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Shepherdson JL, Granas DM, Li J, Shariff Z, Plassmeyer SP, Holehouse AS, White MA, Cohen BA. Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.585809. [PMID: 38585983 PMCID: PMC10996540 DOI: 10.1101/2024.03.21.585809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cone-Rod Homeobox, encoded by CRX, is a transcription factor (TF) essential for the terminal differentiation and maintenance of mammalian photoreceptors. Structurally, CRX comprises an ordered DNA-binding homeodomain and an intrinsically disordered transcriptional effector domain. Although a handful of human variants in CRX have been shown to cause several different degenerative retinopathies with varying cone and rod predominance, as with most human disease genes the vast majority of observed CRX genetic variants are uncharacterized variants of uncertain significance (VUS). We performed a deep mutational scan (DMS) of nearly all possible single amino acid substitution variants in CRX, using an engineered cell-based transcriptional reporter assay. We measured the ability of each CRX missense variant to transactivate a synthetic fluorescent reporter construct in a pooled fluorescence-activated cell sorting assay and compared the activation strength of each variant to that of wild-type CRX to compute an activity score, identifying thousands of variants with altered transcriptional activity. We calculated a statistical confidence for each activity score derived from multiple independent measurements of each variant marked by unique sequence barcodes, curating a high-confidence list of nearly 2,000 variants with significantly altered transcriptional activity compared to wild-type CRX. We evaluated the performance of the DMS assay as a clinical variant classification tool using gold-standard classified human variants from ClinVar, and determined that activity scores could be used to identify pathogenic variants with high specificity. That this performance could be achieved using a synthetic reporter assay in a foreign cell type, even for a highly cell type-specific TF like CRX, suggests that this approach shows promise for DMS of other TFs that function in cell types that are not easily accessible. Per-position average activity scores closely aligned to a predicted structure of the ordered homeodomain and demonstrated position-specific residue requirements. The intrinsically disordered transcriptional effector domain, by contrast, displayed a qualitatively different pattern of substitution effects, following compositional constraints without specific residue position requirements in the peptide chain. The observed compositional constraints of the effector domain were consistent with the acidic exposure model of transcriptional activation. Together, the results of the CRX DMS identify molecular features of the CRX effector domain and demonstrate clinical utility for variant classification.
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Affiliation(s)
- James L. Shepherdson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - David M. Granas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Jie Li
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Zara Shariff
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Stephen P. Plassmeyer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Biomolecular Condensates, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Biomolecular Condensates, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Michael A. White
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Barak A. Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
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Shepherdson JL, Friedman RZ, Zheng Y, Sun C, Oh IY, Granas DM, Cohen BA, Chen S, White MA. Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors. Genome Res 2024; 34:243-255. [PMID: 38355306 PMCID: PMC10984388 DOI: 10.1101/gr.278133.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Dozens of variants in the gene for the homeodomain transcription factor (TF) cone-rod homeobox (CRX) are linked with human blinding diseases that vary in their severity and age of onset. How different variants in this single TF alter its function in ways that lead to a range of phenotypes is unclear. We characterized the effects of human disease-causing variants on CRX cis-regulatory function by deploying massively parallel reporter assays (MPRAs) in mouse retina explants carrying knock-ins of two variants, one in the DNA-binding domain (p.R90W) and the other in the transcriptional effector domain (p.E168d2). The degree of reporter gene dysregulation in these mutant Crx retinas corresponds with their phenotypic severity. The two variants affect similar sets of enhancers, and p.E168d2 has distinct effects on silencers. Cis-regulatory elements (CREs) near cone photoreceptor genes are enriched for silencers that are derepressed in the presence of p.E168d2. Chromatin environments of CRX-bound loci are partially predictive of episomal MPRA activity, and distal elements whose accessibility increases later in retinal development are enriched for CREs with silencer activity. We identified a set of potentially pleiotropic regulatory elements that convert from silencers to enhancers in retinas that lack a functional CRX effector domain. Our findings show that phenotypically distinct variants in different domains of CRX have partially overlapping effects on its cis-regulatory function, leading to misregulation of similar sets of enhancers while having a qualitatively different impact on silencers.
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Affiliation(s)
- James L Shepherdson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Ryan Z Friedman
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Yiqiao Zheng
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Inez Y Oh
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - David M Granas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA;
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Michael A White
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA;
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
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Zheng Y, Chen S. Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research. Front Cell Neurosci 2024; 18:1347436. [PMID: 38414750 PMCID: PMC10896975 DOI: 10.3389/fncel.2024.1347436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
The vertebrate retina is made up of six specialized neuronal cell types and one glia that are generated from a common retinal progenitor. The development of these distinct cell types is programmed by transcription factors that regulate the expression of specific genes essential for cell fate specification and differentiation. Because of the complex nature of transcriptional regulation, understanding transcription factor functions in development and disease is challenging. Research on the Cone-rod homeobox transcription factor CRX provides an excellent model to address these challenges. In this review, we reflect on 25 years of mammalian CRX research and discuss recent progress in elucidating the distinct pathogenic mechanisms of four CRX coding variant classes. We highlight how in vitro biochemical studies of CRX protein functions facilitate understanding CRX regulatory principles in animal models. We conclude with a brief discussion of the emerging systems biology approaches that could accelerate precision medicine for CRX-linked diseases and beyond.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
| | - Shiming Chen
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, Saint Louis, MO, United States
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Li Z, Cheng W, Zi F, Wang J, Huang X, Sheng X, Rong W. Four different gene-related cone-rod dystrophy: clinical and genetic findings in six Chinese families with diverse modes of inheritance. Front Genet 2023; 14:1157156. [PMID: 38028590 PMCID: PMC10652761 DOI: 10.3389/fgene.2023.1157156] [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: 02/02/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose: To investigate pathogenic variants in six families with cone-rod dystrophy (CORD) presenting various inheritance patterns by using whole-exome sequencing (WES) and analyzing phenotypic features. Methods: A total of six families with CORD were enrolled in Ningxia Eye Hospital for this study. The probands and their family members received comprehensive ophthalmic examinations, and DNA was abstracted from patients and family members. Whole-exome sequencing was performed on probands to screen the causative variants, and all suspected pathogenic variants were determined via Sanger sequencing. Furthermore, co-segregation analysis was performed on available family members. The pathogenicity of novel variants was predicted using in silico analysis and evaluated according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results: Of the six families, two families were assigned as X-linked recessive (XL), two families were assigned as autosomal recessive (AR), and two families were assigned as autosomal dominant (AD). Pathogenic variants were detected in CACNA1F in two X-linked recessive probands, among which family 1 had a hemizygous frameshift variant c.2201del (p.Val734Glyfs*17) and family 2 had a hemizygous missense variant c.245G>A (p.Arg82Gln). Both probands had high myopia, with fundus tessellation accompanied by abnormalities in the outer structure of the macular area. The homozygous splice variant c.2373 + 5G>T in PROM1 and the homozygous nonsense variant c.604C>T (p.Arg202Ter) in ADAM9 were detected in two autosomal recessive families of the probands. Both probands showed different degrees of atrophy in the macular area, and the lesions showed hypofluorescence changes in autofluorescence. The heterozygous variation in CRX c.682C>T (p.Gln228Ter) was detected in two autosomal dominant families. The onset age of the two probands was late, with better vision and severe macular atrophy. According to ACMG guidelines and the analysis of online in silico tools, all variations were labeled as potentially harmful or pathogenic. Conclusion: Pathogenic variants in CACNA1F, PROM1, ADAM9, and CRX genes were identified in six families affected by the diverse inheritance patterns of CORD. Furthermore, the potential impact of the nonsense-mediated decay (NMD) mechanism on the manifestation of CORD phenotypes was examined and addressed. Simultaneously, the spectrum of pathogenic variants and clinical phenotypes associated with the CORD gene was extended.
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Affiliation(s)
- Zhen Li
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Wanyu Cheng
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Feiyin Zi
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Juan Wang
- Department of Ophthalmology, Qingdao West Coast New District Central Hospital, Qingdao, China
| | - Xiaoyu Huang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | | | - Weining Rong
- 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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Fujinami-Yokokawa Y, Yang L, Joo K, Tsunoda K, Liu X, Kondo M, Ahn SJ, Li H, Park KH, Tachimori H, Miyata H, Woo SJ, Sui R, Fujinami K. Occult Macular Dysfunction Syndrome: Identification of Multiple Pathologies in a Clinical Spectrum of Macular Dysfunction with Normal Fundus in East Asian Patients: EAOMD Report No. 5. Genes (Basel) 2023; 14:1869. [PMID: 37895218 PMCID: PMC10606510 DOI: 10.3390/genes14101869] [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: 08/13/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Occult macular dystrophy (OMD) is the most prevalent form of macular dystrophy in East Asia. Beyond RP1L1, causative genes and mechanisms remain largely uncharacterised. This study aimed to delineate the clinical and genetic characteristics of OMD syndrome (OMDS). Patients clinically diagnosed with OMDS in Japan, South Korea, and China were enrolled. The inclusion criteria were as follows: (1) macular dysfunction and (2) normal fundus appearance. Comprehensive clinical evaluation and genetic assessment were performed to identify the disease-causing variants. Clinical parameters were compared among the genotype groups. Seventy-two patients with OMDS from fifty families were included. The causative genes were RP1L1 in forty-seven patients from thirty families (30/50, 60.0%), CRX in two patients from one family (1/50, 2.0%), GUCY2D in two patients from two families (2/50, 4.0%), and no genes were identified in twenty-one patients from seventeen families (17/50, 34.0%). Different severities were observed in terms of disease onset and the prognosis of visual acuity reduction. This multicentre large cohort study furthers our understanding of the phenotypic and genotypic spectra of patients with macular dystrophy and normal fundus. Evidently, OMDS encompasses multiple Mendelian retinal disorders, each representing unique pathologies that dictate their respective severity and prognostic patterns.
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Affiliation(s)
- Yu Fujinami-Yokokawa
- Department of Health Policy and Management, Keio University School of Medicine, Tokyo 160-8582, Japan; (Y.F.-Y.)
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo 152-8902, Japan
- UCL Institute of Ophthalmology, London EC1V 9EL, UK
- Division of Public Health, Yokokawa Clinic, Suita 564-0083, Japan
| | - Lizhu Yang
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam 13620, Republic of Korea
| | - Kazushige Tsunoda
- Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo 152-8902, Japan
| | - Xiao Liu
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo 152-8902, Japan
- Southwest Hospital, Army Medical University, Chongqing 400715, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing 400715, China
| | - Mineo Kondo
- Department of Ophthalmology, Mie University Graduate School of Medicine, Mie 514-8507, Japan
| | - Seong Joon Ahn
- Department of Ophthalmology, Hanyang University Hospital, Hanyang University College of Medicine, Seoul 04763, Republic of Korea
| | - Hui Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hisateru Tachimori
- Endowed Course for Health System Innovation, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hiroaki Miyata
- Department of Health Policy and Management, Keio University School of Medicine, Tokyo 160-8582, Japan; (Y.F.-Y.)
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam 13620, Republic of Korea
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Kaoru Fujinami
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo 152-8902, Japan
- UCL Institute of Ophthalmology, London EC1V 9EL, UK
- Moorfields Eye Hospital, London EC1V 2PD, UK
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Bosze B, Suarez-Navarro J, Cajias I, Brzezinski IV JA, Brown NL. Notch pathway mutants do not equivalently perturb mouse embryonic retinal development. PLoS Genet 2023; 19:e1010928. [PMID: 37751417 PMCID: PMC10522021 DOI: 10.1371/journal.pgen.1010928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/16/2023] [Indexed: 09/28/2023] Open
Abstract
In the vertebrate eye, Notch ligands, receptors, and ternary complex components determine the destiny of retinal progenitor cells in part by regulating Hes effector gene activity. There are multiple paralogues for nearly every node in this pathway, which results in numerous instances of redundancy and compensation during development. To dissect such complexity at the earliest stages of eye development, we used seven germline or conditional mutant mice and two spatiotemporally distinct Cre drivers. We perturbed the Notch ternary complex and multiple Hes genes to understand if Notch regulates optic stalk/nerve head development; and to test intracellular pathway components for their Notch-dependent versus -independent roles during retinal ganglion cell and cone photoreceptor competence and fate acquisition. We confirmed that disrupting Notch signaling universally blocks progenitor cell growth, but delineated specific pathway components that can act independently, such as sustained Hes1 expression in the optic stalk/nerve head. In retinal progenitor cells, we found that among the genes tested, they do not uniformly suppress retinal ganglion cell or cone differentiation; which is not due differences in developmental timing. We discovered that shifts in the earliest cell fates correlate with expression changes for the early photoreceptor factor Otx2, but not with Atoh7, a factor required for retinal ganglion cell formation. During photoreceptor genesis we also better defined multiple and simultaneous activities for Rbpj and Hes1 and identify redundant activities that occur downstream of Notch. Given its unique roles at the retina-optic stalk boundary and cone photoreceptor genesis, our data suggest Hes1 as a hub where Notch-dependent and -independent inputs converge.
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Affiliation(s)
- Bernadett Bosze
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
| | - Julissa Suarez-Navarro
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
| | - Illiana Cajias
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
| | - Joseph A. Brzezinski IV
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Nadean L. Brown
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
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Toms M, Ward N, Moosajee M. Nuclear Receptor Subfamily 2 Group E Member 3 (NR2E3): Role in Retinal Development and Disease. Genes (Basel) 2023; 14:1325. [PMID: 37510230 PMCID: PMC10379133 DOI: 10.3390/genes14071325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/11/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
NR2E3 is a nuclear hormone receptor gene required for the correct development of the retinal rod photoreceptors. Expression of NR2E3 protein in rod cell precursors suppresses cone-specific gene expression and, in concert with other transcription factors including NRL, activates the expression of rod-specific genes. Pathogenic variants involving NR2E3 cause a spectrum of retinopathies, including enhanced S-cone syndrome, Goldmann-Favre syndrome, retinitis pigmentosa, and clumped pigmentary retinal degeneration, with limited evidence of genotype-phenotype correlations. A common feature of NR2E3-related disease is an abnormally high number of cone photoreceptors that are sensitive to short wavelength light, the S-cones. This characteristic has been supported by mouse studies, which have also revealed that loss of Nr2e3 function causes photoreceptors to develop as cells that are intermediate between rods and cones. While there is currently no available cure for NR2E3-related retinopathies, there are a number of emerging therapeutic strategies under investigation, including the use of viral gene therapy and gene editing, that have shown promise for the future treatment of patients with NR2E3 variants and other inherited retinal diseases. This review provides a detailed overview of the current understanding of the role of NR2E3 in normal development and disease, and the associated clinical phenotypes, animal models, and therapeutic studies.
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Affiliation(s)
- Maria Toms
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London EC1V 9EL, UK
- Ocular Genomics and Therapeutics, The Francis Crick Institute, London NW1 1AT, UK
| | - Natasha Ward
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | - Mariya Moosajee
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London EC1V 9EL, UK
- Ocular Genomics and Therapeutics, The Francis Crick Institute, London NW1 1AT, UK
- Department of Genetics, Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Department of Ophthalmology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
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Kim DG, Joo K, Han J, Choi M, Kim SW, Park KH, Park SJ, Lee CS, Byeon SH, Woo SJ. Genotypic Profile and Clinical Characteristics of CRX-Associated Retinopathy in Koreans. Genes (Basel) 2023; 14:genes14051057. [PMID: 37239417 DOI: 10.3390/genes14051057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
This study aimed to investigate the clinical characteristics of Korean patients with retinal dystrophy associated with pathogenic variants of cone rod homeobox-containing gene (CRX). We retrospectively enrolled Korean patients with CRX-associated retinal dystrophy (CRX-RD) who visited two tertiary referral hospitals. Pathogenic variants were identified using targeted panel sequencing or whole-exome sequencing. We analyzed clinical features and phenotypic spectra according to genotype. Eleven patients with CRX-RD were included in this study. Six patients with cone-rod dystrophy (CORD), two with macular dystrophy (MD), two with Leber congenital amaurosis (LCA), and one with retinitis pigmentosa (RP) were included. One patient (9.1%) had autosomal recessive inheritance, and the other ten patients (90.9%) had autosomal dominant inheritance. Six patients (54.5%) were male, and the mean age of symptom onset was 27.0 ± 17.9 years. At the first presentation, the mean age was 39.4 ± 20.6 years, and best-corrected visual acuity (BCVA) (logMAR) was 0.76 ± 0.90 in the better eye. Negative electroretinography (ERG) was observed in seven (63.6%) patients. Nine pathogenic variants were identified, including two novel variants, c.101-1G>A and c.898T>C:p.(*300Glnext*118). Taken together with the variants reported in prior studies, all variants within the homeodomain are missense variants, whereas most variants downstream of the homeodomain are truncating variants (88%). The clinical features of pathogenic variants within the homeodomain are either CORD or MD with bull's eye maculopathy, whereas variants downstream of the homeodomain cause more diverse phenotypes, with CORD and MD in 36%, LCA in 40%, and RP in 24%. This is the first case series in Korea to investigate the CRX-RD genotype-phenotype correlation. Pathogenic variants downstream of the homeodomain of the CRX gene are present as RP, LCA, and CORD, whereas pathogenic variants within the homeodomain are mainly present as CORD or MD with bull's eye maculopathy. This trend was similar to previous genotype-phenotype analyses of CRX-RD. Further molecular biologic research on this correlation is required.
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Affiliation(s)
- Dong Geun Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
- Department of Ophthalmology, Inje University College of Medicine, Busan Paik Hospital, Busan 47392, Republic of Korea
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
| | - Jinu Han
- Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Severance Hospital, Seoul 06273, Republic of Korea
| | - Mihyun Choi
- Department of Ophthalmology, Guro Hospital, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Seong-Woo Kim
- Department of Ophthalmology, Guro Hospital, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
| | - Sang Jun Park
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
| | - Christopher Seungkyu Lee
- Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Severance Hospital, Seoul 06273, Republic of Korea
| | - Suk Ho Byeon
- Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Severance Hospital, Seoul 06273, Republic of Korea
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
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9
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D’Antona L, Amato R, Brescia C, Rocca V, Colao E, Iuliano R, Blazer-Yost BL, Perrotti N. Kinase Inhibitors in Genetic Diseases. Int J Mol Sci 2023; 24:ijms24065276. [PMID: 36982349 PMCID: PMC10048847 DOI: 10.3390/ijms24065276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Over the years, several studies have shown that kinase-regulated signaling pathways are involved in the development of rare genetic diseases. The study of the mechanisms underlying the onset of these diseases has opened a possible way for the development of targeted therapies using particular kinase inhibitors. Some of these are currently used to treat other diseases, such as cancer. This review aims to describe the possibilities of using kinase inhibitors in genetic pathologies such as tuberous sclerosis, RASopathies, and ciliopathies, describing the various pathways involved and the possible targets already identified or currently under study.
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Affiliation(s)
- Lucia D’Antona
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
| | - Rosario Amato
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
| | - Carolina Brescia
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
| | - Valentina Rocca
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
- Department of Experimental and Clinical Medicine, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
| | - Emma Colao
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
| | - Rodolfo Iuliano
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
| | - Bonnie L. Blazer-Yost
- Department of Biology, Indiana University Purdue University, Indianapolis, IN 46202, USA
| | - Nicola Perrotti
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
- Correspondence:
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10
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Bosze B, Suarez-Navarro J, Cajias I, Brzezinski JA, Brown NL. Not all Notch pathway mutations are equal in the embryonic mouse retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523641. [PMID: 36711950 PMCID: PMC9882158 DOI: 10.1101/2023.01.11.523641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In the vertebrate retina, combinations of Notch ligands, receptors, and ternary complex components determine the destiny of retinal progenitor cells by regulating Hes effector gene activity. Owing to reiterated Notch signaling in numerous tissues throughout development, there are multiple vertebrate paralogues for nearly every node in this pathway. These Notch signaling components can act redundantly or in a compensatory fashion during development. To dissect the complexity of this pathway during retinal development, we used seven germline or conditional mutant mice and two spatiotemporally distinct Cre drivers. We perturbed the Notch ternary complex and multiple Hes genes with two overt goals in mind. First, we wished to determine if Notch signaling is required in the optic stalk/nerve head for Hes1 sustained expression and activity. Second, we aimed to test if Hes1, 3 and 5 genes are functionally redundant during early retinal histogenesis. With our allelic series, we found that disrupting Notch signaling consistently blocked mitotic growth and overproduced ganglion cells, but we also identified two significant branchpoints for this pathway. In the optic stalk/nerve head, sustained Hes1 is regulated independent of Notch signaling, whereas during photoreceptor genesis both Notch-dependent and -independent roles for Rbpj and Hes1 impact photoreceptor genesis in opposing manners.
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Affiliation(s)
- Bernadett Bosze
- Department of Cell Biology & Human Anatomy, University of California, Davis, CA 95616
| | | | - Illiana Cajias
- Department of Cell Biology & Human Anatomy, University of California, Davis, CA 95616
| | - Joseph A. Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Nadean L Brown
- Department of Cell Biology & Human Anatomy, University of California, Davis, CA 95616
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11
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Sun C, Chen S. Gene Augmentation for Autosomal Dominant CRX-Associated Retinopathies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1415:135-141. [PMID: 37440026 PMCID: PMC11010719 DOI: 10.1007/978-3-031-27681-1_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The cone-rod homeobox (CRX) protein is a key transcription factor essential for photoreceptor function and survival. Mutations in human CRX gene are linked to a wide spectrum of blinding diseases ranging from mild macular dystrophy to severe Leber congenital amaurosis (LCA), cone-rod dystrophy (CRD), and retinitis pigmentosa (RP). These diseases are still incurable and mostly inherited in an autosomal dominant form. Dysfunctional mutant CRX protein interferes with the function of wild-type CRX protein, demonstrating the dominant negative effect. At present, gene augmentation is the most promising treatment strategy for hereditary diseases. This study aims to review the pathogenic mechanisms of various CRX mutations and propose two therapeutic strategies to rescue sick photoreceptors in CRX-associated retinopathies, namely, Tet-On-hCRX system and adeno-associated virus (AAV)-mediated gene augmentation. The outcome of proposed studies will guide future translational research and suggest guidelines for therapy evaluation in terms of treatment safety and efficacy.
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Affiliation(s)
- Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University, St. Louis, MO, USA.
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University, St. Louis, MO, USA
- Department of Developmental Biology, Washington University, St. Louis, MO, USA
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12
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Sun C, Chen S. Disease-causing mutations in genes encoding transcription factors critical for photoreceptor development. Front Mol Neurosci 2023; 16:1134839. [PMID: 37181651 PMCID: PMC10172487 DOI: 10.3389/fnmol.2023.1134839] [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: 12/30/2022] [Accepted: 04/04/2023] [Indexed: 05/16/2023] Open
Abstract
Photoreceptor development of the vertebrate visual system is controlled by a complex transcription regulatory network. OTX2 is expressed in the mitotic retinal progenitor cells (RPCs) and controls photoreceptor genesis. CRX that is activated by OTX2 is expressed in photoreceptor precursors after cell cycle exit. NEUROD1 is also present in photoreceptor precursors that are ready to specify into rod and cone photoreceptor subtypes. NRL is required for the rod fate and regulates downstream rod-specific genes including the orphan nuclear receptor NR2E3 which further activates rod-specific genes and simultaneously represses cone-specific genes. Cone subtype specification is also regulated by the interplay of several transcription factors such as THRB and RXRG. Mutations in these key transcription factors are responsible for ocular defects at birth such as microphthalmia and inherited photoreceptor diseases such as Leber congenital amaurosis (LCA), retinitis pigmentosa (RP) and allied dystrophies. In particular, many mutations are inherited in an autosomal dominant fashion, including the majority of missense mutations in CRX and NRL. In this review, we describe the spectrum of photoreceptor defects that are associated with mutations in the above-mentioned transcription factors, and summarize the current knowledge of molecular mechanisms underlying the pathogenic mutations. At last, we deliberate the outstanding gaps in our understanding of the genotype-phenotype correlations and outline avenues for future research of the treatment strategies.
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Affiliation(s)
- Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, United States
- *Correspondence: Chi Sun,
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, United States
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13
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Clanor PB, Buchholz CN, Hayes JE, Friedman MA, White AM, Enke RA, Berndsen CE. Structural and functional analysis of the human cone‐rod homeobox transcription factor. Proteins 2022; 90:1584-1593. [PMID: 35255174 PMCID: PMC9271546 DOI: 10.1002/prot.26332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/30/2022]
Abstract
The cone‐rod homeobox (CRX) protein is a critical K50 homeodomain transcription factor responsible for the differentiation and maintenance of photoreceptor neurons in the vertebrate retina. Mutant alleles in the human gene encoding CRX result in a variety of distinct blinding retinopathies, including retinitis pigmentosa, cone‐rod dystrophy, and Leber congenital amaurosis. Despite the success of using in vitro biochemistry, animal models, and genomics approaches to study this clinically relevant transcription factor over the past 25 years since its initial characterization, there are no high‐resolution structures in the published literature for the CRX protein. In this study, we use bioinformatic approaches and small‐angle X‐ray scattering (SAXS) structural analysis to further understand the biochemical complexity of the human CRX homeodomain (CRX‐HD). We find that the CRX‐HD is a compact, globular monomer in solution that can specifically bind functional cis‐regulatory elements encoded upstream of retina‐specific genes. This study presents the first structural analysis of CRX, paving the way for a new approach to studying the biochemistry of this protein and its disease‐causing mutant protein variants.
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Affiliation(s)
| | - Christine N. Buchholz
- Department of Chemistry and Biochemistry James Madison University Harrisonburg Virginia USA
| | - Jonathan E. Hayes
- Department of Chemistry and Biochemistry James Madison University Harrisonburg Virginia USA
| | | | - Andrew M. White
- Department of Chemistry and Biochemistry James Madison University Harrisonburg Virginia USA
| | - Ray A. Enke
- Department of Biology James Madison University Harrisonburg Virginia USA
- Center for Genome and Metagenome Studies James Madison University Harrisonburg Virginia USA
| | - Christopher E. Berndsen
- Department of Chemistry and Biochemistry James Madison University Harrisonburg Virginia USA
- Center for Genome and Metagenome Studies James Madison University Harrisonburg Virginia USA
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14
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Gonzalez-Gonzalez LA, Scanga H, Traboulsi E, Nischal KK. Novel clinical presentation of a CRX rod-cone dystrophy. BMJ Case Rep 2021; 14:e233711. [PMID: 33910785 PMCID: PMC8094365 DOI: 10.1136/bcr-2019-233711] [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] [Accepted: 04/09/2021] [Indexed: 11/04/2022] Open
Abstract
We describe a novel clinical presentation of a CRX rod-cone dystrophy in a single family. Two boys ages 6 and 12 years presented with clinical and optical coherence tomography features suggestive of X-linked retinoschisis, but with optic nerve swelling without increased intracranial pressure. One patient had an electronegative electroretinogram (ERG) and the other had rod-cone dysfunction. Neither had retinoschisin (RS1) gene mutations. Biological mother and sister presented with retinal pigment epithelium (RPE) changes and abnormal cone-rod ERG responses. On further testing, next generation sequencing with array comparative genomic hybridisation showed a deletion in exon 4 of the CRX gene. Cystoid maculopathy in young male children can be difficult to distinguish from RS1-associated schisis. Phenotypic variants within a family must prompt a thorough retinal dystrophy evaluation even with electronegative ERG in the presenting child. This novel phenotype for CRX presents with optic nerve swelling and cystoid maculopathy in men, and RPE changes in women.
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Affiliation(s)
- Luis Alonso Gonzalez-Gonzalez
- Ophthalmology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Ophthalmology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, USA
| | - Hannah Scanga
- Ophthalmology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, USA
| | | | - Ken K Nischal
- Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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15
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Padhy SK, Takkar B, Narayanan R, Venkatesh P, Jalali S. Voretigene Neparvovec and Gene Therapy for Leber's Congenital Amaurosis: Review of Evidence to Date. APPLICATION OF CLINICAL GENETICS 2020; 13:179-208. [PMID: 33268999 PMCID: PMC7701157 DOI: 10.2147/tacg.s230720] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/06/2020] [Indexed: 12/13/2022]
Abstract
Gene therapy has now evolved as the upcoming modality for management of many disorders, both inheritable and non-inheritable. Knowledge of genetics pertaining to a disease has therefore become paramount for physicians across most specialities. Inheritable retinal dystrophies (IRDs) are notorious for progressive and relentless vision loss, frequently culminating in complete blindness in both eyes. Leber’s congenital amaurosis (LCA) is a typical example of an IRD that manifests very early in childhood. Research in gene therapy has led to the development and approval of voretigene neparvovec (VN) for use in patients of LCA with a deficient biallelic RPE65 gene. The procedure involves delivery of a recombinant virus vector that carries the RPE65 gene in the subretinal space. This comprehensive review reports the evidence thus far in support of gene therapy for LCA. We explore and compare the various gene targets including but not limited to RPE65, and discuss the choice of vector and method for ocular delivery. The review details the evolution of gene therapy with VN in a phased manner, concluding with the challenges that lie ahead for its translation for use in communities that differ much both genetically and economically.
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Affiliation(s)
- Srikanta Kumar Padhy
- Vitreoretina and Uveitis Services, L V Prasad Eye Institute, Mithu Tulsi Chanrai Campus, Bhubaneswar, India
| | - Brijesh Takkar
- Srimati Kanuri Santhamma Center for Vitreoretinal Diseases, Kallam Anji Reddy Campus, L.V. Prasad Eye Institute, Hyderabad, India.,Center of Excellence for Rare Eye Diseases, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, India
| | - Raja Narayanan
- Srimati Kanuri Santhamma Center for Vitreoretinal Diseases, Kallam Anji Reddy Campus, L.V. Prasad Eye Institute, Hyderabad, India
| | - Pradeep Venkatesh
- Dr RP Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Subhadra Jalali
- Srimati Kanuri Santhamma Center for Vitreoretinal Diseases, Kallam Anji Reddy Campus, L.V. Prasad Eye Institute, Hyderabad, India.,Jasti V. Ramanamma Childrens' Eye Care Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, India
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16
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Ng CC, Carrera WM, McDonald HR, Agarwal A. Heterozygous CRX R90W mutation-associated adult-onset macular dystrophy with phenotype analogous to benign concentric annular macular dystrophy. Ophthalmic Genet 2020; 41:485-490. [PMID: 32689858 DOI: 10.1080/13816810.2020.1795890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Background Historically, CRX mutations have been associated with cone-rod dystrophy, cone dystrophy, Leber's congenital amaurosis, and retinitis pigmentosa. There is recent emerging evidence of an adult-onset macular dystrophy phenotype. We review the published literature and discuss the first case of heterozygous CRX R90 W macular dystrophy. Materials and Methods The patient received serial ophthalmic examination and imaging. Genetic testing was performed by MyRetinaTracker with the use of a retinal dystrophy panel. Results A 55-year-old Caucasian male patient without a prior medical history presented for evaluation of decreased vision in the right eye. Visual acuity was 20/32 both eyes, and his fundus examination was notable for an incomplete ring-shaped macular atrophy with foveolar sparing in both eyes. Fundus autofluorescence was notable for hypo-autofluorescence of the ring and fluorescein angiography for transmission hyperfluorescence. Full-field ERG and EOG were normal, while mfERG showed central depression. His lesion was clinically diagnosed as benign concentric annular macular dystrophy, but genetic testing revealed a heterozygous mutation in CRX (c.268 C > T, p.R90 W). A three-generation family tree did not reveal other members with known macular dystrophy. Given the lack of documentable autosomal dominant inheritance and the presence of a CRX mutation, the patient's diagnosis was revised to adult-onset macular dystrophy. Conclusions We believe this to be the first case of adult onset macular dystrophy associated with heterozygous CRX R90 W mutation.
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Affiliation(s)
- Caleb C Ng
- Department of Ophthalmology, California Pacific Medical Center , San Francisco, CA, USA.,West Coast Retina Medical Group , San Francisco, CA, USA
| | - William M Carrera
- Department of Ophthalmology, California Pacific Medical Center , San Francisco, CA, USA
| | | | - Anita Agarwal
- Department of Ophthalmology, California Pacific Medical Center , San Francisco, CA, USA.,West Coast Retina Medical Group , San Francisco, CA, USA
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17
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Fujinami-Yokokawa Y, Fujinami K, Kuniyoshi K, Hayashi T, Ueno S, Mizota A, Shinoda K, Arno G, Pontikos N, Yang L, Liu X, Sakuramoto H, Katagiri S, Mizobuchi K, Kominami T, Terasaki H, Nakamura N, Kameya S, Yoshitake K, Miyake Y, Kurihara T, Tsubota K, Miyata H, Iwata T, Tsunoda K. Clinical and Genetic Characteristics of 18 Patients from 13 Japanese Families with CRX-associated retinal disorder: Identification of Genotype-phenotype Association. Sci Rep 2020; 10:9531. [PMID: 32533067 PMCID: PMC7293272 DOI: 10.1038/s41598-020-65737-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/06/2020] [Indexed: 11/09/2022] Open
Abstract
Inherited retinal disorder (IRD) is a leading cause of blindness, and CRX is one of a number of genes reported to harbour autosomal dominant (AD) and recessive (AR) causative variants. Eighteen patients from 13 families with CRX-associated retinal disorder (CRX-RD) were identified from 730 Japanese families with IRD. Ophthalmological examinations and phenotype subgroup classification were performed. The median age of onset/latest examination was 45.0/62.5 years (range, 15-77/25-94). The median visual acuity in the right/left eye was 0.52/0.40 (range, -0.08-2.00/-0.18-1.70) logarithm of the minimum angle of resolution (LogMAR) units. There was one family with macular dystrophy, nine with cone-rod dystrophy (CORD), and three with retinitis pigmentosa. In silico analysis of CRX variants was conducted for genotype subgroup classification based on inheritance and the presence of truncating variants. Eight pathogenic CRX variants were identified, including three novel heterozygous variants (p.R43H, p.P145Lfs*42, and p.P197Afs*22). A trend of a genotype-phenotype association was revealed between the phenotype and genotype subgroups. A considerably high proportion of CRX-RD in ADCORD was determined in the Japanese cohort (39.1%), often showing the mild phenotype (CORD) with late-onset disease (sixth decade). Frequently found heterozygous missense variants located within the homeodomain underlie this mild phenotype. This large cohort study delineates the disease spectrum of CRX-RD in the Japanese population.
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Affiliation(s)
- Yu Fujinami-Yokokawa
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, 152-8902, Japan.,Department of Health Policy and Management, Keio University School of Medicine, Tokyo, Japan.,Division of Public Health, Yokokawa Clinic, Suita, 564-0083, Japan
| | - Kaoru Fujinami
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, 152-8902, Japan. .,Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan. .,UCL Institute of Ophthalmology, London, EC1V 9EL, UK. .,Moorfields Eye Hospital, London, EC1V 2PD, UK.
| | - Kazuki Kuniyoshi
- Department of Ophthalmology, Kindai University Faculty of Medicine, Osaka-Sayama, 589-8511, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Shinji Ueno
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Atsushi Mizota
- Department of Ophthalmology, Teikyo University, Tokyo, 173-8605, Japan
| | - Kei Shinoda
- Department of Ophthalmology, Teikyo University, Tokyo, 173-8605, Japan.,Department of Ophthalmology, Saitama Medical University, Saitama, 350-0495, Japan
| | - Gavin Arno
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, 152-8902, Japan.,UCL Institute of Ophthalmology, London, EC1V 9EL, UK.,Moorfields Eye Hospital, London, EC1V 2PD, UK.,North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London WC1N 1EH, London, UK
| | - Nikolas Pontikos
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, 152-8902, Japan.,UCL Institute of Ophthalmology, London, EC1V 9EL, UK.,Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Lizhu Yang
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, 152-8902, Japan.,Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Xiao Liu
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, 152-8902, Japan.,Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan.,Southwest Hospital/Southwest Eye Hospital, Third Military Medical University, Chongqing, 400030, China
| | - Hiroyuki Sakuramoto
- Department of Ophthalmology, Kindai University Faculty of Medicine, Osaka-Sayama, 589-8511, Japan
| | - Satoshi Katagiri
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Kei Mizobuchi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Taro Kominami
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Hiroko Terasaki
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Natsuko Nakamura
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, 152-8902, Japan.,Department of Ophthalmology, The University of Tokyo, Tokyo, 113-8654, Japan
| | - Shuhei Kameya
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital, Inzai, 270-1694, Japan
| | - Kazutoshi Yoshitake
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, 152-8902, Japan
| | - Yozo Miyake
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, 152-8902, Japan.,Aichi Medical University, Nagakute, 480-1195, Japan.,Kobe Eye Center, Next Vision, Kobe, 650-0047, Japan
| | - Toshihide Kurihara
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Kazuo Tsubota
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Hiroaki Miyata
- Department of Health Policy and Management, Keio University School of Medicine, Tokyo, Japan.,Department of Healthcare Quality Assessment, University of Tokyo, Tokyo, 113-8655, Japan
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, 152-8902, Japan
| | - Kazushige Tsunoda
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, 152-8902, Japan
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18
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Nishiguchi KM, Kunikata H, Fujita K, Hashimoto K, Koyanagi Y, Akiyama M, Ikeda Y, Momozawa Y, Sonoda KH, Murakami A, Wada Y, Nakazawa T. Association of CRX genotypes and retinal phenotypes confounded by variable expressivity and electronegative electroretinogram. Clin Exp Ophthalmol 2020; 48:644-657. [PMID: 32112665 DOI: 10.1111/ceo.13743] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/29/2020] [Accepted: 02/26/2020] [Indexed: 11/26/2022]
Abstract
IMPORTANCE A framework for understanding the phenotypic features of CRX retinopathy was established. BACKGROUND To perform a phenotype-genotype correlation analysis in two groups of patients with heterozygous mutations in distinct locations of the CRX gene, encoding the cone-rod homeobox. DESIGN Multicentre retrospective study. PARTICIPANTS Twenty-one Japanese patients from 14 families with a heterozygous CRX mutation. METHODS Retrospective data analysis. MAIN OUTCOME MEASURES Clinical records on CRX mutation, symptoms, best-corrected visual acuity (BCVA), visual field, fundus photography, fundus auto-fluorescence, optical coherence tomography and electroretinograms (ERGs). RESULTS Six different CRX heterozygous mutations were identified in the subjects. Twelve patients from 9 families shared the p.R41W mutation and 1 patient had the p.R43C mutation, both of which affect the homeobox domain of CRX. These patients often displayed adult-onset retinal dystrophy with macular degeneration. In contrast, five patients with downstream mutations (p.S204fs, p.S213fs, p.G243X and p.L299F) displayed retinal degeneration or macular degeneration with bone-spicule pigmentation. Three asymptomatic carriers with different mutations (p.R41W, p.S213fs and p.G243X) were present in both groups. Nearly all patients and carriers had an electronegative ERG in response to a bright flash under dark adaptation. There was no cross-sectional association between patients' age and BCVA, despite progressive decline in BCVA. CONCLUSIONS AND RELEVANCE Heterozygous mutations within or downstream of the homeobox domain in CRX relate to the difference associated retinal phenotypes, which was confounded by variable expressivity and electronegative ERGs. CRX mutations should be considered in patients with an electronegative ERG with minimal or no macular changes.
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Affiliation(s)
- Koji M Nishiguchi
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroshi Kunikata
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kosuke Fujita
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kazuki Hashimoto
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshito Koyanagi
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masato Akiyama
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuhiro Ikeda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akira Murakami
- Department of Ophthalmology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | | | - Toru Nakazawa
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Sendai, Japan
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19
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Khan AO, Neri P, Al Teneiji AM. A recurrent arcuate retinopathy in familial cone-rod dystrophy secondary to heterozygous CRX deletion. Ophthalmic Genet 2019; 40:493-499. [PMID: 31743059 DOI: 10.1080/13816810.2019.1688841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Purpose: To describe an arcuate retinopathy appearance in a familial cone-rod dystrophy and the underlying genetic cause.Methods: Retrospective case series of an affected three-generation family (eight affected members, eight unaffected members)Results: The proband, a 47-year-old male, noted significant visual loss since his early thirties. In addition to central macular atrophic changes, retinal examination was notable for peripapillary atrophy and an arcuate of drusenoid deep yellow lesions in the temporal macula. Spectral-domain optical coherence tomography in the area of the lesions showed regional outer neurosensory retina loss with nasal extension (forming a ring around the central retina) but no drusen. Full-field electroretinography revealed cone-rod dysfunction with an electronegative waveform. Fifteen other available family members were examined, and seven (age range 13-71 years old) showed variable expressivity for similar phenotypic findings, most notably the arcuate lesions in all but the oldest individual who had end-stage atrophy. Exome sequencing of the proband's affected daughter uncovered a heterozygous CRX deletion [NM_000554.4: CRX: c.(100 + 1_101-1)_(c.900 + 1_?)del] that segregated with the disease.Conclusion: An unusual familial cone-rod dystrophy phenotype was associated with heterozygous CRX deletion, a pathogenic variant that had a presumed mechanism of haploinsufficiency. The consistent finding of arcuate temporal macular lesions among affected family members was striking, particularly given the variable expressivity previously associated with CRX-related retinopathy. Additional phenotypic studies are needed to assess how frequently this temporal arcuate retinopathy appearance occurs in individuals harboring a similar deletion who are not from the current family.
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Affiliation(s)
- Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, UAE.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA
| | - Piergiorgio Neri
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, UAE.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA
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20
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Yi Z, Xiao X, Li S, Sun W, Zhang Q. Pathogenicity discrimination and genetic test reference for CRX variants based on genotype-phenotype analysis. Exp Eye Res 2019; 189:107846. [PMID: 31626798 DOI: 10.1016/j.exer.2019.107846] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/27/2019] [Accepted: 10/14/2019] [Indexed: 12/22/2022]
Abstract
The cone-rod homeobox (CRX) gene is specifically expressed in developing and mature photoreceptors and is relatively conserved, with limited polymorphisms in coding regions. Rare variants in CRX are usually considered causative for different forms of retinal degeneration, but this might be problematic based on recent data. This study aimed to classify CRX variants based on a genotype-phenotype analysis of our data and the literature. Twenty-four CRX variants, including 14 novel variants, were detected in 37 Chinese families based on exome sequencing data obtained from 4971 Chinese probands with different forms of eye diseases. After detailed phenotypic analysis and cosegregation analysis in families with CRX variants, the 24 variants could be classified into three groups: benign (six), likely benign (six), and pathogenic (12). Somatic mosaicism was identified in a family with unaffected parents (the father had a mutant allele that was detected in approximately 17% of his leukocyte DNA) and two affected sons. Furthermore, a thorough reassessment was systematically performed for all 113 heterozygous variants as well as for their associated phenotypes from our cohort and patients previously reported. Two critical findings on the pathogenicity of CRX variants were obtained based on the genotype-phenotype correlation, family segregation and ensemble predicting methods: 1) approximately half of heterozygous missense variants are likely benign, and 2) heterozygous truncating variants affecting the homeodomain are likely benign. Truncating mutations after the homeodomain are likely associated with a more severe phenotype. Although most heterozygous pathogenic variants in CRX are associated with autosomal dominant retinal degeneration, a homozygous c.268C> T (p.Arg90Trp) substitution and homozygous complete deletion of CRX have been reported to cause Leber congenital amaurosis. In conclusion, many rare missense variants and some truncating variants in CRX are likely benign, although previously, they might have been predicted to be damaging by some online tools. Evaluation of the pathogenicity of a CRX variant should consider both its nature and location. The information obtained in this study is critical in the era of routine clinical genetic test, not only for CRX but also for many other genes with many more variants. Functional studies and additional genotype-phenotype analyses are expected to confirm these associations.
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Affiliation(s)
- Zhen Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China.
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21
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Xie S, Han S, Qu Z, Liu F, Li J, Yu S, Reilly J, Tu J, Liu X, Lu Z, Hu X, Yimer TA, Qin Y, Huang Y, Lv Y, Jiang T, Shu X, Tang Z, Jia H, Wong F, Liu M. Knockout of Nr2e3 prevents rod photoreceptor differentiation and leads to selective L-/M-cone photoreceptor degeneration in zebrafish. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1273-1283. [PMID: 30684641 DOI: 10.1016/j.bbadis.2019.01.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 01/20/2019] [Accepted: 01/21/2019] [Indexed: 01/28/2023]
Abstract
Mutations in the photoreceptor cell-specific nuclear receptor gene Nr2e3 increased the number of S-cone photoreceptors in human and murine retinas and led to retinal degeneration that involved photoreceptor and non-photoreceptor cells. The mechanisms underlying these complex phenotypes remain unclear. In the hope of understanding the precise role of Nr2e3 in photoreceptor cell fate determination and differentiation, we generated a line of Nr2e3 knockout zebrafish using CRISPR technology. In these Nr2e3-null animals, rod precursors undergo terminal mitoses but fail to differentiate as rods. Rod-specific genes are not expressed and the outer segment (OS) fails to form. Formation and differentiation of cone photoreceptors is normal. Specifically, there is no increase in the number of UV-cone or S-cone photoreceptors. Laminated retinal structure is maintained. After normal development, L-/M-cones selectively degenerate, with progressive shortening of OS that starts at age 1 month. The amount of cone phototransduction proteins is concomitantly reduced, whereas UV- and S-cones have normal OS lengths even at age 10 months. In vitro studies show Nr2e3 synergizes with Crx and Nrl to enhance rhodopsin gene expression. Nr2e3 does not affect cone opsin expression. Our results extend the knowledge of Nr2e3's roles and have specific implications for the interpretation of the phenotypes observed in human and murine retinas. Furthermore, our model may offer new opportunities in finding treatments for enhanced S-cone syndrome (ESCS) and other retinal degenerative diseases.
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Affiliation(s)
- Shanglun Xie
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Shanshan Han
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Zhen Qu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Fei Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Jingzhen Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Shanshan Yu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - James Reilly
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, Scotland, United Kingdom of Great Britain and Northern Ireland
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Xiliang Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Zhaojing Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Xuebin Hu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Tinsae Assefa Yimer
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yayun Qin
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yuexia Lv
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Tao Jiang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Xinhua Shu
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, Scotland, United Kingdom of Great Britain and Northern Ireland
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Haibo Jia
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China.
| | - Fulton Wong
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China.
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22
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Gaspar P, Almudi I, Nunes MDS, McGregor AP. Human eye conditions: insights from the fly eye. Hum Genet 2018; 138:973-991. [PMID: 30386938 DOI: 10.1007/s00439-018-1948-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 10/20/2018] [Indexed: 12/22/2022]
Abstract
The fruit fly Drosophila melanogaster has served as an excellent model to study and understand the genetics of many human diseases from cancer to neurodegeneration. Studying the regulation of growth, determination and differentiation of the compound eyes of this fly, in particular, have provided key insights into a wide range of diseases. Here we review the regulation of the development of fly eyes in light of shared aspects with human eye development. We also show how understanding conserved regulatory pathways in eye development together with the application of tools for genetic screening and functional analyses makes Drosophila a powerful model to diagnose and characterize the genetics underlying many human eye conditions, such as aniridia and retinitis pigmentosa. This further emphasizes the importance and vast potential of basic research to underpin applied research including identifying and treating the genetic basis of human diseases.
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Affiliation(s)
- Pedro Gaspar
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Isabel Almudi
- Centro Andaluz de Biología del Desarrollo, CSIC/ Universidad Pablo de Olavide, Carretera de Utrera Km1, 41013, Sevilla, Spain
| | - Maria D S Nunes
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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23
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Motta FL, Martin RP, Filippelli-Silva R, Salles MV, Sallum JMF. Relative frequency of inherited retinal dystrophies in Brazil. Sci Rep 2018; 8:15939. [PMID: 30374144 PMCID: PMC6206004 DOI: 10.1038/s41598-018-34380-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/15/2018] [Indexed: 11/09/2022] Open
Abstract
Among the Brazilian population, the frequency rates of inherited retinal dystrophies and their causative genes are underreported. To increase the knowledge about these dystrophies in our population, we retrospectively studied the medical records of 1,246 Brazilian patients with hereditary retinopathies during 20 years of specialized outpatient clinic care. Of these patients, 559 had undergone at least one genetic test. In this cohort, the most prevalent dystrophies were non-syndromic retinitis pigmentosa (35%), Stargardt disease (21%), Leber congenital amaurosis (9%), and syndromic inherited retinal dystrophies (12%). Most patients had never undergone genetic testing (55%), and among the individuals with molecular test results, 28.4% had negative or inconclusive results compared to 71.6% with a conclusive molecular diagnosis. ABCA4 was the most frequent disease-causing gene, accounting for 20% of the positive cases. Pathogenic variants also occurred frequently in the CEP290, USH2A, CRB1, RPGR, and CHM genes. The relative frequency rates of different inherited retinal dystrophies in Brazil are similar to those found globally. Although mutations in more than 250 genes lead to hereditary retinopathies, only 66 genes were responsible for 70% of the cases, which indicated that smaller and cheaper gene panels can be just as effective and provide more affordable solutions for implementation by the Brazilian public health system.
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Affiliation(s)
- Fabiana Louise Motta
- Department of Ophthalmology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Renan Paulo Martin
- Department of Biophysics, Universidade Federal de São Paulo, São Paulo, Brazil.,Institute of Genetic Medicine, Johns Hopkins Medicine, Baltimore, USA
| | | | | | - Juliana Maria Ferraz Sallum
- Department of Ophthalmology, Universidade Federal de São Paulo, São Paulo, Brazil. .,Instituto de Genética Ocular, Sao Paulo, Brazil.
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24
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Romdhane K, Vaclavik V, Schorderet DF, Munier FL, Viet Tran H. CRX-linked macular dystrophy with intrafamilial variable expressivity. Ophthalmic Genet 2018; 39:637-641. [PMID: 30067412 DOI: 10.1080/13816810.2018.1502789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND We present a macular dystrophy of differing severity in a single kindred caused by a heterozygous nonsense mutation in CRX. CASE REPORT A 21-year-old Caucasian male from a Swiss family was investigated for decreasing central visual acuity associated with dischromatopsia. Clinical examination revealed posterior pole atrophy, including the maculopapillary bundle. Multimodal imaging, including autofluorescence, showed a hyperautofluorescent paramacular ring in both eyes. Genetic analysis identified a c.313C>T, p.Q105* nonsense mutation in CRX. The same mutation was identified in his father and uncle. Both of them showed signs of the disease, however with different severity. CONCLUSION We describe an intrafamilial variable expressivity of a CRX mutation causing an isolated macular dystrophy.
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Affiliation(s)
- Khaled Romdhane
- a Jules-Gonin Eye Hospital, Department of Ophthalmology , University of Lausanne , Lausanne , Switzerland
| | - Veronika Vaclavik
- a Jules-Gonin Eye Hospital, Department of Ophthalmology , University of Lausanne , Lausanne , Switzerland
| | - Daniel F Schorderet
- a Jules-Gonin Eye Hospital, Department of Ophthalmology , University of Lausanne , Lausanne , Switzerland.,b IRO-Institute for Research in Ophthalmology , Sion , Switzerland.,c Faculty of Life Sciences , Ecole Polytechnique Fédérale de Lausanne , Lausanne , Switzerland
| | - Francis L Munier
- a Jules-Gonin Eye Hospital, Department of Ophthalmology , University of Lausanne , Lausanne , Switzerland
| | - H Viet Tran
- a Jules-Gonin Eye Hospital, Department of Ophthalmology , University of Lausanne , Lausanne , Switzerland
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25
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Wang L, Qi A, Pan H, Liu B, Feng J, Chen W, Wang B. A novel CRX frameshift mutation causing cone-rod dystrophy in a Chinese family: A case report. Medicine (Baltimore) 2018; 97:e11499. [PMID: 30095615 PMCID: PMC6133598 DOI: 10.1097/md.0000000000011499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/20/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Cone-rod dystrophy (CORD) is an inherited, progressive retinal disorder with genetic and phenotypic heterogeneity. Here, we aimed to identify the pathogenic mutation in affected individuals in a Chinese family with autosomal dominant cone-rod dystrophy (adCORD). METHODS Genomic DNA and clinical examination results were collected from a Chinese family presenting with adCORD. The candidate disease-causing mutations were screened with whole-exome sequencing (WES) and bioinformatics analyses. Sanger sequencing was used for validation and cosegregation analysis. RESULTS A novel frameshift mutation (NM_000554.4; c.538dupG:p.Val180fs) in exon 4 of the CRX gene was identified in all affected individuals in the Chinese family with adCORD. Cosegregation analysis confirmed that this mutation was cosegregated with the disease. This variant, which results in premature termination of the protein, was absent from all public variant databases or internal exome databases. CONCLUSIONS We used whole-exome sequencing to identify a novel CRX mutation causing adCORD in a Chinese family. This study broadens the known pathogenic mutation spectrum of the CRX gene and shows the potential of WES in identifying the pathogenic mutations of CORD disease.
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Affiliation(s)
- Lihua Wang
- Department of Ophthalmology, Beijing Haidian Maternal and Child Health Hospital
| | - Anhui Qi
- Graduate School of Peking Union Medical College
- Center for Genetics, National Research Institute for Family Planning, Beijing, China
| | - Hong Pan
- Graduate School of Peking Union Medical College
- Center for Genetics, National Research Institute for Family Planning, Beijing, China
| | - Beihong Liu
- Graduate School of Peking Union Medical College
- Center for Genetics, National Research Institute for Family Planning, Beijing, China
| | - Jingjing Feng
- Department of Ophthalmology, Beijing Haidian Maternal and Child Health Hospital
| | - Wei Chen
- Department of Ophthalmology, Beijing Haidian Maternal and Child Health Hospital
| | - Binbin Wang
- Graduate School of Peking Union Medical College
- Center for Genetics, National Research Institute for Family Planning, Beijing, China
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26
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Wang J, Zibetti C, Shang P, Sripathi SR, Zhang P, Cano M, Hoang T, Xia S, Ji H, Merbs SL, Zack DJ, Handa JT, Sinha D, Blackshaw S, Qian J. ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration. Nat Commun 2018; 9:1364. [PMID: 29636475 PMCID: PMC5893535 DOI: 10.1038/s41467-018-03856-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
Age-related macular degeneration (AMD) is a significant cause of vision loss in the elderly. The extent to which epigenetic changes regulate AMD progression is unclear. Here we globally profile chromatin accessibility using ATAC-Seq in the retina and retinal pigmented epithelium (RPE) from AMD and control patients. Global decreases in chromatin accessibility occur in the RPE with early AMD, and in the retina of advanced disease, suggesting that dysfunction in the RPE drives disease onset. Footprints of photoreceptor and RPE-specific transcription factors are enriched in differentially accessible regions (DARs). Genes associated with DARs show altered expression in AMD. Cigarette smoke treatment of RPE cells recapitulates chromatin accessibility changes seen in AMD, providing an epigenetic link between a known risk factor for AMD and AMD pathology. Finally, overexpression of HDAC11 is partially responsible for the observed reduction in chromatin accessibility, suggesting that HDAC11 may be a potential new therapeutic target for AMD.
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Affiliation(s)
- Jie Wang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Cristina Zibetti
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Peng Shang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Departments of Ophthalmology, Cell Biology and Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
| | - Srinivasa R Sripathi
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Pingwu Zhang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Marisol Cano
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Thanh Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shuli Xia
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Hugo W Moser Research Institute at Kennedy Krieger, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Shannath L Merbs
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Donald J Zack
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - James T Handa
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Debasish Sinha
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Departments of Ophthalmology, Cell Biology and Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
| | - Seth Blackshaw
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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27
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Abstract
Retinal blindness is an important cause of pediatric visual loss. Leber's congenital amaurosis (LCA) is one of these causes, often wrongly included in the spectrum of retinitis pigmentosa. The disease has become the center of research after initial reports of success in management with gene therapy. This review discusses in brief the clinical presentation and investigative modalities used in LCA. Further, the road to gene discovery and details of currently applied gene therapy are presented. LCA is one of the first successfully managed human diseases and offers an entirely new dimension in ocular therapeutics.
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28
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Li S, Xi Q, Zhang X, Yu D, Li L, Jiang Z, Chen Q, Wang QK, Traboulsi EI. Identification of a mutation in CNNM4 by whole exome sequencing in an Amish family and functional link between CNNM4 and IQCB1. Mol Genet Genomics 2018; 293:699-710. [PMID: 29322253 DOI: 10.1007/s00438-018-1417-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 01/06/2018] [Indexed: 12/15/2022]
Abstract
We investigated an Amish family in which three siblings presented with an early-onset childhood retinal dystrophy inherited in an autosomal recessive fashion. Genome-wide linkage analysis identified significant linkage to marker D2S2216 on 2q11 with a two-point LOD score of 1.95 and a multi-point LOD score of 3.76. Whole exome sequencing was then performed for the three affected individuals and identified a homozygous nonsense mutation (c.C1813T, p.R605X) in the cyclin and CBS domain divalent metal cation transport mediator 4 (CNNM4) gene located within the 2p14-2q14 Jalili syndrome locus. The initial assessment and collection of the family were performed before the clinical delineation of Jalili syndrome. Another assessment was made after the discovery of the responsible gene and the dental abnormalities characteristic of Jalili syndrome were retrospectively identified. The p.R605X mutation represents the first probable founder mutation of Jalili syndrome identified in the Amish community. The molecular mechanism underlying Jalili syndrome is unknown. Here we show that CNNM4 interacts with IQCB1, which causes Leber congenital amaurosis (LCA) when mutated. A truncated CNNM4 protein starting at R605 significantly increased the rate of apoptosis, and significantly increased the interaction between CNNM4 and IQCB1. Mutation p.R605X may cause Jalili syndrome by a nonsense-mediated decay mechanism, affecting the function of IQCB1 and apoptosis, or both. Our data, for the first time, functionally link Jalili syndrome gene CNNM4 to LCA gene IQCB1, providing important insights into the molecular pathogenic mechanism of retinal dystrophy in Jalili syndrome.
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Affiliation(s)
- Sisi Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research and Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Quansheng Xi
- Department of Molecular Cardiology, Center for Cardiovascular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA
| | - Xiaoyu Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research and Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Dong Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research and Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Lin Li
- Department of Molecular Cardiology, Center for Cardiovascular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA
| | - Zhenyang Jiang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research and Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qiuyun Chen
- Department of Molecular Cardiology, Center for Cardiovascular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Cleveland, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44195, USA
| | - Qing K Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research and Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Department of Molecular Cardiology, Center for Cardiovascular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Cleveland, USA.
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44195, USA.
| | - Elias I Traboulsi
- Center for Genetic Eye Diseases, Cleveland Clinic Cole Eye Institute, Cleveland, OH, 44195, USA.
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Møller M, Rath MF, Ludvigsen M, Honoré B, Vorum H. Diurnal expression of proteins in the retina of the blind cone-rod homeobox (Crx -/- ) mouse and the 129/Sv mouse: a proteomic study. Acta Ophthalmol 2017; 95:717-726. [PMID: 28371363 DOI: 10.1111/aos.13429] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/06/2017] [Indexed: 01/06/2023]
Abstract
PURPOSE The vertebrate retina contains a circadian clock participating in adaptations to day and night vision. This peripheral clock is independent of the master clock in the suprachiasmatic nucleus (SCN). The retinal clock is located in several cell types, including the photoreceptors. To investigate the role of the circadian clock of the photoreceptor cells in regulation of retinal protein rhythms, we analysed diurnal protein expression in the photoreceptor-deficient cone-rod homeobox knockout mouse (Crx-/- ) and the 129/Sv mouse. METHODS 2D gels were made from retinal homogenates of 129/Sv and Crx-/- mice killed at midday and midnight. Stained gels were analysed by use of PDQuest 2D gel analysis software. After trypsin digestion of differential expressed spots, the proteins were identified by LC-MS/MS using a nano-liquid chromatograph connected to a Q-TOF Premier mass spectrometer. These data were used to search the SWISS-PROT database. RESULTS Both the retinae of the control and the Crx-/- mice exhibited diurnal proteins rhythms. As expected, proteins involved in phototransduction were not detected in the Crx-/- mouse; in this phenotype, however, proteins from spots showing diurnal rhythms were specifically identified as enzymes involved in glucose metabolism, Krebs cycle, and mitochondrial enzymes. Data are available via ProteomeXchange with identifier PXD005556. CONCLUSION We show diurnal protein rhythms in the retina of a mouse lacking the rods and cones. The diurnal protein rhythms in this genotype, lacking the circadian clock of the photoreceptors, might be caused by a circadian clock in other retinal cell types or a direct light input to the retina.
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Affiliation(s)
- Morten Møller
- Department of Neuroscience and Pharmacology; Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Martin Fredensborg Rath
- Department of Neuroscience and Pharmacology; Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Maja Ludvigsen
- Department of Clinical Medicine; Aarhus University; Aarhus Denmark
- Department of Hematology; Aarhus University Hospital; Aarhus Denmark
| | - Bent Honoré
- Department of Biomedicine; Aarhus University; Aarhus Denmark
| | - Henrik Vorum
- Department of Ophthalmology; Aalborg University Hospital; Aalborg Denmark
- Department of Clinical Medicine; Aalborg University; Aalborg Denmark
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30
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Griffith JF, DeBenedictis MJ, Traboulsi EI. A novel dominant CRX mutation causes adult-onset macular dystrophy. Ophthalmic Genet 2017; 39:120-124. [DOI: 10.1080/13816810.2017.1373831] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Occelli LM, Tran NM, Narfström K, Chen S, Petersen-Jones SM. CrxRdy Cat: A Large Animal Model for CRX-Associated Leber Congenital Amaurosis. Invest Ophthalmol Vis Sci 2017; 57:3780-92. [PMID: 27427859 PMCID: PMC4960999 DOI: 10.1167/iovs.16-19444] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Purpose Mutations in the retinal transcription factor cone-rod homeobox (CRX) gene result in severe dominant retinopathies. A large animal model, the Rdy cat, carrying a spontaneous frameshift mutation in Crx, was reported previously. The present study aimed to further understand pathogenesis in this model by thoroughly characterizing the Rdy retina. Methods Structural and functional changes were found in a comparison between the retinas of CrxRdy/+ kittens and those of wild-type littermates and were determined at various ages by fundus examination, electroretinography (ERG), optical coherence tomography, and histologic analyses. RNA and protein expression changes of Crx and key target genes were analyzed using quantitative reverse-transcribed PCR, Western blot analysis, and immunohistochemistry. Transcription activity of the mutant Crx was measured by a dual-luciferase transactivation assay. Results CrxRdy/+ kittens had no recordable cone ERGs. Rod responses were delayed in development and markedly reduced at young ages and lost by 20 weeks. Photoreceptor outer segment development was incomplete and was followed by progressive outer retinal thinning starting in the cone-rich area centralis. Expression of cone and rod Crx target genes was significantly down-regulated. The mutant Crx allele was overexpressed, leading to high levels of the mutant protein lacking transactivation activity. Conclusions The CrxRdy mutation exerts a dominant negative effect on wild-type Crx by overexpressing mutant protein. These findings, consistent with those of studies in a mouse model, support a conserved pathogenic mechanism for CRX frameshift mutations. The similarities between the feline eye and the human eye with the presence of a central region of high cone density makes the CrxRdy/+ cat a valuable model for preclinical testing of therapies for dominant CRX diseases.
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Affiliation(s)
- Laurence M Occelli
- Small Animal Clinical Sciences Michigan State University, East Lansing, Michigan, United States
| | - Nicholas M Tran
- Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Kristina Narfström
- Department of Veterinary Medicine and Surgery, University of Missouri-Columbia, Columbia, Missouri, United States
| | - Shiming Chen
- Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Simon M Petersen-Jones
- Small Animal Clinical Sciences Michigan State University, East Lansing, Michigan, United States
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Corton M, Avila-Fernández A, Campello L, Sánchez M, Benavides B, López-Molina MI, Fernández-Sánchez L, Sánchez-Alcudia R, da Silva LRJ, Reyes N, Martín-Garrido E, Zurita O, Fernández-San José P, Pérez-Carro R, García-García F, Dopazo J, García-Sandoval B, Cuenca N, Ayuso C. Identification of the Photoreceptor Transcriptional Co-Repressor SAMD11 as Novel Cause of Autosomal Recessive Retinitis Pigmentosa. Sci Rep 2016; 6:35370. [PMID: 27734943 PMCID: PMC5062157 DOI: 10.1038/srep35370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/28/2016] [Indexed: 01/09/2023] Open
Abstract
Retinitis pigmentosa (RP), the most frequent form of inherited retinal dystrophy is characterized by progressive photoreceptor degeneration. Many genes have been implicated in RP development, but several others remain to be identified. Using a combination of homozygosity mapping, whole-exome and targeted next-generation sequencing, we found a novel homozygous nonsense mutation in SAMD11 in five individuals diagnosed with adult-onset RP from two unrelated consanguineous Spanish families. SAMD11 is ortholog to the mouse major retinal SAM domain (mr-s) protein that is implicated in CRX-mediated transcriptional regulation in the retina. Accordingly, protein-protein network analysis revealed a significant interaction of SAMD11 with CRX. Immunoblotting analysis confirmed strong expression of SAMD11 in human retina. Immunolocalization studies revealed SAMD11 was detected in the three nuclear layers of the human retina and interestingly differential expression between cone and rod photoreceptors was observed. Our study strongly implicates SAMD11 as novel cause of RP playing an important role in the pathogenesis of human degeneration of photoreceptors.
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Affiliation(s)
- M Corton
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - A Avila-Fernández
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - L Campello
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - M Sánchez
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - B Benavides
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - M I López-Molina
- Department of Ophthalmology, Health Research Institute- Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain
| | - L Fernández-Sánchez
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - R Sánchez-Alcudia
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - L R J da Silva
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Universidade de Mogi das Cruzes, São Paulo, Brazil
| | - N Reyes
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - E Martín-Garrido
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - O Zurita
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - P Fernández-San José
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - R Pérez-Carro
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - F García-García
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Bioinformatics in Rare Diseases (BIER), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Valencia, Spain
| | - J Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Bioinformatics in Rare Diseases (BIER), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Valencia, Spain.,Functional Genomics Node (INB), Valencia, Spain
| | - B García-Sandoval
- Department of Ophthalmology, Health Research Institute- Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain
| | - N Cuenca
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - C Ayuso
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
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Barabino A, Plamondon V, Abdouh M, Chatoo W, Flamier A, Hanna R, Zhou S, Motoyama N, Hébert M, Lavoie J, Bernier G. Loss of Bmi1 causes anomalies in retinal development and degeneration of cone photoreceptors. Development 2016; 143:1571-84. [PMID: 26965367 DOI: 10.1242/dev.125351] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 03/01/2016] [Indexed: 12/17/2022]
Abstract
Retinal development occurs through the sequential but overlapping generation of six types of neuronal cells and one glial cell type. Of these, rod and cone photoreceptors represent the functional unit of light detection and phototransduction and are frequently affected in retinal degenerative diseases. During mouse development, the Polycomb group protein Bmi1 is expressed in immature retinal progenitors and differentiated retinal neurons, including cones. We show here that Bmi1 is required to prevent post natal degeneration of cone photoreceptors and bipolar neurons and that inactivation of Chk2 or p53 could improve but not overcome cone degeneration in Bmi1(-/-) mice. The retinal phenotype of Bmi1(-/-) mice was also characterized by loss of heterochromatin, activation of tandem repeats, oxidative stress and Rip3-associated necroptosis. In the human retina, BMI1 was preferentially expressed in cones at heterochromatic foci. BMI1 inactivation in human embryonic stem cells was compatible with retinal induction but impaired cone terminal differentiation. Despite this developmental arrest, BMI1-deficient cones recapitulated several anomalies observed in Bmi1(-/-) photoreceptors, such as loss of heterochromatin, activation of tandem repeats and induction of p53, revealing partly conserved biological functions between mouse and man.
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Affiliation(s)
- Andrea Barabino
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montréal, Canada H1T 2M4
| | - Vicky Plamondon
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montréal, Canada H1T 2M4
| | - Mohamed Abdouh
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montréal, Canada H1T 2M4
| | - Wassim Chatoo
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montréal, Canada H1T 2M4
| | - Anthony Flamier
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montréal, Canada H1T 2M4
| | - Roy Hanna
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montréal, Canada H1T 2M4
| | - Shufeng Zhou
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montréal, Canada H1T 2M4
| | - Noboru Motoyama
- Department of Cognitive Brain Science, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, 36-3 Gengo, Morioka, Obu, Aichi 474-8522, Japan
| | - Marc Hébert
- Department of Ophthalmology, Otorhinolaryngology and Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Laval, Canada G1V 0A6
| | - Joëlle Lavoie
- Department of Ophthalmology, Otorhinolaryngology and Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Laval, Canada G1V 0A6
| | - Gilbert Bernier
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montréal, Canada H1T 2M4 Department of Neurosciences, Université de Montréal, Montréal, Canada H3T 1J4 Department of Ophthalmology, Université de Montréal, Montréal, Canada H3T 1J4
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34
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Next-generation sequencing-based molecular diagnosis of 12 inherited retinal disease probands of Uyghur ethnicity. Sci Rep 2016; 6:21384. [PMID: 26856745 PMCID: PMC4746660 DOI: 10.1038/srep21384] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 01/22/2016] [Indexed: 01/10/2023] Open
Abstract
Inherited retinal disease (IRD) is a category of genetic disorders affecting retina. Understanding the molecular basis of IRD is vital for clinical and genetic classification of patients. Uyghur people is an isolated ethnic group mainly residing in northwestern China with genetic admixture from Europeans and East Asians. The genetic etiology of IRD in this specific population still remains unknown. Here, by next-generation sequencing (NGS), we screened mutations in over 200 known retinal disease genes in a cohort of 12 unrelated Uyghur IRD probands. Out of the 12 probands, six are solved with high confidence, two with low confidence, while the remaining four are unsolved. We identified known disease-causing alleles in this cohort that suggest ancient Uyghur migration and also discovered eight novel disease-associated variants. Our results showed NGS-based mutation screening as a reliable approach for molecular diagnosis. In addition, this approach can also be applied to reveal the genetic history of a specific ethnic group.
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35
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Wang H, Wang X, Zou X, Xu S, Li H, Soens ZT, Wang K, Li Y, Dong F, Chen R, Sui R. Comprehensive Molecular Diagnosis of a Large Chinese Leber Congenital Amaurosis Cohort. Invest Ophthalmol Vis Sci 2015; 56:3642-55. [PMID: 26047050 DOI: 10.1167/iovs.14-15972] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Leber congenital amaurosis (LCA) is an inherited retinal disease that causes early-onset severe visual impairment. To evaluate the mutation spectrum in the Chinese population, we performed a mutation screen in 145 Chinese LCA families. METHODS First, we performed direct Sanger sequencing of 7 LCA disease genes in 81 LCA families. Next, we developed a capture panel that enriches the entire coding exons and splicing sites of 163 known retinal disease genes and other candidate retinal disease genes. The capture panel allowed us to quickly identify disease-causing mutations in a large number of genes at a relatively low cost. Thus, this method was applied to the 53 LCA families that were unsolved by direct Sanger sequencing of 7 LCA disease genes and an additional 64 LCA families. Systematic next-generation sequencing (NGS) data analysis, Sanger sequencing validation, and segregation analysis were used to identify pathogenic mutations. RESULTS Homozygous or compound heterozygous mutations were identified in 107 families, heterozygous autosomal dominant mutations were identified in 3 families and an X-linked mutation was found in 1 family, for a combined solving rate of 76.6%. In total, 136 novel pathogenic mutations were found in this study. In combination with two previous studies carried out in Chinese LCA patients, we concluded that the mutation spectrum in the Chinese population is distinct compared to that in the European population. After revisiting, we also refined the clinical diagnosis of 10 families based on their molecular diagnosis. CONCLUSIONS Our results highlight the importance of a molecular diagnosis as an integral part of the clinical diagnostic process.
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Affiliation(s)
- Hui Wang
- Institute of Developmental and Regenerative Biology Hangzhou Normal University, Jianggan, Hangzhou, Zhejiang, China
| | - Xia Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States 3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Xuan Zou
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Dongcheng, Beijing, China
| | - Shan Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Hui Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Dongcheng, Beijing, China
| | - Zachry Tore Soens
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Keqing Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States 3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States 3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Fangtian Dong
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Dongcheng, Beijing, China
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States 3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States 5Structural and Computational Biology & Molecular Biophysics
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Dongcheng, Beijing, China
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36
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The pros and cons of vertebrate animal models for functional and therapeutic research on inherited retinal dystrophies. Prog Retin Eye Res 2015; 48:137-59. [DOI: 10.1016/j.preteyeres.2015.04.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/12/2015] [Accepted: 04/16/2015] [Indexed: 01/19/2023]
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37
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Nash BM, Wright DC, Grigg JR, Bennetts B, Jamieson RV. Retinal dystrophies, genomic applications in diagnosis and prospects for therapy. Transl Pediatr 2015; 4:139-63. [PMID: 26835369 PMCID: PMC4729094 DOI: 10.3978/j.issn.2224-4336.2015.04.03] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Retinal dystrophies (RDs) are degenerative diseases of the retina which have marked clinical and genetic heterogeneity. Common presentations among these disorders include night or colour blindness, tunnel vision and subsequent progression to complete blindness. The known causative disease genes have a variety of developmental and functional roles with mutations in more than 120 genes shown to be responsible for the phenotypes. In addition, mutations within the same gene have been shown to cause different disease phenotypes, even amongst affected individuals within the same family highlighting further levels of complexity. The known disease genes encode proteins involved in retinal cellular structures, phototransduction, the visual cycle, and photoreceptor structure or gene regulation. This review aims to demonstrate the high degree of genetic complexity in both the causative disease genes and their associated phenotypes, highlighting the more common clinical manifestation of retinitis pigmentosa (RP). The review also provides insight to recent advances in genomic molecular diagnosis and gene and cell-based therapies for the RDs.
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Affiliation(s)
- Benjamin M Nash
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Dale C Wright
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - John R Grigg
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Bruce Bennetts
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Robyn V Jamieson
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
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Jayakody SA, Gonzalez-Cordero A, Ali RR, Pearson RA. Cellular strategies for retinal repair by photoreceptor replacement. Prog Retin Eye Res 2015; 46:31-66. [PMID: 25660226 DOI: 10.1016/j.preteyeres.2015.01.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 01/13/2015] [Accepted: 01/19/2015] [Indexed: 02/08/2023]
Abstract
Loss of photoreceptors due to retinal degeneration is a major cause of blindness in the developed world. While no effective treatment is currently available, cell replacement therapy, using pluripotent stem cell-derived photoreceptor precursor cells, may be a feasible future treatment. Recent reports have demonstrated rescue of visual function following the transplantation of immature photoreceptors and we have seen major advances in our ability to generate transplantation-competent donor cells from stem cell sources. Moreover, we are beginning to realise the possibilities of using endogenous populations of cells from within the retina itself to mediate retinal repair. Here, we present a review of our current understanding of endogenous repair mechanisms together with recent progress in the use of both ocular and pluripotent stem cells for the treatment of photoreceptor loss. We consider how our understanding of retinal development has underpinned many of the recent major advances in translation and moved us closer to the goal of restoring vision by cellular means.
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Affiliation(s)
- Sujatha A Jayakody
- Gene and Cell Therapy Group, Department of Genetics, UCL Institute of Ophthalmology, 11-43 Bath St, London EC1V 9EL, UK
| | - Anai Gonzalez-Cordero
- Gene and Cell Therapy Group, Department of Genetics, UCL Institute of Ophthalmology, 11-43 Bath St, London EC1V 9EL, UK
| | - Robin R Ali
- Gene and Cell Therapy Group, Department of Genetics, UCL Institute of Ophthalmology, 11-43 Bath St, London EC1V 9EL, UK; NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, City Road, London EC1V 2PD, UK
| | - Rachael A Pearson
- Gene and Cell Therapy Group, Department of Genetics, UCL Institute of Ophthalmology, 11-43 Bath St, London EC1V 9EL, UK.
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Yücel-Yılmaz D, Tarlan B, Kıratlı H, Ozgül RK. Genome-wide homozygosity mapping in families with leber congenital amaurosis identifies mutations in AIPL1 and RDH12 genes. DNA Cell Biol 2015; 33:876-83. [PMID: 25148430 DOI: 10.1089/dna.2014.2554] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Leber congenital amaurosis (LCA) causes severe visual impairment and blindness very early in life. Mutant alleles of several genes acting in different pathways, of which all have critical roles for normal retinal function, were involved in LCA development. The purpose of this study was to use genome-wide genotyping to identify LCA-causing loci in two Turkish families. Genome-wide genotyping and haplotype analysis were performed for prioritization of candidate genes for mutation screening in families with LCA. Identified informative critical choromosomal regions obtained by homozygosity mapping from the families were searched for overlapping of any LCA causative genes. Corresponding clinical phenotypes of the patients with identified mutations were evaluated. In this study, two families were shown to be linked to two different LCA loci covering retinol dehydrogenase 12 (RDH12) and aryl-hydrocarbon-interacting protein-like1 (AIPL1) genes. Mutation screening revealed a novel p.Gln141* mutation in the AIPL1 gene and a previously described p.Thr49Met mutation in the RDH12 gene in a homozygous state. Our patients with the RDH12 mutation had the distinct macular coloboma sign, and the patient with the AIPL1 mutation developed microphthalmia and severe widespread retinal pigment epithelial atrophy, in contrast to previously reported cases. It is currently evident that mutation screening needs to be done in at least 18 genes known to be associated with LCA. Thus, homozygosity mapping is an alternative technique to improve the molecular diagnosis in LCA, which is a group of genetically and clinically heterogeneous diseases causing retinal degeneration. The patients without mutation in known genes may further be analyzed by using next-generation sequencing.
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Affiliation(s)
- Didem Yücel-Yılmaz
- 1 Metabolism Unit, Department of Pediatrics, Institute of Child Health, Hacettepe University , Ankara, Turkey
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Yamamoto S, Jaiswal M, Charng WL, Gambin T, Karaca E, Mirzaa G, Wiszniewski W, Sandoval H, Haelterman NA, Xiong B, Zhang K, Bayat V, David G, Li T, Chen K, Gala U, Harel T, Pehlivan D, Penney S, Vissers LELM, de Ligt J, Jhangiani SN, Xie Y, Tsang SH, Parman Y, Sivaci M, Battaloglu E, Muzny D, Wan YW, Liu Z, Lin-Moore AT, Clark RD, Curry CJ, Link N, Schulze KL, Boerwinkle E, Dobyns WB, Allikmets R, Gibbs RA, Chen R, Lupski JR, Wangler MF, Bellen HJ. A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases. Cell 2014; 159:200-214. [PMID: 25259927 PMCID: PMC4298142 DOI: 10.1016/j.cell.2014.09.002] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 06/04/2014] [Accepted: 09/02/2014] [Indexed: 12/31/2022]
Abstract
Invertebrate model systems are powerful tools for studying human disease owing to their genetic tractability and ease of screening. We conducted a mosaic genetic screen of lethal mutations on the Drosophila X chromosome to identify genes required for the development, function, and maintenance of the nervous system. We identified 165 genes, most of whose function has not been studied in vivo. In parallel, we investigated rare variant alleles in 1,929 human exomes from families with unsolved Mendelian disease. Genes that are essential in flies and have multiple human homologs were found to be likely to be associated with human diseases. Merging the human data sets with the fly genes allowed us to identify disease-associated mutations in six families and to provide insights into microcephaly associated with brain dysgenesis. This bidirectional synergism between fly genetics and human genomics facilitates the functional annotation of evolutionarily conserved genes involved in human health.
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Affiliation(s)
- Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
| | - Manish Jaiswal
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Institute of Computer Science, Warsaw University of Technology, 00-661 Warsaw, Poland
| | - Ender Karaca
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Ghayda Mirzaa
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Hector Sandoval
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Nele A Haelterman
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Bo Xiong
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Ke Zhang
- Program in Structural and Computational Biology and Molecular Biophysics, BCM, Houston, TX 77030, USA
| | - Vafa Bayat
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Gabriela David
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Tongchao Li
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Kuchuan Chen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Upasana Gala
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Samantha Penney
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Joep de Ligt
- Department of Human Genetics, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | - Yajing Xie
- Department of Ophthalmology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yesim Parman
- Neurology Department and Neuropathology Laboratory, Istanbul University Medical School, Istanbul 34390, Turkey
| | - Merve Sivaci
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul 34342, Turkey
| | - Esra Battaloglu
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul 34342, Turkey
| | - Donna Muzny
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, BCM, Houston, TX 77030, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Department of Pediatrics, BCM, Houston, TX 77030, USA
| | | | - Robin D Clark
- Division of Medical Genetics, Department of Pediatrics, Loma Linda University Medical Center, Loma Linda, CA 92354, USA
| | - Cynthia J Curry
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA; Genetic Medicine Central California, Fresno, CA 93701, USA
| | - Nichole Link
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Karen L Schulze
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA; Human Genetics Center, University of Texas, Health Science Center, Houston, TX 77030, USA
| | - William B Dobyns
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Neurology, University of Washington, Seattle WA 98195, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Rui Chen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA; Program in Structural and Computational Biology and Molecular Biophysics, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA.
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Aslanidis A, Karlstetter M, Walczak Y, Jägle H, Langmann T. RETINA-specific expression of Kcnv2 is controlled by cone-rod homeobox (Crx) and neural retina leucine zipper (Nrl). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 801:31-41. [PMID: 24664678 DOI: 10.1007/978-1-4614-3209-8_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Cone dystrophy with supernormal rod response (CDSRR) is an autosomal recessive disorder that leads to progressive retinal degeneration with a distinct electroretinogram (ERG) phenotype. CDSRR patients show reduced sensitivity to dim light, augmented response to suprathreshold light and reduced response to flicker. The disorder is caused by mutations in the KCNV2 gene, which encodes the Kv11.1 subunit of a voltage-gated potassium channel. Here, we studied the retina-specific expression and cis-regulatory activity of the murine Kcnv2 gene using electroporation of explanted retinas. Using qRT-PCR profiling of early postnatal retinas, we showed that Kcnv2 expression increased towards P14, which marks the beginning of visual activity in mice. In vivo electroporation of GFP-Kcnv2 expressing plasmids revealed that Kv11.1 localizes to the inner segment membranes of adult P21 photoreceptors. Using bioinformatic prediction and chromatin immunoprecipitation (ChIP), we identified two Crx binding sites (CBS) and one Nrl binding site (NBS) in the Kcnv2 promoter. Reporter electroporation of the wild type promoter region induced strong DsRed expression, indicating high regulatory activity, whereas shRNA-mediated knockdown of Crx and Nrl resulted in reduced Kcnv2 promoter activity and low endogenous Kcnv2 mRNA expression in the retina. Site-directed mutagenesis of the CBS and NBS demonstrated that CBS2 is crucial for Kcnv2 promoter activity. We conclude that nucleotide changes in evolutionary conserved CBS could impact retina-specific expression levels of Kcnv2.
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Affiliation(s)
- Alexander Aslanidis
- Department of Ophthalmology, University of Cologne, Joseph-Stelzmann-Str. 9, 50931, Cologne, Germany
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Tran NM, Chen S. Mechanisms of blindness: animal models provide insight into distinct CRX-associated retinopathies. Dev Dyn 2014; 243:1153-66. [PMID: 24888636 DOI: 10.1002/dvdy.24151] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/24/2014] [Accepted: 05/10/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The homeodomain transcription factor CRX is a crucial regulator of mammalian photoreceptor gene expression. Mutations in the human CRX gene are associated with dominant inherited retinopathies Retinitis Pigmentosa (RP), Cone-Rod Dystrophy (CoRD), and Leber Congenital Amaurosis (LCA), of varying severity. In vitro and in vivo assessment of mutant CRX proteins have revealed pathogenic mechanisms for several mutations, but no comprehensive mutation-disease correlation has yet been reported. RESULTS Here we describe four different classes of disease-causing CRX mutations, characterized by mutation type, pathogenetic mechanism, and the molecular activity of the mutant protein: (1) hypomorphic missense mutations with reduced DNA binding, (2) antimorphic missense mutations with variable DNA binding, (3) antimorphic frameshift/nonsense mutations with intact DNA binding, and (4) antimorphic frameshift mutations with reduced DNA binding. Mammalian models representing three of these classes have been characterized. CONCLUSIONS Models carrying Class I mutations display a mild dominant retinal phenotype and recessive LCA, while models carrying Class III and IV mutations display characteristically distinct dominant LCA phenotypes. These animal models also reveal unexpected pathogenic mechanisms underlying CRX-associated retinopathies. The complexity of genotype-phenotype correlation for CRX-associated diseases highlights the value of developing comprehensive "true-to-disease" animal models for understanding pathologic mechanisms and testing novel therapeutic approaches.
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Affiliation(s)
- Nicholas M Tran
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, Missouri
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Samuel A, Housset M, Fant B, Lamonerie T. Otx2 ChIP-seq reveals unique and redundant functions in the mature mouse retina. PLoS One 2014; 9:e89110. [PMID: 24558479 PMCID: PMC3928427 DOI: 10.1371/journal.pone.0089110] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/17/2014] [Indexed: 11/18/2022] Open
Abstract
During mouse retinal development and into adulthood, the transcription factor Otx2 is expressed in pigment epithelium, photoreceptors and bipolar cells. In the mature retina, Otx2 ablation causes photoreceptor degeneration through a non-cell-autonomous mechanism involving Otx2 function in the supporting RPE. Surprisingly, photoreceptor survival does not require Otx2 expression in the neural retina, where the related Crx homeobox gene, a major regulator of photoreceptor development, is also expressed. To get a deeper view of mouse Otx2 activities in the neural retina, we performed chromatin-immunoprecipitation followed by massively parallel sequencing (ChIP-seq) on Otx2. Using two independent ChIP-seq assays, we identified consistent sets of Otx2-bound cis-regulatory elements. Comparison with our previous RPE-specific Otx2 ChIP-seq data shows that Otx2 occupies different functional domains of the genome in RPE cells and in neural retina cells and regulates mostly different sets of genes. To assess the potential redundancy of Otx2 and Crx, we compared our data with Crx ChIP-seq data. While Crx genome occupancy markedly differs from Otx2 genome occupancy in the RPE, it largely overlaps that of Otx2 in the neural retina. Thus, in accordance with its essential role in the RPE and its non-essential role in the neural retina, Otx2 regulates different gene sets in the RPE and the neural retina, and shares an important part of its repertoire with Crx in the neural retina. Overall, this study provides a better understanding of gene-regulatory networks controlling photoreceptor homeostasis and disease.
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Affiliation(s)
- Alexander Samuel
- Institut de Biologie Valrose, University of Nice Sophia Antipolis, CNRS UMR7277, Inserm U1091, Nice, France
| | - Michael Housset
- Institut de Biologie Valrose, University of Nice Sophia Antipolis, CNRS UMR7277, Inserm U1091, Nice, France
| | - Bruno Fant
- Institut de Biologie Valrose, University of Nice Sophia Antipolis, CNRS UMR7277, Inserm U1091, Nice, France
| | - Thomas Lamonerie
- Institut de Biologie Valrose, University of Nice Sophia Antipolis, CNRS UMR7277, Inserm U1091, Nice, France
- * E-mail:
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44
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Tran NM, Zhang A, Zhang X, Huecker JB, Hennig AK, Chen S. Mechanistically distinct mouse models for CRX-associated retinopathy. PLoS Genet 2014; 10:e1004111. [PMID: 24516401 PMCID: PMC3916252 DOI: 10.1371/journal.pgen.1004111] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 12/02/2013] [Indexed: 12/02/2022] Open
Abstract
Cone-rod homeobox (CRX) protein is a “paired-like” homeodomain transcription factor that is essential for regulating rod and cone photoreceptor transcription. Mutations in human CRX are associated with the dominant retinopathies Retinitis Pigmentosa (RP), Cone-Rod Dystrophy (CoRD) and Leber Congenital Amaurosis (LCA), with variable severity. Heterozygous Crx Knock-Out (KO) mice (“+/−”) have normal vision as adults and fail to model the dominant human disease. To investigate how different mutant CRX proteins produce distinct disease pathologies, we generated two Crx Knock-IN (K-IN) mouse models: CrxE168d2 (“E168d2”) and CrxR90W (“R90W”). E168d2 mice carry a frameshift mutation in the CRX activation domain, Glu168del2, which is associated with severe dominant CoRD or LCA in humans. R90W mice carry a substitution mutation in the CRX homeodomain, Arg90Trp, which is associated with dominant mild late-onset CoRD and recessive LCA. As seen in human patients, heterozygous E168d2 (“E168d2/+”) but not R90W (“R90W/+”) mice show severely impaired retinal function, while mice homozygous for either mutation are blind and undergo rapid photoreceptor degeneration. E168d2/+ mice also display abnormal rod/cone morphology, greater impairment of CRX target gene expression than R90W/+ or +/− mice, and undergo progressive photoreceptor degeneration. Surprisingly, E168d2/+ mice express more mutant CRX protein than wild-type CRX. E168d2neo/+, a subline of E168d2 with reduced mutant allele expression, displays a much milder retinal phenotype, demonstrating the impact of Crx expression level on disease severity. Both CRX[E168d2] and CRX[R90W] proteins fail to activate transcription in vitro, but CRX[E168d2] interferes more strongly with the function of wild type (WT) CRX, supporting an antimorphic mechanism. E168d2 and R90W are mechanistically distinct mouse models for CRX-associated disease that will allow the elucidation of molecular mechanisms and testing of novel therapeutic approaches for different forms of CRX-associated disease. The transcription factor Cone-Rod Homeobox (CRX) plays a central role in regulating gene expression of rod and cone photoreceptors, the primary light sensing cells of the retina. Mutations in the human CRX gene have been associated with the retinal degeneration diseases Retinitis Pigmentosa (RP), Cone-Rod Dystrophy (CoRD) and Leber Congential Amaurosis (LCA). These diseases cause progressive and permanent loss of vision, vary widely in age of onset and severity, and are currently untreatable. To understand how mutations in CRX cause distinct forms of retinal disease, we have genetically engineered mice to carry human disease-causing mutations in their Crx gene. These mouse lines accurately recapitulate distinct forms of CRX-associated disease, demonstrating that different classes of CRX mutations are responsible for phenotype variability in humans. We have characterized the pathology of these mice and identified critical mechanisms of disease. In addition, we have discovered that modifying the level of mutant protein had a dramatic effect on disease pathology in one mutant model, suggesting that targeted therapy against the mutant CRX could be an effective treatment strategy. These mouse models will allow for the testing of novel therapeutic strategies for retinal diseases caused by CRX mutations.
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Affiliation(s)
- Nicholas M Tran
- Ph.D. program in Molecular Genetics and Genomics, Washington University in Saint Louis, Saint Louis, Missouri, United States of America
| | - Alan Zhang
- College of Arts & Sciences, Washington University in Saint Louis, Saint Louis, Missouri, United States of America
| | - Xiaodong Zhang
- Department of Ophthalmology and Visual Sciences, Washington University in Saint Louis, Saint Louis, Missouri, United States of America
| | - Julie B Huecker
- Department of Ophthalmology and Visual Sciences, Washington University in Saint Louis, Saint Louis, Missouri, United States of America
| | - Anne K Hennig
- Department of Ophthalmology and Visual Sciences, Washington University in Saint Louis, Saint Louis, Missouri, United States of America
| | - Shiming Chen
- Ph.D. program in Molecular Genetics and Genomics, Washington University in Saint Louis, Saint Louis, Missouri, United States of America ; Department of Ophthalmology and Visual Sciences, Washington University in Saint Louis, Saint Louis, Missouri, United States of America ; Department of Developmental Biology, Washington University in Saint Louis, Saint Louis, Missouri, United States of America
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45
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Roger JE, Hiriyanna A, Gotoh N, Hao H, Cheng DF, Ratnapriya R, Kautzmann MAI, Chang B, Swaroop A. OTX2 loss causes rod differentiation defect in CRX-associated congenital blindness. J Clin Invest 2014; 124:631-43. [PMID: 24382353 DOI: 10.1172/jci72722] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/24/2013] [Indexed: 12/14/2022] Open
Abstract
Leber congenital amaurosis (LCA) encompasses a set of early-onset blinding diseases that are characterized by vision loss, involuntary eye movement, and nonrecordable electroretinogram (ERG). At least 19 genes are associated with LCA, which is typically recessive; however, mutations in homeodomain transcription factor CRX lead to an autosomal dominant form of LCA. The mechanism of CRX-associated LCA is not understood. Here, we identified a spontaneous mouse mutant with a frameshift mutation in Crx (CrxRip). We determined that CrxRip is a dominant mutation that results in congenital blindness with nonrecordable response by ERG and arrested photoreceptor differentiation with no associated degeneration. Expression of LCA-associated dominant CRX frameshift mutations in mouse retina mimicked the CrxRip phenotype, which was rescued by overexpression of WT CRX. Whole-transcriptome profiling using deep RNA sequencing revealed progressive and complete loss of rod differentiation factor NRL in CrxRip retinas. Expression of NRL partially restored rod development in CrxRip/+ mice. We show that the binding of homeobox transcription factor OTX2 at the Nrl promoter was obliterated in CrxRip mice and ectopic expression of OTX2 rescued the rod differentiation defect. Together, our data indicate that OTX2 maintains Nrl expression in developing rods to consolidate rod fate. Our studies provide insights into CRX mutation-associated congenital blindness and should assist in therapeutic design.
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Eisenberger T, Neuhaus C, Khan AO, Decker C, Preising MN, Friedburg C, Bieg A, Gliem M, Issa PC, Holz FG, Baig SM, Hellenbroich Y, Galvez A, Platzer K, Wollnik B, Laddach N, Ghaffari SR, Rafati M, Botzenhart E, Tinschert S, Börger D, Bohring A, Schreml J, Körtge-Jung S, Schell-Apacik C, Bakur K, Al-Aama JY, Neuhann T, Herkenrath P, Nürnberg G, Nürnberg P, Davis JS, Gal A, Bergmann C, Lorenz B, Bolz HJ. Increasing the yield in targeted next-generation sequencing by implicating CNV analysis, non-coding exons and the overall variant load: the example of retinal dystrophies. PLoS One 2013; 8:e78496. [PMID: 24265693 PMCID: PMC3827063 DOI: 10.1371/journal.pone.0078496] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/12/2013] [Indexed: 01/30/2023] Open
Abstract
Retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) are major causes of blindness. They result from mutations in many genes which has long hampered comprehensive genetic analysis. Recently, targeted next-generation sequencing (NGS) has proven useful to overcome this limitation. To uncover “hidden mutations” such as copy number variations (CNVs) and mutations in non-coding regions, we extended the use of NGS data by quantitative readout for the exons of 55 RP and LCA genes in 126 patients, and by including non-coding 5′ exons. We detected several causative CNVs which were key to the diagnosis in hitherto unsolved constellations, e.g. hemizygous point mutations in consanguineous families, and CNVs complemented apparently monoallelic recessive alleles. Mutations of non-coding exon 1 of EYS revealed its contribution to disease. In view of the high carrier frequency for retinal disease gene mutations in the general population, we considered the overall variant load in each patient to assess if a mutation was causative or reflected accidental carriership in patients with mutations in several genes or with single recessive alleles. For example, truncating mutations in RP1, a gene implicated in both recessive and dominant RP, were causative in biallelic constellations, unrelated to disease when heterozygous on a biallelic mutation background of another gene, or even non-pathogenic if close to the C-terminus. Patients with mutations in several loci were common, but without evidence for di- or oligogenic inheritance. Although the number of targeted genes was low compared to previous studies, the mutation detection rate was highest (70%) which likely results from completeness and depth of coverage, and quantitative data analysis. CNV analysis should routinely be applied in targeted NGS, and mutations in non-coding exons give reason to systematically include 5′-UTRs in disease gene or exome panels. Consideration of all variants is indispensable because even truncating mutations may be misleading.
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Affiliation(s)
| | | | - Arif O. Khan
- Division of Pediatric Ophthalmology, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | | | - Markus N. Preising
- Department of Ophthalmology, Justus-Liebig-University Giessen, University Hospital Giessen and Marburg GmbH, Giessen Campus, Giessen, Germany
| | - Christoph Friedburg
- Department of Ophthalmology, Justus-Liebig-University Giessen, University Hospital Giessen and Marburg GmbH, Giessen Campus, Giessen, Germany
| | - Anika Bieg
- Bioscientia Center for Human Genetics, Ingelheim, Germany
| | - Martin Gliem
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | | | - Frank G. Holz
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Shahid M. Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | | | - Alberto Galvez
- Division of Pediatric Ophthalmology, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Konrad Platzer
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - Saeed Reza Ghaffari
- Comprehensive Genetic Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Rafati
- Avicenna Biotechnology Research Institute, Tehran, Iran
| | | | - Sigrid Tinschert
- Institute of Clinical Genetics, Technical University Dresden, Dresden, Germany
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | | | - Axel Bohring
- Institute of Human Genetics, Westfälische Wilhelms-University, Münster, Germany
| | - Julia Schreml
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | | | - Khadijah Bakur
- Princess Al Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jumana Y. Al-Aama
- Princess Al Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Peter Herkenrath
- Department of Pediatrics, University Hospital of Cologne, Cologne, Germany
| | - Gudrun Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics and Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics and Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - John S. Davis
- Department of Ophthalmology, Zayed Military Hospital, Abu Dhabi, United Arab Emirates
| | - Andreas Gal
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carsten Bergmann
- Bioscientia Center for Human Genetics, Ingelheim, Germany
- Center for Clinical Research, University Hospital of Freiburg, Freiburg, Germany
| | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University Giessen, University Hospital Giessen and Marburg GmbH, Giessen Campus, Giessen, Germany
| | - Hanno J. Bolz
- Bioscientia Center for Human Genetics, Ingelheim, Germany
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
- * E-mail:
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Arcot Sadagopan K, Battista R, Keep RB, Capasso JE, Levin AV. Autosomal-dominant Leber Congenital Amaurosis Caused by a Heterozygous CRX Mutation in a Father and Son. Ophthalmic Genet 2013; 36:156-9. [PMID: 24093488 DOI: 10.3109/13816810.2013.838273] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Leber congenital amaurosis (LCA) is most often an autosomal recessive disorder. We report a father and son with autosomal dominant LCA due to a mutation in the CRX gene. MATERIALS AND METHODS DNA screening using an allele specific assay of 90 of the most common LCA-causing variations in the coding sequences of AIPL1, CEP290, CRB1, CRX, GUCY2D, RDH12 and RPE65 was performed on the father. Automated DNA sequencing of his son examining exon 3 of the CRX gene was subsequently performed. RESULTS Both father and son have a heterozygous single base pair deletion of an adenine at codon 153 in the coding sequence of the CRX gene resulting in a frameshift mutation. CONCLUSION Mutations involving the CRX gene may demonstrate an autosomal dominant inheritance pattern for LCA.
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Mackay DS, Borman AD, Sui R, van den Born LI, Berson EL, Ocaka LA, Davidson AE, Heckenlively JR, Branham K, Ren H, Lopez I, Maria M, Azam M, Henkes A, Blokland E, Qamar R, Webster AR, Cremers FPM, Moore AT, Koenekoop RK, Andreasson S, de Baere E, Bennett J, Chader GJ, Berger W, Golovleva I, Greenberg J, den Hollander AI, Klaver CCW, Klevering BJ, Lorenz B, Preising MN, Ramsear R, Roberts L, Roepman R, Rohrschneider K, Wissinger B. Screening of a large cohort of leber congenital amaurosis and retinitis pigmentosa patients identifies novel LCA5 mutations and new genotype-phenotype correlations. Hum Mutat 2013; 34:1537-1546. [PMID: 23946133 DOI: 10.1002/humu.22398] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 08/05/2013] [Indexed: 11/11/2022]
Abstract
This study was undertaken to investigate the prevalence of sequence variants in LCA5 in patients with Leber congenital amaurosis (LCA), early-onset retinal dystrophy (EORD), and autosomal recessive retinitis pigmentosa (arRP); to delineate the ocular phenotypes; and to provide an overview of all published LCA5 variants in an online database. Patients underwent standard ophthalmic evaluations after providing informed consent. In selected patients, optical coherence tomography (OCT) and fundus autofluorescence imaging were possible. DNA samples from 797 unrelated patients with LCA and 211 with the various types of retinitis pigmentosa (RP) were screened by Sanger sequence analysis of all LCA5 exons and intron/exon junctions. Some LCA patients were prescreened by APEX technology or selected based on homozygosity mapping. In silico analyses were performed to assess the pathogenicity of the variants. Segregation analysis was performed where possible. Published and novel LCA5 variants were collected, amended for their correct nomenclature, and listed in a Leiden Open Variation Database (LOVD). Sequence analysis identified 18 new probands with 19 different LCA5 variants. Seventeen of the 19 LCA5 variants were novel. Except for two missense variants and one splice site variant, all variants were protein-truncating mutations. Most patients expressed a severe phenotype, typical of LCA. However, some LCA subjects had better vision and intact inner segment/outer segment (IS/OS) junctions on OCT imaging. In two families with LCA5 variants, the phenotype was more compatible with EORD with affected individuals displaying preserved islands of retinal pigment epithelium. One of the families with a milder phenotype harbored a homozygous splice site mutation; a second family was found to have a combination of a stop mutation and a missense mutation. This is the largest LCA5 study to date. We sequenced 1,008 patients (797 with LCA, 211 with arRP) and identified 18 probands with LCA5 mutations. Mutations in LCA5 are a rare cause of childhood retinal dystrophy accounting for ∼2% of disease in this cohort, and the majority of LCA5 mutations are likely null. The LCA5 protein truncating mutations are predominantly associated with LCA. However, in two families with the milder EORD, the LCA5 gene analysis revealed a homozygous splice site mutation in one and a stop mutation in combination with a missense mutation in a second family, suggesting that this milder phenotype is due to residual function of lebercilin and expanding the currently known phenotypic spectrum to include the milder early onset RP. Some patients have remaining foveal cone structures (intact IS/OS junctions on OCT imaging) and remaining visual acuities, which may bode well for upcoming treatment trials.
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Affiliation(s)
- Donna S Mackay
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Arundhati Dev Borman
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK.,Moorfields Eye Hospital, London, UK
| | - Ruifang Sui
- Ophthalmology, Peking Union Med College Hosp, Beijing, China
| | | | - Eliot L Berson
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear, Boston, Massachusetts, USA
| | - Louise A Ocaka
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Alice E Davidson
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - John R Heckenlively
- Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kari Branham
- Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan
| | - Huanan Ren
- McGill Ocular Genetics Laboratory, Departments of Pediatric Surgery, Human Genetics and Ophthalmology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Irma Lopez
- McGill Ocular Genetics Laboratory, Departments of Pediatric Surgery, Human Genetics and Ophthalmology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Maleeha Maria
- Department of Human Genetics, Radboud University Medical Centre, and Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands.,Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Maleeha Azam
- Department of Human Genetics, Radboud University Medical Centre, and Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands.,Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Arjen Henkes
- Department of Human Genetics, Radboud University Medical Centre, and Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Ellen Blokland
- Department of Human Genetics, Radboud University Medical Centre, and Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Raheel Qamar
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan.,Al-Nafees Medical College & Hospital, Isra University, Islamabad, Pakistan
| | - Andrew R Webster
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK.,Moorfields Eye Hospital, London, UK
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Centre, and Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Anthony T Moore
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK.,Moorfields Eye Hospital, London, UK
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory, Departments of Pediatric Surgery, Human Genetics and Ophthalmology, McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Sten Andreasson
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Elfride de Baere
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Jean Bennett
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Gerald J Chader
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Wolfgang Berger
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Irina Golovleva
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Jacquie Greenberg
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | | | | | - B Jeroen Klevering
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Birgit Lorenz
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Markus N Preising
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Raj Ramsear
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Lisa Roberts
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | - Ronald Roepman
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
| | | | - Bernd Wissinger
- Department of Human Genetics, Institute of Ophthalmology, UCL, London, UK
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Zou X, Yao F, Liang X, Xu F, Li H, Sui R, Dong F. De novo mutations in the cone-rod homeobox gene associated with leber congenital amaurosis in Chinese patients. Ophthalmic Genet 2013; 36:21-6. [PMID: 24001014 DOI: 10.3109/13816810.2013.827219] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The cone-rod homeobox (CRX) gene plays an important role in photoreceptor development. Recently, mutant alleles of the CRX gene have been associated with autosomal dominant Leber congenital amaurosis (LCA) and cone-rod dystrophy. The purpose of this study was to analyze the CRX mutations in a cohort of Chinese patients with LCA or early-onset severe retinal dystrophy (EOSRD) and to provide the clinical features of these patients. METHODS Patients with LCA or EOSRD were enrolled from 2003 to 2012. Detailed ocular examinations including optical coherence tomography (OCT) and standardized electrophysiology were performed. Genomic DNA was isolated with standard methods of genetic diagnosis. All three exons of CRX were amplified with PCR and screened for mutations through direct DNA sequencing. A total of 200 unrelated healthy Chinese subjects were screened to exclude nonpathogenic polymorphisms. Offspring-parent relationship was tested to confirm de novo mutation. RESULTS A total of 109 probands from 109 unrelated families were selected for mutation screening of the CRX gene. Two individuals with LCA were confirmed to carry de novo CRX mutations c.421delT (p.Ser141Pro fsX46) and c.571delT (p.Tyr191Met fsX3), respectively. The daughter of Case 1 also carried the same CRX mutation (c.421delT) and had LCA symptoms. Pigmentary retinopathy in the peripheral retina and macular atrophy were observed in the two probands. Macular atrophy without normal lamination structure was the retina phenotype under OCT. CONCLUSIONS Two de novo mutations in CRX were found in Chinese patients with LCA. The CRX mutation might create a dominantly inherited trait.
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Sakuramoto H, Kuniyoshi K, Tsunoda K, Akahori M, Iwata T, Shimomura Y. Two siblings with late-onset cone-rod dystrophy and no visible macular degeneration. Clin Ophthalmol 2013; 7:1703-11. [PMID: 24039390 PMCID: PMC3770715 DOI: 10.2147/opth.s48723] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background We report our findings in two siblings with late-onset cone–rod dystrophy (CRD) with no visible macular degeneration. Cases and methods Case 1 was an 82-year-old man who first noticed a decrease in vision and color blindness in his early seventies. His mother and younger sister also had visual disturbances. His decimal visual acuity was 0.3 in the right eye and 0.2 in the left eye. Ophthalmoscopy showed normal fundi, and fluorescein angiography was also normal in both eyes. The photopic single flash and flicker eletroretinograms (ERGs) were severely attenuated and the scotopic ERGs were slightly reduced in both eyes. Case 2 was the 80-year-old younger sister of Case 1. She first noticed a decline in vision and photophobia in both eyes in her early seventies. Her decimal visual acuity was 0.4 in the right eye and 0.2 in the left eye. Ophthalmoscopy showed mottling of the retinal pigment epithelium in the midperiphery with no visible macular degeneration. The photopic single flash and flicker ERGs were severely attenuated, and the scotopic ERGs were slightly reduced in both eyes. Conclusion These siblings are the oldest reported cases of CRD with no visible macular degeneration. Thus, CRD should be considered in patients with reduced visual acuity, color blindness, and photophobia even if they are older than 70 years.
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Affiliation(s)
- Hiroyuki Sakuramoto
- Department of Ophthalmology, Kinki University Faculty of Medicine, Osaka-Sayama City, Osaka, Japan
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