF family member HIF-2alpha (encoded by Epas1) have a syndrome of multiple-organ pathology, biochemical abnormalities and altered gene expression patterns. Histological and ultrastructural analyses showed retinopathy, hepatic steatosis, cardiac hypertrophy, skeletal myopathy, hypocellular bone marrow, azoospermia and mitochondrial abnormalities in these mice. Serum and urine metabolite studies showed hypoglycemia, lactic acidosis, altered Krebs cycle function and dysregulated fatty acid oxidation. Biochemical assays showed enhanced generation of reactive oxygen species (ROS), whereas molecular analyses indicated reduced expression of genes encoding the primary antioxidant enzymes (AOEs). Transfection analyses showed that HIF-2alpha could efficiently transactivate the promoters of the primary AOEs. Prenatal or postnatal treatment of Epas1-/- mice with a superoxide dismutase (SOD) mimetic reversed several aspects of the null phenotype. We propose a rheostat role for HIF-2alpha that allows for the maintenance of ROS as well as mitochondrial homeostasis.
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Affiliation(s)
- Marzia Scortegagna
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-8573, USA
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35
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Abstract
Hypoxic stress plays a role in pathophysiologic states such as myocardial infarction and cerebral vascular events as well as in normal physiologic conditions including development and hematopoiesis. Members of the hypoxia inducible factor (HIF) family function as transcriptional regulators of genes involved in the hypoxic response. After generating adult mice that globally lack endothelial PAS domain protein 1 (EPAS1, also known as HIF-2alpha/HRF/HLF/MOP3), the second member of the HIF family, characterization of the hematopoietic cell population indicated that the loss of EPAS1/HIF-2alpha resulted in pancytopenia. Using bone marrow reconstitution experiments of lethally irradiated hosts, we have defined the extent and site of hematopoietic impairment in the EPAS1/HIF-2alpha null mice. These data suggest a critical role for EPAS1/HIF-2alpha in maintaining a functional microenvironment in the bone marrow for effective hematopoiesis.
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Affiliation(s)
- Marzia Scortegagna
- University of Texas Southwestern Medical Center, Department of Internal Medicine, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
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