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Davis KW, Bilancia CG, Martin M, Vanzo R, Rimmasch M, Hom Y, Uddin M, Serrano MA. NeuroSCORE is a genome-wide omics-based model that identifies candidate disease genes of the central nervous system. Sci Rep 2022; 12:5427. [PMID: 35361823 PMCID: PMC8971396 DOI: 10.1038/s41598-022-08938-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 03/08/2022] [Indexed: 02/06/2023] Open
Abstract
To identify candidate disease genes of central nervous system (CNS) phenotypes, we created the Neurogenetic Systematic Correlation of Omics-Related Evidence (NeuroSCORE). We identified five genome-wide metrics highly associated with CNS phenotypes to score 19,601 protein-coding genes. Genes scored one point per metric (range: 0-5), identifying 8298 scored genes (scores ≥ 1) and 1601 "high scoring" genes (scores ≥ 3). Using logistic regression, we determined the odds ratio that genes with a NeuroSCORE from 1 to 5 would be associated with known CNS-related phenotypes compared to genes that scored zero. We tested NeuroSCORE using microarray copy number variants (CNVs) in case-control cohorts and aggregate mouse model data. High scoring genes are associated with CNS phenotypes (OR = 5.5, p < 2E-16), enriched in case CNVs, and mouse ortholog genes that cause behavioral and nervous system abnormalities. We identified 1058 high scoring genes with no disease association in OMIM. Transforming the logistic regression results indicates high scoring genes have an 84-92% chance of being associated with a CNS phenotype. Top scoring genes include GRIA1, MAP4K4, SF1, TNPO2, and ZSWIM8. Finally, we interrogated CNVs in the Clinical Genome Resource, finding the majority of clinically significant CNVs contain high scoring genes. These findings can direct future research and improve molecular diagnostics.
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Affiliation(s)
- Kyle W Davis
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA
| | - Colleen G Bilancia
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA
| | - Megan Martin
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA
| | - Rena Vanzo
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA
| | - Megan Rimmasch
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA
| | - Yolanda Hom
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- Cellular Intelligence (Ci) Lab, GenomeArc Inc., Toronto, ON, Canada
| | - Moises A Serrano
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA.
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Hemati P, Revah-Politi A, Bassan H, Petrovski S, Bilancia CG, Ramsey K, Griffin NG, Bier L, Cho MT, Rosello M, Lynch SA, Colombo S, Weber A, Haug M, Heinzen EL, Sands TT, Narayanan V, Primiano M, Aggarwal VS, Millan F, Sattler-Holtrop SG, Caro-Llopis A, Pillar N, Baker J, Freedman R, Kroes HY, Sacharow S, Stong N, Lapunzina P, Schneider MC, Mendelsohn NJ, Singleton A, Loik Ramey V, Wou K, Kuzminsky A, Monfort S, Weiss M, Doyle S, Iglesias A, Martinez F, Mckenzie F, Orellana C, van Gassen KLI, Palomares M, Bazak L, Lee A, Bircher A, Basel-Vanagaite L, Hafström M, Houge G, Goldstein DB, Anyane-Yeboa K. Refining the phenotype associated with GNB1 mutations: Clinical data on 18 newly identified patients and review of the literature. Am J Med Genet A 2018; 176:2259-2275. [PMID: 30194818 DOI: 10.1002/ajmg.a.40472] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 12/31/2017] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 11/05/2022]
Abstract
De novo germline mutations in GNB1 have been associated with a neurodevelopmental phenotype. To date, 28 patients with variants classified as pathogenic have been reported. We add 18 patients with de novo mutations to this cohort, including a patient with mosaicism for a GNB1 mutation who presented with a milder phenotype. Consistent with previous reports, developmental delay in these patients was moderate to severe, and more than half of the patients were non-ambulatory and nonverbal. The most observed substitution affects the p.Ile80 residue encoded in exon 6, with 28% of patients carrying a variant at this residue. Dystonia and growth delay were observed more frequently in patients carrying variants in this residue, suggesting a potential genotype-phenotype correlation. In the new cohort of 18 patients, 50% of males had genitourinary anomalies and 61% of patients had gastrointestinal anomalies, suggesting a possible association of these findings with variants in GNB1. In addition, cutaneous mastocytosis, reported once before in a patient with a GNB1 variant, was observed in three additional patients, providing further evidence for an association to GNB1. We will review clinical and molecular data of these new cases and all previously reported cases to further define the phenotype and establish possible genotype-phenotype correlations.
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Affiliation(s)
- Parisa Hemati
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Haim Bassan
- Pediatric Neurology & Development Center, Assaf Harofe Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Slavé Petrovski
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York.,Department of Medicine, Austin Health and Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Colleen G Bilancia
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Nicole G Griffin
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Louise Bier
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | | | - Monica Rosello
- Unidad de Genetica, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Sally Ann Lynch
- Temple Street Children's University Hospital, Dublin, Ireland
| | - Sophie Colombo
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Astrid Weber
- Department of Clinical Genetics, Liverpool Women's Hospital, Liverpool, United Kingdom
| | - Marte Haug
- Department of Medical Genetics, St. Olav's University Hospital, Trondheim, Norway
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Tristan T Sands
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Michelle Primiano
- Department of Pediatrics, Children's Hospital of New York-Presbyterian, New York, New York
| | - Vimla S Aggarwal
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | | | - Shannon G Sattler-Holtrop
- Carle Physician Group, Urbana, Illinois.,Department of Genetics, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Alfonso Caro-Llopis
- Unidad de Genetica, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Nir Pillar
- Pediatric Neurology & Development Center, Assaf Harofe Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Janice Baker
- Genomics Medicine Program, Children's Hospitals and Clinics of Minnesota, Minneapolis, Minnesota
| | - Rebecca Freedman
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, Western Australia, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia
| | - Hester Y Kroes
- Department of Genetics, University Medical Center Utrecht, The Netherlands
| | - Stephanie Sacharow
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Nick Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Pablo Lapunzina
- INGEMM, Instituto de Genética Médica y Molecular, IdiPAZ, Hospital Universitario la Paz, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER, ISCIII, Madrid, Spain
| | - Michael C Schneider
- Carle Physician Group, Urbana, Illinois.,Biochemical Genetics, Neurology Division, St Christopher's Hospital for Children, Philadelphia, Pennsylvania
| | - Nancy J Mendelsohn
- Genomics Medicine Program, Children's Hospitals and Clinics of Minnesota, Minneapolis, Minnesota
| | | | - Valerie Loik Ramey
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Karen Wou
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center (CUMC), New York, New York
| | - Alla Kuzminsky
- Child development Center, Clalit Health Service, Netanya, Israel
| | - Sandra Monfort
- Unidad de Genetica, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Monica Weiss
- Pediatric Neurology & Development Center, Assaf Harofe Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Samantha Doyle
- Temple Street Children's University Hospital, Dublin, Ireland
| | - Alejandro Iglesias
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center (CUMC), New York, New York
| | - Francisco Martinez
- Unidad de Genetica, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Fiona Mckenzie
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, Western Australia, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia
| | - Carmen Orellana
- Unidad de Genetica, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | | | - Maria Palomares
- INGEMM, Instituto de Genética Médica y Molecular, IdiPAZ, Hospital Universitario la Paz, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER, ISCIII, Madrid, Spain
| | - Lily Bazak
- Pediatric Neurology & Development Center, Assaf Harofe Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Andy Lee
- Brentwood Children's Clinic, Brentwood, Tennessee
| | - Ana Bircher
- Inner Vision Women's Ultrasound & Genetics, Nashville, Tennessee
| | - Lina Basel-Vanagaite
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Maria Hafström
- Department of Pediatrics, St Olav's Hospital, Trondheim, Norway.,Department of Laboratory Medicine, Children's and Women's Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Gunnar Houge
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
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- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
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- DDD Study, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center (CUMC), New York, New York
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Rogers EM, Spracklen AJ, Bilancia CG, Sumigray KD, Allred SC, Nowotarski SH, Schaefer KN, Ritchie BJ, Peifer M. Abelson kinase acts as a robust, multifunctional scaffold in regulating embryonic morphogenesis. Mol Biol Cell 2016; 27:2613-31. [PMID: 27385341 PMCID: PMC4985262 DOI: 10.1091/mbc.e16-05-0292] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 05/11/2016] [Accepted: 06/20/2016] [Indexed: 11/16/2022] Open
Abstract
The importance of Abl kinase activity, the F-actin–binding site, and scaffolding ability in Abl’s many cell biological roles during Drosophila morphogenesis is examined. Abl is a robust multidomain scaffold with different protein motifs and activities contributing differentially to diverse cellular behaviors. Abelson family kinases (Abls) are key regulators of cell behavior and the cytoskeleton during development and in leukemia. Abl’s SH3, SH2, and tyrosine kinase domains are joined via a linker to an F-actin–binding domain (FABD). Research on Abl’s roles in cell culture led to several hypotheses for its mechanism of action: 1) Abl phosphorylates other proteins, modulating their activity, 2) Abl directly regulates the cytoskeleton via its cytoskeletal interaction domains, and/or 3) Abl is a scaffold for a signaling complex. The importance of these roles during normal development remains untested. We tested these mechanistic hypotheses during Drosophila morphogenesis using a series of mutants to examine Abl’s many cell biological roles. Strikingly, Abl lacking the FABD fully rescued morphogenesis, cell shape change, actin regulation, and viability, whereas kinase-dead Abl, although reduced in function, retained substantial rescuing ability in some but not all Abl functions. We also tested the function of four conserved motifs in the linker region, revealing a key role for a conserved PXXP motif known to bind Crk and Abi. We propose that Abl acts as a robust multidomain scaffold with different protein motifs and activities contributing differentially to diverse cellular behaviors.
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Affiliation(s)
- Edward M Rogers
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Andrew J Spracklen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Colleen G Bilancia
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Kaelyn D Sumigray
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - S Colby Allred
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Stephanie H Nowotarski
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Kristina N Schaefer
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Benjamin J Ritchie
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Mark Peifer
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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4
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Bilancia CG, Winkelman JD, Tsygankov D, Nowotarski SH, Sees JA, Comber K, Evans I, Lakhani V, Wood W, Elston TC, Kovar DR, Peifer M. Enabled negatively regulates diaphanous-driven actin dynamics in vitro and in vivo. Dev Cell 2014; 28:394-408. [PMID: 24576424 PMCID: PMC3992947 DOI: 10.1016/j.devcel.2014.01.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [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: 08/13/2013] [Revised: 12/20/2013] [Accepted: 01/15/2014] [Indexed: 11/03/2022]
Abstract
Actin regulators facilitate cell migration by controlling cell protrusion architecture and dynamics. As the behavior of individual actin regulators becomes clear, we must address why cells require multiple regulators with similar functions and how they cooperate to create diverse protrusions. We characterized Diaphanous (Dia) and Enabled (Ena) as a model, using complementary approaches: cell culture, biophysical analysis, and Drosophila morphogenesis. We found that Dia and Ena have distinct biochemical properties that contribute to the different protrusion morphologies each induces. Dia is a more processive, faster elongator, paralleling the long, stable filopodia it induces in vivo, while Ena promotes filopodia with more dynamic changes in number, length, and lifetime. Acting together, Ena and Dia induce protrusions distinct from those induced by either alone, with Ena reducing Dia-driven protrusion length and number. Consistent with this, EnaEVH1 binds Dia directly and inhibits DiaFH1FH2-mediated nucleation in vitro. Finally, Ena rescues hemocyte migration defects caused by activated Dia. Dia and Ena differ biochemically, promoting distinct filopodia dynamics Dia and Ena colocalization negatively regulates filopodia Ena’s EVH1 binds Dia’s FH1 and reduces Dia-driven filopodia and actin nucleation Ena rescues DiaΔDAD inhibition of hemocyte migration speed to wounds in vivo
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Affiliation(s)
- Colleen G Bilancia
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan D Winkelman
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Denis Tsygankov
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie H Nowotarski
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jennifer A Sees
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Kate Comber
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Iwan Evans
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Vinal Lakhani
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Will Wood
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Timothy C Elston
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David R Kovar
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Mark Peifer
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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