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Fan J, Santos da Cruz NF, Negron CI, Zhu AY, Chang TC, Berrocal AM. Foveal photoreceptor atrophy, persistent fetal vasculature, congenital cataracts, and microphthalmia in a pediatric patient with BCOR-associated oculo-facio-cardio-dental (OFCD) syndrome. Am J Ophthalmol Case Rep 2024; 34:102060. [PMID: 38699441 PMCID: PMC11063980 DOI: 10.1016/j.ajoc.2024.102060] [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: 12/06/2023] [Revised: 03/02/2024] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
Purpose To report a case of oculo-facio-cardio-dental (OFCD) syndrome secondary to a novel BCOR variant in a pediatric patient with congenital cataracts, microphthalmia, persistent fetal vasculature (PFV), focal chorioretinal hyperpigmentation, peripheral retinal avascularity, and foveal photoreceptor atrophy. Observations A 3-month-old female patient was referred for bilateral congenital cataracts with microphthalmia. Her past medical history was significant for syndactyly of the toes, left bifid rib, atrial septal defect, patent ductus arteriosus, mitral regurgitation, pulmonary hypertension, anemia of prematurity, vesicoureteral reflux, and duodenal atresia. Examination under anesthesia revealed persistent fetal vasculature (PFV) with peripheral avascularity, foveal photoreceptor atrophy, and focal chorioretinal hyperpigmentation. A bilateral lensectomy with anterior vitrectomy and posterior capsulotomy were performed. Genetic testing identified a novel heterozygous pathogenic variant in the BCOR gene (c.1612C > T (p.Gln538Ter)), confirming a diagnosis of OFCD syndrome. Conclusions and importance This case describes novel posterior segment findings in a patient with OFCD. A detailed examination of both anterior and posterior segments in combination with multimodal imaging should be performed in patients suspected of having OFCD, as this may be critical in determining visual potential and appropriate surgical management.
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Affiliation(s)
- Jason Fan
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, FL, USA
| | | | - Catherin I. Negron
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, FL, USA
| | - Angela Y. Zhu
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, FL, USA
| | - Ta C. Chang
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, FL, USA
| | - Audina M. Berrocal
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, FL, USA
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2
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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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Pfaller AM, Kaplan L, Carido M, Grassmann F, Díaz-Lezama N, Ghaseminejad F, Wunderlich KA, Glänzer S, Bludau O, Pannicke T, Weber BHF, Koch SF, Bonev B, Hauck SM, Grosche A. The glucocorticoid receptor as a master regulator of the Müller cell response to diabetic conditions in mice. J Neuroinflammation 2024; 21:33. [PMID: 38273366 PMCID: PMC10809506 DOI: 10.1186/s12974-024-03021-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: 09/12/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
Diabetic retinopathy (DR) is considered a primarily microvascular complication of diabetes. Müller glia cells are at the centre of the retinal neurovascular unit and play a critical role in DR. We therefore investigated Müller cell-specific signalling pathways that are altered in DR to identify novel targets for gene therapy. Using a multi-omics approach on purified Müller cells from diabetic db/db mice, we found the mRNA and protein expression of the glucocorticoid receptor (GR) to be significantly decreased, while its target gene cluster was down-regulated. Further, oPOSSUM TF analysis and ATAC- sequencing identified the GR as a master regulator of Müller cell response to diabetic conditions. Cortisol not only increased GR phosphorylation. It also induced changes in the expression of known GR target genes in retinal explants. Finally, retinal functionality was improved by AAV-mediated overexpression of GR in Müller cells. Our study demonstrates an important role of the glial GR in DR and implies that therapeutic approaches targeting this signalling pathway should be aimed at increasing GR expression rather than the addition of more ligand.
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Affiliation(s)
- Anna M Pfaller
- Department of Physiological Genomics, Biomedical Center-BMC, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Lew Kaplan
- Department of Physiological Genomics, Biomedical Center-BMC, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Madalena Carido
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Felix Grassmann
- Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
- Institute for Clinical Research and Systems Medicine, Health and Medical University, Potsdam, Germany
| | - Nundehui Díaz-Lezama
- Department of Physiological Genomics, Biomedical Center-BMC, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Farhad Ghaseminejad
- Department of Physiological Genomics, Biomedical Center-BMC, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Kirsten A Wunderlich
- Department of Physiological Genomics, Biomedical Center-BMC, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Institute for Molecular Medicine, Health and Medical University, Potsdam, Germany
| | - Sarah Glänzer
- Department of Physiological Genomics, Biomedical Center-BMC, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Oliver Bludau
- Department of Physiological Genomics, Biomedical Center-BMC, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Thomas Pannicke
- Paul Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Bernhard H F Weber
- Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
- Institute of Human Genetics, University Regensburg, Regensburg, Germany
| | - Susanne F Koch
- Department of Physiological Genomics, Biomedical Center-BMC, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Boyan Bonev
- Department of Physiological Genomics, Biomedical Center-BMC, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Antje Grosche
- Department of Physiological Genomics, Biomedical Center-BMC, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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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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5
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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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6
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Fries M, Brown TW, Jolicoeur C, Boulan B, Boudreau-Pinsonneault C, Javed A, Abram P, Cayouette M. Pou3f1 orchestrates a gene regulatory network controlling contralateral retinogeniculate projections. Cell Rep 2023; 42:112985. [PMID: 37590135 DOI: 10.1016/j.celrep.2023.112985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 05/26/2023] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
The balance of contralateral and ipsilateral retinogeniculate projections is critical for binocular vision, but the transcriptional programs regulating this process remain ill defined. Here we show that the Pou class homeobox protein POU3F1 is expressed in nascent mouse contralateral retinal ganglion cells (cRGCs) but not ipsilateral RGCs (iRGCs). Upon Pou3f1 inactivation, the proportion of cRGCs is reduced in favor of iRGCs, leading to abnormal projection ratios at the optic chiasm. Conversely, misexpression of Pou3f1 in progenitors increases the production of cRGCs. Using CUT&RUN and RNA sequencing in gain- and loss-of-function assays, we demonstrate that POU3F1 regulates expression of several key members of the cRGC gene regulatory network. Finally, we report that POU3F1 is sufficient to induce RGC-like cell production, even in late-stage retinal progenitors of Atoh7 knockout mice. This work uncovers POU3F1 as a regulator of the cRGC transcriptional program, opening possibilities for optic nerve regenerative therapies.
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Affiliation(s)
- Michel Fries
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada; Molecular Biology Program, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Thomas W Brown
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada; Integrated Program in Neuroscience, McGill University, Montreal, QC H3A 1A1, Canada
| | - Christine Jolicoeur
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada
| | - Benoit Boulan
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada
| | - Camille Boudreau-Pinsonneault
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada; Integrated Program in Neuroscience, McGill University, Montreal, QC H3A 1A1, Canada
| | - Awais Javed
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada; Molecular Biology Program, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Pénélope Abram
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada; Molecular Biology Program, Université de Montréal, Montreal, QC H3C 3J7, Canada; Integrated Program in Neuroscience, McGill University, Montreal, QC H3A 1A1, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada.
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