1
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Shepherdson JL, Friedman RZ, Zheng Y, Sun C, Oh IY, Granas DM, Cohen BA, Chen S, White MA. Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors. Genome Res 2024; 34:243-255. [PMID: 38355306 PMCID: PMC10984388 DOI: 10.1101/gr.278133.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Dozens of variants in the gene for the homeodomain transcription factor (TF) cone-rod homeobox (CRX) are linked with human blinding diseases that vary in their severity and age of onset. How different variants in this single TF alter its function in ways that lead to a range of phenotypes is unclear. We characterized the effects of human disease-causing variants on CRX cis-regulatory function by deploying massively parallel reporter assays (MPRAs) in mouse retina explants carrying knock-ins of two variants, one in the DNA-binding domain (p.R90W) and the other in the transcriptional effector domain (p.E168d2). The degree of reporter gene dysregulation in these mutant Crx retinas corresponds with their phenotypic severity. The two variants affect similar sets of enhancers, and p.E168d2 has distinct effects on silencers. Cis-regulatory elements (CREs) near cone photoreceptor genes are enriched for silencers that are derepressed in the presence of p.E168d2. Chromatin environments of CRX-bound loci are partially predictive of episomal MPRA activity, and distal elements whose accessibility increases later in retinal development are enriched for CREs with silencer activity. We identified a set of potentially pleiotropic regulatory elements that convert from silencers to enhancers in retinas that lack a functional CRX effector domain. Our findings show that phenotypically distinct variants in different domains of CRX have partially overlapping effects on its cis-regulatory function, leading to misregulation of similar sets of enhancers while having a qualitatively different impact on silencers.
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Affiliation(s)
- James L Shepherdson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Ryan Z Friedman
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Yiqiao Zheng
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Inez Y Oh
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - David M Granas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA;
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Michael A White
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA;
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
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2
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Bauwens M, Celik E, Zur D, Lin S, Quinodoz M, Michaelides M, Webster AR, Van Den Broeck F, Leroy BP, Rizel L, Moye AR, Meunier A, Tran HV, Moulin AP, Mahieu Q, Van Heetvelde M, Arno G, Rivolta C, De Baere E, Ben-Yosef T. Mutations in SAMD7 cause autosomal-recessive macular dystrophy with or without cone dysfunction. Am J Hum Genet 2024; 111:393-402. [PMID: 38272031 PMCID: PMC10870129 DOI: 10.1016/j.ajhg.2024.01.001] [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: 09/11/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
Sterile alpha motif domain containing 7 (SAMD7) is a component of the Polycomb repressive complex 1, which inhibits transcription of many genes, including those activated by the transcription factor Cone-Rod Homeobox (CRX). Here we report bi-allelic mutations in SAMD7 as a cause of autosomal-recessive macular dystrophy with or without cone dysfunction. Four of these mutations affect splicing, while another mutation is a missense variant that alters the repressive effect of SAMD7 on CRX-dependent promoter activity, as shown by in vitro assays. Immunostaining of human retinal sections revealed that SAMD7 is localized in the nuclei of both rods and cones, as well as in those of cells belonging to the inner nuclear layer. These results place SAMD7 as a gene crucial for human retinal function and demonstrate a significant difference in the role of SAMD7 between the human and the mouse retina.
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Affiliation(s)
- Miriam Bauwens
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Elifnaz Celik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, 4031 Basel, Switzerland
| | - Dinah Zur
- Ophthalmology Division, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Siying Lin
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the Institute of Ophthalmology, London, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Michel Michaelides
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the Institute of Ophthalmology, London, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Andrew R Webster
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the Institute of Ophthalmology, London, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Filip Van Den Broeck
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Head & Skin, Ghent University, 9000 Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Head & Skin, Ghent University, 9000 Ghent, Belgium; Department of Ophthalmology, Ghent University Hospital, 9000 Ghent, Belgium; The Division of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leah Rizel
- The Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Abigail R Moye
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, 4031 Basel, Switzerland
| | - Audrey Meunier
- Department of Ophthalmology, Centre Hospitalier Universitaire Saint-Pierre, 1000 Brussels, Belgium
| | - Hoai Viet Tran
- Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, 1004 Lausanne, Switzerland; Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Alexandre P Moulin
- Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, 1004 Lausanne, Switzerland
| | - Quinten Mahieu
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Mattias Van Heetvelde
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Gavin Arno
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the Institute of Ophthalmology, London, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK; North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3BH, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Tamar Ben-Yosef
- The Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
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3
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Loell KJ, Friedman RZ, Myers CA, Corbo JC, Cohen BA, White MA. Transcription factor interactions explain the context-dependent activity of CRX binding sites. PLoS Comput Biol 2024; 20:e1011802. [PMID: 38227575 PMCID: PMC10817189 DOI: 10.1371/journal.pcbi.1011802] [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: 03/06/2023] [Revised: 01/26/2024] [Accepted: 01/06/2024] [Indexed: 01/18/2024] Open
Abstract
The effects of transcription factor binding sites (TFBSs) on the activity of a cis-regulatory element (CRE) depend on the local sequence context. In rod photoreceptors, binding sites for the transcription factor (TF) Cone-rod homeobox (CRX) occur in both enhancers and silencers, but the sequence context that determines whether CRX binding sites contribute to activation or repression of transcription is not understood. To investigate the context-dependent activity of CRX sites, we fit neural network-based models to the activities of synthetic CREs composed of photoreceptor TFBSs. The models revealed that CRX binding sites consistently make positive, independent contributions to CRE activity, while negative homotypic interactions between sites cause CREs composed of multiple CRX sites to function as silencers. The effects of negative homotypic interactions can be overcome by the presence of other TFBSs that either interact cooperatively with CRX sites or make independent positive contributions to activity. The context-dependent activity of CRX sites is thus determined by the balance between positive heterotypic interactions, independent contributions of TFBSs, and negative homotypic interactions. Our findings explain observed patterns of activity among genomic CRX-bound enhancers and silencers, and suggest that enhancers may require diverse TFBSs to overcome negative homotypic interactions between TFBSs.
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Affiliation(s)
- Kaiser J. Loell
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
| | - Ryan Z. Friedman
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
| | - Connie A. Myers
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
| | - Joseph C. Corbo
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
| | - Barak A. Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
| | - Michael A. White
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
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4
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Shepherdson JL, Friedman RZ, Zheng Y, Sun C, Oh IY, Granas DM, Cohen BA, Chen S, White MA. Pathogenic variants in Crx have distinct cis-regulatory effects on enhancers and silencers in photoreceptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.27.542576. [PMID: 37292699 PMCID: PMC10245955 DOI: 10.1101/2023.05.27.542576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Dozens of variants in the photoreceptor-specific transcription factor (TF) CRX are linked with human blinding diseases that vary in their severity and age of onset. It is unclear how different variants in this single TF alter its function in ways that lead to a range of phenotypes. We examined the effects of human disease-causing variants on CRX cis-regulatory function by deploying massively parallel reporter assays (MPRAs) in live mouse retinas carrying knock-ins of two variants, one in the DNA binding domain (p.R90W) and the other in the transcriptional effector domain (p.E168d2). The degree of reporter gene dysregulation caused by the variants corresponds with their phenotypic severity. The two variants affect similar sets of enhancers, while p.E168d2 has stronger effects on silencers. Cis-regulatory elements (CREs) near cone photoreceptor genes are enriched for silencers that are de-repressed in the presence of p.E168d2. Chromatin environments of CRX-bound loci were partially predictive of episomal MPRA activity, and silencers were notably enriched among distal elements whose accessibility increases later in retinal development. We identified a set of potentially pleiotropic regulatory elements that convert from silencers to enhancers in retinas that lack a functional CRX effector domain. Our findings show that phenotypically distinct variants in different domains of CRX have partially overlapping effects on its cis-regulatory function, leading to misregulation of similar sets of enhancers, while having a qualitatively different impact on silencers.
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Affiliation(s)
- James L. Shepherdson
- Department of Genetics
- Edison Family Center for Genome Sciences & Systems Biology
| | - Ryan Z. Friedman
- Department of Genetics
- Edison Family Center for Genome Sciences & Systems Biology
| | | | - Chi Sun
- Department of Ophthalmology and Visual Sciences
| | - Inez Y. Oh
- Department of Ophthalmology and Visual Sciences
| | - David M. Granas
- Department of Genetics
- Edison Family Center for Genome Sciences & Systems Biology
| | - Barak A. Cohen
- Department of Genetics
- Edison Family Center for Genome Sciences & Systems Biology
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Michael A. White
- Department of Genetics
- Edison Family Center for Genome Sciences & Systems Biology
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5
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Corona-Herrera GA, Navarrete-Ramírez P, Sanchez-Flores FA, Jimenez-Jacinto V, Martínez-Palacios CA, Palomera-Sánchez Z, Volkoff H, Martínez-Chávez CC. Shining light on the transcriptome: Molecular regulatory networks leading to a fast-growth phenotype by continuous light in an environmentally sensitive teleost (Atherinopsidae). JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 235:112550. [PMID: 36049383 DOI: 10.1016/j.jphotobiol.2022.112550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Photoperiod can profoundly affect the physiology of teleost fish, including accelerated growth here defined as "fast growth phenotypes". However, molecular regulatory networks (MRNs) and biological processes being affected by continuous illumination and which allow some teleost species evident plasticity to thrive under this condition are not yet clear. Therefore, to provide a broad perspective of such mechanisms, Chirostoma estor fish were raised and sampled for growth under a simulated control (LD) 12 h Light: 12 h Dark or a continuous illumination (LL) 24 h Light: 0 h Dark since fertilization. The experiment lasted 12 weeks after hatching (wah), the time at which fish were sampled for growth, length, and whole-body cortisol levels. Additionally, 3 heads of fish from each treatment were used to perform a de novo transcriptome analysis using Next-Generation Sequencing. Fish in LL developed the fast growth phenotype with significant differences visible at 4 wah and gained 66% more mass by 12 wah than LD fish. Cortisol levels under LL were below basal levels at all times compared to fish in LD, suggesting circadian dysregulation effects. A strong effect of LL was observed in samples with a generalized down-regulation of genes except for Reactive Oxygen Species responses, genome stability, and growth biological processes. To our knowledge, this work is the first study using a transcriptomic approach to understand environmentally sensitive MRNs that mediate phenotypic plasticity in fish submitted to continuous illumination. This study gives new insights into the plasticity mechanisms of teleost fish under constant illumination.
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Affiliation(s)
- Guillermo A Corona-Herrera
- Laboratorio de Biotecnología Acuícola, Instituto de Investigaciones Agropecuarias y Forestales (IIAF), Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán 58330, Mexico
| | - Pamela Navarrete-Ramírez
- CONACYT-Laboratorio de Biotecnología Acuícola, Instituto de Investigaciones Agropecuarias y Forestales (IIAF), Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | - F Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática del Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Verónica Jimenez-Jacinto
- Unidad Universitaria de Secuenciación Masiva y Bioinformática del Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Carlos A Martínez-Palacios
- Laboratorio de Biotecnología Acuícola, Instituto de Investigaciones Agropecuarias y Forestales (IIAF), Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán 58330, Mexico
| | - Zoraya Palomera-Sánchez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán 58330, Mexico
| | - Helene Volkoff
- Department of Biology, Memorial University of Newfoundland, St John's A1B3X9, Canada
| | - C Cristian Martínez-Chávez
- Laboratorio de Biotecnología Acuícola, Instituto de Investigaciones Agropecuarias y Forestales (IIAF), Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán 58330, Mexico.
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6
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Karademir D, Todorova V, Ebner LJA, Samardzija M, Grimm C. Single-cell RNA sequencing of the retina in a model of retinitis pigmentosa reveals early responses to degeneration in rods and cones. BMC Biol 2022; 20:86. [PMID: 35413909 PMCID: PMC9006580 DOI: 10.1186/s12915-022-01280-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 03/12/2022] [Indexed: 11/18/2022] Open
Abstract
Background In inherited retinal disorders such as retinitis pigmentosa (RP), rod photoreceptor-specific mutations cause primary rod degeneration that is followed by secondary cone death and loss of high-acuity vision. Mechanistic studies of retinal degeneration are challenging because of retinal heterogeneity. Moreover, the detection of early cone responses to rod death is especially difficult due to the paucity of cones in the retina. To resolve heterogeneity in the degenerating retina and investigate events in both types of photoreceptors during primary rod degeneration, we utilized droplet-based single-cell RNA sequencing in an RP mouse model, rd10. Results Using trajectory analysis, we defined two consecutive phases of rod degeneration at P21, characterized by the early transient upregulation of Egr1 and the later induction of Cebpd. EGR1 was the transcription factor most significantly associated with the promoters of differentially regulated genes in Egr1-positive rods in silico. Silencing Egr1 affected the expression levels of two of these genes in vitro. Degenerating rods exhibited changes associated with metabolism, neuroprotection, and modifications to synapses and microtubules. Egr1 was also the most strongly upregulated transcript in cones. Its upregulation in cones accompanied potential early respiratory dysfunction and changes in signaling pathways. The expression pattern of EGR1 in the retina was dynamic during degeneration, with a transient increase of EGR1 immunoreactivity in both rods and cones during the early stages of their degenerative processes. Conclusion Our results identify early and late changes in degenerating rd10 rod photoreceptors and reveal early responses to rod degeneration in cones not expressing the disease-causing mutation, pointing to mechanisms relevant for secondary cone degeneration. In addition, our data implicate EGR1 as a potential key regulator of early degenerative events in rods and cones, providing a potential broad target for modulating photoreceptor degeneration. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01280-9.
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Affiliation(s)
- Duygu Karademir
- Laboratory for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zurich, University of Zurich, Zurich, Switzerland. .,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
| | - Vyara Todorova
- Laboratory for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
| | - Lynn J A Ebner
- Laboratory for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Marijana Samardzija
- Laboratory for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christian Grimm
- Laboratory for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
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7
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Xiang L, Zhang J, Rao FQ, Yang QL, Zeng HY, Huang SH, Xie ZX, Lv JN, Lin D, Chen XJ, Wu KC, Lu F, Huang XF, Chen Q. Depletion of miR-96 Delays, But Does Not Arrest, Photoreceptor Development in Mice. Invest Ophthalmol Vis Sci 2022; 63:24. [PMID: 35481839 PMCID: PMC9055555 DOI: 10.1167/iovs.63.4.24] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Purpose Abundant retinal microRNA-183 cluster (miR-183C) has been reported to be a key player in photoreceptor development and functionality in mice. However, whether there is a protagonist in this cluster remains unclear. Here, we used a mutant mouse model to study the role of miR-96, a member of miR-183C, in photoreceptor development and functionality. Methods The mature miR-96 sequence was removed using the CRISPR/Cas9 genome-editing system. Electroretinogram (ERG) and optical coherence tomography (OCT) investigated the changes in structure and function in mouse retinas. Immunostaining determined the localization and morphology of the retinal cells. RNA sequencing was conducted to observe retinal transcription alterations. Results The miR-96 mutant mice exhibited cone developmental delay, as occurs in miR-183/96 double knockout mice. Immunostaining of cone-specific marker genes revealed cone nucleus mislocalization and exiguous Opn1mw/Opn1sw in the mutant (MT) mouse outer segments at postnatal day 10. Interestingly, this phenomenon could be relieved in the adult stages. Transcriptome analysis revealed activation of microtubule-, actin filament–, and cilia-related pathways, further supporting the findings. Based on ERG and OCT results at different ages, the MT mice displayed developmental delay not only in cones but also in rods. In addition, a group of miR-96 potential direct and indirect target genes was summarized for interpretation and further studies of miR-96–related retinal developmental defects. Conclusions Depletion of miR-96 delayed but did not arrest photoreceptor development in mice. This miRNA is indispensable for mouse photoreceptor maturation, especially for cones.
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Affiliation(s)
- Lue Xiang
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, China
| | - Juan Zhang
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Feng-Qin Rao
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China.,School of Pharmaceutical Sciences of Wenzhou Medical University, Wenzhou, China
| | - Qiao-Li Yang
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Hui-Yi Zeng
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Sheng-Hai Huang
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zhen-Xiang Xie
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ji-Neng Lv
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, China
| | - Dan Lin
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xue-Jiao Chen
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, China
| | - Kun-Chao Wu
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Fan Lu
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, China
| | - Xiu-Feng Huang
- The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qi Chen
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, China
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8
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Friedman RZ, Granas DM, Myers CA, Corbo JC, Cohen BA, White MA. Information content differentiates enhancers from silencers in mouse photoreceptors. eLife 2021; 10:67403. [PMID: 34486522 PMCID: PMC8492058 DOI: 10.7554/elife.67403] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/03/2021] [Indexed: 12/12/2022] Open
Abstract
Enhancers and silencers often depend on the same transcription factors (TFs) and are conflated in genomic assays of TF binding or chromatin state. To identify sequence features that distinguish enhancers and silencers, we assayed massively parallel reporter libraries of genomic sequences targeted by the photoreceptor TF cone-rod homeobox (CRX) in mouse retinas. Both enhancers and silencers contain more TF motifs than inactive sequences, but relative to silencers, enhancers contain motifs from a more diverse collection of TFs. We developed a measure of information content that describes the number and diversity of motifs in a sequence and found that, while both enhancers and silencers depend on CRX motifs, enhancers have higher information content. The ability of information content to distinguish enhancers and silencers targeted by the same TF illustrates how motif context determines the activity of cis-regulatory sequences. Different cell types are established by activating and repressing the activity of specific sets of genes, a process controlled by proteins called transcription factors. Transcription factors work by recognizing and binding short stretches of DNA in parts of the genome called cis-regulatory sequences. A cis-regulatory sequence that increases the activity of a gene when bound by transcription factors is called an enhancer, while a sequence that causes a decrease in gene activity is called a silencer. To establish a cell type, a particular transcription factor will act on both enhancers and silencers that control the activity of different genes. For example, the transcription factor cone-rod homeobox (CRX) is critical for specifying different types of cells in the retina, and it acts on both enhancers and silencers. In rod photoreceptors, CRX activates rod genes by binding their enhancers, while repressing cone photoreceptor genes by binding their silencers. However, CRX always recognizes and binds to the same DNA sequence, known as its binding site, making it unclear why some cis-regulatory sequences bound to CRX act as silencers, while others act as enhancers. Friedman et al. sought to understand how enhancers and silencers, both bound by CRX, can have different effects on the genes they control. Since both enhancers and silencers contain CRX binding sites, the difference between the two must lie in the sequence of the DNA surrounding these binding sites. Using retinas that have been explanted from mice and kept alive in the laboratory, Friedman et al. tested the activity of thousands of CRX-binding sequences from the mouse genome. This showed that both enhancers and silencers have more copies of CRX-binding sites than sequences of the genome that are inactive. Additionally, the results revealed that enhancers have a diverse collection of binding sites for other transcription factors, while silencers do not. Friedman et al. developed a new metric they called information content, which captures the diverse combinations of different transcription binding sites that cis-regulatory sequences can have. Using this metric, Friedman et al. showed that it is possible to distinguish enhancers from silencers based on their information content. It is critical to understand how the DNA sequences of cis-regulatory regions determine their activity, because mutations in these regions of the genome can cause disease. However, since every person has thousands of benign mutations in cis-regulatory sequences, it is a challenge to identify specific disease-causing mutations, which are relatively rare. One long-term goal of models of enhancers and silencers, such as Friedman et al.’s information content model, is to understand how mutations can affect cis-regulatory sequences, and, in some cases, lead to disease.
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Affiliation(s)
- Ryan Z Friedman
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, United States.,Department of Genetics, Washington University School of Medicine, St. Louis, United States
| | - David M Granas
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, United States.,Department of Genetics, Washington University School of Medicine, St. Louis, United States
| | - Connie A Myers
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, United States
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, United States
| | - Barak A Cohen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, United States.,Department of Genetics, Washington University School of Medicine, St. Louis, United States
| | - Michael A White
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, United States.,Department of Genetics, Washington University School of Medicine, St. Louis, United States
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9
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Raeisossadati R, Ferrari MFR, Kihara AH, AlDiri I, Gross JM. Epigenetic regulation of retinal development. Epigenetics Chromatin 2021; 14:11. [PMID: 33563331 PMCID: PMC7871400 DOI: 10.1186/s13072-021-00384-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/28/2021] [Indexed: 01/10/2023] Open
Abstract
In the developing vertebrate retina, retinal progenitor cells (RPCs) proliferate and give rise to terminally differentiated neurons with exquisite spatio-temporal precision. Lineage commitment, fate determination and terminal differentiation are controlled by intricate crosstalk between the genome and epigenome. Indeed, epigenetic regulation plays pivotal roles in numerous cell fate specification and differentiation events in the retina. Moreover, aberrant chromatin structure can contribute to developmental disorders and retinal pathologies. In this review, we highlight recent advances in our understanding of epigenetic regulation in the retina. We also provide insight into several aspects of epigenetic-related regulation that should be investigated in future studies of retinal development and disease. Importantly, focusing on these mechanisms could contribute to the development of novel treatment strategies targeting a variety of retinal disorders.
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Affiliation(s)
- Reza Raeisossadati
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Merari F R Ferrari
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil
| | | | - Issam AlDiri
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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10
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Xu Y, Yang XL, Yang XL, Ren YR, Zhuang XY, Zhang L, Zhang XF. Functional Annotations of Single-Nucleotide Polymorphism (SNP)-Based and Gene-Based Genome-Wide Association Studies Show Genes Affecting Keratitis Susceptibility. MEDICAL SCIENCE MONITOR : INTERNATIONAL MEDICAL JOURNAL OF EXPERIMENTAL AND CLINICAL RESEARCH 2020; 26:e922710. [PMID: 32450567 PMCID: PMC7269196 DOI: 10.12659/msm.922710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background Keratitis is a complex condition in humans and is the second most common cause of legal blindness worldwide. Material/Methods To reveal the genomic loci underlying keratitis, we performed functional annotations of SNP-based and gene-based genome-wide association studies of keratitis in the UK Biobank (UKB) cohort with 337 199 subjects of European ancestry. Results The publicly available SNP-based association results showed a total of 34 SNPs, from 14 distinct loci, associated with keratitis in the UKB. Gene-based association analysis identified 2 significant genes: IQCF3 (p=2.0×10−6) and SOD3 (p=2.0×10−6). Thirty-two candidate genes were then prioritized using information from multiple sources. The overlap of IQCF3 in these 2 analyses resulted in a total of 33 hub genes. Functional annotation of hub genes was performed and transcriptional factors of IQCF3 and SOD3 were predicted. Conclusions A total of 34 SNPs from 14 distinct loci were identified as being associated with keratitis, and 32 candidate genes were then prioritized. In addition, IQCF3 and SOD3 were identified by their p values through gene-based tests on the basis of individual SNP-based tests. The functional relationship between these suspect genes and keratitis suggest that IQCF3 and SOD3 are candidate genes underlying keratitis.
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Affiliation(s)
- Yue Xu
- Department of Ophthalmology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China (mainland)
| | - Xiao-Lin Yang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, China (mainland)
| | - Xiao-Long Yang
- Department of Ophthalmology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China (mainland)
| | - Ya-Ru Ren
- Department of Ophthalmology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China (mainland)
| | - Xin-Yu Zhuang
- Department of Ophthalmology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China (mainland)
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, China (mainland)
| | - Xiao-Feng Zhang
- Department of Ophthalmology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China (mainland)
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11
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Kaufman ML, Park KU, Goodson NB, Chew S, Bersie S, Jones KL, Lamba DA, Brzezinski JA. Transcriptional profiling of murine retinas undergoing semi-synchronous cone photoreceptor differentiation. Dev Biol 2019; 453:155-167. [PMID: 31163126 DOI: 10.1016/j.ydbio.2019.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/24/2019] [Accepted: 05/29/2019] [Indexed: 12/12/2022]
Abstract
Uncovering the gene regulatory networks that control cone photoreceptor formation has been hindered because cones only make up a few percent of the retina and form asynchronously during development. To overcome these limitations, we used a γ-secretase inhibitor, DAPT, to disrupt Notch signaling and force proliferating retinal progenitor cells to rapidly adopt neuronal identity. We treated mouse retinal explants at the peak of cone genesis with DAPT and examined tissues at several time-points by histology and bulk RNA-sequencing. We found that this treatment caused supernumerary cone formation in an overwhelmingly synchronized fashion. This analysis revealed several categorical patterns of gene expression changes over time relative to DMSO treated control explants. These were placed in the temporal context of the activation of Otx2, a transcription factor that is expressed at the onset of photoreceptor development and that is required for both rod and cone formation. One group of interest had genes, such as Mybl1, Ascl1, Neurog2, and Olig2, that became upregulated by DAPT treatment before Otx2. Two other groups showed upregulated gene expression shortly after Otx2, either transiently or permanently. This included genes such as Mybl1, Meis2, and Podxl. Our data provide a developmental timeline of the gene expression events that underlie the initial steps of cone genesis and maturation. Applying this strategy to human retinal organoid cultures was also sufficient to induce a massive increase in cone genesis. Taken together, our results provide a temporal framework that can be used to elucidate the gene regulatory logic controlling cone photoreceptor development.
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Affiliation(s)
- Michael L Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Noah B Goodson
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Shereen Chew
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Stephanie Bersie
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Deepak A Lamba
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Joseph A Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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12
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Samd7 is a cell type-specific PRC1 component essential for establishing retinal rod photoreceptor identity. Proc Natl Acad Sci U S A 2017; 114:E8264-E8273. [PMID: 28900001 DOI: 10.1073/pnas.1707021114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Precise transcriptional regulation controlled by a transcription factor network is known to be crucial for establishing correct neuronal cell identities and functions in the CNS. In the retina, the expression of various cone and rod photoreceptor cell genes is regulated by multiple transcription factors; however, the role of epigenetic regulation in photoreceptor cell gene expression has been poorly understood. Here, we found that Samd7, a rod-enriched sterile alpha domain (SAM) domain protein, is essential for silencing nonrod gene expression through H3K27me3 regulation in rod photoreceptor cells. Samd7-null mutant mice showed ectopic expression of nonrod genes including S-opsin in rod photoreceptor cells and rod photoreceptor cell dysfunction. Samd7 physically interacts with Polyhomeotic homologs (Phc proteins), components of the Polycomb repressive complex 1 (PRC1), and colocalizes with Phc2 and Ring1B in Polycomb bodies. ChIP assays showed a significant decrease of H3K27me3 in the genes up-regulated in the Samd7-deficient retina, showing that Samd7 deficiency causes the derepression of nonrod gene expression in rod photoreceptor cells. The current study suggests that Samd7 is a cell type-specific PRC1 component epigenetically defining rod photoreceptor cell identity.
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13
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Corton M, Avila-Fernández A, Campello L, Sánchez M, Benavides B, López-Molina MI, Fernández-Sánchez L, Sánchez-Alcudia R, da Silva LRJ, Reyes N, Martín-Garrido E, Zurita O, Fernández-San José P, Pérez-Carro R, García-García F, Dopazo J, García-Sandoval B, Cuenca N, Ayuso C. Identification of the Photoreceptor Transcriptional Co-Repressor SAMD11 as Novel Cause of Autosomal Recessive Retinitis Pigmentosa. Sci Rep 2016; 6:35370. [PMID: 27734943 PMCID: PMC5062157 DOI: 10.1038/srep35370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/28/2016] [Indexed: 01/09/2023] Open
Abstract
Retinitis pigmentosa (RP), the most frequent form of inherited retinal dystrophy is characterized by progressive photoreceptor degeneration. Many genes have been implicated in RP development, but several others remain to be identified. Using a combination of homozygosity mapping, whole-exome and targeted next-generation sequencing, we found a novel homozygous nonsense mutation in SAMD11 in five individuals diagnosed with adult-onset RP from two unrelated consanguineous Spanish families. SAMD11 is ortholog to the mouse major retinal SAM domain (mr-s) protein that is implicated in CRX-mediated transcriptional regulation in the retina. Accordingly, protein-protein network analysis revealed a significant interaction of SAMD11 with CRX. Immunoblotting analysis confirmed strong expression of SAMD11 in human retina. Immunolocalization studies revealed SAMD11 was detected in the three nuclear layers of the human retina and interestingly differential expression between cone and rod photoreceptors was observed. Our study strongly implicates SAMD11 as novel cause of RP playing an important role in the pathogenesis of human degeneration of photoreceptors.
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Affiliation(s)
- M Corton
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - A Avila-Fernández
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - L Campello
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - M Sánchez
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - B Benavides
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - M I López-Molina
- Department of Ophthalmology, Health Research Institute- Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain
| | - L Fernández-Sánchez
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - R Sánchez-Alcudia
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - L R J da Silva
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Universidade de Mogi das Cruzes, São Paulo, Brazil
| | - N Reyes
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - E Martín-Garrido
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - O Zurita
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - P Fernández-San José
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - R Pérez-Carro
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - F García-García
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Bioinformatics in Rare Diseases (BIER), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Valencia, Spain
| | - J Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Bioinformatics in Rare Diseases (BIER), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Valencia, Spain.,Functional Genomics Node (INB), Valencia, Spain
| | - B García-Sandoval
- Department of Ophthalmology, Health Research Institute- Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain
| | - N Cuenca
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - C Ayuso
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
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14
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A challenge to the striking genotypic heterogeneity of retinitis pigmentosa: a better understanding of the pathophysiology using the newest genetic strategies. Eye (Lond) 2016; 30:1542-1548. [PMID: 27564722 DOI: 10.1038/eye.2016.197] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 07/13/2016] [Indexed: 11/08/2022] Open
Abstract
Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterized by a complex association between tremendous genotypic multiplicity and great phenotypic heterogeneity. The severity of the clinical manifestation depends on penetrance and expressivity of the disease-gene. Also, various interactions between gene expression and environmental factors have been hypothesized. More than 250 genes with ~4500 causative mutations have been reported to be involved in different RP-related mechanisms. Nowadays, not more than the 50% of RPs are attributable to identified genes, whereas the rest of molecular defects are still undetectable, especially in populations where few genetic screenings have been performed. Therefore, new genetic strategies can be a remarkably useful tool to aid clinical diagnosis, potentially modifying treatment options, and family counseling. Genome-wide analytical techniques (array comparative genomic hybridization and single-nucleotide polymorphism genotyping) and DNA sequencing strategies (arrayed primer extension, Sanger sequencing, and ultra high-throughput sequencing) are successfully used to early make molecular diagnosis detecting single or multiple mutations in the huge heterogeneity of RPs. To date, further research needs to be carried out to better investigate the genotype/phenotype correlation, putting together genetic and clinical findings to provide detailed information concerning the risk of RP development and novel effective treatments.
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15
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Autosomal recessive retinitis pigmentosa with homozygous rhodopsin mutation E150K and non-coding cis-regulatory variants in CRX-binding regions of SAMD7. Sci Rep 2016; 6:21307. [PMID: 26887858 PMCID: PMC4758057 DOI: 10.1038/srep21307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/19/2016] [Indexed: 01/17/2023] Open
Abstract
The aim of this study was to unravel the molecular pathogenesis of an unusual retinitis pigmentosa (RP) phenotype observed in a Turkish consanguineous family. Homozygosity mapping revealed two candidate genes, SAMD7 and RHO. A homozygous RHO mutation c.448G > A, p.E150K was found in two affected siblings, while no coding SAMD7 mutations were identified. Interestingly, four non-coding homozygous variants were found in two SAMD7 genomic regions relevant for binding of the retinal transcription factor CRX (CRX-bound regions, CBRs) in these affected siblings. Three variants are located in a promoter CBR termed CBR1, while the fourth is located more downstream in CBR2. Transcriptional activity of these variants was assessed by luciferase assays and electroporation of mouse retinal explants with reporter constructs of wild-type and variant SAMD7 CBRs. The combined CBR2/CBR1 variant construct showed significantly decreased SAMD7 reporter activity compared to the wild-type sequence, suggesting a cis-regulatory effect on SAMD7 expression. As Samd7 is a recently identified Crx-regulated transcriptional repressor in retina, we hypothesize that these SAMD7 variants might contribute to the retinal phenotype observed here, characterized by unusual, recognizable pigment deposits, differing from the classic spicular intraretinal pigmentation observed in other individuals homozygous for p.E150K, and typically associated with RP in general.
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16
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Holt R, Brown L, Broadgate S, Butler R, Jagannath A, Downes S, Peirson S, Halford S. Identification of rod- and cone-specific expression signatures to identify candidate genes for retinal disease. Exp Eye Res 2015; 132:161-73. [DOI: 10.1016/j.exer.2015.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/22/2014] [Accepted: 01/06/2015] [Indexed: 01/05/2023]
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17
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Early-onset autosomal recessive cerebellar ataxia associated with retinal dystrophy: new human hotfoot phenotype caused by homozygous GRID2 deletion. Genet Med 2014; 17:291-9. [DOI: 10.1038/gim.2014.95] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/19/2014] [Indexed: 11/08/2022] Open
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18
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Prediction of response to preoperative chemoradiotherapy in rectal cancer by using reverse transcriptase polymerase chain reaction analysis of four genes. Dis Colon Rectum 2014; 57:23-31. [PMID: 24316942 DOI: 10.1097/01.dcr.0000437688.33795.9d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Patients with rectal cancer exhibit a wide spectrum of responses to chemoradiotherapy. Several gene expression signatures have been reported to predict the response to chemoradiotherapy in rectal cancer, but the lack of practical assays has restricted the clinical use of this technique. OBJECTIVE We aimed to identify a set of discriminating genes that can be used for the clinical prediction of response to chemoradiotherapy in rectal cancer. DESIGN AND SETTINGS This study is a retrospective analysis of tumor samples in a single institute. PATIENTS Sixty-two patients who underwent preoperative chemoradiotherapy were studied. MAIN OUTCOME MEASURES Gene expression was initially studied in 46 training samples by microarray analysis, and the association between gene expression and response to chemoradiotherapy was evaluated. Quantitative reverse transcriptase polymerase chain reaction was performed to validate the microarray expression levels of the discriminating genes. We developed a gene expression model for the prediction of response to chemoradiotherapy based on the reverse transcriptase polymerase chain reaction findings and validated it by using 16 independent test samples. RESULTS We identified 24 discriminating probes with expression levels that differed significantly between responders and nonresponders. Among 18 genes identified by Gene Symbol, real-time reverse transcriptase polymerase chain reaction showed significant differences in the expression of 16 genes between responders and nonresponders. We constructed a predictive model by using different sets of these 16 genes, and the highest accuracy rate (89.1%) was obtained by using LRRIQ3, FRMD3, SAMD5, and TMC7. The predictive accuracy rate of this 4-gene signature in the independent set of 16 patients was 81.3%. LIMITATIONS Validation in a different and large cohort of patients is necessary. CONCLUSIONS The 4-gene signature identified in this study is closely associated with response to chemoradiotherapy in rectal cancer.
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19
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Song WT, Zhang XY, Xiong SQ, Wen D, Jiang J, Xia XB. Comparison of two methods used to culture and purify rat retinal Müller cells. Int J Ophthalmol 2013; 6:778-84. [PMID: 24392324 DOI: 10.3980/j.issn.2222-3959.2013.06.07] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 10/09/2013] [Indexed: 01/19/2023] Open
Abstract
AIM To study two methods for culturing and purifying Sprague-Dawley (SD) rat retinal Müller cells and determine which one is better. METHODS The passage culture method of Müller cells was respectively carried out by complete pancreatic enzyme digestion method and repeated incomplete pancreatic enzyme digestion method. After culturing retinal cells for one month through these two methods, fluorescence-activated cell sorter (FACS), RT-PCR, and immunohistochemistry technology were performed to examine the enrichment and purity of Müller glial cells, and carried out two-sample approximate t test using SSPS 13.0 to further compare the Müller cell positive rate in both methods. RESULTS The statistical results showed that the purity of Müller cells was 83.2%±5.16% in group A, and the purity was 98.5%±1.08% in group B. The two-sample approximate t test analysis demonstrated that the difference between group A and group B was statistically significant (t=-9.178, P<0.005). The results clearly exhibited a difference between the purity of Müller cells cultured by the complete pancreatic enzyme digestion method (group A) and the repeated incomplete pancreatic enzyme digestion method (group B). CONCLUSION Compared with the complete pancreatic enzyme digestion method, this novel method was more efficient and a higher purity of Müller cells could be obtained using this approach.
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Affiliation(s)
- Wei-Tao Song
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Xue-Yong Zhang
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Si-Qi Xiong
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Dan Wen
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Jian Jiang
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Xiao-Bo Xia
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
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20
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Progressive retinal degeneration and glial activation in the CLN6 (nclf) mouse model of neuronal ceroid lipofuscinosis: a beneficial effect of DHA and curcumin supplementation. PLoS One 2013; 8:e75963. [PMID: 24124525 PMCID: PMC3790850 DOI: 10.1371/journal.pone.0075963] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/19/2013] [Indexed: 01/01/2023] Open
Abstract
Neuronal ceroid lipofuscinosis (NCL) is a group of neurodegenerative lysosomal storage disorders characterized by vision loss, mental and motor deficits, and spontaneous seizures. Neuropathological analyses of autopsy material from NCL patients and animal models revealed brain atrophy closely associated with glial activity. Earlier reports also noticed loss of retinal cells and reactive gliosis in some forms of NCL. To study this phenomenon in detail, we analyzed the ocular phenotype of CLN6nclf mice, an established mouse model for variant-late infantile NCL. Retinal morphometry, immunohistochemistry, optokinetic tracking, electroretinography, and mRNA expression were used to characterize retinal morphology and function as well as the responses of Müller cells and microglia. Our histological data showed a severe and progressive degeneration in the CLN6nclf retina co-inciding with reactive Müller glia. Furthermore, a prominent phenotypic transformation of ramified microglia to phagocytic, bloated, and mislocalized microglial cells was identified in CLN6nclf retinas. These events overlapped with a rapid loss of visual perception and retinal function. Based on the strong microglia reactivity we hypothesized that dietary supplementation with immuno-regulatory compounds, curcumin and docosahexaenoic acid (DHA), could ameliorate microgliosis and reduce retinal degeneration. Our analyses showed that treatment of three-week-old CLN6nclf mice with either 5% DHA or 0.6% curcumin for 30 weeks resulted in a reduced number of amoeboid reactive microglia and partially improved retinal function. DHA-treatment also improved the morphology of CLN6nclf retinas with a preserved thickness of the photoreceptor layer in most regions of the retina. Our results suggest that microglial reactivity closely accompanies disease progression in the CLN6nclf retina and both processes can be attenuated with dietary supplemented immuno-modulating compounds.
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