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Zucco J, Baldan F, Allegri L, Bregant E, Passon N, Franzoni A, D'Elia AV, Faletra F, Damante G, Mio C. A bird's eye view on the use of whole exome sequencing in rare congenital ophthalmic diseases. J Hum Genet 2024; 69:271-282. [PMID: 38459225 PMCID: PMC11126393 DOI: 10.1038/s10038-024-01237-6] [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: 11/20/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/10/2024]
Abstract
Phenotypic and genotypic heterogeneity in congenital ocular diseases, especially in anterior segment dysgenesis (ASD), have created challenges for proper diagnosis and classification of diseases. Over the last decade, genomic research has indeed boosted our understanding in the molecular basis of ASD and genes associated with both autosomal dominant and recessive patterns of inheritance have been described with a wide range of expressivity. Here we describe the molecular characterization of a cohort of 162 patients displaying isolated or syndromic congenital ocular dysgenesis. Samples were analyzed with diverse techniques, such as direct sequencing, multiplex ligation-dependent probe amplification, and whole exome sequencing (WES), over 20 years. Our data reiterate the notion that PAX6 alterations are primarily associated with ASD, mostly aniridia, since the majority of the cohort (66.7%) has a pathogenic or likely pathogenic variant in the PAX6 locus. Unexpectedly, a high fraction of positive samples (20.3%) displayed deletions involving the 11p13 locus, either partially/totally involving PAX6 coding region or abolishing its critical regulatory region, underlying its significance. Most importantly, the use of WES has allowed us to both assess variants in known ASD genes (i.e., CYP1B1, ITPR1, MAB21L1, PXDN, and PITX2) and to identify rarer phenotypes (i.e., MIDAS, oculogastrointestinal-neurodevelopmental syndrome and Jacobsen syndrome). Our data clearly suggest that WES allows expanding the analytical portfolio of ocular dysgenesis, both isolated and syndromic, and that is pivotal for the differential diagnosis of those conditions in which there may be phenotypic overlaps and in general in ASD.
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Affiliation(s)
- Jessica Zucco
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Federica Baldan
- Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Lorenzo Allegri
- Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Elisa Bregant
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Nadia Passon
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Alessandra Franzoni
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Angela Valentina D'Elia
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Flavio Faletra
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy.
| | - Giuseppe Damante
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
- Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Catia Mio
- Department of Medicine (DMED), University of Udine, Udine, Italy
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2
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Shinsato RN, Correa CG, Herai RH. Genetic network analysis indicate that individuals affected by neurodevelopmental conditions have genetic variations associated with ophthalmologic alterations: A critical review of literature. Gene 2024; 908:148246. [PMID: 38325665 DOI: 10.1016/j.gene.2024.148246] [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: 07/21/2023] [Revised: 01/19/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Changes in the nervous system are related to a wide range of mental disorders, which include neurodevelopmental disorders (NDD) that are characterized by early onset mental conditions, such as schizophrenia and autism spectrum disorders and correlated conditions (ASD). Previous studies have shown distinct genetic components associated with diverse schizophrenia and ASD phenotypes, with mostly focused on rescuing neural phenotypes and brain activity, but alterations related to vision are overlooked. Thus, as the vision is composed by the eyes that itself represents a part of the brain, with the retina being formed by neurons and cells originating from the glia, genetic variations affecting the brain can also affect the vision. Here, we performed a critical systematic literature review to screen for all genetic variations in individuals presenting NDD with reported alterations in vision. Using these restricting criteria, we found 20 genes with distinct types of genetic variations, inherited or de novo, that includes SNP, SNV, deletion, insertion, duplication or indel. The variations occurring within protein coding regions have different impact on protein formation, such as missense, nonsense or frameshift. Moreover, a molecular analysis of the 20 genes found revealed that 17 shared a common protein-protein or genetic interaction network. Moreover, gene expression analysis in samples from the brain and other tissues indicates that 18 of the genes found are highly expressed in the brain and retina, indicating their potential role in adult vision phenotype. Finally, we only found 3 genes from our study described in standard public databanks of ophthalmogenetics, suggesting that the other 17 genes could be novel target for vision diseases.
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Affiliation(s)
- Rogério N Shinsato
- Unisalesiano, Araçatuba, São Paulo, Brazil; Laboratory of Bioinformatics and Neurogenetics (LaBiN/LEM), Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, 80215-901, Brazil.
| | - Camila Graczyk Correa
- Laboratory of Bioinformatics and Neurogenetics (LaBiN/LEM), Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, 80215-901, Brazil
| | - Roberto H Herai
- Laboratory of Bioinformatics and Neurogenetics (LaBiN/LEM), Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, 80215-901, Brazil; Research Division, Buko Kaesemodel Institute (IBK), Curitiba, Paraná 80240-000, Brazil; Research Division, 9p Brazil Association (A9pB), Santa Maria, Rio Grande do Sul 97060-580, Brazil.
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3
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Mullin NK, Bohrer LR, Voigt AP, Lozano LP, Wright AT, Bonilha VL, Mullins RF, Stone EM, Tucker BA. NR2E3 loss disrupts photoreceptor cell maturation and fate in human organoid models of retinal development. J Clin Invest 2024:e173892. [PMID: 38652563 DOI: 10.1172/jci173892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
While dysfunction and death of light-detecting photoreceptor cells underlie most inherited retinal dystrophies, knowledge of the species-specific details of human rod and cone photoreceptor cell development remains limited. Here, we generate retinal organoids carrying retinal disease-causing variants in NR2E3, as well as isogenic and unrelated controls. Organoids were sampled using single-cell RNA sequencing across the developmental window encompassing photoreceptor specification, emergence, and maturation. Using scRNAseq data, we reconstruct the rod photoreceptor developmental lineage and identify a branchpoint unique to the disease state. We show that the rod-specific transcription factor NR2E3 is required for the proper expression of genes involved in phototransduction, including rhodopsin, which is absent in divergent rods. NR2E3-null rods additionally misexpress several cone-specific phototransduction genes. Using joint multimodal single-cell sequencing, we further identify putative regulatory sites where rod-specific factors act to steer photoreceptor cell development. Finally, we show that rod-committed photoreceptor cells form and persist throughout life in a patient with NR2E3-associated disease. Importantly, these findings are strikingly different than those observed in Nr2e3 rodent models. Together, these data provide a roadmap of human photoreceptor development and leverage patient iPSCs to define the specific roles of rod transcription factors in photoreceptor cell emergence and maturation in health and disease.
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Affiliation(s)
- Nathaniel K Mullin
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, United States of America
| | - Laura R Bohrer
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, United States of America
| | - Andrew P Voigt
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, United States of America
| | - Lola P Lozano
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, United States of America
| | - Allison T Wright
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, United States of America
| | - Vera L Bonilha
- Department of Ophthalmic Research, Cleveland Clinic, Cleveland, United States of America
| | - Robert F Mullins
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, United States of America
| | - Edwin M Stone
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, United States of America
| | - Budd A Tucker
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, United States of America
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4
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Camerino M, Chang W, Cvekl A. Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers. Epigenetics Chromatin 2024; 17:10. [PMID: 38643244 PMCID: PMC11031936 DOI: 10.1186/s13072-024-00533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/08/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Nuclear organization of interphase chromosomes involves individual chromosome territories, "open" and "closed" chromatin compartments, topologically associated domains (TADs) and chromatin loops. The DNA- and RNA-binding transcription factor CTCF together with the cohesin complex serve as major organizers of chromatin architecture. Cellular differentiation is driven by temporally and spatially coordinated gene expression that requires chromatin changes of individual loci of various complexities. Lens differentiation represents an advantageous system to probe transcriptional mechanisms underlying tissue-specific gene expression including high transcriptional outputs of individual crystallin genes until the mature lens fiber cells degrade their nuclei. RESULTS Chromatin organization between mouse embryonic stem (ES) cells, newborn (P0.5) lens epithelium and fiber cells were analyzed using Hi-C. Localization of CTCF in both lens chromatins was determined by ChIP-seq and compared with ES cells. Quantitative analyses show major differences between number and size of TADs and chromatin loop size between these three cell types. In depth analyses show similarities between lens samples exemplified by overlaps between compartments A and B. Lens epithelium-specific CTCF peaks are found in mostly methylated genomic regions while lens fiber-specific and shared peaks occur mostly within unmethylated DNA regions. Major differences in TADs and loops are illustrated at the ~ 500 kb Pax6 locus, encoding the critical lens regulatory transcription factor and within a larger ~ 15 Mb WAGR locus, containing Pax6 and other loci linked to human congenital diseases. Lens and ES cell Hi-C data (TADs and loops) together with ATAC-seq, CTCF, H3K27ac, H3K27me3 and ENCODE cis-regulatory sites are shown in detail for the Pax6, Sox1 and Hif1a loci, multiple crystallin genes and other important loci required for lens morphogenesis. The majority of crystallin loci are marked by unexpectedly high CTCF-binding across their transcribed regions. CONCLUSIONS Our study has generated the first data on 3-dimensional (3D) nuclear organization in lens epithelium and lens fibers and directly compared these data with ES cells. These findings generate novel insights into lens-specific transcriptional gene control, open new research avenues to study transcriptional condensates in lens fiber cells, and enable studies of non-coding genetic variants linked to cataract and other lens and ocular abnormalities.
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Affiliation(s)
- Michael Camerino
- The Departments Genetics, Albert Einstein College of Medicine, NY10461, Bronx, USA
| | - William Chang
- Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, NY10461, Bronx, USA
| | - Ales Cvekl
- The Departments Genetics, Albert Einstein College of Medicine, NY10461, Bronx, USA.
- Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, NY10461, Bronx, USA.
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5
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Goh J, Wei H, Lai AHM, Chang B, Khan S, Syn Y, Jamuar SS, Tan EC. Novel and recurrent variants in PAX6 in four patients with ocular phenotypes from Southeast Asia. Clin Dysmorphol 2024; 33:63-68. [PMID: 38441200 DOI: 10.1097/mcd.0000000000000487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Aniridia is an autosomal dominant condition characterized by the complete or partial absence of the iris, often with additional presentations such as foveal hypoplasia, nystagmus, cataract, glaucoma and other ocular abnormalities. Most cases are caused by heterozygous mutations in the paired box 6 gene (PAX6), which codes for a transcription factor that regulates eye development. Four patients from our hospital who presented with ocular phenotypes were recruited for research sequencing with informed consent. Sanger sequencing of PAX6 coding exons or exome sequencing was performed on genomic DNA from venous blood samples. Variants in PAX6 were identified in the four patients. Two variants are recurrent single-nucleotide substitutions - one is a substitution found in a patient with bilateral aniridia, whereas the other is a splice variant in a patient with nystagmus and neuroblastoma. The other two variants are novel and found in two patients with isolated aniridia. Both are small duplications that are predicted to lead to premature termination. For the recurrent variants, the comparison of phenotypes for patients with identical variants would shed light on the mechanisms of pathogenesis, and the discovery of two novel variants expands the spectrum of PAX6 mutations.
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Affiliation(s)
- Jeannette Goh
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital
- Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Medical School
| | - Heming Wei
- Research Laboratory, KK Women's and Children's Hospital
| | - Angeline H M Lai
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital
- Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Medical School
| | - Benjamin Chang
- Opthalmology Service, KK Women's and Children's Hospital
| | - Shazia Khan
- Opthalmology Service, KK Women's and Children's Hospital
| | - Yamon Syn
- Singapore National Eye Centre, Singapore
| | - Saumya S Jamuar
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital
- Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Medical School
| | - Ene-Choo Tan
- Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Medical School
- Research Laboratory, KK Women's and Children's Hospital
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6
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Lopez Soriano V, Dueñas Rey A, Mukherjee R, Coppieters F, Bauwens M, Willaert A, De Baere E. Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci. Nat Commun 2024; 15:1600. [PMID: 38383453 PMCID: PMC10881467 DOI: 10.1038/s41467-024-45381-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Cross-species genome comparisons have revealed a substantial number of ultraconserved non-coding elements (UCNEs). Several of these elements have proved to be essential tissue- and cell type-specific cis-regulators of developmental gene expression. Here, we characterize a set of UCNEs as candidate CREs (cCREs) during retinal development and evaluate the contribution of their genomic variation to rare eye diseases, for which pathogenic non-coding variants are emerging. Integration of bulk and single-cell retinal multi-omics data reveals 594 genes under potential cis-regulatory control of UCNEs, of which 45 are implicated in rare eye disease. Mining of candidate cis-regulatory UCNEs in WGS data derived from the rare eye disease cohort of Genomics England reveals 178 ultrarare variants within 84 UCNEs associated with 29 disease genes. Overall, we provide a comprehensive annotation of ultraconserved non-coding regions acting as cCREs during retinal development which can be targets of non-coding variation underlying rare eye diseases.
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Affiliation(s)
- Victor Lopez Soriano
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Alfredo Dueñas Rey
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | | | - Frauke Coppieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Andy Willaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
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7
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Hall HN, Parry D, Halachev M, Williamson KA, Donnelly K, Campos Parada J, Bhatia S, Joseph J, Holden S, Prescott TE, Bitoun P, Kirk EP, Newbury-Ecob R, Lachlan K, Bernar J, van Heyningen V, FitzPatrick DR, Meynert A. Short-read whole genome sequencing identifies causative variants in most individuals with previously unexplained aniridia. J Med Genet 2024; 61:250-261. [PMID: 38050128 DOI: 10.1136/jmg-2023-109181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 09/25/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Classic aniridia is a highly penetrant autosomal dominant disorder characterised by congenital absence of the iris, foveal hypoplasia, optic disc anomalies and progressive opacification of the cornea. >90% of cases of classic aniridia are caused by heterozygous, loss-of-function variants affecting the PAX6 locus. METHODS Short-read whole genome sequencing was performed on 51 (39 affected) individuals from 37 different families who had screened negative for mutations in the PAX6 coding region. RESULTS Likely causative mutations were identified in 22 out of 37 (59%) families. In 19 out of 22 families, the causative genomic changes have an interpretable deleterious impact on the PAX6 locus. Of these 19 families, 1 has a novel heterozygous PAX6 frameshift variant missed on previous screens, 4 have single nucleotide variants (SNVs) (one novel) affecting essential splice sites of PAX6 5' non-coding exons and 2 have deep intronic SNV (one novel) resulting in gain of a donor splice site. In 12 out of 19, the causative variants are large-scale structural variants; 5 have partial or whole gene deletions of PAX6, 3 have deletions encompassing critical PAX6 cis-regulatory elements, 2 have balanced inversions with disruptive breakpoints within the PAX6 locus and 2 have complex rearrangements disrupting PAX6. The remaining 3 of 22 families have deletions encompassing FOXC1 (a known cause of atypical aniridia). Seven of the causative variants occurred de novo and one cosegregated with familial aniridia. We were unable to establish inheritance status in the remaining probands. No plausibly causative SNVs were identified in PAX6 cis-regulatory elements. CONCLUSION Whole genome sequencing proves to be an effective diagnostic test in most individuals with previously unexplained aniridia.
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Affiliation(s)
- Hildegard Nikki Hall
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - David Parry
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
- Illumina United Kingdom, Edinburgh, UK
| | - Mihail Halachev
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Kathleen A Williamson
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Kevin Donnelly
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Jose Campos Parada
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Shipra Bhatia
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Jeffrey Joseph
- MRC Human Genetics Unit, The University of Edinburgh, Edinburgh, UK
| | - Simon Holden
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Trine E Prescott
- Department of Medical Genetics, Telemark Hospital, Skien, Norway
| | - Pierre Bitoun
- Consultations de Génétique médicale, Service de Pédiatrie, CHU Paris-Nord, Hôpital Jean Verdier, Bondy, France
| | - Edwin P Kirk
- Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Katherine Lachlan
- University Hospital Southampton, NHS Foundation Trust Wessex Clinical Genetics Service, Southampton, UK
| | - Juan Bernar
- Department of Genetics, Hospital Ruber Internacional, Madrid, Spain
| | - Veronica van Heyningen
- MRC Human Genetics Unit, The University of Edinburgh, Edinburgh, UK
- Institute of Ophthalmology, University College London, London, UK
| | - David R FitzPatrick
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Alison Meynert
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
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8
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Zhao H, Feng K, Lei J, Shu Y, Bo L, Liu Y, Wang L, Liu W, Ning S, Wang L. Identification of somatic mutation-driven enhancers and their clinical utility in breast cancer. iScience 2024; 27:108780. [PMID: 38303701 PMCID: PMC10831879 DOI: 10.1016/j.isci.2024.108780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/04/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
Somatic mutations contribute to cancer development by altering the activity of enhancers. In the study, a total of 135 mutation-driven enhancers, which displayed significant chromatin accessibility changes, were identified as candidate risk factors for breast cancer (BRCA). Furthermore, we identified four mutation-driven enhancers as independent prognostic factors for BRCA subtypes. In Her2 subtype, enhancer G > C mutation was associated with poorer prognosis through influencing its potential target genes FBXW9, TRIR, and WDR83. We identified aminoglutethimide and quinpirole as candidate drugs targeting the mutated enhancer. In normal subtype, enhancer G > A mutation was associated with poorer prognosis through influencing its target genes ALOX15B, LINC00324, and MPDU1. We identified eight candidate drugs such as erastin, colforsin, and STOCK1N-35874 targeting the mutated enhancer. Our findings suggest that somatic mutations contribute to breast cancer subtype progression by altering enhancer activity, which could be potential candidates for cancer therapy.
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Affiliation(s)
- Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Ke Feng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Junjie Lei
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaopeng Shu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lin Bo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Ying Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lixia Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Wangyang Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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9
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Cole JD, McDaniel JA, Nilak J, Ban A, Rodriguez C, Hameed Z, Grannonico M, Netland PA, Yang H, Provencio I, Liu X. Characterization of neural damage and neuroinflammation in Pax6 small-eye mice. Exp Eye Res 2024; 238:109723. [PMID: 37979905 PMCID: PMC10843716 DOI: 10.1016/j.exer.2023.109723] [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: 06/27/2023] [Revised: 10/17/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Aniridia is a panocular condition characterized by a partial or complete loss of the iris. It manifests various developmental deficits in both the anterior and posterior segments of the eye, leading to a progressive vision loss. The homeobox gene PAX6 plays an important role in ocular development and mutations of PAX6 have been the main causative factors for aniridia. In this study, we assessed how Pax6-haploinsufficiency affects retinal morphology and vision of Pax6Sey mice using in vivo and ex vivo metrics. We used mice of C57BL/6 and 129S1/Svlmj genetic backgrounds to examine the variable severity of symptoms as reflected in human aniridia patients. Elevated intraocular pressure (IOP) was observed in Pax6Sey mice starting from post-natal day 20 (P20). Correspondingly, visual acuity showed a steady age-dependent decline in Pax6Sey mice, though these phenotypes were less severe in the 129S1/Svlmj mice. Local retinal damage with layer disorganization was assessed at P30 and P80 in the Pax6Sey mice. Interestingly, we also observed a greater number of activated Iba1+ microglia and GFAP + astrocytes in the Pax6Sey mice than in littermate controls, suggesting a possible neuroinflammatory response to Pax6 deficiencies.
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Affiliation(s)
- James D Cole
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA; Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - John A McDaniel
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Joelle Nilak
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Ashley Ban
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Carlos Rodriguez
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Zuhaad Hameed
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Marta Grannonico
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Peter A Netland
- Department of Ophthalmology, University of Virginia, Charlottesville, VA, USA
| | - Hu Yang
- Linda and Bipin Doshi Department of Chemical and Biochemical Engineering, Missouri University of Science and Technology, Rolla, MO, USA
| | - Ignacio Provencio
- Department of Biology, University of Virginia, Charlottesville, VA, USA; Department of Ophthalmology, University of Virginia, Charlottesville, VA, USA; Program in Fundamental Neuroscience, University of Virginia, Charlottesville, VA, USA.
| | - Xiaorong Liu
- Department of Biology, University of Virginia, Charlottesville, VA, USA; Department of Ophthalmology, University of Virginia, Charlottesville, VA, USA; Program in Fundamental Neuroscience, University of Virginia, Charlottesville, VA, USA; Department of Psychology, University of Virginia, Charlottesville, VA, USA.
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10
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Fries FN, Moslemani K, Utheim TP, Seitz B, Käsmann-Kellner B, Lagali NS. Early ocular surface and tear film status in congenital aniridia indicates a supportive treatment window. Br J Ophthalmol 2023; 108:30-36. [PMID: 36517210 PMCID: PMC10804021 DOI: 10.1136/bjo-2021-320774] [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: 01/24/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022]
Abstract
AIM To evaluate changes in the ocular surface and tear film with age and mutational status in congenital aniridia. METHODS 45 participants with congenital aniridia (89 eyes) in a prospective, cross-sectional study. Whole-exome sequencing identified the causative mutation. Examinations included slit-lamp biomicroscopy, in vivo confocal microscopy, Ocular Surface Disease Index (OSDI) score, blink rate, Schirmer I test, Oxford Staining Score (OSS), tear film break-up time (TFBUT) and Ocular Protection Index (OPI). RESULTS There were age-dependent increases in OSDI (β=0.34, 95% CI 0.03 to 0.66; p=0.030), blink rate (β=0.18, 95% CI 0.08 to 0.27; p<0.001) and OSS (β=0.05, 95% CI 0.03 to 0.07; p<0.001) and age-dependent reductions in tear production (β=-0.23, 95% CI -0.43 to 0.02; p=0.029) and TFBUT (β=-0.10, 95% CI -0.17 to -0.04; p<0.001). Perturbed OSDI, OSS, blink rate, tear production and TFBUT were noted after the age of ten and OSDI, OSS, blink rate and TFBUT correlated with deficient corneal nerves and limbal stem cell function. OSDI, blink rate, Schirmer, OSS, TFBUT and OPI were not associated with type of PAX6 mutation, but OSDI, OSS and blink rate associated with grade of aniridia-associated keratopathy. CONCLUSIONS Ocular surface damage and dry eye signs appear in congenital aniridia regardless of mutation, appearing after 10 years of age and progressing thereafter. An early treatment window may exist for therapies to protect the ocular surface homoeostasis and limbal function, to possibly delay keratopathy development and progression.
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Affiliation(s)
- Fabian N Fries
- Department of Ophthalmology, Saarland University Hospital and Saarland University Faculty of Medicine, Homburg, Germany
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg, Saar, Germany
| | - Kayed Moslemani
- Department of Ophthalmology, Saarland University Hospital and Saarland University Faculty of Medicine, Homburg, Germany
| | - Tor Paaske Utheim
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- Department of Ophthalmology, Sørlandet Hospital Arendal, Arendal, Norway
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Hospital and Saarland University Faculty of Medicine, Homburg, Germany
| | - Barbara Käsmann-Kellner
- Department of Ophthalmology, Saarland University Hospital and Saarland University Faculty of Medicine, Homburg, Germany
| | - Neil S Lagali
- Department of Ophthalmology, Sørlandet Hospital Arendal, Arendal, Norway
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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11
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Zheng Y, Sun C, Zhang X, Ruzycki PA, Chen S. Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms. eLife 2023; 12:RP87147. [PMID: 37963072 PMCID: PMC10645426 DOI: 10.7554/elife.87147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
Homeodomain transcription factors (HD TFs) are instrumental to vertebrate development. Mutations in HD TFs have been linked to human diseases, but their pathogenic mechanisms remain elusive. Here, we use Cone-Rod Homeobox (CRX) as a model to decipher the disease-causing mechanisms of two HD mutations, p.E80A and p.K88N, that produce severe dominant retinopathies. Through integrated analysis of molecular and functional evidence in vitro and in knock-in mouse models, we uncover two novel gain-of-function mechanisms: p.E80A increases CRX-mediated transactivation of canonical CRX target genes in developing photoreceptors; p.K88N alters CRX DNA-binding specificity resulting in binding at ectopic sites and severe perturbation of CRX target gene expression. Both mechanisms produce novel retinal morphological defects and hinder photoreceptor maturation distinct from loss-of-function models. This study reveals the distinct roles of E80 and K88 residues in CRX HD regulatory functions and emphasizes the importance of transcriptional precision in normal development.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
| | - Chi Sun
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
| | - Xiaodong Zhang
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
| | - Philip A Ruzycki
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Genetics, Washington University in St LouisSaint LouisUnited States
| | - Shiming Chen
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Developmental Biology, Washington University in St LouisSaint LouisUnited States
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12
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Uttley K, Papanastasiou AS, Lahne M, Brisbane JM, MacDonald RB, Bickmore WA, Bhatia S. Unique activities of two overlapping PAX6 retinal enhancers. Life Sci Alliance 2023; 6:e202302126. [PMID: 37643867 PMCID: PMC10465922 DOI: 10.26508/lsa.202302126] [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: 05/01/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
Enhancers play a critical role in development by precisely modulating spatial, temporal, and cell type-specific gene expression. Sequence variants in enhancers have been implicated in diseases; however, establishing the functional consequences of these variants is challenging because of a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development, with a regulatory landscape containing multiple enhancers driving the expression in the eye. Whether these enhancers perform additive, redundant or distinct functions is unknown. Here, we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers, HS5 and NRE. Using a unique combination of live imaging and single-cell RNA sequencing in dual enhancer-reporter zebrafish embryos, we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping, these enhancers have distinct activities in different cell types and therefore likely nonredundant functions. This work demonstrates that unique cell type-specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo.
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Affiliation(s)
- Kirsty Uttley
- https://ror.org/011jsc803 MRC Human Genetics Unithttps://ror.org/01nrxwf90 , Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Andrew S Papanastasiou
- https://ror.org/011jsc803 MRC Human Genetics Unithttps://ror.org/01nrxwf90 , Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Manuela Lahne
- https://ror.org/02jx3x895 UCL Institute of Ophthalmology, University College London, Greater London, UK
| | - Jennifer M Brisbane
- https://ror.org/011jsc803 MRC Human Genetics Unithttps://ror.org/01nrxwf90 , Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Ryan B MacDonald
- https://ror.org/02jx3x895 UCL Institute of Ophthalmology, University College London, Greater London, UK
| | - Wendy A Bickmore
- https://ror.org/011jsc803 MRC Human Genetics Unithttps://ror.org/01nrxwf90 , Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Shipra Bhatia
- https://ror.org/011jsc803 MRC Human Genetics Unithttps://ror.org/01nrxwf90 , Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
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13
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Li Y, Chen J, Zheng Y, Chen Z, Wang T, Sun Q, Wan X, Liu H, Sun X. A novel microdeletion of 517 kb downstream of the PAX6 gene in a Chinese family with congenital aniridia. BMC Ophthalmol 2023; 23:393. [PMID: 37752489 PMCID: PMC10523764 DOI: 10.1186/s12886-023-03147-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 09/19/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND To identify the disease-causing gene in a Chinese family affected with congenital aniridia. METHODS Patients underwent systematic ophthalmic examinations such as anterior segment photography, fundus photography, optical coherence tomography, and fundus fluorescein angiography. The proband was screened for pathogenic variants by whole exome sequencing (WES) and copy number variant (CNV) analysis. Real-time quantitative PCR (RT-qPCR) was applied to confirm the CNV results. Breakpoints were identified by long-range PCR followed by Sanger sequencing. RESULTS All seven members of this Chinese family, including four patients and three normal individuals, were recruited for this study. All patients showed bilateral congenital aniridia with nystagmus, except the son of the proband, who presented with bilateral partial coloboma of the iris. A novel heterozygous deletion (chr11:31,139,019-31,655,997) containing the 3' regulatory enhancers of the PAX6 gene was detected in this family. We also reviewed the reported microdeletions downstream of PAX6 in patients with aniridia. CONCLUSIONS We identified a novel microdeletion, 517 kb in size located about 133 kb downstream of the PAX6 gene, responsible for congenital aniridia in this Chinese family, which expands the spectrum of aniridia-associated mutations in PAX6.
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Affiliation(s)
- Yinwen Li
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Jieqiong Chen
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Ying Zheng
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Zhixuan Chen
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Tao Wang
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Qian Sun
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Xiaoling Wan
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
- National Clinical Research Center for Eye Diseases, Shanghai, China.
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China.
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China.
| | - Haiyun Liu
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
- National Clinical Research Center for Eye Diseases, Shanghai, China.
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China.
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China.
| | - Xiaodong Sun
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
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14
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Lima Cunha D, Sarkar H, Eintracht J, Harding P, Zhou JH, Moosajee M. Restoration of functional PAX6 in aniridia patient iPSC-derived ocular tissue models using repurposed nonsense suppression drugs. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:240-253. [PMID: 37483273 PMCID: PMC10362734 DOI: 10.1016/j.omtn.2023.06.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/22/2023] [Indexed: 07/25/2023]
Abstract
Congenital aniridia is a rare, pan-ocular disease causing severe sight loss, with only symptomatic intervention offered to patients. Approximately 40% of aniridia patients present with heterozygous nonsense variants in PAX6, resulting in haploinsufficiency. Translational readthrough-inducing drugs (TRIDs) have the ability to weaken the recognition of in-frame premature termination codons (PTCs), permitting full-length protein to be translated. We established induced pluripotent stem cell (iPSC)-derived 3D optic cups and 2D limbal epithelial stem cell (LESC) models from two aniridia patients with prevalent PAX6 nonsense mutations. Both in vitro models show reduced PAX6 protein levels, mimicking the disease. The repurposed TRIDs amlexanox and 2,6-diaminopurine (DAP) and the positive control compounds ataluren and G418 were tested for their efficiency. Amlexanox was identified as the most promising TRID, increasing full-length PAX6 levels in both models and rescuing the disease phenotype through normalization of VSX2 and cell proliferation in the optic cups and reduction of ABCG2 protein and SOX10 expression in LESCs. This study highlights the significance of patient iPSC-derived cells as a new model system for aniridia and proposes amlexanox as a new putative treatment for nonsense-mediated aniridia.
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Affiliation(s)
- Dulce Lima Cunha
- UCL Institute of Ophthalmology, London, UK
- Radboud Institute of Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Hajrah Sarkar
- UCL Institute of Ophthalmology, London, UK
- The Francis Crick Institute, London, UK
| | | | | | - Jo Huiqing Zhou
- Radboud Institute of Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, London, UK
- The Francis Crick Institute, London, UK
- Moorfields Eye Hospital, London, UK
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15
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Rodriguez-Martinez AC, Higgins BE, Tailor-Hamblin V, Malka S, Cheloni R, Collins AM, Bladen J, Henderson R, Moosajee M. Foveal Hypoplasia in CRB1-Related Retinopathies. Int J Mol Sci 2023; 24:13932. [PMID: 37762234 PMCID: PMC10531165 DOI: 10.3390/ijms241813932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
The CRB1 gene plays a role in retinal development and its maintenance. When disrupted, it gives a range of phenotypes such as early-onset severe retinal dystrophy/Leber congenital amaurosis (EOSRD/LCA), retinitis pigmentosa (RP), cone-rod dystrophy (CORD) and macular dystrophy (MD). Studies in CRB1 retinopathies have shown thickening and coarse lamination of retinal layers resembling an immature retina. Its role in foveal development has not yet been described; however, this retrospective study is the first to report foveal hypoplasia (FH) presence in a CRB1-related retinopathy cohort. Patients with pathogenic biallelic CRB1 variants from Moorfields Eye Hospital, London, UK, were collected. Demographic, clinical data and SD-OCT analyses with FH structural grading were performed. A total of 15 (48%) patients had EOSRD/LCA, 11 (35%) MD, 3 (9%) CORD and 2 (6%) RP. FH was observed in 20 (65%; CI: 0.47-0.79) patients, all of whom were grade 1. A significant difference in BCVA between patients with FH and without was found (p = 0.014). BCVA continued to worsen over time in both groups (p < 0.001), irrespective of FH. This study reports FH in a CRB1 cohort, supporting the role of CRB1 in foveal development. FH was associated with poorer BCVA and abnormal retinal morphology. Nonetheless, its presence did not alter the disease progression.
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Affiliation(s)
- Ana Catalina Rodriguez-Martinez
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; (A.C.R.-M.); (B.E.H.); (V.T.-H.); (S.M.); (R.C.); (A.M.C.); (R.H.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 1LE, UK
| | - Bethany Elora Higgins
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; (A.C.R.-M.); (B.E.H.); (V.T.-H.); (S.M.); (R.C.); (A.M.C.); (R.H.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Vijay Tailor-Hamblin
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; (A.C.R.-M.); (B.E.H.); (V.T.-H.); (S.M.); (R.C.); (A.M.C.); (R.H.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- UCL Experimental Psychology, London WC1H 0AP, UK
| | - Samantha Malka
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; (A.C.R.-M.); (B.E.H.); (V.T.-H.); (S.M.); (R.C.); (A.M.C.); (R.H.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Riccardo Cheloni
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; (A.C.R.-M.); (B.E.H.); (V.T.-H.); (S.M.); (R.C.); (A.M.C.); (R.H.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Alexander Mark Collins
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; (A.C.R.-M.); (B.E.H.); (V.T.-H.); (S.M.); (R.C.); (A.M.C.); (R.H.)
| | - John Bladen
- King’s College Hospital NHS Foundation Trust, Strand, London WC2R 2LS, UK;
| | - Robert Henderson
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; (A.C.R.-M.); (B.E.H.); (V.T.-H.); (S.M.); (R.C.); (A.M.C.); (R.H.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 1LE, UK
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; (A.C.R.-M.); (B.E.H.); (V.T.-H.); (S.M.); (R.C.); (A.M.C.); (R.H.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 1LE, UK
- The Francis Crick Institute, London NW1 1AT, UK
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16
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Dentel A, Ferrari M, Robert MP, Valleix S, Bremond-Gignac D, Daruich A. Optical Coherence Tomography Angiography Assessment in Congenital Aniridia. Am J Ophthalmol 2023; 253:44-48. [PMID: 37059316 DOI: 10.1016/j.ajo.2023.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/16/2023]
Abstract
PURPOSE This study aims to characterize foveal vasculature assessed by optical coherence tomography angiography (OCT-A) in congenital aniridia which is hallmarked by foveal hypoplasia (FH). DESIGN Cross-sectional case-control analysis. METHODS At the National Referral Center for congenital aniridia, patients with confirmed PAX6-related aniridia and FH diagnosed on spectral-domain OCT (SD-OCT) with available OCT-A and matched control subjects were included. OCT-A was performed in patients with aniridia and control subjects. Foveal avascular zone (FAZ) and vessel density (VD) were collected. VD in the foveal and parafoveal areas at the level of the superficial and deep capillary plexi (SCP and DCP, respectively) were compared between the 2 groups. In patients with congenital aniridia, correlation between VD and the grading of FH was assessed. RESULTS Among 230 patients with confirmed PAX6-related aniridia, high-quality macular B-scans and OCT-A were available in 10 patients. On the foveal area, mean VD was higher in aniridia patients (41.10%, n = 10) than in control subjects (22.65%, n = 10) at the level of the SCP and the DCP (P = .0020 and P = .0273, respectively). On the parafoveal area, mean VD was lower in patients with aniridia (42.34%, n = 10) than in healthy subjects (49.24%, n = 10) at the level of both plexi (P = .0098 and P = .0371, respectively). In patients with congenital aniridia, a positive correlation was found between the grading of FH and the foveal VD at the SCP (r = 0.77, P = .0106). CONCLUSIONS Vasculature is altered in PAX6-related congenital aniridia, higher in foveal and lower in parafoveal areas, especially when FH is severe, which is consistent with the concept that the absence of retinal blood vessels is essential for foveal pit development.
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Affiliation(s)
- Alexandre Dentel
- From the Ophthalmology Department (A.D., M.F., M.P.R., D.B-G., A.D.), Necker-Enfants Malades University Hospital, Paris.
| | - Marco Ferrari
- From the Ophthalmology Department (A.D., M.F., M.P.R., D.B-G., A.D.), Necker-Enfants Malades University Hospital, Paris
| | - Matthieu P Robert
- From the Ophthalmology Department (A.D., M.F., M.P.R., D.B-G., A.D.), Necker-Enfants Malades University Hospital, Paris; Borelli Centre (M.P.R.), UMR 9010, CNRS-SSA-ENS Paris Saclay-Paris Cité University, Paris
| | - Sophie Valleix
- INSERM (S.V., D.B-G., A.D.), UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Sorbonne Paris Cité University, Centre de Recherche des Cordeliers, Paris; Genomic Medicine Department of Systemic and Organ Diseases (S.V.), Cochin Hospital, Paris City University, Paris, France
| | - Dominique Bremond-Gignac
- From the Ophthalmology Department (A.D., M.F., M.P.R., D.B-G., A.D.), Necker-Enfants Malades University Hospital, Paris; INSERM (S.V., D.B-G., A.D.), UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Sorbonne Paris Cité University, Centre de Recherche des Cordeliers, Paris
| | - Alejandra Daruich
- From the Ophthalmology Department (A.D., M.F., M.P.R., D.B-G., A.D.), Necker-Enfants Malades University Hospital, Paris; INSERM (S.V., D.B-G., A.D.), UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Sorbonne Paris Cité University, Centre de Recherche des Cordeliers, Paris
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17
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Yu Y, Jia H, Ma Q, Zhang R, Jiao Y. A novel missense variant expands the phenotype and genotype of PAX6-associated foveal hypoplasia accompanied by various manifestations of anterior segment dysgenesis. BMC Ophthalmol 2023; 23:349. [PMID: 37553561 PMCID: PMC10408164 DOI: 10.1186/s12886-023-03054-5] [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: 09/19/2022] [Accepted: 06/20/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND According to previous reports, PAX6-associated foveal hypoplasia (FH) could usually be accompanied by various anterior segment anomalies including variable iris changes. This study aims to exhibit unusual phenotypes of a novel missense variant of PAX6 from a Chinese pedigree. METHODS Ophthalmic examinations including slit-lamp biomicroscopy, gonioscopy, ophthalmic ultrasound, ultrasonic biomicroscopy, optical coherence tomography, wide-field fundus imaging, and visual field test were performed to evaluate the clinical manifestations. Whole-exome sequencing (WES) and bioinformatics analysis were conducted in eight members from this pedigree to identify the causative mutation. RESULTS WES revealed a novel heterozygous substitution of PAX6 (NM_000280.5:c.157G > A, p.(Val53Met) (chr11:31823309 C > T, hg19)), which cosegregated with the phenotype of this pedigree. All the three patients (a pair of fraternal twins and their mother) exhibited bilateral FH and anterior segment dysgenesis (ASD) including microcornea, sclerocornea, obvious symmetrical corectopia, iris stromal dysplasia, goniodysgenesis, and abnormal distribution of fundus blood vessels. The girl of the fraternal twins also demonstrated bilateral temporal deviation of lenses and abnormal tissue membrane connecting anterior chamber angle and lens anterior capsule in the right eye. The mother additionally showed apparent cataract bilaterally and cupping of the optic disc in her left eye. CONCLUSION A novel missense variant in PAX6 gene was detected in a Chinese pedigree demonstrating bilateral FH and ASD. It is really distinctive that the ASD involves almost all parts of the anterior segment, and bilateral symmetrical corectopia is the most perceptible sign. This study expands the phenotypic and genotypic spectrum of PAX6-associated ocular diseases, and facilitates the understanding of the crucial role that PAX6 plays in the development of the eye. Meanwhile, PAX6 could be considered as a candidate pathogenic gene of bilateral symmetrical corectopia.
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Affiliation(s)
- Yanping Yu
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, No. 1 Dongjiaominxiang Street, Dongcheng District, Beijing, 100730, China
| | - Hongyan Jia
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, No. 1 Dongjiaominxiang Street, Dongcheng District, Beijing, 100730, China.
| | - Qian Ma
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, No. 1 Dongjiaominxiang Street, Dongcheng District, Beijing, 100730, China
| | - Ranran Zhang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, No. 1 Dongjiaominxiang Street, Dongcheng District, Beijing, 100730, China
| | - Yonghong Jiao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, No. 1 Dongjiaominxiang Street, Dongcheng District, Beijing, 100730, China.
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Adair BA, Korecki AJ, Djaksigulova D, Wagner PK, Chiu NY, Lam SL, Lengyell TC, Leavitt BR, Simpson EM. ABE8e Corrects Pax6-Aniridic Variant in Humanized Mouse ESCs and via LNPs in Ex Vivo Cortical Neurons. Ophthalmol Ther 2023; 12:2049-2068. [PMID: 37210469 PMCID: PMC10287867 DOI: 10.1007/s40123-023-00729-6] [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: 03/12/2023] [Accepted: 04/27/2023] [Indexed: 05/22/2023] Open
Abstract
INTRODUCTION Aniridia is a rare congenital vision-loss disease caused by heterozygous variants in the PAX6 gene. There is no vision-saving therapy, but one exciting approach is to use CRISPR/Cas9 to permanently correct the causal genomic variants. Preclinical studies to develop such a therapy in animal models face the challenge of showing efficacy when binding human DNA. Thus, we hypothesized that a CRISPR gene therapy can be developed and optimized in humanized mouse embryonic stem cells (ESCs) that will be able to distinguish between an aniridia patient variant and nonvariant chromosome and lay the foundation for human therapy. METHODS To answer the challenge of binding human DNA, we proposed the "CRISPR Humanized Minimally Mouse Models" (CHuMMMs) strategy. Thus, we minimally humanized Pax6 exon 9, the location of the most common aniridia variant c.718C > T. We generated and characterized a nonvariant CHuMMMs mouse, and a CHuMMMs cell-based disease model, in which we tested five CRISPR enzymes for therapeutic efficacy. We then delivered the therapy via lipid nanoparticles (LNPs) to alter a second variant in ex vivo cortical primary neurons. RESULTS We successfully established a nonvariant CHuMMMs mouse and three novel CHuMMMs aniridia cell lines. We showed that humanization did not disrupt Pax6 function in vivo, as the mouse showed no ocular phenotype. We developed and optimized a CRISPR therapeutic strategy for aniridia in the in vitro system, and found that the base editor, ABE8e, had the highest correction of the patient variant at 76.8%. In the ex vivo system, the LNP-encapsulated ABE8e ribonucleoprotein (RNP) complex altered the second patient variant and rescued 24.8% Pax6 protein expression. CONCLUSION We demonstrated the usefulness of the CHuMMMs approach, and showed the first genomic editing by ABE8e encapsulated as an LNP-RNP. Furthermore, we laid the foundation for translation of the proposed CRISPR therapy to preclinical mouse studies and eventually patients with aniridia.
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Affiliation(s)
- Bethany A Adair
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Diana Djaksigulova
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | | | - Nina Y Chiu
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Siu Ling Lam
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Tess C Lengyell
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
- Incisive Genetics Inc., Vancouver, BC, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
- Department of Medical Genetics, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
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19
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Matsushita I, Izumi H, Ueno S, Hayashi T, Fujinami K, Tsunoda K, Iwata T, Kiuchi Y, Kondo H. Functional Characteristics of Diverse PAX6 Mutations Associated with Isolated Foveal Hypoplasia. Genes (Basel) 2023; 14:1483. [PMID: 37510387 PMCID: PMC10379490 DOI: 10.3390/genes14071483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The human fovea is a specialized pit structure in the central retina. Foveal hypoplasia is a condition where the foveal pit does not fully develop, and it is associated with poor vision. Autosomal dominant isolated foveal hypoplasia (FVH1) is a rare condition of foveal hypoplasia (FH) that lacks any other ocular manifestations. FVH1 is associated with hypomorphic mutations in the PAX6 gene that encodes a sequence-specific DNA-binding transcription factor for morphogenesis and evolution of the eye. We report our findings in 17 patients with PAX6 mutations associated with FVH1 or FH with aniridia and corneal opacities. Patients with three mutations, p.V78E, p.V83F and p.R128H, in the C-terminal subdomain of the paired domain (CTS) consistently have severe FH. Luciferase assays for a single reporter containing a representative PAX6 binding site indicated that the transcriptional activities of these mutations were significantly reduced, comparable to that of the truncation mutation of p.G65Rfs*5. Patients with p.P20S in the N-terminal subdomain of the paired domain, and a patient with p.N365K in the proline-serine-threonine-rich domain (PSTD) had mild FH. A patient with p.Q255L in the homeodomain had severe FH. The P20S and Q255L mutants did not affect the transcriptional activity. Mutant N365K has a retained DNA-binding activity but a reduced transcriptional activity, due to a low PSTD transactivation. These findings demonstrated that mutations associated with FVH1 underlie a functional divergence between DNA-binding ability and transcriptional activity. We conclude that a wide range of mutations in the PAX6 gene is not limited to the CST region and are responsible for FVH1.
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Affiliation(s)
- Itsuka Matsushita
- Department of Ophthalmology, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan;
| | - Hiroto Izumi
- Department of Occupational Pneumology, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan;
| | - Shinji Ueno
- Department of Ophthalmology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan;
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo 105-8461, Japan;
| | - Kaoru Fujinami
- Department of Ophthalmology, National Hospital Organization Tokyo Medical Center, Tokyo 152-8902, Japan; (K.F.); (K.T.)
| | - Kazushige Tsunoda
- Department of Ophthalmology, National Hospital Organization Tokyo Medical Center, Tokyo 152-8902, Japan; (K.F.); (K.T.)
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo 152-8902, Japan;
| | - Yoshiaki Kiuchi
- Department of Ophthalmology and Visual Science, Graduate School of Biomedical and Health Sciences, Hiroshima 734-8551, Japan;
| | - Hiroyuki Kondo
- Department of Ophthalmology, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan;
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20
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Arts JA, Laberthonnière C, Lima Cunha D, Zhou H. Single-Cell RNA Sequencing: Opportunities and Challenges for Studies on Corneal Biology in Health and Disease. Cells 2023; 12:1808. [PMID: 37443842 PMCID: PMC10340756 DOI: 10.3390/cells12131808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
The structure and major cell types of the multi-layer human cornea have been extensively studied. However, various cell states in specific cell types and key genes that define the cell states are not fully understood, hindering our comprehension of corneal homeostasis, related diseases, and therapeutic discovery. Single-cell RNA sequencing is a revolutionary and powerful tool for identifying cell states within tissues such as the cornea. This review provides an overview of current single-cell RNA sequencing studies on the human cornea, highlighting similarities and differences between them, and summarizing the key genes that define corneal cell states reported in these studies. In addition, this review discusses the opportunities and challenges of using single-cell RNA sequencing to study corneal biology in health and disease.
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Affiliation(s)
- Julian A. Arts
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Camille Laberthonnière
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Dulce Lima Cunha
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Huiqing Zhou
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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21
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Grainger RM, Lauderdale JD, Collins JL, Trout KL, McCullen Krantz S, Wolfe SS, Netland PA. Report on the 2021 Aniridia North America symposium on PAX6, aniridia, and beyond. Ocul Surf 2023; 29:423-431. [PMID: 37247841 DOI: 10.1016/j.jtos.2023.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
The inaugural Aniridia North America (ANA) Symposium was held on the first weekend in November 2021 in Charlottesville, VA, at the University of Virginia. The purpose of this meeting was to bring together an international group of scientists, physicians, patient advocacy groups, and individuals with aniridia to discuss recent advances in knowledge about aniridia and other congenital eye diseases and the development of potential treatments for congenital eye disorders using personalized medicine. Leaders in several areas of eye research and clinical treatment provided a broad perspective on new research advances that impact an understanding of the causes of the damage to the eye associated with aniridia and the development of novel treatments for this and related disorders. Here we summarize the research discussed at the symposium.
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Affiliation(s)
- Robert M Grainger
- Aniridia North America, LaGrange, IL, 60525, USA; Department of Biology, 326 Gilmer Hall University of Virginia 485 McCormick Road P.O. Box 400328 Charlottesville, VA 22904, USA.
| | - James D Lauderdale
- Aniridia North America, LaGrange, IL, 60525, USA; Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA.
| | | | | | | | | | - Peter A Netland
- Aniridia North America, LaGrange, IL, 60525, USA; Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
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22
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Daruich A, Duncan M, Robert MP, Lagali N, Semina EV, Aberdam D, Ferrari S, Romano V, des Roziers CB, Benkortebi R, De Vergnes N, Polak M, Chiambaretta F, Nischal KK, Behar-Cohen F, Valleix S, Bremond-Gignac D. Congenital aniridia beyond black eyes: From phenotype and novel genetic mechanisms to innovative therapeutic approaches. Prog Retin Eye Res 2023; 95:101133. [PMID: 36280537 PMCID: PMC11062406 DOI: 10.1016/j.preteyeres.2022.101133] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
Abstract
Congenital PAX6-aniridia, initially characterized by the absence of the iris, has progressively been shown to be associated with other developmental ocular abnormalities and systemic features making congenital aniridia a complex syndromic disorder rather than a simple isolated disease of the iris. Moreover, foveal hypoplasia is now recognized as a more frequent feature than complete iris hypoplasia and a major visual prognosis determinant, reversing the classical clinical picture of this disease. Conversely, iris malformation is also a feature of various anterior segment dysgenesis disorders caused by PAX6-related developmental genes, adding a level of genetic complexity for accurate molecular diagnosis of aniridia. Therefore, the clinical recognition and differential genetic diagnosis of PAX6-related aniridia has been revealed to be much more challenging than initially thought, and still remains under-investigated. Here, we update specific clinical features of aniridia, with emphasis on their genotype correlations, as well as provide new knowledge regarding the PAX6 gene and its mutational spectrum, and highlight the beneficial utility of clinically implementing targeted Next-Generation Sequencing combined with Whole-Genome Sequencing to increase the genetic diagnostic yield of aniridia. We also present new molecular mechanisms underlying aniridia and aniridia-like phenotypes. Finally, we discuss the appropriate medical and surgical management of aniridic eyes, as well as innovative therapeutic options. Altogether, these combined clinical-genetic approaches will help to accelerate time to diagnosis, provide better determination of the disease prognosis and management, and confirm eligibility for future clinical trials or genetic-specific therapies.
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Affiliation(s)
- Alejandra Daruich
- Ophthalmology Department, Necker-Enfants Malades University Hospital, AP-HP, Paris Cité University, Paris, France; INSERM, UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Sorbonne Paris Cité University, Centre de Recherche des Cordeliers, Paris, France
| | - Melinda Duncan
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Matthieu P Robert
- Ophthalmology Department, Necker-Enfants Malades University Hospital, AP-HP, Paris Cité University, Paris, France; Borelli Centre, UMR 9010, CNRS-SSA-ENS Paris Saclay-Paris Cité University, Paris, France
| | - Neil Lagali
- Division of Ophthalmology, Department of Biomedical and Clinical Sciences, Faculty of Medicine, Linköping University, 581 83, Linköping, Sweden; Department of Ophthalmology, Sørlandet Hospital Arendal, Arendal, Norway
| | - Elena V Semina
- Department of Pediatrics, Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Daniel Aberdam
- INSERM, UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Sorbonne Paris Cité University, Centre de Recherche des Cordeliers, Paris, France
| | - Stefano Ferrari
- Fondazione Banca degli Occhi del Veneto, Via Paccagnella 11, Venice, Italy
| | - Vito Romano
- Department of Medical and Surgical Specialties, Radiolological Sciences, and Public Health, Ophthalmology Clinic, University of Brescia, Italy
| | - Cyril Burin des Roziers
- INSERM, UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Sorbonne Paris Cité University, Centre de Recherche des Cordeliers, Paris, France; Service de Médecine Génomique des Maladies de Système et d'Organe, APHP. Centre Université de Paris, Fédération de Génétique et de Médecine Génomique Hôpital Cochin, 27 rue du Fbg St-Jacques, 75679, Paris Cedex 14, France
| | - Rabia Benkortebi
- Ophthalmology Department, Necker-Enfants Malades University Hospital, AP-HP, Paris Cité University, Paris, France
| | - Nathalie De Vergnes
- Ophthalmology Department, Necker-Enfants Malades University Hospital, AP-HP, Paris Cité University, Paris, France
| | - Michel Polak
- Pediatric Endocrinology, Gynecology and Diabetology, Hôpital Universitaire Necker Enfants Malades, AP-HP, Paris Cité University, INSERM U1016, Institut IMAGINE, France
| | | | - Ken K Nischal
- Division of Pediatric Ophthalmology, Strabismus, and Adult Motility, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; UPMC Eye Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Francine Behar-Cohen
- INSERM, UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Sorbonne Paris Cité University, Centre de Recherche des Cordeliers, Paris, France
| | - Sophie Valleix
- INSERM, UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Sorbonne Paris Cité University, Centre de Recherche des Cordeliers, Paris, France; Service de Médecine Génomique des Maladies de Système et d'Organe, APHP. Centre Université de Paris, Fédération de Génétique et de Médecine Génomique Hôpital Cochin, 27 rue du Fbg St-Jacques, 75679, Paris Cedex 14, France
| | - Dominique Bremond-Gignac
- Ophthalmology Department, Necker-Enfants Malades University Hospital, AP-HP, Paris Cité University, Paris, France; INSERM, UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Sorbonne Paris Cité University, Centre de Recherche des Cordeliers, Paris, France.
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23
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Roshandel D, Semnani F, Rayati Damavandi A, Masoudi A, Baradaran-Rafii A, Watson SL, Morgan WH, McLenachan S. Genetic predisposition to ocular surface disorders and opportunities for gene-based therapies. Ocul Surf 2023; 29:150-165. [PMID: 37192706 DOI: 10.1016/j.jtos.2023.05.003] [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: 02/28/2023] [Revised: 04/24/2023] [Accepted: 05/09/2023] [Indexed: 05/18/2023]
Abstract
The ocular surface, comprised of the corneal and conjunctival epithelium, innervation system, immune components, and tear-film apparatus, plays a key role in ocular integrity as well as comfort and vision. Gene defects may result in congenital ocular or systemic disorders with prominent ocular surface involvement. Examples include epithelial corneal dystrophies, aniridia, ectrodactyly-ectodermal dysplasia-clefting (EEC) syndrome, xeroderma pigmentosum (XP), and hereditary sensory and autonomic neuropathy. In addition, genetic factors may interact with environmental risk factors in the development of several multifactorial ocular surface disorders (OSDs) such as autoimmune disorders, allergies, neoplasms, and dry eye disease. Advanced gene-based technologies have already been introduced in disease modelling and proof-of-concept gene therapies for monogenic OSDs. For instance, patient-derived induced pluripotent stem cells have been used for modelling aniridia-associated keratopathy (AAK), XP, and EEC syndrome. Moreover, CRISPR/Cas9 genome editing has been used for disease modelling and/or gene therapy for AAK and Meesmann's epithelial corneal dystrophy. A better understanding of the role of genetic factors in OSDs may be helpful in designing personalized disease models and treatment approaches. Gene-based approaches in monogenic OSDs and genetic predisposition to multifactorial OSDs such as immune-mediated disorders and neoplasms with known or possible genetic risk factors has been seldom reviewed. In this narrative review, we discuss the role of genetic factors in monogenic and multifactorial OSDs and potential opportunities for gene therapy.
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Affiliation(s)
- Danial Roshandel
- Lions Eye Institute, Perth, WA, Australia; Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia
| | - Farbod Semnani
- School of Public Health, Tehran University of Medical Sciences (TUMS), Tehran, Iran; School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Amirmasoud Rayati Damavandi
- School of Public Health, Tehran University of Medical Sciences (TUMS), Tehran, Iran; School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Ali Masoudi
- Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Alireza Baradaran-Rafii
- Department of Ophthalmology, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Ophthalmology, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Stephanie L Watson
- The University of Sydney, Save Sight Institute, Discipline of Ophthalmology, Sydney Medical School, Sydney, New South Wales, Australia
| | - William H Morgan
- Lions Eye Institute, Perth, WA, Australia; Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia
| | - Samuel McLenachan
- Lions Eye Institute, Perth, WA, Australia; Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia.
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24
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Zheng Y, Sun C, Zhang X, Ruzycki PA, Chen S. Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526652. [PMID: 36778408 PMCID: PMC9915647 DOI: 10.1101/2023.02.01.526652] [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: 02/07/2023]
Abstract
Homeodomain transcription factors (HD TFs) are instrumental to vertebrate development. Mutations in HD TFs have been linked to human diseases, but their pathogenic mechanisms remain elusive. Here we use Cone-Rod Homeobox (CRX) as a model to decipher the disease-causing mechanisms of two HD mutations, p.E80A and p.K88N, that produce severe dominant retinopathies. Through integrated analysis of molecular and functional evidence in vitro and in knock-in mouse models, we uncover two novel gain-of-function mechanisms: p.E80A increases CRX-mediated transactivation of canonical CRX target genes in developing photoreceptors; p.K88N alters CRX DNA-binding specificity resulting in binding at ectopic sites and severe perturbation of CRX target gene expression. Both mechanisms produce novel retinal morphological defects and hinder photoreceptor maturation distinct from loss-of-function models. This study reveals the distinct roles of E80 and K88 residues in CRX HD regulatory functions and emphasizes the importance of transcriptional precision in normal development.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
| | - Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
| | - Xiaodong Zhang
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
| | - Philip A. Ruzycki
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
- Department of Genetics, Washington University in St Louis, Saint Louis, Missouri, USA
| | - Shiming Chen
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
- Department of Developmental Biology, Washington University in St Louis, Saint Louis, Missouri, USA
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25
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Damián A, Núñez-Moreno G, Jubin C, Tamayo A, de Alba MR, Villaverde C, Fund C, Delépine M, Leduc A, Deleuze JF, Mínguez P, Ayuso C, Corton M. Long-read genome sequencing identifies cryptic structural variants in congenital aniridia cases. Hum Genomics 2023; 17:45. [PMID: 37269011 DOI: 10.1186/s40246-023-00490-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/08/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Haploinsufficiency of the transcription factor PAX6 is the main cause of congenital aniridia, a genetic disorder characterized by iris and foveal hypoplasia. 11p13 microdeletions altering PAX6 or its downstream regulatory region (DRR) are present in about 25% of patients; however, only a few complex rearrangements have been described to date. Here, we performed nanopore-based whole-genome sequencing to assess the presence of cryptic structural variants (SVs) on the only two unsolved "PAX6-negative" cases from a cohort of 110 patients with congenital aniridia after unsuccessfully short-read sequencing approaches. RESULTS Long-read sequencing (LRS) unveiled balanced chromosomal rearrangements affecting the PAX6 locus at 11p13 in these two patients and allowed nucleotide-level breakpoint analysis. First, we identified a cryptic 4.9 Mb de novo inversion disrupting intron 7 of PAX6, further verified by targeted polymerase chain reaction amplification and sequencing and FISH-based cytogenetic analysis. Furthermore, LRS was decisive in correctly mapping a t(6;11) balanced translocation cytogenetically detected in a second proband with congenital aniridia and considered non-causal 15 years ago. LRS resolved that the breakpoint on chromosome 11 was indeed located at 11p13, disrupting the DNase I hypersensitive site 2 enhancer within the DRR of PAX6, 161 Kb from the causal gene. Patient-derived RNA expression analysis demonstrated PAX6 haploinsufficiency, thus supporting that the 11p13 breakpoint led to a positional effect by cleaving crucial enhancers for PAX6 transactivation. LRS analysis was also critical for mapping the exact breakpoint on chromosome 6 to the highly repetitive centromeric region at 6p11.1. CONCLUSIONS In both cases, the LRS-based identified SVs have been deemed the hidden pathogenic cause of congenital aniridia. Our study underscores the limitations of traditional short-read sequencing in uncovering pathogenic SVs affecting low-complexity regions of the genome and the value of LRS in providing insight into hidden sources of variation in rare genetic diseases.
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Affiliation(s)
- Alejandra Damián
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
- Centre for Biomedical Network Research On Rare Diseases (CIBERER), 28029, Madrid, Spain
| | - Gonzalo Núñez-Moreno
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
- Centre for Biomedical Network Research On Rare Diseases (CIBERER), 28029, Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
| | - Claire Jubin
- Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, 91057, Evry, France
| | - Alejandra Tamayo
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
- Centre for Biomedical Network Research On Rare Diseases (CIBERER), 28029, Madrid, Spain
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, Science and Technology Campus, University of Alcalá, 28871, Alcalá de Henares, Spain
| | - Marta Rodríguez de Alba
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
- Centre for Biomedical Network Research On Rare Diseases (CIBERER), 28029, Madrid, Spain
| | - Cristina Villaverde
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
- Centre for Biomedical Network Research On Rare Diseases (CIBERER), 28029, Madrid, Spain
| | - Cédric Fund
- Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, 91057, Evry, France
| | - Marc Delépine
- Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, 91057, Evry, France
| | - Aurélie Leduc
- Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, 91057, Evry, France
| | - Jean François Deleuze
- Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, 91057, Evry, France
| | - Pablo Mínguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
- Centre for Biomedical Network Research On Rare Diseases (CIBERER), 28029, Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
- Centre for Biomedical Network Research On Rare Diseases (CIBERER), 28029, Madrid, Spain
| | - Marta Corton
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain.
- Centre for Biomedical Network Research On Rare Diseases (CIBERER), 28029, Madrid, Spain.
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Pan Q, Lu K, Luo J, Jiang Y, Xia B, Chen L, Wang M, Dai R, Chen T. Japanese medaka Olpax6.1 mutant as a potential model for spondylo-ocular syndrome. Funct Integr Genomics 2023; 23:168. [PMID: 37204625 DOI: 10.1007/s10142-023-01090-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023]
Abstract
pax6 is a canonic master gene for eye formation. Knockout of pax6 affects the development of craniofacial skeleton and eye in mice. Whether pax6 affects the development of spinal bone has not been reported yet. In the present study, we used CRISPR/Cas9 system to generate Olpax6.1 mutant in Japanese medaka. Phenotype analysis showed that ocular mutation caused by the Olpax6.1 mutation occurred in the homozygous mutant. The phenotype of heterozygotes is not significantly different from that of wild-type. In addition, knockout Olpax6.1 resulted in severe curvature of the spine in the homozygous F2 generation. Comparative transcriptome analysis and qRT-PCR revealed that the defective Olpax6.1 protein caused a decrease in the expression level of sp7, col10a1a, and bglap, while the expression level of xylt2 did not change significantly. The functional enrichment of differentially expressed genes (DEGs) using the Kyoto Encyclopedia of Genes and Genomes database showed that the DEGs between Olpax6.1 mutation and wild-type were enriched in p53 signaling pathway, extracellular matrix (ECM) -receptor interaction, et al. Our results indicated that the defective Olpax6.1 protein results in the reduction of sp7 expression level and the activation of p53 signaling pathway, which leads to a decrease in the expression of genes encoding ECM protein, such as collagen protein family and bone gamma-carboxyglutamate protein, which further inhibits bone development. Based on the phenotype and molecular mechanism of ocular mutation and spinal curvature induced by Olpax6.1 knockout, we believe that the Olpax6.1-/- mutant could be a potential model for the study of spondylo-ocular syndrome.
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Affiliation(s)
- Qihua Pan
- Fisheries College of Jimei University, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Xiamen, 361021, Fujian, China
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ke Lu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Junzhi Luo
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yuewen Jiang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Bilin Xia
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lei Chen
- Fisheries College of Jimei University, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Xiamen, 361021, Fujian, China
| | - Mengyang Wang
- Fisheries College of Jimei University, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Xiamen, 361021, Fujian, China
| | - Ronggui Dai
- Fisheries College of Jimei University, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Xiamen, 361021, Fujian, China
| | - Tiansheng Chen
- Fisheries College of Jimei University, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Xiamen, 361021, Fujian, China.
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Kuchalska K, Wawrocka A, Krawczynski MR. Novel variants in the PAX6 gene related to isolated aniridia. Congenit Anom (Kyoto) 2023. [PMID: 37191119 DOI: 10.1111/cga.12520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/07/2023] [Accepted: 04/25/2023] [Indexed: 05/17/2023]
Abstract
Aniridia, which is a rare congenital defect of the eye, consists of iris hypoplasia or aplasia, and additional ocular abnormalities. It is most commonly caused by autosomal dominant PAX6 gene mutations. However, in about 30% of cases, it is associated with chromosomal rearrangements in the 11p13 region. The aim of this study was to identify the potential PAX6 gene variants, which could cause the isolated aniridia. Eight patients with isolated aniridia were included in this study. MLPA analysis allowed in the past to exclude large structural rearrangements of the PAX6 and adjacent genes like WT1. Blood samples were collected from the patients (and their families in familial cases) and genomic DNA was extracted from peripheral blood leukocytes and buccal cells. The amplification of the 11 exons of the PAX6 gene was performed. Bidirectional Sanger Sequencing was conducted for the identification of the potentially pathogenic variants, and for the segregation analysis of the identified variant in the family. The results were analyzed with the use of CodonCode Aligner software. In three patients, aniridia was sporadic, whereas in another five cases, the eye defect was familial. The potentially pathogenic variants in the PAX6 gene were found in 6 out of 8 patients with aniridia. We identified four known (c.781C > T, c.607C > T, and c.949C > T twice), and two novel variants (c.258_265del and c.495_496insG). Point mutations in the PAX6 gene are the most frequent cause of aniridia. The investigation of the genetic background of the disease is essential for patients to evaluate recurrence risk in the offspring.
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Affiliation(s)
| | - Anna Wawrocka
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Maciej R Krawczynski
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Center of Medical Genetics "Genesis", Poznan, Poland
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28
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Comparing Gene Panels for Non-Retinal Indications: A Systematic Review. Genes (Basel) 2023; 14:genes14030738. [PMID: 36981008 PMCID: PMC10047970 DOI: 10.3390/genes14030738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/16/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Importance: The options for genetic testing continue to grow for ocular conditions, including optic atrophy, anterior segment dysgenesis, cataracts, corneal dystrophy, nystagmus, and glaucoma. Gene panels can vary in content and coverage, as we and others have evaluated in inherited retinal disease (IRD). Objective: To describe gene panel testing options for inherited eye disease phenotypes and their differences. This review is important for making diagnostic decisions. Evidence review: A licensed, certified genetic counselor (RP) used Concert Genetics and the search terms optic atrophy, corneal dystrophy, cataract, glaucoma, anterior segment dysgenesis, microphthalmia/anophthalmia, and nystagmus to identify available testing options performed by CLIA-certified commercial genetic testing laboratories. Other co-authors were surveyed with respect to genetic panels used for the indications of interest. Ophthalmic panels were then compared using Concert Genetics in addition to their own websites. Findings: Panels from each clinical category were included and summarized. This comparison highlighted the differences and similarities between panels so that clinicians can make informed decisions. Conclusions: Access to genetic testing is increasing. The diagnostic yield of genetic testing is increasing. Each panel is different, so phenotyping or characterizing clinical characteristics that may help predict a specific genotype, as well as pre-test hypotheses regarding a genotype, should shape the choice of panels.
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Huang L, Peng J, Xie Y, Zhou Y, Wang X, Wang H, Gui J, Li N. Diversity of clinical phenotypes in a cohort of Han Chinese patients with PAX6 variants. Front Genet 2023; 14:1011060. [PMID: 36816037 PMCID: PMC9934858 DOI: 10.3389/fgene.2023.1011060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
The PAX6 gene plays an important role in ocular development. Mutations of the PAX6 gene may result in a series of ocular abnormalities, including congenital aniridia, anterior segment dysgenesis (ASD), progressive corneal opacification, glaucoma, and hypoplasia of the fovea and optic nerve, leading to reduced visual acuity and even blindness. This study aimed to describe the diversity of clinical features caused by PAX6 pathogenic variants in 45 Han Chinese patients from 23 unrelated families. All patients underwent detailed clinical assessment. Genetic testing was performed to identify pathogenic variations in the PAX6 gene by next-generation sequencing, minigene splicing assay, RT-qPCR, and long-range PCR. Twenty pathogenic variations were detected in the PAX6 gene from 12 pedigrees and 11 sporadic patients, of which 12 were previously reported and 8 were novel. The clinical phenotypes obtained as a result of the PAX6 gene mutations were complicated and vary among patients, even among those who carried the same variants. Genetic testing is helpful for differential diagnosis. Our genetic findings will expand the spectrum of pathogenic variations in the PAX6 gene. PAX6 pathogenic variants not only cause defects in ocular tissues, such as the iris and retina, but also lead to maldevelopment of the whole eye, resulting in microphthalmia.
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Affiliation(s)
- Lijuan Huang
- Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China,Department of Ophthalmology, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Jiajia Peng
- Department of Ophthalmology, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Yan Xie
- Department of Ophthalmology, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Yunyu Zhou
- Department of Ophthalmology, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Xiaolin Wang
- Laboratory of Tumor Immunology, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
| | - Hui Wang
- Laboratory of Tumor Immunology, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
| | - Jingang Gui
- Laboratory of Tumor Immunology, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China,*Correspondence: Jingang Gui, ; Ningdong Li,
| | - Ningdong Li
- Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China,Department of Ophthalmology, Beijing Children’s Hospital, Capital Medical University, Beijing, China,Department of Ophthalmology, Shanghai General Hospital, Shanghai, China,Department of Ophthalmology, Children’s Hospital, Capital Institute of Pediatrics, Beijing, China,*Correspondence: Jingang Gui, ; Ningdong Li,
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Tamayo A, Núñez-Moreno G, Ruiz C, Plaisancie J, Damian A, Moya J, Chassaing N, Calvas P, Ayuso C, Minguez P, Corton M. Minigene Splicing Assays and Long-Read Sequencing to Unravel Pathogenic Deep-Intronic Variants in PAX6 in Congenital Aniridia. Int J Mol Sci 2023; 24:ijms24021562. [PMID: 36675087 PMCID: PMC9863980 DOI: 10.3390/ijms24021562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
PAX6 haploinsufficiency causes aniridia, a congenital eye disorder that involves the iris, and foveal hypoplasia. Comprehensive screening of the PAX6 locus, including the non-coding regions, by next-generation sequencing revealed four deep-intronic variants with potential effects on pre-RNA splicing. Nevertheless, without a functional analysis, their pathogenicity could not be established. We aimed to decipher their impact on the canonical PAX6 splicing using in vitro minigene splicing assays and nanopore-based long-read sequencing. Two multi-exonic PAX6 constructs were generated, and minigene assays were carried out. An aberrant splicing pattern was observed for two variants in intron 6, c.357+136G>A and c.357+334G>A. In both cases, several exonization events, such as pseudoexon inclusions and partial intronic retention, were observed due to the creation or activation of new/cryptic non-canonical splicing sites, including a shared intronic donor site. In contrast, two variants identified in intron 11, c.1032+170A>T and c.1033-275A>C, seemed not to affect splicing processes. We confirmed the high complexity of alternative splicing of PAX6 exon 6, which also involves unreported cryptic intronic sites. Our study highlights the importance of integrating functional studies into diagnostic algorithms to decipher the potential implication of non-coding variants, usually classified as variants of unknown significance, thus allowing variant reclassification to achieve a conclusive genetic diagnosis.
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Affiliation(s)
- Alejandra Tamayo
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, Science and Technology Campus, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Gonzalo Núñez-Moreno
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28240 Madrid, Spain
| | - Carolina Ruiz
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Julie Plaisancie
- Centre de Référence des Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Purpan, CHU Toulouse, 31000 Toulouse, France
- INSERM U1214, Université Toulouse III, 31000 Toulouse, France
| | - Alejandra Damian
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jennifer Moya
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Nicolas Chassaing
- Centre de Référence des Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Purpan, CHU Toulouse, 31000 Toulouse, France
- INSERM U1214, Université Toulouse III, 31000 Toulouse, France
| | - Patrick Calvas
- Centre de Référence des Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Purpan, CHU Toulouse, 31000 Toulouse, France
- INSERM U1214, Université Toulouse III, 31000 Toulouse, France
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Pablo Minguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28240 Madrid, Spain
| | - Marta Corton
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence:
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A new association of PAX6 variation with Juvenile onset open angle glaucoma. J Hum Genet 2023; 68:355-358. [PMID: 36599958 DOI: 10.1038/s10038-022-01115-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/30/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023]
Abstract
Mutations in the PAX6 gene are generally associated with aniridia. We describe a family with Juvenile onset open angle glaucoma (JOAG), where one of the two children had JOAG and the other Juvenile ocular hypertension. Whole exome sequencing was performed for the parents and their two affected children where the proband and her sibling were detected to have a de novo PAX6 gene variant in the absence of aniridia. All previously described gene mutations for glaucoma were looked for in the family. The potential pathogenicity of the identified variants was assessed by determining their frequency in large public exome databases; as well as using the current ACMG guidelines. The same heterozygous variant at NM_000280.6:c.1124 C > A; p. Pro375Gln in the PAX6 gene was detected in the proband and her affected brother. The variant has been described in aniridia patients before and has been shown to cause a weaker DNA binding using functional studies. This report expands the phenotypic spectrum of the PAX6 gene to include Juvenile onset open angle glaucoma.
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Krause MA, Trout KL, Lauderdale JD, Netland PA. Visual Acuity in Aniridia and WAGR Syndrome. Clin Ophthalmol 2023; 17:1255-1261. [PMID: 37152637 PMCID: PMC10162095 DOI: 10.2147/opth.s405003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023] Open
Abstract
Purpose Our purpose was to evaluate visual acuity in aniridia subjects and the more severely affected phenotype in WAGR syndrome subjects, and to assess potential impact on visual function. Materials and Methods This was a retrospective comparative study of 25 aniridia subjects with nonsense mutations of PAX6 (50 eyes) and 25 WAGR syndrome subjects with large deletion mutations involving PAX6 (50 eyes). Aniridia subjects were age- and gender-matched with WAGR syndrome subjects in the Coordination of Rare Diseases at Sanford (CoRDS) database. Best-corrected ETDRS visual acuity measurements were converted to LogMAR visual acuity values, which were used to perform statistical analyses. Results The age and gender distribution of the subjects was not statistically significantly different. The mean LogMAR values in aniridia and WAGR syndrome subjects were 0.95±0.53 and 1.51±0.99, respectively (P<0.001). In the better-seeing eye, mean LogMAR values were 0.78±0.15 in aniridia subjects and 1.40±0.88 in WAGR syndrome subjects (P=0.001). The mean LogMAR values for the better-seeing eye corresponded to Snellen visual acuity of 20/125 in aniridia subjects and 20/500 in WAGR syndrome subjects. This average visual acuity was worse than the threshold for profound visual impairment (WHO criteria) and legal blindness (AAO criteria) in WAGR syndrome but not in aniridia subjects. In analysis of both eyes, the visual efficiency was 34% in aniridia subjects and 2% in WAGR syndrome subjects. Conclusion Visual acuity was significantly worse in WAGR subjects with multi-gene deletion mutations compared with aniridia subjects with nonsense mutations, which corresponded to differences in standard visual function thresholds. Our results suggest that visual acuity may indicate severity of ocular involvement and variability of phenotype in aniridia and WAGR syndrome.
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Affiliation(s)
- Michael A Krause
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kelly L Trout
- International WAGR Syndrome Association, Montgomery Village, MD, USA
| | | | - Peter A Netland
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Correspondence: Peter A Netland, Department of Ophthalmology, University of Virginia School of Medicine, 1300 Jefferson Park Avenue, P.O. Box 800715, Charlottesville, VA, 22908-0715, USA, Tel +1 434-982-1086, Email
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Muacevic A, Adler JR, Xie W, Li M, Zhong L, Zhao S, Liang H. Novel Mutations of PAX6 and WFS1 Associated With Congenital Cataract in a Chinese Family. Cureus 2023; 15:e34208. [PMID: 36843716 PMCID: PMC9957680 DOI: 10.7759/cureus.34208] [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] [Accepted: 01/22/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Congenital cataract is a common cause of blindness in childhood. About half of the cases have a genetic etiology, and more than 100 genes have been associated with congenital cataracts. This study reports the clinical and genetic findings of a two-generation Chinese family affected by congenital cataract. METHODS Ophthalmologic examinations were performed for clinical evaluation of the cataract patients. Whole exome sequencing (WES) and Sanger sequencing were used to identify potentially relevant mutations. The online programsProtein Variation Effect Analyzer (PROVEAN) and Sorting Intolerant from Tolerant (SIFT) were employed to predict the impact of variation on protein function. RESULTS Both the proband and her mother were blind because of bilateral nuclear cataracts, and the elder brother of the proband also manifested obvious bilateral cataracts. Sanger sequencing confirmed the mutations in the proband as well as in her mother. The elder brother simply carried the PAX6 c.221G>A variation. The WFS1 c.2070_2079del variation potentially generates a loss-of-function mutant. CONCLUSION The novel PAX6mutation (c.221G>A) is associated with congenital cataract, and the WFS1 mutation (c.2070_2079del) may interactively aggravates this process. These findings may increase our understanding of the genetic etiology of congenital cataract.
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Guo R, Zhang X, Liu A, Ji J, Liu W. Novel clinical presentation and PAX6 mutation in families with congenital aniridia. Front Med (Lausanne) 2022; 9:1042588. [PMID: 36582291 PMCID: PMC9792480 DOI: 10.3389/fmed.2022.1042588] [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: 09/12/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Purpose To explore the clinical phenotype and genetic defects of families with congenital aniridia. Methods Four Chinese families with aniridia were enrolled in this study. The detailed ocular presentations of the patients were recorded. Whole exome sequencing (BGI MGIEasy V4 chip) was used to detect the gene mutation. Sanger sequencing was performed to validate the potential pathogenic variants, and segregation analysis was performed on all available family members. Results By whole exome sequencing and Sanger sequencing, three recurrent mutations (c.112del, p.Arg38Glyfs*16; c.299G > A, p.Trp100* and c.718C > T, p.Arg240*) and one novel mutation (c.278_281del, p.Glu93Alafs*30) of PAX6 were identified. All the mutations were co-segregated with the phenotype in the families. We also observed spontaneous anterior lens capsule rupture in aniridia for the first time. Conclusion We report spontaneous anterior lens capsule rupture as a novel phenotype of aniridia and three recurrent mutations and one novel mutation of PAX6 in families with aniridia. Our results expanded the phenotype and genotype spectra of aniridia and can help us better understand the disease.
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Affiliation(s)
- Ruru Guo
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Xiaotian Zhang
- Department of Ophthalmology, Nankai University Eye Hospital, Tianjin, China,Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Hospital, Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Aihua Liu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Jian Ji
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Wei Liu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China,*Correspondence: Wei Liu,
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Abdolkarimi D, Cunha DL, Lahne1 M, Moosajee M. PAX6 disease models for aniridia. Indian J Ophthalmol 2022; 70:4119-4129. [PMID: 36453299 PMCID: PMC9940591 DOI: 10.4103/ijo.ijo_316_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/01/2022] [Accepted: 08/10/2022] [Indexed: 12/12/2022] Open
Abstract
Aniridia is a pan-ocular genetic developmental eye disorder characterized by complete or partial iris and foveal hypoplasia, for which there is no treatment currently. Progressive sight loss can arise from cataracts, glaucoma, and aniridia-related keratopathy, which can be managed conservatively or through surgical intervention. The vast majority of patients harbor heterozygous mutations involving the PAX6 gene, which is considered the master transcription factor of early eye development. Over the past decades, several disease models have been investigated to gain a better understanding of the molecular pathophysiology, including several mouse and zebrafish strains and, more recently, human-induced pluripotent stem cells (hiPSCs) derived from aniridia patients. The latter provides a more faithful cellular system to study early human eye development. This review outlines the main aniridia-related animal and cellular models used to study aniridia and highlights the key discoveries that are bringing us closer to a therapy for patients.
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Affiliation(s)
| | - Dulce Lima Cunha
- UCL Institute of Ophthalmology, London, UK
- Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | | | - Mariya Moosajee
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- The Francis Crick Institute, London, UK
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Hall HN, Bengani H, Hufnagel RB, Damante G, Ansari M, Marsh JA, Grimes GR, von Kriegsheim A, Moore D, McKie L, Rahmat J, Mio C, Blyth M, Keng WT, Islam L, McEntargart M, Mannens MM, Heyningen VV, Rainger J, Brooks BP, FitzPatrick DR. Monoallelic variants resulting in substitutions of MAB21L1 Arg51 Cause Aniridia and microphthalmia. PLoS One 2022; 17:e0268149. [PMID: 36413568 PMCID: PMC9681113 DOI: 10.1371/journal.pone.0268149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/06/2022] [Indexed: 11/23/2022] Open
Abstract
Classical aniridia is a congenital and progressive panocular disorder almost exclusively caused by heterozygous loss-of-function variants at the PAX6 locus. We report nine individuals from five families with severe aniridia and/or microphthalmia (with no detectable PAX6 mutation) with ultrarare monoallelic missense variants altering the Arg51 codon of MAB21L1. These mutations occurred de novo in 3/5 families, with the remaining families being compatible with autosomal dominant inheritance. Mice engineered to carry the p.Arg51Leu change showed a highly-penetrant optic disc anomaly in heterozygous animals with severe microphthalmia in homozygotes. Substitutions of the same codon (Arg51) in MAB21L2, a close homolog of MAB21L1, cause severe ocular and skeletal malformations in humans and mice. The predicted nucleotidyltransferase function of MAB21L1 could not be demonstrated using purified protein with a variety of nucleotide substrates and oligonucleotide activators. Induced expression of GFP-tagged wildtype and mutant MAB21L1 in human cells caused only modest transcriptional changes. Mass spectrometry of immunoprecipitated protein revealed that both mutant and wildtype MAB21L1 associate with transcription factors that are known regulators of PAX6 (MEIS1, MEIS2 and PBX1) and with poly(A) RNA binding proteins. Arg51 substitutions reduce the association of wild-type MAB21L1 with TBL1XR1, a component of the NCoR complex. We found limited evidence for mutation-specific interactions with MSI2/Musashi-2, an RNA-binding proteins with effects on many different developmental pathways. Given that biallelic loss-of-function variants in MAB21L1 result in a milder eye phenotype we suggest that Arg51-altering monoallelic variants most plausibly perturb eye development via a gain-of-function mechanism.
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Affiliation(s)
- Hildegard Nikki Hall
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Hemant Bengani
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Robert B. Hufnagel
- National Eye Institute, National Institutes of Health, Bethesda, MD, United States of America
| | | | - Morad Ansari
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, United Kingdom
| | - Joseph A. Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Graeme R. Grimes
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Alex von Kriegsheim
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - David Moore
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, United Kingdom
| | - Lisa McKie
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Jamalia Rahmat
- Ophthalmology Department, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Catia Mio
- Department of Medicine, University of Udine, Udine, Italy
| | - Moira Blyth
- University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Wee Teik Keng
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Lily Islam
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, England
| | - Meriel McEntargart
- Medical Genetics, St George’s University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Marcel M. Mannens
- Genome Diagnostics laboratory, Department of Clinical Genetics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Veronica Van Heyningen
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Joe Rainger
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Brian P. Brooks
- National Eye Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - David R. FitzPatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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Cvekl A, Camerino MJ. Generation of Lens Progenitor Cells and Lentoid Bodies from Pluripotent Stem Cells: Novel Tools for Human Lens Development and Ocular Disease Etiology. Cells 2022; 11:cells11213516. [PMID: 36359912 PMCID: PMC9658148 DOI: 10.3390/cells11213516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
In vitro differentiation of human pluripotent stem cells (hPSCs) into specialized tissues and organs represents a powerful approach to gain insight into those cellular and molecular mechanisms regulating human development. Although normal embryonic eye development is a complex process, generation of ocular organoids and specific ocular tissues from pluripotent stem cells has provided invaluable insights into the formation of lineage-committed progenitor cell populations, signal transduction pathways, and self-organization principles. This review provides a comprehensive summary of recent advances in generation of adenohypophyseal, olfactory, and lens placodes, lens progenitor cells and three-dimensional (3D) primitive lenses, "lentoid bodies", and "micro-lenses". These cells are produced alone or "community-grown" with other ocular tissues. Lentoid bodies/micro-lenses generated from human patients carrying mutations in crystallin genes demonstrate proof-of-principle that these cells are suitable for mechanistic studies of cataractogenesis. Taken together, current and emerging advanced in vitro differentiation methods pave the road to understand molecular mechanisms of cataract formation caused by the entire spectrum of mutations in DNA-binding regulatory genes, such as PAX6, SOX2, FOXE3, MAF, PITX3, and HSF4, individual crystallins, and other genes such as BFSP1, BFSP2, EPHA2, GJA3, GJA8, LIM2, MIP, and TDRD7 represented in human cataract patients.
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Affiliation(s)
- Aleš Cvekl
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Correspondence: ; Tel.: +1-718-430-3217; Fax: +1-718-430-8778
| | - Michael John Camerino
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Weiss JS, Willoughby CE, Abad-Morales V, Turunen JA, Lisch W. Update on the Corneal Dystrophies-Genetic Testing and Therapy. Cornea 2022; 41:1337-1344. [PMID: 36219210 DOI: 10.1097/ico.0000000000002857] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/07/2021] [Indexed: 11/26/2022]
Abstract
ABSTRACT One major purpose of the IC3D Corneal Dystrophy Nomenclature Revision was to include genetic information with a goal of facilitating investigation into the pathogenesis, treatment, and perhaps even prevention of the corneal dystrophies, an ambitious goal. Over a decade has passed since the first publication of the IC3D Corneal Dystrophy Nomenclature Revision. Gene therapy is available for an early-onset form of inherited retinal degeneration called Leber congenital amaurosis, but not yet for corneal degenerations. We review the current state of affairs regarding our original ambitious goal. We discuss genetic testing, gene therapy [RNA interference (RNAi) and genome editing], and ocular delivery of corneal gene therapy for the corneal dystrophies. Why have gene therapy techniques not yet been introduced for the corneal dystrophies?
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Affiliation(s)
- Jayne S Weiss
- Department of Ophthalmology, Pathology and Pharmacology, Louisiana State University School of Medicine, New Orleans, LA
| | - Colin E Willoughby
- Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Víctor Abad-Morales
- Fundació de Recerca de l'Institut de Microcirurgia Ocular, Barcelona, Spain
- Department of Genetics, Institut de Microcirurgia Ocular (IMO), Barcelona, Spain; Dr. Abad-Morales is now with the SpliceBio, Barcelona, Spain, Barcelona, Spain
| | - Joni A Turunen
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland; and
| | - Walter Lisch
- Department of Ophthalmology, University Medical Center of the Johannes Gutenberg, University Mainz, Mainz, Germany
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Zheng Y, Yang X, Wu S, Yi G, Huang X, Feng Z, Qu L, Liu L, Li Q, Xia Z. Paired Box Gene 6 Regulates Heme Oxygenase-1 Expression and Mitigates Hydrogen Peroxide-Induced Oxidative Stress in Lens Epithelial Cells. Curr Eye Res 2022; 47:1516-1524. [PMID: 36149046 DOI: 10.1080/02713683.2022.2110266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
PURPOSE This study aimed to investigate the regulation of heme oxygenase-1 (HO-1) by paired box gene 6 (Pax6) and their roles in hydrogen peroxide (H2O2)-induced oxidative stress and apoptosis in lens epithelial cells (LECs) (SRA01/04, HLE-B3). METHODS Lens anterior capsule membranes of mice of different ages were obtained to compare differences in the expression of Pax6 and HO-1 using Western blotting. Pax6-overexpressing plasmid and small interfering RNA were designed to overexpress and silence Pax6, respectively. Cobalt protoporphyrin (CoPP) was used to promote the expression of HO-1. Oxidative damage in LECs was induced by treatment with H2O2 (400 µM) for 24 h. Cell viability was measured using the Cell Counting Kit-8 assay. Intracellular reactive oxygen species (ROS) were detected using flow cytometry and immunofluorescence. Superoxide dismutase (SOD) level was measured using SOD Assay Kit and apoptotic cells were quantified using annexin V-fluorescein isothiocyanate/propidium iodide staining. RESULTS Pax6 and HO-1 expression levels showed an age-dependent decrease in LECs of mouse. Overexpressing Pax6 upregulated HO-1 expression level. Silencing Pax6 downregulated the HO-1 expression level, resulting in increased generation of ROS, reduced SOD activity, decreased cell viability, and increased apoptotic cells of LECs under H2O2-induced oxidative stress. Overexpressing Pax6 and CoPP both mitigates H2O2-induced oxidative stress by increasing the expression of HO-1 of LECs. CONCLUSION Pax6 and HO-1 expression levels showed an age-dependent decrease in LECs in mouse anterior capsules. Pax6 could regulate the expression of HO-1 in LECs. The decrease of Pax6 weakened the antioxidant ability of LECs under H2O2-induced oxidative stress by downregulating HO-1, which may be a potential mechanism for the formation of age-related cataract.
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Affiliation(s)
- Yuxing Zheng
- Department of Ophthalmology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoxi Yang
- Department of Ophthalmology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuduan Wu
- Department of Ophthalmology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guoguo Yi
- Department of Ophthalmology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaobo Huang
- Department of Ophthalmology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhizhen Feng
- Department of Ophthalmology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lei Qu
- Department of Ophthalmology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Linyu Liu
- Department of Ophthalmology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qianyun Li
- Department of Ophthalmology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhaoxia Xia
- Department of Ophthalmology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Tehreem R, Chen I, Shah MR, Li Y, Khan MA, Afshan K, Chen R, Firasat S. Exome Sequencing Identified Molecular Determinants of Retinal Dystrophies in Nine Consanguineous Pakistani Families. Genes (Basel) 2022; 13:genes13091630. [PMID: 36140798 PMCID: PMC9498396 DOI: 10.3390/genes13091630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) are a heterogeneous group of degenerative disorders of the retina. Retinitis Pigmentosa (RP) is a common type of IRD that causes night blindness and loss of peripheral vision and may progress to blindness. Mutations in more than 300 genes have been associated with syndromic and non-syndromic IRDs. Recessive forms are more frequent in populations where endogamy is a social preference, such as Pakistan. The aim of this study was to identify molecular determinants of IRDs with the common presentation of night blindness in consanguineous Pakistani families. This study included nine consanguineous IRD-affected families that presented autosomal recessive inheritance of the night blindness phenotype. DNA was extracted from blood samples. Targeted exome sequencing of 344 known genes for retinal dystrophies was performed. Screening of nine affected families revealed two novel (c.5571_5576delinsCTAGATand c.471dup in EYS and SPATA7 genes, respectively) and six reported pathogenic mutations (c.304C>A, c.187C>T, c.1560C>A, c.547C>T, c.109del and c.9911_11550del in PDE6A, USH2A, USH2A, NMNAT1, PAX6 and ALMS1 genes, respectively) segregating with disease phenotype in each respective family. Molecular determinants of hereditary retinal dystrophies were identified in all screened families. Identification of novel variants aid future diagnosis of retinal dystrophies and help to provide genetic counseling to affected families.
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Affiliation(s)
- Raeesa Tehreem
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, University Road, Islamabad 45320, Pakistan
| | - Iris Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mudassar Raza Shah
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, University Road, Islamabad 45320, Pakistan
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muzammil Ahmad Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan
- Department of Human Genetics, Sidra Medicine, Doha P.O. Box 26999, Qatar
| | - Kiran Afshan
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, University Road, Islamabad 45320, Pakistan
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: (R.C.); (S.F.); Tel.: +(713)-798-5194 (R.C.); +92-51-9064-4410 (S.F.)
| | - Sabika Firasat
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, University Road, Islamabad 45320, Pakistan
- Correspondence: (R.C.); (S.F.); Tel.: +(713)-798-5194 (R.C.); +92-51-9064-4410 (S.F.)
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Mary L, Leclerc D, Gilot D, Belaud-Rotureau MA, Jaillard S. The TALE never ends: A comprehensive overview of the role of PBX1, a TALE transcription factor, in human developmental defects. Hum Mutat 2022; 43:1125-1148. [PMID: 35451537 DOI: 10.1002/humu.24388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/25/2022] [Accepted: 04/20/2022] [Indexed: 11/07/2022]
Abstract
PBX1 is a highly conserved atypical homeodomain transcription factor (TF) belonging to the TALE (three amino acid loop extension) family. Dimerized with other TALE proteins, it can interact with numerous partners and reach dozens of regulating sequences, suggesting its role as a pioneer factor. PBX1 is expressed throughout the embryonic stages (as early as the blastula stage) in vertebrates. In human, PBX1 germline variations are linked to syndromic renal anomalies (CAKUTHED). In this review, we summarized available data on PBX1 functions, PBX1-deficient animal models, and PBX1 germline variations in humans. Two types of genetic alterations were identified in PBX1 gene. PBX1 missense variations generate a severe phenotype including lung hypoplasia, cardiac malformations, and sexual development defects (DSDs). Conversely, truncating variants generate milder phenotypes (mainly cryptorchidism and deafness). We suggest that defects in PBX1 interactions with various partners, including proteins from the HOX (HOXA7, HOXA10, etc.), WNT (WNT9B, WNT3), and Polycomb (BMI1, EED) families are responsible for abnormal proliferation and differentiation of the embryonic mesenchyme. These alterations could explain most of the defects observed in humans. However, some phenotype variability (especially DSDs) remains poorly understood. Further studies are needed to explore the TALE family in greater depth.
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Affiliation(s)
- Laura Mary
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
| | - Delphine Leclerc
- Inserm U1242, Centre de lutte contre le cancer Eugène Marquis, Université de Rennes, Rennes, France
| | - David Gilot
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- Inserm U1242, Centre de lutte contre le cancer Eugène Marquis, Université de Rennes, Rennes, France
| | - Marc-Antoine Belaud-Rotureau
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
| | - Sylvie Jaillard
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
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Sunny SS, Lachova J, Dupacova N, Kozmik Z. Multiple roles of Pax6 in postnatal cornea development. Dev Biol 2022; 491:1-12. [PMID: 36049534 DOI: 10.1016/j.ydbio.2022.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
Abstract
Mammalian corneal development is a multistep process, including formation of the corneal epithelium (CE), endothelium and stroma during embryogenesis, followed by postnatal stratification of the epithelial layers and continuous renewal of the epithelium to replace the outermost corneal cells. Here, we employed the Cre-loxP system to conditionally deplete Pax6 proteins in two domains of ocular cells, i.e., the ocular surface epithelium (cornea, limbus and conjunctiva) (OSE) or postnatal CE via K14-cre or Aldh3-cre, respectively. Earlier and broader inactivation of Pax6 in the OSE resulted in thickened OSE with CE and limbal cells adopting the conjunctival keratin expression pattern. More restricted depletion of Pax6 in postnatal CE resulted in an abnormal cornea marked by reduced epithelial thickness despite increased epithelial cell proliferation. Immunofluorescence studies revealed loss of intermediate filament Cytokeratin 12 and diffused expression of adherens junction components, together with reduced tight junction protein, Zonula occludens-1. Furthermore, the expression of Cytokeratin 14, a basal cell marker in apical layers, indicates impaired differentiation of CE cells. Collectively, our data demonstrate that Pax6 is essential for maintaining proper differentiation and strong intercellular adhesion in postnatal CE cells, whereas limbal Pax6 is required to prevent the outgrowth of conjunctival cells to the cornea.
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Affiliation(s)
- Sweetu Susan Sunny
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, Praha 4, 142 20, Czech Republic
| | - Jitka Lachova
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, Praha 4, 142 20, Czech Republic
| | - Naoko Dupacova
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, Praha 4, 142 20, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, Praha 4, 142 20, Czech Republic.
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Panikker P, Roy S, Ghosh A, Poornachandra B, Ghosh A. Advancing precision medicines for ocular disorders: Diagnostic genomics to tailored therapies. Front Med (Lausanne) 2022; 9:906482. [PMID: 35911417 PMCID: PMC9334564 DOI: 10.3389/fmed.2022.906482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/29/2022] [Indexed: 11/20/2022] Open
Abstract
Successful sequencing of the human genome and evolving functional knowledge of gene products has taken genomic medicine to the forefront, soon combining broadly with traditional diagnostics, therapeutics, and prognostics in patients. Recent years have witnessed an extraordinary leap in our understanding of ocular diseases and their respective genetic underpinnings. As we are entering the age of genomic medicine, rapid advances in genome sequencing, gene delivery, genome surgery, and computational genomics enable an ever-increasing capacity to provide a precise and robust diagnosis of diseases and the development of targeted treatment strategies. Inherited retinal diseases are a major source of blindness around the world where a large number of causative genes have been identified, paving the way for personalized diagnostics in the clinic. Developments in functional genetics and gene transfer techniques has also led to the first FDA approval of gene therapy for LCA, a childhood blindness. Many such retinal diseases are the focus of various clinical trials, making clinical diagnoses of retinal diseases, their underlying genetics and the studies of natural history important. Here, we review methodologies for identifying new genes and variants associated with various ocular disorders and the complexities associated with them. Thereafter we discuss briefly, various retinal diseases and the application of genomic technologies in their diagnosis. We also discuss the strategies, challenges, and potential of gene therapy for the treatment of inherited and acquired retinal diseases. Additionally, we discuss the translational aspects of gene therapy, the important vector types and considerations for human trials that may help advance personalized therapeutics in ophthalmology. Retinal disease research has led the application of precision diagnostics and precision therapies; therefore, this review provides a general understanding of the current status of precision medicine in ophthalmology.
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Affiliation(s)
| | - Shomereeta Roy
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | - Anuprita Ghosh
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | | | - Arkasubhra Ghosh
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
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Zhang Z, Tang Q, Wang Q, Nie F, Sun L, Luo D, Chen W, Ding X. HODD: A Manually Curated Database of Human Ophthalmic Diseases with Symptom Characteristics and Genetic Variants Towards Facilitating Quick and Definite Diagnosis. Interdiscip Sci 2022; 14:385-393. [PMID: 34846641 DOI: 10.1007/s12539-021-00494-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Ophthalmic diseases are disorders that affect the eyes. Hundreds of causal genes and biological pathways have been reported to be closely correlated with ophthalmic diseases. However, these information are scattered across various resources, which has hindered a thorough and deep understanding of ophthalmic diseases. In the present work, we proposed the Human Ophthalmic Diseases Database (HODD), which currently deposits 730 ophthalmic diseases and 653 related genes and is available at http://bio-bigdata.cn/HODD/ . The disease-related information and genes related to ophthalmic diseases were collected from the several well-known databases. To comprehensively understand the ophthalmic diseases, the basic information was provided for each disease, including disease description, related genes, gene location, ocular and extraocular effect of the disease, protein-protein interaction and disease-associated pathways. All these data were reorganized and made accessible through multiple entrances. We hope that HODD will facilitate studies on ophthalmic diseases. The workflow for the construction of the HODD (Human Ophthalmic Diseases Database, http://bio-bigdata.cn/HODD/ ) database.
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Affiliation(s)
- Zhaotian Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Qiang Tang
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Qiong Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Fulei Nie
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, China
| | - Limei Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Delun Luo
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Chengdu Jingze Biopharmaceutical Co., Ltd, Chengdu, 611137, China
| | - Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, China.
| | - Xiaoyan Ding
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
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Pavlaki I, Shapiro M, Pisignano G, Jones SME, Telenius J, Muñoz-Descalzo S, Williams RJ, Hughes JR, Vance KW. Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells. PLoS Genet 2022; 18:e1010230. [PMID: 35709096 PMCID: PMC9202886 DOI: 10.1371/journal.pgen.1010230] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/02/2022] [Indexed: 11/19/2022] Open
Abstract
Central nervous system-expressed long non-coding RNAs (lncRNAs) are often located in the genome close to protein coding genes involved in transcriptional control. Such lncRNA-protein coding gene pairs are frequently temporally and spatially co-expressed in the nervous system and are predicted to act together to regulate neuronal development and function. Although some of these lncRNAs also bind and modulate the activity of the encoded transcription factors, the regulatory mechanisms controlling co-expression of neighbouring lncRNA-protein coding genes remain unclear. Here, we used high resolution NG Capture-C to map the cis-regulatory interaction landscape of the key neuro-developmental Paupar-Pax6 lncRNA-mRNA locus. The results define chromatin architecture changes associated with high Paupar-Pax6 expression in neurons and identify both promoter selective as well as shared cis-regulatory-promoter interactions involved in regulating Paupar-Pax6 co-expression. We discovered that the TCF7L2 transcription factor, a regulator of chromatin architecture and major effector of the Wnt signalling pathway, binds to a subset of these candidate cis-regulatory elements to coordinate Paupar and Pax6 co-expression. We describe distinct roles for Paupar in Pax6 expression control and show that the Paupar DNA locus contains a TCF7L2 bound transcriptional silencer whilst the Paupar transcript can act as an activator of Pax6. Our work provides important insights into the chromatin interactions, signalling pathways and transcription factors controlling co-expression of adjacent lncRNAs and protein coding genes in the brain.
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Affiliation(s)
- Ioanna Pavlaki
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Michael Shapiro
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Giuseppina Pisignano
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | - Jelena Telenius
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Silvia Muñoz-Descalzo
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Universidad Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Robert J. Williams
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Jim R. Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Keith W. Vance
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- * E-mail:
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46
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van Heyningen V. A Journey Through Genetics to Biology. Annu Rev Genomics Hum Genet 2022; 23:1-27. [PMID: 35567277 DOI: 10.1146/annurev-genom-010622-095109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although my engagement with human genetics emerged gradually, and sometimes serendipitously, it has held me spellbound for decades. Without my teachers, students, postdocs, colleagues, and collaborators, I would not be writing this review of my scientific adventures. Early gene and disease mapping was a satisfying puzzle-solving exercise, but building biological insight was my main goal. The project trajectory was hugely influenced by the evolutionarily conserved nature of the implicated genes and by the pace of progress in genetic technologies. The rich detail of clinical observations, particularly in eye disease, makes humans an excellent model, especially when complemented by the use of multiple other animal species for experimental validation. The contributions of collaborators and rivals also influenced our approach. We are very fortunate to work in this era of unprecedented progress in genetics and genomics. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Veronica van Heyningen
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom;
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47
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Cole JD, McHaney KM, Rabiee B, Gao J, Rodriguez C, Miller DA, Liu M, Grannonico M, Norat P, Zhang HF, Djalilian AR, Liu X. Long-term retinal protection by MEK inhibition in Pax6 haploinsufficiency mice. Exp Eye Res 2022; 218:109012. [PMID: 35245513 PMCID: PMC9050935 DOI: 10.1016/j.exer.2022.109012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/21/2022] [Accepted: 02/22/2022] [Indexed: 11/26/2022]
Abstract
Aniridia is a panocular condition characterized by impaired eye development and vision, which is mainly due to the haploinsufficiency of the paired-box-6 (PAX6) gene. Like what is seen in aniridia patients, Pax6-deficient mice Pax6Sey-Neu/+ exhibit a varied degree of ocular damage and impaired vision. Our previous studies showed that these phenotypes were partially rescued by PD0325901, a mitogen-activated protein kinase kinase (MEK or MAP2K) inhibitor. In this study, we assessed the long-term efficacy of PD0325901 treatment in retinal health and visual behavior. At about one year after the postnatal treatment with PD0325901, Pax6Sey-Neu/+ mice showed robust improvements in retina size and visual acuity, and the elevated intraocular pressure (IOP) was also alleviated, compared to age-matched mice treated with vehicles only. Moreover, the Pax6Sey-Neu/+ eyes showed disorganized retinal ganglion cell (RGC) axon bundles and retinal layers, which we termed as hotspots. We found that the PD treatment reduced the number and size of hotspots in the Pax6Sey-Neu/+ retinas. Taken together, our results suggest that PD0325901 may serve as an efficacious intervention in protecting retina and visual function in aniridia-afflicted subjects.
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Affiliation(s)
- James D Cole
- Department of Biology, University of Virginia, Charlottesville, VA, USA; Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Kara M McHaney
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Behnam Rabiee
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA; Department of Ophthalmology, Nazareth Hospital, Philadelphia, PA, USA
| | - Jingyi Gao
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Carlos Rodriguez
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - David A Miller
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Mingna Liu
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Marta Grannonico
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Pedro Norat
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Ali R Djalilian
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Xiaorong Liu
- Department of Biology, University of Virginia, Charlottesville, VA, USA; Department of Psychology, University of Virginia, Charlottesville, VA, USA; Program in Fundamental Neuroscience, University of Virginia, Charlottesville, VA, USA.
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48
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DARUICH ALEJANDRA, ROBERT MATTHIEUP, LEROY CAMILLE, DE VERGNES NATHALIE, BEUGNET CAROLINE, MALAN VALERIE, VALLEIX SOPHIE, BREMOND-GIGNAC DOMINIQUE. Foveal Hypoplasia Grading in 95 Cases of Congenital Aniridia: Correlation to Phenotype and PAX6 Genotype. Am J Ophthalmol 2022; 237:122-129. [PMID: 34942114 DOI: 10.1016/j.ajo.2021.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/01/2022]
Abstract
PURPOSE To correlate the degree of foveal hypoplasia in congenital aniridia with visual acuity, iris phenotype, and PAX6 mutations. DESIGN Retrospective case series. METHODS Ninety-five consecutive patients with high-quality spectral-domain optical coherence tomography records and available genotype were included in a single referral center. Iris hypoplasia was classified as complete, presence of iris root or remnants, and mild atypical aniridia. Spectral-domain optical coherence tomography images were assessed to classify foveal hypoplasia as grade 1 to 4 and to determine mean thicknesses for retinal layers. For statistical analysis 1 eye for each patient was used and 1 member of the same family has been included (n = 76 eyes). RESULTS Most eyes (n= 158/169, 93.5%) showed variable degree of foveal hypoplasia. PAX6-positive patients presented higher degree of foveal hypoplasia than patients negative for PAX6 (P < .0001). PAX6 deletions, PAX6 variants subjected to nonsense-mediated decay and C-terminal extension variants were mostly associated with grade 3 or 4 foveal hypoplasia. Deletions restricted to the 3' flanking regulatory regions of PAX6 were associated with grade 1 or 2 foveal hypoplasia (P < .0001). Best-corrected visual acuity was higher and foveal outer retinal layers were thicker in patients with deletions in the 3' regulatory region of PAX6 (P = .001 and P < .0001). Patients with missense mutations presented with variable degree of foveal hypoplasia. The degree of foveal hypoplasia was most frequently correlated with the severity of iris defects, with 95% of eyes with complete aniridia presenting grade 3 or 4 foveal hypoplasia (P = .005). However, among eyes with mild iris phenotype, 70% (n=9/13) showed severe foveal hypoplasia. CONCLUSIONS All types of PAX6 variants, even those associated with mild iris defects, may be at risk for severe foveal hypoplasia with poor visual prognosis, except for deletions restricted to the 3' regulatory PAX6 regions.
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McLaughlin T, Medina A, Perkins J, Yera M, Wang JJ, Zhang SX. Cellular stress signaling and the unfolded protein response in retinal degeneration: mechanisms and therapeutic implications. Mol Neurodegener 2022; 17:25. [PMID: 35346303 PMCID: PMC8962104 DOI: 10.1186/s13024-022-00528-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/04/2022] [Indexed: 12/22/2022] Open
Abstract
Background The retina, as part of the central nervous system (CNS) with limited capacity for self-reparation and regeneration in mammals, is under cumulative environmental stress due to high-energy demands and rapid protein turnover. These stressors disrupt the cellular protein and metabolic homeostasis, which, if not alleviated, can lead to dysfunction and cell death of retinal neurons. One primary cellular stress response is the highly conserved unfolded protein response (UPR). The UPR acts through three main signaling pathways in an attempt to restore the protein homeostasis in the endoplasmic reticulum (ER) by various means, including but not limited to, reducing protein translation, increasing protein-folding capacity, and promoting misfolded protein degradation. Moreover, recent work has identified a novel function of the UPR in regulation of cellular metabolism and mitochondrial function, disturbance of which contributes to neuronal degeneration and dysfunction. The role of the UPR in retinal neurons during aging and under disease conditions in age-related macular degeneration (AMD), retinitis pigmentosa (RP), glaucoma, and diabetic retinopathy (DR) has been explored over the past two decades. Each of the disease conditions and their corresponding animal models provide distinct challenges and unique opportunities to gain a better understanding of the role of the UPR in the maintenance of retinal health and function. Method We performed an extensive literature search on PubMed and Google Scholar using the following keywords: unfolded protein response, metabolism, ER stress, retinal degeneration, aging, age-related macular degeneration, retinitis pigmentosa, glaucoma, diabetic retinopathy. Results and conclusion We summarize recent advances in understanding cellular stress response, in particular the UPR, in retinal diseases, highlighting the potential roles of UPR pathways in regulation of cellular metabolism and mitochondrial function in retinal neurons. Further, we provide perspective on the promise and challenges for targeting the UPR pathways as a new therapeutic approach in age- and disease-related retinal degeneration.
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Affiliation(s)
- Todd McLaughlin
- Department of Ophthalmology and Ira G. Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, 955 Main Street, Buffalo, NY, 14203, USA
| | - Andy Medina
- Department of Ophthalmology and Ira G. Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, 955 Main Street, Buffalo, NY, 14203, USA
| | - Jacob Perkins
- Department of Ophthalmology and Ira G. Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, 955 Main Street, Buffalo, NY, 14203, USA
| | - Maria Yera
- Department of Ophthalmology and Ira G. Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, 955 Main Street, Buffalo, NY, 14203, USA.,Neuroscience Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Joshua J Wang
- Department of Ophthalmology and Ira G. Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, 955 Main Street, Buffalo, NY, 14203, USA.,Neuroscience Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Sarah X Zhang
- Department of Ophthalmology and Ira G. Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, 955 Main Street, Buffalo, NY, 14203, USA. .,Neuroscience Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA. .,Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA.
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50
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Saffren BD, Yassin SH, Geddie BE, de Faber JTHN, Blieden LS, Bhate M, Gamio S, Rutar T, Levin AV. Optic Nerve Aplasia. J Neuroophthalmol 2022; 42:e140-e146. [PMID: 33870948 DOI: 10.1097/wno.0000000000001246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Optic nerve aplasia (ONA) is a rare ocular anomaly. We report ophthalmologic, systemic, and genetic findings in ONA. METHODS Patients were identified through an International Pediatric Ophthalmology listserv and from the practice of the senior author. Participating Listserv physicians completed a data collection sheet. Children of all ages were included. Neuroimaging findings were also recorded. RESULTS Nine cases of ONA are reported. Patients' ages ranged from 10 days to 2 years (median 9 months). Seven cases were bilateral. All patients had absence of the optic nerve and retinal vessels in the affected eye or eyes. Ophthalmologic findings included glaucoma, microcornea, persistent pupillary membrane, iris coloboma, aniridia, retinal dysplasia, retinal atrophy, chorioretinal coloboma, and persistent fetal vasculature. Systemic findings included facial dysmorphism, cardiac, genitourinary, skeletal, and developmental defects. A BCOR mutation was found in one patient. One patient had rudimentary optic nerves and chiasm on imaging. CONCLUSION ONA is a unilateral or bilateral condition that may be associated with anomalies of the anterior or posterior segment with or without systemic findings. Rudimentary optic nerve on neuroimaging in one case suggests that ONA is on the continuum of optic nerve hypoplasia.
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Affiliation(s)
- Brooke D Saffren
- Philadelphia College of Osteopathic Medicine (BDS), Philadelphia, Pennsylvania; Pediatric Ophthalmology and Ocular Genetics (BDS, SHY), Wills Eye Hospital, Philadelphia, Pennsylvania; Pediatric Ophthalmology (BEG), Helen DeVos Children's Hospital, Grand Rapids, Michigan; The Rotterdam Eye Hospital (JTHNF), Rotterdam, the Netherlands ; Cullen Eye Institute (LSB), Baylor College of Medicine, Houston, Texas; Department of Pediatric Ophthalmology (MB), LV Prasad Eye Institute, Hyderabad, India ; Ophthalmology Unit (SG), Ricardo Gutiérrez Children Hospital, Buenos Aires, Argentina ; Cataract and Laser Institute of Southern Oregon PC (TR), Medford, Oregon; Flaum Eye Institute and Golisano Children's Hospital (AVL), University of Rochester, New York, New York
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