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Musolf AM, Haarman AEG, Luben RN, Ong JS, Patasova K, Trapero RH, Marsh J, Jain I, Jain R, Wang PZ, Lewis DD, Tedja MS, Iglesias AI, Li H, Cowan CS, Biino G, Klein AP, Duggal P, Mackey DA, Hayward C, Haller T, Metspalu A, Wedenoja J, Pärssinen O, Cheng CY, Saw SM, Stambolian D, Hysi PG, Khawaja AP, Vitart V, Hammond CJ, van Duijn CM, Verhoeven VJM, Klaver CCW, Bailey-Wilson JE. Rare variant analyses across multiethnic cohorts identify novel genes for refractive error. Commun Biol 2023; 6:6. [PMID: 36596879 PMCID: PMC9810640 DOI: 10.1038/s42003-022-04323-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
Refractive error, measured here as mean spherical equivalent (SER), is a complex eye condition caused by both genetic and environmental factors. Individuals with strong positive or negative values of SER require spectacles or other approaches for vision correction. Common genetic risk factors have been identified by genome-wide association studies (GWAS), but a great part of the refractive error heritability is still missing. Some of this heritability may be explained by rare variants (minor allele frequency [MAF] ≤ 0.01.). We performed multiple gene-based association tests of mean Spherical Equivalent with rare variants in exome array data from the Consortium for Refractive Error and Myopia (CREAM). The dataset consisted of over 27,000 total subjects from five cohorts of Indo-European and Eastern Asian ethnicity. We identified 129 unique genes associated with refractive error, many of which were replicated in multiple cohorts. Our best novel candidates included the retina expressed PDCD6IP, the circadian rhythm gene PER3, and P4HTM, which affects eye morphology. Future work will include functional studies and validation. Identification of genes contributing to refractive error and future understanding of their function may lead to better treatment and prevention of refractive errors, which themselves are important risk factors for various blinding conditions.
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Affiliation(s)
- Anthony M Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Annechien E G Haarman
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert N Luben
- MRC Epidemiology, University of Cambridge School of Clinical Medicine, Cambridge, UK
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Jue-Sheng Ong
- Statistical Genetics Laboratory, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Karina Patasova
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Rolando Hernandez Trapero
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Joseph Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Ishika Jain
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Riya Jain
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Paul Zhiping Wang
- Institute for Biomedical Sciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Deyana D Lewis
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Milly S Tedja
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Adriana I Iglesias
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Hengtong Li
- Data Science Unit, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Cameron S Cowan
- Institute for Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council of Italy, Pavia, Italy
| | - Alison P Klein
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Priya Duggal
- The Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, WA, Australia
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Toomas Haller
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Juho Wedenoja
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Olavi Pärssinen
- Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä, Finland
- Gerontology Research Center, Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Ching-Yu Cheng
- Centre for Quantitative Medicine, DUKE-National University of Singapore, Singapore, Singapore
- Ocular Epidemiology Research Group, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Seang-Mei Saw
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore, Singapore
- Myopia Research Group, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Anthony P Khawaja
- MRC Epidemiology, University of Cambridge School of Clinical Medicine, Cambridge, UK
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Christopher J Hammond
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Virginie J M Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
- Institute for Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, The Netherlands.
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA.
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Ornitz DM, Itoh N. New developments in the biology of fibroblast growth factors. WIREs Mech Dis 2022; 14:e1549. [PMID: 35142107 PMCID: PMC10115509 DOI: 10.1002/wsbm.1549] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 01/28/2023]
Abstract
The fibroblast growth factor (FGF) family is composed of 18 secreted signaling proteins consisting of canonical FGFs and endocrine FGFs that activate four receptor tyrosine kinases (FGFRs 1-4) and four intracellular proteins (intracellular FGFs or iFGFs) that primarily function to regulate the activity of voltage-gated sodium channels and other molecules. The canonical FGFs, endocrine FGFs, and iFGFs have been reviewed extensively by us and others. In this review, we briefly summarize past reviews and then focus on new developments in the FGF field since our last review in 2015. Some of the highlights in the past 6 years include the use of optogenetic tools, viral vectors, and inducible transgenes to experimentally modulate FGF signaling, the clinical use of small molecule FGFR inhibitors, an expanded understanding of endocrine FGF signaling, functions for FGF signaling in stem cell pluripotency and differentiation, roles for FGF signaling in tissue homeostasis and regeneration, a continuing elaboration of mechanisms of FGF signaling in development, and an expanding appreciation of roles for FGF signaling in neuropsychiatric diseases. This article is categorized under: Cardiovascular Diseases > Molecular and Cellular Physiology Neurological Diseases > Molecular and Cellular Physiology Congenital Diseases > Stem Cells and Development Cancer > Stem Cells and Development.
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Affiliation(s)
- David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nobuyuki Itoh
- Kyoto University Graduate School of Pharmaceutical Sciences, Sakyo, Kyoto, Japan
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Zhao H, Sun J, Insinna C, Lu Q, Wang Z, Nagashima K, Stauffer J, Andresson T, Specht S, Perera S, Daar IO, Westlake CJ. Male infertility-associated Ccdc108 regulates multiciliogenesis via the intraflagellar transport machinery. EMBO Rep 2022; 23:e52775. [PMID: 35201641 PMCID: PMC8982597 DOI: 10.15252/embr.202152775] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
Motile cilia on the cell surface generate movement and directional fluid flow that is crucial for various biological processes. Dysfunction of these cilia causes human diseases such as sinopulmonary disease and infertility. Here, we show that Ccdc108, a protein linked to male infertility, has an evolutionarily conserved requirement in motile multiciliation. Using Xenopus laevis embryos, Ccdc108 is shown to be required for the migration and docking of basal bodies to the apical membrane in epidermal multiciliated cells (MCCs). We demonstrate that Ccdc108 interacts with the IFT‐B complex, and the ciliation requirement for Ift74 overlaps with Ccdc108 in MCCs. Both Ccdc108 and IFT‐B proteins localize to migrating centrioles, basal bodies, and cilia in MCCs. Importantly, Ccdc108 governs the centriolar recruitment of IFT while IFT licenses the targeting of Ccdc108 to the cilium. Moreover, Ccdc108 is required for the centriolar recruitment of Drg1 and activated RhoA, factors that help establish the apical actin network in MCCs. Together, our studies indicate that Ccdc108 and IFT‐B complex components cooperate in multiciliogenesis.
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Affiliation(s)
- Huijie Zhao
- Laboratory of Cellular and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Jian Sun
- Cancer & Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Christine Insinna
- Laboratory of Cellular and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Quanlong Lu
- Laboratory of Cellular and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Ziqiu Wang
- Cancer Research Technology Program, Electron Microscopy Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Kunio Nagashima
- Cancer Research Technology Program, Electron Microscopy Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Jimmy Stauffer
- Laboratory of Cellular and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory (PCL) Mass Spectrometry Center, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Suzanne Specht
- Laboratory of Cellular and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Sumeth Perera
- Laboratory of Cellular and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Ira O Daar
- Cancer & Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Christopher J Westlake
- Laboratory of Cellular and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
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Shankar SP, Fallurin R, Watson T, Shankar PR, Young TL, Orel-Bixler D, Rauen KA. Ophthalmic manifestations in Costello syndrome caused by Ras pathway dysregulation during development. Ophthalmic Genet 2021; 43:48-57. [PMID: 34612139 DOI: 10.1080/13816810.2021.1978103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Costello syndrome (CS) is a multisystem developmental disorder caused by germline pathogenic variants in HRAS resulting in dysregulation of the Ras pathway. A systematic characterization of ophthalmic manifestations provides a unique opportunity to understand the role of Ras signal transduction in ocular development and guide optimal ophthalmic care in CS individuals. METHODS Visual function, ocular features and genotype/phenotype correlations were evaluated in CS individuals harboring HRAS pathogenic variants, by cross-sectional and retrospective studies, and were recruited through the Costello Syndrome Family Network (CSFN) between 2007 and 2020. RESULTS Fifty-six molecularly diagnosed CS individuals including 34 females and 22 males, ages ranging from 0.5 to 37 years were enrolled. The most common ophthalmic manifestations in the cross-sectional study were lack of stereopsis (96%), refractive errors (83%), strabismus (72%), nystagmus (69%), optic nerve hypoplasia or pallor (55%) and ptosis (13.7%) with higher prevalence than in the retrospective data (refractive errors (41%), strabismus (44%), nystagmus (26%), optic nerve hypoplasia or pallor (7%) and ptosis (11%)). Visual acuities were found to ranged from 20/25 to 20/800 and contrast sensitivity from 1.6% to 44%. HRAS pathogenic variants included p.G12S (84%), p.G13C (7%), p.G12A (5.4%), p.G12C (1.8%) and p.A146V (1.8%). CONCLUSION Majority of individuals with CS have refractive errors, strabismus, nystagmus, absent stereopsis, and optic nerve abnormalities suggesting that HRAS and the Ras pathway play a vital role in visual system development. Ptosis, refractive errors and strabismus are amenable to treatment and early ophthalmic evaluation is crucial to prevent long-term vision impairment and improve overall quality of life in CS.
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Affiliation(s)
- Suma P Shankar
- Department of Pediatrics, University of California Davis, Sacramento, California, USA.,Department of Ophthalmology, University of California Davis, Sacramento, California, USA
| | - Reshmitha Fallurin
- Department of Internal Medicine, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Tonya Watson
- The School of Optometry and Vision Science, University of California Berkeley, Berkeley, California, USA
| | - Prabhu R Shankar
- Department of Public Health, University of California Davis, Sacramento, California, USA
| | - Terri L Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - Deborah Orel-Bixler
- The School of Optometry and Vision Science, University of California Berkeley, Berkeley, California, USA
| | - Katherine A Rauen
- Department of Pediatrics, University of California Davis, Sacramento, California, USA
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