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Marchal C, Singh N, Batz Z, Advani J, Jaeger C, Corso-Díaz X, Swaroop A. High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci. Nat Commun 2022; 13:5827. [PMID: 36207300 PMCID: PMC9547065 DOI: 10.1038/s41467-022-33427-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022] Open
Abstract
Chromatin organization and enhancer-promoter contacts establish unique spatiotemporal gene expression patterns in distinct cell types. Non-coding genetic variants can influence cellular phenotypes by modifying higher-order transcriptional hubs and consequently gene expression. To elucidate genomic regulation in human retina, we mapped chromatin contacts at high resolution and integrated with super-enhancers (SEs), histone marks, binding of CTCF and select transcription factors. We show that topologically associated domains (TADs) with central SEs exhibit stronger insulation and augmented contact with retinal genes relative to TADs with edge SEs. Merging genome-wide expression quantitative trait loci (eQTLs) with topology map reveals physical links between 100 eQTLs and corresponding eGenes associated with retinal neurodegeneration. Additionally, we uncover candidate genes for susceptibility variants linked to age-related macular degeneration and glaucoma. Our study of high-resolution genomic architecture of human retina provides insights into genetic control of tissue-specific functions, suggests paradigms for missing heritability, and enables the dissection of common blinding disease phenotypes.
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Affiliation(s)
- Claire Marchal
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
- In silichrom Ltd, First Floor, Angel Court, 81 St Clements St, Oxford, OX4 1AW, UK
| | - Nivedita Singh
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Zachary Batz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Catherine Jaeger
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Ximena Corso-Díaz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA.
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Taiyab A, Akula M, Dham J, Deschamps P, Sheardown H, Williams T, Borrás T, West-Mays JA. Deletion of transcription factor AP-2β from the developing murine trabecular meshwork region leads to progressive glaucomatous changes. J Neurosci Res 2021; 100:638-652. [PMID: 34822722 DOI: 10.1002/jnr.24982] [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: 08/24/2021] [Revised: 09/28/2021] [Accepted: 10/03/2021] [Indexed: 11/08/2022]
Abstract
Glaucoma is one of the leading causes of irreversible blindness and can result from abnormalities in anterior segment structures required for aqueous humor outflow, including the trabecular meshwork (TM) and Schlemm's canal (SC). Transcription factors such as AP-2β play critical roles in anterior segment development. Here, we show that the Mgp-Cre knock-in (Mgp-Cre.KI) mouse can be used to target the embryonic periocular mesenchyme giving rise to the TM and SC. Fate mapping of male and female mice indicates that AP-2β loss causes a decrease in iridocorneal angle cells derived from Mgp-Cre.KI-expressing populations compared to controls. Moreover, histological analyses revealed peripheral iridocorneal adhesions in AP-2β mutants that were accompanied by a decrease in expression of TM and SC markers, as observed using immunohistochemistry. In addition, rebound tonometry showed significantly higher intraocular pressure (IOP) that was correlated with a progressive significant loss of retinal ganglion cells, reduced retinal thickness, and reduced retinal function, as measured using an electroretinogram, in AP-2β mutants compared with controls, reflecting pathology described in late-stage glaucoma patients. Importantly, elevated IOP in AP-2β mutants was significantly reduced by treatment with latanoprost, a prostaglandin analog that increases unconventional outflow. These findings demonstrate that AP-2β is critical for TM and SC development, and that these mutant mice can serve as a model for understanding and treating progressive human primary angle-closure glaucoma.
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Affiliation(s)
- Aftab Taiyab
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Monica Akula
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Japnit Dham
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Paula Deschamps
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Heather Sheardown
- Department of Chemical Engineering, McMaster University, Hamilton, ON, Canada
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado, Aurora, CO, USA
| | - Teresa Borrás
- Department of Ophthalmology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Judith A West-Mays
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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Conditional Deletion of AP-2β in the Periocular Mesenchyme of Mice Alters Corneal Epithelial Cell Fate and Stratification. Int J Mol Sci 2021; 22:ijms22168730. [PMID: 34445433 PMCID: PMC8395778 DOI: 10.3390/ijms22168730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/16/2022] Open
Abstract
The cornea is an anterior eye structure specialized for vision. The corneal endothelium and stroma are derived from the periocular mesenchyme (POM), which originates from neural crest cells (NCCs), while the stratified corneal epithelium develops from the surface ectoderm. Activating protein-2β (AP-2β) is highly expressed in the POM and important for anterior segment development. Using a mouse model in which AP-2β is conditionally deleted in the NCCs (AP-2β NCC KO), we investigated resulting corneal epithelial abnormalities. Through PAS and IHC staining, we observed structural and phenotypic changes to the epithelium associated with AP-2β deletion. In addition to failure of the mutant epithelium to stratify, we also observed that Keratin-12, a marker of the differentiated epithelium, was absent, and Keratin-15, a limbal and conjunctival marker, was expanded across the central epithelium. Transcription factors PAX6 and P63 were not observed to be differentially expressed between WT and mutant. However, growth factor BMP4 was suppressed in the mutant epithelium. Given the non-NCC origin of the epithelium, we hypothesize that the abnormalities in the AP-2β NCC KO mouse result from changes to regulatory signaling from the POM-derived stroma. Our findings suggest that stromal pathways such as Wnt/β-Catenin signaling may regulate BMP4 expression, which influences cell fate and stratification.
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Tong M, Yu X, Shao J, Shao Z, Li W, Lin W. Automated measuring method based on Machine learning for optomotor response in mice. Neurocomputing 2020. [DOI: 10.1016/j.neucom.2020.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chong RS, Busoy JMF, Tan B, Yeo SW, Lee YS, Barathi AV, Crowston JG, Schmetterer L. A Minimally Invasive Experimental Model of Acute Ocular Hypertension with Acute Angle Closure Characteristics. Transl Vis Sci Technol 2020; 9:24. [PMID: 32832230 PMCID: PMC7414621 DOI: 10.1167/tvst.9.7.24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 05/04/2020] [Indexed: 12/21/2022] Open
Abstract
Purpose To describe a minimally invasive experimental model of acute ocular hypertension (OHT) with characteristics of acute angle closure (AAC). Methods Adult C57/Bl6 mice (n = 31) were subjected to OHT in one eye using a modified circumlimbal suture technique that elevated intraocular pressure (IOP) for 30 minutes. Contralateral un-operated eyes served as controls. IOP, anterior segment optical coherence tomography, and fundus fluorescein angiography (FFA) were performed. The positive scotopic threshold response (pSTR) and a-wave and b-wave amplitudes were also evaluated. Retinal tissues were immunostained for the retinal ganglion cell (RGC) marker RBPMS and the glial marker GFAP. Results OHT eyes developed shallower anterior chambers and dilated pupils. FFA showed focal leakage in 32.2% of OHT eyes, but in none of the control eyes. pSTR was significantly reduced at week 1 in OHT eyes compared to control eyes (57.3 ± 7.2 µV vs. 106.9 ± 24.8 µV; P < 0.05), but a- and b-waves were unaffected. GFAP was upregulated in OHT eyes but not in control eyes or eyes that had been sutured without OHT. RGC density was reduced in OHT eyes after 4 weeks (3857 ± 143.8) vs. control eyes (4469 ± 176.0) (P < 0.05). Conclusions Our minimally invasive model resulted in acute OHT with characteristics of AAC in the absence of non-OHT-related neuroinflammatory changes arising from ocular injury alone. Translational Relevance This model provides a valuable approach to studying specific characteristics of a severe blinding disease in an experimental setting. Focal areas of ischemia were demonstrated, consistent with clinical studies of acute angle closure patients elsewhere, which may indicate the need for further research into how this could affect visual outcome in these patients.
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Affiliation(s)
- Rachel S Chong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Glaucoma Department, Singapore National Eye Centre, Singapore, Singapore.,Agency for Science, Technology and Research, Singapore, Singapore.,Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joanna M F Busoy
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Bingyao Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Sia Wey Yeo
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Ying Shi Lee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Amutha V Barathi
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jonathan G Crowston
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Leopold Schmetterer
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.,School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore.,Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria.,SERI-NTU Advanced Ocular Engineering (STANCE), Singapore, Singapore
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Akula M, Taiyab A, Deschamps P, Yee S, Ball AK, Williams T, West-Mays JA. AP-2β is required for formation of the murine trabecular meshwork and Schlemm's canal. Exp Eye Res 2020; 195:108042. [PMID: 32353428 DOI: 10.1016/j.exer.2020.108042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/02/2020] [Accepted: 04/22/2020] [Indexed: 12/21/2022]
Abstract
Previously, we have shown that Tfap2b, the gene encoding transcription factor AP-2β, is needed for normal mouse eye development. Specifically, targeted loss of Tfap2b in neural crest cells (NCCs)1 and their derivatives, particularly the periocular mesenchyme (POM), resulted in anterior segment defects affecting the cornea and angle tissue. These defects were further associated with an increase in intraocular pressure (IOP). The present study investigates the underlying changes in embryonic and postnatal POM cell development and differentiation caused by loss of AP-2β in the NCCs, particularly in the structures that control aqueous outflow, using Wnt1Cre+/-; Tfap2b-/lox; tdTomatolox/+ mice (AP-2β neural crest cell knockout or AP-2β NCC KO). Toluidine blue-stained sections and ultrathin sections stained with uranyl acetate and lead citrate were used to assess morphology and ultrastructure, respectively. Immunohistochemistry of KO and control eyes was performed at embryonic day (E) 15.5, E18.5, postnatal day (P) 1, P7 and P14 using phospho-histone H3 (PH3), α-smooth muscle actin (α-SMA), myocilin and endomucin antibodies, as well as a TUNEL assay. Conditional deletion of AP-2β in the NCC-derived POM resulted in defects that appeared during both embryogenesis and postnatal stages. Fate mapping of the knockout cells in the mutants revealed that the POM migrated appropriately into the eye during embryogenesis. However, during postnatal stages a significant reduction in POM proliferation in the angle region was observed in the mutants compared to controls. This was accompanied by a lack of expression of appropriate trabecular meshwork and Schlemm's canal markers. This is the first study to show that AP-2β is required for development and differentiation of the trabecular meshwork and Schlemm's canal. Together, these defects likely contributed to the elevated intraocular pressure (IOP) previously reported in the AP-2β NCC KO mice.
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Affiliation(s)
- Monica Akula
- McMaster University, Health Sciences Centre, 1280 Main St. W, L8S 4L8, Hamilton, ON, Canada
| | - Aftab Taiyab
- McMaster University, Health Sciences Centre, 1280 Main St. W, L8S 4L8, Hamilton, ON, Canada
| | - Paula Deschamps
- McMaster University, Health Sciences Centre, 1280 Main St. W, L8S 4L8, Hamilton, ON, Canada
| | - Shannin Yee
- McMaster University, Health Sciences Centre, 1280 Main St. W, L8S 4L8, Hamilton, ON, Canada
| | - Alexander K Ball
- McMaster University, Health Sciences Centre, 1280 Main St. W, L8S 4L8, Hamilton, ON, Canada
| | - Trevor Williams
- University of Colorado, Craniofacial Biology, Mail Stop 8120, RC1-S, Rm L18 111, 12801 E. 17th Ave, Aurora, CO, 80045, USA
| | - Judith A West-Mays
- McMaster University, Health Sciences Centre, 1280 Main St. W, L8S 4L8, Hamilton, ON, Canada.
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Akula M, Park JW, West-Mays JA. Relationship between neural crest cell specification and rare ocular diseases. J Neurosci Res 2018; 97:7-15. [PMID: 29660784 DOI: 10.1002/jnr.24245] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/15/2018] [Accepted: 03/21/2018] [Indexed: 02/06/2023]
Abstract
Development of the eye is closely associated with neural crest cell migration and specification. Eye development is extremely complex, as it requires the working of a combination of local factors, receptors, inductors, and signaling interactions between tissues such as the optic cup and periocular mesenchyme (POM). The POM is comprised of neural crest-derived mesenchymal progenitor cells that give rise to numerous important ocular structures including those tissues that form the optic cup and anterior segment of the eye. A number of genes are involved in the migration and specification of the POM such as PITX2, PITX3, FOXC1, FOXE3, PAX6, LMX1B, GPR48, TFAP2A, and TFAP2B. In this review, we will discuss the relevance of these genes in the development of the POM and how mutations and defects result in rare ocular diseases.
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Affiliation(s)
- Monica Akula
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jeong Won Park
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Judith A West-Mays
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
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