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Calame DG, Wong JH, Panda P, Nguyen DT, Leong NC, Sangermano R, Patankar SG, Abdel-Hamid M, AlAbdi L, Safwat S, Flannery KP, Dardas Z, Fatih JM, Murali C, Kannan V, Lotze TE, Herman I, Ammouri F, Rezich B, Efthymiou S, Alavi S, Murphy D, Firoozfar Z, Nasab ME, Bahreini A, Ghasemi M, Haridy NA, Goldouzi HR, Eghbal F, Karimiani EG, Srinivasan VM, Gowda VK, Du H, Jhangiani SN, Coban-Akdemir Z, Marafi D, Rodan L, Isikay S, Rosenfeld JA, Ramanathan S, Staton M, Kerby C. Oberg, Clark RD, Wenman C, Loughlin S, Saad R, Ashraf T, Male A, Tadros S, Boostani R, Abdel-Salam GM, Zaki M, Abdalla E, Manzini MC, Pehlivan D, Posey JE, Gibbs RA, Houlden H, Alkuraya FS, Bujakowska K, Maroofian R, Lupski JR, Nguyen LN. Biallelic variation in the choline and ethanolamine transporter FLVCR1 underlies a pleiotropic disease spectrum from adult neurodegeneration to severe developmental disorders. medRxiv 2024:2024.02.09.24302464. [PMID: 38405817 PMCID: PMC10888986 DOI: 10.1101/2024.02.09.24302464] [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] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
FLVCR1 encodes Feline leukemia virus subgroup C receptor 1 (FLVCR1), a solute carrier (SLC) transporter within the Major Facilitator Superfamily. FLVCR1 is a widely expressed transmembrane protein with plasma membrane and mitochondrial isoforms implicated in heme, choline, and ethanolamine transport. While Flvcr1 knockout mice die in utero with skeletal malformations and defective erythropoiesis reminiscent of Diamond-Blackfan anemia, rare biallelic pathogenic FLVCR1 variants are linked to childhood or adult-onset neurodegeneration of the retina, spinal cord, and peripheral nervous system. We ascertained from research and clinical exome sequencing 27 individuals from 20 unrelated families with biallelic ultra-rare missense and predicted loss-of-function (pLoF) FLVCR1 variant alleles. We characterize an expansive FLVCR1 phenotypic spectrum ranging from adult-onset retinitis pigmentosa to severe developmental disorders with microcephaly, reduced brain volume, epilepsy, spasticity, and premature death. The most severely affected individuals, including three individuals with homozygous pLoF variants, share traits with Flvcr1 knockout mice and Diamond-Blackfan anemia including macrocytic anemia and congenital skeletal malformations. Pathogenic FLVCR1 missense variants primarily lie within transmembrane domains and reduce choline and ethanolamine transport activity compared with wild-type FLVCR1 with minimal impact on FLVCR1 stability or subcellular localization. Several variants disrupt splicing in a mini-gene assay which may contribute to genotype-phenotype correlations. Taken together, these data support an allele-specific gene dosage model in which phenotypic severity reflects residual FLVCR1 activity. This study expands our understanding of Mendelian disorders of choline and ethanolamine transport and demonstrates the importance of choline and ethanolamine in neurodevelopment and neuronal homeostasis.
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Affiliation(s)
- Daniel G. Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jovi Huixin Wong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Puravi Panda
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Dat Tuan Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Nancy C.P. Leong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Riccardo Sangermano
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Sohil G. Patankar
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Mohamed Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sylvia Safwat
- Department of Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Kyle P. Flannery
- Department of Neuroscience and Cell Biology, Rutgers-Robert Wood Johnson Medical School, Child Health Institute of New Jersey, NY, USA
| | - Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chaya Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Varun Kannan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Timothy E. Lotze
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Boys Town National Research Hospital, Boys Town, NE, USA
| | - Farah Ammouri
- Boys Town National Research Hospital, Boys Town, NE, USA
- The University of Kansas Health System, Westwood, KS, USA
| | - Brianna Rezich
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE, USA
| | - Stephanie Efthymiou
- Department of Neuromuscular diseases, UCL Institute of Neurology, WC1N 3BG, London, UK
| | - Shahryar Alavi
- Department of Neuromuscular diseases, UCL Institute of Neurology, WC1N 3BG, London, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, United Kingdom
| | | | | | - Amir Bahreini
- KaryoGen, Isfahan, Iran
- Department of Human Genetics, University of Pittsburgh, PA, USA
| | - Majid Ghasemi
- Department of Neurology, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Hamid Reza Goldouzi
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Eghbal
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St George’s, University of London, Cranmer Terrace London, London, UK
| | | | - Vykuntaraju K. Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait
| | - Lance Rodan
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Sedat Isikay
- Gaziantep Islam Science and Technology University, Medical Faculty, Department of Pediatric Neurology, Gaziantep, Turkey
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Subhadra Ramanathan
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Michael Staton
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Kerby C. Oberg
- Department of Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Robin D. Clark
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Catharina Wenman
- Rare & Inherited Disease Laboratory, NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3BH, UK
| | - Sam Loughlin
- Rare & Inherited Disease Laboratory, NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3BH, UK
| | - Ramy Saad
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Tazeen Ashraf
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Alison Male
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Shereen Tadros
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Reza Boostani
- Department of Neurology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ghada M.H. Abdel-Salam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Maha Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Ebtesam Abdalla
- Department of Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - M. Chiara Manzini
- Department of Neuroscience and Cell Biology, Rutgers-Robert Wood Johnson Medical School, Child Health Institute of New Jersey, NY, USA
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Henry Houlden
- Department of Neuromuscular diseases, UCL Institute of Neurology, WC1N 3BG, London, UK
| | - Fowzan S. Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Kinga Bujakowska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Reza Maroofian
- Department of Neuromuscular diseases, UCL Institute of Neurology, WC1N 3BG, London, UK
| | - James R. Lupski
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Long Nam Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
- Immunology Program, Life Sciences Institute, National University of Singapore, Singapore 117456
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 117456
- Cardiovascular Disease Research (CVD) Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456
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