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Richard MA, Lupo PJ, Ehli EA, Sahin M, Krueger DA, Wu JY, Bebin EM, Au KS, Northrup H, Farach LS. Common epilepsy variants from the general population are not associated with epilepsy among individuals with tuberous sclerosis complex. Am J Med Genet A 2024; 194:e63569. [PMID: 38366765 PMCID: PMC11060940 DOI: 10.1002/ajmg.a.63569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Common genetic variants identified in the general population have been found to increase phenotypic risks among individuals with certain genetic conditions. Up to 90% of individuals with tuberous sclerosis complex (TSC) are affected by some type of epilepsy, yet the common variants contributing to epilepsy risk in the general population have not been evaluated in the context of TSC-associated epilepsy. Such knowledge is important to help uncover the underlying pathogenesis of epilepsy in TSC which is not fully understood, and critical as uncontrolled epilepsy is a major problem in this population. To evaluate common genetic modifiers of epilepsy, our study pooled phenotypic and genotypic data from 369 individuals with TSC to evaluate known and novel epilepsy common variants. We did not find evidence of enhanced genetic penetrance for known epilepsy variants identified across the largest genome-wide association studies of epilepsy in the general population, but identified support for novel common epilepsy variants in the context of TSC. Specifically, we have identified a novel signal in SLC7A1 that may be functionally involved in pathways relevant to TSC and epilepsy. Our study highlights the need for further evaluation of genetic modifiers in TSC to aid in further understanding of epilepsy in TSC and improve outcomes.
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Affiliation(s)
- Melissa A Richard
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, USA
| | - Mustafa Sahin
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Darcy A Krueger
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Joyce Y Wu
- Epilepsy Center, Division of Pediatric Neurology, Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Division of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Elizabeth M Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kit Sing Au
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Hope Northrup
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Laura S Farach
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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Vong KI, Lee S, Au KS, Crowley TB, Capra V, Martino J, Haller M, Araújo C, Machado HR, George R, Gerding B, James KN, Stanley V, Jiang N, Alu K, Meave N, Nidhiry AS, Jiwani F, Tang I, Nisal A, Jhamb I, Patel A, Patel A, McEvoy-Venneri J, Barrows C, Shen C, Ha YJ, Howarth R, Strain M, Ashley-Koch AE, Azam M, Mumtaz S, Bot GM, Finnell RH, Kibar Z, Marwan AI, Melikishvili G, Meltzer HS, Mutchinick OM, Stevenson DA, Mroczkowski HJ, Ostrander B, Schindewolf E, Moldenhauer J, Zackai EH, Emanuel BS, Garcia-Minaur S, Nowakowska BA, Stevenson RE, Zaki MS, Northrup H, McNamara HK, Aldinger KA, Phelps IG, Deng M, Glass IA, Morrow B, McDonald-McGinn DM, Sanna-Cherchi S, Lamb DJ, Gleeson JG, Koch AEA, Meltzer HS, Le J, Au KS, Northrup H, Bot GM, Capra V, Finnell RH, Kibar Z, Lupo PJ, Machado HR, Araújo C, Magana T, Marwan AI, Melikishvili G, Mutchinick OM, Stevenson RE, Yurrita A, Zaki MS, Mumtaz S, Medina-Bereciartu JR, Kolvenbach CM, Shril S, Hildebrandt F, Noureldeen MM, Salem AM, Takahashi Y, Salimi-Dafsari H, Phillips HW, Hanak B, Kara B, Güneş AS, Gonda DD, Kirmani S, Tkemaladze T, Gleeson JG. Risk of meningomyelocele mediated by the common 22q11.2 deletion. Science 2024; 384:584-590. [PMID: 38696583 DOI: 10.1126/science.adl1624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/27/2024] [Indexed: 05/04/2024]
Abstract
Meningomyelocele is one of the most severe forms of neural tube defects (NTDs) and the most frequent structural birth defect of the central nervous system. We assembled the Spina Bifida Sequencing Consortium to identify causes. Exome and genome sequencing of 715 parent-offspring trios identified six patients with chromosomal 22q11.2 deletions, suggesting a 23-fold increased risk compared with the general population. Furthermore, analysis of a separate 22q11.2 deletion cohort suggested a 12- to 15-fold increased NTD risk of meningomyelocele. The loss of Crkl, one of several neural tube-expressed genes within the minimal deletion interval, was sufficient to replicate NTDs in mice, where both penetrance and expressivity were exacerbated by maternal folate deficiency. Thus, the common 22q11.2 deletion confers substantial meningomyelocele risk, which is partially alleviated by folate supplementation.
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Affiliation(s)
- Keng Ioi Vong
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Sangmoon Lee
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kit Sing Au
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX 77030, USA
| | - T Blaine Crowley
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Valeria Capra
- Genomics and Clinical Genetics Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Jeremiah Martino
- Division of Nephrology, Department of Medicine, Columbia University, NY 10027, USA
| | - Meade Haller
- Center for Reproductive Medicine, Department of Molecular and Cellular Biology and Scott Department of Urology, Baylor College of Medicine, TX 77030, USA
| | - Camila Araújo
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Hélio R Machado
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Renee George
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Bryn Gerding
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kiely N James
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Nan Jiang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kameron Alu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Naomi Meave
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Anna S Nidhiry
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Fiza Jiwani
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Isaac Tang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Ashna Nisal
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Ishani Jhamb
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Arzoo Patel
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Aakash Patel
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Jennifer McEvoy-Venneri
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Chelsea Barrows
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Celina Shen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Yoo-Jin Ha
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Robyn Howarth
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Madison Strain
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Matloob Azam
- Pediatrics and Child Neurology, Wah Medical College, Wah Cantt, Punjab 47000, Pakistan
| | - Sara Mumtaz
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Punjab 46000, Pakistan
| | - Gyang Markus Bot
- Neurosurgery Division, Department of Surgery, Jos University Teaching Hospital, Jos 930105, Nigeria
| | - 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 77030, USA
| | - Zoha Kibar
- Department of Neurosciences, University of Montreal and CHU Sainte Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Ahmed I Marwan
- Division of Pediatric Surgery, University of Colorado School of Medicine, Children's Hospital of Colorado, Colorado Fetal Care Center, Aurora, CO 80045, USA
| | - Gia Melikishvili
- Department of Pediatrics, MediClubGeorgia Medical Center, Tbilisi 0160, Georgia
| | - Hal S Meltzer
- Department of Neurosurgery, University of California San Diego, Rady Children's Hospital, San Diego, CA 92123, USA
| | - Osvaldo M Mutchinick
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, 14080 Mexico City, Mexico
| | - David A Stevenson
- Division of Medical Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Henry J Mroczkowski
- Division of Medical Genetics, University of Tennessee Health Science Campus, Memphis, TN 38163, USA
| | - Betsy Ostrander
- Division of Pediatric Neurology, Primary Children's Hospital, University of Utah, Salt Lake City, UT 84113, USA
| | - Erica Schindewolf
- Center for Fetal Diagnosis and Treatment, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Julie Moldenhauer
- Center for Fetal Diagnosis and Treatment, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elaine H Zackai
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beverly S Emanuel
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sixto Garcia-Minaur
- Clinical Genetics Section, Institute of Medical and Molecular Genetics, University Hospital La Paz, 28046 Madrid, Spain
| | - Beata A Nowakowska
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka, 01-211 Warsaw, Poland
| | - Roger E Stevenson
- JC Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX 77030, USA
| | - Hanna K McNamara
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
- Department of Neurology, University of Washington, Seattle, WA 98105, USA
| | - Ian G Phelps
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Mei Deng
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Ian A Glass
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Bernice Morrow
- Division of Translational Genetics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Donna M McDonald-McGinn
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Human Biology and Medical Genetics, Sapienza University, 00185-Rome RM, Italy
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, NY 10027, USA
| | - Dolores J Lamb
- Center for Reproductive Medicine, Department of Molecular and Cellular Biology and Scott Department of Urology, Baylor College of Medicine, TX 77030, USA
- Department of Urology, Center for Reproductive Genomics, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
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Luo H, Lao L, Au KS, Northrup H, He X, Forget D, Gauthier MS, Coulombe B, Bourdeau I, Shi W, Gagliardi L, Fragoso MCBV, Peng J, Wu J. ARMC5 controls the degradation of most Pol II subunits, and ARMC5 mutation increases neural tube defect risks in mice and humans. Genome Biol 2024; 25:19. [PMID: 38225631 PMCID: PMC10789052 DOI: 10.1186/s13059-023-03147-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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/18/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Neural tube defects (NTDs) are caused by genetic and environmental factors. ARMC5 is part of a novel ubiquitin ligase specific for POLR2A, the largest subunit of RNA polymerase II (Pol II). RESULTS We find that ARMC5 knockout mice have increased incidence of NTDs, such as spina bifida and exencephaly. Surprisingly, the absence of ARMC5 causes the accumulation of not only POLR2A but also most of the other 11 Pol II subunits, indicating that the degradation of the whole Pol II complex is compromised. The enlarged Pol II pool does not lead to generalized Pol II stalling or a generalized decrease in mRNA transcription. In neural progenitor cells, ARMC5 knockout only dysregulates 106 genes, some of which are known to be involved in neural tube development. FOLH1, critical in folate uptake and hence neural tube development, is downregulated in the knockout intestine. We also identify nine deleterious mutations in the ARMC5 gene in 511 patients with myelomeningocele, a severe form of spina bifida. These mutations impair the interaction between ARMC5 and Pol II and reduce Pol II ubiquitination. CONCLUSIONS Mutations in ARMC5 increase the risk of NTDs in mice and humans. ARMC5 is part of an E3 controlling the degradation of all 12 subunits of Pol II under physiological conditions. The Pol II pool size might have effects on NTD pathogenesis, and some of the effects might be via the downregulation of FOLH1. Additional mechanistic work is needed to establish the causal effect of the findings on NTD pathogenesis.
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Affiliation(s)
- Hongyu Luo
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada.
| | - Linjiang Lao
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Kit Sing Au
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Xiao He
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Diane Forget
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Marie-Soleil Gauthier
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Benoit Coulombe
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Isabelle Bourdeau
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
- Division of Endocrinology, CHUM, Montreal, QC, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Wei Shi
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Lucia Gagliardi
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
- Endocrine and Diabetes Unit, Queen Elizabeth Hospital, Adelaide, Australia
| | - Maria Candida Barisson Villares Fragoso
- Unidade de Suprarrenal Disciplina de Endocrinologia E Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Junzheng Peng
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Jiangping Wu
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada.
- Department of Medicine, Université de Montréal, Montreal, QC, Canada.
- Division of Nephrology, CHUM, Montreal, QC, Canada.
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Farach LS, Northrup H, Nellist M, van Unen L, Hillman P, Klonowska K, Ekong R, Crino PB, Sing Au K. Mild TSC Phenotype and Non-Penetrance Associated with a Frameshift Variant in TSC2 Prompts Caution in Evaluating Pathogenicity of Frameshift Variants. Gene 2023:147566. [PMID: 37311496 DOI: 10.1016/j.gene.2023.147566] [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: 04/04/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Technological advances in genetic testing, particularly the adoption of noninvasive prenatal screening (NIPS) for single gene disorders such as tuberous sclerosis complex (TSC, OMIM# 613254), mean that putative/possible pathogenetic DNA variants can be identified prior to the appearance of a disease phenotype. Without a phenotype, accurate prediction of variant pathogenicity is crucial. Here, we report a TSC2 frameshift variant, NM_000548.5(TSC2):c.4255_4256delCA, predicted to result in nonsense-mediated mRNA decay (NMD) and cessation of TSC2 protein production and thus pathogenic according to ACMG criteria, identified by NIPS and subsequently detected in family members with few or no symptoms of TSC. Due to the lack of TSC-associated features in the family, we hypothesized that the deletion created a non-canonical 5' donor site resulting in cryptic splicing and a transcript encoding active TSC2 protein. Verifying the predicted effect of the variant was key to designating pathogenicity in this case and should be considered for other frameshift variants in other genetic disorders. METHODS Phenotypic information on the family members was collected via review of the medical records and patient reports. RNA studies were performed using proband mRNA isolated from blood lymphocytes for RT-PCR and Sanger sequencing. Functional studies were performed by transient expression of the TSC2 variant proteins in cultured cells, followed by immunoblotting. RESULTS No family members harboring the variant met any major clinical diagnostic criteria for TSC, though a few minor features non-specific to TSC were present. RNA studies supported the hypothesis that the variant caused cryptic splicing, resulting in an mRNA transcript with an in-frame deletion of 93 base pairs r.[4255_4256del, 4251_4343del], p.[(Gln1419Valfs*104), (Gln1419_Ser1449del)]. Expression studies demonstrated that the canonical function of the resulting truncated TSC2 p.Gln1419_Ser1449del protein product was maintained and similar to wildtype. CONCLUSION Although most frameshift variants are likely to result in NMD, the NM_000548.5(TSC2):c.4255_4256delCA variant creates a cryptic 5' splice donor site, resulting in an in-frame deletion that retains TSC2 function, explaining why carriers of the variant do not have typical features of TSC. The information is important for this family and others with the same variant. Equally important is the lesson that predictions can be inaccurate, and that caution should be used when designating frameshift variants as pathogenic, especially when phenotypic information to corroborate testing results is unavailable. Our work demonstrates that functional RNA- and protein-based confirmation of the effects of DNA variants improves molecular genetic diagnostics.
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Affiliation(s)
- Laura S Farach
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston) and Children's Memorial Hermann Hospital, Houston, Texas, USA.
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston) and Children's Memorial Hermann Hospital, Houston, Texas, USA
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Leontine van Unen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Paul Hillman
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston) and Children's Memorial Hermann Hospital, Houston, Texas, USA
| | - Katarzyna Klonowska
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rosemary Ekong
- Research Department of Genetics, Evolution and Environment, Darwin Building, University College London, London, United Kingdom
| | - Peter B Crino
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston) and Children's Memorial Hermann Hospital, Houston, Texas, USA
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5
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Bogaert E, Garde A, Gautier T, Rooney K, Duffourd Y, LeBlanc P, van Reempts E, Tran Mau-Them F, Wentzensen IM, Au KS, Richardson K, Northrup H, Gatinois V, Geneviève D, Louie RJ, Lyons MJ, Laulund LW, Brasch-Andersen C, Maxel Juul T, El It F, Marle N, Callier P, Relator R, Haghshenas S, McConkey H, Kerkhof J, Cesario C, Novelli A, Brunetti-Pierri N, Pinelli M, Pennamen P, Naudion S, Legendre M, Courdier C, Trimouille A, Fenzy MD, Pais L, Yeung A, Nugent K, Roeder ER, Mitani T, Posey JE, Calame D, Yonath H, Rosenfeld JA, Musante L, Faletra F, Montanari F, Sartor G, Vancini A, Seri M, Besmond C, Poirier K, Hubert L, Hemelsoet D, Munnich A, Lupski JR, Philippe C, Thauvin-Robinet C, Faivre L, Sadikovic B, Govin J, Dermaut B, Vitobello A. SRSF1 haploinsufficiency is responsible for a syndromic developmental disorder associated with intellectual disability. Am J Hum Genet 2023; 110:790-808. [PMID: 37071997 PMCID: PMC10183470 DOI: 10.1016/j.ajhg.2023.03.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 12/14/2022] [Accepted: 03/23/2023] [Indexed: 04/20/2023] Open
Abstract
SRSF1 (also known as ASF/SF2) is a non-small nuclear ribonucleoprotein (non-snRNP) that belongs to the arginine/serine (R/S) domain family. It recognizes and binds to mRNA, regulating both constitutive and alternative splicing. The complete loss of this proto-oncogene in mice is embryonically lethal. Through international data sharing, we identified 17 individuals (10 females and 7 males) with a neurodevelopmental disorder (NDD) with heterozygous germline SRSF1 variants, mostly de novo, including three frameshift variants, three nonsense variants, seven missense variants, and two microdeletions within region 17q22 encompassing SRSF1. Only in one family, the de novo origin could not be established. All individuals featured a recurrent phenotype including developmental delay and intellectual disability (DD/ID), hypotonia, neurobehavioral problems, with variable skeletal (66.7%) and cardiac (46%) anomalies. To investigate the functional consequences of SRSF1 variants, we performed in silico structural modeling, developed an in vivo splicing assay in Drosophila, and carried out episignature analysis in blood-derived DNA from affected individuals. We found that all loss-of-function and 5 out of 7 missense variants were pathogenic, leading to a loss of SRSF1 splicing activity in Drosophila, correlating with a detectable and specific DNA methylation episignature. In addition, our orthogonal in silico, in vivo, and epigenetics analyses enabled the separation of clearly pathogenic missense variants from those with uncertain significance. Overall, these results indicated that haploinsufficiency of SRSF1 is responsible for a syndromic NDD with ID due to a partial loss of SRSF1-mediated splicing activity.
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Affiliation(s)
- Elke Bogaert
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Aurore Garde
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs", Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Thierry Gautier
- University Grenoble Alpes, Inserm U1209, CNRS UMR 5309, Institute for Advanced Biosciences (IAB), 38000 Grenoble, France
| | - Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Yannis Duffourd
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Pontus LeBlanc
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Emma van Reempts
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Frederic Tran Mau-Them
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | | | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Kate Richardson
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Vincent Gatinois
- Unité de Génétique Chromosomique, CHU Montpellier, Montpellier, France
| | - David Geneviève
- Montpellier University, Inserm U1183, Montpellier, France; Reference center for rare disease developmental anomaly malformative syndrome, Department of Medical Genetics, Montpellier Hospital, Montpellier, France
| | | | | | | | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark; Human Genetics, Department of Clinical Research, Health Faculty, University of Southern Denmark, 5000 Odense, Denmark
| | - Trine Maxel Juul
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Fatima El It
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France
| | - Nathalie Marle
- Laboratoire de Génétique Chromosomique et Moléculaire, Pôle de Biologie, CHU de Dijon, Dijon, France
| | - Patrick Callier
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Laboratoire de Génétique Chromosomique et Moléculaire, Pôle de Biologie, CHU de Dijon, Dijon, France
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Claudia Cesario
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | | | - Sophie Naudion
- Medical Genetics Department, CHU Bordeaux, Bordeaux, France
| | | | | | - Aurelien Trimouille
- INSERM U1211, Laboratoire MRGM, Bordeaux University, Bordeaux, France; Pathology Department, CHU Bordeaux, Bordeaux, France
| | - Martine Doco Fenzy
- Service de génétique, CHU de Reims, Reims, France; Service de génétique médicale, CHU de Nantes, Nantes, France; L'institut du thorax, INSERM, CNRS, UNIV Nantes, CHU de Nantes, Nantes, France
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Kimberly Nugent
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tadahiro Mitani
- 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
| | - Daniel Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Hagith Yonath
- Internal Medicine A, Danek Gertner Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics Laboratories, Houston, TX, USA
| | - Luciana Musante
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Francesca Montanari
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanna Sartor
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Marco Seri
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Claude Besmond
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Karine Poirier
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Laurence Hubert
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Arnold Munnich
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Christophe Philippe
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Christel Thauvin-Robinet
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France; Centre de Référence Maladies Rares « Déficiences intellectuelles de causes rares », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs", Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jérôme Govin
- University Grenoble Alpes, Inserm U1209, CNRS UMR 5309, Institute for Advanced Biosciences (IAB), 38000 Grenoble, France
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium.
| | - Antonio Vitobello
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France.
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6
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Garnett J, Bergh EP, Mann L, Tsao K, Austin M, Johnson A, Northrup H, Au KS, Miller B, Fletcher SA, Papanna R. Differences between myelomeningocele and myeloschisis lesions in patients undergoing open in-utero spina bifida repair. Am J Obstet Gynecol 2023. [DOI: 10.1016/j.ajog.2022.11.669] [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: 01/09/2023]
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7
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Wang C, Seltzsam S, Zheng B, Wu CHW, Nicolas-Frank C, Yousef K, Au KS, Mann N, Pantel D, Schneider S, Schierbaum L, Kitzler TM, Connaughton DM, Mao Y, Dai R, Nakayama M, Kari JA, El Desoky S, Shalaby M, Eid LA, Awad HS, Tasic V, Mane SM, Lifton RP, Baum MA, Shril S, Estrada CR, Hildebrandt F. Whole exome sequencing identifies potential candidate genes for spina bifida derived from mouse models. Am J Med Genet A 2022; 188:1355-1367. [PMID: 35040250 PMCID: PMC8995376 DOI: 10.1002/ajmg.a.62644] [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: 10/27/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 11/11/2022]
Abstract
Spina bifida (SB) is the second most common nonlethal congenital malformation. The existence of monogenic SB mouse models and human monogenic syndromes with SB features indicate that human SB may be caused by monogenic genes. We hypothesized that whole exome sequencing (WES) allows identification of potential candidate genes by (i) generating a list of 136 candidate genes for SB, and (ii) by unbiased exome-wide analysis. We generated a list of 136 potential candidate genes from three categories and evaluated WES data of 50 unrelated SB cases for likely deleterious variants in 136 potential candidate genes, and for potential SB candidate genes exome-wide. We identified 6 likely deleterious variants in 6 of the 136 potential SB candidate genes in 6 of the 50 SB cases, whereof 4 genes were derived from mouse models, 1 gene was derived from human nonsyndromic SB, and 1 gene was derived from candidate genes known to cause human syndromic SB. In addition, by unbiased exome-wide analysis, we identified 12 genes as potential candidates for SB. Identification of these 18 potential candidate genes in larger SB cohorts will help decide which ones can be considered as novel monogenic causes of human SB.
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Affiliation(s)
- Chunyan Wang
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Steve Seltzsam
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bixia Zheng
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chen-Han Wilfred Wu
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Departments of Urology and Genetics, Case Western Reserve University and University Hospitals, Cleveland, Ohio, USA
| | - Camille Nicolas-Frank
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kirollos Yousef
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Nina Mann
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Dalia Pantel
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Sophia Schneider
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Luca Schierbaum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas M Kitzler
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Dervla M Connaughton
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Youying Mao
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rufeng Dai
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Makiko Nakayama
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jameela A Kari
- Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia.,Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Sherif El Desoky
- Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia.,Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Mohammed Shalaby
- Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia.,Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Hazem S Awad
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, North Macedonia
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Michelle A Baum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Carlos R Estrada
- Department of Urology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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8
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Au KS, Hebert L, Hillman P, Baker C, Brown MR, Kim DK, Soldano K, Garrett M, Ashley-Koch A, Lee S, Gleeson J, Hixson JE, Morrison AC, Northrup H. Human myelomeningocele risk and ultra-rare deleterious variants in genes associated with cilium, WNT-signaling, ECM, cytoskeleton and cell migration. Sci Rep 2021; 11:3639. [PMID: 33574475 PMCID: PMC7878900 DOI: 10.1038/s41598-021-83058-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/28/2021] [Indexed: 01/08/2023] Open
Abstract
Myelomeningocele (MMC) affects one in 1000 newborns annually worldwide and each surviving child faces tremendous lifetime medical and caregiving burdens. Both genetic and environmental factors contribute to disease risk but the mechanism is unclear. This study examined 506 MMC subjects for ultra-rare deleterious variants (URDVs, absent in gnomAD v2.1.1 controls that have Combined Annotation Dependent Depletion score ≥ 20) in candidate genes either known to cause abnormal neural tube closure in animals or previously associated with human MMC in the current study cohort. Approximately 70% of the study subjects carried one to nine URDVs among 302 candidate genes. Half of the study subjects carried heterozygous URDVs in multiple genes involved in the structure and/or function of cilium, cytoskeleton, extracellular matrix, WNT signaling, and/or cell migration. Another 20% of the study subjects carried heterozygous URDVs in candidate genes associated with gene transcription regulation, folate metabolism, or glucose metabolism. Presence of URDVs in the candidate genes involving these biological function groups may elevate the risk of developing myelomeningocele in the study cohort.
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Affiliation(s)
- K S Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - L Hebert
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - P Hillman
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - C Baker
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.,Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - M R Brown
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center At Houston, Houston, TX, 77030, USA
| | - D-K Kim
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center At Houston, Houston, TX, 77030, USA
| | - K Soldano
- Department of Medicine, Duke University Medical Center, Durham, NC, 27701, USA
| | - M Garrett
- Department of Medicine, Duke University Medical Center, Durham, NC, 27701, USA
| | - A Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, NC, 27701, USA
| | - S Lee
- Department of Neurosciences and Pediatrics, University of California-San Diego, La Jolla, CA, 92093, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, 92025, USA
| | - J Gleeson
- Department of Neurosciences and Pediatrics, University of California-San Diego, La Jolla, CA, 92093, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, 92025, USA
| | - J E Hixson
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center At Houston, Houston, TX, 77030, USA
| | - A C Morrison
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center At Houston, Houston, TX, 77030, USA
| | - H Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
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9
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Farach LS, Richard MA, Lupo PJ, Sahin M, Krueger DA, Wu JY, Bebin EM, Au KS, Northrup H. Epilepsy Risk Prediction Model for Patients With Tuberous Sclerosis Complex. Pediatr Neurol 2020; 113:46-50. [PMID: 33011641 PMCID: PMC10461434 DOI: 10.1016/j.pediatrneurol.2020.07.015] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/29/2020] [Accepted: 07/25/2020] [Indexed: 01/13/2023]
Abstract
BACKGROUND Individuals with tuberous sclerosis complex are at increased risk of epilepsy. Early seizure control improves developmental outcomes, making identifying at-risk patients critically important. Despite several identified risk factors, it remains difficult to predict. The purpose of the study was to evaluate the combined risk prediction of previously identified risk factors for epilepsy in individuals with tuberous sclerosis complex. METHODS The study group (n = 333) consisted of individuals with tuberous sclerosis complex who were enrolled in the Tuberous Sclerosis Complex Autism Center of Excellence Research Network and UT TSC Biobank. The outcome was defined as having an epilepsy diagnosis. Potential risk factors included sex, TSC genotype, and tuber presence. Logistic regression was used to calculate the odds ratio and P value for the association between each variable and epilepsy. A clinical risk prediction model incorporating all risk factors was built. Area under the curve was calculated to characterize the full model's ability to discriminate individuals with tuberous sclerosis complex with and without epilepsy. RESULTS The strongest risk for epilepsy was presence of tubers (95% confidence interval: 2.39 to 10.89). Individuals with pathogenic TSC2 variants were three times more likely (95% confidence interval: 1.55 to 6.36) to develop seizures compared with those with tuberous sclerosis complex from other causes. The combination of risk factors resulted in an area under the curve 0.73. CONCLUSIONS Simple characteristics of patients with tuberous sclerosis complex can be combined to successfully predict epilepsy risk. A risk assessment model that incorporates sex, TSC genotype, protective TSC2 missense variant, and tuber presence correctly predicts epilepsy in 73% of patients with tuberous sclerosis complex.
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Affiliation(s)
- Laura S Farach
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas.
| | - Melissa A Richard
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Mustafa Sahin
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Darcy A Krueger
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Joyce Y Wu
- Division of Pediatric Neurology, UCLA Mattel Children's Hospital and David Geffen School of Medicine, Los Angeles, California
| | | | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
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10
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Brown HM, Murray SA, Northrup H, Au KS, Niswander LA. Snx3 is important for mammalian neural tube closure via its role in canonical and non-canonical WNT signaling. Development 2020; 147:147/22/dev192518. [PMID: 33214242 DOI: 10.1242/dev.192518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/09/2020] [Indexed: 12/26/2022]
Abstract
Disruptions in neural tube (NT) closure result in neural tube defects (NTDs). To understand the molecular processes required for mammalian NT closure, we investigated the role of Snx3, a sorting nexin gene. Snx3-/- mutant mouse embryos display a fully-penetrant cranial NTD. In vivo, we observed decreased canonical WNT target gene expression in the cranial neural epithelium of the Snx3-/- embryos and a defect in convergent extension of the neural epithelium. Snx3-/- cells show decreased WNT secretion, and live cell imaging reveals aberrant recycling of the WNT ligand-binding protein WLS and mis-trafficking to the lysosome for degradation. The importance of SNX3 in WNT signaling regulation is demonstrated by rescue of NT closure in Snx3-/- embryos with a WNT agonist. The potential for SNX3 to function in human neurulation is revealed by a point mutation identified in an NTD-affected individual that results in functionally impaired SNX3 that does not colocalize with WLS and the degradation of WLS in the lysosome. These data indicate that Snx3 is crucial for NT closure via its role in recycling WLS in order to control levels of WNT signaling.
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Affiliation(s)
- Heather Mary Brown
- Cell Biology, Stem Cells, and Developmental Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | | | - Hope Northrup
- Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Kit Sing Au
- Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lee A Niswander
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
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11
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Hebert L, Hillman P, Baker C, Brown M, Ashley-Koch A, Hixson JE, Morrison AC, Northrup H, Au KS. Burden of rare deleterious variants in WNT signaling genes among 511 myelomeningocele patients. PLoS One 2020; 15:e0239083. [PMID: 32970752 PMCID: PMC7514064 DOI: 10.1371/journal.pone.0239083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/28/2020] [Indexed: 12/22/2022] Open
Abstract
Genes in the noncanonical WNT signaling pathway controlling planar cell polarity have been linked to the neural tube defect myelomeningocele. We hypothesized that some genes in the WNT signaling network have a higher mutational burden in myelomeningocele subjects than in reference subjects in gnomAD. Exome sequencing data from 511 myelomeningocele subjects was obtained in-house and data from 29,940 ethnically matched subjects was provided by version 2 of the publicly available Genome Aggregation Database. To compare mutational burden, we collapsed rare deleterious variants across each of 523 human WNT signaling genes in case and reference populations. Ten WNT signaling genes were disrupted with a higher mutational burden among Mexican American myelomeningocele subjects compared to reference subjects (Fishers exact test, P ≤ 0.05) and seven different genes were disrupted among individuals of European ancestry compared to reference subjects. Gene ontology enrichment analyses indicate that genes disrupted only in the Mexican American population play a role in planar cell polarity whereas genes identified in both populations are important for the regulation of canonical WNT signaling. In summary, evidence for WNT signaling genes that may contribute to myelomeningocele in humans is presented and discussed.
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Affiliation(s)
- Luke Hebert
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, United States of America
| | - Paul Hillman
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, United States of America
| | - Craig Baker
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, United States of America
| | - Michael Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, United States of America
| | - Allison Ashley-Koch
- Department of Medicine and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
| | - James E. Hixson
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, United States of America
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, United States of America
| | - Hope Northrup
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, United States of America
| | - Kit Sing Au
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, United States of America
- * E-mail:
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12
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Hillman P, Baker C, Hebert L, Brown M, Hixson J, Ashley-Koch A, Morrison AC, Northrup H, Au KS. Identification of novel candidate risk genes for myelomeningocele within the glucose homeostasis/oxidative stress and folate/one-carbon metabolism networks. Mol Genet Genomic Med 2020; 8:e1495. [PMID: 32960507 PMCID: PMC7667334 DOI: 10.1002/mgg3.1495] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/17/2020] [Accepted: 08/05/2020] [Indexed: 12/27/2022] Open
Abstract
Background Neural tube defects (NTDs) are the second most common complex birth defect, yet, our understanding of the genetic contribution to their development remains incomplete. Two environmental factors associated with NTDs are Folate and One Carbon Metabolism (FOCM) and Glucose Homeostasis and Oxidative Stress (GHOS). Utilizing next‐generation sequencing of a large patient cohort, we identify novel candidate genes in these two networks to provide insights into NTD mechanisms. Methods Exome sequencing (ES) was performed in 511 patients, born with myelomeningocele, divided between European American and Mexican American ethnicities. Healthy control data from the Genome Aggregation database were ethnically matched and used as controls. Rare, high fidelity, nonsynonymous predicted damaging missense, nonsense, or canonical splice site variants in independently generated candidate gene lists for FOCM and GHOS were identified. We used a gene‐based collapsing approach to quantify mutational burden in case and controls, with the control cohort estimated using cumulative allele frequencies assuming Hardy–Weinberg equilibrium. Results We identified 45 of 837 genes in the FOCM network and 22 of 568 genes in the GHOS network as possible NTD risk genes with p < 0.05. No nominally significant risk genes were shared between ethnicities. Using a novel approach to mutational burden we identify 55 novel NTD risk associations. Conclusions We provide a means of utilizing large publicly available sequencing datasets as controls for sequencing projects examining rare disease. This approach confirmed existing risk genes for myelomeningocele and identified possible novel risk genes. Lastly, it suggests possible distinct genetic etiologies for this malformation between different ethnicities.
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Affiliation(s)
- Paul Hillman
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Craig Baker
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA.,Craig Baker is now affiliated with Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Luke Hebert
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Michael Brown
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - James Hixson
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Allison Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA.,Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
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13
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Farach LS, Pearson DA, Woodhouse JP, Schraw JM, Sahin M, Krueger DA, Wu JY, Bebin EM, Lupo PJ, Au KS, Northrup H. Tuberous Sclerosis Complex Genotypes and Developmental Phenotype. Pediatr Neurol 2019; 96:58-63. [PMID: 31005478 PMCID: PMC6837240 DOI: 10.1016/j.pediatrneurol.2019.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Children with tuberous sclerosis complex (TSC), caused by pathogenic variants in TSC1/TSC2, are at risk for intellectual disability. TSC2 pathogenic variants appear to increase the risk, compared with TSC1. However, the effect of TSC2 pathogenic variants on early and specific domains of development hasn't been studied. Using an extensively phenotyped group, we aimed to characterize differences in early intellectual development between genotypes. METHODS The study group (n = 92) included participants with TSC enrolled in a multicenter study involving genetic testing and detailed prospective phenotyping including the Mullen Scales of Early Learning, a validated measure of cognition, language, and motor development in babies and preschool children. Mean T-scores at 24 months for each Mullen Scales of Early Learning domain were calculated for children with, versus without, a TSC2 pathogenic variant. Multivariable linear regression models were used to compare the groups, adjusting for seizures. RESULTS T-scores on every Mullen Scales of Early Learning domain were significantly worse in the TSC2 group. Below average composite scores were present in three-fourths of the TSC2 group, compared with one-fourth of those without TSC2. Having a TSC2 pathogenic variant was associated with lower composite Mullen Scales of Early Learning scores, even when corrected for seizures. CONCLUSIONS In a well-characterized patient population with standardized assessment of multiple aspects of development, we found that having a TSC2 pathogenic variant was associated with significantly lower Mullen Scales of Early Learning scores at age 24 months, independent of seizures. These data suggest that a baby with a TSC2 pathogenic variant is at high risk for significant developmental delays by 24 months.
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Affiliation(s)
- Laura S. Farach
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas,Communications should he addressed to: Laura S. Farach; 6431 Fannin Street MSB 3.142; Houston, TX 77030., (L.S. Farach)
| | - Deborah A. Pearson
- Department of Psychiatry, Division of Child and Adolescent Psychiatry, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - John P. Woodhouse
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Jeremy M. Schraw
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, Texas
| | - Mustafa Sahin
- Translational Neuroscience Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Darcy A. Krueger
- Division of Neurology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Joyce Y. Wu
- Division of Pediatric Neurology, UCLA Mattel Children’s Hospital and David Geffen School of Medicine, Los Angeles, California
| | | | - Philip J. Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Kit Sing Au
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Hope Northrup
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
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14
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Peron A, Au KS, Northrup H. Genetics, genomics, and genotype-phenotype correlations of TSC: Insights for clinical practice. Am J Med Genet C Semin Med Genet 2018; 178:281-290. [PMID: 30255984 DOI: 10.1002/ajmg.c.31651] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/22/2018] [Indexed: 01/28/2023]
Abstract
Tuberous Sclerosis Complex (TSC) is a multisystem autosomal dominant condition caused by inactivating pathogenic variants in either the TSC1 or the TSC2 gene, leading to hyperactivation of the mTOR pathway. Here, we present an update on the genetic and genomic aspects of TSC, with a focus on clinical and laboratory practice. We briefly summarize the structure of TSC1 and TSC2 as well as their protein products, and discuss current diagnostic testing, addressing mosaicism. We consider genotype-phenotype correlations as an example of precision medicine, and discuss genetic counseling in TSC, with the aim of providing geneticists and health care practitioners involved in the care of TSC individuals with useful tools for their practice.
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Affiliation(s)
- Angela Peron
- Child Neuropsychiatry Unit-Epilepsy Center (Service of Medical Genetics), San Paolo Hospital, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy.,Department of Pediatrics, Division of Medical Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Kit Sing Au
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Hope Northrup
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
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15
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Nguyen MP, Lupo PJ, Northrup H, Morrison AC, Cirino PT, Au KS. Maternal gene-micronutrient interactions related to one-carbon metabolism and the risk of myelomeningocele among offspring. Birth Defects Res 2018; 109:99-105. [PMID: 27384413 DOI: 10.1002/bdra.23538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Few studies have evaluated interactions between maternal genetic variation in 5,10-methylenetetrahydrofolate reductase (MTHFR) and micronutrient intake on the risk of myelomeningocele (MM) in offspring. Therefore, we sought to determine if the role of maternal MTHFR C677T and A1298C on MM risk is altered by maternal intake of micronutrients related to one-carbon metabolism. METHODS The study consisted of 220 MM case-parent trios recruited from 1996 to 2006. A dietary questionnaire was used to obtain information on maternal dietary intake on eight micronutrients including folate and cobalamin. TaqMan assays were used to generate MTHFR C677T and A1298C genotypes. Log-linear models were used to evaluate the joint effects of maternal genotype and micronutrient intake dichotomized as at or above versus below the United States Recommended Dietary Allowance (US RDA) on MM. RESULTS There was little evidence to suggest maternal MTHFR genotypes interacted with micronutrient intake to influence the risk of MM. For instance, the effect of MTHFR 677T was similar for mothers with cobalamin intake below US RDA (relative risk [RR] = 0.97) versus at or above US RDA cobalamin intake (RR = 0.81, interaction p = 0.87). However, some differences were noted. For example, the effect of MTHFR 1298C appeared to be different between those mothers below US RDA folate intake (RR = 0.98) versus those at or above US RDA folate intake (RR = 0.68), but the interaction was not statistically significant (interaction p = 0.27). CONCLUSION There did not appear to be strong effects of maternal micronutrient intake on the role of maternal genetic polymorphisms in MTHFR C677T and A1298C on MM risk. Birth Defects Research 109:99-105, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Margaret P Nguyen
- Divisions of Neonatology, Department of Pediatrics, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas
| | - Philip J Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics & Environmental Sciences, University of Texas Health Science Center at Houston, School of Public Health, Houston, Texas
| | - Paul T Cirino
- Department of Psychology, University of Houston, Houston, Texas
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas
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16
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Davis PE, Filip-Dhima R, Sideridis G, Peters JM, Au KS, Northrup H, Bebin EM, Wu JY, Krueger D, Sahin M. Presentation and Diagnosis of Tuberous Sclerosis Complex in Infants. Pediatrics 2017; 140:peds.2016-4040. [PMID: 29101226 PMCID: PMC5703775 DOI: 10.1542/peds.2016-4040] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [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] [Accepted: 08/25/2017] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVES Tuberous sclerosis complex (TSC) is a neurocutaneous genetic disorder with a high prevalence of epilepsy and neurodevelopmental disorders. TSC can be challenging to diagnose in infants because they often do not show many clinical signs early in life. In this study, we describe the timing and pattern of presenting and diagnostic features in a prospective longitudinal study of infants with TSC. METHODS Two multicenter, prospective studies enrolled 130 infants with definite TSC by clinical or genetic criteria and followed them longitudinally up to 36 months of age. Periodic study visits included medical and seizure histories, physical and neurologic examinations, and developmental assessments. Ages at which major and minor features of TSC and seizures were first identified were analyzed. RESULTS The most common initial presenting features of TSC were cardiac rhabdomyomas (59%) and hypomelanotic macules or other skin findings (39%), and 85% of infants presented with either or both. Ultimately, the most prevalent diagnostic TSC features were hypomelanotic macules (94%), tubers or other cortical dysplasias (94%), subependymal nodules (90%), and cardiac rhabdomyomas (82%). Thirty-five percent of infants presented prenatally, 41% presented at birth or within the first month of life, and 74% met criteria for TSC diagnosis at or within 30 days of presentation. Seizure onset occurred before or at initial presentation in only 15% of infants, but 73% developed epilepsy within the first year of life. CONCLUSIONS Infants with TSC can often be identified early, before the onset of neurologic sequelae, enabling earlier diagnosis, surveillance, and possibly disease-modifying treatment.
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Affiliation(s)
| | - Rajna Filip-Dhima
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Harvard University, Boston, Massachusetts
| | | | - Jurriaan M. Peters
- Division of Epilepsy and Clinical Neurophysiology,,Departments of Neurology and
| | - Kit Sing Au
- Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - E. Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Joyce Y. Wu
- Division of Pediatric Neurology, University of California at Los Angeles Mattel Children’s Hospital, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California; and
| | - Darcy Krueger
- Department of Neurology and Rehabilitation Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Mustafa Sahin
- Departments of Neurology and .,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Harvard University, Boston, Massachusetts
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17
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Au KS, Findley TO, Northrup H. Finding the genetic mechanisms of folate deficiency and neural tube defects-Leaving no stone unturned. Am J Med Genet A 2017; 173:3042-3057. [PMID: 28944587 PMCID: PMC5650505 DOI: 10.1002/ajmg.a.38478] [Citation(s) in RCA: 28] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 08/11/2017] [Accepted: 08/21/2017] [Indexed: 12/21/2022]
Abstract
Neural tube defects (NTDs) occur secondary to failed closure of the neural tube between the third and fourth weeks of gestation. The worldwide incidence ranges from 0.3 to 200 per 10,000 births with the United States of American NTD incidence at around 3-6.3 per 10,000 dependent on race and socioeconomic background. Human NTD incidence has fallen by 35-50% in North America due to mandatory folic acid fortification of enriched cereal grain products since 1998. The US Food and Drug Administration has approved the folic acid fortification of corn masa flour with the goal to further reduce the incidence of NTDs, especially among individuals who are Hispanic. However, the genetic mechanisms determining who will benefit most from folate enrichment of the diet remains unclear despite volumes of literature published on studies of association of genes with functions related to folate metabolism and risk of human NTDs. The advances in omics technologies provides hypothesis-free tools to interrogate every single gene within the genome of NTD affected individuals to discover pathogenic variants and methylation targets throughout the affected genome. By identifying genes with expression regulated by presence of folate through transcriptome profiling studies, the genetic mechanisms leading to human NTDs due to folate deficiency may begin to be more efficiently revealed.
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Affiliation(s)
- KS Au
- Division of Medical Genetics, Department of Pediatrics, University of Texas Health Science Houston – McGovern Medical School, Houston, TX
| | - TO Findley
- Division of Neonatology, Department of Pediatrics, University of Texas Health Science Houston – McGovern Medical School, Houston, TX
| | - H Northrup
- Division of Medical Genetics, Department of Pediatrics, University of Texas Health Science Houston – McGovern Medical School, Houston, TX
- Shriners Hospitals for Children - Houston, Houston, TX
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18
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Farach LS, Gibson WT, Sparagana SP, Nellist M, Stumpel CTRM, Hietala M, Friedman E, Pearson DA, Creighton SP, Wagemans A, Segel R, Ben-Shalom E, Au KS, Northrup H. TSC2 c.1864C>T variant associated with mild cases of tuberous sclerosis complex. Am J Med Genet A 2017; 173:771-775. [PMID: 28211972 DOI: 10.1002/ajmg.a.38083] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/21/2016] [Indexed: 11/08/2022]
Abstract
Tuberous sclerosis complex (TSC) is an autosomal dominantly inherited disorder with variable expressivity associated with hamartomatous tumors, abnormalities of the skin, and neurologic problems including seizures, intellectual disability, and autism. TSC is caused by pathogenic variants in either TSC1 or TSC2. In general, TSC2 pathogenic variants are associated with a more severe phenotype than TSC1 pathogenic variants. Here, we report a pathogenic TSC2 variant, c.1864C>T, p.(Arg622Trp), associated with a mild phenotype, with most carriers meeting fewer than two major clinical diagnostic criteria for TSC. This finding has significant implications for counseling patients regarding prognosis. More patient data are required before changing the surveillance recommendations for patients with the reported variant. However, consideration should be given to tailoring surveillance recommendations for all pathogenic TSC1 and TSC2 variants with documented milder clinical sequelae. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Laura S Farach
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - William T Gibson
- Department of Medical Genetics, BC Children's Hospital and UBC, Vancouver, British Columbia, Canada
| | - Steven P Sparagana
- Division of Neurology, Texas Scottish Rite Hospital for Children and University of Texas Southwestern Medical School, Dallas, Texas
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Connie T R M Stumpel
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center (MUMC), Maastricht, The Netherlands
| | - Marja Hietala
- Department of Clinical Genetics and Department of Medical Biochemistry and Genetics, University of Turku and Turku University Hospital, Turku, Finland
| | - Elliott Friedman
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Deborah A Pearson
- Division of Child and Adolescent Psychiatry, Department of Psychiatry, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Susan P Creighton
- Department of Medical Genetics, BC Women's Hospital and UBC, Vancouver, British Columbia, Canada
| | - Annemiek Wagemans
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center (MUMC), Maastricht, The Netherlands.,Koraalgroep, Maasveld, Maastricht, The Netherlands
| | - Reveel Segel
- Medical Genetics Institute, Shaare Zedek Medical Center and the Hebrew University School of Medicine, Jerusalem, Israel
| | - Efrat Ben-Shalom
- Department of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
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19
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Findley TO, Tenpenny JC, O'Byrne MR, Morrison AC, Hixson JE, Northrup H, Au KS. Mutations in folate transporter genes and risk for human myelomeningocele. Am J Med Genet A 2017; 173:2973-2984. [PMID: 28948692 DOI: 10.1002/ajmg.a.38472] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 07/21/2017] [Accepted: 08/21/2017] [Indexed: 11/09/2022]
Abstract
The molecular mechanisms linking folate deficiency and neural tube defect (NTD) risk in offspring remain unclear. Folate transporters (SLC19A1, SLC46A1, SLC25A32, and FOLH1) and folate receptors (FOLR1, FOLR2, and FOLR3) are suggested to play essential roles in transporting folate from maternal intestinal lumen to the developing embryo. Loss of function variants in these genes may affect folate availability and contribute to NTD risk. This study examines whether variants within the folate transporter and receptor genes are associated with an increased risk for myelomeningocele (MM). Exons and their flanking intron sequences of 348 MM subjects were sequenced using the Sanger sequencing method and/or next generation sequencing to identify variants. Frequencies of alleles of single nucleotide polymorphisms (SNPs) in MM subjects were compared to those from ethnically matched reference populations to evaluate alleles' associated risk for MM. We identified eight novel variants in SLC19A1 and twelve novel variants in FOLR1, FOLR2, and FOLR3. Pathogenic variants include c.1265delG in SLC19A1 resulting in an early stop codon, four large insertion deletion variants in FOLR3, and a stop_gain variant in FOLR3. No new variants were identified in SLC46A1, SLC25A32, or FOLH1. In SLC19A1, c.80A>G (rs1051266) was not associated with our MM cohort; we did observe a variant allele G frequency of 61.7%, higher than previously reported in other NTD populations. In conclusion, we discovered novel loss of function variants in genes involved in folate transport in MM subjects. Our results support the growing evidence of associations between genes involved in folate transport and susceptibility to NTDs.
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Affiliation(s)
- Tina O Findley
- Division of Neonatology, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Joy C Tenpenny
- Division of Neonatology, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Michelle R O'Byrne
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas
| | - James E Hixson
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.,Shriners Hospital for Children, Houston, Texas
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
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20
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Martin KR, Zhou W, Bowman MJ, Shih J, Au KS, Dittenhafer-Reed KE, Sisson KA, Koeman J, Weisenberger DJ, Cottingham SL, DeRoos ST, Devinsky O, Winn ME, Cherniack AD, Shen H, Northrup H, Krueger DA, MacKeigan JP. The genomic landscape of tuberous sclerosis complex. Nat Commun 2017. [PMID: 28643795 PMCID: PMC5481739 DOI: 10.1038/ncomms15816] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [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: 12/15/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is a rare genetic disease causing multisystem growth of benign tumours and other hamartomatous lesions, which leads to diverse and debilitating clinical symptoms. Patients are born with TSC1 or TSC2 mutations, and somatic inactivation of wild-type alleles drives MTOR activation; however, second hits to TSC1/TSC2 are not always observed. Here, we present the genomic landscape of TSC hamartomas. We determine that TSC lesions contain a low somatic mutational burden relative to carcinomas, a subset feature large-scale chromosomal aberrations, and highly conserved molecular signatures for each type exist. Analysis of the molecular signatures coupled with computational approaches reveals unique aspects of cellular heterogeneity and cell origin. Using immune data sets, we identify significant neuroinflammation in TSC-associated brain tumours. Taken together, this molecular catalogue of TSC serves as a resource into the origin of these hamartomas and provides a framework that unifies genomic and transcriptomic dimensions for complex tumours.
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Affiliation(s)
- Katie R Martin
- Center for Cancer and Cell Biology, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Megan J Bowman
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Juliann Shih
- Cancer Program, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Kit Sing Au
- Department of Pediatrics, University of Texas Health Science Center at Houston-McGovern Medical School, 6431 Fannin, Houston, Texas 77030, USA
| | - Kristin E Dittenhafer-Reed
- Center for Cancer and Cell Biology, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Kellie A Sisson
- Center for Cancer and Cell Biology, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Julie Koeman
- Cytogenetics and Pathology Core, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Daniel J Weisenberger
- Norris Comprehensive Cancer Center, University of Southern California, 1450 Biggy Street, Los Angeles, California 90033, USA
| | - Sandra L Cottingham
- Department of Pathology, Spectrum Health System, 100 Michigan Street NE, Grand Rapids, Michigan 49503, USA
| | - Steven T DeRoos
- Division of Pediatric Neurology, Helen DeVos Children's Hospital, Spectrum Health System, 100 Michigan Street NE, Grand Rapids, Michigan 49503, USA
| | - Orrin Devinsky
- Department of Neurology, New York University School of Medicine, 223 E 34 Street, New York, New York 10016, USA
| | - Mary E Winn
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Andrew D Cherniack
- Cancer Program, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA
| | - Hope Northrup
- Department of Pediatrics, University of Texas Health Science Center at Houston-McGovern Medical School, 6431 Fannin, Houston, Texas 77030, USA
| | - Darcy A Krueger
- Division of Neurology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio 45229, USA
| | - Jeffrey P MacKeigan
- Center for Cancer and Cell Biology, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, USA.,College of Human Medicine, Michigan State University, 220 Trowbridge Road, East Lansing, Michigan 48824, USA
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Shah RH, Northrup H, Hixson JE, Morrison AC, Au KS. Genetic association of the glycine cleavage system genes and myelomeningocele. ACTA ACUST UNITED AC 2016; 106:847-853. [PMID: 27620832 DOI: 10.1002/bdra.23552] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 01/20/2023]
Abstract
BACKGROUND Neural tube defects (NTDs) are one of the most common congenital birth defects, with myelomeningocele (MM) being the most severe form compatible with life. Recent studies show a link between mitochondrial folate one carbon metabolism and NTDs by means of the glycine cleavage system (GCS). We hypothesize that single nucleotide polymorphisms and novel variants in the coding regions of the GCS genes increase the risk for MM. METHODS DNA was obtained from 96 subjects with MM born before the United States mandated folic acid fortification of grains in 1998. Primers were designed for polymerase chain reaction amplification and sequencing of all exons in the AMT gene, one of four genes in the GCS, followed by identification of single nucleotide polymorphisms and novel variants. An additional 252 MM subjects underwent whole exome sequencing to examine all four GCS genes (aminomethyltransferase, glycine dehydrogenase, glycine cleavage system protein-H, and dihydrolipoamide dehydrogenase). RESULTS We identified six novel, heterozygous variants in the AMT gene with three predicted to be deleterious to AMT function (p.Val7Leu, p.Pro251Arg, and p.Val380Met). Five extremely rare, known heterozygous variants were found in the AMT gene and one in the GLDC gene. No novel variants in the exons of the other two GCS genes (DLD and GCSH) were identified. CONCLUSION We identified novel and rare, known variants in two of the four GCS genes that may contribute to the development of MM. Consistent with previous findings, the current study provides additional support that genetic variations in GCS genes contribute to the risk of NTDs. Birth Defects Research (Part A) 106:847-853, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rita H Shah
- Division of Neonatology, Department of Pediatrics, The University of Texas Health Science Center at Houston - McGovern Medical School, Houston, Texas
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, The University of Texas Health Science Center at Houston - McGovern Medical School, Houston, Texas
| | - James E Hixson
- Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas Health Science Center at Houston - School of Public Health, Houston, Texas
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas Health Science Center at Houston - School of Public Health, Houston, Texas
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, The University of Texas Health Science Center at Houston - McGovern Medical School, Houston, Texas.
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Yang J, Bassuk AG, Merl-Pham J, Hsu CW, Colgan DF, Li X, Au KS, Zhang L, Smemo S, Justus S, Nagahama Y, Grossbach AJ, Howard MA, Kawasaki H, Feldstein NA, Dobyns WB, Northrup H, Hauck SM, Ueffing M, Mahajan VB, Tsang SH. Catenin delta-1 (CTNND1) phosphorylation controls the mesenchymal to epithelial transition in astrocytic tumors. Hum Mol Genet 2016; 25:4201-4210. [PMID: 27516388 DOI: 10.1093/hmg/ddw253] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/14/2016] [Accepted: 07/21/2016] [Indexed: 11/14/2022] Open
Abstract
Inactivating mutations of the TSC1/TSC2 complex (TSC1/2) cause tuberous sclerosis (TSC), a hereditary syndrome with neurological symptoms and benign hamartoma tumours in the brain. Since TSC effectors are largely unknown in the human brain, TSC patient cortical tubers were used to uncover hyperphosphorylation unique to TSC primary astrocytes, the cell type affected in the brain. We found abnormal hyperphosphorylation of catenin delta-1 S268, which was reversible by mTOR-specific inhibitors. In contrast, in three metastatic astrocytoma cell lines, S268 was under phosphorylated, suggesting S268 phosphorylation controls metastasis. TSC astrocytes appeared epithelial (i.e. tightly adherent, less motile, and epithelial (E)-cadherin positive), whereas wild-type astrocytes were mesenchymal (i.e. E-cadherin negative and highly motile). Despite their epithelial phenotype, TSC astrocytes outgrew contact inhibition, and monolayers sporadically generated tuberous foci, a phenotype blocked by the mTOR inhibitor, Torin1. Also, mTOR-regulated phosphokinase C epsilon (PKCe) activity induced phosphorylation of catenin delta-1 S268, which in turn mediated cell-cell adhesion in astrocytes. The mTOR-dependent, epithelial phenotype of TSC astrocytes suggests TSC1/2 and mTOR tune the phosphorylation level of catenin delta-1 by controlling PKCe activity, thereby regulating the mesenchymal-epithelial-transition (MET). Thus, some forms of TSC could be treated with PKCe inhibitors, while metastasis of astrocytomas might be blocked by PKCe stimulators.
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Affiliation(s)
- Jin Yang
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology & Cell Biology, Institute of Human Nutrition, Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Tianjin Medical University Eye Hospital, Tianjin, People's Republic of China.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Alexander G Bassuk
- Department of Pediatrics and Neurology, Departments of Neurosurgery, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa, IA, USA
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Zentrum Munich, German Research Center for Environmental Health (GmbH), Munich, Germany
| | - Chun-Wei Hsu
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology & Cell Biology, Institute of Human Nutrition, Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | | | - Xiaorong Li
- Tianjin Medical University Eye Hospital, Tianjin, People's Republic of China
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Lijuan Zhang
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology & Cell Biology, Institute of Human Nutrition, Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA.,Shanxi Eye Hospital, affiliated with Shanxi Medical University, Xinghualing, Taiyuan, Shanxi, China
| | - Scott Smemo
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology & Cell Biology, Institute of Human Nutrition, Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Sally Justus
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology & Cell Biology, Institute of Human Nutrition, Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Yasunori Nagahama
- Department of Pediatrics and Neurology, Departments of Neurosurgery, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa, IA, USA
| | - Andrew J Grossbach
- Department of Pediatrics and Neurology, Departments of Neurosurgery, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa, IA, USA
| | - Matthew A Howard
- Department of Pediatrics and Neurology, Departments of Neurosurgery, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa, IA, USA
| | - Hiroto Kawasaki
- Department of Pediatrics and Neurology, Departments of Neurosurgery, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa, IA, USA
| | - Neil A Feldstein
- Departments of Neurosurgery, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY, USA
| | - William B Dobyns
- Division of Genetic Medicine, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington, USA Departments of Pediatrics and Neurology, University of Washington, Seattle, Washington, WA, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum Munich, German Research Center for Environmental Health (GmbH), Munich, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Center of Ophthalmology, University Medical Center, University of Tübingen, Germany
| | - Vinit B Mahajan
- Department of Pediatrics and Neurology, Departments of Neurosurgery, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa, IA, USA.,Omics Laboratory, University of Iowa, Iowa, IA, USA
| | - Stephen H Tsang
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology & Cell Biology, Institute of Human Nutrition, Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA .,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
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Wu JY, Peters JM, Goyal M, Krueger D, Sahin M, Northrup H, Au KS, Cutter G, Bebin EM. Clinical Electroencephalographic Biomarker for Impending Epilepsy in Asymptomatic Tuberous Sclerosis Complex Infants. Pediatr Neurol 2016; 54:29-34. [PMID: 26498039 PMCID: PMC4691569 DOI: 10.1016/j.pediatrneurol.2015.09.013] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/06/2015] [Indexed: 11/18/2022]
Abstract
BACKGROUND We assessed the clinical utility of routine electroencephalography (EEG) in the prediction of epilepsy onset in asymptomatic infants with tuberous sclerosis complex. METHODS This multicenter prospective observational study recruited infants younger than 7 months, seizure-free and on no antiepileptic drugs at enrollment, who all underwent serial physical examinations and video EEGs throughout the study. Parental education on seizure recognition was completed at the time of initial enrollment. Once seizure onset occurred, standard of care was applied, and subjects were followed up until 24 months. RESULTS Forty patients were enrolled, 28 older than 12 months with completed EEG evaluation at the time of this interim analysis. Of those, 19 (67.8%) developed seizures. Epileptic spasms occurred in 10 (52.6%), focal seizures in five (26.3%), generalized tonic-clonic seizure in one (5.3%), and a combination of epileptic spasms and focal seizures in three (15.7%). Fourteen infants (73.6%) had the first emergence of epileptiform abnormalities on EEG at an average age 4.2 months, preceding seizure onset by a median of 1.9 months. Hypsarrhythmia or modified hypsarrhythmia was not found in any infant before onset of epileptic spasms. All children with epileptiform discharges subsequently developed epilepsy (100% positive predictive value), and the negative predictive value for not developing epilepsy after a normal EEG was 64%. CONCLUSIONS Serial routine EEGs in infants with tuberous sclerosis complex is a feasible strategy to identify individuals at high risk for epilepsy. The most frequent clinical presentation was epileptic spasms followed by focal seizures, and then a combination of both seizure types.
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Affiliation(s)
- Joyce Y Wu
- Division of Pediatric Neurology, Mattel Children's Hospital at UCLA, Los Angeles, California
| | - Jurriaan M Peters
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - Monisha Goyal
- Department of Neurology, University of Alabama Birmingham, Birmingham, Alabama
| | | | - Mustafa Sahin
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | | | | | - Gary Cutter
- Department of Neurology, University of Alabama Birmingham, Birmingham, Alabama
| | - E Martina Bebin
- Department of Neurology, University of Alabama Birmingham, Birmingham, Alabama.
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Ruggiero JE, Northrup H, Au KS. Association of facilitated glucose transporter 2 gene variants with the myelomeningocele phenotype. ACTA ACUST UNITED AC 2015; 103:479-87. [PMID: 25776730 DOI: 10.1002/bdra.23358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 02/02/2023]
Abstract
BACKGROUND Neural tube defects (NTDs) remain the second most common cause of congenital malformations. Myelomeningocele (MM), the most common NTD compatible with survival, results from genetic and environmental factors. Epidemiologic studies and murine models support the hypotheses that obesity, diabetes and hyperglycemia confer increased risk of NTDs. Presence of wild-type facilitated glucose transporter, Glut2, in mouse embryos has been shown to increase risk for NTDs in hyperglycemic pregnancy. METHODS The GLUT2 gene of 96 MM patients was amplified, sequenced and compared with the reference sequence (NM_000340). Variants previously unreported in the single nucleotide polymorphisms (SNP) database were considered novel. Allele frequencies of reported SNPs were compared with reference populations using Fisher's exact test. RESULTS Analysis revealed three novel variants: a substitution in the core promoter region (c.-331c>t), a substitution (c.-182g>a) in the 5'-untranslated region, and a single base pair deletion (c.1441delT) in the coding sequences. Polymorphic alleles for 10 SNPs were also identified. Seven SNPs are significantly associated with MM in the Mexican American patients tested (p < 0.05) and two of the seven remained significant after Bonferroni correction. CONCLUSION We identified three novel variants and seven SNPs associated with MM. The novel variants in the core promoter and in the 5'-untranslated region could affect GLUT2 mRNA transcription and stability and translation efficiency. The c.1441delT variant is predicted to alter the reading frame and prematurely terminate translation of the GLUT2 protein at the C-terminus, affecting GLUT2 protein function. Presence of GLUT2 variants may disrupt GLUT2 activity and influence MM susceptibility.
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Affiliation(s)
- Jaclyn E Ruggiero
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, The University of Texas Medical School at Houston, Houston, Texas
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, The University of Texas Medical School at Houston, Houston, Texas.,Shriners Hospitals for Children, Houston, Texas
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, The University of Texas Medical School at Houston, Houston, Texas
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Connealy BD, Northrup H, Au KS. Genetic variations in the GLUT3 gene associated with myelomeningocele. Am J Obstet Gynecol 2014; 211:305.e1-8. [PMID: 24813597 DOI: 10.1016/j.ajog.2014.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 03/11/2014] [Accepted: 05/06/2014] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Our objectives were to examine the extent of described sequence variation in the glucose transporter 3 (GLUT3) gene in children with myelomeningocele (MM), identify novel variations in the GLUT3 gene in these children, and determine whether these variations may confer a risk of MM. STUDY DESIGN We sequenced the 10 exons of GLUT3, including exon-intron boundaries, on 96 children with MM. Sequencing was performed with Sanger methods and results analyzed with deoxyribonucleic acid analysis software. Frequencies of known single-nucleotide polymorphisms were identified, and those differing from the reference sequence (GRCh37/hg19 assembly) were considered variations. RESULTS Six novel and 9 previously described, genetic variations were identified in our population. The novel variations included a large, 83 base pair deletion involving the core promoter region and part of exon 1 (1 of 96 children), and a 2 base pair deletion in the coding sequence of exon 4 (1 of 96 children). The remaining novel variations were located in the introns in the proximity of the splice sites. Novel mutations in GLUT3 were observed among 6.25% of our population. Additionally, the frequency of the rare allele for rs17847972 located in a splice donor site is higher (P < .001) in MM in our population than expected. CONCLUSION We identified previously undescribed deletions and single-nucleotide variations involving the GLUT3 gene that may be associated with increased susceptibility to MM. Of particular interest, the 2 deletions involve both an important core promoter site and a coding region predicted to have a deleterious effect. The functional significance of these findings is under investigation.
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Affiliation(s)
- Brendan D Connealy
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Medicine, University of Texas Medical School at Houston, Houston, TX.
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, University of Texas Medical School at Houston, Houston, TX; Shriners Hospital for Children, Houston, TX
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, University of Texas Medical School at Houston, Houston, TX
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Kase BA, Northrup H, Au KS. Novel single nucleotide polymorphisms in the superoxide dismutase 1 and 2 genes among children with myelomeningocele. Am J Obstet Gynecol 2013; 209:388.e1-7. [PMID: 23792044 DOI: 10.1016/j.ajog.2013.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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: 03/15/2013] [Revised: 05/02/2013] [Accepted: 06/04/2013] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Excessive oxidative stress has been demonstrated as a mechanism for neural tube defects (NTDs). The current exploratory study sought to examine sequence variations in the superoxide dismutase 1 (SOD1) and 2 (SOD2) genes in patients with myelomeningocele and to identify variants altering risk for myelomeningocele. STUDY DESIGN We sequenced deoxyribonucleic acid from 96 patients with myelomeningocele. The 11 exons were amplified by polymerase chain reaction, and the products were sequenced with the Sanger method. Results were compared with reference sequences (NM_000454, NM_000636, and NM_001024466) obtained from University of California Santa Cruz Genome Browser. Observed alleles that differed from the reference sequences were considered novel variants. RESULTS We found 1 novel variant and 1 variant only recently described in phase 1 of the 1000 Genomes Project but not yet validated. The novel variant is located in the 3'-untranslated region (UTR) of SOD2 and is present in 2 of 96 patients (1.0% allele frequency). The other variant is located in the 3'-UTR of SOD1 and is present in 2 of 96 patients (1.0% allele frequency). Minor allele frequencies of known single nucleotide polymorphisms were compared with unaffected population controls. CONCLUSION We identified 1 novel variant and made the second report of an additional variant in the SOD genes studied. The variant located in the 3'-UTR of SOD1 is predicted to alter microribonucleic acid (miRNA) binding. The variant located in the 3'-UTR of SOD2 is predicted to alter 2 miRNA binding sites and potentially affects messenger ribonucleic acid production. We also identified 2 known single-nucleotide polymorphisms that occur in significantly different frequency compared with the unaffected population controls.
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Affiliation(s)
- Benjamin A Kase
- Department of Obstetrics, Gynecology, and Reproductive Sciences, The University of Texas Medical School at Houston, Houston, TX
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Kase B, Northrup H, Au KS. 570: Novel single nucleotide polymorphisms in the superoxide dismutase 1 ( SOD1 ) and 2 ( SOD2 ) genes among patients with non-syndromic myelomeningocele. Am J Obstet Gynecol 2013. [DOI: 10.1016/j.ajog.2012.10.736] [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: 10/27/2022]
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Bassuk AG, Muthuswamy LB, Boland R, Smith TL, Hulstrand AM, Northrup H, Hakeman M, Dierdorff JM, Yung CK, Long A, Brouillette RB, Au KS, Gurnett C, Houston DW, Cornell RA, Manak JR. Copy number variation analysis implicates the cell polarity gene glypican 5 as a human spina bifida candidate gene. Hum Mol Genet 2012; 22:1097-111. [PMID: 23223018 DOI: 10.1093/hmg/dds515] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Neural tube defects (NTDs) are common birth defects of complex etiology. Family and population-based studies have confirmed a genetic component to NTDs. However, despite more than three decades of research, the genes involved in human NTDs remain largely unknown. We tested the hypothesis that rare copy number variants (CNVs), especially de novo germline CNVs, are a significant risk factor for NTDs. We used array-based comparative genomic hybridization (aCGH) to identify rare CNVs in 128 Caucasian and 61 Hispanic patients with non-syndromic lumbar-sacral myelomeningocele. We also performed aCGH analysis on the parents of affected individuals with rare CNVs where parental DNA was available (42 sets). Among the eight de novo CNVs that we identified, three generated copy number changes of entire genes. One large heterozygous deletion removed 27 genes, including PAX3, a known spina bifida-associated gene. A second CNV altered genes (PGPD8, ZC3H6) for which little is known regarding function or expression. A third heterozygous deletion removed GPC5 and part of GPC6, genes encoding glypicans. Glypicans are proteoglycans that modulate the activity of morphogens such as Sonic Hedgehog (SHH) and bone morphogenetic proteins (BMPs), both of which have been implicated in NTDs. Additionally, glypicans function in the planar cell polarity (PCP) pathway, and several PCP genes have been associated with NTDs. Here, we show that GPC5 orthologs are expressed in the neural tube, and that inhibiting their expression in frog and fish embryos results in NTDs. These results implicate GPC5 as a gene required for normal neural tube development.
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Affiliation(s)
- Alexander G Bassuk
- Department of Pediatrics, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Spellicy CJ, Northrup H, Fletcher JM, Cirino PT, Dennis M, Morrison AC, Martinez CA, Au KS. Folate metabolism gene 5,10-methylenetetrahydrofolate reductase (MTHFR) is associated with ADHD in myelomeningocele patients. PLoS One 2012; 7:e51330. [PMID: 23227261 PMCID: PMC3515551 DOI: 10.1371/journal.pone.0051330] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 11/07/2012] [Indexed: 02/06/2023] Open
Abstract
The objective of this study was to examine the relation between the 5, 10-methylenetetrahydrofolate reductase (MTHFR) gene and behaviors related to attention- deficit/hyperactivity disorder (ADHD) in individuals with myelomeningocele. The rationale for the study was twofold: folate metabolizing genes, (e.g. MTHFR), are important not only in the etiology of neural tube defects but are also critical to cognitive function; and individuals with myelomeningocele have an elevated incidence of ADHD. Here, we tested 478 individuals with myelomeningocele for attention-deficit hyperactivity disorder behavior using the Swanson Nolan Achenbach Pelham-IV ADHD rating scale. Myelomeningocele participants in this group for whom DNAs were available were genotyped for seven single nucleotide polymorphisms (SNPs) in the MTHFR gene. The SNPs were evaluated for an association with manifestation of the ADHD phenotype in children with myelomeningocele. The data show that 28.7% of myelomeningocele participants exhibit rating scale elevations consistent with ADHD; of these 70.1% had scores consistent with the predominantly inattentive subtype. In addition, we also show a positive association between the SNP rs4846049 in the 3'-untranslated region of the MTHFR gene and the attention-deficit hyperactivity disorder phenotype in myelomeningocele participants. These results lend further support to the finding that behavior related to ADHD is more prevalent in patients with myelomeningocele than in the general population. These data also indicate the potential importance of the MTHFR gene in the etiology of the ADHD phenotype.
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Affiliation(s)
- Catherine J. Spellicy
- Department of Pediatrics, University of Texas Medical School at Houston, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Hope Northrup
- Department of Pediatrics, University of Texas Medical School at Houston, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Shriners Hospital for Children, Houston, Texas, United States of America
| | - Jack M. Fletcher
- Department of Psychology, University of Houston, Houston, Texas, United States of America
| | - Paul T. Cirino
- Department of Psychology and Texas Institute for Measurement, Evaluation, and Statistics (TIMES), University of Houston, Houston, Texas, United States of America
| | - Maureen Dennis
- Department of Surgery, University of Toronto, and Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Canada
| | - Alanna C. Morrison
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Science, School of Public Health, University of Texas Health Sciences Center at Houston, Houston, Texas, United States of America
| | - Carla A. Martinez
- Department of Obstetrics and Gynecology, Texas Tech University Health Science Center, El Paso, Texas, United States of America
| | - Kit Sing Au
- Department of Pediatrics, University of Texas Medical School at Houston, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
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Kase BA, Northrup H, Morrison AC, Davidson CM, Goiffon AM, Fletcher JM, Ostermaier KK, Tyerman GH, Au KS. Association of copper-zinc superoxide dismutase (SOD1) and manganese superoxide dismutase (SOD2) genes with nonsyndromic myelomeningocele. ACTA ACUST UNITED AC 2012; 94:762-9. [PMID: 22972774 DOI: 10.1002/bdra.23065] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 06/22/2012] [Accepted: 07/06/2012] [Indexed: 11/08/2022]
Abstract
BACKGROUND A common and severe neural tube defect (NTD) phenotype, myelomeningocele (MM), results from the defective closure of the caudal end of the neural tube with herniation of the spinal cord and meninges through the vertebral column. The exact mechanisms for NTDs are unknown, but excessive oxidative stress, particularly in association with maternal diabetes, has been postulated as a mechanism for MM. METHODS The SNPlex Genotyping (ABI, Foster City, CA) platform was used to investigate single nucleotide polymorphisms (SNPs) across the superoxide dismutase (SOD) 1 and 2 genes to assess their association with MM risk. The study population included 329 trio (affected child and both parents) and 281 duo (affected child and one parent) families. Only cases with documented MM were studied. Seventeen SNPs across the SOD1 and SOD2 genes met the quality-control criteria to be considered for statistical analysis. Genetic association was assessed using the family-based transmission disequilibrium test in PLINK (a genome association analysis toolset). RESULTS Four SNPs in the SOD1 gene (rs 202446, rs202447, rs4816405, and rs2070424) and one SNP in the SOD2 gene ( rs5746105) [corrected] appeared to be associated with MM risk in our population. After adjusting for multiple testing, these SNPs remained significant. CONCLUSION This study provides the first genetic evidence to support association of myelomeningocele with superoxide scavenging. The rare alleles of the five specific SNPs within SOD1 and SOD2 appear to confer a protective effect on the susceptibility for MM risk in the MM population tested. Further evaluation of the roles of superoxide scavenging and neural tube development is warranted.
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Affiliation(s)
- Benjamin A Kase
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of Texas Medical School at Houston, Houston, TX 77030, USA
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Aneji CN, Northrup H, Au KS. Deep sequencing study of the MTHFR gene to identify variants associated with myelomeningocele. ACTA ACUST UNITED AC 2012; 94:84-90. [PMID: 22241680 DOI: 10.1002/bdra.22884] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/31/2011] [Accepted: 11/05/2011] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Neural tube defects (NTDs) are congenital anomalies caused by a combination of genetic and environmental influences. A defect below the head region resulting in protuberance of meninges and nervous tissue is termed myelomeningocele (MM). MM, the most common NTD compatible with survival, occurs in approximately 1 in 1000 births worldwide. Maternal preconceptional and periconceptional folate supplementation reduces the risk of NTDs by up to 70%. A key enzyme in folate metabolism is 5, 10-methylene-tetrahydrofolate reductase (MTHFR). OBJECTIVES Sequence the 12 exons of the MTHFR gene among 96 subjects with MM to identify variants potentially contributing to the disease trait. METHODS Exons were amplified by polymerase chain reaction, and the products were sequenced with the Sanger method to reveal sequence variants compared to MTHFR reference sequences. Association of variants was examined by Fisher's test. RESULTS A novel variant c.171+3G>T was identified in intron 1 in one affected subject. The variant was not found in the subject's unaffected mother's DNA, and the unaffected father's DNA was unavailable. We found significant differences in allele frequencies for seven SNPs in MM subjects compared with ethnically matched reference populations reported in the single nucleotide polymorphism database. CONCLUSION We identified a novel variant c.171+3G>T in the MTHFR gene that potentially affects splicing in an affected subject. In addition, we observed five SNPs (rs13306561, rs2274976, rs2066462, rs12121543, and rs1476413) in the MTHFR gene not previously shown to associate with MM. The current study provides additional evidence that multiple variations in the MTHFR gene are associated with MM.
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Affiliation(s)
- Chiamaka N Aneji
- Neonatal-Perinatal Medicine, Department of Pediatrics, University of Texas Houston Health Science Center, Houston, Texas, USA
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Tilley MM, Northrup H, Au KS. Genetic studies of the cystathionine beta-synthase gene and myelomeningocele. ACTA ACUST UNITED AC 2011; 94:52-6. [PMID: 21957013 DOI: 10.1002/bdra.22855] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 07/27/2011] [Accepted: 07/29/2011] [Indexed: 12/24/2022]
Abstract
BACKGROUND Among infants born with spina bifida, the most common defect is myelomeningocele (MM). The prevention of MM by maternal periconceptional folic acid (FA) supplementation has been studied extensively. The protective effect provided by FA suggests that the genes involved in folate metabolism, such as cystathionine beta-synthase (CBS), warrant further investigation. METHODS This study sequenced the DNA from 96 patients with MM to identify novel potential disease-causing variants across the 17 exons of the CBS gene. The frequencies of known single nucleotide polymorphisms (SNPs) were identified, and sequences that differed from the reference sequences were considered novel variants. Statistical analysis was performed using two-sided Fisher's exact test to compare frequencies of SNPs between groups of patients and the known population frequencies. RESULTS We found a new variant in exon 3 in one patient that results in a G/A change subsequently encoding a stop codon. In addition, we found a new variant in the 3'-UTR of exon 17. Allele frequencies for 10 known single nucleotide polymorphisms (SNPs) were determined: rs234706, rs72058776, rs1801181, rs6582281, rs71872941, rs12613, rs706208, rs706209, rs73906420, and rs9982921. Of the remaining 48 known SNPs, all tested DNAs were homozygous for the major allele. CONCLUSION We identified a previously undescribed variant in exon 3 that encodes a stop codon, thus halting downstream translation of the CBS protein. According to the Human Splicing Finder, the 3'-UTR variant found in exon 17 is predicted to abolish the recognition sites for two splice binding factors, SRp40 and SF2/ASF. The functional significance of the 3'-UTR mutation needs to be investigated.
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Affiliation(s)
- Melissa M Tilley
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics The University of Texas Medical School at Houston, Houston, Texas 77030, USA
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Abstract
BACKGROUND X-linked hypophosphatemic rickets, autosomal dominant hypophosphatemic rickets and autosomal recessive hypophosphatemic rickets make up a group of renal phosphate wasting disorders with common clinical and biochemical characteristics. These three types of rickets are related to mutations in PHEX, FGF23 and dentin matrix protein 1 (DMP1), respectively. OBJECTIVE The objective of the study was to evaluate the frequency of mutations that occur in these three genes associated with hypophosphatemic rickets. PATIENTS AND METHODS In this study, we sequenced these genes in 76 members of 46 kindreds from a large hypophosphatemic rickets cohort. RESULTS Forty-two individuals from 27 kindreds were found to have mutations in PHEX; 16 of which were novel. One subject had an FGF23 mutation. No individuals were found to have mutations in DMP1 consistent with the presence of recessive hypophosphatemic rickets. CONCLUSIONS Our data highlight the wide spectrum of genetic variation that can be seen in PHEX, FGF23 and DMP1 when screening a large cohort with hypophosphatemic rickets.
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Affiliation(s)
- Mary D Ruppe
- Department of Medicine, University of Texas Health Science Center at Houston, TX 77030, USA.
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Tran PX, Au KS, Morrison AC, Fletcher JM, Ostermaier KK, Tyerman GH, Northrup H. Association of retinoic acid receptor genes with meningomyelocele. Birth Defects Res A Clin Mol Teratol 2011; 91:39-43. [PMID: 21254357 PMCID: PMC3044482 DOI: 10.1002/bdra.20744] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 08/31/2010] [Accepted: 09/03/2010] [Indexed: 11/06/2022]
Abstract
BACKGROUND Neural tube defects (NTDs) occur in as many as 0.5-2 per 1000 live births in the United States. One of the most common and severe neural tube defects is meningomyelocele (MM) resulting from failed closure of the caudal end of the neural tube. MM has been induced by retinoic acid teratogenicity in rodent models. We hypothesized that genetic variants influencing retinoic acid (RA) induction via retinoic acid receptors (RARs) may be associated with risk for MM. METHODS We analyzed 47 single nucleotide polymorphisms (SNPs) that span across the three retinoic acid receptor genes using the SNPlex genotyping platform. Our cohort consisted of 610 MM families. RESULTS One variant in the RARA gene (rs12051734), three variants in the RARB gene (rs6799734, rs12630816, rs17016462), and a single variant in the RARG gene (rs3741434) were found to be statistically significant at p < 0.05. CONCLUSION RAR genes were associated with risk for MM. For all associated SNPs, the rare allele conferred a protective effect for MM susceptibility.
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Affiliation(s)
- Phong X. Tran
- Department of Pediatrics, University of Texas Medical School at Houston, Houston, Texas
| | - Kit Sing Au
- Department of Pediatrics, University of Texas Medical School at Houston, Houston, Texas
| | - Alanna C. Morrison
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Science, School of Public Health, University of Texas Health Sciences Center at Houston, Texas
| | | | | | | | - Hope Northrup
- Department of Pediatrics, University of Texas Medical School at Houston, Houston, Texas
- Shriners Hospital for Children, Houston, Texas
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O'Byrne MR, Au KS, Morrison AC, Lin JI, Fletcher JM, Ostermaier KK, Tyerman GH, Doebel S, Northrup H. Association of folate receptor (FOLR1, FOLR2, FOLR3) and reduced folate carrier (SLC19A1) genes with meningomyelocele. ACTA ACUST UNITED AC 2010; 88:689-94. [PMID: 20683905 DOI: 10.1002/bdra.20706] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Meningomyelocele (MM) results from lack of closure of the neural tube during embryologic development. Periconceptional folic acid supplementation is a modifier of MM risk in humans, leading toan interest in the folate transport genes as potential candidates for association to MM. METHODS This study used the SNPlex Genotyping (ABI, Foster City, CA) platform to genotype 20 single polymorphic variants across the folate receptor genes (FOLR1, FOLR2, FOLR3) and the folate carrier gene (SLC19A1) to assess their association to MM. The study population included 329 trio and 281 duo families. Only cases with MM were included. Genetic association was assessed using the transmission disequilibrium test in PLINK. RESULTS A variant in the FOLR2 gene (rs13908), three linked variants in the FOLR3 gene (rs7925545, rs7926875, rs7926987), and two variants in the SLC19A1 gene (rs1888530 and rs3788200) were statistically significant for association to MM in our population. CONCLUSION This study involved the analyses of selected single nucleotide polymorphisms across the folate receptor genes and the folate carrier gene in a large population sample. It provided evidence that the rare alleles of specific single nucleotide polymorphisms within these genes appear to be statistically significant for association to MM in the patient population that was tested.
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Affiliation(s)
- Michelle R O'Byrne
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, Texas 77030, USA
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Abstract
We sought to examine the diversity and extent of sequence variations in GLUT1 in patients with myelomeningocele (MM) and to identify variations conferring risk of MM. Sequences of the 10 exons and exon-intron boundaries of GLUT1 for 96 patients with MM (48 Caucasians and 48 Mexican Americans) were determined by direct sequencing of DNA. Two new variants were identified. One is located within intron 7 (c.972+17t>a), 17 bases from exon 7. The other is within exon 8 (c.1016T>C) and results in an amino acid change at isoleucine 339 (p.Ile339Thr). A 10 base pair (bp) deletion within intron 9 was genotyped for 457 patients with MM and showed it to be more common in Caucasian MM patients than in Caucasian controls (P = .02). The physiologic role of the 2 newly identified variants in the GLUT1 gene and the 10 bp deletion associated with risk of MM in Caucasian patients is under investigation.
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Affiliation(s)
- Clint M Cormier
- Department of Obstetrics, Gynecology, and Reproductive Sciences, The University of Texas Medical School at Houston, Houston, TX, USA
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Abstract
The worldwide incidence of neural tube defects (NTDs) ranges from 1.0 to 10.0 per 1,000 births with almost equal frequencies between two major categories: anencephaly and spina bifida (SB). Epidemiological studies have provided valuable insight for (a) researchers to identify nongenetic and genetic factors contributing to etiology, (b) public health officials to design and implement policies to prevent NTD pregnancies, and (c) individuals to take precautions to reduce the chance of having an NTD-affected pregnancy. Despite extensive research, our knowledge of the genetic etiology of human NTDs is limited. Although more than 200 small animal models with NTDs exist, most of these models do not replicate the human disease phenotype. Over a hundred candidate genes have been examined for risk association to human SB. The candidate genes studied include those important in folic acid metabolism, glucose metabolism, retinoid metabolism, and apoptosis. Many genes that regulate transcription in early embryogenesis and maintain planar cell polarity have also been tested as candidates. Additionally, genes identified through mouse models of NTDs have been explored as candidates. We do not know how many genes in the human genome may confer risk for NTDs in human. Less than 20% of the studied candidate genes have been determined to confer even a minor effect on risk association. Many studies have provided conflicting conclusions due to limitations in study design that potentially affect the power of statistical analysis. Future directions such as genomewide association studies (GWAS) and whole exome or even whole genome sequencing are discussed as possible avenues to identify genes that affect risk for human NTDs.
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Affiliation(s)
- Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, The University of Texas, Medical School at Houston, Houston, Texas 77030, USA
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Cormier C, Northrup H, Au KS. 711: Genetic variation in the GLUT1 gene of patients affected with meningomyelocele. Am J Obstet Gynecol 2009. [DOI: 10.1016/j.ajog.2009.10.728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Martinez CA, Northrup H, Lin JI, Morrison AC, Fletcher JM, Tyerman GH, Au KS. Genetic association study of putative functional single nucleotide polymorphisms of genes in folate metabolism and spina bifida. Am J Obstet Gynecol 2009; 201:394.e1-11. [PMID: 19683694 PMCID: PMC2790326 DOI: 10.1016/j.ajog.2009.06.042] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [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: 02/28/2009] [Revised: 05/08/2009] [Accepted: 06/16/2009] [Indexed: 01/15/2023]
Abstract
OBJECTIVE We tested putative functional single nucleotide polymorphisms (SNPs) in genes that regulate the folate/homocysteine metabolism pathway for their contribution to spina bifida (SB) susceptibility. STUDY DESIGN The study consisted of 610 unrelated simplex SB patient families. Genotypes of 46 SNPs located in the coding sequence or promoter region of 11 genes were investigated. Associations between transmission of alleles and SB in the offspring were examined using the reconstruction combined transmission disequilibrium test. RESULTS Significant association of SNP rs5742905 in cystathionine-beta-synthase, rs1643649 in dihydrofolate reductase, rs2853533 in thymidylate synthetase, and rs3737965 in methylenetetrahydrofolate reductase was found (P = .015, .041, .021, and .007 respectively). CONCLUSION Transmission disequilibrium of SNP alleles in cystathionine-beta-synthase, dihydrofolate reductase, methylenetetrahydrofolate reductase, and thymidylate synthetase confers an increased susceptibility to SB.
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Affiliation(s)
- Carla A. Martinez
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Texas Health Science Center at Houston, Houston, Texas
| | - Hope Northrup
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, Texas
| | - Jone-Ing Lin
- Human Genetics Center, University of Texas School of Public Health, Houston, Texas
| | - Alanna C. Morrison
- Human Genetics Center, University of Texas School of Public Health, Houston, Texas
| | - Jack M. Fletcher
- Department of Psychology, University of Houston-Texas Medical Center Annex, Houston, Texas
| | | | - Kit Sing Au
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, Texas
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Au KS, Tran PX, Tsai CC, O’Byrne MR, Lin JI, Morrison AC, Hampson AW, Cirino P, Fletcher JM, Ostermaier KK, Tyerman GH, Doebel S, Northrup H. Characteristics of a spina bifida population including North American Caucasian and Hispanic individuals. Birth Defects Res A Clin Mol Teratol 2008; 82:692-700. [PMID: 18937358 PMCID: PMC2597629 DOI: 10.1002/bdra.20499] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND Meningomyelocele (MM) is a common human birth defect. MM is a disorder of neural development caused by contributions from genes and environmental factors that result in the NTD and lead to a spectrum of physical and neurocognitive phenotypes. METHODS A multidisciplinary approach has been taken to develop a comprehensive understanding of MM through collaborative efforts from investigators specializing in genetics, development, brain imaging, and neurocognitive outcome. Patients have been recruited from five different sites: Houston and the Texas-Mexico border area; Toronto, Canada; Los Angeles, California; and Lexington, Kentucky. Genetic risk factors for MM have been assessed by genotyping and association testing using the transmission disequilibrium test. RESULTS A total of 509 affected child/parent trios and 309 affected child/parent duos have been enrolled to date for genetic association studies. Subsets of the patients have also been enrolled for studies assessing development, brain imaging, and neurocognitive outcomes. The study recruited two major ethnic groups, with 45.9% Hispanics of Mexican descent and 36.2% North American Caucasians of European descent. The remaining patients are African-American, South and Central American, Native American, and Asian. Studies of this group of patients have already discovered distinct corpus callosum morphology and neurocognitive deficits that associate with MM. We have identified maternal MTHFR 667T allele as a risk factor for MM. In addition, we also found that several genes for glucose transport and metabolism are potential risk factors for MM. CONCLUSIONS The enrolled patient population provides a valuable resource for elucidating the disease characteristics and mechanisms for MM development.
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Affiliation(s)
- Kit Sing Au
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX
| | - Phong X. Tran
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX
| | - Chester C. Tsai
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX
| | - Michelle R. O’Byrne
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX
| | - Jone-Ing Lin
- Human Genetics Center, The University of Texas School of Public Health, Houston, TX
| | - Alanna C. Morrison
- Human Genetics Center, The University of Texas School of Public Health, Houston, TX
| | - Amy W. Hampson
- Department of Psychology, University of Houston, Houston, TX
| | - Paul Cirino
- Department of Psychology, University of Houston, Houston, TX
| | | | | | | | - Sabine Doebel
- The Hospital for Sick Children, University of Toronto, Ontario, Canada
| | - Hope Northrup
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX
- Shriners Hospital for Children, Houston, TX
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Abstract
The authors test single nucleotide polymorphisms (SNPs) in coding sequences of 12 candidate genes involved in glucose metabolism and obesity for associations with spina bifida. Genotyping was performed on 507 children with spina bifida and their parents plus anonymous control DNAs from Hispanic and Caucasian individuals. The transmission disequilibrium test was performed to test for genetic associations between transmission of alleles and spina bifida in the offspring (P < .05). A statistically significant association between Lys481 of HK1 (G allele), Arg109Lys of LEPR (G allele), and Pro196 of GLUT1 (A allele) was found ( P = .019, .039, and .040, respectively). Three SNPs on 3 genes involved with glucose metabolism and obesity may be associated with increased susceptibility to spina bifida.
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Affiliation(s)
- Christina M Davidson
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Texas Medical School at Houston, TX 77030, USA
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Lim SD, Stallcup W, Lefkove B, Govindarajan B, Au KS, Northrup H, Lang D, Fisher DE, Patel A, Amin MB, Arbiser JL. Expression of the neural stem cell markers NG2 and L1 in human angiomyolipoma: are angiomyolipomas neoplasms of stem cells? Mol Med 2007. [PMID: 17592550 DOI: 10.2119/2006-00070.lim] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Angiomyolipomas are benign tumors of the kidney which express phenotypes of smooth muscle, fat, and melanocytes. These tumors appear with increased frequency in the autosomal dominant disorder tuberous sclerosis and are the leading cause of morbidity in adults with tuberous sclerosis. While benign, these tumors are capable of provoking life threatening hemorrhage and replacement of the kidney parenchyma, resulting in renal failure. The histogenesis of these tumors is currently unclear, although currently, we believe these tumors arise from "perivascular epithelioid cells" of which no normal counterpart has been convincingly demonstrated. Recently, stem cell precursors have been recognized that can give rise to smooth muscle and melanocytes. These precursors have been shown to express the neural stem cell marker NG2 and L1. In order to determine whether angiomyolipomas, which exhibit smooth muscle and melanocytic phenotypes, express NG2 and L1, we performed immunocytochemistry on a cell line derived from a human angiomyolipoma, and found that these cells are uniformly positive. Immunohistochemistry of human angiomyolipoma specimens revealed uniform staining of tumor cells, while renal cell carcinomas revealed positivity only of angiogenic vessels. These results support a novel histogenesis of angiomyolipoma as a defect in differentiation of stem cell precursors.
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Affiliation(s)
- So Dug Lim
- Department of Urology, Emory University School of Medicine, and Atlanta VA Medical Center, Georgia 30322, USA
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Lim SD, Stallcup W, Lefkove B, Govindarajan B, Au KS, Northrup H, Lang D, Fisher DE, Patel A, Amin MB, Arbiser JL. Expression of the neural stem cell markers NG2 and L1 in human angiomyolipoma: are angiomyolipomas neoplasms of stem cells? Mol Med 2007; 13:160-5. [PMID: 17592550 PMCID: PMC1892760 DOI: 10.2119/2006–00070.lim] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Accepted: 02/22/2007] [Indexed: 11/06/2022]
Abstract
Angiomyolipomas are benign tumors of the kidney which express phenotypes of smooth muscle, fat, and melanocytes. These tumors appear with increased frequency in the autosomal dominant disorder tuberous sclerosis and are the leading cause of morbidity in adults with tuberous sclerosis. While benign, these tumors are capable of provoking life threatening hemorrhage and replacement of the kidney parenchyma, resulting in renal failure. The histogenesis of these tumors is currently unclear, although currently, we believe these tumors arise from "perivascular epithelioid cells" of which no normal counterpart has been convincingly demonstrated. Recently, stem cell precursors have been recognized that can give rise to smooth muscle and melanocytes. These precursors have been shown to express the neural stem cell marker NG2 and L1. In order to determine whether angiomyolipomas, which exhibit smooth muscle and melanocytic phenotypes, express NG2 and L1, we performed immunocytochemistry on a cell line derived from a human angiomyolipoma, and found that these cells are uniformly positive. Immunohistochemistry of human angiomyolipoma specimens revealed uniform staining of tumor cells, while renal cell carcinomas revealed positivity only of angiogenic vessels. These results support a novel histogenesis of angiomyolipoma as a defect in differentiation of stem cell precursors.
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Affiliation(s)
- So Dug Lim
- Department of Urology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - William Stallcup
- Atlanta VA Medical Center, The Burnham Institute for Medical Research, Cancer Research Center, La Jolla, California, USA
| | - Benjamin Lefkove
- Department of Dermatology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Baskaran Govindarajan
- Department of Dermatology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, University of Texas Medical School at Houston, Houston, Texas, USA; Cardiovascular Division, University of Pennsylvania Health System, Philadelphia, Pennsylvania, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, University of Texas Medical School at Houston, Houston, Texas, USA; Cardiovascular Division, University of Pennsylvania Health System, Philadelphia, Pennsylvania, USA
| | - Deborah Lang
- Division of Medical Genetics, Department of Pediatrics, University of Texas Medical School at Houston, Houston, Texas, USA; Cardiovascular Division, University of Pennsylvania Health System, Philadelphia, Pennsylvania, USA
| | - David E Fisher
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Avani Patel
- Department of Urology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Mahul B Amin
- Department of Urology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jack L Arbiser
- Department of Dermatology, Emory University School of Medicine, Atlanta, Georgia, USA
- Address correspondence and reprint requests to Jack L Arbiser, Department of Dermatology, Emory University School of Medicine, 1639 Pierce Drive, WMB 5309, Atlanta, GA 30322. Phone: 404-727-5063; Fax: 404-727-5878; E-mail:
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Kozlowski P, Roberts P, Dabora S, Franz D, Bissler J, Northrup H, Au KS, Lazarus R, Domanska-Pakiela D, Kotulska K, Jozwiak S, Kwiatkowski DJ. Identification of 54 large deletions/duplications in TSC1 and TSC2 using MLPA, and genotype-phenotype correlations. Hum Genet 2007; 121:389-400. [PMID: 17287951 DOI: 10.1007/s00439-006-0308-9] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [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] [Received: 10/23/2006] [Accepted: 11/23/2006] [Indexed: 10/23/2022]
Abstract
Tuberous sclerosis (TSC) is an autosomal dominant disorder caused by mutations in either of two genes, TSC1 and TSC2. Point mutations and small indels account for most TSC1 and TSC2 mutations. We examined 261 TSC DNA samples (209 small-mutation-negative and 52 unscreened) for large deletion/duplication mutations using multiplex ligation-dependent probe amplification (MLPA) probe sets designed to permit interrogation of all TSC1/2 exons, as well as 15-50 kb of flanking sequence. Large deletion/duplication mutations in TSC1 and TSC2 were identified in 54 patients, of which 50 were in TSC2, and 4 were in TSC1. All but two mutations were deletions. Only 13 deletions were intragenic in TSC2, and one in TSC1, so that 39 (73%) deletions extended beyond the 5', 3' or both ends of TSC1 or TSC2. Mutations were identified in 24% of small-mutation-negative and 8% of unscreened samples. Eight of 54 (15%) mutations were mosaic, affecting 34-62% of cells. All intragenic mutations were confirmed by LR-PCR. Genotype/phenotype analysis showed that all (21 of 21) patients with TSC2 deletions extending 3' into the PKD1 gene had kidney cysts. Breakpoints of intragenic deletions were randomly distributed along the TSC2 sequence, and did not preferentially involve repeat sequence elements. Our own 20-plex probe sets gave more robust performance than the 40-plex probe sets from MRC-Holland. We conclude that large deletions in TSC1 and TSC2 account for about 0.5 and 6% of mutations seen in TSC patients, respectively, and MLPA is a highly sensitive and accurate detection method, including for mosaicism.
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Affiliation(s)
- Piotr Kozlowski
- Genetics Laboratory, Division of Translational Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Au KS, Williams AT, Roach ES, Batchelor L, Sparagana SP, Delgado MR, Wheless JW, Baumgartner JE, Roa BB, Wilson CM, Smith-Knuppel TK, Cheung MYC, Whittemore VH, King TM, Northrup H. Genotype/phenotype correlation in 325 individuals referred for a diagnosis of tuberous sclerosis complex in the United States. Genet Med 2007; 9:88-100. [PMID: 17304050 DOI: 10.1097/gim.0b013e31803068c7] [Citation(s) in RCA: 257] [Impact Index Per Article: 15.1] [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] [Indexed: 02/03/2023] Open
Abstract
Tuberous sclerosis complex is an autosomal dominant neurocutaneous disorder marked by hamartoma growth in multiple organ systems. We performed mutational analyses on 325 individuals with definite tuberous sclerosis complex diagnostic status. We identified mutations in 72% (199/257) of de novo and 77% (53/68) of familial cases, with 17% of mutations in the TSC1 gene and 50% in the TSC2 gene. There were 4% unclassified variants and 29% with no mutation identified. Genotype/phenotype analyses of all observed tuberous sclerosis complex findings in probands were performed, including several clinical features not analyzed in two previous large studies. We showed that patients with TSC2 mutations have significantly more hypomelanotic macules and learning disability in contrast to those with TSC1 mutations, findings not noted in previous studies. We also observed results consistent with two similar studies suggesting that individuals with mutations in TSC2 have more severe symptoms. On performing meta-analyses of our data and the other two largest studies in the literature, we found significant correlations for several features that individual studies did not have sufficient power to conclude. Male patients showed more frequent neurologic and eye symptoms, renal cysts, and ungual fibromas. Correlating genotypes with phenotypes should facilitate the disease management of tuberous sclerosis complex.
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Affiliation(s)
- Kit Sing Au
- Department of Pediatrics, The University of Texas Medical School at Houston, 77030, USA.
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Davidson C, Northrup H, King T, Fletcher J, Townsend I, Tyerman G, Au KS. Genes in glucose metabolism and their association with spina bifida. Am J Obstet Gynecol 2006. [DOI: 10.1016/j.ajog.2006.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Khare L, Strizheva GD, Bailey JN, Au KS, Northrup H, Smith M, Smalley SL, Henske EP. A novel missense mutation in the GTPase activating protein homology region of TSC2 in two large families with tuberous sclerosis complex. J Med Genet 2001; 38:347-9. [PMID: 11403047 PMCID: PMC1734876 DOI: 10.1136/jmg.38.5.347] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Astrinidis A, Khare L, Carsillo T, Smolarek T, Au KS, Northrup H, Henske EP. Mutational analysis of the tuberous sclerosis gene TSC2 in patients with pulmonary lymphangioleiomyomatosis. J Med Genet 2000; 37:55-7. [PMID: 10633137 PMCID: PMC1734439 DOI: 10.1136/jmg.37.1.55] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.5] [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: 11/04/2022]
Abstract
Pulmonary lymphangioleiomyomatosis (LAM) is a rare disorder limited almost exclusively to women of reproductive age. LAM affects about 5% of women with tuberous sclerosis complex (TSC). LAM also occurs in women who do not have TSC (sporadic LAM). TSC is a tumour suppressor gene syndrome characterised by seizures, mental retardation, and tumours in the brain, heart, and kidney. Angiomyolipomas, which are benign tumours with smooth muscle, fat, and dysplastic vascular components, are the most common renal tumour in TSC. Renal angiomyolipomas also occur in 63% of sporadic LAM patients. We recently found that 54% of these angiomyolipomas have TSC2 loss of heterozygosity, leading to the hypothesis that sporadic LAM is genetically related to TSC. In this study, we screened DNA from 21 women with sporadic LAM for mutations in all 41 exons of TSC2. Twelve of the patients had known renal angiomyolipomas. No TSC2 mutations were detected. We did find three silent TSC2 polymorphisms. We conclude that patients with sporadic LAM, including those with renal angiomyolipomas, do not have a high frequency of germline mutations in the coding region of TSC2.
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Affiliation(s)
- A Astrinidis
- Department of Medical Oncology, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA
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Abstract
Two-thirds of cases of tuberous sclerosis complex (TSC) are sporadic and usually are attributed to new mutations, but unaffected parents sometimes have more than one affected child. We sought to determine how many of these cases represent germ-line mosaicism, as has been reported for other genetic diseases. In our sample of 120 families with TSC, 7 families had two affected children and clinically unaffected parents. These families were tested for mutations in the TSC1 and TSC2 genes, by Southern blotting and by single-strand conformational analysis. Unique variants were detected in six families. Each variant was present and identical in both affected children of a family but was absent in both parents and the unaffected siblings. Sequencing of the variants yielded two frameshift mutations, one missense mutation, and two nonsense mutations in TSC2 and one nonsense mutation in TSC1. To determine which parent contributed the affected gametes, the families were analyzed for linkage to TSC1 and TSC2, by construction of haplotypes with markers flanking the two genes. Linkage analysis and loss-of-heterozygosity studies indicated maternal origin in three families, paternal origin in one family, and either being possible in two families. To evaluate the possibility of low-level somatic mosaicism for TSC, DNA from lymphocytes of members of the six families were tested by allele-specific PCR. In all the families, the mutant allele was detected only in the known affected individuals. We conclude that germ-line mosaicism was present in five families with mutations in the TSC2 gene and in one family with the causative mutation in the TSC1 gene. The results have implications for genetic counseling of families with seemingly sporadic TSC.
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Affiliation(s)
- V M Rose
- Division of Medical Genetics, Department of Pediatrics, The University of Texas Medical School-Houston, Houston, Texas 77030, USA
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