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Jin L, Zhang L, Yan C, Liu M, Dean DC, Liu Y. Corneal injury repair and the potential involvement of ZEB1. EYE AND VISION (LONDON, ENGLAND) 2024; 11:20. [PMID: 38822380 PMCID: PMC11143703 DOI: 10.1186/s40662-024-00387-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
The cornea, consisting of three cellular and two non-cellular layers, is the outermost part of the eyeball and frequently injured by external physical, chemical, and microbial insults. The epithelial-to-mesenchymal transition (EMT) plays a crucial role in the repair of corneal injuries. Zinc finger E-box binding homeobox 1 (ZEB1), an important transcription factor involved in EMT, is expressed in the corneal tissues. It regulates cell activities like migration, transformation, and proliferation, and thereby affects tissue inflammation, fibrosis, tumor metastasis, and necrosis by mediating various major signaling pathways, including transforming growth factor (TGF)-β. Dysfunction of ZEB1 would impair corneal tissue repair leading to epithelial healing delay, interstitial fibrosis, neovascularization, and squamous cell metaplasia. Understanding the mechanism underlying ZEB1 regulation of corneal injury repair will help us to formulate a therapeutic approach to enhance corneal injury repair.
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Affiliation(s)
- Lin Jin
- Department of Ophthalmology, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, 116033, China
| | - Lijun Zhang
- Department of Ophthalmology, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, 116033, China
| | - Chunxiao Yan
- Department of Ophthalmology, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, 116033, China
| | - Mengxin Liu
- Department of Ophthalmology, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, 116033, China
| | - Douglas C Dean
- James Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
| | - Yongqing Liu
- James Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
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Rice G, Farrelly O, Huang S, Kuri P, Curtis E, Ohman L, Li N, Lengner C, Lee V, Rompolas P. Sox9 marks limbal stem cells and is required for asymmetric cell fate switch in the corneal epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588195. [PMID: 38645161 PMCID: PMC11030424 DOI: 10.1101/2024.04.08.588195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Adult tissues with high cellular turnover require a balance between stem cell renewal and differentiation, yet the mechanisms underlying this equilibrium are unclear. The cornea exhibits a polarized lateral flow of progenitors from the peripheral stem cell niche to the center; attributed to differences in cellular fate. To identify genes that are critical for regulating the asymmetric fates of limbal stem cells and their transient amplified progeny in the central cornea, we utilized an in vivo cell cycle reporter to isolate proliferating basal cells across the anterior ocular surface epithelium and performed single-cell transcriptional analysis. This strategy greatly increased the resolution and revealed distinct basal cell identities with unique expression profiles of structural genes and transcription factors. We focused on Sox9; a transcription factor implicated in stem cell regulation across various organs. Sox9 was found to be differentially expressed between limbal stem cells and their progeny in the central corneal. Lineage tracing analysis confirmed that Sox9 marks long-lived limbal stem cells and conditional deletion led to abnormal differentiation and squamous metaplasia in the central cornea. These data suggest a requirement for Sox9 for the switch to asymmetric fate and commitment toward differentiation, as transient cells exit the limbal niche. By inhibiting terminal differentiation of corneal progenitors and forcing them into perpetual symmetric divisions, we replicated the Sox9 loss-of-function phenotype. Our findings reveal an essential role for Sox9 for the spatial regulation of asymmetric fate in the corneal epithelium that is required to sustain tissue homeostasis.
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Verma S, Lin X, Coulson-Thomas VJ. The Potential Reversible Transition between Stem Cells and Transient-Amplifying Cells: The Limbal Epithelial Stem Cell Perspective. Cells 2024; 13:748. [PMID: 38727284 PMCID: PMC11083486 DOI: 10.3390/cells13090748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Stem cells (SCs) undergo asymmetric division, producing transit-amplifying cells (TACs) with increased proliferative potential that move into tissues and ultimately differentiate into a specialized cell type. Thus, TACs represent an intermediary state between stem cells and differentiated cells. In the cornea, a population of stem cells resides in the limbal region, named the limbal epithelial stem cells (LESCs). As LESCs proliferate, they generate TACs that move centripetally into the cornea and differentiate into corneal epithelial cells. Upon limbal injury, research suggests a population of progenitor-like cells that exists within the cornea can move centrifugally into the limbus, where they dedifferentiate into LESCs. Herein, we summarize recent advances made in understanding the mechanism that governs the differentiation of LESCs into TACs, and thereafter, into corneal epithelial cells. We also outline the evidence in support of the existence of progenitor-like cells in the cornea and whether TACs could represent a population of cells with progenitor-like capabilities within the cornea. Furthermore, to gain further insights into the dynamics of TACs in the cornea, we outline the most recent findings in other organ systems that support the hypothesis that TACs can dedifferentiate into SCs.
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Affiliation(s)
- Sudhir Verma
- College of Optometry, University of Houston, 4901 Calhoun Road, Houston, TX 77204, USA;
- Deen Dayal Upadhyaya College, University of Delhi, Delhi 110078, India
| | - Xiao Lin
- College of Optometry, University of Houston, 4901 Calhoun Road, Houston, TX 77204, USA;
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Kistenmacher S, Schwämmle M, Martin G, Ulrich E, Tholen S, Schilling O, Gießl A, Schlötzer-Schrehardt U, Bucher F, Schlunck G, Nazarenko I, Reinhard T, Polisetti N. Enrichment, Characterization, and Proteomic Profiling of Small Extracellular Vesicles Derived from Human Limbal Mesenchymal Stromal Cells and Melanocytes. Cells 2024; 13:623. [PMID: 38607062 PMCID: PMC11011788 DOI: 10.3390/cells13070623] [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: 03/11/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/13/2024] Open
Abstract
Limbal epithelial progenitor cells (LEPC) rely on their niche environment for proper functionality and self-renewal. While extracellular vesicles (EV), specifically small EVs (sEV), have been proposed to support LEPC homeostasis, data on sEV derived from limbal niche cells like limbal mesenchymal stromal cells (LMSC) remain limited, and there are no studies on sEVs from limbal melanocytes (LM). In this study, we isolated sEV from conditioned media of LMSC and LM using a combination of tangential flow filtration and size exclusion chromatography and characterized them by nanoparticle tracking analysis, transmission electron microscopy, Western blot, multiplex bead arrays, and quantitative mass spectrometry. The internalization of sEV by LEPC was studied using flow cytometry and confocal microscopy. The isolated sEVs exhibited typical EV characteristics, including cell-specific markers such as CD90 for LMSC-sEV and Melan-A for LM-sEV. Bioinformatics analysis of the proteomic data suggested a significant role of sEVs in extracellular matrix deposition, with LMSC-derived sEV containing proteins involved in collagen remodeling and cell matrix adhesion, whereas LM-sEV proteins were implicated in other cellular bioprocesses such as cellular pigmentation and development. Moreover, fluorescently labeled LMSC-sEV and LM-sEV were taken up by LEPC and localized to their perinuclear compartment. These findings provide valuable insights into the complex role of sEV from niche cells in regulating the human limbal stem cell niche.
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Affiliation(s)
- Sebastian Kistenmacher
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106 Freiburg, Germany
| | - Melanie Schwämmle
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D–79104 Freiburg, Germany
| | - Gottfried Martin
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106 Freiburg, Germany
| | - Eva Ulrich
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106 Freiburg, Germany
| | - Stefan Tholen
- Institute of Surgical Pathology, Faculty of Medicine, Freiburg, Medical Center, University of Freiburg, 79085 Freiburg im Breisgau, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, Freiburg, Medical Center, University of Freiburg, 79085 Freiburg im Breisgau, Germany
| | - Andreas Gießl
- Department of Ophthalmology, University Hospital Erlangen, Friedrich-Alexander-University of Erlan-gen-Nürnberg, Schwabachanlage 6, 91054 Erlangen, Germany
| | - Ursula Schlötzer-Schrehardt
- Department of Ophthalmology, University Hospital Erlangen, Friedrich-Alexander-University of Erlan-gen-Nürnberg, Schwabachanlage 6, 91054 Erlangen, Germany
| | - Felicitas Bucher
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106 Freiburg, Germany
| | - Günther Schlunck
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106 Freiburg, Germany
| | - Irina Nazarenko
- Institute for Infection Prevention and Hospital Epidemiology, Faculty of Medicine, Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Thomas Reinhard
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106 Freiburg, Germany
| | - Naresh Polisetti
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106 Freiburg, Germany
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Alam J, Yaman E, Silva GCV, Chen R, de Paiva CS, Stepp MA, Pflugfelder SC. Single cell analysis of short-term dry eye induced changes in cornea immune cell populations. Front Med (Lausanne) 2024; 11:1362336. [PMID: 38560382 PMCID: PMC10978656 DOI: 10.3389/fmed.2024.1362336] [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: 12/28/2023] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
Background Dry eye causes corneal inflammation, epitheliopathy and sensorineural changes. This study evaluates the hypothesis that dry eye alters the percentages and transcriptional profiles of immune cell populations in the cornea. Methods Desiccating stress (DS) induced dry eye was created by pharmacologic suppression of tear secretion and exposure to drafty low humidity environment. Expression profiling of corneal immune cells was performed by single-cell RNA sequencing (scRNA-seq). Cell differentiation trajectories and cell fate were modeled through RNA velocity analysis. Confocal microscopy was used to immunodetect corneal immune cells. Irritation response to topical neurostimulants was assessed. Results Twelve corneal immune cell populations based on their transcriptional profiles were identified at baseline and consist of monocytes, resident (rMP) and MMP12/13 high macrophages, dendritic cells (cDC2), neutrophils, mast cells, pre T/B cells, and innate (γDT, ILC2, NK) and conventional T and B lymphocytes. T cells and resident macrophages (rMP) were the largest populations in the normal cornea comprising 18.6 and 18.2 percent, respectively. rMP increased to 55.2% of cells after 5 days of DS. Significant changes in expression of 1,365 genes (adj p < 0.0001) were noted in rMP with increases in cytokines and chemokines (Tnf, Cxcl1, Ccl12, Il1rn), inflammatory markers (Vcam, Adam17, Junb), the TAM receptor (Mertk), and decreases in complement and MHCII genes. A differentiation trajectory from monocytes to terminal state rMP was found. Phagocytosis, C-type lectin receptor signaling, NF-kappa B signaling and Toll-like receptor signaling were among the pathways with enhanced activity in these cells. The percentage of MRC1+ rMPs increased in the cornea and they were observed in the basal epithelium adjacent to epithelial nerve plexus. Concentration of the chemokine CXCL1 increased in the cornea and it heightened irritation/pain responses to topically applied hypertonic saline. Conclusion These findings indicate that DS recruits monocytes that differentiate to macrophages with increased expression of inflammation associated genes. The proximity of these macrophages to cornea nerves and their expression of neurosensitizers suggests they contribute to the corneal sensorineural changes in dry eye.
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Affiliation(s)
- Jehan Alam
- Ocular Surface Center, Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
| | - Ebru Yaman
- Ocular Surface Center, Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
| | - Gerda Cristal Villalba Silva
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Rui Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Cintia S. de Paiva
- Ocular Surface Center, Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
| | - Mary Ann Stepp
- Departments of Anatomy, Regenerative Biology and Ophthalmology, The George Washington University Medical School and Health Sciences, Washington, DC, United States
| | - Stephen C. Pflugfelder
- Ocular Surface Center, Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
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Brookins E, Serrano SE, Yacu GS, Finer G, Thomson BR. Non-endothelial expression of Endomucin in the mouse and human choroid. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584133. [PMID: 38559191 PMCID: PMC10979916 DOI: 10.1101/2024.03.08.584133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Endomucin (EMCN) is a 261 AA transmembrane glycoprotein that is highly expressed by venous and capillary endothelial cells where it plays a role in VEGF-mediated angiogenesis and regulation of immune cell recruitment. However, it is better known as a histological marker, where it has become widespread due to the commercial availability of high-quality antibodies that work under a wide range of conditions and in many tissues. The specificity of EMCN staining has been well-validated in retinal vessels, but while it has been used extensively as a marker in other tissues of the eye, including the choroid, the pattern of expression has not been described in detail. Here, in addition to endothelial expression in the choriocapillaris and deeper vascular layers, we characterize a population of EMCN-positive perivascular cells in the mouse choroid that did not co-localize with cells expressing other endothelial markers such as PECAM1 or PODXL. To confirm that these cells represented a new population of EMCN-expressing stromal cells, we then performed single cell RNA sequencing in choroids from adult wild-type mice. Analysis of this new dataset confirmed that, in addition to endothelial cells, Emcn mRNA expression was present in choroidal pericytes and a subset of fibroblasts, but not vascular smooth muscle cells. Besides Emcn , no known endothelial gene expression was detected in these cell populations, confirming that they did not represent endothelial-stromal doublets, a common technical artifact in single cell RNA seq datasets. Instead, choroidal Emcn -expressing fibroblasts exhibited high levels of chemokine and interferon signaling genes, while Emcn -negative fibroblasts were enriched in genes encoding extracellular matrix proteins. Emcn expressing fibroblasts were also detected in published datasets from mouse brain and human choroid, suggesting that stromal Emcn expression was not unique to the choroid and was evolutionarily conserved. Together, these findings highlight unique fibroblast and pericyte populations in the choroid and provide new context for the role of EMCN in angiogenesis and immune cell recruitment.
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7
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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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8
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Tyler SR, Lozano-Ojalvo D, Guccione E, Schadt EE. Anti-correlated feature selection prevents false discovery of subpopulations in scRNAseq. Nat Commun 2024; 15:699. [PMID: 38267438 PMCID: PMC10808220 DOI: 10.1038/s41467-023-43406-9] [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: 12/13/2022] [Accepted: 11/07/2023] [Indexed: 01/26/2024] Open
Abstract
While sub-clustering cell-populations has become popular in single cell-omics, negative controls for this process are lacking. Popular feature-selection/clustering algorithms fail the null-dataset problem, allowing erroneous subdivisions of homogenous clusters until nearly each cell is called its own cluster. Using real and synthetic datasets, we find that anti-correlated gene selection reduces or eliminates erroneous subdivisions, increases marker-gene selection efficacy, and efficiently scales to millions of cells.
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Affiliation(s)
- Scott R Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Daniel Lozano-Ojalvo
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ernesto Guccione
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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9
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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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Peng H, Kaplan N, Liu M, Jiang H, Lavker RM. Keeping an Eye Out for Autophagy in the Cornea: Sample Preparation for Single-Cell RNA-Sequencing. Methods Mol Biol 2023:10.1007/7651_2023_502. [PMID: 37930627 PMCID: PMC11162605 DOI: 10.1007/7651_2023_502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Single-cell RNA-sequencing (scRNA-seq) is a powerful technique that can barcode individual cells and thus used to obtain a gene expression profile for every individual cell within a tissue. This makes scRNA-seq an excellent method for characterizing rare cell populations such as stem cells. We describe how scRNA-seq can be utilized to examine limbal epithelial stem cell population as well as investigate the contribution of autophagy to the function of limbal epithelial stem cells. To accomplish this, we used the Beclin1 heterozygous (Beclin1 het) mouse, a well-established model of autophagy deficiency. We provide a protocol that we developed for the isolation of viable, single-cell suspensions of limbal/corneal tissues, as well as the analysis of scRNA-seq data.
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Affiliation(s)
- Han Peng
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Nihal Kaplan
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Min Liu
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Huimin Jiang
- Department of Dermatology, Northwestern University, Chicago, IL, USA
- Department of Ophthalmology, The Second Hospital of Anhui Medical University, Hefei, China
| | - Robert M Lavker
- Department of Dermatology, Northwestern University, Chicago, IL, USA.
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11
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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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12
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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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13
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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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14
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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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15
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Yang W, Lee SK, Lehmann OJ, Wu Z, Hiriyanna S, Swaroop A, Lavker RM, Peng H, Kume T. FoxC1 activates limbal epithelial stem cells following corneal epithelial debridement. Exp Eye Res 2023; 234:109599. [PMID: 37488009 PMCID: PMC10530263 DOI: 10.1016/j.exer.2023.109599] [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: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023]
Abstract
Limbal epithelial stem cells are not only critical for corneal epithelial homeostasis but also have the capacity to change from a relatively quiescent mitotic phenotype to a rapidly proliferating cell in response to population depletion following corneal epithelial wounding. Pax6+/- mice display many abnormalities including corneal vascularization and these aberrations are consistent with a limbal stem cell deficiency (LSCD) phenotype. FoxC1 has an inhibitory effect on corneal avascularity and a positive role in stem cell maintenance in many tissues. However, the role of FoxC1 in limbal epithelial stem cells remains unknown. To unravel FoxC1's role(s) in limbal epithelial stem cell homeostasis, we utilized an adeno-associated virus (AAV) vector to topically deliver human FOXC1 proteins into Pax6 +/- mouse limbal epithelium. Under unperturbed conditions, overexpression of FOXC1 in the limbal epithelium had little significant change in differentiation (PAI-2, Krt12) and proliferation (BrdU, Ki67). Conversely, such overexpression resulted in a marked increase in the expression of putative limbal epithelial stem cell markers, N-cadherin and Lrig1. After corneal injuries in Pax6 +/- mice, FOXC1 overexpression enhanced the behavior of limbal epithelial stem cells from quiescence to a highly proliferative status. Overall, the treatment of AAV8-FOXC1 may be beneficial to the function of limbal epithelial stem cells in the context of a deficiency of Pax6 function.
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Affiliation(s)
- Wending Yang
- Departments of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Sun Kyong Lee
- Departments of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Ordan J Lehmann
- Department of Ophthalmology and Medical Genetics, University of Alberta, Edmonton, Alberta, T6G, 2H7, Canada
| | - Zhijian Wu
- Neurobiology Neurodegeneration& Repair Laboratory (N-NRL), National Eye Institute, NIH, Bethesda, MD, 20892, USA
| | - Suja Hiriyanna
- Neurobiology Neurodegeneration& Repair Laboratory (N-NRL), National Eye Institute, NIH, Bethesda, MD, 20892, USA
| | - Anand Swaroop
- Neurobiology Neurodegeneration& Repair Laboratory (N-NRL), National Eye Institute, NIH, Bethesda, MD, 20892, USA
| | - Robert M Lavker
- Departments of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
| | - Han Peng
- Departments of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
| | - Tsutomu Kume
- Departments of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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16
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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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17
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Swamynathan SK, Swamynathan S. Corneal epithelial development and homeostasis. Differentiation 2023; 132:4-14. [PMID: 36870804 PMCID: PMC10363238 DOI: 10.1016/j.diff.2023.02.002] [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: 10/26/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
The corneal epithelium (CE), the most anterior cellular structure of the eye, is a self-renewing stratified squamous tissue that protects the rest of the eye from external elements. Each cell in this exquisite three-dimensional structure needs to have proper polarity and positional awareness for the CE to serve as a transparent, refractive, and protective tissue. Recent studies have begun to elucidate the molecular and cellular events involved in the embryonic development, post-natal maturation, and homeostasis of the CE, and how they are regulated by a well-coordinated network of transcription factors. This review summarizes the status of related knowledge and aims to provide insight into the pathophysiology of disorders caused by disruption of CE development, and/or homeostasis.
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Affiliation(s)
| | - Sudha Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
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18
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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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19
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Cancedda R, Mastrogiacomo M. Transit Amplifying Cells (TACs): a still not fully understood cell population. Front Bioeng Biotechnol 2023; 11:1189225. [PMID: 37229487 PMCID: PMC10203484 DOI: 10.3389/fbioe.2023.1189225] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Maintenance of tissue homeostasis and tissue regeneration after an insult are essential functions of adult stem cells (SCs). In adult tissues, SCs proliferate at a very slow rate within "stem cell niches", but, during tissue development and regeneration, before giving rise to differentiated cells, they give rise to multipotent and highly proliferative cells, known as transit-amplifying cells (TACs). Although differences exist in diverse tissues, TACs are not only a transitory phase from SCs to post-mitotic cells, but they also actively control proliferation and number of their ancestor SCs and proliferation and differentiation of their progeny toward tissue specific functional cells. Autocrine signals and negative and positive feedback and feedforward paracrine signals play a major role in these controls. In the present review we will consider the generation and the role played by TACs during development and regeneration of lining epithelia characterized by a high turnover including epidermis and hair follicles, ocular epithelial surfaces, and intestinal mucosa. A comparison between these different tissues will be made. There are some genes and molecular pathways whose expression and activation are common to most TACs regardless their tissue of origin. These include, among others, Wnt, Notch, Hedgehog and BMP pathways. However, the response to these molecular signals can vary in TACs of different tissues. Secondly, we will consider cultured cells derived from tissues of mesodermal origin and widely adopted for cell therapy treatments. These include mesenchymal stem cells and dedifferentiated chondrocytes. The possible correlation between cell dedifferentiation and reversion to a transit amplifying cell stage will be discussed.
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Affiliation(s)
- Ranieri Cancedda
- Emeritus Professor, Università degli Studi di Genova, Genoa, Italy
| | - Maddalena Mastrogiacomo
- Dipartimento di Medicina Interna e Specialità Mediche (DIMI), Università Degli Studi di Genova, Genova, Italy
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20
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Zhang Y, Do KK, Wang F, Lu X, Liu JY, Li C, Ceresa BP, Zhang L, Dean DC, Liu Y. Zeb1 facilitates corneal epithelial wound healing by maintaining corneal epithelial cell viability and mobility. Commun Biol 2023; 6:434. [PMID: 37081200 PMCID: PMC10119281 DOI: 10.1038/s42003-023-04831-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/11/2023] [Indexed: 04/22/2023] Open
Abstract
The cornea is the outmost ocular tissue and plays an important role in protecting the eye from environmental insults. Corneal epithelial wounding provokes pain and fear and contributes to the most ocular trauma emergency assessments worldwide. ZEB1 is an essential transcription factor in development; but its roles in adult tissues are not clear. We identify Zeb1 is an intrinsic factor that facilitates corneal epithelial wound healing. In this study, we demonstrate that monoallelic deletion of Zeb1 significantly expedites corneal cell death and inhibits corneal epithelial EMT-related cell migration upon an epithelial debridement. We provide evidence that Zeb1-regulation of corneal epithelial wound healing is through the repression of genes required for Tnfa-induced epithelial cell death and the induction of genes beneficial for epithelial cell migration. We suggest utilizing TNF-α antagonists would reduce TNF/TNFR1-induced cell death in the corneal epithelium and inflammation in the corneal stroma to help corneal wound healing.
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Affiliation(s)
- Yingnan Zhang
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- The Rosenberg School of Optometry, University of the Incarnate Word, San Antonio, TX, 78229, USA
| | - Khoi K Do
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Fuhua Wang
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Eye Institute and Eye Hospital of Shangdong First Medical University, 250021, Jinan, China
| | - Xiaoqin Lu
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- James Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - John Y Liu
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Chi Li
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- James Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Brian P Ceresa
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Lijun Zhang
- Department of Ophthalmology, Third People's Hospital of Dalian, Dalian Medical University, 116033, Dalian, China
| | - Douglas C Dean
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- James Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
| | - Yongqing Liu
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- James Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
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21
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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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22
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Bonnet C, Ruiz M, Gonzalez S, Tseng CH, Bourges JL, Behar-Cohen F, Deng SX. Single mRNA detection of Wnt signaling pathway in the human limbus. Exp Eye Res 2023; 229:109337. [PMID: 36702232 DOI: 10.1016/j.exer.2022.109337] [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: 08/16/2022] [Revised: 11/02/2022] [Accepted: 11/23/2022] [Indexed: 01/24/2023]
Abstract
Limbal epithelial stem/progenitor cells (LSCs) are adult stem cells located at the limbus, tightly regulated by their close microenvironment. It has been shown that Wnt signaling pathway is crucial for LSCs regulation. Previous differential gene profiling studies confirmed the preferential expression of specific Wnt ligands (WNT2, WNT6, WNT11, WNT16) and Wnt inhibitors (DKK1, SFRP5, WIF1, FRZB) in the limbal region compared to the cornea. Among all frizzled receptors, frizzled7 (Fzd7) was found to be preferentially expressed in the basal limbal epithelium. However, the exact localization of Wnt signaling molecules-producing cells in the limbus remains unknown. The current study aims to evaluate the in situ spatial expression of these 4 Wnt ligands, 4 Wnt inhibitors, and Fzd7. Wnt ligands, DKK1, and Fzd7 expression were scattered within the limbal epithelium, at a higher abundance in the basal layer than the superficial layer. SFRP5 expression was diffuse among the limbal epithelium, whereas WIF1 and FRZB expression was clustered at the basal limbal epithelial layer corresponding to the areas of high levels of Fzd7 expression. Quantitation of the fluorescence intensity showed that all 4 Wnt ligands, 3 Wnt inhibitors (WIF1, DKK1, FRZB), and Fzd7 were highly expressed at the basal layer of the limbus, then in a decreasing gradient toward the superficial layer (P < 0.05). The expression levels of all 4 Wnt ligands, FRZB, and Fzd7 in the basal epithelial layer were higher in the limbus than the central cornea (P < 0.05). All 4 Wnt ligands, 4 Wnt inhibitors, and Fzd7 were also highly expressed in the limbal stroma immediately below the epithelium but not in the corneal stroma (P < 0.05). In addition, Fzd7 had a preferential expression in the superior limbus compared to other limbal quadrants (P < 0.05). Taken together, the unique expression patterns of the Wnt molecules in the limbus suggests the involvement of both paracrine and autocrine effects in LSCs regulation, and a fine balance between Wnt activators and inhibitors to govern LSC fate.
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Affiliation(s)
- Clémence Bonnet
- Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; INSERM, UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Centre de Recherche des Cordeliers, Paris University, And Cornea Departement, Cochin Hospital, AP-HP, F-75014, Paris, France
| | - Maxime Ruiz
- Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Sheyla Gonzalez
- Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Chi-Hong Tseng
- David Geffen School of Medicine, Division of General Internal Medicine and Health Services Research, University of California, Los Angeles, USA
| | - Jean-Louis Bourges
- INSERM, UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Centre de Recherche des Cordeliers, Paris University, And Cornea Departement, Cochin Hospital, AP-HP, F-75014, Paris, France
| | - Francine Behar-Cohen
- INSERM, UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Centre de Recherche des Cordeliers, Paris University, And Cornea Departement, Cochin Hospital, AP-HP, F-75014, Paris, France
| | - Sophie X Deng
- Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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23
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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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24
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Liton PB, Boesze-Battaglia K, Boulton ME, Boya P, Ferguson TA, Ganley IG, Kauppinnen A, Laurie GW, Mizushima N, Morishita H, Russo R, Sadda J, Shyam R, Sinha D, Thompson DA, Zacks DN. AUTOPHAGY IN THE EYE: FROM PHYSIOLOGY TO PATHOPHYSOLOGY. AUTOPHAGY REPORTS 2023; 2:2178996. [PMID: 37034386 PMCID: PMC10078619 DOI: 10.1080/27694127.2023.2178996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/26/2023] [Indexed: 03/05/2023]
Abstract
Autophagy is a catabolic self-degradative pathway that promotes the degradation and recycling of intracellular material through the lysosomal compartment. Although first believed to function in conditions of nutritional stress, autophagy is emerging as a critical cellular pathway, involved in a variety of physiological and pathophysiological processes. Autophagy dysregulation is associated with an increasing number of diseases, including ocular diseases. On one hand, mutations in autophagy-related genes have been linked to cataracts, glaucoma, and corneal dystrophy; on the other hand, alterations in autophagy and lysosomal pathways are a common finding in essentially all diseases of the eye. Moreover, LC3-associated phagocytosis, a form of non-canonical autophagy, is critical in promoting visual cycle function. This review collects the latest understanding of autophagy in the context of the eye. We will review and discuss the respective roles of autophagy in the physiology and/or pathophysiology of each of the ocular tissues, its diurnal/circadian variation, as well as its involvement in diseases of the eye.
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Affiliation(s)
- Paloma B. Liton
- Departments of Ophthalmology & Pathology, Duke School of Medicine, Duke University, Durham, NC 27705, USA
| | - Kathleen Boesze-Battaglia
- Department of Basic and Translational Sciences, University of Pennsylvania, School of Dental Medicine, Philadelphia, PA 19104, USA
| | - Michael E. Boulton
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Patricia Boya
- Department of Neuroscience and Movement Science. Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Thomas A. Ferguson
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Ian G. Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Anu Kauppinnen
- Faculty of Health and Sciences, School of Pharmacy, University of Eastern Finland, 70210 Kuopio, Finland
| | - Gordon W. Laurie
- Departments of Cell Biology, Ophthalmology and Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, 113-0033, Japan
| | - Hideaki Morishita
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, 113-0033, Japan
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Rossella Russo
- Preclinical and Translational Pharmacology, Glaucoma Unit, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Jaya Sadda
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Debasish Sinha
- Department of Ophthalmology, Cell Biology, and Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Debra A. Thompson
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - David N. Zacks
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
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25
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Soleimani M, Cheraqpour K, Koganti R, Baharnoori SM, Djalilian AR. Concise Review: Bioengineering of Limbal Stem Cell Niche. BIOENGINEERING (BASEL, SWITZERLAND) 2023; 10:bioengineering10010111. [PMID: 36671683 PMCID: PMC9855097 DOI: 10.3390/bioengineering10010111] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/01/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
The corneal epithelium is composed of nonkeratinized stratified squamous cells and has a significant turnover rate. Limbal integrity is vital to maintain the clarity and avascularity of the cornea as well as regeneration of the corneal epithelium. Limbal epithelial stem cells (LESCs) are located in the basal epithelial layer of the limbus and preserve this homeostasis. Proper functioning of LESCs is dependent on a specific microenvironment, known as the limbal stem cell niche (LSCN). This structure is made up of various cells, an extracellular matrix (ECM), and signaling molecules. Different etiologies may damage the LSCN, leading to limbal stem cell deficiency (LSCD), which is characterized by conjunctivalization of the cornea. In this review, we first summarize the basics of the LSCN and then focus on current and emerging bioengineering strategies for LSCN restoration to combat LSCD.
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Affiliation(s)
- Mohammad Soleimani
- Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran 1336616351, Iran
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Kasra Cheraqpour
- Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran 1336616351, Iran
| | - Raghuram Koganti
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Seyed Mahbod Baharnoori
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Ali R. Djalilian
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
- Correspondence:
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26
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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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27
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Dias-Teixeira KL, Sharifian Gh M, Romano J, Norouzi F, Laurie GW. Autophagy in the normal and diseased cornea. Exp Eye Res 2022; 225:109274. [PMID: 36252655 PMCID: PMC10083687 DOI: 10.1016/j.exer.2022.109274] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 01/18/2023]
Abstract
The cornea and covering tear film are together the 'objective lens' of the eye through which 80% of light is refracted. Despite exposure to a physically harsh and at times infectious or toxic environment, transparency essential for sight is in most cases maintained. Such resiliency makes the avascular cornea a superb model for the exploration of autophagy in the regulation of homeostasis with relevancy to all organs. Nonetheless, missense mutations and inflammation respectively clog or apparently overwhelm autophagic flux to create dystrophies much like in neurodegenerative diseases or further exacerbate inflammation. Here there is opportunity to generate novel topical therapies towards the restoration of homeostasis with potential broad application.
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Affiliation(s)
| | | | - Jeff Romano
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
| | - Fatemeh Norouzi
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
| | - Gordon W Laurie
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA; Department of Ophthalmology, University of Virginia, Charlottesville, VA, USA.
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28
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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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29
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Di Girolamo N, Park M. Cell identity changes in ocular surface Epithelia. Prog Retin Eye Res 2022:101148. [DOI: 10.1016/j.preteyeres.2022.101148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/13/2022] [Accepted: 11/09/2022] [Indexed: 11/21/2022]
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30
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Masood F, Chang JH, Akbar A, Song A, Hu WY, Azar DT, Rosenblatt MI. Therapeutic Strategies for Restoring Perturbed Corneal Epithelial Homeostasis in Limbal Stem Cell Deficiency: Current Trends and Future Directions. Cells 2022; 11:3247. [PMID: 36291115 PMCID: PMC9600167 DOI: 10.3390/cells11203247] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 02/03/2023] Open
Abstract
Limbal stem cells constitute an important cell population required for regeneration of the corneal epithelium. If insults to limbal stem cells or their niche are sufficiently severe, a disease known as limbal stem cell deficiency occurs. In the absence of functioning limbal stem cells, vision-compromising conjunctivalization of the corneal epithelium occurs, leading to opacification, inflammation, neovascularization, and chronic scarring. Limbal stem cell transplantation is the standard treatment for unilateral cases of limbal stem cell deficiency, but bilateral cases require allogeneic transplantation. Herein we review the current therapeutic utilization of limbal stem cells. We also describe several limbal stem cell markers that impact their phenotype and function and discuss the possibility of modulating limbal stem cells and other sources of stem cells to facilitate the development of novel therapeutic interventions. We finally consider several hurdles for widespread adoption of these proposed methodologies and discuss how they can be overcome to realize vision-restoring interventions.
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Affiliation(s)
- Faisal Masood
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Jin-Hong Chang
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Anosh Akbar
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Amy Song
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Wen-Yang Hu
- Department of Urology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Dimitri T. Azar
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Mark I. Rosenblatt
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
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31
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Liu Q, Zhang P, Yuan X, Ya O, Li Q, Li J, Long Q. Investigate the stemness of adult adipose-derived stromal cells based on single-cell RNA-sequencing. Cell Biol Int 2022; 46:2118-2131. [PMID: 36150081 DOI: 10.1002/cbin.11898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/15/2022] [Accepted: 08/20/2022] [Indexed: 11/06/2022]
Abstract
The cellular heterogeneity and genetic features of stemness of adipose-derived stromal cells (ADSCs) remain unclear. Using single-cell RNA sequencing (scRNA-seq), we investigated the genomic features of the stemness gene in ADSCs with genetic variability. We cultured the ADSCs isolated from the fat waste of a healthy adult volunteers undergoing cosmetic plastic surgery to the third generation, used the BD Rhapsody platform to perform scRNA-seq, then used Monocle2 to analyze the growth and development trajectory of ADSCs, Cellular Trajectory Reconstruction Analysis Using Gene Counts and Expression (CytoTRACE) to evaluate the stemness gene characteristics in ADSCs clusters, and Beam to analyze the expression change characteristics of the main stemness related genes of ADSCs. According to the scRNA-seq data of 5325 ADSCs, they could be classified into nine cell clusters. According to CytoTRACE analysis, Cluster 3 of ADSCs had the highest stemness, whereas Cluster 8 had the lowest stemness. Pseudotime analysis revealed that Cluster 3 of ADSCs was primarily dispersed in the middle part of the growth and development trajectory, whereas Cluster 8 was primarily distributed at the end. We summarized the stemness of Cluster 3 in ADSCs with high expression of TPM1 and CCND1 genes in the metaphase of growth and development is the strongest, whereas the stemness of Cluster 8 with high expression of FICD, CREBRF, SDF2L1, HERPUD1, and HYOU1 genes in the telophase of growth and development is the weakest, providing a theoretical basis for screening and improving the therapeutic effect of ADSCs in cell transplantation research.
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Affiliation(s)
- Qing Liu
- Department of Neurology, Kailuan General Hospital, Affiliated North China University of Science and Technology, Tangshan
| | - Pingshu Zhang
- Department of Neurology, Kailuan General Hospital, Affiliated North China University of Science and Technology, Tangshan
| | - Xiaodong Yuan
- Department of Neurology, Kailuan General Hospital, Affiliated North China University of Science and Technology, Tangshan
| | - Ou Ya
- Department of Neurology, Kailuan General Hospital, Affiliated North China University of Science and Technology, Tangshan
| | - Qi Li
- Hebei Provincial Key Laboratory of Neurobiological Function, Tangshan, China
| | - Jing Li
- Radiology Department, Tangshan Maternal and Child Health Hospital, Tangshan, China
| | - Qingxi Long
- Department of Neurology, Kailuan General Hospital, Affiliated North China University of Science and Technology, Tangshan
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32
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Sasamoto Y, Lee CAA, Wilson BJ, Buerger F, Martin G, Mishra A, Kiritoshi S, Tran J, Gonzalez G, Hildebrandt F, Jo VY, Lian CG, Murphy GF, Ksander BR, Frank MH, Frank NY. Limbal BCAM expression identifies a proliferative progenitor population capable of holoclone formation and corneal differentiation. Cell Rep 2022; 40:111166. [PMID: 35947947 PMCID: PMC9480518 DOI: 10.1016/j.celrep.2022.111166] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 04/14/2022] [Accepted: 07/13/2022] [Indexed: 12/13/2022] Open
Abstract
The corneal epithelium is renowned for high regenerative potential, which is dependent on the coordinated function of its diverse progenitor subpopulations. However, the molecular pathways governing corneal epithelial progenitor differentiation are incompletely understood. Here, we identify a highly proliferative limbal epithelial progenitor subpopulation characterized by expression of basal cell adhesion molecule (BCAM) that is capable of holocone formation and corneal epithelial sheet generation. BCAM-positive cells can be found among ABCB5-positive limbal stem cells (LSCs) as well as among ABCB5-negative limbal epithelial cell populations. Mechanistically, we show that BCAM is functionally required for cellular migration and differentiation and that its expression is regulated by the transcription factor p63. In aggregate, our study identifies limbal BCAM expression as a marker of highly proliferative corneal epithelial progenitor cells and defines the role of BCAM as a critical molecular mediator of corneal epithelial differentiation. Using scRNA sequencing of ABCB5-positive human limbal stem cells, Sasamoto et al. identify a BCAM-positive highly proliferative limbal epithelial progenitor subpopulation that is capable of holocone formation and corneal epithelial sheet generation. BCAM regulated by the stem cell transcription factor p63 is functionally required for corneal cell migration and differentiation.
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Affiliation(s)
- Yuzuru Sasamoto
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Transplant Research Program, Boston Children's Hospital, Boston, MA, USA
| | - Catherine A A Lee
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Transplant Research Program, Boston Children's Hospital, Boston, MA, USA
| | - Brian J Wilson
- Transplant Research Program, Boston Children's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Florian Buerger
- Department of Nephrology, Boston Children's Hospital, Boston, MA, USA
| | - Gabrielle Martin
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Transplant Research Program, Boston Children's Hospital, Boston, MA, USA
| | - Ananda Mishra
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Transplant Research Program, Boston Children's Hospital, Boston, MA, USA
| | - Shoko Kiritoshi
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Johnathan Tran
- Transplant Research Program, Boston Children's Hospital, Boston, MA, USA
| | - Gabriel Gonzalez
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, VA Boston Healthcare System, Boston, MA, USA
| | | | - Vickie Y Jo
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Christine G Lian
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - George F Murphy
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce R Ksander
- Massachusetts Eye and Ear Infirmary, Schepens Eye Research Institute, Boston, MA, USA
| | - Markus H Frank
- Transplant Research Program, Boston Children's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Harvard Skin Disease Research Center, Department of Dermatology, Brigham and Women's Hospital, Boston, MA, USA; School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia.
| | - Natasha Y Frank
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Department of Medicine, VA Boston Healthcare System, Boston, MA, USA.
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33
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Abstract
The single-cell revolution in the field of genomics is in full bloom, with clever new molecular biology tricks appearing regularly that allow researchers to explore new modalities or scale up their projects to millions of cells and beyond. Techniques abound to measure RNA expression, DNA alterations, protein abundance, chromatin accessibility, and more, all with single-cell resolution and often in combination. Despite such a rapidly changing technology landscape, there are several fundamental principles that are applicable to the majority of experimental workflows to help users avoid pitfalls and exploit the advantages of the chosen platform. In this overview article, we describe a variety of popular single-cell genomics technologies and address some common questions pertaining to study design, sample preparation, quality control, and sequencing strategy. As the majority of relevant publications currently revolve around single-cell RNA-seq, we will prioritize this genomics modality in our discussion. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Claire Regan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
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Puri S, Moreno IY, Sun M, Verma S, Lin X, Gesteira TF, Coulson-Thomas VJ. Hyaluronan supports the limbal stem cell phenotype during ex vivo culture. Stem Cell Res Ther 2022; 13:384. [PMID: 35907870 PMCID: PMC9338506 DOI: 10.1186/s13287-022-03084-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/21/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Hyaluronan (HA) has previously been identified as an integral component of the limbal stem cell niche in vivo. In this study, we investigated whether a similar HA matrix is also expressed in vitro providing a niche supporting limbal epithelial stem cells (LESCs) during ex vivo expansion. We also investigated whether providing exogenous HA in vitro is beneficial to LESCs during ex vivo expansion. METHOD Human LESCs (hLESCs) were isolated from donor corneas and a mouse corneal epithelial progenitor cell line (TKE2) was obtained. The HA matrix was identified surrounding LESCs in vitro using immunocytochemistry, flow cytometry and red blood exclusion assay. Thereafter, LESCs were maintained on HA coated dishes or in the presence of HA supplemented in the media, and viability, proliferation, cell size, colony formation capabilities and expression of putative stem cell markers were compared with cells maintained on commonly used coated dishes. RESULTS hLESCs and TKE2 cells express an HA-rich matrix in vitro, and this matrix is essential for maintaining LESCs. Further supplying exogenous HA, as a substrate and supplemented to the media, increases LESC proliferation, colony formation capabilities and the expression levels of putative limbal stem cell markers. CONCLUSION Our data show that both exogenous and endogenous HA help to maintain the LESC phenotype. Exogenous HA provides improved culture conditions for LESC during ex vivo expansion. Thus, HA forms a favorable microenvironment for LESCs during ex vivo expansion and, therefore, could be considered as an easy and cost-effective substrate and/or supplement for culturing LESCs in the clinic.
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Affiliation(s)
- Sudan Puri
- College of Optometry, University of Houston, Houston, TX, USA
| | - Isabel Y Moreno
- College of Optometry, University of Houston, Houston, TX, USA
| | - Mingxia Sun
- College of Optometry, University of Houston, Houston, TX, USA
| | - Sudhir Verma
- College of Optometry, University of Houston, Houston, TX, USA
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Xiao Lin
- College of Optometry, University of Houston, Houston, TX, USA
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Gheiratmand L, Brown DJ, Sandkuijl D, Loboda A, Jester JV. Immuno Tomography (IT) and Imaging Mass Cytometry (IMC) for constructing spatially resolved, multiplexed 3D IMC data sets. Ocul Surf 2022; 25:49-54. [PMID: 35489589 PMCID: PMC10411503 DOI: 10.1016/j.jtos.2022.04.008] [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: 01/31/2022] [Revised: 04/20/2022] [Accepted: 04/23/2022] [Indexed: 10/18/2022]
Abstract
PURPOSE We have previously used Immuno Tomography (IT) to identify label-retaining stem cell populations in the cornea and meibomian gland. While this method provides the unique ability to quantify stem cell populations comprised of 1-4 cells, the number of antigens that can be sequentially used to characterize these unique cells is limited by antigen stability after antibody stripping and re-probing. To address this deficiency, we have evaluated the capability of Imaging Mass Cytometry™ (IMC™) to generate multiplexed images using metal-conjugated antibodies to label IT plastic sections and generate 3-dimensional IMC data sets (3D IMC). METHODS K5-H2B-GFP mice, 56 days after doxycycline chase, were sacrificed and eyelid tissue processed for IT. A total of 400 serial, plastic sections, 2 μm thick, were then probed using metal-tagged antibodies specific for sox 9, collagen type I, E-cadherin, Ki67, GFP, αSMA, vimentin, and DNA intercalator. Multiplexed images were then generated using an Imaging Mass Cytometry system (Fluidigm®), and 3D reconstructions were assembled. RESULTS All 8 metal-labeled tags were detected and their images were successfully assembled into 3D IMC data sets. GFP-labeled nuclei were identified within the meibomian glands in comparable numbers to those previously reported for slow-cycling meibomian gland stem cells. CONCLUSIONS These findings demonstrate that IMC can be used on plastic sections to generate multiplexed, 3D data sets that can be reconstructed to show the spatial localization of meibomian gland stem cells. We propose that 3D IMC might prove valuable in more fully characterizing stem cell populations in different tissues.
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Affiliation(s)
- Ladan Gheiratmand
- Standard BioTools Canada Inc. (formerly Fluidigm), 1380 Rodick Road, Suite 400, Markham, ON, Canada.
| | - Donald J Brown
- Department of Ophthalmology, University of California Irvine, Irvine, CA, USA
| | - Daaf Sandkuijl
- Standard BioTools Canada Inc. (formerly Fluidigm), 1380 Rodick Road, Suite 400, Markham, ON, Canada
| | - Alexander Loboda
- Standard BioTools Canada Inc. (formerly Fluidigm), 1380 Rodick Road, Suite 400, Markham, ON, Canada
| | - James V Jester
- Department of Ophthalmology, University of California Irvine, Irvine, CA, USA
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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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Zhang W, Lan X, Zhu J, Zhang C, Huang Y, Mo K, Tan J, Guo H, Huang H, Li M, Ouyang H, Wang L. Healing Ability of Central Corneal Epithelium in Rabbit Ocular Surface Injury Models. Transl Vis Sci Technol 2022; 11:28. [PMID: 35771535 PMCID: PMC9251814 DOI: 10.1167/tvst.11.6.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Purpose Wound healing of the corneal epithelium mainly involves two types of cells: limbal stem/progenitor cells (LSCs) and differentiated central corneal epithelial cells (CECs). The healing ability of CECs is still debatable, and its correlated transcriptomic alterations during wound healing are yet to be elucidated. This study aimed to determine the healing ability and mechanisms underlying the actions of CECs using rabbit ocular surface injury models. Methods A central corneal ring-like residual epithelium model was used to investigate the healing ability of CECs. Uninjured and injury-stimulated LSCs and CECs were collected for transcriptomic analysis. The analysis results were verified by quantitative reverse transcriptase polymerase chain reaction, immunofluorescence staining, and two types of rabbit corneal injury models. Results During wound healing, the upregulated genes in LSCs were mostly enriched in the mitotic cell cycle–related processes, but those in CECs were mostly enriched in cell adhesion and migration. CECs could repair the epithelial defects successfully at one-time injuries. However, after repetitive injuries, the CECs repaired notably slower and failed to completely heal the defect, but the LSCs repaired even faster than the one-time injury. Conclusions Our results indicated rabbit CECs repair the epithelial defect mainly depending on migration and its proliferative ability is limited, and LSCs are the main source of regenerative epithelial cells. Translational Relevance This study provides information on gene expression in the corneal epithelium during wound healing, indicating that regulation of the cell cycle, cell adhesion, and migration may be the basis for future treatment strategies for corneal wound healing.
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Affiliation(s)
- Wang Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xihong Lan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jin Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Canwei Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Ying Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Kunlun Mo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jieying Tan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Huizhen Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Huaxing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Mingsen Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Hong Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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Chen X, Yang J, Li M, Zhu S, Zhao M, Yang C, Liu B, Gao H, Lu A, Ge L, Mo L, Gu Z, Xu H. Fullerenol protects cornea from ultraviolet B exposure. Redox Biol 2022; 54:102360. [PMID: 35690049 PMCID: PMC9190064 DOI: 10.1016/j.redox.2022.102360] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/20/2022] [Accepted: 05/31/2022] [Indexed: 02/07/2023] Open
Abstract
The eyes are highly susceptible to the oxidative stress induced by ultraviolet B (UVB, wavelength between 280 ∼ 320 nm), which could cause severe damage to the cornea. Fullerenols are effective antioxidants to alleviate UVB-induced injury, while their application for the eyes is still rare. In present study, we investigated the protective performance and mechanism of fullerenols on cornea under UVB radiation in vivo and in vitro. The synthesized fullerenols exhibited broad-spectrum free radical scavenging properties (applicable to both reactive oxygen species (ROS) and reactive nitrogen species (RNS)) and photo-stability. When compared with another widely used antioxidant glutathione (GSH), the administration of fullerenols markedly decreased the injured area, corneal edema, cell death, and increased the cell proliferation in UVB-induced rat cornea. The effects of fullerenols were confirmed in UVB-exposed human corneal epithelial cells (hCECs), where elevated cell viability and proliferation, decreased oxidative free radical production, repaired mitochondrial dysfunction and DNA lesions were observed. RNA sequencing (RNA-Seq) analysis demonstrated that fullerenol alleviated UVB-induced corneal injury through down-regulation of oxidative stress-related genes and up-regulation of proliferation-associated genes. Our results demonstrate the suitability of fullerenols as a potential exogenous treatment in ameliorating UVB-induced cornea damage. Fullerenol produces significant precaution on UVB-induced corneal damage. Fullerenol exhibits broader spectrum free radical scavenging properties than GSH. Fullerenol mitigates the LSCs loss in the cornea caused by UVB. Fullerenol down-regulates oxidative stress genes and up-regulates proliferation-related genes.
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Thomson BR, Quaggin SE. Preparation of a Single Cell Suspension from the Murine Iridocorneal Angle. Bio Protoc 2022; 12:e4426. [PMID: 35865116 PMCID: PMC9257837 DOI: 10.21769/bioprotoc.4426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 12/29/2022] Open
Abstract
Single cell RNA sequencing is a powerful tool that can be used to identify distinct cell types and transcriptomic differences within complex tissues. It has proven to be especially useful in tissues of the eye, where investigators have identified novel cell types within the retina, anterior chamber, and iridocorneal angle and explored transcriptomic contribution to disease phenotypes in age-related macular degeneration. However, to obtain high quality results, the technique requires isolation of healthy single cells from the tissue of interest, seeking complete tissue digestion while minimizing stress and transcriptomic changes in the isolated cells prior to library preparation. Here, we present a protocol developed in our laboratory for isolation of live single cells from the murine iridocorneal angle, which includes Schlemm's canal and the trabecular meshwork, suitable for single cell RNA sequencing, flow cytometry, or other downstream analysis. Graphical abstract.
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Affiliation(s)
- Benjamin R. Thomson
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Susan E. Quaggin
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Wang Q, Dou S, Zhang B, Jiang H, Qi X, Duan H, Wang X, Dong C, Zhang BN, Xie L, Cao Y, Zhou Q, Shi W. Heterogeneity of human corneal endothelium implicates lncRNA NEAT1 in Fuchs endothelial corneal dystrophy. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 27:880-893. [PMID: 35141048 PMCID: PMC8807987 DOI: 10.1016/j.omtn.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/07/2022] [Indexed: 11/05/2022]
Abstract
The corneal endothelium is critical for maintaining corneal clarity by mediating hydration through barrier and pump functions. Progressive loss of corneal endothelial cells during aging has been associated with the development of Fuchs endothelial corneal dystrophy (FECD), one of the main causes of cornea-related vision loss. The mechanisms underlying FECD development remain elusive. Single-cell RNA sequencing of isolated healthy human corneas discovered 4 subpopulations of corneal endothelial cells with distinctive signatures. Unsupervised clustering analysis uncovered nuclear enriched abundant transcript 1 (NEAT1), a long non-coding RNA (lncRNA), as the top expressed gene in the C0-endothelial subpopulation, but markedly downregulated in FECD. Consistent with human corneas, a UVA-induced mouse FECD model validated the loss of NEAT1 expression. Loss of NEAT1 function by an in vivo genetic approach reproduced the exacerbated phenotype of FECD by ablating corneal endothelial cells. Conversely, gain of function by a CRISPR-activated adenoviral delivery system protected corneas from UVA-induced FECD. Our findings provide novel mechanistic insights into the development of FECD, and targeting NEAT1 offers an attractive approach for treating FECD.
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Ji X, Zheng M, Fan T, Xu B. Commentary: Novel Cell Culture Paradigm Prolongs Mouse Corneal Epithelial Cell Proliferative Activity In Vitro and In Vivo. Front Cell Dev Biol 2022; 10:822728. [PMID: 35252189 PMCID: PMC8894700 DOI: 10.3389/fcell.2022.822728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Xiuna Ji
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Mingyue Zheng
- Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Tingjun Fan
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Bin Xu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- *Correspondence: Bin Xu,
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Qin Z, Luo K, Liu Y, Liao S, He J, He M, Xie T, Jiang X, Li B, Liu H, Huang Q, Tang H, Feng W, Zhan X. ATG16L1 is a Potential Prognostic Biomarker and Immune Signature for Osteosarcoma: A Study Based on Bulk RNA and Single-Cell RNA-Sequencing. Int J Gen Med 2022; 15:1033-1045. [PMID: 35140506 PMCID: PMC8818976 DOI: 10.2147/ijgm.s341879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background Osteosarcoma is a common solid malignancy of the bone in children and adolescents, and its metastasis and recurrence are the principal causes of poor treatment outcomes. Methods Autophagy-related genes were used to cluster osteosarcoma patients by consensus clustering analysis using the GSE21257 database. Differentially expressed genes (DEGs) were identified by limma package. Multiple-gene risk signature was constructed using least absolute shrinkage and selection operator (LASSO) analysis and Cox regression analyses. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to determine gene expression levels. Then, single-cell RNA-sequencing dataset GSE152048 were used to identify the correlation between the DEGs and effector molecules expressed in specific tumor-infiltrating immune cells. Results Two clusters were identified in the consensus clustering analysis, which were confirmed by principal component analysis. Limma analysis revealed that 15 genes were related, and 9 genes were screened using protein-protein interaction network and LASSO regression analysis. Cox regression analyses identified 5 genes. Combined with survival analysis, only the autophagy related 16 like 1 gene (ATG16L1) was significant. The results of qRT-PCR showed low expression levels of ATG16L1 in tumor cells group. Immune infiltration analysis revealed significantly lower expression of CD8+ T cells in the high ATG16L1 gene expression group. ScRNA-seq revealed that in the ATG16L1+CD8+ T cell group, the expression of GZMB was lower, whereas the expression of ITGA1 was higher. These results showed that ATG16L1 is an immune-related gene, which is associated with poor prognosis in patients with osteosarcoma. Conclusion ATG16L1 is a potential prognostic biomarker and immune signature and may be a therapeutic target for osteosarcoma.
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Affiliation(s)
- Zhaojie Qin
- Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
- Department of Orthopedic, The People’s Hospital of Hechi, Hechi, 547600, Guangxi, People’s Republic of China
| | - Kai Luo
- Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Yun Liu
- Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Shijie Liao
- Department of Trauma Orthopedic and Hand Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Juliang He
- Department of Bone and Soft Tissue Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, People’s Republic of China
| | - Mingwei He
- Department of Trauma Orthopedic and Hand Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Tianyu Xie
- Department of Trauma Orthopedic and Hand Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Xiaohong Jiang
- Department of Orthopedic, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Boxiang Li
- Department of Orthopedic, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Huijiang Liu
- Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
- Department of Orthopedics, The First People’s Hospital of Nanning, Nanning, 530021, Guangxi, People’s Republic of China
| | - Qian Huang
- Department of Orthopedics, The First People’s Hospital of Nanning, Nanning, 530021, Guangxi, People’s Republic of China
| | - Haijun Tang
- Department of Orthopedic, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Wenyu Feng
- Department of Trauma Orthopedic and Hand Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
- Correspondence: Xinli Zhan, Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China, Tel +86 771-5350189, Fax +867715350001, Email ; Wenyu Feng, Department of Trauma Orthopedic and Hand Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China, Tel +86 18277185646, Fax +867715350001, Email
| | - Xinli Zhan
- Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
- Correspondence: Xinli Zhan, Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China, Tel +86 771-5350189, Fax +867715350001, Email ; Wenyu Feng, Department of Trauma Orthopedic and Hand Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China, Tel +86 18277185646, Fax +867715350001, Email
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Arunachalam D, Ramanathan SM, Menon A, Madhav L, Ramaswamy G, Namperumalsamy VP, Prajna L, Kuppamuthu D. Expression of immune response genes in human corneal epithelial cells interacting with Aspergillus flavus conidia. BMC Genomics 2022; 23:5. [PMID: 34983375 PMCID: PMC8728928 DOI: 10.1186/s12864-021-08218-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022] Open
Abstract
Background Aspergillus flavus, one of the causative agents of human fungal keratitis, can be phagocytosed by human corneal epithelial (HCE) cells and the conidia containing phagosomes mature into phagolysosomes. But the immunological responses of human corneal epithelial cells interacting with A. flavus are not clear. In this study, we report the expression of immune response related genes of HCE cells exposed to A. flavus spores using targeted transcriptomics. Methods Human corneal epithelial cell line and primary cultures were grown in a six-well plate and used for coculture experiments. Internalization of the conidia was confirmed by immunofluorescence microscopy of the colocalized endosomal markers CD71 and LAMP1. Total RNA was isolated, and the quantity and quality of the isolated RNA were assessed using Qubit and Bioanalyzer. NanoString nCounter platform was used for the analysis of mRNA abundance using the Human Immunology panel. R-package and nSolver software were used for data analysis. KEGG and FunRich 3.1.3 tools were used to analyze the differentially expressed genes. Results Different morphotypes of conidia were observed after 6 h of coculture with human corneal epithelial cells and found to be internalized by epithelial cells. NanoString profiling showed more than 20 differentially expressed genes in immortalized human corneal epithelial cell line and more than ten differentially expressed genes in primary corneal epithelial cells. Distinct set of genes were altered in their expression in cell line and primary corneal epithelial cells. KEGG pathway analysis revealed that genes associated with TNF signaling, NF-KB signaling, and Th17 signaling were up-regulated, and genes associated with chemokine signaling and B cell receptor signaling were down regulated. FunRich pathway analysis showed that pathways such as CDC42 signaling, PI3K signaling, and Arf6 trafficking events were activated by the clinical isolates CI1123 and CI1698 in both type of cells. Conclusions Combining the transcript analysis data from cell lines and primary cultures, we showed the up regulation of immune defense genes in A. flavus infected cells. At the same time, chemokine signaling and B cell signaling pathways are downregulated. The variability in the expression levels in the immortalized cell line and the primary cultures is likely due to the variable epigenetic reprogramming in the immortalized cells and primary cultures in the absence of any changes in the genome. It highlights the importance of using both cell types in host-pathogen interaction studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08218-5.
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Affiliation(s)
- Divya Arunachalam
- Proteomics Department, Aravind Medical Research Foundation, Dr. G. Venkataswamy Eye Research Institute, Aravind Eye Care System, Madurai, Tamil Nadu, India.,Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Shruthi Mahalakshmi Ramanathan
- Proteomics Department, Aravind Medical Research Foundation, Dr. G. Venkataswamy Eye Research Institute, Aravind Eye Care System, Madurai, Tamil Nadu, India
| | - Athul Menon
- Theracues Innovations Private Limited, Bangalore, India, Karnataka
| | - Lekshmi Madhav
- Theracues Innovations Private Limited, Bangalore, India, Karnataka
| | | | | | - Lalitha Prajna
- Department of Ocular Microbiology, Aravind Eye Hospital, Aravind Eye Care System, Madurai, Tamil Nadu, India
| | - Dharmalingam Kuppamuthu
- Proteomics Department, Aravind Medical Research Foundation, Dr. G. Venkataswamy Eye Research Institute, Aravind Eye Care System, Madurai, Tamil Nadu, India. .,Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India. .,Aravind Medical Research Foundation, Dr. G.Venkataswamy Eye Research Institute, Aravind Eye Care System, No.1 Anna Nagar, Madurai, Tamil Nadu, India.
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Transcriptome Analysis of Pterygium and Pinguecula Reveals Evidence of Genomic Instability Associated with Chronic Inflammation. Int J Mol Sci 2021; 22:ijms222112090. [PMID: 34769520 PMCID: PMC8584501 DOI: 10.3390/ijms222112090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 12/24/2022] Open
Abstract
Solar damage due to ultraviolet radiation (UVR) is implicated in the development of two proliferative lesions of the ocular surface: pterygium and pinguecula. Pterygium and pinguecula specimens were collected, along with adjacent healthy conjunctiva specimens. RNA was extracted and sequenced. Pairwise comparisons were made of differentially expressed genes (DEGs). Computational methods were used for analysis. Transcripts from 18,630 genes were identified. Comparison of two subgroups of pterygium specimens uncovered evidence of genomic instability associated with inflammation and the immune response; these changes were also observed in pinguecula, but to a lesser extent. Among the top DEGs were four genes encoding tumor suppressors that were downregulated in pterygium: C10orf90, RARRES1, DMBT1 and SCGB3A1; C10orf90 and RARRES1 were also downregulated in pinguecula. Ingenuity Pathway Analysis overwhelmingly linked DEGs to cancer for both lesions; however, both lesions are clearly still benign, as evidenced by the expression of other genes indicating their well-differentiated and non-invasive character. Pathways for epithelial cell proliferation were identified that distinguish the two lesions, as well as genes encoding specific pathway components. Upregulated DEGs common to both lesions, including KRT9 and TRPV3, provide a further insight into pathophysiology. Our findings suggest that pterygium and pinguecula, while benign lesions, are both on the pathological pathway towards neoplastic transformation.
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Català P, Groen N, Dehnen JA, Soares E, van Velthoven AJH, Nuijts RMMA, Dickman MM, LaPointe VLS. Single cell transcriptomics reveals the heterogeneity of the human cornea to identify novel markers of the limbus and stroma. Sci Rep 2021; 11:21727. [PMID: 34741068 PMCID: PMC8571304 DOI: 10.1038/s41598-021-01015-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/21/2021] [Indexed: 12/13/2022] Open
Abstract
The cornea is the clear window that lets light into the eye. It is composed of five layers: epithelium, Bowman's layer, stroma, Descemet's membrane and endothelium. The maintenance of its structure and transparency are determined by the functions of the different cell types populating each layer. Attempts to regenerate corneal tissue and understand disease conditions requires knowledge of how cell profiles vary across this heterogeneous tissue. We performed a single cell transcriptomic profiling of 19,472 cells isolated from eight healthy donor corneas. Our analysis delineates the heterogeneity of the corneal layers by identifying cell populations and revealing cell states that contribute in preserving corneal homeostasis. We identified expression of CAV1, HOMER3 and CPVL in the corneal epithelial limbal stem cell niche, CKS2, STMN1 and UBE2C were exclusively expressed in highly proliferative transit amplifying cells, CXCL14 was expressed exclusively in the suprabasal/superficial limbus, and NNMT was exclusively expressed by stromal keratocytes. Overall, this research provides a basis to improve current primary cell expansion protocols, for future profiling of corneal disease states, to help guide pluripotent stem cells into different corneal lineages, and to understand how engineered substrates affect corneal cells to improve regenerative therapies.
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Affiliation(s)
- Pere Català
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
- University Eye Clinic Maastricht, Maastricht University Medical Center+, PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | | | - Jasmin A Dehnen
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
- University Eye Clinic Maastricht, Maastricht University Medical Center+, PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Eduardo Soares
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
- University Eye Clinic Maastricht, Maastricht University Medical Center+, PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Arianne J H van Velthoven
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
- University Eye Clinic Maastricht, Maastricht University Medical Center+, PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Rudy M M A Nuijts
- University Eye Clinic Maastricht, Maastricht University Medical Center+, PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Mor M Dickman
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
- University Eye Clinic Maastricht, Maastricht University Medical Center+, PO Box 5800, 6202 AZ, Maastricht, The Netherlands.
| | - Vanessa L S LaPointe
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
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46
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Youkilis JC, Bassnett S. Single-cell RNA-sequencing analysis of the ciliary epithelium and contiguous tissues in the mouse eye. Exp Eye Res 2021; 213:108811. [PMID: 34717927 PMCID: PMC8860325 DOI: 10.1016/j.exer.2021.108811] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/08/2021] [Accepted: 10/24/2021] [Indexed: 12/12/2022]
Abstract
The ciliary epithelium plays a central role in ocular homeostasis but cells of the pigmented and non-pigmented layers are difficult to isolate physically and study. Here we used single-cell RNA-sequencing (scRNA-seq) to analyze the transcriptional signatures of cells harvested from the ciliary body and contiguous tissues. Microdissected tissue was dissociated by collagenase digestion and the transcriptomes of individual cells were obtained using a droplet-based scRNA-seq approach. In situ hybridization was used to verify the expression patterns of selected differentially-expressed genes. High quality transcriptomes were obtained from 10,024 cells and unsupervised clustering distinguished 22 cell types. Although efforts were made to specifically isolate the ciliary body, approximately half of the sequenced cells were derived from the adjacent retina. Cluster identities were assigned using expression of canonical markers or cluster-specific genes. The transcriptional signature of cells in the PCE and NPCE were distinct from each other and from cells in contiguous tissues. PCE cell transcriptomes were characterized by genes involved in melanin synthesis and transport proteins such as Slc4a4. Among the most differentially expressed genes in NPCE cells were those encoding members of the Zic family of transcription factors (Zic1, 2, 4), collagen XVIII (Col18a1), and corticotrophin-releasing hormone-binding protein (Crhbp). The ocular melanocyte population was distinguished by expression of the gap junction genes Gjb2 and Gjb6. Two fibroblast signatures were detected in the ciliary body preparation and shown by in situ hybridization to correspond to uveal and scleral populations. This cell atlas for the ciliary body and contiguous layers represents a useful resource that may facilitate studies into the development of the ciliary epithelium, the production of the aqueous and vitreous humors, and the synthesis of the ciliary zonule.
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Affiliation(s)
- J C Youkilis
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - S Bassnett
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA.
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47
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Bonnet C, González S, Roberts JS, Robertson SYT, Ruiz M, Zheng J, Deng SX. Human limbal epithelial stem cell regulation, bioengineering and function. Prog Retin Eye Res 2021; 85:100956. [PMID: 33676006 PMCID: PMC8428188 DOI: 10.1016/j.preteyeres.2021.100956] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/21/2021] [Accepted: 02/26/2021] [Indexed: 12/13/2022]
Abstract
The corneal epithelium is continuously renewed by limbal stem/progenitor cells (LSCs), a cell population harbored in a highly regulated niche located at the limbus. Dysfunction and/or loss of LSCs and their niche cause limbal stem cell deficiency (LSCD), a disease that is marked by invasion of conjunctival epithelium into the cornea and results in failure of epithelial wound healing. Corneal opacity, pain, loss of vision, and blindness are the consequences of LSCD. Successful treatment of LSCD depends on accurate diagnosis and staging of the disease and requires restoration of functional LSCs and their niche. This review highlights the major advances in the identification of potential LSC biomarkers and components of the LSC niche, understanding of LSC regulation, methods and regulatory standards in bioengineering of LSCs, and diagnosis and staging of LSCD. Overall, this review presents key points for researchers and clinicians alike to consider in deepening the understanding of LSC biology and improving LSCD therapies.
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Affiliation(s)
- Clémence Bonnet
- Cornea Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA; Cornea Department, Paris University, Cochin Hospital, AP-HP, F-75014, Paris, France
| | - Sheyla González
- Cornea Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA
| | - JoAnn S Roberts
- Cornea Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA
| | - Sarah Y T Robertson
- Cornea Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA
| | - Maxime Ruiz
- Cornea Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA
| | - Jie Zheng
- Basic Science Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA
| | - Sophie X Deng
- Cornea Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA.
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Ali D, Alhattab D, Jafar H, Alzubide M, Sharar N, Bdour S, Awidi A. Differential Marker Expression between Keratinocyte Stem Cells and Their Progeny Generated from a Single Colony. Int J Mol Sci 2021; 22:ijms221910810. [PMID: 34639148 PMCID: PMC8509450 DOI: 10.3390/ijms221910810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 01/31/2023] Open
Abstract
The stemness in keratinocyte stem cells (KSCs) is determined by their gene expression patterns. KSCs are crucial in maintaining epidermal homeostasis and wound repair and are widely used candidates for therapeutic applications. Although several studies have reported their positive identifiers, unique biomarkers for KSCs remain elusive. Here, we aim to identify potential candidate stem cell markers. Human epidermal keratinocytes (HEKs) from neonatal foreskin tissues were isolated and cultured. Single-cell clonal analysis identified and characterized three types of cells: KSCs (holoclones), transient amplifying cells (TACs; meroclones), and differentiated cells (DSCs; paraclones). The clonogenic potential of KSCs demonstrated the highest proliferation potential of KSCs, followed by TACs and DSCs, respectively. Whole-transcriptome analysis using microarray technology unraveled the molecular signatures of these cells. These results were validated by quantitative real-time polymerase chain reaction and flow cytometry analysis. A total of 301 signature upregulated and 149 downregulated differentially expressed genes (DEGs) were identified in the KSCs, compared to TACs and DSCs. Furthermore, DEG analyses revealed new sets of genes related to cell proliferation, cell adhesion, surface makers, and regulatory factors. In conclusion, this study provides a useful source of information for the identification of potential SC-specific candidate markers.
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Affiliation(s)
- Dema Ali
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; (D.A.); (D.A.); (H.J.); (M.A.); (N.S.)
- Department of Biological Sciences, Faculty of Science, The University of Jordan, Amman 11942, Jordan
| | - Dana Alhattab
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; (D.A.); (D.A.); (H.J.); (M.A.); (N.S.)
- Laboratory for Nanomedicine, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Hanan Jafar
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; (D.A.); (D.A.); (H.J.); (M.A.); (N.S.)
- Department of Anatomy and Histology, School of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Malak Alzubide
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; (D.A.); (D.A.); (H.J.); (M.A.); (N.S.)
| | - Nour Sharar
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; (D.A.); (D.A.); (H.J.); (M.A.); (N.S.)
| | - Salwa Bdour
- Department of Clinical Laboratory Sciences, Faculty of Science, The University of Jordan, Amman 11942, Jordan
- Correspondence: (S.B.); (A.A.)
| | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; (D.A.); (D.A.); (H.J.); (M.A.); (N.S.)
- Department of Hematology and Oncology, Faculty of Medicine, The University of Jordan, Amman 11942, Jordan
- Correspondence: (S.B.); (A.A.)
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Kapoor D, Khan A, O'Donnell MJ, Kolosov D. Novel mechanisms of epithelial ion transport: insights from the cryptonephridial system of lepidopteran larvae. CURRENT OPINION IN INSECT SCIENCE 2021; 47:53-61. [PMID: 33866042 DOI: 10.1016/j.cois.2021.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Lepidopterans are among the most widespread and easily recognized insects. Whereas adult lepidopterans are known for their beauty and ecological importance as pollinators and sources of food for other animals, larvae are economically important pests of forests and agricultural crops. In the larval body, rapid growth while feeding on plant-based diet is associated with extreme alkalinity (up to pH = 11) of the midgut lumen that helps digest plant proteins. Additionally, the presence of plant secondary metabolites which serve as anti-herbivory agents requires uninterrupted excretory function, accomplished primarily by the Malpighian tubules (MTs). The so-called cryptonephridial condition, along with extreme regional heterogeneity of the MTs, and the ability to rapidly and reversibly alter the direction of epithelial ion transport are features that allow uninterrupted MT functioning and recycling of base equivalents. Studies of MTs in lepidopteran larvae have revealed that rapid adjustments in epithelial ion transport include unexpected roles for voltage-gated, ligand-gated and mechanosensitive ion channels, as well as gap junctions. These molecular components are present in epithelia of a variety of vertebrates and invertebrates and thus are likely to constitute a universal epithelial toolkit for rapid autonomous regulation of epithelial function.
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Affiliation(s)
| | - Aliyyah Khan
- Department of Biology, McMaster University, Hamilton, Canada
| | | | - Dennis Kolosov
- Department of Biological Sciences, California State University San Marcos, San Marcos, USA.
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50
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Ligocki AJ, Fury W, Gutierrez C, Adler C, Yang T, Ni M, Bai Y, Wei Y, Lehmann GL, Romano C. Molecular characteristics and spatial distribution of adult human corneal cell subtypes. Sci Rep 2021; 11:16323. [PMID: 34381080 PMCID: PMC8357950 DOI: 10.1038/s41598-021-94933-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/19/2021] [Indexed: 12/13/2022] Open
Abstract
Bulk RNA sequencing of a tissue captures the gene expression profile from all cell types combined. Single-cell RNA sequencing identifies discrete cell-signatures based on transcriptomic identities. Six adult human corneas were processed for single-cell RNAseq and 16 cell clusters were bioinformatically identified. Based on their transcriptomic signatures and RNAscope results using representative cluster marker genes on human cornea cross-sections, these clusters were confirmed to be stromal keratocytes, endothelium, several subtypes of corneal epithelium, conjunctival epithelium, and supportive cells in the limbal stem cell niche. The complexity of the epithelial cell layer was captured by eight distinct corneal clusters and three conjunctival clusters. These were further characterized by enriched biological pathways and molecular characteristics which revealed novel groupings related to development, function, and location within the epithelial layer. Moreover, epithelial subtypes were found to reflect their initial generation in the limbal region, differentiation, and migration through to mature epithelial cells. The single-cell map of the human cornea deepens the knowledge of the cellular subsets of the cornea on a whole genome transcriptional level. This information can be applied to better understand normal corneal biology, serve as a reference to understand corneal disease pathology, and provide potential insights into therapeutic approaches.
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Affiliation(s)
- Ann J Ligocki
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Wen Fury
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | | | - Tao Yang
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Min Ni
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Yu Bai
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Yi Wei
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | - Carmelo Romano
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA.
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