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Poli G, Barravecchia I, Demontis GC, Sodi A, Saba A, Rizzo S, Macchia M, Tuccinardi T. Predicting potentially pathogenic effects of hRPE65 missense mutations: a computational strategy based on molecular dynamics simulations. J Enzyme Inhib Med Chem 2022; 37:1765-1772. [PMID: 35726567 PMCID: PMC9225791 DOI: 10.1080/14756366.2022.2090547] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The human retinal pigment epithelium-specific 65-kDa protein (hRPE65) plays a crucial role within the retinoid visual cycle and several mutations affecting either its expression level or its enzymatic function are associated with inherited retinal diseases such as Retinitis Pigmentosa. The gene therapy product voretigene neparvovec (Luxturna) has been recently approved for treating hereditary retinal dystrophies; however, the treatment is currently accessible only to patients presenting confirmed biallelic mutations that severely impair hRPE65 function, and many reported hRPE65 missense mutations lack sufficient evidences for proving their pathogenicity. In this context, we developed a computational approach aimed at evaluating the potential pathogenic effect of hRPE65 missense variants located on the dimerisation domain of the protein. The protocol evaluates how mutations may affect folding and conformation stability of this protein region, potentially helping clinicians to evaluate the eligibility for gene therapy of patients diagnosed with this type of hRPE65 variant of uncertain significance.
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Affiliation(s)
- Giulio Poli
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Ivana Barravecchia
- Department of Pharmacy, University of Pisa, Pisa, Italy.,Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | | | - Andrea Sodi
- Department of Neurosciences, Psychology, Drug Research and Child Health Eye Clinic, University of Florence, AOU Careggi, Florence, Italy
| | - Alessandro Saba
- Department of Surgical Pathology, Molecular Medicine and of the Critical Area, University of Pisa, Pisa, Italy
| | - Stanislao Rizzo
- Ophthalmology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Catholic University Sacro Cuore, Rome, Italy.,Consiglio Nazionale delle Ricerche, Istituto di Neuroscienze, Pisa, Italy
| | - Marco Macchia
- Department of Pharmacy, University of Pisa, Pisa, Italy
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Wu W, Takahashi Y, Shin HY, Ma X, Moiseyev G, Ma JX. The interplay of environmental luminance and genetics in the retinal dystrophy induced by the dominant RPE65 mutation. Proc Natl Acad Sci U S A 2022; 119:e2115202119. [PMID: 35271391 PMCID: PMC8931212 DOI: 10.1073/pnas.2115202119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/11/2022] [Indexed: 01/09/2023] Open
Abstract
SignificanceIn humans, genetic mutations in the retinal pigment epithelium (RPE) 65 are associated with blinding diseases, for which there is no effective therapy alleviating progressive retinal degeneration in affected patients. Our findings uncovered that the increased free opsin caused by enhancing the ambient light intensity increased retinal activation, and when compounded with the RPE visual cycle dysfunction caused by the heterozygous D477G mutation and aggregation, led to the onset of retinal degeneration.
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Affiliation(s)
- Wenjing Wu
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Yusuke Takahashi
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Henry Younghwa Shin
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Xiang Ma
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Gennadiy Moiseyev
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Jian-Xing Ma
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
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Kiser PD. Retinal pigment epithelium 65 kDa protein (RPE65): An update. Prog Retin Eye Res 2021; 88:101013. [PMID: 34607013 PMCID: PMC8975950 DOI: 10.1016/j.preteyeres.2021.101013] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 12/21/2022]
Abstract
Vertebrate vision critically depends on an 11-cis-retinoid renewal system known as the visual cycle. At the heart of this metabolic pathway is an enzyme known as retinal pigment epithelium 65 kDa protein (RPE65), which catalyzes an unusual, possibly biochemically unique, reaction consisting of a coupled all-trans-retinyl ester hydrolysis and alkene geometric isomerization to produce 11-cis-retinol. Early work on this isomerohydrolase demonstrated its membership to the carotenoid cleavage dioxygenase superfamily and its essentiality for 11-cis-retinal production in the vertebrate retina. Three independent studies published in 2005 established RPE65 as the actual isomerohydrolase instead of a retinoid-binding protein as previously believed. Since the last devoted review of RPE65 enzymology appeared in this journal, major advances have been made in a number of areas including our understanding of the mechanistic details of RPE65 isomerohydrolase activity, its phylogenetic origins, the relationship of its membrane binding affinity to its catalytic activity, its role in visual chromophore production for rods and cones, its modulation by macromolecules and small molecules, and the involvement of RPE65 mutations in the development of retinal diseases. In this article, I will review these areas of progress with the goal of integrating results from the varied experimental approaches to provide a comprehensive picture of RPE65 biochemistry. Key outstanding questions that may prove to be fruitful future research pursuits will also be highlighted.
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Affiliation(s)
- Philip D Kiser
- Research Service, VA Long Beach Healthcare System, Long Beach, CA, 90822, USA; Department of Physiology & Biophysics, University of California, Irvine School of Medicine, Irvine, CA, 92697, USA; Department of Ophthalmology and Center for Translational Vision Research, Gavin Herbert Eye Institute, University of California, Irvine School of Medicine, Irvine, CA, 92697, USA.
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Skorczyk-Werner A, Niedziela Z, Stopa M, Krawczyński MR. Novel gene variants in Polish patients with Leber congenital amaurosis (LCA). Orphanet J Rare Dis 2020; 15:345. [PMID: 33308271 PMCID: PMC7731562 DOI: 10.1186/s13023-020-01634-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/27/2020] [Indexed: 12/26/2022] Open
Abstract
Background Leber congenital amaurosis (LCA) is a rare retinal disease that is the most frequent cause of congenital blindness in children and the most severe form of inherited retinal dystrophies. To date, 25 genes have been implicated in the pathogenesis of LCA. As gene therapy is becoming available, the identification of potential treatment candidates is crucial. The aim of the study was to report the molecular basis of Leber congenital amaurosis in 22 Polish families.
Methods Single Nucleotide Polymorphism-microarray for LCA genes or Next Generation Sequencing diagnostic panel for LCA genes (or both tests) were performed to identify potentially pathogenic variants. Bidirectional Sanger sequencing was carried out for validation and segregation analysis of the variants identified within the families. Results The molecular background was established in 22 families. From a total of 24 identified variants, 23 were predicted to affect protein-coding or splicing, including 10 novel variants. The variants were identified in 7 genes: CEP290, GUCY2D, RPE65, NMNAT1, CRB1, RPGRIP1, and CRX. More than one-third of the patients, with clinical LCA diagnosis confirmed by the results of molecular analysis, appeared to be affected with a severe form of the disease: LCA10 caused by the CEP290 gene variants. Intronic mutation c.2991+1655A>G in the CEP290 gene was the most frequent variant identified in the studied group. Conclusions This study provides the first molecular genetic characteristics of patients with Leber congenital amaurosis from the previously unexplored Polish population. Our study expands the mutational spectrum as we report 10 novel variants identified in LCA genes. The fact that the most frequent causes of the disease in the studied group of Polish patients are mutations in one out of three genes that are currently the targets for gene therapy (CEP290, GUCY2D, and RPE65) strongly emphasizes the importance of the molecular background analyses of LCA in Polish patients.
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Affiliation(s)
- Anna Skorczyk-Werner
- Department of Medical Genetics, Poznan University of Medical Sciences, 8, Rokietnicka St, 60-806, Poznan, Poland.
| | - Zuzanna Niedziela
- Department of Medical Genetics, Poznan University of Medical Sciences, 8, Rokietnicka St, 60-806, Poznan, Poland.,Department of Ophthalmology, Chair of Ophthalmology and Optometry, Poznan University of Medical Sciences, Poznan, Poland
| | - Marcin Stopa
- Department of Ophthalmology, Chair of Ophthalmology and Optometry, Poznan University of Medical Sciences, Poznan, Poland
| | - Maciej Robert Krawczyński
- Department of Medical Genetics, Poznan University of Medical Sciences, 8, Rokietnicka St, 60-806, Poznan, Poland.,Centers for Medical Genetics GENESIS, Poznan, Poland
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Motta FL, Martin RP, Porto FBO, Wohler ES, Resende RG, Gomes CP, Pesquero JB, Sallum JMF. Pathogenicity Reclasssification of RPE65 Missense Variants Related to Leber Congenital Amaurosis and Early-Onset Retinal Dystrophy. Genes (Basel) 2019; 11:E24. [PMID: 31878136 PMCID: PMC7016655 DOI: 10.3390/genes11010024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
A challenge in molecular diagnosis and genetic counseling is the interpretation of variants of uncertain significance. Proper pathogenicity classification of new variants is important for the conclusion of molecular diagnosis and the medical management of patient treatments. The purpose of this study was to reclassify two RPE65 missense variants, c.247T>C (p.Phe83Leu) and c.560G>A (p.Gly187Glu), found in Brazilian families. To achieve this aim, we reviewed the sequencing data of a 224-gene retinopathy panel from 556 patients (513 families) with inherited retinal dystrophies. Five patients with p.Phe83Leu and seven with p.Gly187Glu were selected and their families investigated. To comprehend the pathogenicity of these variants, we evaluated them based on the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) classification guidelines. Initially, these RPE65 variants met only three pathogenic criteria: (i) absence or low frequency in the population, (ii) several missense pathogenic RPE65 variants, and (iii) 15 out of 16 lines of computational evidence supporting them as damaging, which together allowed the variants to be classified as uncertain significance. Two other pieces of evidence were accepted after further analysis of these Brazilian families: (i) p.Phe83Leu and p.Gly187Glu segregate with childhood retinal dystrophy within families, and (ii) their prevalence in Leber congenital amaurosis (LCA)/early-onset retinal dystrophy (EORD) patients can be considered higher than in other inherited retinal dystrophy patients. Therefore, these variants can now be classified as likely pathogenic according to ACMG/AMP classification guidelines.
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Affiliation(s)
- Fabiana L. Motta
- Department of Ophthalmology, Universidade Federal de São Paulo, Sao Paulo SP 04039-032, Brazil;
- Instituto de Genética Ocular, Sao Paulo SP 04552-050, Brazil
| | - Renan P. Martin
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins Medicine, Baltimore, MD 21205, USA; (R.P.M.); (E.S.W.)
| | - Fernanda B. O. Porto
- INRET Clínica e Centro de Pesquisa, Belo Horizonte MG 30150-270, Brazil;
- Centro Oftalmológico de Minas Gerais, Belo Horizonte MG 30180-070, Brazil
| | - Elizabeth S. Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins Medicine, Baltimore, MD 21205, USA; (R.P.M.); (E.S.W.)
| | | | - Caio P. Gomes
- Department of Biophysics, Universidade Federal de São Paulo, São Paulo SP 04039-032, Brazil; (C.P.G.); (J.B.P.)
| | - João B. Pesquero
- Department of Biophysics, Universidade Federal de São Paulo, São Paulo SP 04039-032, Brazil; (C.P.G.); (J.B.P.)
| | - Juliana M. F. Sallum
- Department of Ophthalmology, Universidade Federal de São Paulo, Sao Paulo SP 04039-032, Brazil;
- Instituto de Genética Ocular, Sao Paulo SP 04552-050, Brazil
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Yu B, Egbejimi A, Dharmat R, Xu P, Zhao Z, Long B, Miao H, Chen R, Wensel TG, Cai J, Chen Y. Phagocytosed photoreceptor outer segments activate mTORC1 in the retinal pigment epithelium. Sci Signal 2018; 11:11/532/eaag3315. [PMID: 29844054 DOI: 10.1126/scisignal.aag3315] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The retinal pigment epithelium (RPE) transports nutrients and metabolites between the microvascular bed that maintains the outer retina and photoreceptor neurons. The RPE removes photoreceptor outer segments (POS) by receptor-mediated phagocytosis, a process that peaks in the morning. Uptake and degradation of POS initiates signaling cascades in the RPE. Upstream stimuli from various metabolic activities converge on mechanistic target of rapamycin complex 1 (mTORC1), and aberrant mTORC1 signaling is implicated in aging and age-related degeneration of the RPE. We measured mTORC1-mediated responses to RPE phagocytosis in vivo and in vitro. During the morning burst of POS shedding, there was transient activation of mTORC1-mediated signaling in the RPE. POS activated mTORC1 through lysosome-independent mechanisms, and engulfed POS served as a docking platform for mTORC1 assembly. The identification of POS as endogenous stimuli of mTORC1 in the RPE provides a mechanistic link underlying the photoreceptor-RPE interaction in the outer retina.
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Affiliation(s)
- Bo Yu
- Department of Ophthalmology and Visual Science, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Anuoluwapo Egbejimi
- Department of Ophthalmology and Visual Science, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Rachayata Dharmat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pei Xu
- Department of Ophthalmology and Visual Science, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Zhenyang Zhao
- Department of Ophthalmology and Visual Science, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Bo Long
- Department of Ophthalmology and Visual Science, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Hongyu Miao
- Department of Biostatistics and Data Science, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Theodore G Wensel
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiyang Cai
- Department of Ophthalmology and Visual Science, University of Texas Medical Branch, Galveston, TX 77555, USA.,Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Yan Chen
- Department of Ophthalmology and Visual Science, University of Texas Medical Branch, Galveston, TX 77555, USA. .,Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX 77555, USA
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Comparative sequence analyses of rhodopsin and RPE65 reveal patterns of selective constraint across hereditary retinal disease mutations. Vis Neurosci 2016; 33:e002. [DOI: 10.1017/s0952523815000322] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractRetinitis pigmentosa (RP) comprises several heritable diseases that involve photoreceptor, and ultimately retinal, degeneration. Currently, mutations in over 50 genes have known links to RP. Despite advances in clinical characterization, molecular characterization of RP remains challenging due to the heterogeneous nature of causal genes, mutations, and clinical phenotypes. In this study, we compiled large datasets of two important visual genes associated with RP: rhodopsin, which initiates the phototransduction cascade, and the retinoid isomerase RPE65, which regenerates the visual cycle. We used a comparative evolutionary approach to investigate the relationship between interspecific sequence variation and pathogenic mutations that lead to degenerative retinal disease. Using codon-based likelihood methods, we estimated evolutionary rates (dN/dS) across both genes in a phylogenetic context to investigate differences between pathogenic and nonpathogenic amino acid sites. In both genes, disease-associated sites showed significantly lower evolutionary rates compared to nondisease sites, and were more likely to occur in functionally critical areas of the proteins. The nature of the dataset (e.g., vertebrate or mammalian sequences), as well as selection of pathogenic sites, affected the differences observed between pathogenic and nonpathogenic sites. Our results illustrate that these methods can serve as an intermediate step in understanding protein structure and function in a clinical context, particularly in predicting the relative pathogenicity (i.e., functional impact) of point mutations and their downstream phenotypic effects. Extensions of this approach may also contribute to current methods for predicting the deleterious effects of candidate mutations and to the identification of protein regions under strong constraint where we expect pathogenic mutations to occur.
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Yang GQ, Chen T, Tao Y, Zhang ZM. Recent advances in the dark adaptation investigations. Int J Ophthalmol 2015; 8:1245-52. [PMID: 26682182 DOI: 10.3980/j.issn.2222-3959.2015.06.31] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/28/2015] [Indexed: 12/15/2022] Open
Abstract
Dark adaptation is a highly sensitive neural function and may be the first symptom of many status including the physiologic and pathologic entity, suggesting that it could be instrumental for diagnose. However, shortcomings such as the lack of standardized parameters, the long duration of examination, and subjective randomness would substantially impede the use of dark adaptation in clinical work. In this review we summarize the recent research about the dark adaptation, including two visual cycles-canonical and cone-specific visual cycle, affecting factors and the methods for measuring dark adaptation. In the opinions of authors, intensive investigations are needed to be done for the widely use of this significant visual function in clinic.
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Affiliation(s)
- Guo-Qing Yang
- Department of Clinical Aerospace Medicine, the Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
| | - Tao Chen
- Department of Clinical Aerospace Medicine, the Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
| | - Ye Tao
- Department of Ophthalmology, Beidaihe Hospital of PLA, Beidaihe 066100, Hebei Province, China
| | - Zuo-Ming Zhang
- Department of Clinical Aerospace Medicine, the Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
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