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Ha YJJ, Nisal A, Tang I, Lee C, Jhamb I, Wallace C, Howarth R, Schroeder S, Vong KI, Meave N, Jiwani F, Barrows C, Lee S, Jiang N, Patel A, Bagga K, Banka N, Friedman L, Blanco FA, Yu S, Rhee S, Jeong HS, Plutzer I, Major MB, Benoit B, Poüs C, Heffner C, Kibar Z, Bot GM, Northrup H, Au KS, Strain M, Ashley-Koch AE, Finnell RH, Le JT, Meltzer HS, Araujo C, Machado HR, Stevenson RE, Yurrita A, Mumtaz S, Ahmed A, Khara MH, Mutchinick OM, Medina-Bereciartu JR, Hildebrandt F, Melikishvili G, Marwan AI, Capra V, Noureldeen MM, Salem AMS, Issa MY, Zaki MS, Xu L, Lee JE, Shin D, Alkelai A, Shuldiner AR, Kingsmore SF, Murray SA, Gee HY, Miller WT, Tolias KF, Wallingford JB, Kim S, Gleeson JG. The contribution of de novo coding mutations to meningomyelocele. Nature 2025; 641:419-426. [PMID: 40140573 DOI: 10.1038/s41586-025-08676-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 01/20/2025] [Indexed: 03/28/2025]
Abstract
Meningomyelocele (also known as spina bifida) is considered to be a genetically complex disease resulting from a failure of the neural tube to close. Individuals with meningomyelocele display neuromotor disability and frequent hydrocephalus, requiring ventricular shunting. A few genes have been proposed to contribute to disease susceptibility, but beyond that it remains unexplained1. We postulated that de novo mutations under purifying selection contribute to the risk of developing meningomyelocele2. Here we recruited a cohort of 851 meningomyelocele trios who required shunting at birth and 732 control trios, and found that de novo likely gene disruption or damaging missense mutations occurred in approximately 22.3% of subjects, with 28% of such variants estimated to contribute to disease risk. The 187 genes with damaging de novo mutations collectively define networks including actin cytoskeleton and microtubule-based processes, Netrin-1 signalling and chromatin-modifying enzymes. Gene validation demonstrated partial or complete loss of function, impaired signalling and defective closure of the neural tube in Xenopus embryos. Our results indicate that de novo mutations make key contributions to meningomyelocele risk, and highlight critical pathways required for neural tube closure in human embryogenesis.
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Affiliation(s)
- Yoo-Jin Jiny Ha
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ashna Nisal
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Isaac Tang
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Chanjae Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Ishani Jhamb
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Cassidy Wallace
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Robyn Howarth
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Sarah Schroeder
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Keng Ioi Vong
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Naomi Meave
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Fiza Jiwani
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Chelsea Barrows
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Sangmoon Lee
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Nan Jiang
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Arzoo Patel
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Krisha Bagga
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Niyati Banka
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Liana Friedman
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Francisco A Blanco
- Department of Neuroscience, Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Seyoung Yu
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Soeun Rhee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Hui Su Jeong
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Isaac Plutzer
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA
| | - Michael B Major
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA
| | - Béatrice Benoit
- INSERM UMR-S 1193, UFR de Pharmacie, University Paris-Saclay, Orsay, France
| | - Christian Poüs
- INSERM UMR-S 1193, UFR de Pharmacie, University Paris-Saclay, Orsay, France
- Biochimie-Hormonologie, Assistance Publique - Hôpitaux de Paris Université Paris-Saclay, Clamart, France
| | | | - Zoha Kibar
- Department of Neurosciences, Research Center of CHU Sainte Justine, University of Montreal, Montreal, Quebec, Canada
| | - Gyang Markus Bot
- Neurosurgery Division, Department of Surgery, Jos University Teaching Hospital, Jos, Nigeria
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston and Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Kit Sing Au
- Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston and Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Madison Strain
- Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | | | - Richard H Finnell
- Center for Precision Environmental Health, Departments of Molecular and Human Genetics, Molecular and Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Joan T Le
- Rady Children's Hospital, San Diego, CA, USA
| | | | - Camila Araujo
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Helio R Machado
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Roger E Stevenson
- J. C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC, USA
| | - Anna Yurrita
- Catedrática de Ciencias Ómicas, Facultad de Medicina, Universidad Francisco Marroquín, Guatemala City, Guatemala
| | - Sara Mumtaz
- National University of Medical Sciences, Rawalpindi, Pakistan
| | | | | | - Osvaldo M Mutchinick
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | | | - Gia Melikishvili
- Department of Pediatrics, MediClubGeorgia Medical Center, Tbilisi, Georgia
| | - Ahmed I Marwan
- Division of Pediatric General, Thoracic and Fetal Surgery, Department of Surgery, University of Missouri School of Medicine, Columbia, MO, USA
| | - Valeria Capra
- Genomics and Clinical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Mahmoud M Noureldeen
- Department of Pediatrics, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Aida M S Salem
- Department of Pediatrics, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Mahmoud Y Issa
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Ji Eun Lee
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Donghyuk Shin
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | | | | | | | | | - Heon Yung Gee
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA
- VA Medical Center, Northport, NY, USA
| | - Kimberley F Tolias
- Department of Neuroscience, Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea.
- POSTECH Biotechnology Center, Pohang University of Science and Technology, Pohang, Republic of Korea.
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
- Department of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA, USA.
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