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Suanno G, Genna VG, Maurizi E, Dieh AA, Griffith M, Ferrari G. Cell therapy in the cornea: the emerging role of microenvironment. Prog Retin Eye Res 2024:101275. [PMID: 38797320 DOI: 10.1016/j.preteyeres.2024.101275] [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: 10/11/2023] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
The cornea is an ideal testing field for cell therapies. Its highly ordered structure, where specific cell populations are sequestered in different layers, together with its accessibility, has allowed the development of the first stem cell-based therapy approved by the European Medicine Agency. Today, different techniques have been proposed for autologous and allogeneic limbal and non-limbal cell transplantation. Cell replacement has also been attempted in cases of endothelial cell decompensation as it occurs in Fuchs dystrophy: injection of cultivated allogeneic endothelial cells is now in advanced phases of clinical development. Recently, stromal substitutes have been developed with excellent integration capability and transparency. Finally, cell-derived products, such as exosomes obtained from different sources, have been investigated for the treatment of severe corneal diseases with encouraging results. Optimization of the success rate of cell therapies obviously requires high-quality cultured cells/products, but the role of the surrounding microenvironment is equally important to allow engraftment of transplanted cells, to preserve their functions and, ultimately, lead to restoration of tissue integrity and transparency of the cornea.
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Affiliation(s)
- Giuseppe Suanno
- Vita-Salute San Raffaele University, Milan, Italy; Eye Repair Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Eleonora Maurizi
- Centre for Regenerative Medicine ''S. Ferrari'', University of Modena and Reggio Emilia, Modena, Italy
| | - Anas Abu Dieh
- Maisonneuve-Rosemont Hospital Research Centre, Montreal, Quebec, Canada
| | - May Griffith
- Maisonneuve-Rosemont Hospital Research Centre, Montreal, Quebec, Canada.
| | - Giulio Ferrari
- Vita-Salute San Raffaele University, Milan, Italy; Eye Repair Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Ophthalmology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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2
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Davidson KC, Sung M, Brown KD, Contet J, Belluschi S, Hamel R, Moreno-Moral A, Dos Santos RL, Gough J, Polo JM, Daniell M, Parfitt GJ. Single nuclei transcriptomics of the in situ human limbal stem cell niche. Sci Rep 2024; 14:6749. [PMID: 38514716 PMCID: PMC10957941 DOI: 10.1038/s41598-024-57242-4] [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: 09/06/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
The corneal epithelium acts as a barrier to pathogens entering the eye; corneal epithelial cells are continuously renewed by uni-potent, quiescent limbal stem cells (LSCs) located at the limbus, where the cornea transitions to conjunctiva. There has yet to be a consensus on LSC markers and their transcriptome profile is not fully understood, which may be due to using cadaveric tissue without an intact stem cell niche for transcriptomics. In this study, we addressed this problem by using single nuclei RNA sequencing (snRNAseq) on healthy human limbal tissue that was immediately snap-frozen after excision from patients undergoing cataract surgery. We identified the quiescent LSCs as a sub-population of corneal epithelial cells with a low level of total transcript counts. Moreover, TP63, KRT15, CXCL14, and ITGβ4 were found to be highly expressed in LSCs and transiently amplifying cells (TACs), which constitute the corneal epithelial progenitor populations at the limbus. The surface markers SLC6A6 and ITGβ4 could be used to enrich human corneal epithelial cell progenitors, which were also found to specifically express the putative limbal progenitor cell markers MMP10 and AC093496.1.
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Affiliation(s)
- Kathryn C Davidson
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | | | - Karl D Brown
- Centre for Eye Research Australia (CERA), Melbourne, Australia
| | - Julian Contet
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | | | | | | | | | - Julian Gough
- Mogrify Limited, Cambridge, England, UK
- MRC Laboratory of Molecular Biology, Cambridge, England, UK
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.
- Mogrify Limited, Cambridge, England, UK.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.
- Adelaide Centre for Epigenetics, Faculty of Medicine Nursing and Medical Sciences, The University of Adelaide, Adelaide, Australia.
- The South Australian Immunogenomics Cancer Institute, Faculty of Medicine Nursing and Medical Sciences, The University of Adelaide, Adelaide, Australia.
| | - Mark Daniell
- Centre for Eye Research Australia (CERA), Melbourne, Australia.
| | - Geraint J Parfitt
- Mogrify Limited, Cambridge, England, UK.
- Ophthalmology Discovery Research, AbbVie, Irvine, CA, USA.
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3
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Wolosin JM. A Keratin 12 Expression-Based Analysis of Stem-Precursor Cells and Differentiation in the Limbal-Corneal Epithelium Using Single-Cell RNA-Seq Data. BIOLOGY 2024; 13:145. [PMID: 38534415 DOI: 10.3390/biology13030145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 03/28/2024]
Abstract
The corneal epithelium (CE) is spread between two domains, the outer vascularized limbus and the avascular cornea proper. Epithelial cells undergo constant migration from the limbus to the vision-critical central cornea. Coordinated with this migration, the cells undergo differentiation changes where a pool of unique stem/precursor cells at the limbus yields the mature cells that reach the corneal center. Differentiation is heralded by the expression of the corneal-specific Krt12. Processing data acquired by scRNA-Seq showed that the increase in Krt12 expression occurs in four distinct steps within the limbus, plus a single continuous increase in the cornea. Differential gene analysis demonstrated that these domains reflect discreet stages of CE differentiation and yielded extensive information of the genes undergoing down- or upregulation in the sequential transition from less to more differentiate conditions. The approach allowed the identification of multiple gene cohorts, including (a) the genes which have maximal expression in the most primitive, Krt12-negative cell cohort, which is likely to include the stem/precursor cells; (b) the sets of genes that undergo continuous increase or decrease along the whole differentiation path; and (c) the genes showing maximal positive or negative correlation with the changes in Krt12.
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Affiliation(s)
- J Mario Wolosin
- Department of Ophthalmology, Black Family Stem Cell Institute and Vision Research Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029, USA
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4
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Altshuler A, Amitai-Lange A, Nasser W, Dimri S, Bhattacharya S, Tiosano B, Barbara R, Aberdam D, Shimmura S, Shalom-Feuerstein R. Eyes open on stem cells. Stem Cell Reports 2023; 18:2313-2327. [PMID: 38039972 PMCID: PMC10724227 DOI: 10.1016/j.stemcr.2023.10.023] [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: 08/02/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 12/03/2023] Open
Abstract
Recently, the murine cornea has reemerged as a robust stem cell (SC) model, allowing individual SC tracing in living animals. The cornea has pioneered seminal discoveries in SC biology and regenerative medicine, from the first corneal transplantation in 1905 to the identification of limbal SCs and their transplantation to successfully restore vision in the early 1990s. Recent experiments have exposed unexpected properties attributed to SCs and progenitors and revealed flexibility in the differentiation program and a key role for the SC niche. Here, we discuss the limbal SC model and its broader relevance to other tissues, disease, and therapy.
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Affiliation(s)
- Anna Altshuler
- Department of Genetics & Developmental Biology, The Rappaport Faculty of Medicine & Research Institute, Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa 31096, Israel.
| | - Aya Amitai-Lange
- Department of Genetics & Developmental Biology, The Rappaport Faculty of Medicine & Research Institute, Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Waseem Nasser
- Department of Genetics & Developmental Biology, The Rappaport Faculty of Medicine & Research Institute, Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Shalini Dimri
- Department of Genetics & Developmental Biology, The Rappaport Faculty of Medicine & Research Institute, Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Swarnabh Bhattacharya
- Department of Genetics & Developmental Biology, The Rappaport Faculty of Medicine & Research Institute, Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Beatrice Tiosano
- Department of Ophthalmology, Hillel Yaffe Medical Center, Hadera, Israel
| | - Ramez Barbara
- Department of Ophthalmology, Hillel Yaffe Medical Center, Hadera, Israel
| | - Daniel Aberdam
- Université Paris-Cité, INSERM U1138, Centre des Cordeliers, 75270 Paris, France
| | - Shigeto Shimmura
- Department of Clinical Regenerative Medicine, Fujita Medical Innovation Center, Tokyo, Japan
| | - Ruby Shalom-Feuerstein
- Department of Genetics & Developmental Biology, The Rappaport Faculty of Medicine & Research Institute, Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa 31096, Israel.
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5
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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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6
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Wu YF, Chang NW, Chu LA, Liu HY, Zhou YX, Pai YL, Yu YS, Kuan CH, Wu YC, Lin SJ, Tan HY. Single-Cell Transcriptomics Reveals Cellular Heterogeneity and Complex Cell-Cell Communication Networks in the Mouse Cornea. Invest Ophthalmol Vis Sci 2023; 64:5. [PMID: 37792336 PMCID: PMC10565710 DOI: 10.1167/iovs.64.13.5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 06/30/2023] [Indexed: 10/05/2023] Open
Abstract
Purpose To generate a single-cell RNA-sequencing (scRNA-seq) map and construct cell-cell communication networks of mouse corneas. Methods C57BL/6 mouse corneas were dissociated to single cells and subjected to scRNA-seq. Cell populations were clustered and annotated for bioinformatic analysis using the R package "Seurat." Differential expression patterns were validated and spatially mapped with whole-mount immunofluorescence staining. Global intercellular signaling networks were constructed using CellChat. Results Unbiased clustering of scRNA-seq transcriptomes of 14,732 cells from 40 corneas revealed 17 cell clusters of six major cell types: nine epithelial cell, three keratocyte, two corneal endothelial cell, and one each of immune cell, vascular endothelial cell, and fibroblast clusters. The nine epithelial cell subtypes included quiescent limbal stem cells, transit-amplifying cells, and differentiated cells from corneas and two minor conjunctival epithelial clusters. CellChat analysis provided an atlas of the complex intercellular signaling communications among all cell types. Conclusions We constructed a complete single-cell transcriptomic map and the complex signaling cross-talk among all cell types of the cornea, which can be used as a foundation atlas for further research on the cornea. This study also deepens the understanding of the cellular heterogeneity and heterotypic cell-cell interaction within corneas.
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Affiliation(s)
- Yueh-Feng Wu
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
| | - Nai-Wen Chang
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-An Chu
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Hsin-Yu Liu
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Ophthalmology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Yu-Xian Zhou
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
| | - Yun-Lin Pai
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Sheng Yu
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
| | - Chen-Hsiang Kuan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Plastic Surgery, Department of Surgery, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Ching Wu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Sung-Jan Lin
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Hsin-Yuan Tan
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
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7
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Li W, Gurdziel K, Pitchaikannu A, Gupta N, Hazlett LD, Xu S. The miR-183/96/182 cluster is a checkpoint for resident immune cells and shapes the cellular landscape of the cornea. Ocul Surf 2023; 30:17-41. [PMID: 37536656 PMCID: PMC10834862 DOI: 10.1016/j.jtos.2023.07.012] [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: 01/30/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
PURPOSE The conserved miR-183/96/182 cluster (miR-183C) regulates both corneal sensory innervation and corneal resident immune cells (CRICs). This study is to uncover its role in CRICs and in shaping the corneal cellular landscape at a single-cell (sc) level. METHODS Corneas of naïve, young adult [2 and 6 months old (mo)], female miR-183C knockout (KO) mice and wild-type (WT) littermates were harvested and dissociated into single cells. Dead cells were removed using a Dead Cell Removal kit. CD45+ CRICs were enriched by Magnetic Activated Cell Sorting (MACS). scRNA libraries were constructed and sequenced followed by comprehensive bioinformatic analyses. RESULTS The composition of major cell types of the cornea stays relatively stable in WT mice from 2 to 6 mo, however the compositions of subtypes of corneal cells shift with age. Inactivation of miR-183C disrupts the stability of the major cell-type composition and age-related transcriptomic shifts of subtypes of corneal cells. The diversity of CRICs is enhanced with age. Naïve mouse cornea contains previously-unrecognized resident fibrocytes and neutrophils. Resident macrophages (ResMφ) adopt cornea-specific function by expressing abundant extracellular matrix (ECM) and ECM organization-related genes. Naïve cornea is endowed with partially-differentiated proliferative ResMφ and contains microglia-like Mφ. Resident lymphocytes, including innate lymphoid cells (ILCs), NKT and γδT cells, are the major source of innate IL-17a. miR-183C limits the diversity and polarity of ResMφ. CONCLUSION miR-183C serves as a checkpoint for CRICs and imposes a global regulation of the cellular landscape of the cornea.
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Affiliation(s)
- Weifeng Li
- Predoctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine, Department of Genetic Medicine, USA; Wilmer Eye Institute, School of Medicine, The Johns Hopkins University, Baltimore, MD, USA
| | | | - Ahalya Pitchaikannu
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Naman Gupta
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Linda D Hazlett
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Shunbin Xu
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, MI, USA.
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8
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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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9
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Abd-Elmonem EM, Makky AM, Antar A, Abd-Elsalam WH, Khalil IA. Corneal targeted Amorolfine HCl-mixed micelles for the management of ocular candidiasis: Preparation, in vitro characterization, ex vivo and in vivo assessments. J Drug Deliv Sci Technol 2023; 85:104614. [DOI: 10.1016/j.jddst.2023.104614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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10
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Arts JA, Laberthonnière C, Lima Cunha D, Zhou H. Single-Cell RNA Sequencing: Opportunities and Challenges for Studies on Corneal Biology in Health and Disease. Cells 2023; 12:1808. [PMID: 37443842 PMCID: PMC10340756 DOI: 10.3390/cells12131808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
The structure and major cell types of the multi-layer human cornea have been extensively studied. However, various cell states in specific cell types and key genes that define the cell states are not fully understood, hindering our comprehension of corneal homeostasis, related diseases, and therapeutic discovery. Single-cell RNA sequencing is a revolutionary and powerful tool for identifying cell states within tissues such as the cornea. This review provides an overview of current single-cell RNA sequencing studies on the human cornea, highlighting similarities and differences between them, and summarizing the key genes that define corneal cell states reported in these studies. In addition, this review discusses the opportunities and challenges of using single-cell RNA sequencing to study corneal biology in health and disease.
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Affiliation(s)
- Julian A. Arts
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Camille Laberthonnière
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Dulce Lima Cunha
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Huiqing Zhou
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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Tsedilina TR, Sharova E, Iakovets V, Skorodumova LO. Systematic review of SLC4A11, ZEB1, LOXHD1, and AGBL1 variants in the development of Fuchs' endothelial corneal dystrophy. Front Med (Lausanne) 2023; 10:1153122. [PMID: 37441688 PMCID: PMC10333596 DOI: 10.3389/fmed.2023.1153122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/30/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction The pathogenic role of variants in TCF4 and COL8A2 in causing Fuchs' endothelial corneal dystrophy (FECD) is not controversial and has been confirmed by numerous studies. The causal role of other genes, SLC4A11, ZEB1, LOXHD1, and AGBL1, which have been reported to be associated with FECD, is more complicated and less obvious. We performed a systematic review of the variants in the above-mentioned genes in FECD cases, taking into account the currently available population frequency information, transcriptomic data, and the results of functional studies to assess their pathogenicity. Methods Search for articles published in 2005-2022 was performed manually between July 2022 and February 2023. We searched for original research articles in peer-reviewed journals, written in English. Variants in the genes of interest identified in patients with FECD were extracted for the analysis. We classified each presented variant by pathogenicity status according to the ACMG criteria implemented in the Varsome tool. Diagnosis, segregation data, presence of affected relatives, functional analysis results, and gene expression in the corneal endothelium were taken into account. Data on the expression of genes of interest in the corneal endothelium were extracted from articles in which transcriptome analysis was performed. The identification of at least one variant in a gene classified as pathogenic or significantly associated with FECD was required to confirm the causal role of the gene in FECD. Results The analysis included 34 articles with 102 unique ZEB1 variants, 20 articles with 64 SLC4A11 variants, six articles with 26 LOXHD1 variants, and five articles with four AGBL1 variants. Pathogenic status was confirmed for seven SLC4A11 variants found in FECD. No variants in ZEB1, LOXHD1, and AGBL1 genes were classified as pathogenic for FECD. According to the transcriptome data, AGBL1 and LOXHD1 were not expressed in the corneal endothelium. Functional evidence for the association of LOXHD1, and AGBL1 with FECD was conflicting. Conclusion Our analysis confirmed the causal role of SLC4A11 variants in the development of FECD. The causal role of ZEB1, LOXHD1, and AGBL1 variants in FECD has not been confirmed. Further evidence from familial cases and functional analysis is needed to confirm their causal roles in FECD.
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Affiliation(s)
- Tatiana Romanovna Tsedilina
- Laboratory of Human Molecular Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Elena Sharova
- Laboratory of Human Molecular Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Valeriia Iakovets
- Laboratory of Human Molecular Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Liubov Olegovna Skorodumova
- Laboratory of Human Molecular Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
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12
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Liu X, Zhang S, Mao Y, Lin S, Wu H, Ou S. Optimization of method for achieving a single-cell suspension from mouse corneas. Exp Eye Res 2023:109544. [PMID: 37336469 DOI: 10.1016/j.exer.2023.109544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 05/28/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
The single-cell RNA-sequencing (scRNA-seq) technique is used to explore the biological characteristics of tissues under pathological and physiological conditions that include certain chronic eye diseases. Harvesting of single-cell suspensions is one challenge inherent to scRNA-seq procedures. This study aimed to use an optimized method to digest a whole mouse cornea to harvest single-cell suspensions. We utilized five different mouse cornea digestion methods to obtain single-cell suspensions: (1) 5 dissected mouse corneas were cut into pieces (∼0.5 mm) and digested in trypsin for 10 min, and this digestion was repeated for 10 cycles; (2) 5 dissected mouse corneas were cut into pieces and incubated with 5 mg/ml collagenase A at 37 °C for 1h and then further digested in trypsin at 37 °C for 10 min; (3) used the same approach as that used in method 2, but the second digestion step was performed in TrypLE for 20 min; (4) used the same approach as that used in method 2, but the concentration of collagenase A was 2 mg/ml and the incubation time was 2h; (5) used the same approach as that used in method 3, but the corneas were incubated in 2 mg/ml collagenase A at 37 °C for 2h. Trypan blue staining was used to calculate the cell viability and agglomeration rate. The cell types and percentages were determined using immunofluorescence staining. RNA integrity number (RIN) was measured by Agilent 2100. Method 1 showed the lowest cell yield (0.375 × 105), epithelial cell percentage, and less than 70% cell viability, thus not a proper protocol. Method 2 showed the highest cell viability (over 90%), percentage of single-cell (89.53%), and high cell quantity (1.05 × 105). Method 3 had a significantly lower cell viability (55.30%). Cell agglomeration rates of method 4 and 5 reached up to 20% and 13%, and with lower cell viability (72.51%, 59.87%, respectively) and decreased epithelial cell rate compared to method 2 and 3. The results suggest that method 2 (5 mg/ml collagenase A and trypsin) is a preferred protocol for digesting mouse cornea to obtain single-cell suspension which achieves the criterion of single-cell RNA sequencing.
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Affiliation(s)
- Xiaodong Liu
- Eye Institute and Affiliated Xiamen Eye Center of Xiamen University, Fujian Provincial Key Laboratory of Cornea & Ocular Surface Diseases, Xiamen, Fujian, 361002, China; School of Medicine, Xiamen University, Xiamen, Fujian, 361002, China; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Xiamen, Fujian, 361002, China
| | - Shengpeng Zhang
- Eye Institute and Affiliated Xiamen Eye Center of Xiamen University, Fujian Provincial Key Laboratory of Cornea & Ocular Surface Diseases, Xiamen, Fujian, 361002, China; School of Medicine, Xiamen University, Xiamen, Fujian, 361002, China; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Xiamen, Fujian, 361002, China
| | - Yi Mao
- The Affiliated Hospital of Guizhou Medical University, Guiyang, 350000, Guizhou, China; Eye Institute and Affiliated Xiamen Eye Center of Xiamen University, Fujian Provincial Key Laboratory of Cornea & Ocular Surface Diseases, Xiamen, Fujian, 361002, China; School of Medicine, Xiamen University, Xiamen, Fujian, 361002, China
| | - Sijie Lin
- Eye Institute and Affiliated Xiamen Eye Center of Xiamen University, Fujian Provincial Key Laboratory of Cornea & Ocular Surface Diseases, Xiamen, Fujian, 361002, China
| | - Huping Wu
- Eye Institute and Affiliated Xiamen Eye Center of Xiamen University, Fujian Provincial Key Laboratory of Cornea & Ocular Surface Diseases, Xiamen, Fujian, 361002, China; School of Medicine, Xiamen University, Xiamen, Fujian, 361002, China; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Xiamen, Fujian, 361002, China.
| | - Shangkun Ou
- The Affiliated Hospital of Guizhou Medical University, Guiyang, 350000, Guizhou, China; Eye Institute and Affiliated Xiamen Eye Center of Xiamen University, Fujian Provincial Key Laboratory of Cornea & Ocular Surface Diseases, Xiamen, Fujian, 361002, China; School of Medicine, Xiamen University, Xiamen, Fujian, 361002, China; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Xiamen, Fujian, 361002, China.
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13
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Polisetti N, Martin G, Cristina Schmitz HR, Schlötzer-Schrehardt U, Schlunck G, Reinhard T. Characterization of Porcine Ocular Surface Epithelial Microenvironment. Int J Mol Sci 2023; 24:ijms24087543. [PMID: 37108705 PMCID: PMC10145510 DOI: 10.3390/ijms24087543] [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: 02/28/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
The porcine ocular surface is used as a model of the human ocular surface; however, a detailed characterization of the porcine ocular surface has not been documented. This is due, in part, to the scarcity of antibodies produced specifically against the porcine ocular surface cell types or structures. We performed a histological and immunohistochemical investigation on frozen and formalin-fixed, paraffin-embedded ocular surface tissue from domestic pigs using a panel of 41 different antibodies related to epithelial progenitor/differentiation phenotypes, extracellular matrix and associated molecules, and various niche cell types. Our observations suggested that the Bowman's layer is not evident in the cornea; the deep invaginations of the limbal epithelium in the limbal zone are analogous to the limbal interpalisade crypts of human limbal tissue; and the presence of goblet cells in the bulbar conjunctiva. Immunohistochemistry analysis revealed that the epithelial progenitor markers cytokeratin (CK)15, CK14, p63α, and P-cadherin were expressed in both the limbal and conjunctival basal epithelium, whereas the basal cells of the limbal and conjunctival epithelium did not stain for CK3, CK12, E-cadherin, and CK13. Antibodies detecting marker proteins related to the extracellular matrix (collagen IV, Tenascin-C), cell-matrix adhesion (β-dystroglycan, integrin α3 and α6), mesenchymal cells (vimentin, CD90, CD44), neurons (neurofilament), immune cells (HLA-ABC; HLA-DR, CD1, CD4, CD14), vasculature (von Willebrand factor), and melanocytes (SRY-homeobox-10, human melanoma black-45, Tyrosinase) on the normal human ocular surface demonstrated similar immunoreactivity on the normal porcine ocular surface. Only a few antibodies (directed against N-cadherin, fibronectin, agrin, laminin α3 and α5, melan-A) appeared unreactive on porcine tissues. Our findings characterize the main immunohistochemical properties of the porcine ocular surface and provide a morphological and immunohistochemical basis useful to research using porcine models. Furthermore, the analyzed porcine ocular structures are similar to those of humans, confirming the potential usefulness of pig eyes to study ocular surface physiology and pathophysiology.
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Affiliation(s)
- Naresh Polisetti
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106 Freiburg, Germany
| | - Gottfried Martin
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106 Freiburg, Germany
| | - Heidi R Cristina Schmitz
- CEMT-Freiburg, Experimental Surgery, Hospital-Medical Center, Faculty of Medicine, University of Freiburg, Breisacher Str. 66, 79106 Freiburg, Germany
| | - Ursula Schlötzer-Schrehardt
- Department of Ophthalmology, University Hospital Erlangen, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054 Erlangen, Germany
| | - Günther Schlunck
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106 Freiburg, Germany
| | - Thomas Reinhard
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106 Freiburg, Germany
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14
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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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15
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Lu ZJ, Ye JG, Wang DL, Li MK, Zhang QK, Liu Z, Huang YJ, Pan CN, Lin YH, Shi ZX, Zheng YF. Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Mouse Corneal Epithelial Cells. Invest Ophthalmol Vis Sci 2023; 64:30. [PMID: 36943152 PMCID: PMC10043503 DOI: 10.1167/iovs.64.3.30] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Purpose Corneal epithelial homeostasis is maintained by coordinated gene expression across distinct cell populations, but the gene regulatory programs underlying this cellular diversity remain to be characterized. Here we applied single-cell multi-omics analysis to delineate the gene regulatory profile of mouse corneal epithelial cells under normal homeostasis. Methods Single cells isolated from the cornea epithelium (with marginal conjunctiva) of adult mice were subjected to scRNA-seq and scATAC-seq using the 10×Genomics platform. Cell types were clustered by the graph-based visualization method uniform manifold approximation and projection and unbiased computational informatics analysis. The scRNA-seq and scATAC-seq datasets were integrated following the integration pipeline described in ArchR and Seurat. Results We characterized diverse corneal epithelial cell types based on gene expression signatures and chromatin accessibility. We found that cell type-specific accessibility regions were mainly located at distal regions, suggesting essential roles of distal regulatory elements in determining corneal epithelial cell diversity. Trajectory analyses revealed a continuum of cell state transition and higher coordination between transcription factor (TF) motif accessibility and gene expression during corneal epithelial cell differentiation. By integrating transcriptomic and chromatin accessibility analysis, we identified cell type-specific and shared gene regulation programs. We also uncovered critical TFs driving corneal epithelial cell differentiation, such as nuclear factor I (NFI) family members, Rarg, Elf3. We found that nuclear factor-κB (NF-κB) family members were positive TFs in limbal cells and some superficial cells, but they were involved in regulating distinct biological processes. Conclusions Our study presents a comprehensive gene regulatory landscape of mouse cornea epithelial cells, and provides valuable foundations for future investigation of corneal epithelial homeostasis in the context of cornea pathologies and regenerative medicine.
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Affiliation(s)
- Zhao-Jing Lu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, China
| | - Jin-Guo Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Dong-Liang Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Meng-Ke Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qi-Kai Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhong Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yan-Jing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Cai-Neng Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yu-Heng Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhuo-Xing Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Ying-Feng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, China
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16
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Talpan D, Salla S, Meusel L, Walter P, Kuo CC, Franzen J, Fuest M. Cytoprotective Effects of Human Platelet Lysate during the Xeno-Free Culture of Human Donor Corneas. Int J Mol Sci 2023; 24:ijms24032882. [PMID: 36769200 PMCID: PMC9917909 DOI: 10.3390/ijms24032882] [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: 10/28/2022] [Revised: 01/18/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
We evaluated the suitability of 2% human platelet lysate medium (2%HPL) as a replacement for 2% fetal bovine serum medium (2%FBS) for the xeno-free organ culture of human donor corneas. A total of 32 corneas from 16 human donors were cultured in 2%FBS for 3 days (TP1), then evaluated using phase contrast microscopy (endothelial cell density (ECD) and cell morphology). Following an additional 25-day culture period (TP2) in either 2%FBS or 2%HPL, the pairs were again compared using microscopy; then stroma and Descemet membrane/endothelium (DmE) were processed for next generation sequencing (NGS). At TP2 the ECD was higher in the 2%HPL group (2179 ± 288 cells/mm2) compared to 2%FBS (2113 ± 331 cells/mm2; p = 0.03), and endothelial cell loss was lower (ECL HPL = -0.7% vs. FBS = -3.8%; p = 0.01). There were no significant differences in cell morphology between TP1 and 2, or between 2%HPL and 2%FBS. NGS showed the differential expression of 1644 genes in endothelial cells and 217 genes in stromal cells. It was found that 2%HPL led to the upregulation of cytoprotective, anti-inflammatory and anti-fibrotic genes (HMOX1, SERPINE1, ANGPTL4, LEFTY2, GADD45B, PLIN2, PTX3, GFRA1/2), and the downregulation of pro-inflammatory/apoptotic genes (e.g., CXCL14, SIK1B, PLK5, PPP2R3B, FABP5, MAL, GATA3). 2%HPL is a suitable xeno-free substitution for 2%FBS in human cornea organ culture, inducing less ECL and producing potentially beneficial alterations in gene expression.
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Affiliation(s)
- Delia Talpan
- Department of Ophthalmology, RWTH Aachen University, 52074 Aachen, Germany
| | - Sabine Salla
- Department of Ophthalmology, RWTH Aachen University, 52074 Aachen, Germany
- Cornea Bank Aachen, RWTH Aachen University, 52074 Aachen, Germany
| | - Linus Meusel
- Department of Ophthalmology, RWTH Aachen University, 52074 Aachen, Germany
- Cornea Bank Aachen, RWTH Aachen University, 52074 Aachen, Germany
| | - Peter Walter
- Department of Ophthalmology, RWTH Aachen University, 52074 Aachen, Germany
- Cornea Bank Aachen, RWTH Aachen University, 52074 Aachen, Germany
| | - Chao-Chung Kuo
- Genomics Facility, Interdisciplinary Center for Clinical Research (IZKF), RWTH Aachen University, 52074 Aachen, Germany
| | - Julia Franzen
- Genomics Facility, Interdisciplinary Center for Clinical Research (IZKF), RWTH Aachen University, 52074 Aachen, Germany
| | - Matthias Fuest
- Department of Ophthalmology, RWTH Aachen University, 52074 Aachen, Germany
- Cornea Bank Aachen, RWTH Aachen University, 52074 Aachen, Germany
- Correspondence:
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17
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Dry eye disease in mice activates adaptive corneal epithelial regeneration distinct from constitutive renewal in homeostasis. Proc Natl Acad Sci U S A 2023; 120:e2204134120. [PMID: 36595669 PMCID: PMC9926235 DOI: 10.1073/pnas.2204134120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Many epithelial compartments undergo constitutive renewal in homeostasis but activate unique regenerative responses following injury. The clear corneal epithelium is crucial for vision and is renewed from limbal stem cells (LSCs). Using single-cell RNA sequencing, we profiled the mouse corneal epithelium in homeostasis, aging, diabetes, and dry eye disease (DED), where tear deficiency predisposes the cornea to recurrent injury. In homeostasis, we capture the transcriptional states that accomplish continuous tissue turnover. We leverage our dataset to identify candidate genes and gene networks that characterize key stages across homeostatic renewal, including markers for LSCs. In aging and diabetes, there were only mild changes with <15 dysregulated genes. The constitutive cell types that accomplish homeostatic renewal were conserved in DED but were associated with activation of cell states that comprise "adaptive regeneration." We provide global markers that distinguish cell types in homeostatic renewal vs. adaptive regeneration and markers that specifically define DED-elicited proliferating and differentiating cell types. We validate that expression of SPARC, a marker of adaptive regeneration, is also induced in corneal epithelial wound healing and accelerates wound closure in a corneal epithelial cell scratch assay. Finally, we propose a classification system for LSC markers based on their expression fidelity in homeostasis and disease. This transcriptional dissection uncovers the dramatically altered transcriptional landscape of the corneal epithelium in DED, providing a framework and atlas for future study of these ocular surface stem cells in health and disease.
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18
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Lee V, Rompolas P. Corneal regeneration: insights in epithelial stem cell heterogeneity and dynamics. Curr Opin Genet Dev 2022; 77:101981. [PMID: 36084496 PMCID: PMC9938714 DOI: 10.1016/j.gde.2022.101981] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 01/27/2023]
Abstract
The discovery of slow-cycling cells at the corneal periphery three decades ago established the limbus as the putative corneal stem cell niche. Since then, studies have underscored the importance of the limbal stem cells in maintaining the health and function of the ocular surface. Advancements in our understanding of stem cell biology have been successfully translated into stem cell therapies for corneal diseases. Here, we review recent developments in mouse genetics, intravital imaging, and single-cell genomics that have revealed an underappreciated complexity of the limbal stem cells, from their molecular identity, function, and interactions with their niche environment. Continued efforts to elucidate stem cell dynamics of this extraordinary tissue are critical for not only understanding stem cell biology but also for advancing therapeutic innovation and development.
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Affiliation(s)
- Vivian Lee
- Department of Ophthalmology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Panteleimon Rompolas
- Department of Ophthalmology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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19
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Transcriptomic Landscape and Functional Characterization of Human Induced Pluripotent Stem Cell-Derived Limbal Epithelial Progenitor Cells. Cells 2022; 11:cells11233752. [PMID: 36497012 PMCID: PMC9737332 DOI: 10.3390/cells11233752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022] Open
Abstract
Limbal stem cell deficiency (LSCD) is a complex, multifactorial disease affecting limbal epithelial progenitor cells (LEPC), which are essential for maintaining corneal stability and transparency. Human induced pluripotent stem cell-derived (hiPSC-) LEPC are a promising cell source for the treatment of LSCD. However, their similarity to native tissue-derived (T-) LEPC and their functional characterization has not been studied in detail. Here, we show that hiPSC-LEPC and T-LEPC have rather similar gene expression patterns, colony-forming ability, wound-healing capacity, and melanosome uptake. In addition, hiPSC-LEPC exhibited lower immunogenicity and reduced the proliferation of peripheral blood mononuclear cells compared with T-LEPC. Similarly, the hiPSC-LEPC secretome reduced the proliferation of vascular endothelial cells more than the T-LEPC secretome. Moreover, hiPSC-LEPC successfully repopulated decellularized human corneolimbal (DHC/L) scaffolds with multilayered epithelium, while basal deposition of fibrillary material was observed. These findings suggest that hiPSC-LEPC exhibited functional properties close to native LEPC and that hiPSC-LEPC-DHC/L scaffolds might be feasible for transplantation in patients suffering from LSCD in the future. Although hiPSC-LEPC-based stem cell therapy is promising, the current study also revealed new challenges, such as abnormal extracellular matrix deposition, that need to be overcome before hiPSC-LEPC-based stem cell therapies are viable.
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20
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Sonam S, Bangru S, Perry KJ, Chembazhi UV, Kalsotra A, Henry JJ. Cellular and molecular profiles of larval and adult Xenopus corneal epithelia resolved at the single-cell level. Dev Biol 2022; 491:13-30. [PMID: 36049533 PMCID: PMC10241109 DOI: 10.1016/j.ydbio.2022.08.007] [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: 01/20/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022]
Abstract
Corneal Epithelial Stem Cells (CESCs) and their proliferative progeny, the Transit Amplifying Cells (TACs), are responsible for homeostasis and maintaining corneal transparency. Owing to our limited knowledge of cell fates and gene activity within the cornea, the search for unique markers to identify and isolate these cells remains crucial for ocular surface reconstruction. We performed single-cell RNA sequencing of corneal cells from larval and adult stages of Xenopus. Our results indicate that as the cornea develops and matures, there is an increase in cellular diversity, which is accompanied by a substantial shift in transcriptional profile, gene regulatory network and cell-cell communication dynamics. Our data also reveals several novel genes expressed in corneal cells and changes in gene expression during corneal differentiation at both developmental time-points. Importantly, we identify specific basal cell clusters in both the larval and adult cornea that comprise a relatively undifferentiated cell type and express distinct stem cell markers, which we propose are the putative larval and adult CESCs, respectively. This study offers a detailed atlas of single-cell transcriptomes in the frog cornea. In the future, this work will be useful to elucidate the function of novel genes in corneal epithelial homeostasis, wound healing and regeneration.
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Affiliation(s)
- Surabhi Sonam
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA; Cancer Center@Illinois, University of Illinois, Urbana-Champaign, IL, USA
| | - Kimberly J Perry
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL, USA
| | - Ullas V Chembazhi
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, USA; Cancer Center@Illinois, University of Illinois, Urbana-Champaign, IL, USA.
| | - Jonathan J Henry
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL, USA.
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21
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Maiti G, Monteiro de Barros MR, Hu N, Dolgalev I, Roshan M, Foster JW, Tsirigos A, Wahlin KJ, Chakravarti S. Single cell RNA-seq of human cornea organoids identifies cell fates of a developing immature cornea. PNAS NEXUS 2022; 1:pgac246. [PMID: 36712326 PMCID: PMC9802453 DOI: 10.1093/pnasnexus/pgac246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 10/26/2022] [Indexed: 11/27/2022]
Abstract
The cornea is a protective and refractive barrier in the eye crucial for vision. Understanding the human cornea in health, disease, and cell-based treatments can be greatly advanced with cornea organoids developed in culture from induced pluripotent stem cells. While a limited number of studies have investigated the single-cell transcriptomic composition of the human cornea, its organoids have not been examined similarly. Here, we elucidated the transcriptomic cell fate map of 4-month-old human cornea organoids and human donor corneas. The organoids harbor cell clusters that resemble cells of the corneal epithelium, stroma, and endothelium, with subpopulations that capture signatures of early developmental states. Unlike the adult cornea where the largest cell population is stromal, the organoids contain large proportions of epithelial and endothelial-like cells. These corneal organoids offer a 3D model to study corneal diseases and integrated responses of different cell types.
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Affiliation(s)
- George Maiti
- Department of Ophthalmology, NYU Grossman School of Medicine, Science Building, Fifth Floor 435 E 30th, New York, NY 10016, USA
| | - Maithê Rocha Monteiro de Barros
- Department of Ophthalmology, NYU Grossman School of Medicine, Science Building, Fifth Floor 435 E 30th, New York, NY 10016, USA
| | - Nan Hu
- Department of Ophthalmology, NYU Grossman School of Medicine, Science Building, Fifth Floor 435 E 30th, New York, NY 10016, USA
| | - Igor Dolgalev
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, Science Building, Eighth Floor, 435 E 30th, New York, NY 10016, USA
| | - Mona Roshan
- University of California San Diego, ACTRI Building Rm Lower level 3E419, 9452 Medical Center Drive, La Jolla, CA 92037, USA
| | - James W Foster
- Wilmer Eye Institute, Johns Hopkins school of Medicine, Smith M037, 400 Broadway, Baltimore, MD 21287, USA
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, Science Building, Eighth Floor, 435 E 30th, New York, NY 10016, USA,Department of Pathology, NYU Grossman School of Medicine, Science Building, Fifth Floor 435 E 30th, New York, NY 10016, USA
| | - Karl J Wahlin
- University of California San Diego, ACTRI Building Rm Lower level 3E419, 9452 Medical Center Drive, La Jolla, CA 92037, USA
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22
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van Zyl T, Yan W, McAdams AM, Monavarfeshani A, Hageman GS, Sanes JR. Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types. Proc Natl Acad Sci U S A 2022; 119:e2200914119. [PMID: 35858321 PMCID: PMC9303934 DOI: 10.1073/pnas.2200914119] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/26/2022] [Indexed: 01/17/2023] Open
Abstract
The anterior segment of the eye consists of the cornea, iris, ciliary body, crystalline lens, and aqueous humor outflow pathways. Together, these tissues are essential for the proper functioning of the eye. Disorders of vision have been ascribed to defects in all of them; some disorders, including glaucoma and cataract, are among the most prevalent causes of blindness in the world. To characterize the cell types that compose these tissues, we generated an anterior segment cell atlas of the human eye using high-throughput single-nucleus RNA sequencing (snRNAseq). We profiled 195,248 nuclei from nondiseased anterior segment tissues of six human donors, identifying >60 cell types. Many of these cell types were discrete, whereas others, especially in the lens and cornea, formed continua corresponding to known developmental transitions that persist in adulthood. Having profiled each tissue separately, we performed an integrated analysis of the entire anterior segment, revealing that some cell types are unique to a single structure, whereas others are shared across tissues. The integrated cell atlas was then used to investigate cell type-specific expression patterns of more than 900 human ocular disease genes identified through either Mendelian inheritance patterns or genome-wide association studies.
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Affiliation(s)
- Tavé van Zyl
- Department of Ophthalmology, Harvard Medical School, Boston, MA 02115
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Wenjun Yan
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Alexi M. McAdams
- Department of Ophthalmology, Harvard Medical School, Boston, MA 02115
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Aboozar Monavarfeshani
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Boston Children’s Hospital, F.M. Kirby Neurobiology Center, Boston, MA 02115
| | - Gregory S. Hageman
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, University of Utah, Salt Lake City, UT 84132
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT 84132
| | - Joshua R. Sanes
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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23
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Song Z, Chen B, Tsai CH, Wu D, Liu E, Hawkins IS, Phan A, Auman JT, Tao Y, Mei H. Differentiation Trajectory of Limbal Stem and Progenitor Cells under Normal Homeostasis and upon Corneal Wounding. Cells 2022; 11:cells11131983. [PMID: 35805068 PMCID: PMC9266118 DOI: 10.3390/cells11131983] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/06/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
Limbal stem cells (LSCs) reside discretely at limbus surrounded by niche cells and progenitor cells. The aim of this study is to identify the heterogeneous cell populations at limbus under normal homeostasis and upon wounding using single-cell RNA sequencing in a mouse model. Two putative LSC types were identified which showed a differentiation trajectory into limbal progenitor cell (LPC) types under normal homeostasis and during wound healing. They were designated as “putative active LSCs” and “putative quiescent LSCs”, respectively, because the former type actively divided upon wounding while the later type stayed at a quiescent status upon wounding. The “putative quiescent LSCs” might contribute to a barrier function due to their characteristic markers regulating vascular and epithelial barrier and growth. Different types of LPCs at different proliferative statuses were identified in unwounded and wounded corneas with distinctive markers. Four maturation markers (Aldh3, Slurp1, Tkt, and Krt12) were screened out for corneal epithelium, which showed an increased expression along the differentiation trajectory during corneal epithelial maturation. In conclusion, our study identified two different types of putative LSCs and several types of putative LPCs under normal homeostasis and upon wounding, which will facilitate the understanding of corneal epithelial regeneration and wound healing.
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Affiliation(s)
- Zhenwei Song
- Department of Ophthalmology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (Z.S.); (C.-H.T.); (E.L.); (I.S.H.)
- School of Medicine, Hunan Normal University, 371 Tongzipo Road, Changsha 410081, China
| | - Brian Chen
- Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (B.C.); (D.W.)
| | - Chi-Hao Tsai
- Department of Ophthalmology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (Z.S.); (C.-H.T.); (E.L.); (I.S.H.)
| | - Di Wu
- Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (B.C.); (D.W.)
- Division of Oral and Craniofacial Health Research, Adams School of Dentistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emily Liu
- Department of Ophthalmology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (Z.S.); (C.-H.T.); (E.L.); (I.S.H.)
| | - Isha Sharday Hawkins
- Department of Ophthalmology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (Z.S.); (C.-H.T.); (E.L.); (I.S.H.)
| | - Andrew Phan
- Department of Psychology and Neuroscience, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - James Todd Auman
- Department of Pathology and Laboratory Medicine, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (J.T.A.); (Y.T.)
| | - Yazhong Tao
- Department of Pathology and Laboratory Medicine, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (J.T.A.); (Y.T.)
| | - Hua Mei
- Department of Ophthalmology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (Z.S.); (C.-H.T.); (E.L.); (I.S.H.)
- Department of Cell Biology and Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence:
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24
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Li Y, Jeong J, Song W. Molecular Characteristics and Distribution of Adult Human Corneal Immune Cell Types. Front Immunol 2022; 13:798346. [PMID: 35280984 PMCID: PMC8905655 DOI: 10.3389/fimmu.2022.798346] [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: 10/20/2021] [Accepted: 01/19/2022] [Indexed: 11/22/2022] Open
Abstract
Background The limbus is located at a 2-mm-wide area between the bulbar conjunctiva and the cornea and has been suggested to be the niche of corneal epithelial stem cells and immune cells. Like the skin and intestines, the cornea is also an important mucosal surface, and immune cells on the cornea play critical roles in immune surveillance to ensure barrier surface homeostasis and protection from various environmental damage and infections. Single-cell RNA sequencing (scRNA-seq) analysis of protein tyrosine phosphatase receptor type C positive (PTPRC+) hematopoietic cells from the corneal limbus could provide a single cell atlas of all the immune cell subsets. Methods We performed single-cell RNA sequencing to generate transcriptomic profile for 804 sort-purified hematopoietic cells from the corneal limbus of three healthy donors. Results Our analysis identified a primary transcriptomic pattern for multiple immune cell subtypes, including naive T cells, antiviral effector CD8+ T cells, and innate immune cells such as IDO1+ mature regulatory dendritic cells (mregDCs), macrophages, monocytes, and basophils in the human corneal limbus. Conclusion Overall, single-cell transcriptomic analysis of limbal immune cells suggested the possible contribution of these cells on the adaptive and innate immune response of the human cornea.
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Affiliation(s)
- Yanxiu Li
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, China.,Eye Center of Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Joyce Jeong
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, United States
| | - Weitao Song
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, China.,Eye Center of Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
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