1
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Wang S, Tong S, Jin X, Li N, Dang P, Sui Y, Liu Y, Wang D. Single-cell RNA sequencing analysis of the retina under acute high intraocular pressure. Neural Regen Res 2024; 19:2522-2531. [PMID: 38526288 PMCID: PMC11090430 DOI: 10.4103/1673-5374.389363] [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: 05/24/2023] [Revised: 07/27/2023] [Accepted: 09/13/2023] [Indexed: 03/26/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202419110-00032/figure1/v/2024-03-08T184507Z/r/image-tiff High intraocular pressure causes retinal ganglion cell injury in primary and secondary glaucoma diseases, yet the molecular landscape characteristics of retinal cells under high intraocular pressure remain unknown. Rat models of acute hypertension ocular pressure were established by injection of cross-linked hyaluronic acid hydrogel (Healaflow®). Single-cell RNA sequencing was then used to describe the cellular composition and molecular profile of the retina following high intraocular pressure. Our results identified a total of 12 cell types, namely retinal pigment epithelial cells, rod-photoreceptor cells, bipolar cells, Müller cells, microglia, cone-photoreceptor cells, retinal ganglion cells, endothelial cells, retinal progenitor cells, oligodendrocytes, pericytes, and fibroblasts. The single-cell RNA sequencing analysis of the retina under acute high intraocular pressure revealed obvious changes in the proportions of various retinal cells, with ganglion cells decreased by 23%. Hematoxylin and eosin staining and TUNEL staining confirmed the damage to retinal ganglion cells under high intraocular pressure. We extracted data from retinal ganglion cells and analyzed the retinal ganglion cell cluster with the most distinct expression. We found upregulation of the B3gat2 gene, which is associated with neuronal migration and adhesion, and downregulation of the Tsc22d gene, which participates in inhibition of inflammation. This study is the first to reveal molecular changes and intercellular interactions in the retina under high intraocular pressure. These data contribute to understanding of the molecular mechanism of retinal injury induced by high intraocular pressure and will benefit the development of novel therapies.
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Affiliation(s)
- Shaojun Wang
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Siti Tong
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Xin Jin
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Na Li
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Pingxiu Dang
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Yang Sui
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Ying Liu
- Department of Ophthalmology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Dajiang Wang
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
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2
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Wu J, Wang C, Sun S, Ren T, Pan L, Liu H, Hou S, Wu S, Yan X, Zhang J, Zhao X, Liu W, Zhu S, Wei S, Zhang C, Jia X, Zhang Q, Yu Z, Zhuo Y, Zhao Q, Yang C, Wang N. Single-cell transcriptomic Atlas of aging macaque ocular outflow tissues. Protein Cell 2024; 15:594-611. [PMID: 38366188 PMCID: PMC11259549 DOI: 10.1093/procel/pwad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/24/2023] [Indexed: 02/18/2024] Open
Abstract
The progressive degradation in the trabecular meshwork (TM) is related to age-related ocular diseases like primary open-angle glaucoma. However, the molecular basis and biological significance of the aging process in TM have not been fully elucidated. Here, we established a dynamic single-cell transcriptomic landscape of aged macaque TM, wherein we classified the outflow tissue into 12 cell subtypes and identified mitochondrial dysfunction as a prominent feature of TM aging. Furthermore, we divided TM cells into 13 clusters and performed an in-depth analysis on cluster 0, which had the highest aging score and the most significant changes in cell proportions between the two groups. Ultimately, we found that the APOE gene was an important differentially expressed gene in cluster 0 during the aging process, highlighting the close relationship between cell migration and extracellular matrix regulation, and TM function. Our work further demonstrated that silencing the APOE gene could increase migration and reduce apoptosis by releasing the inhibition on the PI3K-AKT pathway and downregulating the expression of extracellular matrix components, thereby increasing the aqueous outflow rate and maintaining intraocular pressure within the normal range. Our work provides valuable insights for future clinical diagnosis and treatment of glaucoma.
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Affiliation(s)
- Jian Wu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Chaoye Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianmin Ren
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
| | - Lijie Pan
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
| | - Hongyi Liu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
| | - Simeng Hou
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
| | - Shen Wu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
| | - Xuejing Yan
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
| | - Jingxue Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
| | - Xiaofang Zhao
- Department of Neurosurgery, Peking University Third Hospital, Center for Precision Neurosurgery and Oncology of Peking University Health Science Center, Beijing 100191, China
| | - Weihai Liu
- Department of Neurosurgery, Peking University Third Hospital, Center for Precision Neurosurgery and Oncology of Peking University Health Science Center, Beijing 100191, China
| | - Sirui Zhu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
| | - Shuwen Wei
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
| | - Chi Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
| | - Xu Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Qi Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Ziyu Yu
- Spencer Center for Vision Research, Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Chenlong Yang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Department of Neurosurgery, Peking University Third Hospital, Center for Precision Neurosurgery and Oncology of Peking University Health Science Center, Beijing 100191, China
| | - Ningli Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
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3
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Yang GN, Sun YBY, Roberts PK, Moka H, Sung MK, Gardner-Russell J, El Wazan L, Toussaint B, Kumar S, Machin H, Dusting GJ, Parfitt GJ, Davidson K, Chong EW, Brown KD, Polo JM, Daniell M. Exploring single-cell RNA sequencing as a decision-making tool in the clinical management of Fuchs' endothelial corneal dystrophy. Prog Retin Eye Res 2024; 102:101286. [PMID: 38969166 DOI: 10.1016/j.preteyeres.2024.101286] [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: 01/17/2024] [Revised: 06/14/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has enabled the identification of novel gene signatures and cell heterogeneity in numerous tissues and diseases. Here we review the use of this technology for Fuchs' Endothelial Corneal Dystrophy (FECD). FECD is the most common indication for corneal endothelial transplantation worldwide. FECD is challenging to manage because it is genetically heterogenous, can be autosomal dominant or sporadic, and progress at different rates. Single-cell RNA sequencing has enabled the discovery of several FECD subtypes, each with associated gene signatures, and cell heterogeneity. Current FECD treatments are mainly surgical, with various Rho kinase (ROCK) inhibitors used to promote endothelial cell metabolism and proliferation following surgery. A range of emerging therapies for FECD including cell therapies, gene therapies, tissue engineered scaffolds, and pharmaceuticals are in preclinical and clinical trials. Unlike conventional disease management methods based on clinical presentations and family history, targeting FECD using scRNA-seq based precision-medicine has the potential to pinpoint the disease subtypes, mechanisms, stages, severities, and help clinicians in making the best decision for surgeries and the applications of therapeutics. In this review, we first discuss the feasibility and potential of using scRNA-seq in clinical diagnostics for FECD, highlight advances from the latest clinical treatments and emerging therapies for FECD, integrate scRNA-seq results and clinical notes from our FECD patients and discuss the potential of applying alternative therapies to manage these cases clinically.
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Affiliation(s)
- Gink N Yang
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Yu B Y Sun
- Department of Anatomy and Development Biology, Monash University, Clayton, Australia
| | - Philip Ke Roberts
- Department of Ophthalmology, Medical University Vienna, 18-20 Währinger Gürtel, Vienna, Austria
| | - Hothri Moka
- Mogrify Limited, 25 Cambridge Science Park Milton Road, Milton, Cambridge, UK
| | - Min K Sung
- Mogrify Limited, 25 Cambridge Science Park Milton Road, Milton, Cambridge, UK
| | - Jesse Gardner-Russell
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Layal El Wazan
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Bridget Toussaint
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Satheesh Kumar
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Heather Machin
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Lions Eye Donation Service, Level 7, Smorgon Family Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia
| | - Gregory J Dusting
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Geraint J Parfitt
- Mogrify Limited, 25 Cambridge Science Park Milton Road, Milton, Cambridge, UK
| | - Kathryn Davidson
- Department of Anatomy and Development Biology, Monash University, Clayton, Australia
| | - Elaine W Chong
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Department of Ophthalmology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Karl D Brown
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Jose M Polo
- Department of Anatomy and Development Biology, Monash University, Clayton, Australia
| | - Mark Daniell
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Lions Eye Donation Service, Level 7, Smorgon Family Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia.
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4
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Zhang X, Zhang F, Xu X. Single-cell RNA sequencing in exploring the pathogenesis of diabetic retinopathy. Clin Transl Med 2024; 14:e1751. [PMID: 38946005 PMCID: PMC11214886 DOI: 10.1002/ctm2.1751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 07/02/2024] Open
Abstract
Diabetic retinopathy (DR) is a leading cause of irreversible blindness in the working-age populations. Despite decades of research on the pathogenesis of DR for clinical care, a comprehensive understanding of the condition is still lacking due to the intricate cellular diversity and molecular heterogeneity involved. Single-cell RNA sequencing (scRNA-seq) has made the high-throughput molecular profiling of cells across modalities possible which has provided valuable insights into complex biological systems. In this review, we summarise the application of scRNA-seq in investigating the pathogenesis of DR, focusing on four aspects. These include the identification of differentially expressed genes, characterisation of key cell subpopulations and reconstruction of developmental 'trajectories' to unveil their state transition, exploration of complex cell‒cell communication in DR and integration of scRNA-seq with genome-wide association studies to identify cell types that are most closely related to DR risk genetic loci. Finally, we discuss the future challenges and expectations associated with studying DR using scRNA-seq. We anticipate that scRNA-seq will facilitate the discovery of mechanisms and new treatment targets in the clinical care landscape for patients with DR. KEY POINTS: Progress in scRNA-seq for diabetic retinopathy (DR) research includes studies on DR patients, non-human primates, and the prevalent mouse models. scRNA-seq facilitates the identification of differentially expressed genes, pivotal cell subpopulations, and complex cell-cell interactions in DR at single-cell level. Future scRNA-seq applications in DR should target specific patient subsets and integrate with single-cell and spatial multi-omics approaches.
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Affiliation(s)
- Xinzi Zhang
- National Clinical Research Center for Eye DiseasesDepartment of OphthalmologyShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Eye Institute of Shanghai Jiao Tong University SchoolShanghaiChina
- Shanghai Key Laboratory of Ocular Fundus DiseasesShanghaiChina
- Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye DiseasesShanghaiChina
| | - Fang Zhang
- National Clinical Research Center for Eye DiseasesDepartment of OphthalmologyShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Eye Institute of Shanghai Jiao Tong University SchoolShanghaiChina
- Shanghai Key Laboratory of Ocular Fundus DiseasesShanghaiChina
- Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye DiseasesShanghaiChina
| | - Xun Xu
- National Clinical Research Center for Eye DiseasesDepartment of OphthalmologyShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Eye Institute of Shanghai Jiao Tong University SchoolShanghaiChina
- Shanghai Key Laboratory of Ocular Fundus DiseasesShanghaiChina
- Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye DiseasesShanghaiChina
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5
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Xi G, Feng P, Zhang X, Wu S, Zhang J, Wang X, Xiang A, Xu W, Wang N, Zhu W. iPSC-derived cells stimulate ABCG2 +/NES + endogenous trabecular meshwork cell proliferation and tissue regeneration. Cell Prolif 2024; 57:e13611. [PMID: 38356373 PMCID: PMC11216930 DOI: 10.1111/cpr.13611] [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: 11/06/2023] [Revised: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
A major risk factor for glaucoma, the first leading cause of irreversible blindness worldwide, is the decellularisation of the trabecular meshwork (TM) in the conventional outflow pathway. Stem cell-based therapy, particularly the utilisation of induced pluripotent stem cells (iPSCs), presents an enticing potential for tissue regeneration and intraocular pressure (IOP) maintenance in glaucoma. We have previously observed that differentiated iPSCs can stimulate endogenous cell proliferation in the TM, a pivotal factor in TM regeneration and aqueous humour outflow restoration. In this study, we investigated the response of TM cells in vivo after interacting with iPSC-derived cells and identified two subpopulations responsible for this relatively long-term tissue regeneration: ATP Binding Cassette Subfamily G Member 2 (ABCG2)-positive cells and Nestin (NES)-positive cells. We further uncovered that alterations of these responsive cells are linked to ageing and different glaucoma etiologies, suggesting that ABCG2+ subpopulation decellularization could serve as a potential risk factor for TM decellularization in glaucoma. Taken together, our findings illustrated the proliferative subpopulations in the conventional outflow pathway when stimulated with iPSC-derived cells and defined them as TM precursors, which may be applied to develop novel therapeutic approaches for glaucoma.
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Affiliation(s)
- Gaiping Xi
- Department of Pharmacology, School of PharmacyQingdao UniversityQingdaoChina
| | - Pengchao Feng
- Department of Pharmacology, School of PharmacyQingdao UniversityQingdaoChina
| | - Xiaoyan Zhang
- Department of Pharmacology, School of PharmacyQingdao UniversityQingdaoChina
| | - Shen Wu
- Beijing Institute of OphthalmologyBeijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key LaboratoryBeijingChina
- Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain DisordersCapital Medical UniversityBeijingChina
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical ApplicationCapital Medical UniversityBeijingChina
| | - Jingxue Zhang
- Beijing Institute of OphthalmologyBeijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key LaboratoryBeijingChina
- Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain DisordersCapital Medical UniversityBeijingChina
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical ApplicationCapital Medical UniversityBeijingChina
| | - Xiangji Wang
- Department of Pharmacology, School of PharmacyQingdao UniversityQingdaoChina
| | - Ailing Xiang
- Qingdao Xikai Biotechnology Co., LtdQingdaoChina
| | - Wenhua Xu
- Department of InspectionQingdao UniversityQingdaoChina
| | - Ningli Wang
- Beijing Institute of OphthalmologyBeijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key LaboratoryBeijingChina
- Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain DisordersCapital Medical UniversityBeijingChina
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical ApplicationCapital Medical UniversityBeijingChina
- Advanced Innovation Center for Big Data‐Based Precision MedicineBeijing University of Aeronautics and Astronautics‐Capital Medical UniversityBeijingChina
| | - Wei Zhu
- Department of Pharmacology, School of PharmacyQingdao UniversityQingdaoChina
- Advanced Innovation Center for Big Data‐Based Precision MedicineBeijing University of Aeronautics and Astronautics‐Capital Medical UniversityBeijingChina
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6
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Lotfollahi M, Yuhan Hao, Theis FJ, Satija R. The future of rapid and automated single-cell data analysis using reference mapping. Cell 2024; 187:2343-2358. [PMID: 38729109 PMCID: PMC11184658 DOI: 10.1016/j.cell.2024.03.009] [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: 01/05/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 05/12/2024]
Abstract
As the number of single-cell datasets continues to grow rapidly, workflows that map new data to well-curated reference atlases offer enormous promise for the biological community. In this perspective, we discuss key computational challenges and opportunities for single-cell reference-mapping algorithms. We discuss how mapping algorithms will enable the integration of diverse datasets across disease states, molecular modalities, genetic perturbations, and diverse species and will eventually replace manual and laborious unsupervised clustering pipelines.
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Affiliation(s)
- Mohammad Lotfollahi
- Institute of Computational Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA; New York Genome Center, New York, NY, USA
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Mathematics, Technical University of Munich, Garching, Germany.
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY, USA; New York Genome Center, New York, NY, USA.
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7
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Bou Ghanem GO, Wareham LK, Calkins DJ. Addressing neurodegeneration in glaucoma: Mechanisms, challenges, and treatments. Prog Retin Eye Res 2024; 100:101261. [PMID: 38527623 DOI: 10.1016/j.preteyeres.2024.101261] [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: 12/28/2023] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 03/27/2024]
Abstract
Glaucoma is the leading cause of irreversible blindness globally. The disease causes vision loss due to neurodegeneration of the retinal ganglion cell (RGC) projection to the brain through the optic nerve. Glaucoma is associated with sensitivity to intraocular pressure (IOP). Thus, mainstay treatments seek to manage IOP, though many patients continue to lose vision. To address neurodegeneration directly, numerous preclinical studies seek to develop protective or reparative therapies that act independently of IOP. These include growth factors, compounds targeting metabolism, anti-inflammatory and antioxidant agents, and neuromodulators. Despite success in experimental models, many of these approaches fail to translate into clinical benefits. Several factors contribute to this challenge. Firstly, the anatomic structure of the optic nerve head differs between rodents, nonhuman primates, and humans. Additionally, animal models do not replicate the complex glaucoma pathophysiology in humans. Therefore, to enhance the success of translating these findings, we propose two approaches. First, thorough evaluation of experimental targets in multiple animal models, including nonhuman primates, should precede clinical trials. Second, we advocate for combination therapy, which involves using multiple agents simultaneously, especially in the early and potentially reversible stages of the disease. These strategies aim to increase the chances of successful neuroprotective treatment for glaucoma.
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Affiliation(s)
- Ghazi O Bou Ghanem
- Vanderbilt Eye Institute, Department of Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Lauren K Wareham
- Vanderbilt Eye Institute, Department of Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - David J Calkins
- Vanderbilt Eye Institute, Department of Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.
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8
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Tian A, Baidouri H, Kim S, Li J, Cheng X, Li Y, Chen R, Raghunathan V. To be or not to be - Decoding the Trabecular Meshwork Cell Identity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591346. [PMID: 38746421 PMCID: PMC11092480 DOI: 10.1101/2024.04.26.591346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The trabecular meshwork within the conventional outflow apparatus is critical in maintaining intraocular pressure homeostasis. In vitro studies employing primary cell cultures of the human trabecular meshwork (hTM) have conventionally served as surrogates for investigating the pathobiology of TM dysfunction. Despite its abundant use, translation of outcomes from in vitro studies to ex vivo and/or in vivo studies remains a challenge. Given the cell heterogeneity, performing single-cell RNA sequencing comparing primary hTM cell cultures to hTM tissue may provide important insights on cellular identity and translatability, as such an approach has not been reported before. In this study, we assembled a total of 14 primary hTM in vitro samples across passages 1-4, including 4 samples from individuals diagnosed with glaucoma. This dataset offers a comprehensive transcriptomic resource of primary hTM in vitro scRNA-seq data to study global changes in gene expression in comparison to cells in tissue in situ. We have performed extensive preprocessing and quality control, allowing the research community to access and utilize this public resource.
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Affiliation(s)
- Alice Tian
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hasna Baidouri
- University of Houston, College of Optomtery, Houston, TX, 77204, USA
| | - Sangbae Kim
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jin Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xuesen Cheng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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9
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Greatbatch CJ, Lu Q, Hung S, Barnett AJ, Wing K, Liang H, Han X, Zhou T, Siggs OM, Mackey DA, Cook AL, Senabouth A, Liu GS, Craig JE, MacGregor S, Powell JE, Hewitt AW. High throughput functional profiling of genes at intraocular pressure loci reveals distinct networks for glaucoma. Hum Mol Genet 2024; 33:739-751. [PMID: 38272457 PMCID: PMC11031357 DOI: 10.1093/hmg/ddae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/18/2023] [Accepted: 04/06/2024] [Indexed: 01/27/2024] Open
Abstract
INTRODUCTION Primary open angle glaucoma (POAG) is a leading cause of blindness globally. Characterized by progressive retinal ganglion cell degeneration, the precise pathogenesis remains unknown. Genome-wide association studies (GWAS) have uncovered many genetic variants associated with elevated intraocular pressure (IOP), one of the key risk factors for POAG. We aimed to identify genetic and morphological variation that can be attributed to trabecular meshwork cell (TMC) dysfunction and raised IOP in POAG. METHODS 62 genes across 55 loci were knocked-out in a primary human TMC line. Each knockout group, including five non-targeting control groups, underwent single-cell RNA-sequencing (scRNA-seq) for differentially-expressed gene (DEG) analysis. Multiplexed fluorescence coupled with CellProfiler image analysis allowed for single-cell morphological profiling. RESULTS Many gene knockouts invoked DEGs relating to matrix metalloproteinases and interferon-induced proteins. We have prioritized genes at four loci of interest to identify gene knockouts that may contribute to the pathogenesis of POAG, including ANGPTL2, LMX1B, CAV1, and KREMEN1. Three genetic networks of gene knockouts with similar transcriptomic profiles were identified, suggesting a synergistic function in trabecular meshwork cell physiology. TEK knockout caused significant upregulation of nuclear granularity on morphological analysis, while knockout of TRIOBP, TMCO1 and PLEKHA7 increased granularity and intensity of actin and the cell-membrane. CONCLUSION High-throughput analysis of cellular structure and function through multiplex fluorescent single-cell analysis and scRNA-seq assays enabled the direct study of genetic perturbations at the single-cell resolution. This work provides a framework for investigating the role of genes in the pathogenesis of glaucoma and heterogenous diseases with a strong genetic basis.
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Affiliation(s)
- Connor J Greatbatch
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Qinyi Lu
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Sandy Hung
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, 32 Gisborne St, East Melbourne 3002, Australia
| | - Alexander J Barnett
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Kristof Wing
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Helena Liang
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, 32 Gisborne St, East Melbourne 3002, Australia
| | - Xikun Han
- QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane 4006, Australia
| | - Tiger Zhou
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, 1 Flinders Dr, Bedford Park, South Australia 5042, Australia
| | - Owen M Siggs
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, Short Street, St George Hospital KOGARAH UNSW, Sydney 2217, Australia
| | - David A Mackey
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
- Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, 2 Verdun Street Nedlands WA 6009, Australia
| | - Anthony L Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Anne Senabouth
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, 1 Flinders Dr, Bedford Park, South Australia 5042, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane 4006, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, 32 Gisborne St, East Melbourne 3002, Australia
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10
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Pan Y, Iwata T. Exploring the Genetic Landscape of Childhood Glaucoma. CHILDREN (BASEL, SWITZERLAND) 2024; 11:454. [PMID: 38671671 PMCID: PMC11048810 DOI: 10.3390/children11040454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024]
Abstract
Childhood glaucoma, a significant cause of global blindness, represents a heterogeneous group of disorders categorized into primary or secondary forms. Primary childhood glaucoma stands as the most prevalent subtype, comprising primary congenital glaucoma (PCG) and juvenile open-angle glaucoma (JOAG). Presently, multiple genes are implicated in inherited forms of primary childhood glaucoma. This comprehensive review delves into genetic investigations into primary childhood glaucoma, with a focus on identifying causative genes, understanding their inheritance patterns, exploring essential biological pathways in disease pathogenesis, and utilizing animal models to study these mechanisms. Specifically, attention is directed towards genes such as CYP1B1 (cytochrome P450 family 1 subfamily B member 1), LTBP2 (latent transforming growth factor beta binding protein 2), TEK (TEK receptor tyrosine kinase), ANGPT1 (angiopoietin 1), and FOXC1 (forkhead box C1), all associated with PCG; and MYOC (myocilin), associated with JOAG. Through exploring these genetic factors, this review aims to deepen our understanding of the intricate pathogenesis of primary childhood glaucoma, thereby facilitating the development of enhanced diagnostic and therapeutic strategies.
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Affiliation(s)
| | - Takeshi Iwata
- National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo 152-8902, Japan;
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11
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Ikegami K. Circadian rhythm of intraocular pressure. J Physiol Sci 2024; 74:14. [PMID: 38431563 PMCID: PMC10908160 DOI: 10.1186/s12576-024-00905-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/04/2024] [Indexed: 03/05/2024]
Abstract
Intraocular pressure (IOP) plays a crucial role in glaucoma development, involving the dynamics of aqueous humor (AH). AH flows in from the ciliary body and exits through the trabecular meshwork (TM). IOP follows a circadian rhythm synchronized with the suprachiasmatic nucleus (SCN), the circadian pacemaker. The SCN resets peripheral clocks through sympathetic nerves or adrenal glucocorticoids (GCs). IOP's circadian rhythm is governed by circadian time signals, sympathetic noradrenaline (NE), and GCs, rather than the local clock. The activity of Na+/K+-ATPase in non-pigmented epithelial cells in the ciliary body can influence the nocturnal increase in IOP by enhancing AH inflow. Conversely, NE, not GCs, can regulate the IOP rhythm by suppressing TM macrophage phagocytosis and AH outflow. The activation of the β1-adrenergic receptor (AR)-mediated EPAC-SHIP1 signal through the ablation of phosphatidylinositol triphosphate may govern phagocytic cup formation. These findings could offer insights for better glaucoma management, such as chronotherapy.
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Affiliation(s)
- Keisuke Ikegami
- Laboratory of Regulation in Metabolism and Behavior, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka, 819-0395, Japan.
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12
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Xiao Y, McGhee CNJ, Zhang J. Adult stem cells in the eye: Identification, characterisation, and therapeutic application in ocular regeneration - A review. Clin Exp Ophthalmol 2024; 52:148-166. [PMID: 38214071 DOI: 10.1111/ceo.14309] [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: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 01/13/2024]
Abstract
Adult stem cells, present in various parts of the human body, are undifferentiated cells that can proliferate and differentiate to replace dying cells within tissues. Stem cells have specifically been identified in the cornea, trabecular meshwork, crystalline lens, iris, ciliary body, retina, choroid, sclera, conjunctiva, eyelid, lacrimal gland, and orbital fat. The identification of ocular stem cells broadens the potential therapeutic strategies for untreatable eye diseases. Currently, stem cell transplantation for corneal and conjunctival diseases remains the most common stem cell-based therapy in ocular clinical management. Lens epithelial stem cells have been applied in the treatment of paediatric cataracts. Several early-phase clinical trials for corneal and retinal regeneration using ocular stem cells are also underway. Extensive preclinical studies using ocular stem cells have been conducted, showing encouraging outcomes. Ocular stem cells currently demonstrate great promise in potential treatments of eye diseases. In this review, we focus on the identification, characterisation, and therapeutic application of adult stem cells in the eye.
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Affiliation(s)
- Yuting Xiao
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Charles N J McGhee
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Jie Zhang
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
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13
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Jing L, Liu K, Wang F, Su Y. Role of mechanically-sensitive cation channels Piezo1 and TRPV4 in trabecular meshwork cell mechanotransduction. Hum Cell 2024; 37:394-407. [PMID: 38316716 DOI: 10.1007/s13577-024-01035-4] [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: 12/05/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Glaucoma is one of the leading causes of irreversible blindness in developed countries, and intraocular pressure (IOP) is primary and only treatable risk factor, suggesting that to a significant extent, glaucoma is a disease of IOP disorder and pathological mechanotransduction. IOP-lowering ways are limited to decreaseing aqueous humour (AH) production or increasing the uveoscleral outflow pathway. Still, therapeutic approaches have been lacking to control IOP by enhancing the trabecular meshwork (TM) pathway. Trabecular meshwork cells (TMCs) have endothelial and myofibroblast properties and are responsible for the renewal of the extracellular matrix (ECM). Mechanosensitive cation channels, including Piezo1 and TRPV4, are abundantly expressed in primary TMCs and trigger mechanostress-dependent ECM and cytoskeletal remodelling. However, prolonged mechanical stimulation severely affects cellular biosynthesis through TMC mechanotransduction, including signaling, gene expression, ECM remodelling, and cytoskeletal structural changes, involving outflow facilities and elevating IOP. As for the functional coupling relationship between Piezo1 and TRPV4 channels, inspired by VECs and osteoblasts, we hypothesized that Piezo1 may also act upstream of TRPV4 in glaucomatous TM tissue, mediating the activation of TRPV4 via Ca2+ inflow or Ca2+ binding to phospholipase A2(PLA2), and thus be involved in increasing TM outflow resistance and elevated IOP. Therefore, this review aims to help identify new potential targets for IOP stabilization in ocular hypertension and primary open-angle glaucoma by understanding the mechanical transduction mechanisms associated with the development of glaucoma and may provide ideas into novel treatments for preventing the progression of glaucoma by targeting mechanotransduction.
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Affiliation(s)
- Lingling Jing
- Department of Ophthalmology, The Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Kexin Liu
- Department of Ophthalmology, The Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Feng Wang
- Department of Ophthalmology, The Fourth Affiliated Hospital, Harbin Medical University, Harbin, China.
| | - Ying Su
- Eye Hospital, The First Affiliated Hospital, Harbin Medical University, Harbin, China.
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14
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Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J. Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. Nat Methods 2024:10.1038/s41592-024-02191-z. [PMID: 38366243 DOI: 10.1038/s41592-024-02191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint analysis of cross-species datasets to homologous genes. Here we present SATURN, a deep learning method for learning universal cell embeddings that encodes genes' biological properties using protein language models. By coupling protein embeddings from language models with RNA expression, SATURN integrates datasets profiled from different species regardless of their genomic similarity. SATURN can detect functionally related genes coexpressed across species, redefining differential expression for cross-species analysis. Applying SATURN to three species whole-organism atlases and frog and zebrafish embryogenesis datasets, we show that SATURN can effectively transfer annotations across species, even when they are evolutionarily remote. We also demonstrate that SATURN can be used to find potentially divergent gene functions between glaucoma-associated genes in humans and four other species.
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Affiliation(s)
- Yanay Rosen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Maria Brbić
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Yusuf Roohani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kyle Swanson
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziang Li
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA.
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15
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Mah JL, Dunn CW. Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data. Nat Ecol Evol 2024; 8:325-338. [PMID: 38182680 DOI: 10.1038/s41559-023-02281-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/16/2023] [Indexed: 01/07/2024]
Abstract
The origin and evolution of cell types has emerged as a key topic in evolutionary biology. Driven by rapidly accumulating single-cell datasets, recent attempts to infer cell type evolution have largely been limited to pairwise comparisons because we lack approaches to build cell phylogenies using model-based approaches. Here we approach the challenges of applying explicit phylogenetic methods to single-cell data by using principal components as phylogenetic characters. We infer a cell phylogeny from a large, comparative single-cell dataset of eye cells from five distantly related mammals. Robust cell type clades enable us to provide a phylogenetic, rather than phenetic, definition of cell type, allowing us to forgo marker genes and phylogenetically classify cells by topology. We further observe evolutionary relationships between diverse vessel endothelia and identify the myelinating and non-myelinating Schwann cells as sister cell types. Finally, we examine principal component loadings and describe the gene expression dynamics underlying the function and identity of cell type clades that have been conserved across the five species. A cell phylogeny provides a rigorous framework towards investigating the evolutionary history of cells and will be critical to interpret comparative single-cell datasets that aim to ask fundamental evolutionary questions.
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Affiliation(s)
- Jasmine L Mah
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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16
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Balasubramanian R, Kizhatil K, Li T, Tolman N, Bhandari A, Clark G, Bupp-Chickering V, Kelly RA, Zhou S, Peregrin J, Simón M, Montgomery C, Stamer WD, Qian J, John SWM. Transcriptomic profiling of Schlemm's canal cells reveals a lymphatic-biased identity and three major cell states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.31.555823. [PMID: 37886472 PMCID: PMC10602040 DOI: 10.1101/2023.08.31.555823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Schlemm's canal (SC) is central in intraocular pressure regulation but requires much characterization. It has distinct inner and outer walls, each composed of Schlemm's canal endothelial cells (SECs) with different morphologies and functions. Recent transcriptomic studies of the anterior segment added important knowledge, but were limited in power by SEC numbers or did not focus on SC. To gain a more comprehensive understanding of SC biology, we performed bulk RNA sequencing on C57BL/6J SC, blood vessel, and lymphatic endothelial cells from limbal tissue (~4500 SECs). We also analyzed mouse limbal tissues by single-cell and single-nucleus RNA sequencing (C57BL/6J and 129/Sj strains), successfully sequencing 903 individual SECs. Together, these datasets confirm that SC has molecular characteristics of both blood and lymphatic endothelia with a lymphatic phenotype predominating. SECs are enriched in pathways that regulate cell-cell junction formation pointing to the importance of junctions in determining SC fluid permeability. Importantly, and for the first time, our analyses characterize 3 molecular classes of SECs, molecularly distinguishing inner wall from outer wall SECs and discovering two inner wall cell states that likely result from local environmental differences. Further, and based on ligand and receptor expression patterns, we document key interactions between SECs and cells of the adjacent trabecular meshwork (TM) drainage tissue. Also, we present cell type expression for a collection of human glaucoma genes. These data provide a new molecular foundation that will enable the functional dissection of key homeostatic processes mediated by SECs as well as the development of new glaucoma therapeutics.
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Affiliation(s)
| | | | - Taibo Li
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD
| | - Nicholas Tolman
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA
| | - Aakriti Bhandari
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY
- Neuroscience Graduate Program, University of Utah, Salt Lake City, UT
| | | | | | - Ruth A Kelly
- Department of Ophthalmology, Duke University, NC
| | - Sally Zhou
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY
- SUNY Downstate Health Sciences University, New York, NY
| | - John Peregrin
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY
| | - Marina Simón
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY
| | - Christa Montgomery
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY
| | | | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Simon W M John
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY
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17
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Hamel AR, Yan W, Rouhana JM, Monovarfeshani A, Jiang X, Mehta PA, Advani J, Luo Y, Liang Q, Rajasundaram S, Shrivastava A, Duchinski K, Mantena S, Wang J, van Zyl T, Pasquale LR, Swaroop A, Gharahkhani P, Khawaja AP, MacGregor S, Chen R, Vitart V, Sanes JR, Wiggs JL, Segrè AV. Integrating genetic regulation and single-cell expression with GWAS prioritizes causal genes and cell types for glaucoma. Nat Commun 2024; 15:396. [PMID: 38195602 PMCID: PMC10776627 DOI: 10.1038/s41467-023-44380-y] [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: 05/11/2022] [Accepted: 12/12/2023] [Indexed: 01/11/2024] Open
Abstract
Primary open-angle glaucoma (POAG), characterized by retinal ganglion cell death, is a leading cause of irreversible blindness worldwide. However, its molecular and cellular causes are not well understood. Elevated intraocular pressure (IOP) is a major risk factor, but many patients have normal IOP. Colocalization and Mendelian randomization analysis of >240 POAG and IOP genome-wide association study (GWAS) loci and overlapping expression and splicing quantitative trait loci (e/sQTLs) in 49 GTEx tissues and retina prioritizes causal genes for 60% of loci. These genes are enriched in pathways implicated in extracellular matrix organization, cell adhesion, and vascular development. Analysis of single-nucleus RNA-seq of glaucoma-relevant eye tissues reveals that the POAG and IOP colocalizing genes and genome-wide associations are enriched in specific cell types in the aqueous outflow pathways, retina, optic nerve head, peripapillary sclera, and choroid. This study nominates IOP-dependent and independent regulatory mechanisms, genes, and cell types that may contribute to POAG pathogenesis.
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Affiliation(s)
- Andrew R Hamel
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Wenjun Yan
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - John M Rouhana
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aboozar Monovarfeshani
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Xinyi Jiang
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Puja A Mehta
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MA, USA
| | - Yuyang Luo
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Qingnan Liang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Skanda Rajasundaram
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Centre for Evidence-Based Medicine, University of Oxford, Oxford, UK
- Faculty of Medicine, Imperial College London, London, UK
| | - Arushi Shrivastava
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Katherine Duchinski
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics (BIG) PhD Program, Harvard Medical School, Boston, MA, USA
| | - Sreekar Mantena
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
| | - Jiali Wang
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Tavé van Zyl
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Ophthalmology and Visual Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MA, USA
| | - Puya Gharahkhani
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4029, Australia
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4029, Australia
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Janey L Wiggs
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ayellet V Segrè
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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18
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Wu J, Lin C, Yang C, Pan L, Liu H, Zhu S, Wei S, Jia X, Zhang Q, Yu Z, Zhao X, Liu W, Zhuo Y, Wang N. Identification and validation of key biomarkers and potential therapeutic targets for primary open-angle glaucoma. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2837-2850. [PMID: 37610681 DOI: 10.1007/s11427-022-2344-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/06/2023] [Indexed: 08/24/2023]
Abstract
Primary open-angle glaucoma (POAG) is a prevalent cause of blindness worldwide, resulting in degeneration of retinal ganglion cells and permanent damage to the optic nerve. However, the underlying pathogenetic mechanisms of POAG are currently indistinct, and there has been no effective nonsurgical treatment regimen. The objective of this study is to identify novel biomarkers and potential therapeutic targets for POAG. The mRNA expression microarray datasets GSE27276 and GSE138125, as well as the single-cell high-throughput RNA sequencing (scRNA-seq) dataset GSE148371 were utilized to screen POAG-related differentially expressed genes (DEGs). Functional enrichment analyses, protein-protein interaction (PPI) analysis, and weighted gene co-expression network analysis (WGCNA) of the DEGs were performed. Subsequently, the hub genes were validated at a single-cell level, where trabecular cells were annotated, and the mRNA expression levels of target genes in different cell clusters were analyzed. Immunofluorescence and quantitative real-time PCR (qPCR) were performed for further validation. DEGs analysis identified 43 downregulated and 32 upregulated genes in POAG, which were mainly enriched in immune-related pathways, oxidative stress, and endoplasmic reticulum (ER) stress. PPI networks showed that FN1 and DUSP1 were the central hub nodes, while GPX3 and VAV3 were screened out as hub genes through WGCNA and subsequently validated by qPCR. Finally, FN1, GPX3, and VAV3 were determined to be pivotal core genes via single-cell validation. The relevant biomarkers involved in the pathogenesis of POAG, may serve as potential therapeutic targets. Further studies are necessary to unveil the mechanisms underlying the expression variations of these genes in POAG.
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Affiliation(s)
- Jian Wu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing, 100730, China
| | - Caixia Lin
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Chenlong Yang
- Department of Neurosurgery, Peking University Third Hospital, Center for Precision Neurosurgery and Oncology of Peking University Health Science Center, Beijing, 100191, China
- North America Medical Education Foundation, Union City, CA, 94539, USA
| | - Lijie Pan
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing, 100730, China
| | - Hongyi Liu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing, 100730, China
| | - Sirui Zhu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing, 100730, China
| | - Shuwen Wei
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing, 100730, China
| | - Xu Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Qi Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Ziyu Yu
- Spencer Center for Vision Research, Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, CA, 94304, USA
| | - Xiaofang Zhao
- Department of Neurosurgery, Peking University Third Hospital, Center for Precision Neurosurgery and Oncology of Peking University Health Science Center, Beijing, 100191, China
| | - Weihai Liu
- Department of Neurosurgery, Peking University Third Hospital, Center for Precision Neurosurgery and Oncology of Peking University Health Science Center, Beijing, 100191, China
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
| | - Ningli Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing, 100730, China.
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19
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Rajasundaram S, Zebardast N, Mehta P, Khawaja AP, Warwick A, Duchinski K, Burgess S, Gill D, Segrè AV, Wiggs J. TIE1 and TEK signalling, intraocular pressure, and primary open-angle glaucoma: a Mendelian randomization study. J Transl Med 2023; 21:847. [PMID: 37996923 PMCID: PMC10668387 DOI: 10.1186/s12967-023-04737-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND In primary open-angle glaucoma (POAG), lowering intraocular pressure (IOP) is the only proven way of slowing vision loss. Schlemm's canal (SC) is a hybrid vascular and lymphatic vessel that mediates aqueous humour drainage from the anterior ocular chamber. Animal studies support the importance of SC endothelial angiopoietin-TEK signalling, and more recently TIE1 signalling, in maintaining normal IOP. However, human genetic support for a causal role of TIE1 and TEK signalling in lowering IOP is currently lacking. METHODS GWAS summary statistics were obtained for plasma soluble TIE1 (sTIE1) protein levels (N = 35,559), soluble TEK (sTEK) protein levels (N = 35,559), IOP (N = 139,555) and POAG (Ncases = 16,677, Ncontrols = 199,580). Mendelian randomization (MR) was performed to estimate the association of genetically proxied TIE1 and TEK protein levels with IOP and POAG liability. Where significant MR estimates were obtained, genetic colocalization was performed to assess the probability of a shared causal variant (PPshared) versus distinct (PPdistinct) causal variants underlying TIE1/TEK signalling and the outcome. Publicly available single-nucleus RNA-sequencing data were leveraged to investigate differential expression of TIE1 and TEK in the human ocular anterior segment. RESULTS Increased genetically proxied TIE1 signalling and TEK signalling associated with a reduction in IOP (- 0.21 mmHg per SD increase in sTIE1, 95% CI = - 0.09 to - 0.33 mmHg, P = 6.57 × 10-4, and - 0.14 mmHg per SD decrease in sTEK, 95% CI = - 0.03 to - 0.25 mmHg, P = 0.011), but not with POAG liability. Colocalization analysis found that the probability of a shared causal variant was greater for TIE1 and IOP than for TEK and IOP (PPshared/(PPdistinct + PPshared) = 0.98 for TIE1 and 0.30 for TEK). In the anterior segment, TIE1 and TEK were preferentially expressed in SC, lymphatic, and vascular endothelium. CONCLUSIONS This study provides novel human genetic support for a causal role of both TIE1 and TEK signalling in regulating IOP. Here, combined evidence from cis-MR and colocalization analyses provide stronger support for TIE1 than TEK as a potential IOP-lowering therapeutic target.
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Affiliation(s)
- Skanda Rajasundaram
- Faculty of Medicine, Imperial College London, London, UK.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
| | - Nazlee Zebardast
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Boston, MA, USA
| | - Puja Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
- UCL Institute of Cardiovascular Science, London, UK
| | | | - Alasdair Warwick
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Katherine Duchinski
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Ayellet V Segrè
- Faculty of Medicine, Imperial College London, London, UK
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Boston, MA, USA
| | - Janey Wiggs
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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20
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Jia X, Wu J, Chen X, Hou S, Li Y, Zhao L, Zhu Y, Li Z, Deng C, Su W, Zhuo Y. Cell atlas of trabecular meshwork in glaucomatous non-human primates and DEGs related to tissue contract based on single-cell transcriptomics. iScience 2023; 26:108024. [PMID: 37867950 PMCID: PMC10589847 DOI: 10.1016/j.isci.2023.108024] [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: 11/03/2022] [Revised: 05/22/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023] Open
Abstract
As the major channel of aqueous humor outflow, dysfunction of trabecular meshwork (TM) can lead to intraocular pressure elevating, which can trigger primary open-angle glaucoma (POAG). In this study, we use single-cell RNA sequencing (scRNA-seq) technique to build an atlas and further explore the spontaneous POAG and healthy macaques cellular heterogeneity associated with the dysfunction of TM contraction. We built the TM atlas, which identified 14 different cell types. In Beam A, Beam B, Beam C, and smooth muscle cell (SMC) cell types, we first found multiple genes associated with TM contraction (e.g., TPM1, ACTC1, TNNT1), determining their differential expression in the POAG and healthy groups. In addition, the microstructural alterations in TM of POAG non-human primates were observed, which was compact and collapsed. Thus, our study indicated that TPM1 may be a key target for regulating TM structure, contraction function, and resistance of aqueous humor outflow.
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Affiliation(s)
- Xu Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
- The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Jian Wu
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Xiaohong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Simeng Hou
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Yangyang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Ling Zhao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Yingting Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Zhidong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Caibin Deng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Wenru Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
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21
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Passaro ML, Matarazzo F, Abbadessa G, Pezone A, Porcellini A, Tranfa F, Rinaldi M, Costagliola C. Glaucoma as a Tauopathy-Is It the Missing Piece in the Glaucoma Puzzle? J Clin Med 2023; 12:6900. [PMID: 37959365 PMCID: PMC10650423 DOI: 10.3390/jcm12216900] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Glaucoma is a chronic neurodegenerative disorder affecting the visual system which can result in vision loss and blindness. The pathogenetic mechanisms underlying glaucomatous optic neuropathy are ultimately enigmatic, prompting ongoing investigations into its potential shared pathogenesis with other neurodegenerative neurological disorders. Tauopathies represent a subclass of neurodegenerative diseases characterized by the abnormal deposition of tau protein within the brain and consequent microtubule destabilization. The extended spectrum of tauopathies includes conditions such as frontotemporal dementias, progressive supranuclear palsy, chronic traumatic encephalopathy, and Alzheimer's disease. Notably, recent decades have witnessed emerging documentation of tau inclusion among glaucoma patients, providing substantiation that this ocular disease may similarly manifest features of tauopathies. These studies found that: (i) aggregated tau inclusions are present in the somatodendritic compartment of RGCs in glaucoma patients; (ii) the etiology of the disease may affect tau splicing, phosphorylation, oligomerization, and subcellular localization; and (iii) short interfering RNA against tau, administered intraocularly, significantly decreased retinal tau accumulation and enhanced RGC somas and axon survival, demonstrating a crucial role for tau modifications in ocular hypertension-induced neuronal injury. Here, we examine the most recent evidence surrounding the interplay between tau protein dysregulation and glaucomatous neurodegeneration. We explore the novel perspective of glaucoma as a tau-associated disorder and open avenues for cross-disciplinary collaboration and new treatment strategies.
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Affiliation(s)
- Maria Laura Passaro
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (M.L.P.); (F.T.); (C.C.)
| | | | - Gianmarco Abbadessa
- Division of Neurology, Department of Advanced Medical and Surgical Sciences, University of Campania Luigi Vanvitelli, 80138 Naples, Italy;
| | - Antonio Pezone
- Department of Biology, University of Naples “Federico II”, 80126 Naples, Italy; (A.P.); (A.P.)
| | - Antonio Porcellini
- Department of Biology, University of Naples “Federico II”, 80126 Naples, Italy; (A.P.); (A.P.)
| | - Fausto Tranfa
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (M.L.P.); (F.T.); (C.C.)
| | - Michele Rinaldi
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (M.L.P.); (F.T.); (C.C.)
| | - Ciro Costagliola
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (M.L.P.); (F.T.); (C.C.)
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22
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Ahsanuddin S, Wu AY. Single-cell transcriptomics of the ocular anterior segment: a comprehensive review. Eye (Lond) 2023; 37:3334-3350. [PMID: 37138096 PMCID: PMC10156079 DOI: 10.1038/s41433-023-02539-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/07/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Elucidating the cellular and genetic composition of ocular tissues is essential for uncovering the pathophysiology of ocular diseases. Since the introduction of single-cell RNA sequencing (scRNA-seq) in 2009, vision researchers have performed extensive single-cell analyses to better understand transcriptome complexity and heterogeneity of ocular structures. This technology has revolutionized our ability to identify rare cell populations and to make cross-species comparisons of gene expression in both steady state and disease conditions. Importantly, single-cell transcriptomic analyses have enabled the identification of cell-type specific gene markers and signalling pathways between ocular cell populations. While most scRNA-seq studies have been conducted on retinal tissues, large-scale transcriptomic atlases pertaining to the ocular anterior segment have also been constructed in the past three years. This timely review provides vision researchers with an overview of scRNA-seq experimental design, technical limitations, and clinical applications in a variety of anterior segment-related ocular pathologies. We review open-access anterior segment-related scRNA-seq datasets and illustrate how scRNA-seq can be an indispensable tool for the development of targeted therapeutics.
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Affiliation(s)
- Sofia Ahsanuddin
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Ophthalmology, New York Eye and Ear Infirmary of Mount Sinai, New York City, NY, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Albert Y Wu
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Stanford, CA, USA.
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23
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Zhu Y, Garcia-Sanchez J, Dalal R, Sun Y, Kapiloff MS, Goldberg JL, Liu WW. Differential expression of PIEZO1 and PIEZO2 mechanosensitive channels in ocular tissues implicates diverse functional roles. Exp Eye Res 2023; 236:109675. [PMID: 37820892 PMCID: PMC10843266 DOI: 10.1016/j.exer.2023.109675] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/08/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023]
Abstract
PIEZO1 and PIEZO2 are mechanosensitive ion channels that regulate many important physiological processes including vascular blood flow, touch, and proprioception. As the eye is subject to mechanical stress and is highly perfused, these channels may play important roles in ocular function and intraocular pressure regulation. PIEZO channel expression in the eye has not been well defined, in part due to difficulties in validating available antibodies against PIEZO1 and PIEZO2 in ocular tissues. It is also unclear if PIEZO1 and PIEZO2 are differentially expressed. To address these questions, we used single-molecule fluorescence in situ hybridization (smFISH) together with transgenic reporter mice expressing PIEZO fusion proteins under the control of their endogenous promoters to compare the expression and localization of PIEZO1 and PIEZO2 in mouse ocular tissues relevant to glaucoma. We detected both PIEZO1 and PIEZO2 expression in the trabecular meshwork, ciliary body, and in the ganglion cell layer (GCL) of the retina. Piezo1 mRNA was more abundantly expressed than Piezo2 mRNA in these ocular tissues. Piezo1 but not Piezo2 mRNA was detected in the inner nuclear layer and outer nuclear layer of the retina. Our results suggest that PIEZO1 and PIEZO2 are differentially expressed and may have distinct roles as mechanosensors in glaucoma-relevant ocular tissues.
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Affiliation(s)
- Ying Zhu
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Julian Garcia-Sanchez
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Roopa Dalal
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Yang Sun
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Michael S Kapiloff
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Jeffrey L Goldberg
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Wendy W Liu
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA.
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24
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Wolf J, Rasmussen DK, Sun YJ, Vu JT, Wang E, Espinosa C, Bigini F, Chang RT, Montague AA, Tang PH, Mruthyunjaya P, Aghaeepour N, Dufour A, Bassuk AG, Mahajan VB. Liquid-biopsy proteomics combined with AI identifies cellular drivers of eye aging and disease in vivo. Cell 2023; 186:4868-4884.e12. [PMID: 37863056 PMCID: PMC10720485 DOI: 10.1016/j.cell.2023.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/26/2023] [Accepted: 09/13/2023] [Indexed: 10/22/2023]
Abstract
Single-cell analysis in living humans is essential for understanding disease mechanisms, but it is impractical in non-regenerative organs, such as the eye and brain, because tissue biopsies would cause serious damage. We resolve this problem by integrating proteomics of liquid biopsies with single-cell transcriptomics from all known ocular cell types to trace the cellular origin of 5,953 proteins detected in the aqueous humor. We identified hundreds of cell-specific protein markers, including for individual retinal cell types. Surprisingly, our results reveal that retinal degeneration occurs in Parkinson's disease, and the cells driving diabetic retinopathy switch with disease stage. Finally, we developed artificial intelligence (AI) models to assess individual cellular aging and found that many eye diseases not associated with chronological age undergo accelerated molecular aging of disease-specific cell types. Our approach, which can be applied to other organ systems, has the potential to transform molecular diagnostics and prognostics while uncovering new cellular disease and aging mechanisms.
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Affiliation(s)
- Julian Wolf
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Ditte K Rasmussen
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA; Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Young Joo Sun
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Jennifer T Vu
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Elena Wang
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Fabio Bigini
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Robert T Chang
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Artis A Montague
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Peter H Tang
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; Retina Consultants of Minnesota, Edina, MN 55435, USA
| | - Prithvi Mruthyunjaya
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Antoine Dufour
- Departments of Physiology and Pharmacology & Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Alexander G Bassuk
- Departments of Pediatrics and Neurology, The Iowa Neuroscience Institute (INI), University of Iowa, Iowa City, IA 52242, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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25
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Faralli JA, Filla MS, Peters DM. Role of integrins in the development of fibrosis in the trabecular meshwork. FRONTIERS IN OPHTHALMOLOGY 2023; 3:1274797. [PMID: 38983065 PMCID: PMC11182094 DOI: 10.3389/fopht.2023.1274797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/09/2023] [Indexed: 07/11/2024]
Abstract
Primary open angle glaucoma (POAG) is a progressive and chronic disease exhibiting many of the features of fibrosis. The extracellular matrix (ECM) in the trabecular meshwork (TM) undergoes extensive remodeling and enhanced rigidity, resembling fibrotic changes. In addition, there are changes associated with myofibroblast activation and cell contractility that further drives tissue fibrosis and stiffening. This review discusses what is known about the integrins in the TM and their involvement in fibrotic processes.
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Affiliation(s)
- Jennifer A Faralli
- Department of Pathology & Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Mark S Filla
- Department of Pathology & Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Donna M Peters
- Department of Pathology & Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
- Department of Ophthalmology & Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
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26
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Dobrzycka M, Sulewska A, Biecek P, Charkiewicz R, Karabowicz P, Charkiewicz A, Golaszewska K, Milewska P, Michalska-Falkowska A, Nowak K, Niklinski J, Konopińska J. miRNA Studies in Glaucoma: A Comprehensive Review of Current Knowledge and Future Perspectives. Int J Mol Sci 2023; 24:14699. [PMID: 37834147 PMCID: PMC10572595 DOI: 10.3390/ijms241914699] [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: 09/05/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Glaucoma, a neurodegenerative disorder that leads to irreversible blindness, remains a challenge because of its complex nature. MicroRNAs (miRNAs) are crucial regulators of gene expression and are associated with glaucoma and other diseases. We aimed to review and discuss the advantages and disadvantages of miRNA-focused molecular studies in glaucoma through discussing their potential as biomarkers for early detection and diagnosis; offering insights into molecular pathways and mechanisms; and discussing their potential utility with respect to personalized medicine, their therapeutic potential, and non-invasive monitoring. Limitations, such as variability, small sample sizes, sample specificity, and limited accessibility to ocular tissues, are also addressed, underscoring the need for robust protocols and collaboration. Reproducibility and validation are crucial to establish the credibility of miRNA research findings, and the integration of bioinformatics tools for miRNA database creation is a valuable component of a comprehensive approach to investigate miRNA aberrations in patients with glaucoma. Overall, miRNA research in glaucoma has provided significant insights into the molecular mechanisms of the disease, offering potential biomarkers, diagnostic tools, and therapeutic targets. However, addressing challenges such as variability and limited tissue accessibility is essential, and further investigations and validation will contribute to a deeper understanding of the functional significance of miRNAs in glaucoma.
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Affiliation(s)
- Margarita Dobrzycka
- Department of Ophthalmology, Medical University of Bialystok, 15-276 Bialystok, Poland; (M.D.); (K.G.)
| | - Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (A.C.); (J.N.)
| | - Przemyslaw Biecek
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland;
| | - Radoslaw Charkiewicz
- Center of Experimental Medicine, Medical University of Bialystok, 15-369 Bialystok, Poland;
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (A.M.-F.)
| | - Piotr Karabowicz
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (A.M.-F.)
| | - Angelika Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (A.C.); (J.N.)
| | - Kinga Golaszewska
- Department of Ophthalmology, Medical University of Bialystok, 15-276 Bialystok, Poland; (M.D.); (K.G.)
| | - Patrycja Milewska
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (A.M.-F.)
| | | | - Karolina Nowak
- Department of Obstetrics and Gynecology, C.S. Mott Center for Human Growth and Development, School of Medicine, Wayne State University, Detroit, MI 48201, USA;
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (A.C.); (J.N.)
| | - Joanna Konopińska
- Department of Ophthalmology, Medical University of Bialystok, 15-276 Bialystok, Poland; (M.D.); (K.G.)
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27
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Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J. Towards Universal Cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.526939. [PMID: 36778387 PMCID: PMC9915700 DOI: 10.1101/2023.02.03.526939] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, inter-species genomic differences limit the joint analysis of cross-species datasets to homologous genes. Here, we present SATURN, a deep learning method for learning universal cell embeddings that encodes genes' biological properties using protein language models. By coupling protein embeddings from language models with RNA expression, SATURN integrates datasets profiled from different species regardless of their genomic similarity. SATURN has a unique ability to detect functionally related genes co-expressed across species, redefining differential expression for cross-species analysis. We apply SATURN to three species whole-organism atlases and frog and zebrafish embryogenesis datasets. We show that cell embeddings learnt in SATURN can be effectively used to transfer annotations across species and identify both homologous and species-specific cell types, even across evolutionarily remote species. Finally, we use SATURN to reannotate the five species Cell Atlas of Human Trabecular Meshwork and Aqueous Outflow Structures and find evidence of potentially divergent functions between glaucoma associated genes in humans and other species.
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Affiliation(s)
- Yanay Rosen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Maria Brbić
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Yusuf Roohani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kyle Swanson
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziang Li
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA
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Zhang Y, Ma Y, Liu Q, Du Y, Peng L, Zhou J, Zhao Z, Li C, Wang S. Single-cell transcriptome sequencing reveals tumor heterogeneity in family neuroblastoma. Front Immunol 2023; 14:1197773. [PMID: 37790931 PMCID: PMC10543897 DOI: 10.3389/fimmu.2023.1197773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/01/2023] [Indexed: 10/05/2023] Open
Abstract
Neuroblastoma(NB) is the most common extracranial solid tumor in childhood, and it is now believed that some patients with NB have an underlying genetic susceptibility, which may be one of the reasons for the multiplicity of NB patients within a family line. Even within the same family, the samples show great variation and can present as ganglioneuroblastoma or even benign ganglioneuroma. The genomics of NB is still unclear and more in-depth studies are needed to reveal its key components. We first performed single-cell RNA sequencing(sc-RNAseq) analysis on clinical specimens of two family neuroblastoma(FNB) and four sporadic NB cases. A complete transcriptional profile of FNB was constructed from 18,394 cells from FNB, and we found that SDHD may be genetically associated with FNB and identified a prognostic related CAF subtype in FNB: Fib-4. Single-cell flux estimation analysis (scFEA) results showed that malignant cells were associated with arginine spermine, oxaloacetate and hypoxanthine, and that malignant cells metabolize lactate at lower levels than T cells. Our study provides new resources and ideas for the development of the genomics of family NB, and the mechanisms of cell-to-cell interactions and communication and the metabolic landscape will provide new therapeutic targets.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shan Wang
- Department of Pediatric Surgical Oncology Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
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Kizhatil K, Clark G, Sunderland D, Bhandari A, Horbal L, Balasubramanian R, John S. FYN regulates aqueous humor outflow and IOP through the phosphorylation of VE-cadherin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.04.556253. [PMID: 37886565 PMCID: PMC10602025 DOI: 10.1101/2023.09.04.556253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The exact sites and molecules that determine resistance to aqueous humor drainage and control intraocular pressure (IOP) need further elaboration. Proposed sites include the inner wall of Schlemms's canal and the juxtacanalicular trabecular meshwork ocular drainage tissues. The adherens junctions (AJs) of Schlemm's canal endothelial cells (SECs) must both preserve the blood-aqueous humor (AQH) barrier and be conducive to AQH drainage. How homeostatic control of AJ permeability in SC occurs and how such control impacts IOP is unclear. We hypothesized that mechano-responsive phosphorylation of the junctional molecule VE-CADHERIN (VEC) by SRC family kinases (SFKs) regulates the permeability of SEC AJs. We tested this by clamping IOP at either 16 mmHg, 25 mmHg, or 45 mmHg in mice and then measuring AJ permeability and VEC phosphorylation. We found that with increasing IOP: 1) SEC AJ permeability increased, 2) VEC phosphorylation was increased at tyrosine-658, and 3) SFKs were activated at the AJ. Among the two SFKs known to phosphorylate VEC, FYN, but not SRC, localizes to the SC. Furthermore, FYN mutant mice had decreased phosphorylation of VEC at SEC AJs, dysregulated IOP, and reduced AQH outflow. Together, our data demonstrate that increased IOP activates FYN in the inner wall of SC, leading to increased phosphorylation of AJ VEC and, thus, decreased resistance to AQH outflow. These findings support a crucial role of mechanotransduction signaling in IOP homeostasis within SC in response to IOP. These data strongly suggest that the inner wall of SC partially contributes to outflow resistance.
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Madadi Y, Monavarfeshani A, Chen H, Stamer WD, Williams RW, Yousefi S. Artificial Intelligence Models for Cell Type and Subtype Identification Based on Single-Cell RNA Sequencing Data in Vision Science. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2837-2852. [PMID: 37294649 PMCID: PMC10631573 DOI: 10.1109/tcbb.2023.3284795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) provides a high throughput, quantitative and unbiased framework for scientists in many research fields to identify and characterize cell types within heterogeneous cell populations from various tissues. However, scRNA-seq based identification of discrete cell-types is still labor intensive and depends on prior molecular knowledge. Artificial intelligence has provided faster, more accurate, and user-friendly approaches for cell-type identification. In this review, we discuss recent advances in cell-type identification methods using artificial intelligence techniques based on single-cell and single-nucleus RNA sequencing data in vision science. The main purpose of this review paper is to assist vision scientists not only to select suitable datasets for their problems, but also to be aware of the appropriate computational tools to perform their analysis. Developing novel methods for scRNA-seq data analysis remains to be addressed in future studies.
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Swamy VS, Batz ZA, McGaughey DM. PLAE Web App Enables Powerful Searching and Multiple Visualizations Across One Million Unified Single-Cell Ocular Transcriptomes. Transl Vis Sci Technol 2023; 12:18. [PMID: 37747415 PMCID: PMC10578359 DOI: 10.1167/tvst.12.9.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 07/02/2023] [Indexed: 09/26/2023] Open
Abstract
Purpose To create a high-performance reactive web application to query single-cell gene expression data across cell type, species, study, and other factors. Methods We updated the content and structure of the underlying data (single cell Eye in a Disk [scEiaD]) and wrote the web application PLAE (https://plae.nei.nih.gov) to visualize and explore the data. Results The new portal provides quick visualization of over a million individual cells from vertebrate eye and body transcriptomes encompassing four species, 60 cell types, six ocular tissues, and 23 body tissues across 35 publications. To demonstrate the value of this unified pan-eye dataset, we replicated known neurogenic and cone macula markers in addition to proposing six new cone human region markers. Conclusions The PLAE web application offers the eye community a powerful and quick means to test hypotheses related to gene expression across a highly diverse, community-derived database. Translational Relevance The PLAE resource enables any researcher or clinician to study and research gene expression patterning across a wide variety of curated ocular cell types with a responsive web app.
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Affiliation(s)
- Vinay S Swamy
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Zachary A Batz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - David M McGaughey
- Bioinformatics Group, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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Raghunathan V, Nartey A, Dhamodaran K, Baidouri H, Staverosky JA, Keller KE, Zientek K, Reddy A, Acott T, Vranka JA. Characterization of extracellular matrix deposited by segmental trabecular meshwork cells. Exp Eye Res 2023; 234:109605. [PMID: 37506755 PMCID: PMC11104015 DOI: 10.1016/j.exer.2023.109605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/14/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
PURPOSE Biophysical and biochemical attributes of the extracellular matrix are major determinants of cell fate in homeostasis and disease. Ocular hypertension and glaucoma are diseases where the trabecular meshwork tissue responsible for aqueous humor egress becomes stiffer accompanied by changes in its matrisome in a segmental manner with regions of high or low flow. Prior studies demonstrate these alterations in the matrix are dynamic in response to age and pressure changes. The underlying reason for segmentation or differential response to pressure and stiffening are unknown. This is largely due to a lack of appropriate models (in vitro or ex vivo) to study this phenomena. METHODS Primary trabecular meshwork cells were isolated from segmental flow regions, and cells were cultured for 4 weeks in the presence or absence or dexamethasone to obtain cell derived matrices (CDM). The biomechanical attributes of the CDM, composition of the matrisome, and incidence of crosslinks were determined by atomic force microscopy and mass spectrometry. RESULTS Data demonstrate that matrix deposited by cells from low flow regions are stiffer and exhibit a greater number of immature and mature crosslinks, and that these are exacerbated in the presence of steroid. We also show a differential response of high or low flow cells to steroid via changes observed in the matrix composition. However, no correlations were observed between elastic moduli and presence or absence of mature and immature crosslinks in the CDMs. CONCLUSION Regardless of a direct correlation between matrix stiffness and crosslinks, we observed distinct differences in the composition and mechanics of the matrices deposited by segmental flow cells. These results suggest distinct differences in cellular identify and likely a basis for mechanical memory post isolation and culture. Nevertheless, we conclude that although a mechanistic basis for matrix stiffness was undetermined in this study, it is a viable tool to study cell-matrix interactions and further our understanding of trabecular meshwork pathobiology.
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Affiliation(s)
| | - Andrews Nartey
- Department of Basic Sciences, College of Optometry, University of Houston, Houston, TX, USA
| | - Kamesh Dhamodaran
- Department of Basic Sciences, College of Optometry, University of Houston, Houston, TX, USA
| | - Hasna Baidouri
- Department of Basic Sciences, College of Optometry, University of Houston, Houston, TX, USA
| | | | - Kate E Keller
- Ophthalmology and Visual Sciences, Casey Eye Institute, USA
| | - Keith Zientek
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Ashok Reddy
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Ted Acott
- Ophthalmology and Visual Sciences, Casey Eye Institute, USA
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Ujiie N, Norden PR, Fang R, Beckmann L, Cai Z, Kweon J, Liu T, Tan C, Kuhn MS, Stamer WD, Aoto K, Quaggin SE, Zhang HF, Kume T. Differential roles of FOXC2 in the trabecular meshwork and Schlemm's canal in glaucomatous pathology. Life Sci Alliance 2023; 6:e202201721. [PMID: 37414529 PMCID: PMC10326420 DOI: 10.26508/lsa.202201721] [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: 09/12/2022] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
Impaired development and maintenance of Schlemm's canal (SC) are associated with perturbed aqueous humor outflow and intraocular pressure. The angiopoietin (ANGPT)/TIE2 signaling pathway regulates SC development and maintenance, whereas the molecular mechanisms of crosstalk between SC and the neural crest (NC)-derived neighboring tissue, the trabecular meshwork (TM), are poorly understood. Here, we show NC-specific forkhead box (Fox)c2 deletion in mice results in impaired SC morphogenesis, loss of SC identity, and elevated intraocular pressure. Visible-light optical coherence tomography analysis further demonstrated functional impairment of the SC in response to changes in intraocular pressure in NC-Foxc2 -/- mice, suggesting altered TM biomechanics. Single-cell RNA-sequencing analysis identified that this phenotype is predominately characterized by transcriptional changes associated with extracellular matrix organization and stiffness in TM cell clusters, including increased matrix metalloproteinase expression, which can cleave the TIE2 ectodomain to produce soluble TIE2. Moreover, endothelial-specific Foxc2 deletion impaired SC morphogenesis because of reduced TIE2 expression, which was rescued by deleting the TIE2 phosphatase VE-PTP. Thus, Foxc2 is critical in maintaining SC identity and morphogenesis via TM-SC crosstalk.
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Affiliation(s)
- Naoto Ujiie
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Pieter R Norden
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Raymond Fang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Lisa Beckmann
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Zhen Cai
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Junghun Kweon
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Ting Liu
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Can Tan
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Megan S Kuhn
- Duke Eye Center, Duke University, Durham, NC, USA
| | | | - Kazushi Aoto
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Susan E Quaggin
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Department of Ophthalmology, Northwestern University, Chicago, IL, USA
| | - Tsutomu Kume
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Ophthalmology, Northwestern University, Chicago, IL, USA
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Yam GHF, Pi S, Du Y, Mehta JS. Posterior corneoscleral limbus: Architecture, stem cells, and clinical implications. Prog Retin Eye Res 2023; 96:101192. [PMID: 37392960 DOI: 10.1016/j.preteyeres.2023.101192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/03/2023]
Abstract
The limbus is a transition from the cornea to conjunctiva and sclera. In human eyes, this thin strip has a rich variation of tissue structures and composition, typifying a change from scleral irregularity and opacity to corneal regularity and transparency; a variation from richly vascularized conjunctiva and sclera to avascular cornea; the neural passage and drainage of aqueous humor. The limbal stroma is enriched with circular fibres running parallel to the corneal circumference, giving its unique role in absorbing small pressure changes to maintain corneal curvature and refractivity. It contains specific niches housing different types of stem cells for the corneal epithelium, stromal keratocytes, corneal endothelium, and trabecular meshwork. This truly reflects the important roles of the limbus in ocular physiology, and the limbal functionality is crucial for corneal health and the entire visual system. Since the anterior limbus containing epithelial structures and limbal epithelial stem cells has been extensively reviewed, this article is focused on the posterior limbus. We have discussed the structural organization and cellular components of the region beneath the limbal epithelium, the characteristics of stem cell types: namely corneal stromal stem cells, endothelial progenitors and trabecular meshwork stem cells, and recent advances leading to the emergence of potential cell therapy options to replenish their respective mature cell types and to correct defects causing corneal abnormalities. We have reviewed different clinical disorders associated with defects of the posterior limbus and summarized the available preclinical and clinical evidence about the developing topic of cell-based therapy for corneal disorders.
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Affiliation(s)
- Gary Hin-Fai Yam
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore; McGowan Institute for Regenerative Medicine, Pittsburgh, PA, USA.
| | - Shaohua Pi
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yiqin Du
- Department of Ophthalmology, University of South Florida, Tampa, FL, USA
| | - Jodhbir S Mehta
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore; Department of Cornea and External Eye Disease, Singapore National Eye Centre, Singapore; Ophthalmology and Visual Sciences Academic Clinical Program, Duke-National University of Singapore (NUS) Medical School, Singapore.
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Wang X, Wang M, Liu H, Mercieca K, Prinz J, Feng Y, Prokosch V. The Association between Vascular Abnormalities and Glaucoma-What Comes First? Int J Mol Sci 2023; 24:13211. [PMID: 37686017 PMCID: PMC10487550 DOI: 10.3390/ijms241713211] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Glaucoma is a leading cause of irreversible blindness worldwide. While intraocular pressure (IOP) presents a major risk factor, the underlying pathophysiology still remains largely unclear. The correlation between vascular abnormalities and glaucoma has been deliberated for decades. Evidence for a role played by vascular factors in the pathogenesis of glaucomatous neurodegeneration has already been postulated. In addition, the fact that glaucoma causes both structural and functional changes to retinal blood vessels has been described. This review aims to investigate the published evidence concerning the relationship between vascular abnormalities and glaucoma, and to provide an overview of the "chicken or egg" dilemma in glaucoma. In this study, several biomarkers of glaucoma progression from a vascular perspective, including endothelin-1 (ET-1), nitric oxide, vascular endothelial growth factor (VEGF), and matrix metalloproteinases (MMPs), were identified and subsequently assessed for their potential as pharmacological intervention targets.
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Affiliation(s)
- Xiaosha Wang
- Department of Ophthalmology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; (X.W.); (M.W.); (H.L.); (J.P.); (Y.F.)
| | - Maoren Wang
- Department of Ophthalmology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; (X.W.); (M.W.); (H.L.); (J.P.); (Y.F.)
- Department of Ophthalmology, University Medical Center, Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Hanhan Liu
- Department of Ophthalmology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; (X.W.); (M.W.); (H.L.); (J.P.); (Y.F.)
| | - Karl Mercieca
- Glaucoma Section, University Hospital Eye Clinic, 53127 Bonn, Germany;
- Faculty of Biology, Medicine and Health, School of Health Sciences, University of Manchester, Manchester M13 9WH, UK
| | - Julia Prinz
- Department of Ophthalmology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; (X.W.); (M.W.); (H.L.); (J.P.); (Y.F.)
- Department of Ophthalmology, RWTH Aachen University, 52074 Aachen, Germany
| | - Yuan Feng
- Department of Ophthalmology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; (X.W.); (M.W.); (H.L.); (J.P.); (Y.F.)
| | - Verena Prokosch
- Department of Ophthalmology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; (X.W.); (M.W.); (H.L.); (J.P.); (Y.F.)
- Department of Ophthalmology, University Medical Center, Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
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Monavarfeshani A, Yan W, Pappas C, Odenigbo KA, He Z, Segrè AV, van Zyl T, Hageman GS, Sanes JR. Transcriptomic analysis of the ocular posterior segment completes a cell atlas of the human eye. Proc Natl Acad Sci U S A 2023; 120:e2306153120. [PMID: 37566633 PMCID: PMC10450437 DOI: 10.1073/pnas.2306153120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/29/2023] [Indexed: 08/13/2023] Open
Abstract
Although the visual system extends through the brain, most vision loss originates from defects in the eye. Its central element is the neural retina, which senses light, processes visual signals, and transmits them to the rest of the brain through the optic nerve (ON). Surrounding the retina are numerous other structures, conventionally divided into anterior and posterior segments. Here, we used high-throughput single-nucleus RNA sequencing (snRNA-seq) to classify and characterize cells in six extraretinal components of the posterior segment: ON, optic nerve head (ONH), peripheral sclera, peripapillary sclera (PPS), choroid, and retinal pigment epithelium (RPE). Defects in each of these tissues are associated with blinding diseases-for example, glaucoma (ONH and PPS), optic neuritis (ON), retinitis pigmentosa (RPE), and age-related macular degeneration (RPE and choroid). From ~151,000 single nuclei, we identified 37 transcriptomically distinct cell types, including multiple types of astrocytes, oligodendrocytes, fibroblasts, and vascular endothelial cells. Our analyses revealed a differential distribution of many cell types among distinct structures. Together with our previous analyses of the anterior segment and retina, the data presented here complete a "Version 1" cell atlas of the human eye. We used this atlas to map the expression of >180 genes associated with the risk of developing glaucoma, which is known to involve ocular tissues in both anterior and posterior segments as well as the neural retina. Similar methods can be used to investigate numerous additional ocular diseases, many of which are currently untreatable.
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Affiliation(s)
- Aboozar Monavarfeshani
- Center for Brain Science, Harvard University, Cambridge, MA02138
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA02115
| | - Wenjun Yan
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
| | - Christian Pappas
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT84132
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT84132
| | - Kenechukwu A. Odenigbo
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA02115
| | - Ayellet V. Segrè
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA02114
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA02142
| | - Tavé van Zyl
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA02114
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT065101
| | - Gregory S. Hageman
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT84132
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT84132
| | - Joshua R. Sanes
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
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Tan JK, Xiao Y, Liu G, Huang LX, Ma WH, Xia Y, Wang XZ, Zhu XJ, Cai SP, Wu XB, Wang Y, Liu XY. Evaluation of trabecular meshwork-specific promoters in vitro and in vivo using scAAV2 vectors expressing C3 transferase. Int J Ophthalmol 2023; 16:1196-1209. [PMID: 37602341 PMCID: PMC10398517 DOI: 10.18240/ijo.2023.08.03] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/14/2023] [Indexed: 08/22/2023] Open
Abstract
AIM To evaluate the potential of two trabecular meshwork (TM)-specific promoters, Chitinase 3-like 1 (Ch3L1) and matrix gla protein (MGP), for improving specificity and safety in glaucoma gene therapy based on self-complementary AAV2 (scAAV2) vector technologies. METHODS An scAAV2 vector with C3 transferase (C3) as the reporter gene (scAAV2-C3) was selected. The scAAV2-C3 vectors were driven by Ch3L1 (scAAV2-Ch3L1-C3), MGP (scAAV2-MGP-C3), enhanced MGP (scAAV2-eMGP-C3) and cytomegalovirus (scAAV2-CMV-C3), respectively. The cultured primary human TM cells were treated with each vector at different multiplicities of infections. Changes in cell morphology were observed by phase contrast microscopy. Actin stress fibers and Rho GTPases/Rho-associated protein kinase pathway-related molecules were assessed by immunofluorescence staining, real-time quantitative polymerase chain reaction and Western blot. Each vector was injected intracamerally into the one eye of each rat at low and high doses respectively. In vivo green fluorescence was visualized by a Micron III Retinal Imaging Microscope. Intraocular pressure (IOP) was monitored using a rebound tonometer. Ocular responses were evaluated by slit-lamp microscopy. Ocular histopathology analysis was examined by hematoxylin and eosin staining. RESULTS In TM cell culture studies, the vector-mediated C3 expression induced morphologic changes, disruption of actin cytoskeleton and reduction of fibronectin expression in TM cells by inhibiting the Rho GTPases/Rho-associated protein kinase signaling pathway. At the same dose, these changes were significant in TM cells treated with scAAV2-CMV-C3 or scAAV2-Ch3L1-C3, but not in cells treated with scAAV2-eMGP-C3 or scAAV2-MGP-C3. At low-injected dose, the IOP was significantly decreased in the scAAV2-Ch3L1-C3-injected eyes but not in scAAV2-MGP-C3-injected and scAAV2-eMGP-C3-injected eyes. At high-injected dose, significant IOP reduction was observed in the scAAV2-eMGP-C3-injected eyes but not in scAAV2-MGP-C3-injected eyes. Similar to scAAV2-CMV-C3, scAAV2-Ch3L1-C3 vector showed efficient transduction both in the TM and corneal endothelium. In anterior segment tissues of scAAV2-eMGP-C3-injected eyes, no obvious morphological changes were found except for the TM. Inflammation was absent. CONCLUSION In scAAV2-transduced TM cells, the promoter-driven efficiency of Ch3L1 is close to that of cytomegalovirus, but obviously higher than that of MGP. In the anterior chamber of rat eye, the transgene expression pattern of scAAV2 vector is presumably affected by MGP promoter, but not by Ch3L1 promoter. These findings would provide a useful reference for improvement of specificity and safety in glaucoma gene therapy using scAAV2 vector.
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Affiliation(s)
- Jun-Kai Tan
- Xiamen Eye Center, Xiamen University, Xiamen 361004, Fujian Province, China
| | - Ying Xiao
- Department of Pathology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610032, Sichuan Province, China
| | - Guo Liu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan Province, China
| | - Long-Xiang Huang
- The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, Fujian Province, China
| | - Wen-Hao Ma
- Beijing FivePlus Molecular Medicine Institute Co., Ltd., Beijing 102600, China
| | - Yan Xia
- Beijing FivePlus Molecular Medicine Institute Co., Ltd., Beijing 102600, China
| | - Xi-Zhen Wang
- Shenzhen Key Laboratory of Ophthalmology, Shenzhen Eye Hospital, School of Optometry, Jinan University, Shenzhen 518040, Guangdong Province, China
| | - Xian-Jun Zhu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan Province, China
| | - Su-Ping Cai
- Shenzhen Key Laboratory of Ophthalmology, Shenzhen Eye Hospital, School of Optometry, Jinan University, Shenzhen 518040, Guangdong Province, China
| | - Xiao-Bing Wu
- Beijing FivePlus Molecular Medicine Institute Co., Ltd., Beijing 102600, China
| | - Yun Wang
- Shenzhen Key Laboratory of Ophthalmology, Shenzhen Eye Hospital, School of Optometry, Jinan University, Shenzhen 518040, Guangdong Province, China
| | - Xu-Yang Liu
- Xiamen Eye Center, Xiamen University, Xiamen 361004, Fujian Province, China
- Department of Ophthalmology, Shenzhen People's Hospital, the 2 Clinical Medical College, Jinan University, Shenzhen 518020, Guangdong Province, China
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38
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Cousins HC, Cousins CC, Valluru G, Altman RB, Liu Y, Pasquale LR, Ahmad S. Genetic Correlations Among Corneal Biophysical Parameters and Anthropometric Traits. Transl Vis Sci Technol 2023; 12:8. [PMID: 37561511 PMCID: PMC10424803 DOI: 10.1167/tvst.12.8.8] [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: 01/25/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023] Open
Abstract
Purpose The genetic architecture of corneal dysfunction remains poorly understood. Epidemiological and clinical evidence suggests a relationship between corneal structural features and anthropometric measures. We used global and local genetic similarity analysis to identify genomic features that may underlie structural corneal dysfunction. Methods We assembled genome-wide association study summary statistics for corneal features (central corneal thickness, corneal hysteresis [CH], corneal resistance factor [CRF], and the 3 mm index of keratometry) and anthropometric traits (body mass index, weight, and height) in Europeans. We calculated global genetic correlations (rg) between traits using linkage disequilibrium (LD) score regression and local genetic covariance using ρ-HESS, which partitions the genome and performs regression with LD regions. Finally, we identified genes located within regions of significant genetic covariance and analyzed patterns of tissue expression and pathway enrichment. Results Global LD score regression revealed significant negative correlations between height and both CH (rg = -0.12; P = 2.0 × 10-7) and CRF (rg = -0.11; P = 6.9 × 10-7). Local analysis revealed 68 genomic regions exhibiting significant local genetic covariance between CRF and height, containing 2874 unique genes. Pathway analysis of genes in regions with significant local rg revealed enrichment among signaling pathways with known keratoconus associations, including cadherin and Wnt signaling, as well as enrichment of genes modulated by copper and zinc ions. Conclusions Corneal biophysical parameters and height share a common genomic architecture, which may facilitate identification of disease-associated genes and therapies for corneal ectasias. Translational Relevance Local genetic covariance analysis enables the identification of associated genes and therapeutic targets for corneal ectatic disease.
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Affiliation(s)
- Henry C. Cousins
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Clara C. Cousins
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Girish Valluru
- Department of Ophthalmology, New York Eye and Ear Infirmary of Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Russ B. Altman
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA
| | - Louis R. Pasquale
- Department of Ophthalmology, New York Eye and Ear Infirmary of Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sumayya Ahmad
- Department of Ophthalmology, New York Eye and Ear Infirmary of Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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39
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Aboobakar IF, Collantes ERA, Hauser MA, Stamer WD, Wiggs JL. Rare protective variants and glaucoma-relevant cell stressors modulate Angiopoietin-like 7 expression. Hum Mol Genet 2023; 32:2523-2531. [PMID: 37220876 PMCID: PMC10360392 DOI: 10.1093/hmg/ddad083] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/25/2023] Open
Abstract
Rare missense and nonsense variants in the Angiopoietin-like 7 (ANGPTL7) gene confer protection from primary open-angle glaucoma (POAG), though the functional mechanism remains uncharacterized. Interestingly, a larger variant effect size strongly correlates with in silico predictions of increased protein instability (r = -0.98), suggesting that protective variants lower ANGPTL7 protein levels. Here, we show that missense and nonsense variants cause aggregation of mutant ANGPTL7 protein in the endoplasmic reticulum (ER) and decreased levels of secreted protein in human trabecular meshwork (TM) cells; a lower secreted:intracellular protein ratio strongly correlates with variant effects on intraocular pressure (r = 0.81). Importantly, accumulation of mutant protein in the ER does not increase expression of ER stress proteins in TM cells (P > 0.05 for all variants tested). Cyclic mechanical stress, a glaucoma-relevant physiologic stressor, also significantly lowers ANGPTL7 expression in primary cultures of human Schlemm's canal (SC) cells (-2.4-fold-change, P = 0.01). Collectively, these data suggest that the protective effects of ANGPTL7 variants in POAG stem from lower levels of secreted protein, which may modulate responses to physiologic and pathologic ocular cell stressors. Downregulation of ANGPTL7 expression may therefore serve as a viable preventative and therapeutic strategy for this common, blinding disease.
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Affiliation(s)
- Inas F Aboobakar
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
| | - Edward Ryan A Collantes
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
| | - Michael A Hauser
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - W Daniel Stamer
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biomedical Engineering, Duke University School of Medicine, Durham, NC 27710, USA
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
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40
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Tang Y, Gutmann DH. Neurofibromatosis Type 1-Associated Optic Pathway Gliomas: Current Challenges and Future Prospects. Cancer Manag Res 2023; 15:667-681. [PMID: 37465080 PMCID: PMC10351533 DOI: 10.2147/cmar.s362678] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/06/2023] [Indexed: 07/20/2023] Open
Abstract
Optic pathway glioma (OPG) occurs in as many as one-fifth of individuals with the neurofibromatosis type 1 (NF1) cancer predisposition syndrome. Generally considered low-grade and slow growing, many children with NF1-OPGs remain asymptomatic. However, due to their location within the optic pathway, ~20-30% of those harboring NF1-OPGs will experience symptoms, including progressive vision loss, proptosis, diplopia, and precocious puberty. While treatment with conventional chemotherapy is largely effective at attenuating tumor growth, it is not clear whether there is much long-term recovery of visual function. Additionally, because these tumors predominantly affect young children, there are unique challenges to NF1-OPG diagnosis, monitoring, and longitudinal management. Over the past two decades, the employment of authenticated genetically engineered Nf1-OPG mouse models have provided key insights into the function of the NF1 protein, neurofibromin, as well as the molecular and cellular pathways that contribute to optic gliomagenesis. Findings from these studies have resulted in the identification of new molecular targets whose inhibition blocks murine Nf1-OPG growth in preclinical studies. Some of these promising compounds have now entered into early clinical trials. Future research focused on defining the determinants that underlie optic glioma initiation, expansion, and tumor-induced optic nerve injury will pave the way to personalized risk assessment strategies, improved tumor monitoring, and optimized treatment plans for children with NF1-OPG.
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Affiliation(s)
- Yunshuo Tang
- Department of Ophthalmology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
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41
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Oikawa K, Torne O, Sun D, Moon AKB, Kiland JA, Trane RM, McLellan GJ. Aqueous Humor TGF-β2 and Its Association With Intraocular Pressure in a Naturally Occurring Large Animal Model of Glaucoma. Invest Ophthalmol Vis Sci 2023; 64:18. [PMID: 37459065 PMCID: PMC10362923 DOI: 10.1167/iovs.64.10.18] [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: 01/26/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023] Open
Abstract
Purpose Transforming growth factor (TGF)-β2 has been widely implicated in human glaucoma pathology. The purpose of this study was to determine the source of TGF-β2 in aqueous humor (AH) and its relationship with intraocular pressure (IOP) in an inherited large animal model of glaucoma. Methods Sixty-six glaucomatous cats homozygous for LTBP2 mutation, and 42 normal cats were studied. IOP was measured weekly by rebound tonometry. AH was collected by anterior chamber paracentesis from each eye under general anesthesia, and serum samples collected from venous blood concurrently. Concentrations of total, active and latent TGF-β2 in AH and serum samples were measured by quantitative sandwich immunoassay. For comparisons between groups, unpaired t-test or Mann Whitney test were used, with P < 0.05 considered significant. The relationships between TGF-β2 concentrations and IOP values were examined by Pearson's correlation coefficient and generalized estimating equation. Results IOP and AH TGF-β2 concentrations were significantly higher in glaucomatous than in normal cats. AH TGF-β2 showed a significant, robust positive correlation with IOP in glaucomatous cats (r = 0.83, R2 = 0.70, P < 0.0001). Serum TGF-β2 did not correlate with AH TGF-β2 and was not significantly different between groups. TGF-β2 mRNA and protein expression were significantly increased in local ocular tissues in glaucomatous cats. Conclusions Enhanced, local ocular production of TGF-β2 with a robust positive association with IOP was identified in this spontaneous feline glaucoma model, providing a foundation for preclinical testing of novel therapeutics to limit disease-associated AH TGF-β2 elevation and signaling in glaucoma.
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Affiliation(s)
- Kazuya Oikawa
- Surgical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
- McPherson Eye Research Institute, Madison, Wisconsin, United States
| | - Odalys Torne
- Surgical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
- McPherson Eye Research Institute, Madison, Wisconsin, United States
| | - David Sun
- Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Alaina K. B. Moon
- Surgical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Julie A. Kiland
- Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Ralph Møller Trane
- Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Gillian J. McLellan
- Surgical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
- McPherson Eye Research Institute, Madison, Wisconsin, United States
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42
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Vöcking O, Famulski JK. Single cell transcriptome analyses of the developing zebrafish eye- perspectives and applications. Front Cell Dev Biol 2023; 11:1213382. [PMID: 37457291 PMCID: PMC10346855 DOI: 10.3389/fcell.2023.1213382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
Within a relatively short period of time, single cell transcriptome analyses (SCT) have become increasingly ubiquitous with transcriptomic research, uncovering plentiful details that boost our molecular understanding of various biological processes. Stemming from SCT analyses, the ever-growing number of newly assigned genetic markers increases our understanding of general function and development, while providing opportunities for identifying genes associated with disease. SCT analyses have been carried out using tissue from numerous organisms. However, despite the great potential of zebrafish as a model organism, other models are still preferably used. In this mini review, we focus on eye research as an example of the advantages in using zebrafish, particularly its usefulness for single cell transcriptome analyses of developmental processes. As studies have already shown, the unique opportunities offered by zebrafish, including similarities to the human eye, in combination with the possibility to analyze and extract specific cells at distinct developmental time points makes the model a uniquely powerful one. Particularly the practicality of collecting large numbers of embryos and therefore isolation of sufficient numbers of developing cells is a distinct advantage compared to other model organisms. Lastly, the advent of highly efficient genetic knockouts methods offers opportunities to characterize target gene function in a more cost-efficient way. In conclusion, we argue that the use of zebrafish for SCT approaches has great potential to further deepen our molecular understanding of not only eye development, but also many other organ systems.
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Affiliation(s)
| | - Jakub K. Famulski
- Department of Biology, University of Kentucky, Lexington, KY, United States
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43
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Huang X, Bajpai AK, Sun J, Xu F, Lu L, Yousefi S. A new gene-scoring method for uncovering novel glaucoma-related genes using non-negative matrix factorization based on RNA-seq data. Front Genet 2023; 14:1204909. [PMID: 37377596 PMCID: PMC10292752 DOI: 10.3389/fgene.2023.1204909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Early diagnosis and treatment of glaucoma are challenging. The discovery of glaucoma biomarkers based on gene expression data could potentially provide new insights for early diagnosis, monitoring, and treatment options of glaucoma. Non-negative Matrix Factorization (NMF) has been widely used in numerous transcriptome data analyses in order to identify subtypes and biomarkers of different diseases; however, its application in glaucoma biomarker discovery has not been previously reported. Our study applied NMF to extract latent representations of RNA-seq data from BXD mouse strains and sorted the genes based on a novel gene scoring method. The enrichment ratio of the glaucoma-reference genes, extracted from multiple relevant resources, was compared using both the classical differentially expressed gene (DEG) analysis and NMF methods. The complete pipeline was validated using an independent RNA-seq dataset. Findings showed our NMF method significantly improved the enrichment detection of glaucoma genes. The application of NMF with the scoring method showed great promise in the identification of marker genes for glaucoma.
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Affiliation(s)
- Xiaoqin Huang
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Akhilesh K. Bajpai
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Jian Sun
- Integrated Data Science Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institute of Health (NIH), Bethesda, MD, United States
| | - Fuyi Xu
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Lu Lu
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Siamak Yousefi
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
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44
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Nandadasa S, Martin D, Deshpande G, Robert KL, Stack MS, Itoh Y, Apte SS. Degradomic Identification of Membrane Type 1-Matrix Metalloproteinase as an ADAMTS9 and ADAMTS20 Substrate. Mol Cell Proteomics 2023; 22:100566. [PMID: 37169079 PMCID: PMC10267602 DOI: 10.1016/j.mcpro.2023.100566] [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: 09/14/2022] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/13/2023] Open
Abstract
The secreted metalloproteases ADAMTS9 and ADAMTS20 are implicated in extracellular matrix proteolysis and primary cilium biogenesis. Here, we show that clonal gene-edited RPE-1 cells in which ADAMTS9 was inactivated, and which constitutively lack ADAMTS20 expression, have morphologic characteristics distinct from parental RPE-1 cells. To investigate underlying proteolytic mechanisms, a quantitative terminomics method, terminal amine isotopic labeling of substrates was used to compare the parental and gene-edited RPE-1 cells and their medium to identify ADAMTS9 substrates. Among differentially abundant neo-amino (N) terminal peptides arising from secreted and transmembrane proteins, a peptide with lower abundance in the medium of gene-edited cells suggested cleavage at the Tyr314-Gly315 bond in the ectodomain of the transmembrane metalloprotease membrane type 1-matrix metalloproteinase (MT1-MMP), whose mRNA was also reduced in gene-edited cells. This cleavage, occurring in the MT1-MMP hinge, that is, between the catalytic and hemopexin domains, was orthogonally validated both by lack of an MT1-MMP catalytic domain fragment in the medium of gene-edited cells and restoration of its release from the cell surface by reexpression of ADAMTS9 and ADAMTS20 and was dependent on hinge O-glycosylation. A C-terminally semitryptic MT1-MMP peptide with greater abundance in WT RPE-1 medium identified a second ADAMTS9 cleavage site in the MT1-MMP hemopexin domain. Consistent with greater retention of MT1-MMP on the surface of gene-edited cells, pro-MMP2 activation, which requires cell surface MT1-MMP, was increased. MT1-MMP knockdown in gene-edited ADAMTS9/20-deficient cells restored focal adhesions but not ciliogenesis. The findings expand the web of interacting proteases at the cell surface, suggest a role for ADAMTS9 and ADAMTS20 in regulating cell surface activity of MT1-MMP, and indicate that MT1-MMP shedding does not underlie their observed requirement in ciliogenesis.
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Affiliation(s)
- Sumeda Nandadasa
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA; Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
| | - Daniel Martin
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Gauravi Deshpande
- Imaging Core Facility, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Karyn L Robert
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - M Sharon Stack
- Department of Chemistry and Biochemistry and Harper Cancer Center, University of Notre Dame, Notre Dame, Indiana, USA
| | - Yoshifumi Itoh
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA.
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45
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Sharif NA. Recently Approved Drugs for Lowering and Controlling Intraocular Pressure to Reduce Vision Loss in Ocular Hypertensive and Glaucoma Patients. Pharmaceuticals (Basel) 2023; 16:791. [PMID: 37375739 DOI: 10.3390/ph16060791] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Serious vision loss occurs in patients affected by chronically raised intraocular pressure (IOP), a characteristic of many forms of glaucoma where damage to the optic nerve components causes progressive degeneration of retinal and brain neurons involved in visual perception. While many risk factors abound and have been validated for this glaucomatous optic neuropathy (GON), the major one is ocular hypertension (OHT), which results from the accumulation of excess aqueous humor (AQH) fluid in the anterior chamber of the eye. Millions around the world suffer from this asymptomatic and progressive degenerative eye disease. Since clinical evidence has revealed a strong correlation between the reduction in elevated IOP/OHT and GON progression, many drugs, devices, and surgical techniques have been developed to lower and control IOP. The constant quest for new pharmaceuticals and other modalities with superior therapeutic indices has recently yielded health authority-approved novel drugs with unique pharmacological signatures and mechanism(s) of action and AQH drainage microdevices for effectively and durably treating OHT. A unique nitric oxide-donating conjugate of latanoprost, an FP-receptor prostaglandin (PG; latanoprostene bunod), new rho kinase inhibitors (ripasudil; netarsudil), a novel non-PG EP2-receptor-selective agonist (omidenepag isopropyl), and a form of FP-receptor PG in a slow-release intracameral implant (Durysta) represent the additions to the pharmaceutical toolchest to mitigate the ravages of OHT. Despite these advances, early diagnosis of OHT and glaucoma still lags behind and would benefit from further concerted effort and attention.
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Affiliation(s)
- Najam A Sharif
- Eye-APC Duke-NUS Medical School, Singapore 169856, Singapore
- Singapore Eye Research Institute, Singapore 169856, Singapore
- Department of Pharmacology and Neuroscience, University of North Texas Health Sciences Center, Fort Worth, TX 76107, USA
- Department of Pharmacy Sciences, Creighton University, Omaha, NE 68178, USA
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
- Imperial College of Science and Technology, St. Mary's Campus, London SW7 2BX, UK
- Institute of Ophthalmology, University College London, London WC1E 6BT, UK
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46
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Monavarfeshani A, Yan W, Pappas C, Odenigbo KA, He Z, Segrè AV, van Zyl T, Hageman GS, Sanes JR. Transcriptomic Analysis of the Ocular Posterior Segment Completes a Cell Atlas of the Human Eye. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538447. [PMID: 37162855 PMCID: PMC10168356 DOI: 10.1101/2023.04.26.538447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Although the visual system extends through the brain, most vision loss originates from defects in the eye. Its central element is the neural retina, which senses light, processes visual signals, and transmits them to the rest of the brain through the optic nerve (ON). Surrounding the retina are numerous other structures, conventionally divided into anterior and posterior segments. Here we used high-throughput single nucleus RNA sequencing (snRNA-seq) to classify and characterize cells in the extraretinal components of the posterior segment: ON, optic nerve head (ONH), peripheral sclera, peripapillary sclera (PPS), choroid, and retinal pigment epithelium (RPE). Defects in each of these tissues are associated with blinding diseases - for example, glaucoma (ONH and PPS), optic neuritis (ON), retinitis pigmentosa (RPE), and age-related macular degeneration (RPE and choroid). From ∼151,000 single nuclei, we identified 37 transcriptomically distinct cell types, including multiple types of astrocytes, oligodendrocytes, fibroblasts, and vascular endothelial cells. Our analyses revealed a differential distribution of many cell types among distinct structures. Together with our previous analyses of the anterior segment and retina, the new data complete a "Version 1" cell atlas of the human eye. We used this atlas to map the expression of >180 genes associated with the risk of developing glaucoma, which is known to involve ocular tissues in both anterior and posterior segments as well as neural retina. Similar methods can be used to investigate numerous additional ocular diseases, many of which are currently untreatable.
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Affiliation(s)
- Aboozar Monavarfeshani
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Equal contributions
| | - Wenjun Yan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Equal contributions
| | - Christian Pappas
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Kenechukwu A. Odenigbo
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
| | - Ayellet V. Segrè
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Tavé van Zyl
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114
- Present address: Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT 06510
| | - Gregory S. Hageman
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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47
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Vöcking O, Famulski JK. A temporal single cell transcriptome atlas of zebrafish anterior segment development. Sci Rep 2023; 13:5656. [PMID: 37024546 PMCID: PMC10079958 DOI: 10.1038/s41598-023-32212-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Anterior segment dysgenesis (ASD), resulting in vision impairment, stems from maldevelopment of anterior segment (AS) tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells (POM). POM cells specify into anterior segment mesenchyme (ASM) cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS. Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development, Tg[foxc1b:GFP], we isolated GFP+ ASM cells at several developmental timepoints (48-144 hpf) and performed single cell RNA sequencing. Clustering analysis indicates subdifferentiation of ASM as early as 48 hpf and subsequent diversification into corneal epithelium/endothelium/stroma, or annular ligament (AL) lineages. Tracking individual clusters reveals common developmental pathways, up to 72 hpf, for the AL and corneal endothelium/stroma and distinct pathways for corneal epithelium starting at 48 hpf. Spatiotemporal validation of over 80 genes found associated with AS development demonstrates a high degree of conservation with mammalian trabecular meshwork and corneal tissues. In addition, we characterize thirteen novel genes associated with annular ligament and seven with corneal development. Overall, the data provide a molecular verification of the long-standing hypothesis that POM derived ASM give rise to AS tissues and highlight the high degree of conservation between zebrafish and mammals.
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Affiliation(s)
- Oliver Vöcking
- Department of Biology, University of Kentucky, Lexington, USA
| | - J K Famulski
- Department of Biology, University of Kentucky, Lexington, USA.
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48
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Feng P, Wang W, Xu W, Cao Q, Zhu W. Application of a Magnetic Platform in α6 Integrin-Positive iPSC-TM Purification. Bioengineering (Basel) 2023; 10:bioengineering10040410. [PMID: 37106597 PMCID: PMC10135729 DOI: 10.3390/bioengineering10040410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
The emergence of induced pluripotent stem cell (iPSC) technology has provided a new approach to regenerating decellularized trabecular meshwork (TM) in glaucoma. We have previously generated iPSC-derived TM (iPSC-TM) using a medium conditioned by TM cells and verified its function in tissue regeneration. Because of the heterogeneity of iPSCs and the isolated TM cells, iPSC-TM cells appear to be heterogeneous, which impedes our understanding of how the decellularized TM may be regenerated. Herein, we developed a protocol based on a magnetic-activated cell sorting (MACS) system or an immunopanning (IP) method for sorting integrin subunit alpha 6 (ITGA6)-positive iPSC-TM, an example of the iPSC-TM subpopulation. We first analyzed the purification efficiency of these two approaches by flow cytometry. In addition, we also determined cell viability by analyzing the morphologies of the purified cells. To conclude, the MACS-based purification could yield a higher ratio of ITGA6-positive iPSC-TM and maintain a relatively higher cell viability than the IP-based method, allowing for the preparation of any iPSC-TM subpopulation of interest and facilitating a better understanding of the regenerative mechanism of iPSC-based therapy.
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Affiliation(s)
- Pengchao Feng
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao 266021, China
| | - Wenyan Wang
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao 266021, China
| | - Wenhua Xu
- Institute of Regenerative Medicine and Laboratory Technology Innovation, Qingdao University, Qingdao 266021, China
| | - Qilong Cao
- Qingdao Haier Biotech Co., Ltd., Qingdao 266109, China
- Correspondence: (Q.C.); (W.Z.)
| | - Wei Zhu
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao 266021, China
- Advanced Innovation Center for Big Data-Based Precision Medicine, Beijing University of Aeronautics and Astronautics-Capital Medical University, Beijing 100083, China
- Correspondence: (Q.C.); (W.Z.)
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Yao X, Yang H, Han H, Kou X, Jiang Y, Luo M, Zhou Y, Wang J, Fan X, Wang X, Li MJ, Yan H. Genome-wide analysis of genetic pleiotropy and causal genes across three age-related ocular disorders. Hum Genet 2023; 142:507-522. [PMID: 36917350 DOI: 10.1007/s00439-023-02542-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/04/2023] [Indexed: 03/16/2023]
Abstract
Age-related macular degeneration (AMD), cataract, and glaucoma are leading causes of blindness worldwide. Previous genome-wide association studies (GWASs) have revealed a variety of susceptible loci associated with age-related ocular disorders, yet the genetic pleiotropy and causal genes across these diseases remain poorly understood. By leveraging large-scale genetic and observational data from ocular disease GWASs and UK Biobank (UKBB), we found significant pairwise genetic correlations and consistent epidemiological associations among these ocular disorders. Cross-disease meta-analysis uncovered seven pleiotropic loci, three of which were replicated in an additional cohort. Integration of variants in pleiotropic loci and multiple single-cell omics data identified that Müller cells and astrocytes were likely trait-related cell types underlying ocular comorbidity. In addition, we comprehensively integrated eye-specific gene expression quantitative loci (eQTLs), epigenomic profiling, and 3D genome data to prioritize causal pleiotropic genes. We found that pleiotropic genes were essential in nerve development and eye pigmentation, and targetable by aflibercept and pilocarpine for the treatment of AMD and glaucoma. These findings will not only facilitate the mechanistic research of ocular comorbidities but also benefit the therapeutic optimization of age-related ocular diseases.
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Affiliation(s)
- Xueming Yao
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Hongxi Yang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Han Han
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Xuejing Kou
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Yuhan Jiang
- Department of Bioinformatics, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Menghan Luo
- Department of Bioinformatics, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yao Zhou
- Department of Bioinformatics, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Jianhua Wang
- Department of Bioinformatics, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xutong Fan
- Department of Bioinformatics, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xiaohong Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
| | - Mulin Jun Li
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China. .,Department of Bioinformatics, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
| | - Hua Yan
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, 300052, China. .,Laboratory of Molecular Ophthalmology, Tianjin Medical University, Tianjin, 300070, China. .,School of Medicine, Nankai University, Tianjin, 300071, China.
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Raghunathan V, Nartey A, Dhamodaran K, Baidouri H, Staverosky JA, Keller KE, Zientek K, Reddy A, Acott T, Vranka JA. Characterization of extracellular matrix deposited by segmental trabecular meshwork cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.11.532242. [PMID: 36945588 PMCID: PMC10028995 DOI: 10.1101/2023.03.11.532242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Biophysical and biochemical attributes of the extracellular matrix are major determinants of cell fate in homeostasis and disease. Ocular hypertension and glaucoma are diseases where the trabecular meshwork tissue responsible for aqueous humor egress becomes stiffer accompanied by changes in its matrisome in a segmental manner with regions of high or low flow. Prior studies demonstrate these alterations in the matrix are dynamic in response to age and pressure changes. The underlying reason for segmentation or differential response to pressure and stiffening are unknown. This is largely due to a lack of appropriate models ( in vitro or ex vivo ) to study this phenomena. In this study, we characterize the biomechanical attributes, matrisome, and incidence of crosslinks in the matrix deposited by primary cells isolated from segmental flow regions and when treated with glucocorticosteroid. Data demonstrate that matrix deposited by cells from low flow regions are stiffer and exhibit a greater number of immature and mature crosslinks, and that these are exacerbated in the presence of steroid. We also show a differential response of high or low flow cells to steroid via changes observed in the matrix composition. We conclude that although a mechanistic basis for matrix stiffness was undetermined in this study, it is a viable tool to study cell-matrix interactions and further our understanding of trabecular meshwork pathobiology.
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