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Ye L, Guo YM, Cai YX, Wei J, Huang J, Bi J, Chen D, Li FF, Huang XF. Trio-based whole-exome sequencing reveals mutations in early-onset high myopia. BMJ Open Ophthalmol 2024; 9:e001720. [PMID: 38789272 PMCID: PMC11129018 DOI: 10.1136/bmjophth-2024-001720] [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: 03/21/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
PURPOSE Myopia, especially high myopia (HM), represents a widespread visual impairment with a globally escalating prevalence. This study aimed to elucidate the genetic foundations associated with early-onset HM (eoHM) while delineating the genetic landscape specific to Shaanxi province, China. METHODS A comprehensive analysis of whole-exome sequencing was conducted involving 26 familial trios displaying eoHM. An exacting filtration protocol identified potential candidate mutations within acknowledged myopia-related genes and susceptibility loci. Subsequently, computational methodologies were employed for functional annotations and pathogenicity assessments. RESULTS Our investigation identified 7 genes and 10 variants associated with HM across 7 families, including a novel mutation in the ARR3 gene (c.139C>T, p.Arg47*) and two mutations in the P3H2 gene (c.1865T>C, p.Phe622Ser and c.212T>C, p.Leu71Pro). Pathogenic mutations were found in syndromic myopia genes, notably encompassing VPS13B, TRPM1, RPGR, NYX and RP2. Additionally, a thorough comparison of previously reported causative genes of syndromic myopia and myopia risk genes with the negative sequencing results pinpointed various types of mutations within risk genes. CONCLUSIONS This investigation into eoHM within Shaanxi province adds to the current understanding of myopic genetic factors. Our results warrant further functional validation and ocular examinations, yet they provide foundational insights for future genetic research and therapeutic innovations in HM.
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Affiliation(s)
- Lu Ye
- Shaanxi Eye Hospital, Xi'an People's Hospital (Xi'an Fourth Hospital), Affiliated People's Hospital of Northwest University, Xi'an, Shaanxi, China
| | - Yi-Ming Guo
- Shaanxi Eye Hospital, Xi'an People's Hospital (Xi'an Fourth Hospital), Affiliated People's Hospital of Northwest University, Xi'an, Shaanxi, China
| | - Yi-Xin Cai
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junhan Wei
- Shaanxi Eye Hospital, Xi'an People's Hospital (Xi'an Fourth Hospital), Affiliated People's Hospital of Northwest University, Xi'an, Shaanxi, China
| | - Juan Huang
- Shaanxi Eye Hospital, Xi'an People's Hospital (Xi'an Fourth Hospital), Affiliated People's Hospital of Northwest University, Xi'an, Shaanxi, China
| | - Jiejing Bi
- Shaanxi Eye Hospital, Xi'an People's Hospital (Xi'an Fourth Hospital), Affiliated People's Hospital of Northwest University, Xi'an, Shaanxi, China
| | - Ding Chen
- National Clinical Research Center for Ocular Diseases, Wenzhou Medical University Eye Hospital, Wenzhou, Zhejiang, China
- State Key Laboratory of Ophthalmology Optometry and Visual Science, Wenzhou Medical University Eye Hospital, Wenzhou, Zhejiang, China
| | - Fen-Fen Li
- National Clinical Research Center for Ocular Diseases, Wenzhou Medical University Eye Hospital, Wenzhou, Zhejiang, China
- State Key Laboratory of Ophthalmology Optometry and Visual Science, Wenzhou Medical University Eye Hospital, Wenzhou, Zhejiang, China
| | - Xiu-Feng Huang
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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Govers BM, van Huet RAC, Roosing S, Keijser S, Los LI, den Hollander AI, Klevering BJ. The genetics and disease mechanisms of rhegmatogenous retinal detachment. Prog Retin Eye Res 2023; 97:101158. [PMID: 36621380 DOI: 10.1016/j.preteyeres.2022.101158] [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: 08/25/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023]
Abstract
Rhegmatogenous retinal detachment (RRD) is a sight threatening condition that warrants immediate surgical intervention. To date, 29 genes have been associated with monogenic disorders involving RRD. In addition, RRD can occur as a multifactorial disease through a combined effect of multiple genetic variants and non-genetic risk factors. In this review, we provide a comprehensive overview of the spectrum of hereditary disorders involving RRD. We discuss genotype-phenotype correlations of these monogenic disorders, and describe genetic variants associated with RRD through multifactorial inheritance. Furthermore, we evaluate our current understanding of the molecular disease mechanisms of RRD-associated genetic variants on collagen proteins, proteoglycan versican, and the TGF-β pathway. Finally, we review the role of genetics in patient management and prevention of RRD. We provide recommendations for genetic testing and prophylaxis of at-risk patients, and hypothesize on novel therapeutic approaches beyond surgical intervention.
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Affiliation(s)
- Birgit M Govers
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ramon A C van Huet
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sander Keijser
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leonoor I Los
- Department of Ophthalmology, University Medical Center Groningen, Groningen, the Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands; AbbVie, Genomics Research Center, Cambridge, MA, USA
| | - B Jeroen Klevering
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands.
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Chen J, Lian P, Zhao X, Li J, Yu X, Huang X, Chen S, Lu L. PSMD3 gene mutations cause pathological myopia. J Med Genet 2023; 60:918-924. [PMID: 36948574 DOI: 10.1136/jmg-2022-108978] [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: 10/05/2022] [Accepted: 02/08/2023] [Indexed: 03/24/2023]
Abstract
PURPOSE Genetic factors play a prominent role in the pathogenesis of pathological myopia (PM). However, the exact genetic mechanism of PM remains unclear. This study aimed to determine the candidate mutation of PM in a Chinese family and explore the potential mechanism. METHODS We performed exome sequencing and Sanger sequencing in a Chinese family and 179 sporadic PM cases. The gene expression in human tissue was investigated by RT-quantitative real-time PCR (RT-qPCR) and immunofluorescence. Cell apoptotic rates were tested by annexin V-APC/7AAD and flow cytometry. Psmd3 knock-in mice with point mutation were generated for measuring myopia-related parameters. RESULTS We screened a novel PSMD3 variant (c.689T>C; p.F230S) in a Chinese family with PM, and another rare mutation (c.1015C>A; p.L339M) was identified in 179 unrelated cases with PM. RT-qPCR and immunofluorescence confirmed the expression of PSMD3 in human eye tissue. Mutation of PSMD3 decreased the mRNA and protein expression, causing apoptosis of human retinal pigment epithelial cells. In in vivo experiments, the axial length (AL) of mutant mice increased significantly compared with that of wild-type mice (p<0.001). CONCLUSIONS A new potential pathogenic gene, PSMD3, in a PM family was identified, and it may be involved in the elongation of AL and the development of PM.
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Affiliation(s)
- Jing 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, Guangdong, China
| | - Ping Lian
- 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, Guangdong, China
| | - Xiujuan Zhao
- 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, Guangdong, China
| | - Jun Li
- 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, Guangdong, China
| | - Xiling Yu
- 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, Guangdong, China
| | - Xia Huang
- 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, Guangdong, China
| | - Shida 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, Guangdong, China
| | - Lin Lu
- 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, Guangdong, China
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Jackson D, Moosajee M. The Genetic Determinants of Axial Length: From Microphthalmia to High Myopia in Childhood. Annu Rev Genomics Hum Genet 2023; 24:177-202. [PMID: 37624667 DOI: 10.1146/annurev-genom-102722-090617] [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] [Indexed: 08/27/2023]
Abstract
The axial length of the eye is critical for normal visual function by enabling light to precisely focus on the retina. The mean axial length of the adult human eye is 23.5 mm, but the molecular mechanisms regulating ocular axial length remain poorly understood. Underdevelopment can lead to microphthalmia (defined as a small eye with an axial length of less than 19 mm at 1 year of age or less than 21 mm in adulthood) within the first trimester of pregnancy. However, continued overgrowth can lead to axial high myopia (an enlarged eye with an axial length of 26.5 mm or more) at any age. Both conditions show high genetic and phenotypic heterogeneity associated with significant visual morbidity worldwide. More than 90 genes can contribute to microphthalmia, and several hundred genes are associated with myopia, yet diagnostic yields are low. Crucially, the genetic pathways underpinning the specification of eye size are only now being discovered, with evidence suggesting that shared molecular pathways regulate under- or overgrowth of the eye. Improving our mechanistic understanding of axial length determination will help better inform us of genotype-phenotype correlations in both microphthalmia and myopia, dissect gene-environment interactions in myopia, and develop postnatal therapies that may influence overall eye growth.
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Affiliation(s)
- Daniel Jackson
- Institute of Ophthalmology, University College London, London, United Kingdom;
| | - Mariya Moosajee
- Institute of Ophthalmology, University College London, London, United Kingdom;
- The Francis Crick Institute, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
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5
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Ben Yosef T, Banin E, Chervinsky E, Shalev SA, Leibu R, Mezer E, Rotenstreich Y, Goldenberg-Cohen N, Weiss S, Khan MI, Panneman DM, Hitti-Malin RJ, Weiner C, Roosing S, Cremers FPM, Pras E, Zur D, Newman H, Deitch I, Sharon D, Ehrenberg M. Genetic causes of inherited retinal diseases among Israeli Jews of Ethiopian ancestry. Mol Vis 2023; 29:1-12. [PMID: 37287645 PMCID: PMC10243676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 04/20/2023] [Indexed: 06/09/2023] Open
Abstract
Purpose This study sought to describe the phenotype frequency and genetic basis of inherited retinal diseases (IRDs) among a nationwide cohort of Israeli Jewish patients of Ethiopian ancestry. Methods Patients' data-including demographic, clinical, and genetic information-were obtained through members of the Israeli Inherited Retinal Disease Consortium (IIRDC). Genetic analysis was performed by either Sanger sequencing for founder mutations or next-generation sequencing (targeted next-generation sequencing or whole-exome sequencing). Results Forty-two patients (58% female) from 36 families were included, and their ages ranged from one year to 82 years. Their most common phenotypes were Stargardt disease (36%) and nonsyndromic retinitis pigmentosa (33%), while their most common mode of inheritance was autosomal recessive inheritance. Genetic diagnoses were ascertained for 72% of genetically analyzed patients. The most frequent gene involved was ABCA4. Overall, 16 distinct IRD mutations were identified, nine of which are novel. One of them, ABCA4-c.6077delT, is likely a founder mutation among the studied population. Conclusions This study is the first to describe IRDs' phenotypic and molecular characteristics in the Ethiopian Jewish community. Most of the identified variants are rare. Our findings can help caregivers with clinical and molecular diagnosis and, we hope, enable adequate therapy in the near future.
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Affiliation(s)
| | - Eyal Banin
- Division of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | | | - Stavit A. Shalev
- Rappaport Faculty of Medicine, Technion, Haifa, Israel
- Genetics Institute, Emek Medical Center, Afula, Israel
| | - Rina Leibu
- Department of Ophthalmology, Rambam Health Care Campus, Haifa, Israel
| | - Eedy Mezer
- Rappaport Faculty of Medicine, Technion, Haifa, Israel
- Department of Ophthalmology, Rambam Health Care Campus, Haifa, Israel
| | - Ygal Rotenstreich
- Goldschleger Eye Institute, Sheba Medical Center, Tel Hashomer, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Nitza Goldenberg-Cohen
- Rappaport Faculty of Medicine, Technion, Haifa, Israel
- Department of Ophthalmology, Bnai Zion Medical Center, Haifa, Israel
- The Krieger Eye Research Laboratory, Petach Tikva, Israel
| | - Shirel Weiss
- The Krieger Eye Research Laboratory, Petach Tikva, Israel
| | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Chen Weiner
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Ophthalmology Department, Shamir Medical Center, Zerifin, Israel
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eran Pras
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Ophthalmology Department, Shamir Medical Center, Zerifin, Israel
| | - Dinah Zur
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Division of Ophthalmology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Hadas Newman
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Division of Ophthalmology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Iris Deitch
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Ophthalmology, Rabin Medical Center, Petach Tikva, Israel
| | - Dror Sharon
- Division of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | - Miriam Ehrenberg
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Ophthalmology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
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6
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Magliyah MS, Almarek F, Nowilaty SR, Al-Abdi L, Alkuraya FS, Alowain M, Schatz P, Alfaadhel T, Khan AO, Alsulaiman SM. LEPREL1 -RELATED GIANT RETINAL TEAR DETACHMENTS MIMIC THE PHENOTYPE OF OCULAR STICKLER SYNDROME. Retina 2023; 43:498-505. [PMID: 36729830 DOI: 10.1097/iae.0000000000003691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE To describe the features of retinal detachments and high myopia in patients with novel pathogenic variants in LEPREL1 and report a possible association with nephropathy. METHODS Retrospective study of 10 children with biallelic LEPREL1 pathogenic variants. Data included ophthalmic features, surgical interventions, and genetic and laboratory findings. RESULTS 10 patients (8 females) from three families with homozygous (2) or compound heterozygous (1) variants in LEPREL1 were included. At presentation, mean age was 9.9 ± 2.6 years. Mean axial length was 28.9 ± 1.9 mm and mean refraction was -13.9 ± 2.8 diopters. Bilateral posterior subcapsular cataracts were present in eight patients (80%), with lens subluxation in five eyes of three patients (30%). Rhegmatogenous retinal detachments (RRD), associated with giant retinal tears (GRT), developed in seven eyes of five patients (50%) at a mean age of 14.14 ± 5.9 years. Six were successfully reattached with mean Snellen best-corrected visual acuity improving from 20/120 preoperatively to 20/60 at last follow-up. Urinalysis in nine patients revealed microhematuria and/or mild proteinuria in six patients (67%). CONCLUSION LEPREL1 -related high myopia confers a high risk of early-onset GRT-related RRD. The ocular phenotype may be confused with that of ocular Stickler syndrome if genetic testing is not performed. Further investigations into a potential association with renal dysfunction are warranted.
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Affiliation(s)
- Moustafa S Magliyah
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
- Department of Ophthalmology, Prince Mohammed Medical City, AlJouf, Saudi Arabia
| | - Faisal Almarek
- Department of Ophthalmology, Imam Mohammed Bin Saud Islamic University, Riyadh, Saudi Arabia
| | - Sawsan R Nowilaty
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Lama Al-Abdi
- Department of Translational Genomics, Center 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
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center 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
| | - Mohammed Alowain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Patrik Schatz
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
- Department of Ophthalmology, Clinical Sciences, Skane University Hospital, Lund University, Lund, Sweden
| | - Talal Alfaadhel
- Department of Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates; and
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
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Key Factors in Early Diagnosis of Myopia Progression within Ocular Biometric Parameters by Scheimpflug Technology. Life (Basel) 2023; 13:life13020447. [PMID: 36836804 PMCID: PMC9960747 DOI: 10.3390/life13020447] [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: 01/04/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
The aim of this study was to evaluate the relationship between myopia and ocular biometric variables using the Pentacam AXL® single rotation Scheimpflug camera. This prospective, cross-sectional, single-center study was performed in fifty Caucasian patients aged between 18 and 30 years (24.84 ± 3.04 years). The measured variables included maximum and minimum keratometry (K1 and K2, respectively), anterior chamber depth (ACD), corneal horizontal diameter or white to white (WTW), central corneal thickness (CCT), corneal asphericity (Q), and axial length (AXL). The tomographic and biometric measurements were considered optimal when the quality factor was greater than 95% according to the manufacturer's software instructions. The AXL presented a significant correlation with the spherical equivalent without cycloplegia (SE without CP), age at onset of myopia (r = -0.365, p = 0.012), mean keratometry (Km) (r = -0.339, p = 0.016), ACD (r = 0.304, p = 0.032), and WTW (r = 0.406, p = 0.005). The eyes with AXL higher than 25 mm had earlier onset; higher SE without CP, AXL, and Q; and a flatter Km. AXL is the biometric variable with the greatest influence on the final refractive state in the adult myopic eye. Ophthalmologists and optometric management must consider these biometric differences in order to identify the most appropriate correction techniques in each case. The use of the Pentacam AXL in ocular biometric measurement is effective, reproducible, and non-invasive.
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The Differential Expression of Circular RNAs and the Role of circAFF1 in Lens Epithelial Cells of High-Myopic Cataract. J Clin Med 2023; 12:jcm12030813. [PMID: 36769461 PMCID: PMC9918043 DOI: 10.3390/jcm12030813] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/02/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023] Open
Abstract
High-myopic cataract (HMC) is a complex cataract with earlier onset and more rapid progress than age-related cataract (ARC). Circular RNAs (circRNAs) have been implicated in many diseases. However, their involvement in HMC remain largely unexplored. To investigate the role of dysregulated circRNAs in HMC, lens epithelium samples from 24 HMC and 24 ARC patients were used for whole transcriptome sequencing. Compared with ARC, HMC had 3687 uniquely expressed circRNAs and 1163 significantly differentially expressed circRNAs (DEcRs) (|log2FC| > 1, p < 0.05). A putative circRNA-miRNA-mRNA network was constructed based on correlation analysis. We validated the differential expression of 3 DEcRs by quantitative polymerase chain reaction (qPCR) using different sets of samples. We further investigated the role of circAFF1 in cultured lens epithelial cells (LECs) and found that the overexpression of circAFF1 promoted cell proliferation, migration and inhibited apoptosis. We also showed that circAFF1 upregulated Tropomyosin 1 (TPM1) expression by sponging miR-760, which was consistent with the network prediction. Collectively, our study suggested the involvement of circRNAs in the pathogenesis of HMC and provide a resource for further study on this topic.
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Du Z, Cai S, Yan D, Li H, Zhang X, Yang W, Cao J, Yi N, Tang Z. Development and Validation of a Radiosensitivity Prediction Model for Lower Grade Glioma Based on Spike-and-Slab Lasso. Front Oncol 2021; 11:701500. [PMID: 34395274 PMCID: PMC8363254 DOI: 10.3389/fonc.2021.701500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/16/2021] [Indexed: 12/25/2022] Open
Abstract
Background and Purpose Lower grade glioma (LGG) is one of the leading causes of death world worldwide. We attempted to develop and validate a radiosensitivity model for predicting the survival of lower grade glioma by using spike-and-slab lasso Cox model. Methods In this research, differentially expressed genes based on tumor microenvironment was obtained to further analysis. Log-rank test was used to identify genes in patients who received radiotherapy and patients who did not receive radiotherapy, respectively. Then, spike-and-slab lasso was performed to select genes in patients who received radiotherapy. Finally, three genes (INA, LEPREL1 and PTCRA) were included in the model. A radiosensitivity-related risk score model was established based on overall rate of TCGA dataset in patients who received radiotherapy. The model was validated in TCGA dataset that PFS as endpoint and two CGGA datasets that OS as endpoint. A novel nomogram integrated risk score with age and tumor grade was developed to predict the OS of LGG patients. Results We developed and verified a radiosensitivity-related risk score model. The radiosensitivity-related risk score is served as an independent prognostic indicator. This radiosensitivity-related risk score model has prognostic prediction ability. Moreover, the nomogram integrated risk score with age and tumor grade was established to perform better for predicting 1, 3, 5-year survival rate. Conclusions This model can be used by clinicians and researchers to predict patient’s survival rates and achieve personalized treatment of LGG.
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Affiliation(s)
- Zixuan Du
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Shang Cai
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Derui Yan
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Huijun Li
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Xinyan Zhang
- School of Data Science and Analytics, Kennesaw State University, Kennesaw, GA, United States
| | - Wei Yang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Jianping Cao
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Nengjun Yi
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Zaixiang Tang
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
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10
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Liu Y, Zhang JJ, Piao SY, Shen RJ, Ma Y, Xue ZQ, Zhang W, Liu J, Jin ZB, Zhuang WJ. Whole-Exome Sequencing in a Cohort of High Myopia Patients in Northwest China. Front Cell Dev Biol 2021; 9:645501. [PMID: 34222226 PMCID: PMC8250434 DOI: 10.3389/fcell.2021.645501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/27/2021] [Indexed: 11/22/2022] Open
Abstract
High myopia (HM) is one of the leading causes of visual impairment worldwide. In order to expand the myopia gene spectrum in the Chinese population, we investigated genetic mutations in a cohort of 27 families with HM from Northwest China by using whole-exome sequencing (WES). Genetic variations were filtered using bioinformatics tools and cosegregation analysis. A total of 201 candidate mutations were detected, and 139 were cosegregated with the disease in the families. Multistep analysis revealed four missense variants in four unrelated families, including c.904C>T (p.R302C) in CSMD1, c.860G>A (p.R287H) in PARP8, c.G848A (p.G283D) in ADAMTSL1, and c.686A>G (p.H229R) in FNDC3B. These mutations were rare or absent in the Exome Aggregation Consortium (ExAC), 1000 Genomes Project, and Genome Aggregation Database (gnomAD), indicating that they are new candidate disease-causing genes. Our findings not only expand the myopia gene spectrum but also provide reference information for further genetic study of heritable HM.
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Affiliation(s)
- Yang Liu
- School of Basic Medical Sciences, Third Clinical Medical College of Ningxia Medical University (People’s Hospital of Ningxia Hui Autonomous Region), Yinchuan, China
| | - Jin-Jin Zhang
- Clinical Medical College, Ningxia Medical University, Yinchuan, China
| | - Shun-Yu Piao
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China
| | - Ya Ma
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China
| | - Zhong-Qi Xue
- Department of Ophthalmology, Affiliated Hospital of Qingdao Binhai University, Qingdao, China
| | - Wen Zhang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Juan Liu
- School of Basic Medical Sciences, Third Clinical Medical College of Ningxia Medical University (People’s Hospital of Ningxia Hui Autonomous Region), Yinchuan, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China
| | - Wen-Juan Zhuang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
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11
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Tideman JWL, Pärssinen O, Haarman AEG, Khawaja AP, Wedenoja J, Williams KM, Biino G, Ding X, Kähönen M, Lehtimäki T, Raitakari OT, Cheng CY, Jonas JB, Young TL, Bailey-Wilson JE, Rahi J, Williams C, He M, Mackey DA, Guggenheim JA. Evaluation of Shared Genetic Susceptibility to High and Low Myopia and Hyperopia. JAMA Ophthalmol 2021; 139:601-609. [PMID: 33830181 DOI: 10.1001/jamaophthalmol.2021.0497] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Importance Uncertainty currently exists about whether the same genetic variants are associated with susceptibility to low myopia (LM) and high myopia (HM) and to myopia and hyperopia. Addressing this question is fundamental to understanding the genetics of refractive error and has clinical relevance for genotype-based prediction of children at risk for HM and for identification of new therapeutic targets. Objective To assess whether a common set of genetic variants are associated with susceptibility to HM, LM, and hyperopia. Design, Setting, and Participants This genetic association study assessed unrelated UK Biobank participants 40 to 69 years of age of European and Asian ancestry. Participants 40 to 69 years of age living in the United Kingdom were recruited from January 1, 2006, to October 31, 2010. Of the total sample of 502 682 participants, 117 279 (23.3%) underwent an ophthalmic assessment. Data analysis was performed from December 12, 2019, to June 23, 2020. Exposures Four refractive error groups were defined: HM, -6.00 diopters (D) or less; LM, -3.00 to -1.00 D; hyperopia, +2.00 D or greater; and emmetropia, 0.00 to +1.00 D. Four genome-wide association study (GWAS) analyses were performed in participants of European ancestry: (1) HM vs emmetropia, (2) LM vs emmetropia, (3) hyperopia vs emmetropia, and (4) LM vs hyperopia. Polygenic risk scores were generated from GWAS summary statistics, yielding 4 sets of polygenic risk scores. Performance was assessed in independent replication samples of European and Asian ancestry. Main Outcomes and Measures Odds ratios (ORs) of polygenic risk scores in replication samples. Results A total of 51 841 unrelated individuals of European ancestry and 2165 unrelated individuals of Asian ancestry were assigned to a specific refractive error group and included in our analyses. Polygenic risk scores derived from all 4 GWAS analyses were predictive of all categories of refractive error in both European and Asian replication samples. For example, the polygenic risk score derived from the HM vs emmetropia GWAS was predictive in the European sample of HM vs emmetropia (OR, 1.58; 95% CI, 1.41-1.77; P = 1.54 × 10-15) as well as LM vs emmetropia (OR, 1.15; 95% CI, 1.07-1.23; P = 8.14 × 10-5), hyperopia vs emmetropia (OR, 0.83; 95% CI, 0.77-0.89; P = 4.18 × 10-7), and LM vs hyperopia (OR, 1.45; 95% CI, 1.33-1.59; P = 1.43 × 10-16). Conclusions and Relevance Genetic risk variants were shared across HM, LM, and hyperopia and across European and Asian samples. Individuals with HM inherited a higher number of variants from among the same set of myopia-predisposing alleles and not different risk alleles compared with individuals with LM. These findings suggest that treatment interventions targeting common genetic risk variants associated with refractive error could be effective against both LM and HM.
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Affiliation(s)
- J Willem L Tideman
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Olavi Pärssinen
- Gerontology Research Center and Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland.,Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä, Finland
| | - Annechien E G Haarman
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital National Health Service (NHS) Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - Juho Wedenoja
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Katie M Williams
- Section of Academic Ophthalmology, Faculty of Life Sciences and Medicine, King's College London School of Life Course Sciences, London, United Kingdom.,Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council of Italy, Pavia, Italy
| | - Xiaohu Ding
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Mika Kähönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Terho Lehtimäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland.,Department of Clinical Chemistry, Finnish Cardiovascular Research Center, Tampere, Finland
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Finland.,Research Centre of Applied and Preventive Medicine, University of Turku, Turku, Finland.,Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Ching-Yu Cheng
- Duke-NUS Medical School, Singapore, Singapore.,Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Jost B Jonas
- Department of Ophthalmology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Terri L Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - Jugnoo Rahi
- UCL Great Ormond Street Institute of Child Health and Institute of Ophthalmology, University College London, London, United Kingdom
| | - Cathy Williams
- Centre for Academic Child Health, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Mingguang He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Centre for Eye Research Australia; Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Western Australia, Australia
| | - Jeremy A Guggenheim
- Cardiff University School of Optometry and Vision Sciences, Cardiff, United Kingdom
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12
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Prolyl 3-Hydroxylase 2 Is a Molecular Player of Angiogenesis. Int J Mol Sci 2021; 22:ijms22083896. [PMID: 33918807 PMCID: PMC8069486 DOI: 10.3390/ijms22083896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
Prolyl 3-hydroxylase 2 (P3H2) catalyzes the post-translational formation of 3-hydroxyproline on collagens, mainly on type IV. Its activity has never been directly associated to angiogenesis. Here, we identified P3H2 gene through a deep-sequencing transcriptome analysis of human umbilical vein endothelial cells (HUVECs) stimulated with vascular endothelial growth factor A (VEGF-A). Differently from many previous studies we carried out the stimulation not on starved HUVECs, but on cells grown to maintain the best condition for their in vitro survival and propagation. We showed that P3H2 is induced by VEGF-A in two primary human endothelial cell lines and that its transcription is modulated by VEGF-A/VEGF receptor 2 (VEGFR-2) signaling pathway through p38 mitogen-activated protein kinase (MAPK). Then, we demonstrated that P3H2, through its activity on type IV Collagen, is essential for angiogenesis properties of endothelial cells in vitro by performing experiments of gain- and loss-of-function. Immunofluorescence studies showed that the overexpression of P3H2 induced a more condensed status of Collagen IV, accompanied by an alignment of the cells along the Collagen IV bundles, so towards an evident pro-angiogenic status. Finally, we found that P3H2 knockdown prevents pathological angiogenesis in vivo, in the model of laser-induced choroid neovascularization. Together these findings reveal that P3H2 is a new molecular player involved in new vessels formation and could be considered as a potential target for anti-angiogenesis therapy.
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13
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Abstract
Collagen is the most abundant protein in mammals. A unique feature of collagen is its triple-helical structure formed by the Gly-Xaa-Yaa repeats. Three single chains of procollagen make a trimer, and the triple-helical structure is then folded in the endoplasmic reticulum (ER). This unique structure is essential for collagen's functions in vivo, including imparting bone strength, allowing signal transduction, and forming basement membranes. The triple-helical structure of procollagen is stabilized by posttranslational modifications and intermolecular interactions, but collagen is labile even at normal body temperature. Heat shock protein 47 (Hsp47) is a collagen-specific molecular chaperone residing in the ER that plays a pivotal role in collagen biosynthesis and quality control of procollagen in the ER. Mutations that affect the triple-helical structure or result in loss of Hsp47 activity cause the destabilization of procollagen, which is then degraded by autophagy. In this review, we present the current state of the field regarding quality control of procollagen.
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Affiliation(s)
- Shinya Ito
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan;
| | - Kazuhiro Nagata
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan; .,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto 603-8555, Japan; .,JT Biohistory Research Hall, Osaka, 569-1125, Japan
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14
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Variants in FLRT3 and SLC35E2B identified using exome sequencing in seven high myopia families from Central Europe. Adv Med Sci 2021; 66:192-198. [PMID: 33711669 DOI: 10.1016/j.advms.2021.02.005] [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] [Received: 07/14/2020] [Revised: 02/09/2021] [Accepted: 02/26/2021] [Indexed: 12/28/2022]
Abstract
PURPOSE High myopia (HM) is an eye disorder with both environmental and genetic factors involved. Many genetic factors responsible for HM were recognized worldwide, but little is known about genetic variants underlying HM in Central Europe. Thus, the aim of this study was to identify rare sequence variants involved in HM in families from Central Europe to better understand the genetic basis of HM. MATERIALS AND METHODS We assessed 17 individuals from 7 unrelated Central European families with hereditary HM using exome sequencing (ES). Segregation of selected variants in other available family members was performed using Sanger sequencing. RESULTS Detected 73 rare variants were selected for verification. We observed 2 missense variants, c.938C>T in SLC35E2B - encoding solute carrier family 35 member E2B, and c.1642G>C in FLRT3 - encoding fibronectin leucine rich transmembrane protein, segregating with HM in one family. CONCLUSIONS FLRT3 and/or SLC35E2B could represent disease candidate genes and identified sequence variants might be responsible for HM in the studied family.
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15
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Salo AM, Myllyharju J. Prolyl and lysyl hydroxylases in collagen synthesis. Exp Dermatol 2020; 30:38-49. [PMID: 32969070 DOI: 10.1111/exd.14197] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]
Abstract
Collagens are the most abundant proteins in the extracellular matrix. They provide a framework to build organs and tissues and give structural support to make them resistant to mechanical load and forces. Several intra- and extracellular modifications are needed to make functional collagen molecules, intracellular post-translational modifications of proline and lysine residues having key roles in this. In this article, we provide a review on the enzymes responsible for the proline and lysine modifications, that is collagen prolyl 4-hydroxylases, 3-hydroxylases and lysyl hydroxylases, and discuss their biological functions and involvement in diseases.
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Affiliation(s)
- Antti M Salo
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Johanna Myllyharju
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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16
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Taga Y, Kusubata M, Mizuno K. Quantitative Analysis of the Positional Distribution of Hydroxyproline in Collagenous Gly-Xaa-Yaa Sequences by LC-MS with Partial Acid Hydrolysis and Precolumn Derivatization. Anal Chem 2020; 92:8427-8434. [PMID: 32437599 DOI: 10.1021/acs.analchem.0c01098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Collagen is extensively modified by various enzymes, including prolyl hydroxylases. Pro residues at the Yaa position of repeating Gly-Xaa-Yaa amino acid sequences are mostly hydroxylated to 4-hydroxyproline (4Hyp), which is essential for the thermal stability of collagen triple helix. In contrast, Pro residues at the Xaa position are rarely modified to 3Hyp and 4Hyp, the biological function of which is poorly understood. Overall estimation of prolyl hydroxylation with discrimination of the position (Xaa or Yaa) and hydroxylation type (4Hyp or 3Hyp) has been difficult to perform using traditional methods. In the present study, we developed a novel position-specific analytical method featuring LC-MS detection of collagenous Gly-containing dipeptides, including Gly-Pro, Pro-Gly, Gly-4Hyp, Gly-3Hyp, and 4Hyp-Gly, after partial acid hydrolysis and precolumn derivatization using 3-aminopyridyl-N-hydroxysuccinimidyl carbamate (APDS). We performed acid hydrolysis at 55 °C with HCl/trifluoroacetic acid/water (2:1:1, v/v) to avoid peptide inversion and imbalanced peptide generation observed for collagenous model peptides. The positional distribution of Pro, 4Hyp, and 3Hyp can be calculated from the relative concentrations of the APDS-derivatized dipeptides, and in combination with amino acid analysis, we can determine their absolute contents at the Xaa and Yaa positions. Bovine type I, III, and V collagens were analyzed by the established method, and the amount of 4Hyp was higher than that of 3Hyp at the Xaa position in type I and III collagens. In addition, we clearly showed that collagen extracted from earthworm cuticles has an extremely high content of Xaa position 4Hyp, reaching over 10% of the total amino acids.
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Affiliation(s)
- Yuki Taga
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Masashi Kusubata
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Kazunori Mizuno
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
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17
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Liu F, Wang J, Xing Y, Li T. Mutation screening of 17 candidate genes in a cohort of 67 probands with early-onset high myopia. Ophthalmic Physiol Opt 2020; 40:271-280. [PMID: 32215939 DOI: 10.1111/opo.12683] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 02/17/2020] [Indexed: 12/22/2022]
Abstract
PURPOSE To detect variants in 17 known potentially causative genes for non-syndromic myopia in 67 Tujia Chinese patients with early-onset high myopia (eo-HM). METHODS DNA from 67 unrelated patients with early onset (<7 years old) high myopia (refraction error ≤ -6.00D or axial length > 26 mm) were subjected to whole-exome sequencing (WES). Variants in 17 candidate genes were analysed by multistep bioinformatics analysis. Subsequently, Sanger sequencing was used to verify identified candidate mutations and to assess available family members for co-segregation with myopia. RESULTS A multistep systematic analysis of variants in 17 potentially causative genes for eo-HM revealed four novel pathogenic mutations and three potential pathogenic mutations in 4 of 17 genes in 7 of 67 (10.4%) probands. The pathogenic group included one missense mutation (c.100G > C, p.Asp34His) and one splice donor mutation (c.989 + 1G >A) in ARR3, one missense mutation (c.995C > A, p.Thr332Lys) in NDUFAF7 and one novel frameshift mutation (c.726dupA, p.Arg243fs*140) in SLC39A5. The potential pathogenic group included two missense mutations (c.3266A > G, p.Tyr1089Cys; c.913G > A, p.Glu305Lys) in ZNF644 and one missense mutation (c.960T > A, p.His320Gln) in NDUFAF7. Sequence changes were confirmed by Sanger sequencing; all had an allele frequency <0.01 in the 1000G, EVS, ExAC and gnomAD databases. Additionally, both the pathogenic and potentially pathogenic mutations were predicted to be damaging by SIFT, Polyphen-2, PROVEAN, MutationTaster2, CADD and REVEL except the p.Tyr1089Cys and p.Glu305Lys changes were predicted to be neutral by PROVEAN. CONCLUSION Our research provides more evidence to support the hypothesis that mutations in ARR3, SLC39A5 and NDUFAF7 are disease-causing genes for eo-HM and broadens the eo-HM mutation spectrum among different ethnic groups. It also deepens understanding of the contributions of ARR3, SLC39A5, and NDUFAF7 to eo-HM.
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Affiliation(s)
- Fang Liu
- Department of Ophthalmology, The Central Hospital of Enshi Tujia And Miao Autonomous Prefecture, Enshi Clinical College of Wuhan University, Enshi, China.,Department of Eye Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Junwen Wang
- Department of Ophthalmology, The Central Hospital of Enshi Tujia And Miao Autonomous Prefecture, Enshi Clinical College of Wuhan University, Enshi, China
| | - Yiqiao Xing
- Department of Eye Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tuo Li
- Department of Ophthalmology, The Central Hospital of Enshi Tujia And Miao Autonomous Prefecture, Enshi Clinical College of Wuhan University, Enshi, China
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18
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Rhegmatogenous Retinal Detachment in Nonsyndromic High Myopia Associated with Recessive Mutations in LRPAP1. ACTA ACUST UNITED AC 2020; 4:77-83. [DOI: 10.1016/j.oret.2019.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 01/19/2023]
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19
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Cai XB, Shen SR, Chen DF, Zhang Q, Jin ZB. An overview of myopia genetics. Exp Eye Res 2019; 188:107778. [DOI: 10.1016/j.exer.2019.107778] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/27/2019] [Accepted: 08/23/2019] [Indexed: 11/15/2022]
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20
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Cai XB, Zheng YH, Chen DF, Zhou FY, Xia LQ, Wen XR, Yuan YM, Han F, Piao SY, Zhuang W, Lu F, Qu J, Yu AY, Jin ZB. Expanding the Phenotypic and Genotypic Landscape of Nonsyndromic High Myopia: A Cross-Sectional Study in 731 Chinese Patients. ACTA ACUST UNITED AC 2019; 60:4052-4062. [PMID: 31560770 DOI: 10.1167/iovs.19-27921] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Xue-Bi Cai
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, National Center for International Research in Regenerative Medicine and Neurogenetics, National Clinical Research Center for Ophthalmology, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - Yi-Han Zheng
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, National Center for International Research in Regenerative Medicine and Neurogenetics, National Clinical Research Center for Ophthalmology, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - De-Fu Chen
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, National Center for International Research in Regenerative Medicine and Neurogenetics, National Clinical Research Center for Ophthalmology, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - Fang-Yue Zhou
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, National Center for International Research in Regenerative Medicine and Neurogenetics, National Clinical Research Center for Ophthalmology, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - Lu-Qi Xia
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, National Center for International Research in Regenerative Medicine and Neurogenetics, National Clinical Research Center for Ophthalmology, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - Xin-Ran Wen
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, National Center for International Research in Regenerative Medicine and Neurogenetics, National Clinical Research Center for Ophthalmology, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - Yi-Min Yuan
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, National Center for International Research in Regenerative Medicine and Neurogenetics, National Clinical Research Center for Ophthalmology, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - Fang Han
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, National Center for International Research in Regenerative Medicine and Neurogenetics, National Clinical Research Center for Ophthalmology, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - Shun-Yu Piao
- Ningxia Medical University, People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Wenjuan Zhuang
- Ningxia Medical University, People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Fan Lu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, National Center for International Research in Regenerative Medicine and Neurogenetics, National Clinical Research Center for Ophthalmology, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - Jia Qu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, National Center for International Research in Regenerative Medicine and Neurogenetics, National Clinical Research Center for Ophthalmology, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - A-Yong Yu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, National Center for International Research in Regenerative Medicine and Neurogenetics, National Clinical Research Center for Ophthalmology, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - Zi-Bing Jin
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, National Center for International Research in Regenerative Medicine and Neurogenetics, National Clinical Research Center for Ophthalmology, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
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21
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Role of prolyl hydroxylation in the molecular interactions of collagens. Essays Biochem 2019; 63:325-335. [PMID: 31350381 PMCID: PMC6744578 DOI: 10.1042/ebc20180053] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022]
Abstract
Co- and post-translational hydroxylation of proline residues is critical for the stability of the triple helical collagen structure. In this review, we summarise the biology of collagen prolyl 4-hydroxylases and collagen prolyl 3-hydroxylases, the enzymes responsible for proline hydroxylation. Furthermore, we describe the potential roles of hydroxyproline residues in the complex interplay between collagens and other proteins, especially integrin and discoidin domain receptor type cell adhesion receptors. Qualitative and quantitative regulation of collagen hydroxylation may have remarkable effects on the properties of the extracellular matrix and consequently on the cell behaviour.
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22
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Weatherbee BAT, Barton JR, Siddam AD, Anand D, Lachke SA. Molecular characterization of the human lens epithelium-derived cell line SRA01/04. Exp Eye Res 2019; 188:107787. [PMID: 31479653 DOI: 10.1016/j.exer.2019.107787] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 12/18/2022]
Abstract
Cataract-associated gene discovery in human and animal models have informed on key aspects of human lens development, homeostasis and pathology. Additionally, in vitro models such as the culture of permanent human lens epithelium-derived cell lines (LECs) have also been utilized to understand the molecular biology of lens cells. However, these resources remain uncharacterized, specifically regarding their global gene expression and suitability to model lens cell biology. Therefore, we sought to molecularly characterize gene expression in the human LEC, SRA01/04, which is commonly used in lens studies. We first performed short tandem repeat (STR) analysis and validated SRA01/04 LEC for its human origin, as recommended by the eye research community. Next, we used Illumina HumanHT-12 v3.0 Expression BeadChip arrays to gain insights into the global gene expression profile of SRA01/04. Comparative analysis of SRA01/04 microarray data was performed using other resources such as the lens expression database iSyTE (integrated Systems Tool for Eye gene discovery), the cataract gene database Cat-Map and the published lens literature. This analysis showed that SRA01/04 significantly expresses >40% of the top iSyTE lens-enriched genes (313 out of 749) across different developmental stages. Further, SRA01/04 also significantly expresses ~53% (168 out of 318) of cataract-associated genes in Cat-Map. We also performed comparative gene expression analysis between SRA01/04 cells and the previously validated mouse LEC 21EM15. To gain insight into whether SRA01/04 reflects epithelial or fiber cell characteristics, we compared its gene expression profile to previously reported differentially expressed genes in isolated mouse lens epithelial and fiber cells. This analysis suggests that SRA01/04 has reduced expression of several fiber cell-enriched genes. In agreement with these findings, cell culture analysis demonstrates that SRA01/04 has reduced potential to initiate spontaneous lentoid body formation compared to 21EM15 cells. Next, to independently validate SRA01/04 microarray gene expression, we subjected several candidate genes to RT-PCR and RT-qPCR assays. This analysis demonstrates that SRA01/04 supports expression of many key genes associated with lens development and cataract, including CRYAB, CRYBB2, CRYGS, DKK3, EPHA2, ETV5, GJA1, HSPB1, INPPL1, ITGB1, PAX6, PVRL3, SFRP1, SPARC, TDRD7, and VIM, among others, and therefore can be relevant for understanding the mechanistic basis of these factors. At the same time, SRA01/04 cells do not exhibit robust expression of several genes known to be important to lens biology and cataract such as ALDH1A1, COL4A6, CP, CRYBA4, FOXE3, HMX1, HSF4, MAF, MEIS1, PITX3, PRX, SIX3, and TRPM3, among many others. Therefore, the present study offers a rich transcript-level resource for case-by-case evaluation of the potential advantages and limitations of SRA01/04 cells prior to their use in downstream investigations. In sum, these data show that the human LEC, SRA01/04, exhibits lens epithelial cell-like character reflected in the expression of several lens-enriched and cataract-associated genes, and therefore can be considered as a useful in vitro resource when combined with in vivo studies to gain insight into specific aspects of human lens epithelial cells.
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Affiliation(s)
| | - Joshua R Barton
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, 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, 19716, USA.
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23
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Wen Y, Zhu C, Li N, Li Z, Cheng Y, Dong J, Zhu M, Wang Y, Dai J, Ma H, Jin G, Dai M, Hu Z, Shen H. Fine Mapping in Chromosome 3q28 Identified Two Variants Associated with Lung Cancer Risk in Asian Population. J Cancer 2019; 10:1862-1869. [PMID: 31205543 PMCID: PMC6547980 DOI: 10.7150/jca.28379] [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: 07/08/2018] [Accepted: 01/20/2019] [Indexed: 11/23/2022] Open
Abstract
Genome-wide association studies (GWASs) have consistently identified chromosome 3q28 as a lung cancer susceptibility region. To further characterize the potential genetic mechanism of the variants in this region, we conducted a fine-mapping study on chromosome 3q28 region. We performed a target resequencing in 200 lung cancer cases and 300 controls in the screening and followed by validation in multi-ethnic lung cancer GWASs with 12,843 cases and 12,639 controls. For our identified novel variants, we conducted expression quantitative trait loci (eQTL) analysis to reveal the potential target genes. Two susceptibility variants were identified (rs4396880: G>A, OR = 0.35, 95%CI: 0.20-0.62, P = 3.01×10-4; and rs3856776: C>T, OR = 2.05, 95%CI: 1.32-3.18, P = 1.49×10-3) and further supported in Asian population (rs4396880: OR = 0.88, P = 7.43×10-6; and rs3856776: OR =1.17, P = 1.64×10-4). The eQTL analysis showed the A allele of rs4396880 was significantly associated with higher mRNA expression of TP63 (P = 1.70×10-4) in lung tissues, while rs3856776 showed significant association with the expression of LEPREL1-AS1 (P = 6.90×10-3), which was the antisense RNA of LEPREL1 and could suppress the translation of LEPREL1. Notably, LEPREL1 was aberrantly downregulated (P = 2.54×10-18) in lung tumor tissues based on TCGA database. In conclusion, this is the first fine-mapping analysis of 3q28 region in Han Chinese, and we found two variants associated with lung cancer susceptibility in Asian population. What's more, rs3856776 was newly identified and might modulate lung cancer susceptibility by suppressing the function of LEPREL1.
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Affiliation(s)
- Yang Wen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chen Zhu
- Zhejiang Provincial Office for Cancer Prevention and Control, Zhejiang Cancer Center/Zhejiang Cancer Hospital, Hangzhou 310004, China
| | - Ni Li
- National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhihua Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Cheng
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Dong
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuzhuo Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center of Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center of Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center of Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Min Dai
- National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center of Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center of Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
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24
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Quantitative proteomic profiling of extracellular matrix and site-specific collagen post-translational modifications in an in vitro model of lung fibrosis. Matrix Biol Plus 2019; 1:100005. [PMID: 33543004 PMCID: PMC7852317 DOI: 10.1016/j.mbplus.2019.04.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 12/21/2022] Open
Abstract
Lung fibrosis is characterized by excessive deposition of extracellular matrix (ECM), in particular collagens, by fibroblasts in the interstitium. Transforming growth factor-β1 (TGF-β1) alters the expression of many extracellular matrix (ECM) components produced by fibroblasts, but such changes in ECM composition as well as modulation of collagen post-translational modification (PTM) levels have not been comprehensively investigated. Here, we performed mass spectrometry (MS)-based proteomics analyses to assess changes in the ECM deposited by cultured lung fibroblasts from idiopathic pulmonary fibrosis (IPF) patients upon stimulation with transforming growth factor β1 (TGF-β1). In addition to the ECM changes commonly associated with lung fibrosis, MS-based label-free quantification revealed profound effects on enzymes involved in ECM crosslinking and turnover as well as multiple positive and negative feedback mechanisms of TGF-β1 signaling. Notably, the ECM changes observed in this in vitro model correlated significantly with ECM changes observed in patient samples. Because collagens are subject to multiple PTMs with major implications in disease, we implemented a new bioinformatic platform to analyze MS data that allows for the comprehensive mapping and site-specific quantitation of collagen PTMs in crude ECM preparations. These analyses yielded a comprehensive map of prolyl and lysyl hydroxylations as well as lysyl glycosylations for 15 collagen chains. In addition, site-specific PTM analysis revealed novel sites of prolyl-3-hydroxylation and lysyl glycosylation in type I collagen. Interestingly, the results show, for the first time, that TGF-β1 can modulate prolyl-3-hydroxylation and glycosylation in a site-specific manner. Taken together, this proof of concept study not only reveals unanticipated TGF-β1 mediated regulation of collagen PTMs and other ECM components but also lays the foundation for dissecting their key roles in health and disease. The proteomic data has been deposited to the ProteomeXchange Consortium via the MassIVE partner repository with the data set identifier MSV000082958. Quantitative proteomics of TGF-β-induced changes in ECM composition and collagen PTM in pulmonary fibroblasts TGF-β promotes crosslinking and turnover as well as complex feedback mechanisms that alter fibroblast ECM homeostasis. A novel bioinformatic workflow for MS data analysis enabled global mapping and quantitation of known and novel collagen PTMs Quantitative assessment of prolyl-3-hydroxylation site occupancy and lysine-O-glycosylation microheterogeneity TGF-β1 modulates collagen PTMs in a site-specific manner that may favor collagen accumulation in lung fibrosis
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Key Words
- 3-HyP, 3-hydroxyproline
- 4-HyP, 4-hydroxyproline
- AGC, automatic gain control
- ANXA11, annexin A11
- BGN, biglycan
- COL1A1, collagen-I alpha 1 chain
- Collagen
- Collagen post-translational modifications
- DCN, decorin
- ECM, extracellular matrix
- Extracellular matrix
- FN1, fibronectin 1
- G-HyK, galactosylhydroxylysine
- GG-HyK, glucosylgalactosylhydroxylysine
- HyK, hydroxylysine
- HyP, hydroxyproline
- ILD, interstitial lung disease
- IPF, idiopathic pulmonary fibrosis
- LH, lysyl hydroxylase
- LOX(L), lysyl oxidase(-like)
- LTBP2, latent-transforming growth factor β -binding protein 2
- Lysyl glycosylation
- Lysyl hydroxylation
- P3H, prolyl-3-hydroxylase
- P4H, prolyl-4-hydroxylase
- PAI1, plasminogen activator inhibitor 1
- PCA, principal component analysis
- PLOD (LH), procollagen-lysine,2-oxoglutarate 5-dioxygenases (lysyl hydroxylases)
- PTM, post-translational modification
- Prolyl hydroxylation
- Pulmonary fibrosis
- SEMA7A, semaphorin 7a
- TGF-β, transforming growth factor β
- TGM2, transglutaminase 1
- Transforming growth factor-β
- VCAN, versican
- Xaa, Xaa position in the Gly-Xaa-Yaa repeat in triple-helical collagen
- Yaa, Yaa position in the Gly-Xaa-Yaa repeat in triple-helical collagen
- α-SMA, α-smooth muscle actin
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25
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Troilo D, Smith EL, Nickla DL, Ashby R, Tkatchenko AV, Ostrin LA, Gawne TJ, Pardue MT, Summers JA, Kee CS, Schroedl F, Wahl S, Jones L. IMI - Report on Experimental Models of Emmetropization and Myopia. Invest Ophthalmol Vis Sci 2019; 60:M31-M88. [PMID: 30817827 PMCID: PMC6738517 DOI: 10.1167/iovs.18-25967] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 10/20/2018] [Indexed: 11/24/2022] Open
Abstract
The results of many studies in a variety of species have significantly advanced our understanding of the role of visual experience and the mechanisms of postnatal eye growth, and the development of myopia. This paper surveys and reviews the major contributions that experimental studies using animal models have made to our thinking about emmetropization and development of myopia. These studies established important concepts informing our knowledge of the visual regulation of eye growth and refractive development and have transformed treatment strategies for myopia. Several major findings have come from studies of experimental animal models. These include the eye's ability to detect the sign of retinal defocus and undergo compensatory growth, the local retinal control of eye growth, regulatory changes in choroidal thickness, and the identification of components in the biochemistry of eye growth leading to the characterization of signal cascades regulating eye growth and refractive state. Several of these findings provided the proofs of concepts that form the scientific basis of new and effective clinical treatments for controlling myopia progression in humans. Experimental animal models continue to provide new insights into the cellular and molecular mechanisms of eye growth control, including the identification of potential new targets for drug development and future treatments needed to stem the increasing prevalence of myopia and the vision-threatening conditions associated with this disease.
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Affiliation(s)
- David Troilo
- SUNY College of Optometry, State University of New York, New York, New York, United States
| | - Earl L. Smith
- College of Optometry, University of Houston, Houston, Texas, United States
| | - Debora L. Nickla
- Biomedical Sciences and Disease, New England College of Optometry, Boston, Massachusetts, United States
| | - Regan Ashby
- Health Research Institute, University of Canberra, Canberra, Australia
| | - Andrei V. Tkatchenko
- Department of Ophthalmology, Department of Pathology and Cell Biology, Columbia University, New York, New York, United States
| | - Lisa A. Ostrin
- College of Optometry, University of Houston, Houston, Texas, United States
| | - Timothy J. Gawne
- School of Optometry, University of Alabama Birmingham, Birmingham, Alabama, United States
| | - Machelle T. Pardue
- Biomedical Engineering, Georgia Tech College of Engineering, Atlanta, Georgia, United States31
| | - Jody A. Summers
- College of Medicine, University of Oklahoma, Oklahoma City, Oklahoma, United States
| | - Chea-su Kee
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong, SAR, China
| | - Falk Schroedl
- Departments of Ophthalmology and Anatomy, Paracelsus Medical University, Salzburg, Austria
| | - Siegfried Wahl
- Institute for Ophthalmic Research, University of Tuebingen, Zeiss Vision Science Laboratory, Tuebingen, Germany
| | - Lyndon Jones
- CORE, School of Optometry and Vision Science, University of Waterloo, Ontario, Canada
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26
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Affiliation(s)
- Arif O Khan
- a Eye Institute , Cleveland Clinic Abu Dhabi , Abu Dhabi , United Arab Emirates.,b Department of Ophthalmology , Cleveland Clinic Lerner College of Medicine of Case Western University , Cleveland , OH , USA
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27
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Wormser O, Gradstein L, Kadar E, Yogev Y, Perez Y, Mashkit E, Elbedour K, Drabkin M, Markus B, Kadir R, Halperin D, Khalaila S, Levy J, Lifshitz T, Manor E, Birk OS. Combined CNV, haplotyping and whole exome sequencing enable identification of two distinct novel EYS mutations causing RP in a single inbred tribe. Am J Med Genet A 2018; 176:2695-2703. [PMID: 30513137 DOI: 10.1002/ajmg.a.40668] [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: 06/20/2018] [Revised: 09/17/2018] [Accepted: 09/28/2018] [Indexed: 11/10/2022]
Abstract
Whole exome sequencing (WES) has become routine in clinical practice, especially in studies of recessive hereditary diseases in inbred consanguineous families, where homozygosity of a founder mutation is assumed. Multiple members of two consanguineous families of a single Bedouin tribe were diagnosed with apparently autosomal recessive/pseudo-dominant retinitis pigmentosa (RP). Affected individuals exhibited severe visual impairment with nyctalopia, marked constriction of visual fields, markedly reduced and delayed responses on electro-retinography (ERG) and eventual loss of central vision. Combined copy-number variant (CNV) analysis, haplotype reconstruction and WES of the kindred identified two distinct novel mutations in EYS (RP25): a p.(W1817*) nonsense mutation (identified through WES) and a large deletion encompassing 9 of the 43 exons, that was missed by WES and was identified through microarray CNV analysis. Segregation analysis of both mutations demonstrated that all affected individuals were either homozygous for one of the mutations, or compound heterozygous for both. The two mutations are predicted to cause loss of function of the encoded protein and were not present in screening of 200 ethnically-matched controls. Our findings of two distinct mutations in the same gene in a single inbred kindred, identified only through combined WES and microarray CNV analysis, highlight the limitations of either CNV or WES alone, as the heterozygous deletion had normal WES read-depth values. Moreover, they demonstrate pitfalls in homozygosity mapping for disease-causing variant identification in inbred communities.
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Affiliation(s)
- Ohad Wormser
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Libe Gradstein
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Einat Kadar
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yonatan Perez
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Elena Mashkit
- Genetics Institute, Soroka Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Khalil Elbedour
- Genetics Institute, Soroka Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Max Drabkin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Barak Markus
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Kadir
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Daniel Halperin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Soltan Khalaila
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jaime Levy
- Department of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Tova Lifshitz
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Esther Manor
- Genetics Institute, Soroka Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,Genetics Institute, Soroka Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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28
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Liu Y, Lusk CM, Cho MH, Silverman EK, Qiao D, Zhang R, Scheurer ME, Kheradmand F, Wheeler DA, Tsavachidis S, Armstrong G, Zhu D, Wistuba II, Chow CWB, Behrens C, Pikielny CW, Neslund-Dudas C, Pinney SM, Anderson M, Kupert E, Bailey-Wilson J, Gaba C, Mandal D, You M, de Andrade M, Yang P, Field JK, Liloglou T, Davies M, Lissowska J, Swiatkowska B, Zaridze D, Mukeriya A, Janout V, Holcatova I, Mates D, Milosavljevic S, Scelo G, Brennan P, McKay J, Liu G, Hung RJ, Christiani DC, Schwartz AG, Amos CI, Spitz MR. Rare Variants in Known Susceptibility Loci and Their Contribution to Risk of Lung Cancer. J Thorac Oncol 2018; 13:1483-1495. [PMID: 29981437 PMCID: PMC6366341 DOI: 10.1016/j.jtho.2018.06.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/06/2018] [Accepted: 06/17/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Genome-wide association studies are widely used to map genomic regions contributing to lung cancer (LC) susceptibility, but they typically do not identify the precise disease-causing genes/variants. To unveil the inherited genetic variants that cause LC, we performed focused exome-sequencing analyses on genes located in 121 genome-wide association study-identified loci previously implicated in the risk of LC, chronic obstructive pulmonary disease, pulmonary function level, and smoking behavior. METHODS Germline DNA from 260 case patients with LC and 318 controls were sequenced by utilizing VCRome 2.1 exome capture. Filtering was based on enrichment of rare and potential deleterious variants in cases (risk alleles) or controls (protective alleles). Allelic association analyses of single-variant and gene-based burden tests of multiple variants were performed. Promising candidates were tested in two independent validation studies with a total of 1773 case patients and 1123 controls. RESULTS We identified 48 rare variants with deleterious effects in the discovery analysis and validated 12 of the 43 candidates that were covered in the validation platforms. The top validated candidates included one well-established truncating variant, namely, BRCA2, DNA repair associated gene (BRCA2) K3326X (OR = 2.36, 95% confidence interval [CI]: 1.38-3.99), and three newly identified variations, namely, lymphotoxin beta gene (LTB) p.Leu87Phe (OR = 7.52, 95% CI: 1.01-16.56), prolyl 3-hydroxylase 2 gene (P3H2) p.Gln185His (OR = 5.39, 95% CI: 0.75-15.43), and dishevelled associated activator of morphogenesis 2 gene (DAAM2) p.Asp762Gly (OR = 0.25, 95% CI: 0.10-0.79). Burden tests revealed strong associations between zinc finger protein 93 gene (ZNF93), DAAM2, bromodomain containing 9 gene (BRD9), and the gene LTB and LC susceptibility. CONCLUSION Our results extend the catalogue of regions associated with LC and highlight the importance of germline rare coding variants in LC susceptibility.
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Affiliation(s)
- Yanhong Liu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine M. Lusk
- Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ruyang Zhang
- Harvard University School of Public Health, Boston, MA 02115, USA
| | - Michael E. Scheurer
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Farrah Kheradmand
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Michael E. DeBakey Veterans Affairs Medical Center; Houston, TX 77030, USA
| | - David A. Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequence Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Spiridon Tsavachidis
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Georgina Armstrong
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dakai Zhu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chi-Wan B. Chow
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Claudio W. Pikielny
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03755, USA
| | | | - Susan M. Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Marshall Anderson
- University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Elena Kupert
- University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | | | - Colette Gaba
- The University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Ming You
- Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Ping Yang
- Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - John K. Field
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Triantafillos Liloglou
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Michael Davies
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Jolanta Lissowska
- The M. Sklodowska-Curie Institute of Oncology Center, Warsaw 02781, Poland
| | - Beata Swiatkowska
- Nofer Institute of Occupational Medicine, Department of Environmental Epidemiology, Lodz 91348, Poland
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow 115478, Russian Federation
| | - Anush Mukeriya
- Russian N.N. Blokhin Cancer Research Centre, Moscow 115478, Russian Federation
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc 77515, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Charles University, 2nd Faculty of Medicine, Prague 12800, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest 050463, Romania
| | - Sasa Milosavljevic
- International Organization for Cancer Prevention and Research (IOCPR), Belgrade, Serbia
| | | | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Geoffrey Liu
- Princess Margaret Cancer Center, Toronto, ON, M5G 2M9, Canada
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5 Canada
| | | | | | - Ann G. Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Christopher I Amos
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret R. Spitz
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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Wan L, Deng B, Wu Z, Chen X. Exome sequencing study of 20 patients with high myopia. PeerJ 2018; 6:e5552. [PMID: 30245926 PMCID: PMC6148412 DOI: 10.7717/peerj.5552] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 08/07/2018] [Indexed: 02/05/2023] Open
Abstract
Background High myopia is a common ocular disease worldwide. To expand our current understanding of the genetic basis of high myopia, we carried out a whole exome sequencing (WES) study to identify potential causal gene mutations. Methods A total of 20 individuals with high myopia were exome sequenced. A novel filtering strategy combining phenotypes and functional impact of variants was applied to identify candidate genes by multi-step bioinformatics analyses. Network and enrichment analysis were employed to examine the biological pathways involved in the candidate genes. Results In 16 out of 20 patients, we identified 20 potential pathogenic gene variants for high myopia. A total of 18 variants were located in myopia-associated chromosomal regions. In addition to the novel mutations found in five known myopia genes (ADAMTS18, CSMD1, P3H2, RPGR, and SLC39A5), we also identified pathogenic variants in seven ocular disease genes (ABCA4, CEP290, HSPG2, PCDH15, SAG, SEMA4A, and USH2A) as novel candidate genes. The biological processes associated with vision were significantly enriched in our candidate genes, including visual perception, photoreceptor cell maintenance, retinoid metabolic process, and cellular response to zinc ion starvation. Discussion Systematic mutation analysis of candidate genes was performed using WES data, functional interaction (FI) network, Gene Ontology and pathway enrichment. FI network analysis revealed important network modules and regulator linker genes (EP300, CTNNB1) potentially related to high myopia development. Our study expanded the list of candidate genes associated with high myopia, which increased the genetic screening performance and provided implications for future studies on the molecular genetics of myopia.
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Affiliation(s)
- Ling Wan
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Ophthalmology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital and Affiliated Hospital of University of Electronic Science and Technology, Chengdu, Sichuan, China
| | - Boling Deng
- Department of Ophthalmology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital and Affiliated Hospital of University of Electronic Science and Technology, Chengdu, Sichuan, China
| | - Zhengzheng Wu
- Department of Ophthalmology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital and Affiliated Hospital of University of Electronic Science and Technology, Chengdu, Sichuan, China
| | - Xiaoming Chen
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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30
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Liu KY, Sengillo JD, Velez G, Jauregui R, Sakai LY, Maumenee IH, Bassuk AG, Mahajan VB, Tsang SH. Missense mutation in SLIT2 associated with congenital myopia, anisometropia, connective tissue abnormalities, and obesity. Orphanet J Rare Dis 2018; 13:138. [PMID: 30111362 PMCID: PMC6094464 DOI: 10.1186/s13023-018-0885-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 07/31/2018] [Indexed: 12/26/2022] Open
Abstract
Background SLIT2 is a protein ligand for the Roundabout (ROBO) receptor and was found to play a major role in repulsive midline axon guidance in central nervous system development. Based on studies utilizing knockout models, it has been postulated that SLIT2 is important for preventing inappropriate axonal routing during mammalian optic chiasm development. Methods Case report. Results Here, we report a case of congenital myopia, anisometropia, and obesity in a patient with a SLIT2 point mutation. Examination of the patient’s skin biopsy revealed abnormalities in elastin and collagen fibrils that suggest an underlying connective tissue disorder. Structural modeling placed the novel mutation (p.D1407G) in the EGF-like domain 8 and was predicted to affect interactions with SLIT2 binding partners. Conclusions To the authors’ knowledge, this is the first report of a SLIT2 variant in the context of these ocular findings. Electronic supplementary material The online version of this article (10.1186/s13023-018-0885-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine Y Liu
- Stony Brook University School of Medicine, Stony Brook, NY, USA
| | - Jesse D Sengillo
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Department of Medicine, Reading Hospital, West Reading, PA, USA
| | - Gabriel Velez
- Omics Laboratory, Stanford University, Palo Alto, CA, USA.,Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA.,Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Ruben Jauregui
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Lynn Y Sakai
- Departments of Molecular and Medical Genetics and Biochemistry and Molecular Biology, Oregon Health and Science University and Shriners Hospital for Children, Portland, USA
| | - Irene H Maumenee
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | | | - Vinit B Mahajan
- Omics Laboratory, Stanford University, Palo Alto, CA, USA.,Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA.,Palo Alto Veterans Administration, Palo Alto, CA, USA
| | - Stephen H Tsang
- Jonas Children's Vision Care, and Bernard and Shirlee Brown Glaucoma Laboratory, New York, USA. .,Department of Ophthalmology, Columbia University, New York, NY, USA. .,Department of Pathology and Cell Biology, Stem Cell Initiative (CSCI), Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY, USA. .,Harkness Eye Institute, Columbia University Medical Center, 635 West 165th Street, Box 212, New York, NY, 10032, USA.
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31
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32
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Ma F, Sun R, Tremmel D, Sackett S, Odorico J, Li L. Large-Scale Differentiation and Site Specific Discrimination of Hydroxyproline Isomers by Electron Transfer/Higher-Energy Collision Dissociation (EThcD) Mass Spectrometry. Anal Chem 2018; 90:5857-5864. [PMID: 29624053 PMCID: PMC6481173 DOI: 10.1021/acs.analchem.8b00413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
3- and 4-Hydroxyprolines (HyP) are regioisomers that play different roles in various species and organs. Despite their distinct functions inside cells, they are generally considered indistinguishable using mass spectrometry due to their identical masses. Here, we demonstrate, for the first time, that characteristic w ions can be produced by electron-transfer/higher energy collision dissociation (EThcD) dual fragmentation technique to confidently discriminate 3-HyP/4-HyP isomers. An integrated and high throughput strategy was developed which combined online LC separation with EThcD for large-scale differentiation of 3-HyP/4-HyP in complex samples. An automated algorithm was developed for charge state dependent characterization of 3-HyP/4-HyP isomers. Using this combined discrimination approach, we identified 108 3-HyP sites and 530 4-HyP sites from decellularized pancreas, allowing more than 5-fold increase of both 3-HyP and 4-HyP identifications compared to previous reports. This approach outperformed ETD and HCD in the analysis of HyP-containing peptides with unique capacity to generate w ions for HyP discrimination, improved fragmentation of precursor ions, as well as unambiguous localization of modifications. A high content of 3-HyP was observed in the C-terminal (GPP)n domain of human CO1A1, which was previously only identified in vertebrate fibrillar collagens from tendon. Unexpectedly, some unusual HyP sites at Xaa position in Gly-HyP-Ala, Gly-HyP-Val, Gly-HyP-Gln, Gly-HyP-Ser, and Gly-HyP-Arg were also confirmed to be 3-hydroxylated, whose functions and enzymes are yet to be discovered. Overall, this novel discrimination strategy can be readily implemented into de novo sequencing or other proteomic search engines.
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Affiliation(s)
- Fengfei Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Ruixiang Sun
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Daniel Tremmel
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Sara Sackett
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Jon Odorico
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
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33
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Napolitano F, Di Iorio V, Testa F, Tirozzi A, Reccia MG, Lombardi L, Farina O, Simonelli F, Gianfrancesco F, Di Iorio G, Melone MAB, Esposito T, Sampaolo S. Autosomal-dominant myopia associated to a novel P4HA2 missense variant and defective collagen hydroxylation. Clin Genet 2018; 93:982-991. [PMID: 29364500 DOI: 10.1111/cge.13217] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/10/2018] [Accepted: 01/18/2018] [Indexed: 12/30/2022]
Abstract
We recently described a complex multisystem syndrome in which mild-moderate myopia segregated as an independent trait. A plethora of genes has been related to sporadic and familial myopia. More recently, in Chinese patients severe myopia (MYP25, OMIM:617238) has been linked to mutations in P4HA2 gene. Seven family members complaining of reduced distance vision especially at dusk underwent complete ophthalmological examination. Whole-exome sequencing was performed to identify the gene responsible for myopia in the pedigree. Moderate myopia was diagnosed in the family which was associated to the novel missense variant c.1147A > G p.(Lys383Glu) in the prolyl 4-hydroxylase,alpha-polypeptide 2 (P4HA2) gene, which catalyzes the formation of 4-hydroxyproline residues in the collagen strands. In vitro studies demonstrated P4HA2 mRNA and protein reduced expression level as well as decreased collagen hydroxylation and deposition in mutated fibroblast primary cultures compared to healthy cell lines. This study suggests that P4HA2 mutations may lead to myopic axial elongation of eyeball as a consequence of quantitative and structural alterations of collagen. This is the first confirmatory study which associates a novel dominant missense variant in P4HA2 with myopia in Caucasian patients. Further studies in larger cohorts are advisable to fully clarify genotype-phenotype correlations.
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Affiliation(s)
- F Napolitano
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council, Naples, Italy.,Neurology Clinic II, Department of Medical Sciences, Surgery, Neurology, Metabolic Diseases and Geriatrics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - V Di Iorio
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - F Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - A Tirozzi
- IRCCS INM Neuromed, Pozzilli, IS, Italy
| | | | - L Lombardi
- Neurology Clinic II, Department of Medical Sciences, Surgery, Neurology, Metabolic Diseases and Geriatrics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - O Farina
- Neurology Clinic II, Department of Medical Sciences, Surgery, Neurology, Metabolic Diseases and Geriatrics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - F Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - F Gianfrancesco
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council, Naples, Italy
| | - G Di Iorio
- Neurology Clinic II, Department of Medical Sciences, Surgery, Neurology, Metabolic Diseases and Geriatrics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - M A B Melone
- Neurology Clinic II, Department of Medical Sciences, Surgery, Neurology, Metabolic Diseases and Geriatrics, University of Campania Luigi Vanvitelli, Naples, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania
| | - T Esposito
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council, Naples, Italy.,IRCCS INM Neuromed, Pozzilli, IS, Italy
| | - S Sampaolo
- Neurology Clinic II, Department of Medical Sciences, Surgery, Neurology, Metabolic Diseases and Geriatrics, University of Campania Luigi Vanvitelli, Naples, Italy
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Montgomery NT, Zientek KD, Pokidysheva EN, Bächinger HP. Post-translational modification of type IV collagen with 3-hydroxyproline affects its interactions with glycoprotein VI and nidogens 1 and 2. J Biol Chem 2018; 293:5987-5999. [PMID: 29491144 DOI: 10.1074/jbc.ra117.000406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/15/2018] [Indexed: 01/18/2023] Open
Abstract
Type IV collagen is a major component of the basement membrane and interacts with numerous other basement membrane proteins. Many of these interactions are poorly characterized. Type IV collagen is abundantly post-translationally modified with 3-hydroxyproline (3-Hyp), but 3-Hyp's biochemical role in type IV collagen's interactions with other proteins is not well established. In this work, we present binding data consistent with a major role of 3-Hyp in interactions of collagen IV with glycoprotein VI and nidogens 1 and 2. The increased binding interaction between type IV collagen without 3-Hyp and glycoprotein VI has been the subject of some controversy, which we sought to explore, whereas the lack of binding of nidogens to type IV collagen without 3-Hyp is novel. Using tandem MS, we show that the putative glycoprotein VI-binding site is 3-Hyp-modified in WT PFHR-9 type IV collagen, but not in PFHR-9 cells in which prolyl-3-hydroxylase 2 (P3H2) has been knocked out (KO). Moreover, we observed altered 3-Hyp occupancy across many other sites. Using amino acid analysis of type IV collagen from the WT and P3H2 KO cell lines, we confirm that P3H2 is the major, but not the only 3-Hyp-modifying enzyme of type IV collagen. These findings underscore the importance of post-translational modifications of type IV collagen for interactions with other proteins.
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Affiliation(s)
- Nathan T Montgomery
- From the Research Department, Shriners Hospital for Children, Portland, Oregon 97239.,the Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon 97239, and
| | - Keith D Zientek
- From the Research Department, Shriners Hospital for Children, Portland, Oregon 97239
| | - Elena N Pokidysheva
- the Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University, Nashville, Tennessee 37232
| | - Hans Peter Bächinger
- From the Research Department, Shriners Hospital for Children, Portland, Oregon 97239, .,the Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon 97239, and
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35
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Zimmerman SM, Besio R, Heard-Lipsmeyer ME, Dimori M, Castagnola P, Swain FL, Gaddy D, Diekman AB, Morello R. Expression characterization and functional implication of the collagen-modifying Leprecan proteins in mouse gonadal tissue and mature sperm. AIMS GENETICS 2018; 5:24-40. [PMID: 30417103 PMCID: PMC6221197 DOI: 10.3934/genet.2018.1.24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Leprecan protein family which includes the prolyl 3-hydroxylase enzymes (P3H1, P3H2, and P3H3), the closely related cartilage-associated protein (CRTAP), and SC65 (Synaptonemal complex 65, aka P3H4, LEPREL4), is involved in the post-translational modification of fibrillar collagens. Mutations in CRTAP, P3H1 and P3H2 cause human genetic diseases. We recently showed that SC65 forms a stable complex in the endoplasmic reticulum with P3H3 and lysyl hydroxylase 1 and that loss of this complex leads to defective collagen lysyl hydroxylation and causes low bone mass and skin fragility. Interestingly, SC65 was initially described as a synaptonemal complex-associated protein, suggesting a potential additional role in germline cells. In the present study, we describe the expression of SC65, CRTAP and other Leprecan proteins in postnatal mouse reproductive organs. We detect SC65 expression in peritubular cells of testis up to 4 weeks of age but not in cells within seminiferous tubules, while its expression is maintained in ovarian follicles until adulthood. Similar to bone and skin, SC65 and P3H3 are also tightly co-expressed in testis and ovary. Moreover, we show that CRTAP, a protein normally involved in collagen prolyl 3-hydroxylation, is highly expressed in follicles and stroma of the ovary and in testes interstitial cells at 4 weeks of age, germline cells and mature sperm. Importantly, CrtapKO mice have a mild but significant increase in morphologically abnormal mature sperm (17% increase compared to WT). These data suggest a role for the Leprecans in the post-translational modification of collagens expressed in the stroma of the reproductive organs. While we could not confirm that SC65 is part of the synaptonemal complex, the expression of CRTAP in the seminiferous tubules and in mature sperm suggest a role in the testis germ cell lineage and sperm morphogenesis.
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Affiliation(s)
- Sarah M Zimmerman
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Roberta Besio
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Melissa E Heard-Lipsmeyer
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Milena Dimori
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Frances L Swain
- Department of Orthopaedic Surgery, Center for Orthopaedic Research, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Dana Gaddy
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Alan B Diekman
- Department of Biochemistry, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Roy Morello
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Department of Orthopaedic Surgery, Center for Orthopaedic Research, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Division of Genetics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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36
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Li J, Zhang Q. Insight into the molecular genetics of myopia. Mol Vis 2017; 23:1048-1080. [PMID: 29386878 PMCID: PMC5757860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 12/29/2017] [Indexed: 11/18/2022] Open
Abstract
Myopia is the most common cause of visual impairment worldwide. Genetic and environmental factors contribute to the development of myopia. Studies on the molecular genetics of myopia are well established and have implicated the important role of genetic factors. With linkage analysis, association studies, sequencing analysis, and experimental myopia studies, many of the loci and genes associated with myopia have been identified. Thus far, there has been no systemic review of the loci and genes related to non-syndromic and syndromic myopia based on the different approaches. Such a systemic review of the molecular genetics of myopia will provide clues to identify additional plausible genes for myopia and help us to understand the molecular mechanisms underlying myopia. This paper reviews recent genetic studies on myopia, summarizes all possible reported genes and loci related to myopia, and suggests implications for future studies on the molecular genetics of myopia.
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Affiliation(s)
- Jiali Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Li Y, Chen Y, Ma Y, Nenkov M, Haase D, Petersen I. Collagen prolyl hydroxylase 3 has a tumor suppressive activity in human lung cancer. Exp Cell Res 2017; 363:121-128. [PMID: 29277505 DOI: 10.1016/j.yexcr.2017.12.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 12/18/2017] [Accepted: 12/21/2017] [Indexed: 11/27/2022]
Abstract
Collagen prolyl hydroxylases (P3H) are required for proper collagen biosynthesis. One of the family members P3H3 was downregulated in breast cancer and lymphoma due to DNA methylation. However the role of P3H3 in lung cancer has not yet been elucidated. In this study, we analyzed P3H3 expression in a panel of lung cancer cell lines and primary lung tumors. Epigenetic regulation was explored and the function of P3H3 was investigated by stable transfection and RNA interference. We found that P3H3 was downregulated in 6 out of 10 lung cancer cell lines. A heterogeneous methylation pattern of P3H3 was found in the exon region. In primary lung tumors, immunohistochemistry on tissue microarray (TMA) showed that higher expression of P3H3 was significantly associated with lower tumor N stage and grade (p = 0.035 and p = 0.026, respectively). Ectopic expression of P3H3 inhibited cell proliferation, colony formation, migration as well as invasion, and induced apoptosis together with cell cycle arrest in the G2/M phase. Knockdown of P3H3 led to increased migratory and invasive potential. These Phenomena are accompanied by enhanced p21, decreased cyclin A1 levels and increased caspase 3/7 activities. Taken together, we feel that P3H3 is a novel tumor suppressor and its protein expression is inversely related to lymph node metastasis and tumor differentiation in lung cancer.
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Affiliation(s)
- Yong Li
- Institute of Pathology, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Yuan Chen
- Institute of Pathology, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Yunxia Ma
- Institute of Pathology, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Miljana Nenkov
- Institute of Pathology, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany.
| | - Daniela Haase
- Institute of Pathology, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Iver Petersen
- Institute of Pathology, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany.
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Abeshi A, Coppola P, Beccari T, Dundar M, Colombo L, Bertelli M. Genetic testing for Mendelian myopia. EUROBIOTECH JOURNAL 2017. [DOI: 10.24190/issn2564-615x/2017/s1.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Abstract
We studied the scientific literature and disease guidelines in order to summarize the clinical utility of genetic testing for Mendelian myopia (MM), a large and heterogeneous group of inherited refraction disorders. Variations in the SLC39A5, SCO2 and COL2A1 genes have an autosomal dominant transmission, whereas those in the LRPAP1, P3H2, LRP2 and SLITRK6 genes have autosomal recessive transmission. The prevalence of MM is currently unknown. Clinical diagnosis is based on clinical findings, family history, ophthalmological examination and other tests depending on complications. The genetic test is useful for confirming diagnosis, and for differential diagnosis, couple risk assessment and access to clinical trials.
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Affiliation(s)
- Andi Abeshi
- MAGI Balkans, Tirana , Albania
- MAGI’S Lab, Rovereto , Italy
| | | | - Tommaso Beccari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia , Italy
| | - Munis Dundar
- Department of Medical Genetics, Erciyes University Medical School, Kayseri , Turkey
| | - Leonardo Colombo
- Department of Ophthalmology, ASST Santi Paolo e Carlo, University of Milan, Milan , Italy
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Li J, Jiao X, Zhang Q, Hejtmancik JF. Association and interaction of myopia with SNP markers rs13382811 and rs6469937 at ZFHX1B and SNTB1 in Han Chinese and European populations. Mol Vis 2017; 23:588-604. [PMID: 28848321 PMCID: PMC5561140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/09/2017] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Previously, a genome-wide association study (GWAS) identified rs13382811 (near ZFHX1B) and rs6469937 (near SNTB1) to be associated with high myopia. The present study evaluates the association of these two single nucleotide polymorphisms (SNPs) with moderate to high myopia in two Chinese cohorts and two cohorts of European populations. METHODS Two Chinese university student cohorts, including one with 300 unrelated subjects with high myopia and 308 emmetropic controls from Guangzhou and a second with 96 unrelated individuals with moderate to high myopia and 96 emmetropic controls of Chaoshanese origin in Guangzhou, were enrolled in this study. Two SNPs, rs6469937 and rs13382811, were selected for genotyping based on their reported associations with severe myopia. The SNPs were genotyped via DNA sequencing. In addition, association analysis of both SNPs was performed using genotype data from the database of Genotypes and Phenotypes (dbGaP) involving a total of 2,423 samples in two independent cohorts of European-derived populations, as follows: Kooperative Gesundheitsforschung in der Region Augsburg (KORA) and TwinsUK. The allelic and genotypic distribution among cases and controls were analyzed using the Chi-square test. Logistic regression was used to evaluate the SNP-SNP interaction. Fisher's exact test was used for two-SNP comparisons. RESULTS In the Guangzhou cohort, SNP rs13382811 near ZFHX1B showed significant association with high myopia (pallelic = 0.0001, pgenotypic = 4.07 × 10-5), with the minor T allele showing an increased risk of high myopia (odds ratio [OR] = 1.68, 95% confidence interval [CI] = 1.28-2.20). SNP rs6469937 near SNTB1 showed nominal evidence of association (pallelic = 0.0085, pgenotypic = 0.0166), which did not withstand correction for multiple testing. No significant association was detected in the smaller Chaoshan cohort alone. The association of SNPs rs13382811 and rs6469937 remained significant when both Han Chinese cohorts were combined (pallelic = 0.0033 and 0.0016, respectively), and it was also significant under the genotypic test (pgenotypic = 0.0036 and 0.0053, respectively). When both SNPs were considered together under a recessive model, their significance increased (p = 8.37 × 10-4), as did their effect (OR = 4.09, 95%CI = 1.7-9.8). The association between either of these two SNPs alone and myopia did not replicate significantly in the combined cohorts of European descent, providing only suggestive results (pallelic = 0.0088 for rs13382811 and pallelic = 0.0319 for rs6469937). However, the effects of the combined SNPs showed significant association (p = 8.2 × 10-4; OR = 1.56, 95%CI = 1.2-2.0). While the risk for myopia increased with risk alleles from both SNPs, the increase was additive rather representing a multiplicative interaction in both populations. CONCLUSIONS Our study confirms that the two susceptibility loci ZFHX1B and SNTB1 are associated with moderate to high myopia in a Han Chinese population, as well as in a European population, when both SNPs are combined. These results confirm previous reports of their associations, extend these observations to a European population, and suggest that additional interactive and possibly population-specific genetic or environmental factors may affect their contribution to myopia.
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Affiliation(s)
- Jiali Li
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, MD,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, MD
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, MD
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Kloss BA, Tompson SW, Whisenhunt KN, Quow KL, Huang SJ, Pavelec DM, Rosenberg T, Young TL. Exome Sequence Analysis of 14 Families With High Myopia. Invest Ophthalmol Vis Sci 2017; 58:1982-1990. [PMID: 28384719 PMCID: PMC5382835 DOI: 10.1167/iovs.16-20883] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Purpose To identify causal gene mutations in 14 families with autosomal dominant (AD) high myopia using exome sequencing. Methods Select individuals from 14 large Caucasian families with high myopia were exome sequenced. Gene variants were filtered to identify potential pathogenic changes. Sanger sequencing was used to confirm variants in original DNA, and to test for disease cosegregation in additional family members. Candidate genes and chromosomal loci previously associated with myopic refractive error and its endophenotypes were comprehensively screened. Results In 14 high myopia families, we identified 73 rare and 31 novel gene variants as candidates for pathogenicity. In seven of these families, two of the novel and eight of the rare variants were within known myopia loci. A total of 104 heterozygous nonsynonymous rare variants in 104 genes were identified in 10 out of 14 probands. Each variant cosegregated with affection status. No rare variants were identified in genes known to cause myopia or in genes closest to published genome-wide association study association signals for refractive error or its endophenotypes. Conclusions Whole exome sequencing was performed to determine gene variants implicated in the pathogenesis of AD high myopia. This study provides new genes for consideration in the pathogenesis of high myopia, and may aid in the development of genetic profiling of those at greatest risk for attendant ocular morbidities of this disorder.
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Affiliation(s)
- Bethany A Kloss
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, Wisconsin, United States
| | - Stuart W Tompson
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, Wisconsin, United States
| | - Kristina N Whisenhunt
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, Wisconsin, United States
| | - Krystina L Quow
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina, United States
| | - Samuel J Huang
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, Wisconsin, United States
| | - Derek M Pavelec
- Biotechnology Center, University of Wisconsin, Madison, Wisconsin, United States
| | - Thomas Rosenberg
- The National Eye Clinic, Rigshospitalet, Kennedy Center, Glostrup, Denmark 5Institute of Clinical Medicine, University of Copenhagen, Denmark
| | - Terri L Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, Wisconsin, United States
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Hudson DM, Garibov M, Dixon DR, Popowics T, Eyre DR. Distinct post-translational features of type I collagen are conserved in mouse and human periodontal ligament. J Periodontal Res 2017. [PMID: 28631261 DOI: 10.1111/jre.12475] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND AND OBJECTIVE Specifics of the biochemical pathways that modulate collagen cross-links in the periodontal ligament (PDL) are not fully defined. Better knowledge of the collagen post-translational modifications that give PDL its distinct tissue properties is needed to understand the pathogenic mechanisms of human PDL destruction in periodontal disease. In this study, the post-translational phenotypes of human and mouse PDL type I collagen were surveyed using mass spectrometry. PDL is a highly specialized connective tissue that joins tooth cementum to alveolar bone. The main function of the PDL is to support the tooth within the alveolar bone while under occlusal load after tooth eruption. Almost half of the adult population in the USA has periodontal disease resulting from inflammatory destruction of the PDL, leading to tooth loss. Interestingly, PDL is unique from other ligamentous connective tissues as it has a high rate of turnover. Rapid turnover is believed to be an important characteristic for this specialized ligament to function within the oral-microbial environment. Like other ligaments, PDL is composed predominantly of type I collagen. Collagen synthesis is a complex process with multiple steps and numerous post-translational modifications including hydroxylation, glycosylation and cross-linking. The chemistry, placement and quantity of intermolecular cross-links are believed to be important regulators of tissue-specific structural and mechanical properties of collagens. MATERIAL AND METHODS Type I collagen was isolated from several mouse and human tissues, including PDL, and analyzed by mass spectrometry for post-translational variances. RESULTS The collagen telopeptide cross-linking lysines of PDL were found to be partially hydroxylated in human and mouse, as well as in other types of ligament. However, the degree of hydroxylation and glycosylation at the helical Lys87 cross-linking residue varied across species and between ligaments. These data suggest that different types of ligament collagen, notably PDL, appear to have evolved distinctive lysine/hydroxylysine cross-linking variations. Another distinguishing feature of PDL collagen is that, unlike other ligaments, it lacks any of the known prolyl 3-hydroxylase 2-catalyzed 3-hydroxyproline site modifications that characterize tendon and ligament collagens. This gives PDL a novel modification profile, with hybrid features of both ligament and skin collagens. CONCLUSION This distinctive post-translational phenotype may be relevant for understanding why some individuals are at risk of rapid PDL destruction in periodontal disease and warrants further investigation. In addition, developing a murine model for studying PDL collagen may be useful for exploring potential clinical strategies for promoting PDL regeneration.
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Affiliation(s)
- D M Hudson
- Department of Orthopaedics, University of Washington, Seattle, WA, USA
| | - M Garibov
- Department of Periodontics, University of Washington, Seattle, WA, USA
| | - D R Dixon
- Department of Periodontics, University of Washington, Seattle, WA, USA
| | - T Popowics
- Department of Oral Health Sciences, University of Washington, Seattle, WA, USA
| | - D R Eyre
- Department of Orthopaedics, University of Washington, Seattle, WA, USA
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Mutational screening of SLC39A5, LEPREL1 and LRPAP1 in a cohort of 187 high myopia patients. Sci Rep 2017; 7:1120. [PMID: 28442722 PMCID: PMC5430800 DOI: 10.1038/s41598-017-01285-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/24/2017] [Indexed: 12/13/2022] Open
Abstract
High myopia (HM) is a leading cause of mid-way blindness with a high heritability in East Asia. Although only a few disease genes have been reported, a small proportion of patients could be identified with genetic predispositions. In order to expand the mutation spectrum of the causative genes in Chinese adult population, we investigated three genes, SLC39A5, LEPREL1 and LRPAP1, in a cohort of 187 independent Chinese patients with high myopia. Sanger sequencing was used to find possible pathogenic mutations, which were further screened in normal controls. After a pipeline of database and predictive assessments filtering, we, thereby, identified totally seven heterozygous mutations in the three genes. Among them, three novel missense mutations, c.860C > T, p.Pro287Leu and c.956G > C, p.Arg319Thr in SLC39A5, c.1982A > G, p.Lys661Arg in LEPREL1, were identified as potentially causative mutations. Additionally, the two heterozygous mutations (c.1582G > A, p.Ala528Thr; c.1982A > G, p.Lys661Arg) in one patient in LEPREL1 gene were reported in this study. Our findings will not only augment the mutation spectrum of these three genes, but also provide insights of the contribution of these genes to adult high myopia in Chinese. However, further studies are still needed to address the pathogenicity of each of the mutations reported in this study.
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Trio-based exome sequencing arrests de novo mutations in early-onset high myopia. Proc Natl Acad Sci U S A 2017; 114:4219-4224. [PMID: 28373534 DOI: 10.1073/pnas.1615970114] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The etiology of the highly myopic condition has been unclear for decades. We investigated the genetic contributions to early-onset high myopia (EOHM), which is defined as having a refraction of less than or equal to -6 diopters before the age of 6, when children are less likely to be exposed to high educational pressures. Trios (two nonmyopic parents and one child) were examined to uncover pathogenic mutations using whole-exome sequencing. We identified parent-transmitted biallelic mutations or de novo mutations in as-yet-unknown or reported genes in 16 probands. Interestingly, an increased rate of de novo mutations was identified in the EOHM patients. Among the newly identified candidate genes, a BSG mutation was identified in one EOHM proband. Expanded screening of 1,040 patients found an additional four mutations in the same gene. Then, we generated Bsg mutant mice to further elucidate the functional impact of this gene and observed typical myopic phenotypes, including an elongated axial length. Using a trio-based exonic screening study in EOHM, we deciphered a prominent role for de novo mutations in EOHM patients without myopic parents. The discovery of a disease gene, BSG, provides insights into myopic development and its etiology, which expands our current understanding of high myopia and might be useful for future treatment and prevention.
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Gradstein L, Hansen RM, Cox GF, Altschwager P, Fulton AB. Progressive retinal degeneration in a girl with Knobloch syndrome who presented with signs of ocular albinism. Doc Ophthalmol 2017; 134:135-140. [DOI: 10.1007/s10633-017-9574-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/16/2017] [Indexed: 10/20/2022]
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Hudson DM, Weis M, Rai J, Joeng KS, Dimori M, Lee BH, Morello R, Eyre DR. P3h3-null and Sc65-null Mice Phenocopy the Collagen Lysine Under-hydroxylation and Cross-linking Abnormality of Ehlers-Danlos Syndrome Type VIA. J Biol Chem 2017; 292:3877-3887. [PMID: 28115524 DOI: 10.1074/jbc.m116.762245] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/18/2017] [Indexed: 11/06/2022] Open
Abstract
Tandem mass spectrometry was applied to tissues from targeted mutant mouse models to explore the collagen substrate specificities of individual members of the prolyl 3-hydroxylase (P3H) gene family. Previous studies revealed that P3h1 preferentially 3-hydroxylates proline at a single site in collagen type I chains, whereas P3h2 is responsible for 3-hydroxylating multiple proline sites in collagen types I, II, IV, and V. In screening for collagen substrate sites for the remaining members of the vertebrate P3H family, P3h3 and Sc65 knock-out mice revealed a common lysine under-hydroxylation effect at helical domain cross-linking sites in skin, bone, tendon, aorta, and cornea. No effect on prolyl 3-hydroxylation was evident on screening the spectrum of known 3-hydroxyproline sites from all major tissue collagen types. However, collagen type I extracted from both Sc65-/- and P3h3-/- skin revealed the same abnormal chain pattern on SDS-PAGE with an overabundance of a γ112 cross-linked trimer. The latter proved to be from native molecules that had intramolecular aldol cross-links at each end. The lysine under-hydroxylation was shown to alter the divalent aldimine cross-link chemistry of mutant skin collagen. Furthermore, the ratio of mature HP/LP cross-links in bone of both P3h3-/- and Sc65-/- mice was reversed compared with wild type, consistent with the level of lysine under-hydroxylation seen in individual chains at cross-linking sites. The effect on cross-linking lysines was quantitatively very similar to that previously observed in EDS VIA human and Plod1-/- mouse tissues, suggesting that P3H3 and/or SC65 mutations may cause as yet undefined EDS variants.
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Affiliation(s)
- David M Hudson
- From the Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington 98195,
| | - MaryAnn Weis
- From the Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington 98195
| | - Jyoti Rai
- From the Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington 98195
| | - Kyu Sang Joeng
- the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, and
| | - Milena Dimori
- the Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Brendan H Lee
- the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, and
| | - Roy Morello
- the Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - David R Eyre
- From the Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington 98195
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Jiang B, Chen Y, Xu B, Hong N, Liu R, Qi M, Shen L. Identification of a novel missense mutation of MIP in a Chinese family with congenital cataracts by target region capture sequencing. Sci Rep 2017; 7:40129. [PMID: 28059152 PMCID: PMC5216388 DOI: 10.1038/srep40129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 12/02/2016] [Indexed: 11/09/2022] Open
Abstract
Congenital cataract is both clinically diverse and genetically heterogeneous. To investigate the underlying genetic defect in three-generations of a Chinese family with autosomal dominant congenital cataracts, we recruited family members who underwent comprehensive ophthalmic examinations. A heterozygous missense mutation c.634G > C (p.G212R) substitution was identified in the MIP gene through target region capture sequencing. The prediction results of PolyPhen-2 and SIFT indicated that this mutation was likely to damage the structure and function of MIP. Confocal microscopy images showed that the intensity of the green fluorescent signal revealed much weaker signal from the mutant compared to the wild-type MIP. The expressed G212R-MIP was diminished and almost exclusively cytoplasmic in the HeLa cells; whereas the WT-MIP was stable dispersed throughout the cytoplasm, and it appeared to be in the membrane structure. Western blot analysis indicated that the protein expression level of the mutant form of MIP was remarkably reduced compared with that of the wild type, however, the mRNA levels of the wild-type and mutant cells were comparable. In conclusion, our study presented genetic and functional evidence for a novel MIP mutation of G212R, which leads to congenital progressive cortical punctate with or without Y suture.
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Affiliation(s)
- Bo Jiang
- Department of Ophthalmology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanhua Chen
- BGI-Shenzhen, Shenzhen, China.,School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China.,Casey Eye Institute Molecular Diagnostic Laboratory, Portland, Oregon, USA
| | - Baisheng Xu
- Department of Ophthalmology, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Nan Hong
- Department of Ophthalmology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Rongrong Liu
- Division of Hematology-oncology, Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Ming Qi
- Department of Cell Biology and Medical Genetics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology and Laboratory of Medicine, University of Rochester Medical Centre, Rochester, New York, USA
| | - Liping Shen
- Department of Ophthalmology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Gjaltema RAF, Bank RA. Molecular insights into prolyl and lysyl hydroxylation of fibrillar collagens in health and disease. Crit Rev Biochem Mol Biol 2016; 52:74-95. [PMID: 28006962 DOI: 10.1080/10409238.2016.1269716] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Collagen is a macromolecule that has versatile roles in physiology, ranging from structural support to mediating cell signaling. Formation of mature collagen fibrils out of procollagen α-chains requires a variety of enzymes and chaperones in a complex process spanning both intracellular and extracellular post-translational modifications. These processes include modifications of amino acids, folding of procollagen α-chains into a triple-helical configuration and subsequent stabilization, facilitation of transportation out of the cell, cleavage of propeptides, aggregation, cross-link formation, and finally the formation of mature fibrils. Disruption of any of the proteins involved in these biosynthesis steps potentially result in a variety of connective tissue diseases because of a destabilized extracellular matrix. In this review, we give a revised overview of the enzymes and chaperones currently known to be relevant to the conversion of lysine and proline into hydroxyproline and hydroxylysine, respectively, and the O-glycosylation of hydroxylysine and give insights into the consequences when these steps are disrupted.
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Affiliation(s)
- Rutger A F Gjaltema
- a MATRIX Research Group, Department of Pathology and Medical Biology , University Medical Center Groningen, University of Groningen , Groningen , the Netherlands
| | - Ruud A Bank
- a MATRIX Research Group, Department of Pathology and Medical Biology , University Medical Center Groningen, University of Groningen , Groningen , the Netherlands
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X-linked heterozygous mutations in ARR3 cause female-limited early onset high myopia. Mol Vis 2016; 22:1257-1266. [PMID: 27829781 PMCID: PMC5082638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/24/2016] [Indexed: 11/01/2022] Open
Abstract
PURPOSE To identify genetic mutations in three families with early onset high myopia (eoHM) limited to female members. METHODS Genomic DNA was collected from participating members of families XF1, XF2, and XF3. Genome-wide linkage scans were performed on the largest family (XF1). Whole exome sequencing was performed on seven samples, including five samples (four affected and one unaffected) from family XF1, as well as the two probands from family XF2 and XF3. Variants were analyzed with multistep bioinformatics analyses. Sanger-dideoxy sequencing was used to verify candidate variations in families and controls. RESULTS The genome-wide linkage scans performed on family XF1 detected a candidate locus on chromosome Xp11.1-Xq13.3 with a maximum logarithm of the odds (LOD) score of 2.48 and 3.01 for markers DXS991 and DXS986, respectively. Parallel whole exome sequencing identified a novel c.893C>A (p.Ala298Asp) mutation in ARR3 located on Xq13.1 in family XF1, which was shared by all four affected individuals but not the unaffected individual. Two other novel mutations in ARR3, c.298C>T (p.Arg100*) and c.239T>C (p.Leu80Pro), were detected in families XF2 and XF3, respectively. These mutations were predicted to be damaging and were not present in the normal controls and existing databases. All three mutations cosegregated with eoHM in each of the three families, in which all heterozygous female members are affected whereas all hemizygous male family members are not affected. Transmission of the mutations and eoHM in the three families demonstrates an unusual pattern of X-linked female-limited inheritance. CONCLUSIONS These data suggest that heterozygous mutations in ARR3 might be responsible for X-linked female-limited eoHM in the three families, a pattern contrary to the standard X-linked recessive trait. To our knowledge, eoHM is the first human disease associated with mutations in ARR3 and the second X-linked female-limited disease identified thus far. Identification of ARR3 associated with X-linked female-limited trait provides not only additional evidence of this unusual hereditary pattern but also an additional model for investigating the molecular mechanism responsible for female-limited phenotypes.
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Gradstein L, Zolotushko J, Sergeev YV, Lavy I, Narkis G, Perez Y, Guigui S, Sharon D, Banin E, Walter E, Lifshitz T, Birk OS. Novel GUCY2D mutation causes phenotypic variability of Leber congenital amaurosis in a large kindred. BMC MEDICAL GENETICS 2016; 17:52. [PMID: 27475985 PMCID: PMC4967317 DOI: 10.1186/s12881-016-0314-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/21/2016] [Indexed: 11/25/2022]
Abstract
Background Leber congenital amaurosis (LCA) is a severe retinal degenerative disease that manifests as blindness or poor vision in infancy. The purpose of this study was to clinically characterize and identify the cause of disease in a large inbred Bedouin Israeli tribe with LCA. Methods Thirty individuals of a single kindred, including eight affected with LCA, were recruited for this study. Patients’ clinical data and electroretinography (ERG) findings were collected. Molecular analysis included homozygosity mapping with polymorphic markers and Sanger sequencing of candidate genes. Results Of the eight affected individuals of the kindred, nystagmus was documented in five subjects and keratoconus in three. Cataract was found in 5 of 16 eyes. Photopic and scotopic ERG performed in 5 patients were extinguished. All affected subjects were nearly blind, their visual acuity ranged between finger counting and uncertain light perception. Assuming autosomal recessive heredity of a founder mutation, studies using polymorphic markers excluded homozygosity of affected individuals at the genomic loci of all previously known genes associated with LCA, except GUCY2D. Sequencing of GUCY2D identified a novel missense mutation (c.2129C>T; p.Ala710Val) resulting in substitution of alanine by valine at position 710 within the protein kinase domain of the retina-specific enzyme guanylate cyclase 1 (GC1) encoded by GUCY2D. Molecular modeling implied that the mutation changes the conformation of the regulatory segment within the kinase styk-domain of GC1 and causes loss of its helical structure, likely inhibiting phosphorylation of threonine residue within this segment, which is needed to activate the catalytic domain of the protein. Conclusions This is the first documentation of the p.Ala710Val mutation in GC1 and the second ever described mutation in its protein kinase domain. Our findings enlarge the scope of genetic variability of LCA, highlight the phenotypic heterogeneity found amongst individuals harboring an identical LCA mutation, and possibly provide hope for gene therapy in patients with this congenital blinding disease. As the Bedouin kindred studied originates from Saudi Arabia, the mutation found might be an ancient founder mutation in that large community.
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Affiliation(s)
- Libe Gradstein
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, 84101, Israel
| | - Jenny Zolotushko
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Yuri V Sergeev
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Itay Lavy
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, 84101, Israel
| | - Ginat Narkis
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Yonatan Perez
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Sarah Guigui
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, 84101, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eyal Walter
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, 84101, Israel
| | - Tova Lifshitz
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, 84101, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, 84105, Israel. .,Genetics Institute, Soroka Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84101, Israel.
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50
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Abstract
Myopia is a major cause of visual impairment worldwide. In particular, high myopia is associated with serious blinding complications, including retinal detachment, chorioretinal degeneration, and choroidal neovascularization. Myopia is multifactorial in etiology, resulting from the interaction of environmental and genetic risk factors. During the past 2 decades, a large number of gene loci and variants have been identified for myopia. There are more than 20 myopia-associated loci spanning all chromosomes. Earlier findings were obtained mainly from family linkage analyses and candidate gene studies, and more recent results are principally from genome-wide association studies and exome sequencing. Some genetic associations have been successfully validated and replicated in populations of different geographic localities and ethnicities, but some have not. Compared with Whites, Asian populations-in particular Japanese, Korean, and Chinese-have a much higher prevalence of myopia, especially high myopia. Both genetic and environmental factors contribute to such ethnic variations. This review attempts to summarize and compare the allelic frequencies of gene variants known to be associated with myopia in different ethnic groups, especially in the Asia-Pacific region.
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Affiliation(s)
- Shi Song Rong
- From the *Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong Eye Hospital, Kowloon, Hong Kong; and †Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA
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