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Calame DG, Herman I, Marshall AE, Maroofian R, Donis KC, Fatih JM, Mitani T, Du H, Grochowski CM, Sousa S, Bakhtiari S, Ito YA, Rocca C, Hunter JV, Sutton VR, Emrick LT, Boycott KM, Lossos A, Fellig Y, Prus E, Kalish Y, Meiner V, Suerink M, Ruivenkamp C, Muirhead K, Saadi NW, Zaki MS, Skidmore DL, Osmond M, Silva TO, Houlden H, Murphy D, Ghayoorarimiani E, Jamshidi Y, Jaddoa AG, Tajsharghi H, Jin SC, Coban-Akdemir Z, Travaglini L, Nicita F, Jhangiani SN, Gibbs RA, Posey JE, Kruer MC, Kernohan KD, Morales Saute JA, Vanderver A, Pehlivan D, Marafi D, Lupski JR. Biallelic Variants in the Ectonucleotidase ENTPD1 Cause a Complex Neurodevelopmental Disorder with Intellectual Disability, Distinct White Matter Abnormalities, and Spastic Paraplegia. Ann Neurol 2022; 92:304-321. [PMID: 35471564 PMCID: PMC10054521 DOI: 10.1002/ana.26381] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Human genomics established that pathogenic variation in diverse genes can underlie a single disorder. For example, hereditary spastic paraplegia is associated with >80 genes, with frequently only few affected individuals described for each gene. Herein, we characterize a large cohort of individuals with biallelic variation in ENTPD1, a gene previously linked to spastic paraplegia 64 (Mendelian Inheritance in Man # 615683). METHODS Individuals with biallelic ENTPD1 variants were recruited worldwide. Deep phenotyping and molecular characterization were performed. RESULTS A total of 27 individuals from 17 unrelated families were studied; additional phenotypic information was collected from published cases. Twelve novel pathogenic ENTPD1 variants are described (NM 001776.6): c.398_399delinsAA; p.(Gly133Glu), c.540del; p.(Thr181Leufs*18), c.640del; p.(Gly216Glufs*75), c.185 T > G; p.(Leu62*), c.1531 T > C; p.(*511Glnext*100), c.967C > T; p.(Gln323*), c.414-2_414-1del, and c.146 A > G; p.(Tyr49Cys) including 4 recurrent variants c.1109 T > A; p.(Leu370*), c.574-6_574-3del, c.770_771del; p.(Gly257Glufs*18), and c.1041del; p.(Ile348Phefs*19). Shared disease traits include childhood onset, progressive spastic paraplegia, intellectual disability (ID), dysarthria, and white matter abnormalities. In vitro assays demonstrate that ENTPD1 expression and function are impaired and that c.574-6_574-3del causes exon skipping. Global metabolomics demonstrate ENTPD1 deficiency leads to impaired nucleotide, lipid, and energy metabolism. INTERPRETATION The ENTPD1 locus trait consists of childhood disease onset, ID, progressive spastic paraparesis, dysarthria, dysmorphisms, and white matter abnormalities, with some individuals showing neurocognitive regression. Investigation of an allelic series of ENTPD1 (1) expands previously described features of ENTPD1-related neurological disease, (2) highlights the importance of genotype-driven deep phenotyping, (3) documents the need for global collaborative efforts to characterize rare autosomal recessive disease traits, and (4) provides insights into disease trait neurobiology. ANN NEUROL 2022;92:304-321.
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Affiliation(s)
- Daniel G. Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Aren E. Marshall
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Karina Carvalho Donis
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | | | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ, 85016, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine–Phoenix, Phoenix, AZ, USA
| | - Yoko A. Ito
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Clarissa Rocca
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Jill V. Hunter
- Texas Children’s Hospital, Houston, Texas, 77030, USA
- Division of Neuroradiology, Edward B. Singleton Department of Radiology, Texas Children’s Hospital, Houston, Texas
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Lisa T. Emrick
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Alexander Lossos
- Department of Neurology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Yakov Fellig
- Department of Pathology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Eugenia Prus
- Hematology and Bone Marrow Transplantation Division, Hadassah Medical Center and the Hebrew University, POB 12000, 91120, Jerusalem, Israel
| | - Yosef Kalish
- Hematology and Bone Marrow Transplantation Division, Hadassah Medical Center and the Hebrew University, POB 12000, 91120, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Genetics, Hadassah Medical Center and the Hebrew University, POB 12000, 91120, Jerusalem, Israel
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Kayla Muirhead
- Division of Neurology, Children’s Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Nebal W. Saadi
- College of Medicine / University of Baghdad, Children Welfare Teaching Hospital, Medical City Complex, Baghdad 10001, Iraq
| | - Maha S. Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - David L. Skidmore
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Matthew Osmond
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Thiago Oliveira Silva
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Henry Houlden
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, United Kingdom
| | - Ehsan Ghayoorarimiani
- Genetics Section, Molecular and Clinical Sciences Institute, St. George’s University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Yalda Jamshidi
- Genetics Section, Molecular and Clinical Sciences Institute, St. George’s University of London, Cranmer Terrace, London SW17 0RE, UK
| | | | - Homa Tajsharghi
- School of Health Sciences, Division Biomedicine, University of Skovde, Skovde, Sweden
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, 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, Texas, USA
| | - Lorena Travaglini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Laboratory of Molecular Medicine, Department of Neuroscience, IRCCS Bambino Gesù Children’s Hospital, 00146 Rome, Italy
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Laboratory of Molecular Medicine, Department of Neuroscience, IRCCS Bambino Gesù Children’s Hospital, 00146 Rome, Italy
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Michael C. Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ, 85016, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine–Phoenix, Phoenix, AZ, USA
| | - Kristin D. Kernohan
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
- Newborn Screening Ontario, Ottawa, Canada, K1H 8L1, Canada
| | - Jonas A. Morales Saute
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Internal Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Neurology Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Adeline Vanderver
- Division of Neurology, Children’s Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
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