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Zhang JJ, Cao ZF, Zhou BT, Yang JH, Li Z, Lin S, Chen XL, Zhang NW, Ye Q, Ma X, Zhu YH. Abnormal function of EPHA2/p.R957P mutant in congenital cataract. Int J Ophthalmol 2024; 17:1007-1017. [PMID: 38895685 PMCID: PMC11144770 DOI: 10.18240/ijo.2024.06.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/18/2024] [Indexed: 06/21/2024] Open
Abstract
AIM To identify genetic defects in a Chinese family with congenital posterior polar cataracts and assess the pathogenicity. METHODS A four-generation Chinese family affected with autosomal dominant congenital cataract was recruited. Nineteen individuals took part in this study including 5 affected and 14 unaffected individuals. Sanger sequencing targeted hot-spot regions of 27 congenital cataract-causing genes for variant discovery. The pathogenicity of the variant was evaluated by the guidelines of American College of Medical Genetics and InterVar software. Confocal microscopy was applied to detect the subcellular localization of fluorescence-labeled ephrin type-A receptor 2 (EPHA2). Co-immunoprecipitation assay was implemented to estimate the interaction between EphA2 and other lens membrane proteins. The mRNA and protein expression were analyzed by reverse transcription-polymerase chain reaction (qRT-PCR) and Western blotting assay, respectively. The cell migration was analyzed by wound healing assay. Zebrafish model was generated by ectopic expression of human EPHA2/p.R957P mutant to demonstrate whether the mutant could cause lens opacity in vivo. RESULTS A novel missense and pathogenic variant c.2870G>C was identified in the sterile alpha motif (SAM) domain of EPHA2. Functional studies demonstrated the variant's impact: reduced EPHA2 protein expression, altered subcellular localization, and disrupted interactions with other lens membrane proteins. This mutant notably enhanced human lens epithelial cell migration, and induced a central cloudy region and roughness in zebrafish lenses with ectopic expression of human EPHA2/p.R957P mutant under differential interference contrast (DIC) optics. CONCLUSION Novel pathogenic c.2870G>C variant of EPHA2 in a Chinese congenital cataract family contributes to disease pathogenesis.
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Affiliation(s)
- Jing-Jin Zhang
- Department of Ophthalmology, the First Affiliated Hospital of Fujian Medical University; Fujian Institute of Ophthalmology; Fujian Provincial Clinical Medical Research Center of Eye Diseases and Optometry, Fuzhou 350005, Fujian Province, China
- Department of Ophthalmology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian Province, China
| | - Zong-Fu Cao
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100000, China
- National Human Genetic Resources Center, National Research Institute for Family Planning, Beijing 100081, China
| | - Bi-Ting Zhou
- Department of Ophthalmology, the First Affiliated Hospital of Fujian Medical University; Fujian Institute of Ophthalmology; Fujian Provincial Clinical Medical Research Center of Eye Diseases and Optometry, Fuzhou 350005, Fujian Province, China
- Department of Ophthalmology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian Province, China
| | - Ju-Hua Yang
- Department of Ophthalmology, the First Affiliated Hospital of Fujian Medical University; Fujian Institute of Ophthalmology; Fujian Provincial Clinical Medical Research Center of Eye Diseases and Optometry, Fuzhou 350005, Fujian Province, China
- Department of Ophthalmology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian Province, China
- Department of Bioengineering and Biopharmaceutics, School of Pharmacy, Fujian Medical University, Fuzhou 350004, Fujian Province, China
| | - Zhong Li
- Department of Bioengineering and Biopharmaceutics, School of Pharmacy, Fujian Medical University, Fuzhou 350004, Fujian Province, China
| | - Shuang Lin
- Department of Bioengineering and Biopharmaceutics, School of Pharmacy, Fujian Medical University, Fuzhou 350004, Fujian Province, China
| | - Xiao-Le Chen
- Department of Bioengineering and Biopharmaceutics, School of Pharmacy, Fujian Medical University, Fuzhou 350004, Fujian Province, China
| | - Nan-Wen Zhang
- Department of Bioengineering and Biopharmaceutics, School of Pharmacy, Fujian Medical University, Fuzhou 350004, Fujian Province, China
| | - Qin Ye
- Department of Ophthalmology, the First Affiliated Hospital of Fujian Medical University; Fujian Institute of Ophthalmology; Fujian Provincial Clinical Medical Research Center of Eye Diseases and Optometry, Fuzhou 350005, Fujian Province, China
- Department of Ophthalmology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian Province, China
| | - Xu Ma
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100000, China
- National Human Genetic Resources Center, National Research Institute for Family Planning, Beijing 100081, China
| | - Yi-Hua Zhu
- Department of Ophthalmology, the First Affiliated Hospital of Fujian Medical University; Fujian Institute of Ophthalmology; Fujian Provincial Clinical Medical Research Center of Eye Diseases and Optometry, Fuzhou 350005, Fujian Province, China
- Department of Ophthalmology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian Province, China
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Shiels A. Through the Cat-Map Gateway: A Brief History of Cataract Genetics. Genes (Basel) 2024; 15:785. [PMID: 38927721 PMCID: PMC11202810 DOI: 10.3390/genes15060785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/06/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Clouding of the transparent eye lens, or cataract(s), is a leading cause of visual impairment that requires surgical replacement with a synthetic intraocular lens to effectively restore clear vision. Most frequently, cataract is acquired with aging as a multifactorial or complex trait. Cataract may also be inherited as a classic Mendelian trait-often with an early or pediatric onset-with or without other ocular and/or systemic features. Since the early 1990s, over 85 genes and loci have been genetically associated with inherited and/or age-related forms of cataract. While many of these underlying genes-including those for lens crystallins, connexins, and transcription factors-recapitulate signature features of lens development and differentiation, an increasing cohort of unpredicted genes, including those involved in cell-signaling, membrane remodeling, and autophagy, has emerged-providing new insights regarding lens homeostasis and aging. This review provides a brief history of gene discovery for inherited and age-related forms of cataract compiled in the Cat-Map database and highlights potential gene-based therapeutic approaches to delay, reverse, or even prevent cataract formation that may help to reduce the increasing demand for cataract surgery.
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Affiliation(s)
- Alan Shiels
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
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Köroğlu M, Karakaplan M, Gündüz E, Kesriklioğlu B, Ergen E, Aslantürk O, Özdemir ZM. Cerebrotendinous Xanthomatosis patients with late diagnosed in single orthopedic clinic: two novel variants in the CYP27A1 gene. Orphanet J Rare Dis 2024; 19:53. [PMID: 38336741 PMCID: PMC10858589 DOI: 10.1186/s13023-024-03082-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 02/05/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Cerebrotendinous Xanthomatosis (CTX) is a rare autosomal recessive lipid storage disorder caused by loss of function variants in the CYP27A1 gene which encodes sterol 27-hydroxylase, on chromosome 2q35. Although the symptoms begin commonly in infancy, CTX diagnosis is often delayed. The aim of this study is to review the orthopedic findings of the disease by providing an overview of the clinical features of the disease. It is to raise awareness of this condition for which early diagnosis and treatment are important. METHODS We retrospectively evaluated the clinical, laboratory, radiological, and genetic findings of eight patients from four families who were admitted to our Orthopedics and Traumatology Department between 2017 and 2022 due to bilateral Achilles tendon xanthomas, were found to have high cholestanol and CYP27A1 gene mutations. RESULTS The mean age of patients was 37, and five of them were male. The mean age at the onset of symptoms was 9.25 years. The mean age of initial diagnosis was 33.75 years. Between symptom onset and clinical diagnosis, an average delay of 24.5 years was observed. All patients had bilateral Achilles tendon xanthoma. Notably, a novel variant (c.670_671delAA) in CYP27A1 gene was identified in three patients who also presented with peripheral neuropathy and bilateral pes cavus. One patient had osteoporosis and four patients had osteopenia. Five patients had a history of bilateral cataracts. Furthermore, three of the patients had early-onset chronic diarrhea and three of the patients had ataxia. Two of the patients had epilepsy and seven of the patients had behavior-personality disorder. All patients had low intelligence, but none of them had cardiac disease. CONCLUSION We present the diagnostic process and clinical features which the largest CTX case series ever reported from single orthopedic clinic. We suggest that patients with normal cholesterol levels presenting with xanthoma being genetically analyzed by testing at their serum cholestanol level, and that all siblings of patients diagnosed with CTX be examined.
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Affiliation(s)
- Muhammed Köroğlu
- Orthopaedics and Traumatology Department, Turgut Özal Medical Center, İnönü University Medical School, Malatya, 44280, Turkey
| | - Mustafa Karakaplan
- Orthopaedics and Traumatology Department, Turgut Özal Medical Center, İnönü University Medical School, Malatya, 44280, Turkey.
| | - Enes Gündüz
- Orthopaedics and Traumatology Department, Şarkışla State Hospital, Sivas, Turkey
| | - Betül Kesriklioğlu
- Department of Medical Genetics, Cerrahpaşa Faculty of Medicine, İstanbul University, Istanbul, Turkey
| | - Emre Ergen
- Orthopaedics and Traumatology Department, Turgut Özal Medical Center, İnönü University Medical School, Malatya, 44280, Turkey
| | - Okan Aslantürk
- Orthopaedics and Traumatology Department, Turgut Özal Medical Center, İnönü University Medical School, Malatya, 44280, Turkey
| | - Zeynep Maraş Özdemir
- Department of Radiology, Turgut Özal Medical Center, İnönü University Medical School, Malatya, Turkey
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Delas F, Koller S, Feil S, Dacheva I, Gerth-Kahlert C, Berger W. Novel CRYGC Mutation in Conserved Ultraviolet-Protective Tryptophan (p.Trp131Arg) Is Linked to Autosomal Dominant Congenital Cataract. Int J Mol Sci 2023; 24:16594. [PMID: 38068917 PMCID: PMC10706789 DOI: 10.3390/ijms242316594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/13/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Congenital cataract (CC), the most prevalent cause of childhood blindness and amblyopia, necessitates prompt and precise genetic diagnosis. The objective of this study is to identify the underlying genetic cause in a Swiss patient with isolated CC. Whole exome sequencing (WES) and copy number variation (CNV) analysis were conducted for variant identification in a patient born with a total binocular CC without a family history of CC. Sanger Sequencing was used to confirm the variant and segregation analysis was used to screen the non-affected parents. The first de novo missense mutation at c.391T>C was identified in exon 3 of CRYGC on chromosome 2 causing the substitution of a highly conserved Tryptophan to an Arginine located at p.Trp131Arg. Previous studies exhibit significant changes in the tertiary structure of the crystallin family in the following variant locus, making CRYGC prone to aggregation aggravated by photodamage resulting in cataract. The variant can be classified as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) criteria (PP3 + PM1 + PM2 + PS2; scoring 10 points). The identification of this novel variant expands the existing knowledge on the range of variants found in the CRYGC gene and contributes to a better comprehension of cataract heterogeneity.
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Affiliation(s)
- Flora Delas
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (F.D.); (S.K.); (S.F.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (F.D.); (S.K.); (S.F.)
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (F.D.); (S.K.); (S.F.)
| | - Ivanka Dacheva
- Department of Ophthalmology, Cantonal Hospital of St. Gallen, 9007 St. Gallen, Switzerland;
| | | | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (F.D.); (S.K.); (S.F.)
- Neuroscience Center Zürich (ZNZ), University of Zurich and ETH Zurich, 8006 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8006 Zurich, Switzerland
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Tan Y, Jiang W, Hu LY, Shen YY, Chen H, Zou YS, Luo LX, Jin GM, Liu ZZ. Hotspots and frontiers of genetic research on pediatric cataracts from 2013 to 2022: a scientometric analysis. Int J Ophthalmol 2023; 16:1682-1691. [PMID: 37854365 PMCID: PMC10559021 DOI: 10.18240/ijo.2023.10.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/02/2023] [Indexed: 10/20/2023] Open
Abstract
AIM To explore the hotspots and frontiers of genetic research on pediatric cataracts. METHODS Global publications from 2013 to 2022 related to genes in pediatric cataracts were extracted from the Web of Science Core Collection, and were analyzed in terms of the publication counts, countries, journals, authors, keywords, cited references, subject categories, and the underlying hotspots and frontiers. RESULTS Totally 699 publications were included in the final analysis. The predominant actors were identified, with China (n=240) and PLoS One (n=33) being the most productive country and journal respectively. The research hotspots extracted from keywords were crystallin gene mutations, pathogenicity evaluation, phenotypes of ocular and neurodevelopmental abnormalities, genes encoding membrane proteins, and diagnosis of multisystemic disorders. The co-cited articles formed 10 clusters of research topics, including FYCO1 (56 items), mutation screening (43 items), gap junction (29 items), the Warburg Micro syndrome (29 items), ephrin-A5 (28 items), novel mutation (24 items), eye development and function (22 items), cholestanol (7 items), OCRL (6 items), and pathogenicity prediction (3 items). The research frontiers were FYCO1, ephrin-A5, and cholestanol. Cell biology showed the strongest bridging effects among different disciplines in the field (betweenness centrality=0.44). CONCLUSION With the progress in next-generation sequencing and multidisciplinary collaboration, genetic research on pediatric cataracts broadens the knowledge scope of the crystalline lens, as well as other organs and systems, shedding light on the molecular mechanisms of systemic diseases. Cell biology may integrate multidisciplinary content to address cutting-edge issues in the field.
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Affiliation(s)
- Yuan Tan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou 510060, Guangdong Province, China
| | - Wei Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou 510060, Guangdong Province, China
- Zhongshan Medical School, Sun Yat-sen University, Guangzhou 510060, Guangdong Province, China
| | - Le-Yi Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou 510060, Guangdong Province, China
| | - Yan-Yu Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou 510060, Guangdong Province, China
| | - Hui Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou 510060, Guangdong Province, China
| | - Ying-Shi Zou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou 510060, Guangdong Province, China
| | - Li-Xia Luo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou 510060, Guangdong Province, China
| | - Guang-Ming Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou 510060, Guangdong Province, China
| | - Zhen-Zhen Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou 510060, Guangdong Province, China
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Rodríguez-Solana P, Arruti N, Nieves-Moreno M, Mena R, Rodríguez-Jiménez C, Guerrero-Carretero M, Acal JC, Blasco J, Peralta JM, Del Pozo Á, Montaño VEF, Dios-Blázquez LD, Fernández-Alcalde C, González-Atienza C, Sánchez-Cazorla E, Gómez-Cano MDLÁ, Delgado-Mora L, Noval S, Vallespín E. Whole Exome Sequencing of 20 Spanish Families: Candidate Genes for Non-Syndromic Pediatric Cataracts. Int J Mol Sci 2023; 24:11429. [PMID: 37511188 PMCID: PMC10380485 DOI: 10.3390/ijms241411429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/23/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Non-syndromic pediatric cataracts are defined as opacification of the crystalline lens that occurs during the first years of life without affecting other organs. Given that this disease is one of the most frequent causes of reversible blindness in childhood, the main objective of this study was to propose new responsible gene candidates that would allow a more targeted genetic approach and expand our genetic knowledge about the disease. We present a whole exome sequencing (WES) study of 20 Spanish families with non-syndromic pediatric cataracts and a previous negative result on an ophthalmology next-generation sequencing panel. After ophthalmological evaluation and collection of peripheral blood samples from these families, WES was performed. We were able to reach a genetic diagnosis in 10% of the families analyzed and found genes that could cause pediatric cataracts in 35% of the cohort. Of the variants found, 18.2% were classified as pathogenic, 9% as likely pathogenic, and 72.8% as variants of uncertain significance. However, we did not find conclusive results in 55% of the families studied, which suggests further studies are needed. The results of this WES study allow us to propose LONP1, ACACA, TRPM1, CLIC5, HSPE1, ODF1, PIKFYVE, and CHMP4A as potential candidates to further investigate for their role in pediatric cataracts, and AQP5 and locus 2q37 as causal genes.
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Affiliation(s)
- Patricia Rodríguez-Solana
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
| | - Natalia Arruti
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
- European Reference Network on Eye Diseases (ERN-EYE), La Paz University Hospital, 28046 Madrid, Spain
| | - María Nieves-Moreno
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
- European Reference Network on Eye Diseases (ERN-EYE), La Paz University Hospital, 28046 Madrid, Spain
| | - Rocío Mena
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (Á.D.P.); (M.d.L.Á.G.-C.); (L.D.-M.)
| | - Carmen Rodríguez-Jiménez
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
| | - Marta Guerrero-Carretero
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
| | - Juan Carlos Acal
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
| | - Joana Blasco
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
| | - Jesús M. Peralta
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
| | - Ángela Del Pozo
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (Á.D.P.); (M.d.L.Á.G.-C.); (L.D.-M.)
- Clinical Bioinformatics Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, CIBERER, La Paz University Hospital, 28046 Madrid, Spain;
| | - Victoria E. F. Montaño
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (Á.D.P.); (M.d.L.Á.G.-C.); (L.D.-M.)
| | - Lucía De Dios-Blázquez
- Clinical Bioinformatics Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, CIBERER, La Paz University Hospital, 28046 Madrid, Spain;
| | - Celia Fernández-Alcalde
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
| | - Carmen González-Atienza
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
| | - Eloísa Sánchez-Cazorla
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
| | - María de Los Ángeles Gómez-Cano
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (Á.D.P.); (M.d.L.Á.G.-C.); (L.D.-M.)
- Clinical Genetics Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, CIBERER, La Paz University Hospital, 28046 Madrid, Spain
| | - Luna Delgado-Mora
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (Á.D.P.); (M.d.L.Á.G.-C.); (L.D.-M.)
- Clinical Genetics Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, CIBERER, La Paz University Hospital, 28046 Madrid, Spain
| | - Susana Noval
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
- European Reference Network on Eye Diseases (ERN-EYE), La Paz University Hospital, 28046 Madrid, Spain
| | - Elena Vallespín
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
- European Reference Network on Eye Diseases (ERN-EYE), La Paz University Hospital, 28046 Madrid, Spain
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (Á.D.P.); (M.d.L.Á.G.-C.); (L.D.-M.)
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Villalba MF, Li CM, Pakravan P, Bademci G, Chang TCP. Commercial Gene Panels for Congenital Anterior Segment Anomalies: Are They All the Same? Am J Ophthalmol 2023; 251:90-103. [PMID: 36906093 PMCID: PMC10247492 DOI: 10.1016/j.ajo.2023.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023]
Abstract
PURPOSE We compared next generation sequencing multigene panels (NGS-MGP) from 5 commercial laboratories to inform ophthalmologists' decision making in diagnostic genetic testing for congenital anterior segment anomalies (CASAs). DESIGN Comparison of commercial genetic testing panels. METHODS This observational study gathered publicly available information on NGS-MGP from 5 commercial laboratories for the following: cataracts, glaucoma, anterior segment dysgenesis (ASD), microphthalmia-anophthalmia-coloboma (MAC), corneal dystrophies, and Axenfeld-Rieger syndrome (ARS). We compared gene panel composition, consensus rate (genes covered by all the panels per condition, "concurrent"), dissensus rate (genes covered by only 1 panel per condition, "standalone"), and intronic variant coverage. For individual genes, we compared publication history and association with systemic conditions. RESULTS Altogether, cataract, glaucoma, corneal dystrophies, MAC, ASD, and ARS panels tested 239, 60, 36, 292, and 10 discrete genes, respectively. The consensus rate varied between 16% and 50%, and the dissensus rate varied between 14% and 74%. After pooling concurrent genes from all conditions, 20% of these genes were concurrent in 2 or more conditions. For both cataract and glaucoma, concurrent genes had significantly stronger correlation with the condition than standalone genes. CONCLUSIONS The genetic testing of CASAs using NGS-MGPs is complicated, owing to their number, variety, and phenotypic and genetic overlap. Although the inclusion of additional genes, such as the standalone ones, might increase diagnostic yield, these genes are also less well studied, indicating uncertainty over their role in CASA pathogenesis. Rigorous prospective diagnostic yield studies of NGS-MGPs will aid in making decisions of panel selection for the diagnosis of CASAs.
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Affiliation(s)
- Maria Fernanda Villalba
- From the Bascom Palmer Eye Institute (M.F.V., T.C.P.C.), University of Miami Miller School of Medicine, Miami, Florida, USA; John P. Hussmann Institute for Human Genomics (M.F.V., G.B.), University of Miami Miller School of Medicine, Miami, Florida, USA; University of Miami Miller School of Medicine (M.F.V., C.M.L., P.P.), Miami, Florida, USA
| | - Chris Michael Li
- University of Miami Miller School of Medicine (M.F.V., C.M.L., P.P.), Miami, Florida, USA
| | - Parastou Pakravan
- University of Miami Miller School of Medicine (M.F.V., C.M.L., P.P.), Miami, Florida, USA
| | - Guney Bademci
- John P. Hussmann Institute for Human Genomics (M.F.V., G.B.), University of Miami Miller School of Medicine, Miami, Florida, USA; Department of Human Genetics (G.B.), University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Ta Chen Peter Chang
- From the Bascom Palmer Eye Institute (M.F.V., T.C.P.C.), University of Miami Miller School of Medicine, Miami, Florida, USA.
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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. Hum Genet 2023; 142:927-947. [PMID: 37191732 PMCID: PMC10680127 DOI: 10.1007/s00439-023-02570-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3300 proteins per sample (n = 5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ≥ 2.5 average spectral counts, ≥ 2.0 fold-enrichment, false discovery rate < 0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE ( https://research.bioinformatics.udel.edu/iSyTE/ ), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA.
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9
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Tan Y, Chen H, Gong S, Zou Y, Shen Y, Luo L, Jin G, Liu Z. Evolution and trends of childhood cataract research in the past 10 years: A scientometric analysis. Heliyon 2023; 9:e17590. [PMID: 37416629 PMCID: PMC10320269 DOI: 10.1016/j.heliyon.2023.e17590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023] Open
Abstract
Purpose To present a panoramic review of childhood cataract knowledge networks, hotspots and trends. Methods The Web of Science Core Collection was used to retrieve the global literature on childhood cataract published between 2012 and 2021. Scientometric data were analyzed and visualized using VOSviewer and CiteSpace for metrics including publication count, citation count, country, journal, author, cited reference, subject category and their temporal trends. Results A total of 3395 analyzed publications showed an inconsistent annual increasing trend. The USA (n = 939) was the leading contributor among countries. The Journal of American Association for Pediatric Ophthalmology and Strabismus (n = 113) had the highest number of publications among journals. Eight clusters of author collaboration network including 183 authors were identified. Gene mutation, cataract surgery management, intraocular lens implantation complications, prevalence, and glaucoma were identified as the research hotspots. Pediatric cataract surgery, new mutations, artificial intelligence, and cerebrotendinous xanthomatosis were identified as frontier research topics. "Biochemistry and molecular biology", "neurosciences", and "radiology, nuclear medicine and medical imaging" had the highest betweenness centrality values (0.38, 0.32, and 0.22). Multidisciplinary (burst years: 2020 to 2021; strength = 4.32) had the greatest strength as of 2021. Conclusions Childhood cataract research intensely focuses on revealing the genetic background and pheno-spectrum of the diseases, innovating and/or optimizing surgical techniques, and preventing and treating postoperative complications. Artificial intelligence has shed light on the diagnosis and treatment of childhood cataracts. The advance in the research on molecular mechanisms of childhood cataracts depends on multidisciplinary cooperation.
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Affiliation(s)
- Yuan Tan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Hui Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Shaoyi Gong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
- Zhongshan Medical School, Sun Yat-sen University, Guangzhou, China
| | - Yingshi Zou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Yanyu Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Lixia Luo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Guangming Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Zhenzhen Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
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10
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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. RESEARCH SQUARE 2023:rs.3.rs-2652395. [PMID: 36993571 PMCID: PMC10055508 DOI: 10.21203/rs.3.rs-2652395/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3,300 proteins per sample (n=5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ³2.5 average spectral counts, ³2.0 fold-enrichment, False Discovery Rate <0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Hongzhan Huang
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
| | - Ashok P. Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Larry L. David
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
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11
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A tapt1 knock-out zebrafish line with aberrant lens development and impaired vision models human early-onset cataract. Hum Genet 2023; 142:457-476. [PMID: 36697720 DOI: 10.1007/s00439-022-02518-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023]
Abstract
Bi-allelic mutations in the gene coding for human trans-membrane anterior-posterior transformation protein 1 (TAPT1) result in a broad phenotypic spectrum, ranging from syndromic disease with severe skeletal and congenital abnormalities to isolated early-onset cataract. We present here the first patient with a frameshift mutation in the TAPT1 gene, resulting in both bilateral early-onset cataract and skeletal abnormalities, in addition to several dysmorphic features, in this way further expanding the phenotypic spectrum associated with TAPT1 mutations. A tapt1a/tapt1b double knock-out (KO) zebrafish model generated by CRISPR/Cas9 gene editing revealed an early larval phenotype with eye malformations, loss of vision, increased photokinetics and hyperpigmentation, without visible skeletal involvement. Ultrastructural analysis of the eyes showed a smaller condensed lens, loss of integrity of the lens capsule with formation of a secondary lens and hyperplasia of the cells in the ganglion and inner plexiform layers of the retina. Transcriptomic analysis pointed to an impaired lens development with aberrant expression of many of the crystallin and other lens-specific genes. Furthermore, the phototransduction and visual perception pathways were found to be significantly disturbed. Differences in light perception are likely the cause of the increased dark photokinetics and generalized hyperpigmentation observed in this zebrafish model. In conclusion, this study validates TAPT1 as a new gene for early-onset cataract and sheds light on its ultrastructural and molecular characteristics.
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Nabavizadeh N, Bressin A, Shboul M, Moreno Traspas R, Chia PH, Bonnard C, Szenker‐Ravi E, Sarıbaş B, Beillard E, Altunoglu U, Hojati Z, Drutman S, Freier S, El‐Khateeb M, Fathallah R, Casanova J, Soror W, Arafat A, Escande‐Beillard N, Mayer A, Reversade B. A progeroid syndrome caused by a deep intronic variant in TAPT1 is revealed by RNA/SI-NET sequencing. EMBO Mol Med 2023; 15:e16478. [PMID: 36652330 PMCID: PMC9906387 DOI: 10.15252/emmm.202216478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 01/19/2023] Open
Abstract
Exome sequencing has introduced a paradigm shift for the identification of germline variations responsible for Mendelian diseases. However, non-coding regions, which make up 98% of the genome, cannot be captured. The lack of functional annotation for intronic and intergenic variants makes RNA-seq a powerful companion diagnostic. Here, we illustrate this point by identifying six patients with a recessive Osteogenesis Imperfecta (OI) and neonatal progeria syndrome. By integrating homozygosity mapping and RNA-seq, we delineated a deep intronic TAPT1 mutation (c.1237-52 G>A) that segregated with the disease. Using SI-NET-seq, we document that TAPT1's nascent transcription was not affected in patients' fibroblasts, indicating instead that this variant leads to an alteration of pre-mRNA processing. Predicted to serve as an alternative splicing branchpoint, this mutation enhances TAPT1 exon 12 skipping, creating a protein-null allele. Additionally, our study reveals dysregulation of pathways involved in collagen and extracellular matrix biology in disease-relevant cells. Overall, our work highlights the power of transcriptomic approaches in deciphering the repercussions of non-coding variants, as well as in illuminating the molecular mechanisms of human diseases.
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Affiliation(s)
- Nasrinsadat Nabavizadeh
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
- Division of Genetics, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
| | | | - Mohammad Shboul
- Department of Medical Laboratory SciencesJordan University of Science and TechnologyIrbidJordan
| | - Ricardo Moreno Traspas
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
| | - Poh Hui Chia
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
| | - Carine Bonnard
- Model Development, A*STAR Skin Research Labs (A*SRL)Singapore CitySingapore
| | - Emmanuelle Szenker‐Ravi
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
| | - Burak Sarıbaş
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
| | | | - Umut Altunoglu
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
| | - Zohreh Hojati
- Division of Genetics, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
| | - Scott Drutman
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller BranchRockefeller UniversityNew YorkNYUSA
| | - Susanne Freier
- Max Planck Institute for Molecular GeneticsBerlinGermany
| | | | - Rajaa Fathallah
- National Center for Diabetes, Endocrinology and GeneticsAmmanJordan
| | - Jean‐Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller BranchRockefeller UniversityNew YorkNYUSA
- Laboratory of Human Genetics of Infectious Diseases, Necker BranchINSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine InstituteUniversity of ParisParisFrance
- Howard Hughes Medical InstituteNew YorkNYUSA
- Pediatric Hematology and Immunology UnitNecker Hospital for Sick ChildrenParisFrance
| | - Wesam Soror
- National Center for Diabetes, Endocrinology and GeneticsAmmanJordan
| | - Alaa Arafat
- National Center for Diabetes, Endocrinology and GeneticsAmmanJordan
| | - Nathalie Escande‐Beillard
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
- Institute of Molecular and Cell Biology, A*STARSingapore CitySingapore
| | - Andreas Mayer
- Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Bruno Reversade
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
- Institute of Molecular and Cell Biology, A*STARSingapore CitySingapore
- Department of PaediatricsNational University of SingaporeSingapore CitySingapore
- Smart‐Health Initiative, BESE, KAUSTThuwalKingdom of Saudi Arabia
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Highly Accessible Computational Prediction and In Vivo/In Vitro Experimental Validation: Novel Synthetic Phenyl Ketone Derivatives as Promising Agents against NAFLD via Modulating Oxidoreductase Activity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:3782230. [PMID: 36659905 PMCID: PMC9844233 DOI: 10.1155/2023/3782230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) has reached epidemic proportions with no pharmacological treatment approved. Several highly accessible computational tools were employed to predict the activities of twelve novel compounds prior to actual chemical synthesis. We began our work by designing two or three hydroxyl groups appended to the phenyl ketone core, followed by prediction of drug-likeness and targets. Most predicted targets for each compound overlapped with NAFLD targets (≥80%). Enrichment analysis showed that these compounds might regulate oxidoreductase activity. Then, these compounds were synthesized and confirmed by IR, MS, 1H, and 13C NMR. Their cell viability demonstrated that twelve compounds exhibited appreciable potencies against NAFLD (EC50 values ≤ 13.5 μM). Furthermore, the most potent compound 5f effectively prevented NAFLD progression as evidenced by the change in histological features. 5f significantly reduced total cholesterol and triglyceride levels in vitro/in vivo, and the effects of 5f were significantly stronger than those of the control drug. The proteomic data showed that oxidoreductase activity was the most significantly enriched, and this finding was consistent with docking results. In summary, this validated presynthesis prediction approach was cost-saving and worthy of popularization. The novel synthetic phenyl ketone derivative 5f holds great therapeutic potential by modulating oxidoreductase activity to counter NAFLD.
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14
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Lansdon LA, Dickinson A, Arlis S, Liu H, Hlas A, Hahn A, Bonde G, Long A, Standley J, Tyryshkina A, Wehby G, Lee NR, Daack-Hirsch S, Mohlke K, Girirajan S, Darbro BW, Cornell RA, Houston DW, Murray JC, Manak JR. Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes. Am J Hum Genet 2023; 110:71-91. [PMID: 36493769 PMCID: PMC9892779 DOI: 10.1016/j.ajhg.2022.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex, heterogeneous etiology. It is well established that common and rare sequence variants contribute to the formation of CL/P, but the contribution of copy-number variants (CNVs) to cleft formation remains relatively understudied. To fill this knowledge gap, we conducted a large-scale comparative analysis of genome-wide CNV profiles of 869 individuals from the Philippines and 233 individuals of European ancestry with CL/P with three primary goals: first, to evaluate whether differences in CNV number, amount of genomic content, or amount of coding genomic content existed within clefting subtypes; second, to assess whether CNVs in our cohort overlapped with known Mendelian clefting loci; and third, to identify unestablished Mendelian clefting genes. Significant differences in CNVs across cleft types or in individuals with non-syndromic versus syndromic clefts were not observed; however, several CNVs in our cohort overlapped with known syndromic and non-syndromic Mendelian clefting loci. Moreover, employing a filtering strategy relying on population genetics data that rare variants are on the whole more deleterious than common variants, we identify several CNV-associated gene losses likely driving non-syndromic clefting phenotypes. By prioritizing genes deleted at a rare frequency across multiple individuals with clefts yet enriched in our cohort of individuals with clefts compared to control subjects, we identify COBLL1, RIC1, and ARHGEF38 as clefting genes. CRISPR-Cas9 mutagenesis of these genes in Xenopus laevis and Danio rerio yielded craniofacial dysmorphologies, including clefts analogous to those seen in human clefting disorders.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology, University of Missouri - Kansas City School of Medicine, Kansas City, MO 64108, USA
| | | | - Sydney Arlis
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Huan Liu
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Arman Hlas
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Alyssa Hahn
- Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Greg Bonde
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Abby Long
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Standley
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | | | - George Wehby
- College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Nanette R Lee
- Office of Population Studies Foundation, Inc., University of San Carlos, Cebu City, Philippines
| | | | - Karen Mohlke
- University of North Carolina, Chapel Hill, NC 27514, USA
| | | | - Benjamin W Darbro
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Robert A Cornell
- Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA; Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Douglas W Houston
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - J Robert Manak
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA.
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15
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Tang Y, Liu YX, Sheng Y, Fan LL, Zhang AQ, Zheng ZF. The first case report of CODAS syndrome in Chinese population caused by two LONP1 pathogenic mutations. Front Genet 2023; 13:1031856. [PMID: 36685982 PMCID: PMC9845248 DOI: 10.3389/fgene.2022.1031856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/02/2022] [Indexed: 01/06/2023] Open
Abstract
Background: CODAS syndrome (MIM 600373) is a multi-system developmental disorder characterized by cerebral, ocular, dental, auricular, and skeletal anomalies. CODAS syndrome is rare in the world and no cases have been reported in Chinese population so far. Mutations in the LONP1 gene can contribute to CODAS syndrome, while the underlying molecular mechanisms requires further investigation. Method: We described a Chinese boy who has suffered from cognition impairment, cataracts, caries, abnormal auricle and skeletal anomalies since birth. The patient's parents are non-consanguineous and healthy. Whole-exome sequencing (WES) was employed to explore the genetic entity of this family. Results: A compound heterozygous missense mutation (NM_004793: c.2009C>T/p.A670V and c.2014C>T/p.R672C) of LONP1 was identified in the patient. Considering the clinical phenotypes and genetic results, the patient was diagnosed as CODAS syndrome. Conclusion: Here we reported the first case with CODAS syndrome in Chinese population. WES identified a compound heterozygous missense mutation of LONP1 gene in the patients. Our study not only provided data for genetic counseling and clinical diagnosis to this family, but also expanded the clinical spectrum of LONP1-related CODAS syndrome.
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Affiliation(s)
- Yi Tang
- Department of Cardiology, Hunan Provincial People’s Hospital, The First Afliated Hospital of Hunan Normal University, Clinical Medicine Research Center of Heart Failure of Hunan Province, Hunan Normal University, Changsha, China
| | - Yu-Xing Liu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Yue Sheng
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Liang-Liang Fan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Ai-Qian Zhang
- Department of Obstetrics and Gynecology, Third Xiangya Hospital of Central South University, Changsha, China,*Correspondence: Ai-Qian Zhang, ; Zhao-Fen Zheng,
| | - Zhao-Fen Zheng
- Department of Cardiology, Hunan Provincial People’s Hospital, The First Afliated Hospital of Hunan Normal University, Clinical Medicine Research Center of Heart Failure of Hunan Province, Hunan Normal University, Changsha, China,*Correspondence: Ai-Qian Zhang, ; Zhao-Fen Zheng,
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16
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Liao HQ, Guo ZY, Huang LH, Liu G, Lu JF, Zhang YF, Xing XW. WDR87 interacts with CFAP47 protein in the middle piece of spermatozoa flagella to participate in sperm tail assembly. Mol Hum Reprod 2022; 29:6960929. [PMID: 36571501 DOI: 10.1093/molehr/gaac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 12/07/2022] [Indexed: 12/27/2022] Open
Abstract
Spermatogenesis is a complex process that includes spermatogonia self-renewal, spermatocyte meiosis and spermatozoa assembly. Recent studies have revealed that WD40-repeat domain-containing (WDR) proteins play important roles in spermatocyte division, spermatozoa flagella assembly and head shaping. In this study, we investigated the expression pattern of WDR87 and found that it was highly expressed in the testis of both humans and mice. Immunofluorescence staining revealed that mouse WDR87 was distributed in the perinuclear cytoplasm of primary spermatocytes, secondary spermatocytes and round spermatids. In the spermiogenesis stage, with extension of the nucleus, WDR87 migrated to the manchette and finally localized to the middle piece of the spermatozoa tail. Furthermore, we identified a cilia- and flagella-associated protein, CFAP47, which interacted with WDR87 in the flagellar midpiece of the spermatozoa, suggesting that WDR87 may be associated with multiple morphological abnormalities of the flagella (MMAF). Subsequently, we screened gene mutations in seven MMAF individuals and found two novel mutations in CFAP47 (c.706G>A, Val236Met; c.1337C>T, Thr446Met) in one case. Immunoblotting and immunofluorescence revealed that CFAP47 was dramatically reduced in spermatozoa from the CFAP47-mutated man. Meanwhile, the expression of WDR87 was also significantly decreased, and weak signals were detected adjacent to the spermatozoa nuclei, indicating that CFAP47 was necessary for WDR87 transportation during spermatozoa flagella biogenesis. These data indicate that WDR87 is located in the middle piece of the sperm tail and interacts with CFAP47 to form a complex which is involved in spermatozoa tail assembly.
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Affiliation(s)
- Hong-Qing Liao
- The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China.,Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang, China
| | - Zi-Yi Guo
- The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China.,Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang, China
| | - Li-Hua Huang
- Center for Experimental Medicine, Third Xiangya Hospital, Central South University, Changsha, China
| | - Gang Liu
- The Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Jin-Feng Lu
- Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang, China
| | - Yun-Fei Zhang
- Center for Experimental Medicine, Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiao-Wei Xing
- Center for Experimental Medicine, Third Xiangya Hospital, Central South University, Changsha, China
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17
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Jones JL, Burdon KP. Evaluating gap junction variants for a role in pediatric cataract: an overview of the genetic landscape and clinical classification of variants in the GJA3 and GJA8 genes. EXPERT REVIEW OF OPHTHALMOLOGY 2022. [DOI: 10.1080/17469899.2023.2160320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Johanna L Jones
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
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18
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Altassan R, Qudair A, Alokaili R, Alhasan K, Faqeih EA, Alhashem A, Alowain M, Alsayed M, Rahbeeni Z, Albadi L, Alkuraya FS, Anderson EN, Rajan D, Pandey UB. Further delineation of GEMIN4 related neurodevelopmental disorder with microcephaly, cataract, and renal abnormalities syndrome. Am J Med Genet A 2022; 188:2932-2940. [PMID: 35861185 DOI: 10.1002/ajmg.a.62894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 01/31/2023]
Abstract
Pathogenic variants in GEMIN4 have recently been linked to an inherited autosomal recessive neurodevelopmental disorder characterized with microcephaly, cataracts, and renal abnormalities (NEDMCR syndrome). This report provides a retrospective review of 16 patients from 11 unrelated Saudi consanguineous families with GEMIN4 mutations. The cohort comprises 11 new and unpublished clinical details from five previously described patients. Only two missense, homozygous, pathogenic variants were found in all affected patients, suggesting a founder effect. All patients shared global developmental delay with variable ophthalmological, renal, and skeletal manifestations. In addition, we knocked down endogenous Drosophila GEMIN4 in neurons to further investigate the mechanism of the functional defects in affected patients. Our fly model findings demonstrated developmental defects and motor dysfunction suggesting that loss of GEMIN4 function is detrimental in vivo; likely similar to human patients. To date, this study presents the largest cohort of patients affected with GEMIN4 mutations. Considering that identifying GEMIN4 defects in patients presenting with neurodevelopmental delay and congenital cataract will help in early diagnosis, appropriate management and prevention plans that can be made for affected families.
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Affiliation(s)
- Ruqaiah Altassan
- Department of Medical Genetics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Ahmad Qudair
- Department of Medical Genetics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Riyadh Alokaili
- Department of Radiology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Khalid Alhasan
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Pediatrics, King Saud University Medical City, Riyadh, Saudi Arabia
| | - Eissa A Faqeih
- Medical Genetics Section, King Fahad Medical City, Children's Hospital, Riyadh, Kingdom of Saudi Arabia
| | - Amal Alhashem
- Division of Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Muhammed Alowain
- Department of Medical Genetics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Moeanaldeen Alsayed
- Department of Medical Genetics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genetics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lama Albadi
- Department of Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Deepa Rajan
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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19
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Ahmad I. CRISPR/Cas9—A Promising Therapeutic Tool to Cure Blindness: Current Scenario and Future Prospects. Int J Mol Sci 2022; 23:ijms231911482. [PMID: 36232782 PMCID: PMC9569777 DOI: 10.3390/ijms231911482] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
CRISPR-based targeted genome editing is bringing revolutionary changes in the research arena of biological sciences. CRISPR/Cas9 has been explored as an efficient therapeutic tool for the treatment of genetic diseases. It has been widely used in ophthalmology research by using mouse models to correct pathogenic mutations in the eye stem cells. In recent studies, CRISPR/Cas9 has been used to correct a large number of mutations related to inherited retinal disorders. In vivo therapeutic advantages for retinal diseases have been successfully achieved in some rodents. Current advances in the CRISPR-based gene-editing domain, such as modified Cas variants and delivery approaches have optimized its application to treat blindness. In this review, recent progress and challenges of the CRISPR-Cas system have been discussed to cure blindness and its prospects.
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Affiliation(s)
- Irshad Ahmad
- Department of Bioengineering, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia; ; Tel.: +966-13-8608393
- Interdisciplinary Research Center for Membranes and Water Security, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia
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20
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Fell CW, Hagelkruys A, Cicvaric A, Horrer M, Liu L, Li JSS, Stadlmann J, Polyansky AA, Mereiter S, Tejada MA, Kokotović T, Achuta VS, Scaramuzza A, Twyman KA, Morrow MM, Juusola J, Yan H, Wang J, Burmeister M, Choudhury B, Andersen TL, Wirnsberger G, Holmskov U, Perrimon N, Žagrović B, Monje FJ, Moeller JB, Penninger JM, Nagy V. FIBCD1 is an endocytic GAG receptor associated with a novel neurodevelopmental disorder. EMBO Mol Med 2022; 14:e15829. [PMID: 35916241 PMCID: PMC9449597 DOI: 10.15252/emmm.202215829] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/21/2022] Open
Abstract
Whole-exome sequencing of two patients with idiopathic complex neurodevelopmental disorder (NDD) identified biallelic variants of unknown significance within FIBCD1, encoding an endocytic acetyl group-binding transmembrane receptor with no known function in the central nervous system. We found that FIBCD1 preferentially binds and endocytoses glycosaminoglycan (GAG) chondroitin sulphate-4S (CS-4S) and regulates GAG content of the brain extracellular matrix (ECM). In silico molecular simulation studies and GAG binding analyses of patient variants determined that such variants are loss-of-function by disrupting FIBCD1-CS-4S association. Gene knockdown in flies resulted in morphological disruption of the neuromuscular junction and motor-related behavioural deficits. In humans and mice, FIBCD1 is expressed in discrete brain regions, including the hippocampus. Fibcd1 KO mice exhibited normal hippocampal neuronal morphology but impaired hippocampal-dependent learning. Further, hippocampal synaptic remodelling in acute slices from Fibcd1 KO mice was deficient but restored upon enzymatically modulating the ECM. Together, we identified FIBCD1 as an endocytic receptor for GAGs in the brain ECM and a novel gene associated with an NDD, revealing a critical role in nervous system structure, function and plasticity.
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Affiliation(s)
- Christopher W Fell
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Astrid Hagelkruys
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Ana Cicvaric
- Department of Neurophysiology and Neuropharmacology, Centre for Physiology and PharmacologyMedical University of ViennaViennaAustria
- Department of Psychiatry and Behavioral Sciences, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Marion Horrer
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Lucy Liu
- Department of Genetics, Harvard Medical SchoolHoward Hughes Medical InstituteBostonMAUSA
| | - Joshua Shing Shun Li
- Department of Genetics, Harvard Medical SchoolHoward Hughes Medical InstituteBostonMAUSA
| | - Johannes Stadlmann
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Institute of BiochemistryUniversity of Natural Resource and Life SciencesViennaAustria
| | - Anton A Polyansky
- Department of Structural and Computational Biology, Max Perutz LabsUniversity of ViennaViennaAustria
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
| | - Stefan Mereiter
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Miguel Angel Tejada
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Research Unit on Women's Health‐Institute of Health Research INCLIVAValenciaSpain
| | - Tomislav Kokotović
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Venkat Swaroop Achuta
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Angelica Scaramuzza
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | | | | | | | - Huifang Yan
- Department of PediatricsPeking University First HospitalBeijingChina
- Joint International Research Center of Translational and Clinical ResearchBeijingChina
| | - Jingmin Wang
- Department of PediatricsPeking University First HospitalBeijingChina
- Joint International Research Center of Translational and Clinical ResearchBeijingChina
| | - Margit Burmeister
- Michigan Neuroscience InstituteUniversity of MichiganAnn ArborMIUSA
- Departments of Computational Medicine & Bioinformatics, Psychiatry and Human GeneticsUniversity of MichiganAnn ArborMIUSA
| | - Biswa Choudhury
- Department of Cellular and Molecular MedicineUCSDLa JollaCAUSA
| | - Thomas Levin Andersen
- Clinical Cell Biology, Department of PathologyOdense University HospitalOdenseDenmark
- Pathology Research Unit, Department of Clinical Research and Department of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
| | - Gerald Wirnsberger
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Apeiron Biologics AG, Vienna BioCenter CampusViennaAustria
| | - Uffe Holmskov
- Cancer and Inflammation Research, Department of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical SchoolHoward Hughes Medical InstituteBostonMAUSA
| | - Bojan Žagrović
- Department of Structural and Computational Biology, Max Perutz LabsUniversity of ViennaViennaAustria
| | - Francisco J Monje
- Department of Neurophysiology and Neuropharmacology, Centre for Physiology and PharmacologyMedical University of ViennaViennaAustria
| | - Jesper Bonnet Moeller
- Cancer and Inflammation Research, Department of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
- Danish Institute for Advanced StudyUniversity of Southern DenmarkOdenseDenmark
| | - Josef M Penninger
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Department of Medical Genetics, Life Science InstituteUniversity of British ColumbiaVancouverBCCanada
| | - Vanja Nagy
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
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21
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Shirzadeh E, Piryaei F, Naddaf H, Barabadi Z. Two New Variants in FYCO1 Are Responsible for Autosomal Recessive Congenital Cataract in Iranian Population. CELL JOURNAL 2022; 24:546-551. [PMID: 36274208 PMCID: PMC9594866 DOI: 10.22074/cellj.2022.8116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Indexed: 11/18/2022]
Abstract
The purpose of this experimental study was to investigate the genetic etiology of congenital cataract (CC) manifesting an autosomal recessive pattern of inheritance in four Iranian families. Affected individuals and their normal first-degree relatives in each family were included in the present study. The genomic DNA of the blood samples was extracted from all participants, and one affected member belonging to each family was subjected to Whole Exome Sequencing (WES). Using bidirectional Sanger sequencing, the identified variants were validated by co-segregation analysis. Two different mutations were detected in the FYCO1 gene encoding FYVE and coiled-coil domain-containing protein. A previously reported missense mutation, c.265C>T (p.Arg89Cys), was found in one Iranian family for the first time, and a combination of two variants in a single codon, c.[265C>T;267C>A] (p.Arg89X), was identified in the three other families. On the other hand, accompanying the c.265C>T mutation, the presence of the c.267C>A polymorphism leads to a premature stop codon. In-Silico Analysis of FYCO1 protein demonstrated that RUN domain will be interrupted so that the large part of functional protein will be eliminated due to this novel variant. FYCO1 has been proved to be involved in human lens development and transparency. Its mutations, therefore, result in CC. Herein, we reported the first autosomal recessive CC patients with c.265C>T (p.Arg89Cys) or c.[265C>T;267C>A] variant in Iranian population for the FYCO1 gene. FYCO1 mutations could be tracked for preventive objectives or even be targeted as therapeutic candidates via treatment approaches in the future.
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Affiliation(s)
- Ebrahim Shirzadeh
- Department of Ophthalmology, School of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran,*Corresponding Addresses:P.O.Box: 9613873137Department of OphthalmologySchool of MedicineSabzevar University of Medical SciencesSabzevarIranP.O.Box: 6517838696Department of Tissue EngineeringSchool of MedicineHamadan University of Medical SciencesHamadanIran
Emails:,
| | - Fahimeh Piryaei
- Department of Molecular Medicine and Genetics, Research Center for Molecular Medicine, School of Medicine, Hamadan University
of Medical Sciences, Hamadan, Iran
| | - Hanieh Naddaf
- Core facility of Hamadan University of Medical Sciences, Hamadan, Iran
| | - Zahra Barabadi
- Department of Tissue Engineering, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran,School of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran,*Corresponding Addresses:P.O.Box: 9613873137Department of OphthalmologySchool of MedicineSabzevar University of Medical SciencesSabzevarIranP.O.Box: 6517838696Department of Tissue EngineeringSchool of MedicineHamadan University of Medical SciencesHamadanIran
Emails:,
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22
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Patel SD, Anand D, Motohashi H, Katsuoka F, Yamamoto M, Lachke SA. Deficiency of the bZIP transcription factors Mafg and Mafk causes misexpression of genes in distinct pathways and results in lens embryonic developmental defects. Front Cell Dev Biol 2022; 10:981893. [PMID: 36092713 PMCID: PMC9459095 DOI: 10.3389/fcell.2022.981893] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/28/2022] [Indexed: 01/11/2023] Open
Abstract
Deficiency of the small Maf proteins Mafg and Mafk cause multiple defects, namely, progressive neuronal degeneration, cataract, thrombocytopenia and mid-gestational/perinatal lethality. Previous data shows Mafg -/-:Mafk +/- compound knockout (KO) mice exhibit cataracts age 4-months onward. Strikingly, Mafg -/-:Mafk -/- double KO mice develop lens defects significantly early in life, during embryogenesis, but the pathobiology of these defects is unknown, and is addressed here. At embryonic day (E)16.5, the epithelium of lens in Mafg -/-:Mafk -/- animals appears abnormally multilayered as demonstrated by E-cadherin and nuclear staining. Additionally, Mafg -/-:Mafk -/- lenses exhibit abnormal distribution of F-actin near the "fulcrum" region where epithelial cells undergo apical constriction prior to elongation and reorientation as early differentiating fiber cells. To identify the underlying molecular changes, we performed high-throughput RNA-sequencing of E16.5 Mafg -/-:Mafk -/- lenses and identified a cohort of differentially expressed genes that were further prioritized using stringent filtering criteria and validated by RT-qPCR. Several key factors associated with the cytoskeleton, cell cycle or extracellular matrix (e.g., Cdk1, Cdkn1c, Camsap1, Col3a1, Map3k12, Sipa1l1) were mis-expressed in Mafg -/-:Mafk -/- lenses. Further, the congenital cataract-linked extracellular matrix peroxidase Pxdn was significantly overexpressed in Mafg -/-:Mafk -/- lenses, which may cause abnormal cell morphology. These data also identified the ephrin signaling receptor Epha5 to be reduced in Mafg -/-:Mafk -/- lenses. This likely contributes to the Mafg -/-:Mafk -/- multilayered lens epithelium pathology, as loss of an ephrin ligand, Efna5 (ephrin-A5), causes similar lens defects. Together, these findings uncover a novel early function of Mafg and Mafk in lens development and identify their new downstream regulatory relationships with key cellular factors.
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Affiliation(s)
- Shaili D. Patel
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, United States,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States,*Correspondence: Salil A. Lachke,
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23
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Peng Y, Zheng Y, Deng Z, Zhang S, Tan Y, Hu Z, Tao L, Luo Y. Case Report: A de novo Variant of CRYGC Gene Associated With Congenital Cataract and Microphthalmia. Front Genet 2022; 13:866246. [PMID: 35719371 PMCID: PMC9198712 DOI: 10.3389/fgene.2022.866246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Congenital cataract is one of the most common causes of blindness in children. A rapid and accurate genetic diagnosis benefit the patients in the pediatric department. The current study aims to identify the genetic defects in a congenital cataract patient without a family history. Case presentation: A congenital cataract patient with microphthalmia and nystagmus was recruited for this study. Trio-based whole-exome sequencing revealed a de novo variant (c.394delG, p.V132Sfs*15) in CRYGC gene. According to the American College of Medical Genetics and Genomics (ACMG) criteria, the variant could be annontated as pathogenic. Conclusion: Our findings provide new knowledge of the variant spectrum of CRYGC gene and are essential for understanding the heterogeneity of cataracts in the Chinese population.
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Affiliation(s)
- Yu Peng
- Department of Ophthalmology & Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, China
| | - Yu Zheng
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, China
| | - Zifeng Deng
- Department of Ophthalmology, Hunan Children's Hospital, Changsha, China
| | - Shuju Zhang
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, China
| | - Yilan Tan
- Department of Ophthalmology, Hunan Children's Hospital, Changsha, China
| | - Zhengmao Hu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Lijuan Tao
- Department of Ophthalmology, Hunan Children's Hospital, Changsha, China
| | - Yulin Luo
- Department of Ophthalmology, Hunan Children's Hospital, Changsha, China
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24
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Ghosh R, León-Ruiz M, Sardar SS, Naga D, Ghosh T, Dutta S, Benito-León J. Cerebellar Cognitive Affective Syndrome in a Case of Cerebrotendinous Xanthomatosis. CEREBELLUM (LONDON, ENGLAND) 2022:10.1007/s12311-022-01421-4. [PMID: 35668283 DOI: 10.1007/s12311-022-01421-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Ritwik Ghosh
- Department of General Medicine, Burdwan Medical College & Hospital, Burdwan, West Bengal, India
| | - Moisés León-Ruiz
- Section of Clinical Neurophysiology, Department of Neurology, University Hospital "La Paz", Madrid, Spain
| | - Sona Singh Sardar
- Department of General Medicine, Burdwan Medical College & Hospital, Burdwan, West Bengal, India
| | - Dinobandhu Naga
- Department of General Medicine, Burdwan Medical College & Hospital, Burdwan, West Bengal, India
| | - Tapas Ghosh
- Department of Anatomy, Burdwan Medical College & Hospital, Burdwan, West Bengal, India
| | - Souvik Dutta
- Department of Radiodiagnosis, Burdwan Medical College and Hospital, Burdwan, West Bengal, India
| | - Julián Benito-León
- Department of Neurology, University Hospital "12 de Octubre", Madrid, Spain.
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
- Department of Medicine, Complutense University, Madrid, Spain.
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25
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A Novel Mutation in CRYGC Mutation Associated with Autosomal Dominant Congenital Cataracts and Microcornea. OPHTHALMOLOGY SCIENCE 2022; 2:100093. [PMID: 36246175 PMCID: PMC9560566 DOI: 10.1016/j.xops.2021.100093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 11/22/2022]
Abstract
Purpose Crystallin protein mutations are associated with congenital cataract (CC), and several disease-causing mutations in the CRYGC gene have been identified. We present the location of a new mutation in CRYGC in members of a Chinese family who presented with CCs with or without microcornea. Design Observational study. Participants A Chinese family diagnosed with autosomal dominant (AD) CCs with or without microphthalmia. Methods Because this was an observational study, it was not registered as a clinical trial. The proband and her 2 children were diagnosed with AD CCs and microcornea and were recruited for the study. Participants underwent complete ophthalmological examinations, and blood samples were used for genomic extraction. Main Outcome Measures We detected 1 disease-associated variant using Exomiser analysis by matching the proband’s phenotype and the inheritance pattern. The variant was determined to be pathogenic according to American College of Medical Genetics and Genomics (ACMG) guidelines. Results We detected 1 disease-associated variant using Exomiser analysis by matching the proband’s phenotype and the inheritance pattern. The variant was determined to be pathogenic according to the American College of Medical Genetics and Genomics guidelines. Next-generation sequencing was verified using Sanger sequencing, and we confirmed that the proband and her children carried the same mutation. We identified the heterozygous variant c.389_390insGCTG (p.C130fs), which includes a frameshift mutation. The residues in p.C130fs are all highly conserved across species. This disease-causing frameshift mutation in the CRYGC gene is not currently present in the ClinVar database. Conclusions Our findings expand the repertoire of known mutations in the CRYGC gene that cause CCs and provide new insights into the etiology and molecular diagnosis of CCs; however, the molecular mechanism of this mutation warrants further investigation.
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Murugan S, Cheng C. Roles of Eph-Ephrin Signaling in the Eye Lens Cataractogenesis, Biomechanics, and Homeostasis. Front Cell Dev Biol 2022; 10:852236. [PMID: 35295853 PMCID: PMC8918484 DOI: 10.3389/fcell.2022.852236] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/04/2022] [Indexed: 01/26/2023] Open
Abstract
The eye lens is responsible for fine focusing of light onto the retina, and its function relies on tissue transparency and biomechanical properties. Recent studies have demonstrated the importance of Eph-ephrin signaling for the maintenance of life-long lens homeostasis. The binding of Eph receptor tyrosine kinases to ephrin ligands leads to a bidirectional signaling pathway that controls many cellular processes. In particular, dysfunction of the receptor EphA2 or the ligand ephrin-A5 lead to a variety of congenital and age-related cataracts, defined as any opacity in the lens, in human patients. In addition, a wealth of animal studies reveal the unique and overlapping functions of EphA2 and ephrin-A5 in lens cell shape, cell organization and patterning, and overall tissue optical and biomechanical properties. Significant differences in lens phenotypes of mouse models with disrupted EphA2 or ephrin-A5 signaling indicate that genetic modifiers likely affect cataract phenotypes and progression, suggesting a possible reason for the variability of human cataracts due to Eph-ephrin dysfunction. This review summarizes the roles of EphA2 and ephrin-A5 in the lens and suggests future avenues of study.
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Gao Y, Ren X, Fu X, Lin Y, Xiao L, Wang X, Yan N, Zhang M. Case Report: A Novel Mutation in the CRYGD Gene Causing Congenital Cataract Associated with Nystagmus in a Chinese Family. Front Genet 2022; 13:824550. [PMID: 35222542 PMCID: PMC8866695 DOI: 10.3389/fgene.2022.824550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: Congenital cataract (CC) is a common disease resulting in leukocoria and the leading cause of blindness in children worldwide. Approximately 50% of congenital cataract is inherited. Our aim is to identify mutations in a Chinese family with congenital cataract.Methods: A four-generation Chinese family diagnosed with congenital cataract was recruited in West China Hospital of Sichuan University. Genomic DNA was extracted from the peripheral blood of these participants. All coding exons and flanking regions were amplified and sequenced, and the variants were validated using Sanger sequencing. AlphaFold2 was used to predict possible protein structural changes in this variant.Results: The proband had congenital nuclear cataract with nystagmus. A heterozygous variant c.233C > T was identified in exon 2 of the CRYGD gene in chromosome 2. This mutation resulted in a substitution of serine with phenylalanine at amino acid residue 78 (p.S78F). The variant might result in a less stable structure with a looser loop and broken hydrogen bond predicted by AlphaFold2, and this mutation was co-segregated with the disease phenotype in this family.Conclusion: We described cases of human congenital cataract caused by a novel mutation in the CRYGD gene and provided evidence of further phenotypic heterogeneity associated with this variant. Our study further extends the mutation spectrum of the CRYGD gene in congenital cataract.
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Affiliation(s)
- Yunxia Gao
- Department of Ophthalmology, Ophthalmic Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Xiang Ren
- Department of Ophthalmology, Ophthalmic Laboratory, West China Hospital, Sichuan University, Chengdu, China
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xiangyu Fu
- Department of Ophthalmology, Ophthalmic Laboratory, West China Hospital, Sichuan University, Chengdu, China
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Lin
- Department of Ophthalmology, Ophthalmic Laboratory, West China Hospital, Sichuan University, Chengdu, China
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Lirong Xiao
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoyue Wang
- Department of Ophthalmology, Ophthalmic Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Naihong Yan
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ming Zhang
- Department of Ophthalmology, Ophthalmic Laboratory, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Ming Zhang,
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Hellicar J, Stevenson NL, Stephens DJ, Lowe M. Supply chain logistics - the role of the Golgi complex in extracellular matrix production and maintenance. J Cell Sci 2022; 135:273996. [PMID: 35023559 PMCID: PMC8767278 DOI: 10.1242/jcs.258879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The biomechanical and biochemical properties of connective tissues are determined by the composition and quality of their extracellular matrix. This, in turn, is highly dependent on the function and organisation of the secretory pathway. The Golgi complex plays a vital role in directing matrix output by co-ordinating the post-translational modification and proteolytic processing of matrix components prior to their secretion. These modifications have broad impacts on the secretion and subsequent assembly of matrix components, as well as their function in the extracellular environment. In this Review, we highlight the role of the Golgi in the formation of an adaptable, healthy matrix, with a focus on proteoglycan and procollagen secretion as example cargoes. We then discuss the impact of Golgi dysfunction on connective tissue in the context of human disease and ageing.
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Affiliation(s)
- John Hellicar
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.,Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673
| | - Nicola L Stevenson
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - David J Stephens
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Martin Lowe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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Lachke SA. RNA-binding proteins and post-transcriptional regulation in lens biology and cataract: Mediating spatiotemporal expression of key factors that control the cell cycle, transcription, cytoskeleton and transparency. Exp Eye Res 2022; 214:108889. [PMID: 34906599 PMCID: PMC8792301 DOI: 10.1016/j.exer.2021.108889] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 01/03/2023]
Abstract
Development of the ocular lens - a transparent tissue capable of sustaining frequent shape changes for optimal focusing power - pushes the boundaries of what cells can achieve using the molecular toolkit encoded by their genomes. The mammalian lens contains broadly two types of cells, the anteriorly located monolayer of epithelial cells which, at the equatorial region of the lens, initiate differentiation into fiber cells that contribute to the bulk of the tissue. This differentiation program involves massive upregulation of select fiber cell-expressed RNAs and their subsequent translation into high amounts of proteins, such as crystallins. But intriguingly, fiber cells achieve this while also simultaneously undergoing significant morphological changes such as elongation - involving about 1000-fold length-wise increase - and migration, which requires modulation of cytoskeletal and cell adhesion factors. Adding further to the challenges, these molecular and cellular events have to be coordinated as fiber cells progress toward loss of their nuclei and organelles, which irreversibly compromises their potential for harnessing genetically hardwired information. A long-standing question is how processes downstream of signaling and transcription, which may also participate in feedback regulation, contribute toward orchestrating these cellular differentiation events in the lens. It is now becoming clear from findings over the past decade that post-transcriptional gene expression regulatory mechanisms are critical in controlling cellular proteomes and coordinating key processes in lens development and fiber cell differentiation. Indeed, RNA-binding proteins (RBPs) such as Caprin2, Celf1, Rbm24 and Tdrd7 have now been described in mediating post-transcriptional control over key factors (e.g. Actn2, Cdkn1a (p21Cip1), Cdkn1b (p27Kip1), various crystallins, Dnase2b, Hspb1, Pax6, Prox1, Sox2) that are variously involved in cell cycle, transcription, cytoskeleton maintenance and differentiation in the lens. Furthermore, deficiencies of these RBPs have been shown to result in various eye and lens defects and/or cataract. Because fiber cell differentiation in the lens occurs throughout life, the underlying regulatory mechanisms operational in development are expected to also be recruited for the maintenance of transparency in aged lenses. Indeed, in support of this, TDRD7 and CAPRIN2 loci have been linked to age-related cataract in humans. Here, I will review the role of key RBPs in the lens and their importance in understanding the pathology of lens defects. I will discuss advances in RBP-based gene expression control, in general, and the important challenges that need to be addressed in the lens to define the mechanisms that determine the epithelial and fiber cell proteome. Finally, I will also discuss in detail several key future directions including the application of bioinformatics approaches such as iSyTE to study RBP-based post-transcriptional gene expression control in the aging lens and in the context of age-related cataract.
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Affiliation(s)
- Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA; Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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Aldhalaan H, AlBakheet A, AlRuways S, AlMutairi N, AlNakiyah M, AlGhofaili R, Cardona-Londoño KJ, Alahmadi KO, AlQudairy H, AlRasheed MM, Colak D, Arold ST, Kaya N. A Novel GEMIN4 Variant in a Consanguineous Family Leads to Neurodevelopmental Impairment with Severe Microcephaly, Spastic Quadriplegia, Epilepsy, and Cataracts. Genes (Basel) 2021; 13:genes13010092. [PMID: 35052432 PMCID: PMC8774908 DOI: 10.3390/genes13010092] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 12/24/2022] Open
Abstract
Pathogenic variants in GEMIN4 contribute to a hereditary disorder characterized by neurodevelopmental features, microcephaly, cataracts, and renal abnormalities (known as NEDMCR). To date, only two homoallelic variations have been linked to the disease. Moreover, clinical features associated with the variants have not been fully elucidated yet. Here, we identified a novel variant in GEMIN4 (NM_015721:exon2:c.440A>G:p.His147Arg) in two siblings from a consanguineous Saudi family by using whole exome sequencing followed by Sanger sequence verification. We comprehensively investigated the patients’ clinical features, including brain imaging and electroencephalogram findings, and compared their phenotypic characteristics with those of previously reported cases. In silico prediction and structural modeling support that the p.His147Arg variant is pathogenic.
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Affiliation(s)
- Hesham Aldhalaan
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Albandary AlBakheet
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
| | - Sarah AlRuways
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
- Clinical Pharmacy Department, College of Pharmacy, King Saud University, Riyadh 11211, Saudi Arabia;
| | - Nouf AlMutairi
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
- Clinical Pharmacy Department, College of Pharmacy, King Saud University, Riyadh 11211, Saudi Arabia;
| | - Maha AlNakiyah
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
- Clinical Pharmacy Department, College of Pharmacy, King Saud University, Riyadh 11211, Saudi Arabia;
| | - Reema AlGhofaili
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
- Clinical Pharmacy Department, College of Pharmacy, King Saud University, Riyadh 11211, Saudi Arabia;
| | - Kelly J. Cardona-Londoño
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.J.C.-L.); (S.T.A.)
| | - Khalid Omar Alahmadi
- Department of Radiology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Hanan AlQudairy
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
| | - Maha M. AlRasheed
- Clinical Pharmacy Department, College of Pharmacy, King Saud University, Riyadh 11211, Saudi Arabia;
| | - Dilek Colak
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Stefan T. Arold
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.J.C.-L.); (S.T.A.)
| | - Namik Kaya
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
- Correspondence: ; Tel.: +966-11-4647272 (ext. 39612)
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Idriss LT, Hussain M, Khan M, Ahmad T, Muhammad K, Baig M, Khan MM, Inamullah. Mapping of global research output in congenital cataracts from 1903 to 2021. Medicine (Baltimore) 2021; 100:e27756. [PMID: 35049169 PMCID: PMC9191315 DOI: 10.1097/md.0000000000027756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/27/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND AND AIM Globally, congenital cataract remains one of the main causes of visual loss in children. This study was designed to plot the overall research output and evaluate some key bibliometric indicators in congenital cataracts research. METHODS Publications on congenital cataracts were retrieved from the Web of Science Core Collection database. The published literature was searched using the keywords "congenital cataract" OR "congenital cataracts" in the title filed with document types and language restrictions. The data were exported into HistCite to analyze; publication year, top authors, countries, institutions, journals, keywords, and most cited studies. VOSviewer software was used to construct network visualization mapping. RESULTS A total of 1427 publications (1903-2021) published in English language were included in this study. Over the past few decades, the total number of publications in congenital cataracts was found to be increased. The most productive year was 2016 (n = 72), while the most cited year was 1941 (1268 citations). The Investigative Ophthalmology & Visual Science (Impact Factor: 4.799) was the most attractive journal with 161 publications, and the Molecular Vision (Impact Factor : 2.367) was the most cited journal with 1915 citations and 161.723 citations per year. The most productive country was the United States of America (USA) (n = 325), while the most active institute was Sun Yat-sen University, China (n = 36). The most prolific author was Yao K (n = 27). The most studied Web of Science category was ophthalmology (n = 852). The most widely used keyword was congenital (n = 1427). The most cited paper in congenital cataracts was "Congenital cataract following German measles in the mother, cited 1268 times. The USA and author keyword congenital cataract had the highest total link strength. CONCLUSION These findings provide useful insights, current status, and trends in clinical research in congenital cataracts. This study can be used to identify future research areas and standard bibliography references for better diagnosis and disease control.
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Affiliation(s)
- Lujain Talaat Idriss
- Department of Ophthalmology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maryam Hussain
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra, Khyber Pakhtunkhwa, Islamic Republic of Pakistan
| | - Muhammad Khan
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra, Khyber Pakhtunkhwa, Islamic Republic of Pakistan
| | - Tauseef Ahmad
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Khushi Muhammad
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra, Khyber Pakhtunkhwa, Islamic Republic of Pakistan
| | - Mukhtiar Baig
- Department of Clinical Biochemistry, Faculty of Medicine Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Mumtaz Khan
- Department of Microbiology, University of Haripur, Haripur, Khyber Pakhtunkhwa, Islamic Republic of Pakistan
| | - Inamullah
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra, Khyber Pakhtunkhwa, Islamic Republic of Pakistan
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Mutation of the EPHA2 Tyrosine-Kinase Domain Dysregulates Cell Pattern Formation and Cytoskeletal Gene Expression in the Lens. Cells 2021; 10:cells10102606. [PMID: 34685586 PMCID: PMC8534143 DOI: 10.3390/cells10102606] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/13/2022] Open
Abstract
Genetic variations in ephrin type-A receptor 2 (EPHA2) have been associated with inherited and age-related forms of cataract in humans. Here, we have characterized the eye lens phenotype and transcript profile of germline Epha2 knock-in mutant mice homozygous for either a missense variant associated with age-related cataract in humans (Epha2-Q722) or a novel insertion-deletion mutation (Epha2-indel722) that were both located within the tyrosine-kinase domain of EPHA2. Confocal imaging of ex vivo lenses from Epha2-indel722 mice on a fluorescent reporter background revealed misalignment of epithelial-to-fiber cell meridional-rows at the lens equator and severe disturbance of Y-suture formation at the lens poles, whereas Epha2-Q722 lenses displayed mild disturbance of posterior sutures. Immunofluorescent labeling showed that EPHA2 was localized to radial columns of hexagonal fiber cell membranes in Epha2-Q722 lenses, whereas Epha2-indel722 lenses displayed disorganized radial cell columns and cytoplasmic retention of EPHA2. Immunoprecipitation/blotting studies indicated that EPHA2 formed strong complexes with Src kinase and was mostly serine phosphorylated in the lens. RNA sequencing analysis revealed differential expression of several cytoskeleton-associated genes in Epha2-mutant and Epha2-null lenses including shared downregulation of Lgsn and Clic5. Collectively, our data suggest that mutations within the tyrosine-kinase domain of EPHA2 result in lens cell patterning defects and dysregulated expression of several cytoskeleton-associated proteins.
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Jones JL, Corbett MA, Yeaman E, Zhao D, Gecz J, Gasperini RJ, Charlesworth JC, Mackey DA, Elder JE, Craig JE, Burdon KP. A 127 kb truncating deletion of PGRMC1 is a novel cause of X-linked isolated paediatric cataract. Eur J Hum Genet 2021; 29:1206-1215. [PMID: 33867527 PMCID: PMC8385038 DOI: 10.1038/s41431-021-00889-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/10/2021] [Accepted: 04/02/2021] [Indexed: 02/02/2023] Open
Abstract
Inherited paediatric cataract is a rare Mendelian disease that results in visual impairment or blindness due to a clouding of the eye's crystalline lens. Here we report an Australian family with isolated paediatric cataract, which we had previously mapped to Xq24. Linkage at Xq24-25 (LOD = 2.53) was confirmed, and the region refined with a denser marker map. In addition, two autosomal regions with suggestive evidence of linkage were observed. A segregating 127 kb deletion (chrX:g.118373226_118500408del) in the Xq24-25 linkage region was identified from whole-genome sequencing data. This deletion completely removed a commonly deleted long non-coding RNA gene LOC101928336 and truncated the protein coding progesterone receptor membrane component 1 (PGRMC1) gene following exon 1. A literature search revealed a report of two unrelated males with non-syndromic intellectual disability, as well as congenital cataract, who had contiguous gene deletions that accounted for their intellectual disability but also disrupted the PGRMC1 gene. A morpholino-induced pgrmc1 knockdown in a zebrafish model produced significant cataract formation, supporting a role for PGRMC1 in lens development and cataract formation. We hypothesise that the loss of PGRMC1 causes cataract through disrupted PGRMC1-CYP51A1 protein-protein interactions and altered cholesterol biosynthesis. The cause of paediatric cataract in this family is the truncating deletion of PGRMC1, which we report as a novel cataract gene.
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Affiliation(s)
- Johanna L. Jones
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, Hobart, TAS Australia
| | - Mark A. Corbett
- grid.1010.00000 0004 1936 7304Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, SA Australia
| | - Elise Yeaman
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, Hobart, TAS Australia
| | - Duran Zhao
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, Hobart, TAS Australia
| | - Jozef Gecz
- grid.1010.00000 0004 1936 7304Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, SA Australia
| | - Robert J. Gasperini
- grid.1009.80000 0004 1936 826XSchool of Medicine, University of Tasmania, Hobart, TAS Australia
| | - Jac C. Charlesworth
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, Hobart, TAS Australia
| | - David A. Mackey
- grid.1489.40000 0000 8737 8161Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, WA Australia
| | - James E. Elder
- grid.1008.90000 0001 2179 088XDepartment of Paediatrics, University of Melbourne, Melbourne, VIC Australia
| | - Jamie E. Craig
- grid.1014.40000 0004 0367 2697Department of Ophthalmology, Flinders University, Bedford Park, SA Australia
| | - Kathryn P. Burdon
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, Hobart, TAS Australia ,grid.1014.40000 0004 0367 2697Department of Ophthalmology, Flinders University, Bedford Park, SA Australia
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Li D, Han X, Zhao Z, Lu Y, Yang J. Functional analysis of deleterious EPHA2 SNPs in lens epithelial cells. Mol Vis 2021; 27:403-414. [PMID: 34267496 PMCID: PMC8254660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/29/2021] [Indexed: 10/29/2022] Open
Abstract
Purpose Ephrin (Eph) receptor A2 (EPHA2) polymorphism has been associated with age-related cataract (ARC) in different populations worldwide, but the mechanisms by which this polymorphism results in the development of ARC are unclear. Here, we chose four EPHA2 single nucleotide polymorphisms (SNPs; rs35903225, rs145592908, rs137853199, and rs116506614) and studied their function in human lens epithelial cells (LECs). Methods The four EPHA2 mutants were overexpressed using lentiviral transduction in human LECs. Cells expressing wild-type (WT) and mutated EPHA2 were subjected to quantitative PCR (qPCR), western blot, immunoprecipitation (IP), and transwell migration assay. MG132 and chloroquine were used to inhibit the degradation of the WT and mutated EPHA2. The structural changes induced by rs137853199 were predicted and optimized using Schrödinger software. IP-mass spectrometry (IP-MS) was performed to examine the proteins that directly interact with WT and rs137853199 EPHA2. Sanger sequencing was performed to determine the frequency of rs137853199 in 184 patients with ARC (73 cortical cataracts, 56 nuclear cataracts, and 55 posterior subcapsular cataracts) and 49 normal controls. Results Compared with the WT and the other three mutations, the rs137853199 mutation specifically resulted in a significant decrease in the expression of EPHA2. We identified that EPHA2 rs137853199 is degraded via the ubiquitin-proteasomal pathway through a lysine-48 (K48) residue linkage. Furthermore, the knockdown of EPHA2 reduced cell migration; while the overexpression of WT EPHA2 rescued this defect, the overexpression of rs137853199 EPHA2 did not. In addition, in cells overexpressing rs137853199 EPHA2, the expression of β-catenin, a key protein that regulates cell migration, significantly decreased. We predicted that rs137853199 would induce a conformational change at a linker position in the carboxyl terminal of EPHA2. The IP-MS results showed that the main molecular functions of the proteins that specifically bind WT or rs137853199 EPHA2 are binding and catalysis, while the main protein class is the protein-modifying enzyme. Finally, we discovered that the minor allele frequency of rs137853199 was significantly higher in cortical cataract patients than it was in normal controls. Conclusions In summary, these findings suggest a mechanism by which a point mutation in EPHA2 disrupts protein stability, expedites protein degradation, and decreases cell mobility. Importantly, this mutant is associated with cortical cataracts.
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Affiliation(s)
- Dan Li
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China,Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Xiaoyan Han
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China,Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Zhennan Zhao
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China,Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yi Lu
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China,Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Jin Yang
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China,Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
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Li D, Han X, Zhao Z, Lu Y, Yang J. Functional analysis of deleterious EPHA2 SNPs in lens epithelial cells. Mol Vis 2021; 27:384-395. [PMID: 34220184 PMCID: PMC8219505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/21/2021] [Indexed: 11/03/2022] Open
Abstract
Purpose Ephrin (Eph) receptor A2 (EPHA2) polymorphism has been associated with age-related cataract (ARC) in different populations worldwide, but the mechanisms by which this polymorphism results in the development of ARC are unclear. Here, we chose four EPHA2 single nucleotide polymorphisms (SNPs; rs35903225, rs145592908, rs137853199, and rs116506614) and studied their function in human lens epithelial cells (LECs). Methods The four EPHA2 mutants were overexpressed using lentiviral transduction in human LECs. Cells expressing wild-type (WT) and mutated EPHA2 were subjected to quantitative PCR (qPCR), western blot, immunoprecipitation (IP), and transwell migration assay. MG132 and chloroquine were used to inhibit the degradation of the WT and mutated EPHA2. The structural changes induced by rs137853199 were predicted and optimized using Schrödinger software. IP-mass spectrometry (IP-MS) was performed to examine the proteins that directly interact with WT and rs137853199 EPHA2. Sanger sequencing was performed to determine the frequency of rs137853199 in 184 patients with ARC (73 cortical cataracts, 56 nuclear cataracts, and 55 posterior subcapsular cataracts) and 49 normal controls. Results Compared with the WT and the other three mutations, the rs137853199 mutation specifically resulted in a significant decrease in the expression of EPHA2. We identified that EPHA2 rs137853199 is degraded via the ubiquitin-proteasomal pathway through a lysine-48 (K48) residue linkage. Furthermore, the knockdown of EPHA2 reduced cell migration; while the overexpression of WT EPHA2 rescued this defect, the overexpression of rs137853199 EPHA2 did not. In addition, in cells overexpressing rs137853199 EPHA2, the expression of β-catenin, a key protein that regulates cell migration, significantly decreased. We predicted that rs137853199 would induce a conformational change at a linker position in the carboxyl terminal of EPHA2. The IP-MS results showed that the main molecular functions of the proteins that specifically bind WT or rs137853199 EPHA2 are binding and catalysis, while the main protein class is the protein-modifying enzyme. Finally, we discovered that the minor allele frequency of rs137853199 was significantly higher in cortical cataract patients than it was in normal controls. Conclusions In summary, these findings suggest a mechanism by which a point mutation in EPHA2 disrupts protein stability, expedites protein degradation, and decreases cell mobility. Importantly, this mutant is associated with cortical cataracts.
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Affiliation(s)
- Dan Li
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China,NHC Key Laboratory of Myopia, Fudan University, Fudan China,Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Xiaoyan Han
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China,NHC Key Laboratory of Myopia, Fudan University, Fudan China,Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Zhennan Zhao
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China,NHC Key Laboratory of Myopia, Fudan University, Fudan China,Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yi Lu
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China,NHC Key Laboratory of Myopia, Fudan University, Fudan China,Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Jin Yang
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China,NHC Key Laboratory of Myopia, Fudan University, Fudan China,Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
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Choquet H, Melles RB, Anand D, Yin J, Cuellar-Partida G, Wang W, Hoffmann TJ, Nair KS, Hysi PG, Lachke SA, Jorgenson E. A large multiethnic GWAS meta-analysis of cataract identifies new risk loci and sex-specific effects. Nat Commun 2021; 12:3595. [PMID: 34127677 PMCID: PMC8203611 DOI: 10.1038/s41467-021-23873-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 05/17/2021] [Indexed: 01/16/2023] Open
Abstract
Cataract is the leading cause of blindness among the elderly worldwide and cataract surgery is one of the most common operations performed in the United States. As the genetic etiology of cataract formation remains unclear, we conducted a multiethnic genome-wide association meta-analysis, combining results from the GERA and UK Biobank cohorts, and tested for replication in the 23andMe research cohort. We report 54 genome-wide significant loci, 37 of which were novel. Sex-stratified analyses identified CASP7 as an additional novel locus specific to women. We show that genes within or near 80% of the cataract-associated loci are significantly expressed and/or enriched-expressed in the mouse lens across various spatiotemporal stages as per iSyTE analysis. Furthermore, iSyTE shows 32 candidate genes in the associated loci have altered gene expression in 9 different gene perturbation mouse models of lens defects/cataract, suggesting their relevance to lens biology. Our work provides further insight into the complex genetic architecture of cataract susceptibility.
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Affiliation(s)
- Hélène Choquet
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA.
| | | | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Jie Yin
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA
| | | | | | | | - Thomas J Hoffmann
- Institute for Human Genetics, UCSF, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA
| | - K Saidas Nair
- Departments of Ophthalmology and Anatomy, School of Medicine, UCSF, San Francisco, CA, USA
| | - Pirro G Hysi
- King's College London, Section of Ophthalmology, School of Life Course Sciences, London, UK.,King's College London, Department of Twin Research and Genetic Epidemiology, London, UK.,University College London, Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Eric Jorgenson
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA
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Barashkov NA, Konovalov FA, Borisova TV, Teryutin FM, Solovyev AV, Pshennikova VG, Sapojnikova NV, Vychuzhina LS, Romanov GP, Gotovtsev NN, Morozov IV, Bondar AA, Platonov FA, Burtseva TE, Khusnutdinova EK, Posukh OL, Fedorova SA. Autosomal recessive cataract (CTRCT18) in the Yakut population isolate of Eastern Siberia: a novel founder variant in the FYCO1 gene. Eur J Hum Genet 2021; 29:965-976. [PMID: 33767456 PMCID: PMC8187664 DOI: 10.1038/s41431-021-00833-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/19/2020] [Accepted: 02/10/2021] [Indexed: 11/09/2022] Open
Abstract
Congenital autosomal recessive cataract with unknown genetic etiology is one of the most common Mendelian diseases among the Turkic-speaking Yakut population (Eastern Siberia, Russia). To identify the genetic cause of congenital cataract spread in this population, we performed whole-exome sequencing (Illumina NextSeq 500) in one Yakut family with three affected siblings whose parents had preserved vision. We have revealed the novel homozygous c.1621C>T transition leading to premature stop codon p.(Gln541*) in exon 8 of the FYCO1 gene (NM_024513.4). Subsequent screening of c.1621C>T p.(Gln541*) revealed this variant in a homozygous state in 25 out of 29 Yakut families with congenital cataract (86%). Among 424 healthy individuals from seven populations of Eastern Siberia (Russians, Yakuts, Evenks, Evens, Dolgans, Chukchi, and Yukaghirs), the highest carrier frequency of c.1621C>T p.(Gln541*) was found in the Yakut population (7.9%). DNA samples of 25 homozygous for c.1621C>T p.(Gln541*) patients with congenital cataract and 114 unaffected unrelated individuals without this variant were used for a haplotype analysis based on the genotyping of six STR markers (D3S3512, D3S3685, D3S3582, D3S3561, D3S1289, and D3S3698). The structure of the identified haplotypes indicates a common origin for all of the studied mutant chromosomes bearing c.1621C>T p.(Gln541*). The age of the с.1621C>T p.(Gln541*) founder haplotype was estimated to be approximately 260 ± 65 years (10 generations). These findings characterize Eastern Siberia as the region of the world with the most extensive accumulation of the unique variant c.1621C>T p.(Gln541*) in the FYCO1 gene as a result of the founder effect.
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Affiliation(s)
- Nikolay A Barashkov
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation.
- Laboratory of Molecular Biology, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation.
| | | | - Tuyara V Borisova
- Laboratory of Molecular Biology, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Fedor M Teryutin
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
| | - Aisen V Solovyev
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
- Laboratory of Molecular Biology, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Vera G Pshennikova
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
| | - Nadejda V Sapojnikova
- Department of Ophthalmology, Republican Hospital #1 - National Centre of Medicine, Yakutsk, Russian Federation
| | - Lyubov S Vychuzhina
- Department of Ophthalmology, Republican Hospital #1 - National Centre of Medicine, Yakutsk, Russian Federation
| | - Georgii P Romanov
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
- Laboratory of Molecular Biology, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Nyurgun N Gotovtsev
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
| | - Igor V Morozov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
| | - Alexander A Bondar
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Fedor A Platonov
- Medical Institute, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Tatiana E Burtseva
- Medical Institute, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
- Laboratory of the Children Health Monitoring and Medical-environmental Research, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
| | - Elza K Khusnutdinova
- Laboratory of Molecular Biology, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
- Laboratory of Human Molecular Genetics, Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, Ufa, Russian Federation
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russian Federation
| | - Olga L Posukh
- Novosibirsk State University, Novosibirsk, Russian Federation
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Sardana A Fedorova
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
- Laboratory of Molecular Biology, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
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Ni SH, Zhang JM, Zhao J. A novel missense mutation of CRYBA1 in a northern Chinese family with inherited coronary cataract with blue punctate opacities. Eur J Ophthalmol 2021; 32:193-199. [PMID: 33827296 DOI: 10.1177/11206721211008355] [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: 11/17/2022]
Abstract
PURPOSE To demonstrate the underlying genetic defect that contribute to inherited cataract in a northern Chinese pedigree. METHODS The study recruited a family pedigree with a diagnosis of bilateral coronary cataract with blue punctate opacities. Fourteen family members and 100 healthy volunteers were enrolled. DNA sample of the proband in this family were analyzed by high-throughput sequencing, which was then demonstrated by Sanger sequencing in the remained people in the family and 100 controls. The functional effect of mutant genes was investigated via bioinformatics analysis, including Polymorphism Phenotyping version2 (PolyPhen-2), Protein Variation Effect Analyzer (PROVEAN v1.1.3) Scale-Invariant Feature Transform (SIFT), and Mutation Taster. RESULTS In this three-generation family, a novel heterozygous mutation was found in the kinase domain of CRYBA1 gene (c.340C > T, p.R114C), which was only detected in patients in the family with inherited cataract and were not detected in the remained people in the family nor in normal people. The pathogenic effect of the mutation was verified via bioinformatics analysis. CONCLUSION Our study presented the molecular experiments to confirm that a novel missense mutation of c.340 C > T located in exon 4 of CRYBA1 gene results in a bilateral coronary cataract with blue punctate opacities, which enriches the mutation spectrum of CRYBA1 gene in inherited cataract and deepens the understanding of the pathogenesis of inherited cataract.
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Affiliation(s)
- Shu-Hua Ni
- School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Juan-Mei Zhang
- Department of Ophthalmology, Linyi People's Hospital, Linyi, China
| | - Jun Zhao
- Department of Ophthalmology, Linyi People's Hospital, Linyi, China
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Reis LM, Costakos D, Wheeler PG, Bardakjian T, Schneider A, Fung SSM, Semina EV. Dominant variants in PRR12 result in unilateral or bilateral complex microphthalmia. Clin Genet 2021; 99:437-442. [PMID: 33314030 PMCID: PMC8259391 DOI: 10.1111/cge.13897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 11/25/2022]
Abstract
Complex microphthalmia is characterized by small eyes with additional abnormalities that may include anterior segment dysgenesis. While many genes are known, a genetic cause is identified in only 4-30% of microphthalmia, with the lowest rate in unilateral cases. We identified four novel pathogenic loss-of-function alleles in PRR12 in families affected by complex microphthalmia and/or Peters anomaly, including two de novo, the first dominantly transmitted allele, as well as the first splicing variant. The ocular phenotypes were isolated with no additional systemic features observed in two unrelated families. Remarkably, ocular phenotypes were asymmetric in all individuals and unilateral (with structurally normal contralateral eye) in three. There are only three previously reported PRR12 variants identified in probands with intellectual disability, neuropsychiatric disorders, and iris anomalies. While some overlap with previously reported cases is seen, nonsyndromic developmental ocular anomalies are a novel phenotype for this gene. Additional phenotypic expansions included short stature and normal development/cognition, each noted in two individuals in this cohort, as well as absence of neuropsychiatric disorders in all. This study identifies new associations for PRR12 disruption in humans and presents a genetic diagnosis resulting in unilateral ocular phenotypes in a significant proportion of cases.
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Affiliation(s)
- Linda M Reis
- Department of Pediatrics, Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI 53226, USA
| | - Deborah Costakos
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Tanya Bardakjian
- Einstein Medical Center Philadelphia 5501 Old York Rd, Levy 2 West Philadelphia, PA 19141, USA
| | - Adele Schneider
- Einstein Medical Center Philadelphia 5501 Old York Rd, Levy 2 West Philadelphia, PA 19141, USA
- Current position: Wills Eye Hospital, Department of Pediatric Ophthalmology and Ocular Genetics, 840 Walnut Street, Philadelphia, PA 19107, USA
| | - Simon S M Fung
- Department of Ophthalmology, University of California Los Angeles, Los Angeles, California, 90095, USA
| | | | - Elena V Semina
- Department of Pediatrics, Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI 53226, USA
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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40
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Wang X, Qin Y, Abudoukeremuahong A, Dongye M, Zhang X, Wang D, Li J, Lin Z, Yang Y, Ding L, Lin H. Elongated axial length and myopia-related fundus changes associated with the Arg130Cys mutation in the LIM2 gene in four Chinese families with congenital cataracts. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:235. [PMID: 33708862 PMCID: PMC7940952 DOI: 10.21037/atm-20-4275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background Congenital cataract (CC) is a congenital abnormality characterized by lens opacity present at birth and is associated with highly heterogeneous clinical manifestations. Lens-specific integral membrane protein (LIM2) gene expression is localized to tight junctional domains of different lens fiber membranes. To date, only four mutations in LIM2 have been reported to be associated with congenital or presenile cataracts. Due to the rarity of variants detected in the gene, there is limited progress in understanding the correlation between the genotype and phenotype of patients with mutations in LIM2. Methods A total of four Chinese families with CCs were recruited for this study, including three families inheriting in an autosomal dominant (AD) pattern and one sporadic case. Genomic DNA was extracted from the leukocytes of peripheral blood collected from all available patients. Whole-exome sequencing (WES) was performed on all probands and at least one of their parents. Bioinformatics analysis was performed to evaluate the pathogenicity of the candidate variants. Exon 4 of LIM2 was amplified by polymerase chain reaction and directly sequenced. All patients underwent full ocular examinations. This was an observational study to explore the genotype-phenotype relationships in the four families with a common candidate variant. Results Various ocular phenotypes were detected in these families, mainly including CCs, elongated axial length, and myopia-related fundus changes. The LIM2 gene mutation, p.Arg130Cys, was detected in all patients. This was further confirmed by Sanger sequencing. The proportion of probands with this mutation in our CCs database was 3.1% (4/130), which indicated that this mutation appears to be a frequent cause of cataracts in the Han Chinese population. This variation has been reported by other investigators before and was correlated with isolated cataracts. Conclusions This is the first study that reports various ocular phenotypes associated with the p.Arg130Cys mutation in the LIM2 gene, which indicated the phenotypic heterogeneity of this gene. LIM2 might not only function as an integral membrane protein in lens fiber cells but also be associated with the axial development of the eyeball. Functional studies of the LIM2 gene are important and should receive more attention.
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Affiliation(s)
- Xun Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yanli Qin
- Department of Ophthalmology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | | | - Meimei Dongye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xulin Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Dongni Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhuoling Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yahan Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Lin Ding
- Department of Ophthalmology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Haotian Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Yu Y, Xu J, Qiao Y, Li J, Yao K. A new heterozygous mutation in the stop codon of CRYAB (p.X176Y) is liable for congenital posterior pole cataract in a Chinese family. Ophthalmic Genet 2020; 42:139-143. [PMID: 33272090 DOI: 10.1080/13816810.2020.1855665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Background: The present study aims to identify the underlying genetic defects in a Chinese family with autosomal dominant congenital cataracts (ADCC).Methods: Detailed family histories and clinical data were recorded. Targeted exome sequencing of 54 known cataract-associated genes combined with high-throughput next-generation sequencing was conducted followed by Sanger sequencing and bioinformatic analysis to identify the causative gene lesion for the family.Results: A four-generation Chinese family with posterior pole type cataract were enrolled. Enrichment of targeted genes revealed a new heterozygous p.X176Y mutation in the stop codon of αB-crystallin (CRYAB) gene, which resulted in the loss of the stop codon and prolongation of the mutant protein by 19 amino acid residues (p.X176Yfs19*). Sanger sequencing showed complete co-segregation with the disease. The elongated mutant protein was predicted to be pathogenic by forming new α-helix and random-coil in the secondary structure as well as producing an extended strand in the tertiary structure, potentially leading to increased hydrophobicity and reduced protein stability.Conclusions: Our report added a new mutation in the spectrum of congenital cataracts. The data suggested that X176 residue in the COOH-terminal is of crucial importance for the αB-crystallin protein function which was valuable for further study of the pathogenesis of congenital cataracts.Abbreviations: CRYAB: αB-crystallin; DNA: deoxyribonucleic acid; PCR: polymerase chain reaction; TES: targeted exome sequencing; ACD: αB-crystallin domain.
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Affiliation(s)
- Yinhui Yu
- Department of Eye Center, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.,Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province, China
| | - Jingjie Xu
- Department of Eye Center, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.,Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province, China
| | - Yue Qiao
- Department of Eye Center, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.,Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province, China
| | - Jinyu Li
- Department of Eye Center, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.,Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province, China
| | - Ke Yao
- Department of Eye Center, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.,Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province, China
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Berry V, Ionides A, Pontikos N, Georgiou M, Yu J, Ocaka LA, Moore AT, Quinlan RA, Michaelides M. The genetic landscape of crystallins in congenital cataract. Orphanet J Rare Dis 2020; 15:333. [PMID: 33243271 PMCID: PMC7691105 DOI: 10.1186/s13023-020-01613-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/10/2020] [Indexed: 02/01/2023] Open
Abstract
Background The crystalline lens is mainly composed of a large family of soluble proteins called the crystallins, which are responsible for its development, growth, transparency and refractive index. Disease-causing sequence variants in the crystallins are responsible for nearly 50% of all non-syndromic inherited congenital cataracts, as well as causing cataract associated with other diseases, including myopathies. To date, more than 300 crystallin sequence variants causing cataract have been identified. Methods Here we aimed to identify the genetic basis of disease in five multi-generation British families and five sporadic cases with autosomal dominant congenital cataract using whole exome sequencing, with identified variants validated using Sanger sequencing. Following bioinformatics analysis, rare or novel variants with a moderate to damaging pathogenicity score, were filtered out and tested for segregation within the families. Results We have identified 10 different heterozygous crystallin variants. Five recurrent variants were found: family-A, with a missense variant (c.145C>T; p.R49C) in CRYAA associated with nuclear cataract; family-B, with a deletion in CRYBA1 (c.272delGAG; p.G91del) associated with nuclear cataract; and family-C, with a truncating variant in CRYGD (c.470G>A; W157*) causing a lamellar phenotype; individuals I and J had variants in CRYGC (c.13A>C; T5P) and in CRYGD (c.418C>T; R140*) causing unspecified congenital cataract and nuclear cataract, respectively. Five novel disease-causing variants were also identified: family D harboured a variant in CRYGC (c.179delG; R60Qfs*) responsible for a nuclear phenotype; family E, harboured a variant in CRYBB1 (c.656G>A; W219*) associated with lamellar cataract; individual F had a variant in CRYGD (c.392G>A; W131*) associated with nuclear cataract; and individuals G and H had variants in CRYAA (c.454delGCC; A152del) and in CRYBB1 (c.618C>A; Y206*) respectively, associated with unspecified congenital cataract. All novel variants were predicted to be pathogenic and to be moderately or highly damaging. Conclusions We report five novel variants and five known variants. Some are rare variants that have been reported previously in small ethnic groups but here we extend this to the wider population and record a broader phenotypic spectrum for these variants.
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Affiliation(s)
- Vanita Berry
- Department of Genetics, UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK. .,Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK.
| | - Alex Ionides
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | - Nikolas Pontikos
- Department of Genetics, UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | - Michalis Georgiou
- Department of Genetics, UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | - Jing Yu
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Louise A Ocaka
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Anthony T Moore
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK.,Ophthalmology Department, University of California School of Medicine, San Francisco, CA, 94158, USA
| | - Roy A Quinlan
- Department of Biosciences, University of Durham, Upper Mountjoy Science Site, Durham, DH1 3LE, UK
| | - Michel Michaelides
- Department of Genetics, UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK. .,Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK.
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Cokan KB, Urlep Ž, Lorbek G, Matz-Soja M, Skubic C, Perše M, Jeruc J, Juvan P, Režen T, Rozman D. Chronic Disruption of the Late Cholesterol Synthesis Leads to Female-Prevalent Liver Cancer. Cancers (Basel) 2020; 12:cancers12113302. [PMID: 33182326 PMCID: PMC7695248 DOI: 10.3390/cancers12113302] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/29/2020] [Accepted: 11/05/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Hepatocellular carcinoma is a disease with a variety of molecular triggers and is usually reported to prevail in males. However, after the menopause, the disease is also increasing in the female population. Herein, we discovered that chronic depletion of cholesterol synthesis due to the knock-out of the gene Cyp51 from this pathway leads to female prevalent hepatocarcinogenesis in aging mice. There is a high similarity between our mouse model and the situation in humans. Multiple deregulated pathways of hepatocarcinogenesis are shared. A female-dependent metabolic reprogramming leading to this type of liver cancer is exposed for the first time and reflects on deregulated cholesterol synthesis as the metabolic trigger. These data are of crucial importance. Despite the higher overall prevalence of hepatocellular carcinoma in males, we need tools and biomarkers to further stratify patients and offer better diagnosis and treatment options to both sexes. Abstract While the role of cholesterol in liver carcinogenesis remains controversial, hepatocellular carcinoma generally prevails in males. Herein, we uncover pathways of female-prevalent progression to hepatocellular carcinoma due to chronic repression of cholesterogenic lanosterol 14α-demethylase (CYP51) in hepatocytes. Tumors develop in knock-out mice after year one, with 2:1 prevalence in females. Metabolic and transcription factor networks were deduced from the liver transcriptome data, combined by sterol metabolite and blood parameter analyses, and interpreted with relevance to humans. Female knock-outs show increased plasma cholesterol and HDL, dampened lipid-related transcription factors FXR, LXRα:RXRα, and importantly, crosstalk between reduced LXRα and activated TGF-β signalling, indicating a higher susceptibility to HCC in aging females. PI3K/Akt signalling and ECM-receptor interaction are common pathways that are disturbed by sex-specific altered genes. Additionally, transcription factors (SOX9)2 and PPARα were recognized as important for female hepatocarcinogenesis, while overexpressed Cd36, a target of nuclear receptor RORC, is a new male-related regulator of ECM-receptor signalling in hepatocarcinogenesis. In conclusion, we uncover the sex-dependent metabolic reprogramming of cholesterol-related pathways that predispose for hepatocarcinogenesis in aging females. This is important in light of increased incidence of liver cancers in post-menopausal women.
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Affiliation(s)
- Kaja Blagotinšek Cokan
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (K.B.C.); (Ž.U.); (G.L.); (C.S.); (P.J.); (T.R.)
| | - Žiga Urlep
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (K.B.C.); (Ž.U.); (G.L.); (C.S.); (P.J.); (T.R.)
| | - Gregor Lorbek
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (K.B.C.); (Ž.U.); (G.L.); (C.S.); (P.J.); (T.R.)
| | - Madlen Matz-Soja
- Rudol-Schönheimer-Institute of Biochemistry, Divison of General Biochemistry, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany;
| | - Cene Skubic
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (K.B.C.); (Ž.U.); (G.L.); (C.S.); (P.J.); (T.R.)
| | - Martina Perše
- Medical Experimental Centre, Institute of Pathology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia;
| | - Jera Jeruc
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia;
| | - Peter Juvan
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (K.B.C.); (Ž.U.); (G.L.); (C.S.); (P.J.); (T.R.)
| | - Tadeja Režen
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (K.B.C.); (Ž.U.); (G.L.); (C.S.); (P.J.); (T.R.)
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (K.B.C.); (Ž.U.); (G.L.); (C.S.); (P.J.); (T.R.)
- Correspondence: ; Tel.: +386-1-543-7591
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Bremond-Gignac D, Daruich A, Robert MP, Valleix S. Recent developments in the management of congenital cataract. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1545. [PMID: 33313290 PMCID: PMC7729375 DOI: 10.21037/atm-20-3033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Congenital cataract is a rare eye disease, one of the leading treatable causes of low vision in children worldwide. Hereditary cataracts can be divided in syndromic and non-syndromic cataracts. Early diagnosis in congenital cataracts is key to reach good visual function. Current surgical techniques, that combine microincision cataract extraction and primary intraocular lens (IOL) implantation, have improved childhood cataract outcome. Complications include posterior capsule opacification (PCO), aphakic or pseudophakic glaucoma, uveitis, pupil displacement and IOL decentration. A recent study using a modified Delphi approach identified areas of consensus and disagreement in the management of pediatric cataract. A consensus or near consensus was achieved for 79% of the questions, however 21% of the questions remained controversial, as for IOL implantation strategy. Congenital cataracts show a highly variable phenotype and genotype, and can be related to different mutations, genetic variance, and other risk factors. Congenital cataracts can be associated with other ocular developmental abnormalities, including microphthalmia, microcornea, or aniridia and with systemic findings. Next-generation sequencing (NGS) and forthcoming new ultra-high-throughput sequencing represent excellent tools to investigate the genetic causes of congenital cataracts. A better recognition of different clinical presentations and underlying etiologies of congenital cataracts may lead to the development of new approaches to improve visual outcome after cataract surgery and promote early detection of systemic associated syndromes.
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Affiliation(s)
- Dominique Bremond-Gignac
- Ophthalmology Department, Necker-Enfants Malades Hospital, Paris University, Paris, France.,INSERM UMRS 1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Université Sorbonne Paris Cité, Centre de Recherche des Cordeliers, Paris, France
| | - Alejandra Daruich
- Ophthalmology Department, Necker-Enfants Malades Hospital, Paris University, Paris, France.,INSERM UMRS 1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Université Sorbonne Paris Cité, Centre de Recherche des Cordeliers, Paris, France
| | - Matthieu P Robert
- Ophthalmology Department, Necker-Enfants Malades Hospital, Paris University, Paris, France.,Borelli Centre, UMR 9010 CNRS-SSA-ENS Paris Saclay-Paris University, Paris, France
| | - Sophie Valleix
- INSERM UMRS 1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Université Sorbonne Paris Cité, Centre de Recherche des Cordeliers, Paris, France.,Molecular Genetics, University Hospital Necker-Enfants Malades, APHP, OPHTARA Center, Paris, France
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Sun W, Xu J, Gu Y, Du C. The relationship between major intrinsic protein genes and cataract. Int Ophthalmol 2020; 41:375-387. [PMID: 32920712 DOI: 10.1007/s10792-020-01583-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/29/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Genetic factors play an essential role in the development of cataracts, and the major intrinsic protein (MIP) gene is a type of causative genes. Our study aims to discuss the current research progress of MIP genes responsible for cataractogenesis in DNA and protein levels, which is essential in achieving a response to the molecular deficiencies and pathophysiologic features of cataract. METHODS We developed a search strategy using a combination of the words "Cataract", "Mutation", "MIP gene", and "AQP0" to identify all articles from PubMed, Web of Science, Scopus, and Google Scholar up to December 2019. To find more articles and to ensure that databases were thoroughly searched, the reference lists of selected items were also reviewed. RESULTS A total of 29 MIP gene mutations causing congenital cataract were obtained by searching these databases and analyzing the results of genetic mutation pathogenicity prediction software tools; most of them caused amino acid codon changes in the H4, H5, H6, C-TIDs, and loop C in the structure of the MIP protein. However, there was no clear causality between lens morphology, phenotypes, and genotypes. The genotype TC in polymorphism c.-4T > C and haplotype CCG of rs2269348, c.-4T > C, and rs74641138 in MIP may attach an additional genetic risk factor for age-related cataract. CONCLUSION These single-base mutations and single nucleotide polymorphisms might be importantly involved in the pathogenesis of congenital cataract and age-related cataract, respectively. This review provides a significant reference for clinical trials and theoretical studies.
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Affiliation(s)
- Wen Sun
- Department of Ophthalmology, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, 310003, Hangzhou, China
| | - Jiawei Xu
- Department of Ophthalmology, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, 310003, Hangzhou, China
| | - Yangshun Gu
- Department of Ophthalmology, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, 310003, Hangzhou, China
| | - Chixin Du
- Department of Ophthalmology, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, 310003, Hangzhou, China.
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46
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The cholesterol synthesis enzyme lanosterol 14α-demethylase is post-translationally regulated by the E3 ubiquitin ligase MARCH6. Biochem J 2020; 477:541-555. [PMID: 31904814 PMCID: PMC6993871 DOI: 10.1042/bcj20190647] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/22/2019] [Accepted: 01/02/2020] [Indexed: 01/07/2023]
Abstract
Cholesterol synthesis is a tightly controlled pathway, with over 20 enzymes involved. Each of these enzymes can be distinctly regulated, helping to fine-tune the production of cholesterol and its functional intermediates. Several enzymes are degraded in response to increased sterol levels, whilst others remain stable. We hypothesised that an enzyme at a key branch point in the pathway, lanosterol 14α-demethylase (LDM) may be post-translationally regulated. Here, we show that the preceding enzyme, lanosterol synthase is stable, whilst LDM is rapidly degraded. Surprisingly, this degradation is not triggered by sterols. However, the E3 ubiquitin ligase membrane-associated ring-CH-type finger 6 (MARCH6), known to control earlier rate-limiting steps in cholesterol synthesis, also control levels of LDM and the terminal cholesterol synthesis enzyme, 24-dehydrocholesterol reductase. Our work highlights MARCH6 as the first example of an E3 ubiquitin ligase that targets multiple steps in a biochemical pathway and indicates new facets in the control of cholesterol synthesis.
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Iqbal H, Khan SY, Zhou L, Irum B, Ali M, Ahmed MR, Shahzad M, Ali MH, Naeem MA, Riazuddin S, Hejtmancik JF, Riazuddin SA. Mutations in FYCO1 identified in families with congenital cataracts. Mol Vis 2020; 26:334-344. [PMID: 32355443 PMCID: PMC7190580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 04/26/2020] [Indexed: 11/04/2022] Open
Abstract
Purpose This study was designed to identify the pathogenic variants in three consanguineous families with congenital cataracts segregating as a recessive trait. Methods Consanguineous families with multiple individuals manifesting congenital cataracts were ascertained. All participating members underwent an ophthalmic examination. A small aliquot of the blood sample was collected from all participating individuals, and genomic DNAs were extracted. Homozygosity-based linkage analysis was performed using short tandem repeat (STR) markers. The haplotypes were constructed with alleles of the STR markers, and the two-point logarithm of odds (LOD) scores were calculated. The candidate gene was sequenced bidirectionally to identify the disease-causing mutations. Results Linkage analysis localized the disease interval to chromosome 3p in three families. Subsequently, bidirectional Sanger sequencing identified two novel mutations-a single base deletion resulting in a frameshift (c.3196delC; p.His1066IlefsTer10) mutation and a single base substitution resulting in a nonsense (c.4270C>T; p.Arg1424Ter) mutation-and a known missense (c.4127T>C, p.Leu1376Pro) mutation in FYCO1. All three mutations showed complete segregation with the disease phenotype and were absent in 96 ethnically matched control individuals. Conclusions We report two novel mutations and a previously reported mutation in FYCO1 in three large consanguineous families. Taken together, mutations in FYCO1 contribute nearly 15% to the total genetic load of autosomal recessive congenital cataracts in this cohort.
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Affiliation(s)
- Hira Iqbal
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shahid Y. Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lin Zhou
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Bushra Irum
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Ali
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Mariya R. Ahmed
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Mohsin Shahzad
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | | | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan,Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
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48
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Gibellini L, De Gaetano A, Mandrioli M, Van Tongeren E, Bortolotti CA, Cossarizza A, Pinti M. The biology of Lonp1: More than a mitochondrial protease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 354:1-61. [PMID: 32475470 DOI: 10.1016/bs.ircmb.2020.02.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Initially discovered as a protease responsible for degradation of misfolded or damaged proteins, the mitochondrial Lon protease (Lonp1) turned out to be a multifaceted enzyme, that displays at least three different functions (proteolysis, chaperone activity, binding of mtDNA) and that finely regulates several cellular processes, within and without mitochondria. Indeed, LONP1 in humans is ubiquitously expressed, and is involved in regulation of response to oxidative stress and, heat shock, in the maintenance of mtDNA, in the regulation of mitophagy. Furthermore, its proteolytic activity can regulate several biochemical pathways occurring totally or partially within mitochondria, such as TCA cycle, oxidative phosphorylation, steroid and heme biosynthesis and glutamine production. Because of these multiple activities, Lon protease is highly conserved throughout evolution, and mutations occurring in its gene determines severe diseases in humans, including a rare syndrome characterized by Cerebral, Ocular, Dental, Auricular and Skeletal anomalies (CODAS). Finally, alterations of LONP1 regulation in humans can favor tumor progression and aggressiveness, further highlighting the crucial role of this enzyme in mitochondrial and cellular homeostasis.
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Affiliation(s)
- Lara Gibellini
- Department of Medical and Surgical Sciences of Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Anna De Gaetano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Mauro Mandrioli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Elia Van Tongeren
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Andrea Cossarizza
- Department of Medical and Surgical Sciences of Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Marcello Pinti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
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Unlu G, Qi X, Gamazon ER, Melville DB, Patel N, Rushing AR, Hashem M, Al-Faifi A, Chen R, Li B, Cox NJ, Alkuraya FS, Knapik EW. Phenome-based approach identifies RIC1-linked Mendelian syndrome through zebrafish models, biobank associations and clinical studies. Nat Med 2020; 26:98-109. [PMID: 31932796 PMCID: PMC7147997 DOI: 10.1038/s41591-019-0705-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/15/2019] [Indexed: 12/17/2022]
Abstract
Discovery of genotype-phenotype relationships remains a major challenge in clinical medicine. Here, we combined three sources of phenotypic data to uncover a novel mechanism for rare and common diseases resulting from collagen secretion deficits. Using zebrafish genetic screen, we identified the ric1 gene to be essential for skeletal biology. Using a gene-based phenome-wide association study (PheWAS) in the EHR-linked BioVU biobank, we show that reduced genetically determined expression of RIC1 is associated with musculoskeletal and dental conditions. Whole exome sequencing (WES) identified individuals homozygous-by-descent for a rare variant in RIC1, and, through a guided clinical re-evaluation, they were discovered to share signs with the BioVU-associated phenome. We named this novel Mendelian syndrome CATIFA (Cleft lip, cAtaract, Tooth abnormality, Intellectual disability, Facial dysmorphism, ADHD), and revealed further disease mechanisms. This gene-based PheWAS-guided approach can accelerate the discovery of clinically relevant disease phenome and associated biological mechanisms.
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Affiliation(s)
- Gokhan Unlu
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.,Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Xinzi Qi
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Clare Hall, University of Cambridge, Cambridge, UK
| | - David B Melville
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amy R Rushing
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abdullah Al-Faifi
- Department of Pediatrics, Security Forces Hospital, Riyadh, Saudi Arabia
| | - Rui Chen
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Bingshan Li
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ela W Knapik
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA. .,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA. .,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
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50
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Clinical utility of genetic testing in 201 preschool children with inherited eye disorders. Genet Med 2019; 22:745-751. [PMID: 31848469 PMCID: PMC7118019 DOI: 10.1038/s41436-019-0722-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
Purpose A key property to consider in all genetic tests is clinical utility, the ability of the test to influence patient management and health outcomes. Here we assess the current clinical utility of genetic testing in diverse pediatric inherited eye disorders (IEDs). Methods Two hundred one unrelated children (0–5 years old) with IEDs were ascertained through the database of the North West Genomic Laboratory Hub, Manchester, UK. The cohort was collected over a 7-year period (2011–2018) and included 74 children with bilateral cataracts, 8 with bilateral ectopia lentis, 28 with bilateral anterior segment dysgenesis, 32 with albinism, and 59 with inherited retinal disorders. All participants underwent panel-based genetic testing. Results The diagnostic yield of genetic testing for the cohort was 64% (ranging from 39% to 91% depending on the condition). The test result led to altered management (including preventing additional investigations or resulting in the introduction of personalized surveillance measures) in 33% of probands (75% for ectopia lentis, 50% for cataracts, 33% for inherited retinal disorders, 7% for anterior segment dysgenesis, 3% for albinism). Conclusion Genetic testing helped identify an etiological diagnosis in the majority of preschool children with IEDs. This prevented additional unnecessary testing and provided the opportunity for anticipatory guidance in significant subsets of patients.
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