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Vattulainen M, Smits JGA, Arts JA, Lima Cunha D, Ilmarinen T, Skottman H, Zhou H. Deciphering the heterogeneity of differentiating hPSC-derived corneal limbal stem cells through single-cell RNA sequencing. Stem Cell Reports 2024; 19:1010-1023. [PMID: 38942029 PMCID: PMC11252539 DOI: 10.1016/j.stemcr.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/30/2024] Open
Abstract
A comprehensive understanding of the human pluripotent stem cell (hPSC) differentiation process stands as a prerequisite for the development of hPSC-based therapeutics. In this study, single-cell RNA sequencing (scRNA-seq) was performed to decipher the heterogeneity during differentiation of three hPSC lines toward corneal limbal stem cells (LSCs). The scRNA-seq data revealed nine clusters encompassing the entire differentiation process, among which five followed the anticipated differentiation path of LSCs. The remaining four clusters were previously undescribed cell states that were annotated as either mesodermal-like or undifferentiated subpopulations, and their prevalence was hPSC line dependent. Distinct cluster-specific marker genes identified in this study were confirmed by immunofluorescence analysis and employed to purify hPSC-derived LSCs, which effectively minimized the variation in the line-dependent differentiation efficiency. In summary, scRNA-seq offered molecular insights into the heterogeneity of hPSC-LSC differentiation, allowing a data-driven strategy for consistent and robust generation of LSCs, essential for future advancement toward clinical translation.
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Affiliation(s)
- Meri Vattulainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jos G A Smits
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Julian A Arts
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Dulce Lima Cunha
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Tanja Ilmarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Heli Skottman
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| | - Huiqing Zhou
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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2
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Wang J, Luo H, Zhao X, Wang C, Yang L. Impact of Combined Phototherapy and Melanocyte Transplantation on Indicators of Vitiligo Activity. Dermatol Surg 2024:00042728-990000000-00875. [PMID: 38984521 DOI: 10.1097/dss.0000000000004320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
OBJECTIVE To investigate the effect of phototherapy combined with melanocyte transplantation on the activity index of vitiligo. METHODS One hundred twenty patients with stable vitiligo were selected and divided into 2 groups: phototherapy group (n = 60) and phototherapy combined with melanocyte therapy group (n = 60). Patients' vitiligo activity scores before and 6 months after treatment, patients' skin pigmentation responses 6 months after treatment, and patients' new Koebner cases 6 months after treatment were compared. The expression of tyrosinase and Melan-A in the skin samples was analyzed by immunohistochemistry. RESULTS The effect of skin surface repigmentation in the observation group was better than that in the control group (p < .05). The expression of tyrosinase and Melan-A in the observation group was higher than that in the control group (p < .05), indicating that the combined treatment could enhance the function of melanocytes. After 6 months of treatment, the incidence of the Koebner phenomenon in the observation group was lower than that in the control group (p < .05). CONCLUSION The combination of phototherapy and melanocyte transplantation can obviously improve the activity index of vitiligo, slow down the spread of white spots, reduce the formation of new white spots, and reduce the occurrence of the Koebner phenomenon.
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Affiliation(s)
- Junlong Wang
- Department of Dermatology, Xingtai People's Hospital Affiliated to Hebei Medical University, Xingtai, China
| | - Hongyu Luo
- Department of Cardiology, Xingtai Central Hospital, Xingtai, China
| | - Xiaoling Zhao
- Cancer Laboratory, Xingtai People's Hospital Affiliated to Hebei Medical University, Xingtai, China
| | - Chengcheng Wang
- Department of Dermatology, Xingtai People's Hospital Affiliated to Hebei Medical University, Xingtai, China
| | - Linfang Yang
- Department of Dermatology, Xingtai People's Hospital Affiliated to Hebei Medical University, Xingtai, China
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3
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Sun D, Zhang X, Chen R, Sang T, Li Y, Wang Q, Xie L, Zhou Q, Dou S. Decoding cellular plasticity and niche regulation of limbal stem cells during corneal wound healing. Stem Cell Res Ther 2024; 15:201. [PMID: 38971839 PMCID: PMC11227725 DOI: 10.1186/s13287-024-03816-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 06/25/2024] [Indexed: 07/08/2024] Open
Abstract
BACKGROUND Dysfunction or deficiency of corneal epithelium results in vision impairment or blindness in severe cases. The rapid and effective regeneration of corneal epithelial cells relies on the limbal stem cells (LSCs). However, the molecular and functional responses of LSCs and their niche cells to injury remain elusive. METHODS Single-cell RNA sequencing was performed on corneal tissues from normal mice and corneal epithelium defect models. Bioinformatics analysis was performed to confirm the distinct characteristics and cell fates of LSCs. Knockdown of Creb5 and OSM treatment experiment were performed to determine their roles of in corneal epithelial wound healing. RESULTS Our data defined the molecular signatures of LSCs and reconstructed the pseudotime trajectory of corneal epithelial cells. Gene network analyses characterized transcriptional landmarks that potentially regulate LSC dynamics, and identified a transcription factor Creb5, that was expressed in LSCs and significantly upregulated after injury. Loss-of-function experiments revealed that silencing Creb5 delayed the corneal epithelial healing and LSC mobilization. Through cell-cell communication analysis, we identified 609 candidate regeneration-associated ligand-receptor interaction pairs between LSCs and distinct niche cells, and discovered a unique subset of Arg1+ macrophages infiltrated after injury, which were present as the source of Oncostatin M (OSM), an IL-6 family cytokine, that were demonstrated to effectively accelerate the corneal epithelial wound healing. CONCLUSIONS This research provides a valuable single-cell resource and reference for the discovery of mechanisms and potential clinical interventions aimed at ocular surface reconstruction.
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Affiliation(s)
- Di Sun
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Xiaowen Zhang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Rong Chen
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Tian Sang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Ya Li
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Qun Wang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Lixin Xie
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Qingjun Zhou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China.
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China.
| | - Shengqian Dou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China.
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China.
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4
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Yang GN, Sun YBY, Roberts PK, Moka H, Sung MK, Gardner-Russell J, El Wazan L, Toussaint B, Kumar S, Machin H, Dusting GJ, Parfitt GJ, Davidson K, Chong EW, Brown KD, Polo JM, Daniell M. Exploring single-cell RNA sequencing as a decision-making tool in the clinical management of Fuchs' endothelial corneal dystrophy. Prog Retin Eye Res 2024; 102:101286. [PMID: 38969166 DOI: 10.1016/j.preteyeres.2024.101286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 06/14/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has enabled the identification of novel gene signatures and cell heterogeneity in numerous tissues and diseases. Here we review the use of this technology for Fuchs' Endothelial Corneal Dystrophy (FECD). FECD is the most common indication for corneal endothelial transplantation worldwide. FECD is challenging to manage because it is genetically heterogenous, can be autosomal dominant or sporadic, and progress at different rates. Single-cell RNA sequencing has enabled the discovery of several FECD subtypes, each with associated gene signatures, and cell heterogeneity. Current FECD treatments are mainly surgical, with various Rho kinase (ROCK) inhibitors used to promote endothelial cell metabolism and proliferation following surgery. A range of emerging therapies for FECD including cell therapies, gene therapies, tissue engineered scaffolds, and pharmaceuticals are in preclinical and clinical trials. Unlike conventional disease management methods based on clinical presentations and family history, targeting FECD using scRNA-seq based precision-medicine has the potential to pinpoint the disease subtypes, mechanisms, stages, severities, and help clinicians in making the best decision for surgeries and the applications of therapeutics. In this review, we first discuss the feasibility and potential of using scRNA-seq in clinical diagnostics for FECD, highlight advances from the latest clinical treatments and emerging therapies for FECD, integrate scRNA-seq results and clinical notes from our FECD patients and discuss the potential of applying alternative therapies to manage these cases clinically.
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Affiliation(s)
- Gink N Yang
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Yu B Y Sun
- Department of Anatomy and Development Biology, Monash University, Clayton, Australia
| | - Philip Ke Roberts
- Department of Ophthalmology, Medical University Vienna, 18-20 Währinger Gürtel, Vienna, Austria
| | - Hothri Moka
- Mogrify Limited, 25 Cambridge Science Park Milton Road, Milton, Cambridge, UK
| | - Min K Sung
- Mogrify Limited, 25 Cambridge Science Park Milton Road, Milton, Cambridge, UK
| | - Jesse Gardner-Russell
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Layal El Wazan
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Bridget Toussaint
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Satheesh Kumar
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Heather Machin
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Lions Eye Donation Service, Level 7, Smorgon Family Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia
| | - Gregory J Dusting
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Geraint J Parfitt
- Mogrify Limited, 25 Cambridge Science Park Milton Road, Milton, Cambridge, UK
| | - Kathryn Davidson
- Department of Anatomy and Development Biology, Monash University, Clayton, Australia
| | - Elaine W Chong
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Department of Ophthalmology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Karl D Brown
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Jose M Polo
- Department of Anatomy and Development Biology, Monash University, Clayton, Australia
| | - Mark Daniell
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Lions Eye Donation Service, Level 7, Smorgon Family Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia.
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5
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Suanno G, Genna VG, Maurizi E, Dieh AA, Griffith M, Ferrari G. Cell therapy in the cornea: The emerging role of microenvironment. Prog Retin Eye Res 2024; 102:101275. [PMID: 38797320 DOI: 10.1016/j.preteyeres.2024.101275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
The cornea is an ideal testing field for cell therapies. Its highly ordered structure, where specific cell populations are sequestered in different layers, together with its accessibility, has allowed the development of the first stem cell-based therapy approved by the European Medicine Agency. Today, different techniques have been proposed for autologous and allogeneic limbal and non-limbal cell transplantation. Cell replacement has also been attempted in cases of endothelial cell decompensation as it occurs in Fuchs dystrophy: injection of cultivated allogeneic endothelial cells is now in advanced phases of clinical development. Recently, stromal substitutes have been developed with excellent integration capability and transparency. Finally, cell-derived products, such as exosomes obtained from different sources, have been investigated for the treatment of severe corneal diseases with encouraging results. Optimization of the success rate of cell therapies obviously requires high-quality cultured cells/products, but the role of the surrounding microenvironment is equally important to allow engraftment of transplanted cells, to preserve their functions and, ultimately, lead to restoration of tissue integrity and transparency of the cornea.
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Affiliation(s)
- Giuseppe Suanno
- Vita-Salute San Raffaele University, Milan, Italy; Eye Repair Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Eleonora Maurizi
- Centre for Regenerative Medicine ''S. Ferrari'', University of Modena and Reggio Emilia, Modena, Italy
| | - Anas Abu Dieh
- Maisonneuve-Rosemont Hospital Research Centre, Montreal, Quebec, Canada
| | - May Griffith
- Maisonneuve-Rosemont Hospital Research Centre, Montreal, Quebec, Canada.
| | - Giulio Ferrari
- Vita-Salute San Raffaele University, Milan, Italy; Eye Repair Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Ophthalmology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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6
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Ge X, Weis K, Raetzman L. Glycoprotein hormone subunit alpha 2 (GPHA2): A pituitary stem cell-expressed gene associated with NOTCH2 signaling. Mol Cell Endocrinol 2024; 586:112163. [PMID: 38246572 DOI: 10.1016/j.mce.2024.112163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/03/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
Abstract
NOTCH2 is expressed in pituitary stem cells and is necessary for stem cell maintenance, proliferation, and differentiation. However, the pathways NOTCH2 engages to affect pituitary development remain unclear. In this study, we hypothesized that glycoprotein hormone subunit A2 (GPHA2), a corneal stem cell factor and ligand for the thyroid stimulating hormone receptor (TSHR), is downstream of NOTCH2 signaling. We found Gpha2 is expressed in quiescent pituitary stem cells by RNAscope in situ hybridization and scRNA seq. In Notch2 conditional knockout pituitaries, Gpha2 mRNA is reduced compared with control littermates. We then investigated the possible functions of GPHA2. Pituitaries treated with a GPHA2 peptide do not have a change in proliferation. However, in dissociated adult pituitary cells, GPHA2 increased pCREB expression and this induction was reversed by co-treatment with a TSHR inhibitor. These data suggest GPHA2 is a NOTCH2 related stem cell factor that activates TSHR signaling, potentially impacting pituitary development.
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Affiliation(s)
- Xiyu Ge
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, 524 Burrill Hall, 407 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Karen Weis
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, 524 Burrill Hall, 407 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Lori Raetzman
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, 524 Burrill Hall, 407 South Goodwin Avenue, Urbana, IL, 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA.
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7
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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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8
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Su Y, He S, Chen Q, Zhang H, Huang C, Zhao Q, Pu Y, He X, Jiang L, Ma Y, Zhao Q. Integrative ATAC-seq and RNA-seq analysis of myogenic differentiation of ovine skeletal muscle satellite cell. Genomics 2024; 116:110851. [PMID: 38692440 DOI: 10.1016/j.ygeno.2024.110851] [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: 01/29/2024] [Revised: 04/01/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
Skeletal muscle satellite cells (SMSCs) play an important role in regulating muscle growth and regeneration. Chromatin accessibility allows physical interactions that synergistically regulate gene expression through enhancers, promoters, insulators, and chromatin binding factors. However, the chromatin accessibility altas and its regulatory role in ovine myoblast differentiation is still unclear. Therefore, ATAC-seq and RNA-seq analysis were performed on ovine SMSCs at the proliferation stage (SCG) and differentiation stage (SCD). 17,460 DARs (differential accessibility regions) and 3732 DEGs (differentially expressed genes) were identified. Based on joint analysis of ATAC-seq and RNA-seq, we revealed that PI3K-Akt, TGF-β and other signaling pathways regulated SMSCs differentiation. We identified two novel candidate genes, FZD5 and MAP2K6, which may affect the proliferation and differentiation of SMSCs. Our data identify potential cis regulatory elements of ovine SMSCs. This study can provide a reference for exploring the mechanisms of the differentiation and regeneration of SMSCs in the future.
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Affiliation(s)
- Yingxiao Su
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China
| | - Siqi He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China; College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Qian Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China; College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Hechun Zhang
- Chaoyang Chaomu Breeding Farm Co., LTD, Chaoyang, Liaoning 122629, China
| | - Chang Huang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China; College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Qian Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China; College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yabin Pu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China
| | - Xiaohong He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China
| | - Lin Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China.
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Cui W, Chen S, Hu T, Zhou T, Qiu C, Jiang L, Cheng X, Ji J, Yao K, Han H. Nanoceria-Mediated Cyclosporin A Delivery for Dry Eye Disease Management through Modulating Immune-Epithelial Crosstalk. ACS NANO 2024; 18:11084-11102. [PMID: 38632691 DOI: 10.1021/acsnano.3c11514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Dry eye disease (DED) affects a substantial worldwide population with increasing frequency. Current single-targeting DED management is severely hindered by the existence of an oxidative stress-inflammation vicious cycle and complicated intercellular crosstalk within the ocular microenvironment. Here, a nanozyme-based eye drop, namely nanoceria loading cyclosporin A (Cs@P/CeO2), is developed, which possesses long-term antioxidative and anti-inflammatory capacities due to its regenerative antioxidative activity and sustained release of cyclosporin A (CsA). In vitro studies showed that the dual-functional Cs@P/CeO2 not only inhibits cellular reactive oxygen species production, sequentially maintaining mitochondrial integrity, but also downregulates inflammatory processes and repolarizes macrophages. Moreover, using flow cytometric and single-cell sequencing data, the in vivo therapeutic effect of Cs@P/CeO2 was systemically demonstrated, which rebalances the immune-epithelial communication in the corneal microenvironment with less inflammatory macrophage polarization, restrained oxidative stress, and enhanced epithelium regeneration. Collectively, our data proved that the antioxidative and anti-inflammatory Cs@P/CeO2 may provide therapeutic insights into DED management.
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Affiliation(s)
- Wenyu Cui
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, P. R. China
| | - Sheng Chen
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, P. R. China
| | - Tianyi Hu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, P. R. China
| | - Tinglian Zhou
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, P. R. China
| | - Chen Qiu
- MOE Laboratory of Biosystems Homeostasis & Protection and iCell Biotechnology Regenerative Biomedicine Laboratory of College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Luyang Jiang
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, P. R. China
| | - Xiaoyu Cheng
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, P. R. China
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, P. R. China
| | - Ke Yao
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, P. R. China
| | - Haijie Han
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, P. R. China
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10
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Dorgau B, Collin J, Rozanska A, Zerti D, Unsworth A, Crosier M, Hussain R, Coxhead J, Dhanaseelan T, Patel A, Sowden JC, FitzPatrick DR, Queen R, Lako M. Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina. Nat Commun 2024; 15:3567. [PMID: 38670973 PMCID: PMC11053058 DOI: 10.1038/s41467-024-47933-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The emergence of retinal progenitor cells and differentiation to various retinal cell types represent fundamental processes during retinal development. Herein, we provide a comprehensive single cell characterisation of transcriptional and chromatin accessibility changes that underline retinal progenitor cell specification and differentiation over the course of human retinal development up to midgestation. Our lineage trajectory data demonstrate the presence of early retinal progenitors, which transit to late, and further to transient neurogenic progenitors, that give rise to all the retinal neurons. Combining single cell RNA-Seq with spatial transcriptomics of early eye samples, we demonstrate the transient presence of early retinal progenitors in the ciliary margin zone with decreasing occurrence from 8 post-conception week of human development. In retinal progenitor cells, we identified a significant enrichment for transcriptional enhanced associate domain transcription factor binding motifs, which when inhibited led to loss of cycling progenitors and retinal identity in pluripotent stem cell derived organoids.
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Affiliation(s)
- Birthe Dorgau
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Agata Rozanska
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Darin Zerti
- Biosciences Institute, Newcastle University, Newcastle, UK
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Moira Crosier
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | | | | | - Aara Patel
- UCL Great Ormond Street Institute of Child Health and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Jane C Sowden
- UCL Great Ormond Street Institute of Child Health and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle, UK.
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle, UK.
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11
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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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12
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Verma S, Moreno IY, Prinholato da Silva C, Sun M, Cheng X, Gesteira TF, Coulson-Thomas VJ. Endogenous TSG-6 modulates corneal inflammation following chemical injury. Ocul Surf 2024; 32:26-38. [PMID: 38151073 PMCID: PMC11056311 DOI: 10.1016/j.jtos.2023.12.007] [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: 08/01/2023] [Revised: 11/21/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
PURPOSE Tumor necrosis factor (TNF)-stimulated gene-6 (TSG-6) is upregulated in various pathophysiological contexts, where it has a diverse repertoire of immunoregulatory functions. Herein, we investigated the expression and function of TSG-6 during corneal homeostasis and after injury. METHODS Human corneas, eyeballs from BALB/c (TSG-6+/+), TSG-6+/- and TSG-6-/- mice, human immortalized corneal epithelial cells and murine corneal epithelial progenitor cells were prepared for immunostaining and real time PCR analysis of endogenous expression of TSG-6. Mice were subjected to unilateral corneal debridement or alkali burn (AB) injuries and wound healing assessed over time using fluorescein stain, in vivo confocal microscopy and histology. RESULTS TSG-6 is endogenously expressed in the human and mouse cornea and established corneal epithelial cell lines and is upregulated after injury. A loss of TSG-6 has no structural and functional effect in the cornea during homeostasis. No differences were noted in the rate of corneal epithelial wound closure between BALB/c, TSG-6+/- and TSG-6-/- mice. TSG-6-/- mice presented decreased inflammatory response within the first 24 h of injury and accelerated corneal wound healing following AB when compared to control mice. CONCLUSION TSG-6 is endogenously expressed in the cornea and upregulated after injury where it propagates the inflammatory response following chemical injury.
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Affiliation(s)
- Sudhir Verma
- College of Optometry, University of Houston, Houston, TX, United States; Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, Delhi, India
| | - Isabel Y Moreno
- College of Optometry, University of Houston, Houston, TX, United States
| | | | - Mingxia Sun
- College of Optometry, University of Houston, Houston, TX, United States
| | - Xuhong Cheng
- College of Optometry, University of Houston, Houston, TX, United States
| | - Tarsis F Gesteira
- College of Optometry, University of Houston, Houston, TX, United States
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13
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Davidson KC, Sung M, Brown KD, Contet J, Belluschi S, Hamel R, Moreno-Moral A, Dos Santos RL, Gough J, Polo JM, Daniell M, Parfitt GJ. Single nuclei transcriptomics of the in situ human limbal stem cell niche. Sci Rep 2024; 14:6749. [PMID: 38514716 PMCID: PMC10957941 DOI: 10.1038/s41598-024-57242-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
The corneal epithelium acts as a barrier to pathogens entering the eye; corneal epithelial cells are continuously renewed by uni-potent, quiescent limbal stem cells (LSCs) located at the limbus, where the cornea transitions to conjunctiva. There has yet to be a consensus on LSC markers and their transcriptome profile is not fully understood, which may be due to using cadaveric tissue without an intact stem cell niche for transcriptomics. In this study, we addressed this problem by using single nuclei RNA sequencing (snRNAseq) on healthy human limbal tissue that was immediately snap-frozen after excision from patients undergoing cataract surgery. We identified the quiescent LSCs as a sub-population of corneal epithelial cells with a low level of total transcript counts. Moreover, TP63, KRT15, CXCL14, and ITGβ4 were found to be highly expressed in LSCs and transiently amplifying cells (TACs), which constitute the corneal epithelial progenitor populations at the limbus. The surface markers SLC6A6 and ITGβ4 could be used to enrich human corneal epithelial cell progenitors, which were also found to specifically express the putative limbal progenitor cell markers MMP10 and AC093496.1.
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Affiliation(s)
- Kathryn C Davidson
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | | | - Karl D Brown
- Centre for Eye Research Australia (CERA), Melbourne, Australia
| | - Julian Contet
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | | | | | | | | | - Julian Gough
- Mogrify Limited, Cambridge, England, UK
- MRC Laboratory of Molecular Biology, Cambridge, England, UK
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.
- Mogrify Limited, Cambridge, England, UK.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.
- Adelaide Centre for Epigenetics, Faculty of Medicine Nursing and Medical Sciences, The University of Adelaide, Adelaide, Australia.
- The South Australian Immunogenomics Cancer Institute, Faculty of Medicine Nursing and Medical Sciences, The University of Adelaide, Adelaide, Australia.
| | - Mark Daniell
- Centre for Eye Research Australia (CERA), Melbourne, Australia.
| | - Geraint J Parfitt
- Mogrify Limited, Cambridge, England, UK.
- Ophthalmology Discovery Research, AbbVie, Irvine, CA, USA.
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14
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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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15
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Barvaux S, Okawa S, Del Sol A. SinCMat: A single-cell-based method for predicting functional maturation transcription factors. Stem Cell Reports 2024; 19:270-284. [PMID: 38215756 PMCID: PMC10874865 DOI: 10.1016/j.stemcr.2023.12.006] [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: 07/18/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
A major goal of regenerative medicine is to generate tissue-specific mature and functional cells. However, current cell engineering protocols are still unable to systematically produce fully mature functional cells. While existing computational approaches aim at predicting transcription factors (TFs) for cell differentiation/reprogramming, no method currently exists that specifically considers functional cell maturation processes. To address this challenge, here, we develop SinCMat, a single-cell RNA sequencing (RNA-seq)-based computational method for predicting cell maturation TFs. Based on a model of cell maturation, SinCMat identifies pairs of identity TFs and signal-dependent TFs that co-target genes driving functional maturation. A large-scale application of SinCMat to the Mouse Cell Atlas and Tabula Sapiens accurately recapitulates known maturation TFs and predicts novel candidates. We expect SinCMat to be an important resource, complementary to preexisting computational methods, for studies aiming at producing functionally mature cells.
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Affiliation(s)
- Sybille Barvaux
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Esch-Belval Esch-sur-Alzette, Luxembourg
| | - Satoshi Okawa
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Esch-Belval Esch-sur-Alzette, Luxembourg; University of Pittsburgh School of Medicine, Vascular Medicine Institute, Department of Computational and Systems Biology, McGowan Institute for Regenerative Medicine, Pittsburgh, PA, USA
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Esch-Belval Esch-sur-Alzette, Luxembourg; CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
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16
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Li W, Bazaz SR, Mayoh C, Salomon R. Analytical Workflows for Single-Cell Multiomic Data Using the BD Rhapsody Platform. Curr Protoc 2024; 4:e963. [PMID: 38353375 DOI: 10.1002/cpz1.963] [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] [Indexed: 02/16/2024]
Abstract
The conversion of raw sequencing reads to biologically relevant data in high-throughput single-cell RNA sequencing experiments is a complex and involved process. Drawing meaning from thousands of individual cells to provide biological insight requires ensuring not only that the data are of the highest quality but also that the signal can be separated from noise. In this article, we describe a detailed analytical workflow, including six pipelines, that allows high-quality data analysis in single-cell multiomics. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Image analysis Basic Protocol 2: Sequencing quality control and generation of a gene expression matrix Basic Protocol 3: Gene expression matrix data pre-processing and analysis Basic Protocol 4: Advanced analysis Basic Protocol 5: Conversion to flow cytometry standard (FCS) format Basic Protocol 6: Visualization using graphical interfaces.
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Affiliation(s)
- Wenyan Li
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Sajad Razavi Bazaz
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Robert Salomon
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
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17
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Bannier-Hélaouët M, Korving J, Ma Z, Begthel H, Giladi A, Lamers MM, van de Wetering WJ, Yawata N, Yawata M, LaPointe VLS, Dickman MM, Kalmann R, Imhoff SM, van Es JH, López-Iglesias C, Peters PJ, Haagmans BL, Wu W, Clevers H. Human conjunctiva organoids to study ocular surface homeostasis and disease. Cell Stem Cell 2024; 31:227-243.e12. [PMID: 38215738 DOI: 10.1016/j.stem.2023.12.008] [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: 07/11/2023] [Revised: 09/14/2023] [Accepted: 12/11/2023] [Indexed: 01/14/2024]
Abstract
The conjunctival epithelium covering the eye contains two main cell types: mucus-producing goblet cells and water-secreting keratinocytes, which present mucins on their apical surface. Here, we describe long-term expanding organoids and air-liquid interface representing mouse and human conjunctiva. A single-cell RNA expression atlas of primary and cultured human conjunctiva reveals that keratinocytes express multiple antimicrobial peptides and identifies conjunctival tuft cells. IL-4/-13 exposure increases goblet and tuft cell differentiation and drastically modifies the conjunctiva secretome. Human NGFR+ basal cells are identified as bipotent conjunctiva stem cells. Conjunctival cultures can be infected by herpes simplex virus 1 (HSV1), human adenovirus 8 (hAdV8), and SARS-CoV-2. HSV1 infection was reversed by acyclovir addition, whereas hAdV8 infection, which lacks an approved drug therapy, was inhibited by cidofovir. We document transcriptional programs induced by HSV1 and hAdV8. Finally, conjunctival organoids can be transplanted. Together, human conjunctiva organoid cultures enable the study of conjunctival (patho)-physiology.
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Affiliation(s)
- Marie Bannier-Hélaouët
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center, Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands.
| | - Jeroen Korving
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center, Utrecht, the Netherlands
| | - Ziliang Ma
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), and Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center, Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Amir Giladi
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center, Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Mart M Lamers
- Viroscience Department, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Willine J van de Wetering
- Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Nobuyo Yawata
- Department of Ocular Pathology and Imaging Science, Kyushu University, Fukuoka, Japan; Singapore Eye Research Institute, Singapore, Singapore; Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Makoto Yawata
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; National University Health System, Singapore, Singapore; Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore; NUSMED Immunology Translational Research Program, National University of Singapore, Singapore, Singapore; Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore; International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Vanessa L S LaPointe
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht, the Netherlands
| | - Mor M Dickman
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht, the Netherlands; University Eye Clinic Maastricht, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Rachel Kalmann
- Department of Ophthalmology, University Medical Center, Utrecht, the Netherlands
| | - Saskia M Imhoff
- Department of Ophthalmology, University Medical Center, Utrecht, the Netherlands
| | - Johan H van Es
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center, Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Carmen López-Iglesias
- Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Wei Wu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), and Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center, Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands.
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18
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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19
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Pan J, Pany S, Martinez-Carrasco R, Fini ME. Differential Efficacy of Small Molecules Dynasore and Mdivi-1 for the Treatment of Dry Eye Epitheliopathy or as a Countermeasure for Nitrogen Mustard Exposure of the Ocular Surface. J Pharmacol Exp Ther 2024; 388:506-517. [PMID: 37442618 PMCID: PMC10801785 DOI: 10.1124/jpet.123.001697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/19/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023] Open
Abstract
The ocular surface comprises the wet mucosal epithelia of the cornea and conjunctiva, the associated glands, and the overlying tear film. Epitheliopathy is the common pathologic outcome when the ocular surface is subjected to oxidative stress. Whether different stresses act via the same or different mechanisms is not known. Dynasore and dyngo-4a, small molecules developed to inhibit the GTPase activity of classic dynamins DNM1, DNM2, and DNM3, but not mdivi-1, a specific inhibitor of DNM1L, protect corneal epithelial cells exposed to the oxidant tert-butyl hydroperoxide (tBHP). Here we report that, while dyngo-4a is the more potent inhibitor of endocytosis, dynasore is the better cytoprotectant. Dynasore also protects corneal epithelial cells against exposure to high salt in an in vitro model of dysfunctional tears in dry eye. We now validate this finding in vivo, demonstrating that dynasore protects against epitheliopathy in a mouse model of dry eye. Knockdown of classic dynamin DNM2 was also cytoprotective against tBHP exposure, suggesting that dynasore's effect is at least partially on target. Like tBHP and high salt, exposure of corneal epithelial cells to nitrogen mustard upregulated the unfolded protein response and inflammatory markers, but dynasore did not protect against nitrogen mustard exposure. In contrast, mdivi-1 was cytoprotective. Interestingly, mdivi-1 did not inhibit the nitrogen mustard-induced expression of inflammatory cytokines. We conclude that exposure to tBHP or nitrogen mustard, two different oxidative stress agents, cause corneal epitheliopathy via different pathologic pathways. SIGNIFICANCE STATEMENT: Results presented in this paper, for the first time, implicate the dynamin DNM2 in ocular surface epitheliopathy. The findings suggest that dynasore could serve as a new topical treatment for dry eye epitheliopathy and that mdivi-1 could serve as a medical countermeasure for epitheliopathy due to nitrogen mustard exposure, with potentially increased efficacy when combined with anti-inflammatory agents and/or UPR modulators.
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Affiliation(s)
- Jinhong Pan
- New England Eye Center, Tufts Medical Center and Department of Ophthalmology, Tufts University School of Medicine (J.P., S.P., R.M.-C., M.E.F.) and Program in Pharmacology and Drug Development, Tufts Graduate School of Biomedical Sciences (M.E.F.), Tufts University, Boston, Massachusetts
| | - Satyabrata Pany
- New England Eye Center, Tufts Medical Center and Department of Ophthalmology, Tufts University School of Medicine (J.P., S.P., R.M.-C., M.E.F.) and Program in Pharmacology and Drug Development, Tufts Graduate School of Biomedical Sciences (M.E.F.), Tufts University, Boston, Massachusetts
| | - Rafael Martinez-Carrasco
- New England Eye Center, Tufts Medical Center and Department of Ophthalmology, Tufts University School of Medicine (J.P., S.P., R.M.-C., M.E.F.) and Program in Pharmacology and Drug Development, Tufts Graduate School of Biomedical Sciences (M.E.F.), Tufts University, Boston, Massachusetts
| | - M Elizabeth Fini
- New England Eye Center, Tufts Medical Center and Department of Ophthalmology, Tufts University School of Medicine (J.P., S.P., R.M.-C., M.E.F.) and Program in Pharmacology and Drug Development, Tufts Graduate School of Biomedical Sciences (M.E.F.), Tufts University, Boston, Massachusetts
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20
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Lapp T, Kammrath Betancor P, Schlunck G, Auw-Hädrich C, Maier P, Lange C, Reinhard T, Wolf J. Transcriptional profiling specifies the pathogen-specific human host response to infectious keratitis. Front Cell Infect Microbiol 2024; 13:1285676. [PMID: 38274739 PMCID: PMC10808294 DOI: 10.3389/fcimb.2023.1285676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Purpose Corneal infections are a leading cause of visual impairment and blindness worldwide. Here we applied high-resolution transcriptomic profiling to assess the general and pathogen-specific molecular and cellular mechanisms during human corneal infection. Methods Clinical diagnoses of herpes simplex virus (HSV) (n=5) and bacterial/fungal (n=5) keratitis were confirmed by histology. Healthy corneas (n=7) and keratoconus (n=4) samples served as controls. Formalin-fixed, paraffin-embedded (FFPE) human corneal specimens were analyzed using the 3' RNA sequencing method Massive Analysis of cDNA Ends (MACE RNA-seq). The cellular host response was investigated using comprehensive bioinformatic deconvolution (xCell and CYBERSORTx) analyses and by integration with published single cell RNA-seq data of the human cornea. Results Our analysis identified 216 and 561 genes, that were specifically overexpressed in viral or bacterial/fungal keratitis, respectively, and allowed to distinguish the two etiologies. The virus-specific host response was driven by adaptive immunity and associated molecular signaling pathways, whereas the bacterial/fungal-specific host response mainly involved innate immunity signaling pathways and cell types. We identified several genes and pathways involved in the host response to infectious keratitis, including CXCL9, CXCR3, and MMP9 for viral, and S100A8/A9, MMP9, and the IL17 pathway for bacterial/fungal keratitis. Conclusions High-resolution molecular profiling provides new insights into the human corneal host response to viral and bacterial/fungal infection. Pathogen-specific molecular profiles may provide the foundation for novel diagnostic biomarker and therapeutic approaches that target inflammation-induced damage to corneal host cells with the goal to improve the outcome of infectious keratitis.
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Affiliation(s)
- Thabo Lapp
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
- Ophtha-Lab, Department of Ophthalmology, St. Franziskus Hospital, Münster, Germany
| | - Paola Kammrath Betancor
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Günther Schlunck
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Claudia Auw-Hädrich
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Philip Maier
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Clemens Lange
- Ophtha-Lab, Department of Ophthalmology, St. Franziskus Hospital, Münster, Germany
| | - Thomas Reinhard
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Julian Wolf
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
- Omics Laboratory, Stanford University, Palo Alto, CA, United States
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, United States
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21
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Li M, Guo H, Wang B, Han Z, Wu S, Liu J, Huang H, Zhu J, An F, Lin Z, Mo K, Tan J, Liu C, Wang L, Deng X, Li G, Ji J, Ouyang H. The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation. Nat Commun 2024; 15:256. [PMID: 38177186 PMCID: PMC10766623 DOI: 10.1038/s41467-023-44471-w] [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: 08/16/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024] Open
Abstract
Proper differentiation of corneal epithelial cells (CECs) from limbal stem/progenitor cells (LSCs) is required for maintenance of ocular homeostasis and clear vision. Here, using a single-cell transcriptomic atlas, we delineate the comprehensive and refined molecular regulatory dynamics during human CEC development and differentiation. We find that RORA is a CEC-specific molecular switch that initiates and drives LSCs to differentiate into mature CECs by activating PITX1. RORA dictates CEC differentiation by establishing CEC-specific enhancers and chromatin interactions between CEC gene promoters and distal regulatory elements. Conversely, RORA silences LSC-specific promoters and disrupts promoter-anchored chromatin loops to turn off LSC genes. Collectively, our work provides detailed and comprehensive insights into the transcriptional dynamics and RORA-mediated epigenetic remodeling underlying human corneal epithelial differentiation.
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Affiliation(s)
- Mingsen Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
| | - Huizhen Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Bofeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Zhuo Han
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Siqi Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Jiafeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Huaxing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Jin Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Fengjiao An
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Zesong Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Kunlun Mo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Jieying Tan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Chunqiao Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, 999077, China
| | - Guigang Li
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jianping Ji
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
| | - Hong Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
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22
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Swarup A, Phansalkar R, Morri M, Agarwal A, Subramaniam V, Li B, Wu AY. Single-cell transcriptomic analysis of corneal organoids during development. Stem Cell Reports 2023; 18:2482-2497. [PMID: 38039970 PMCID: PMC10724212 DOI: 10.1016/j.stemcr.2023.10.022] [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: 04/21/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 12/03/2023] Open
Abstract
Corneal organoids are useful tools for disease modeling and tissue transplantation; however, they have not yet been well studied during maturation. We characterized human iPSC-derived corneal organoids at 1, 2, 3, and 4 months of development using single-cell RNA sequencing to determine the cellular heterogeneity at each stage. We found pluripotent cell clusters committed to epithelial cell lineage at 1 month; early corneal epithelial, endothelial, and stromal cell markers at 2 months; keratocytes as the largest cell population at 3 months; and a large epithelial cell population at 4 months. We compared organoid to fetal corneal development at different stages and found that 4-month organoids closely resemble the corneal cellular complexity of the fetal (16 post conception week) and adult cornea. Using RNA velocity trajectory analysis, we found that less differentiated cells appear to give rise to corneal epithelial cells during development.
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Affiliation(s)
- Aditi Swarup
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ragini Phansalkar
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maurizio Morri
- Chan Zuckerberg Biohub, Stanford University, San Francisco, CA, USA
| | - Aditi Agarwal
- Chan Zuckerberg Biohub, Stanford University, San Francisco, CA, USA
| | - Varun Subramaniam
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - BaoXiang Li
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - Albert Y Wu
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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23
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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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24
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Hu D, Lin Z, Li P, Zhang Z, Jiang J, Yang C. Investigation of Potential Crucial Genes and Key Pathways in Keratoconus: An Analysis of Gene Expression Omnibus Data. Biochem Genet 2023; 61:2724-2740. [PMID: 37233843 DOI: 10.1007/s10528-023-10398-6] [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: 01/08/2023] [Accepted: 05/07/2023] [Indexed: 05/27/2023]
Abstract
Keratoconus is one of the most common causes leading to visual impairment in young adult population. The pathogenesis of keratoconus remains poorly understood. The aim of this study was to identify the potential key genes and pathways associated with keratoconus and to further analyze its molecular mechanism. Two RNA-sequencing datasets of keratoconus and paired normal corneal tissues from the Gene Expression Omnibus database were obtained. Differentially expressed genes (DEGs) were identified, and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted. The protein-protein interaction (PPI) network of the DEGs was established, and the hub genes and significant gene modules of PPI were further constructed. Lastly, the GO and KEGG analyses of the hub gene were performed. In total, 548 common DEGs were identified. GO enrichment analysis showed that the DEGs were primarily associated with regulation of cell adhesion, the response to molecule of bacterial origin, lipopolysaccharide and biotic stimulus, collagen-containing extracellular matrix, extracellular matrix, and structure organization. KEGG pathway analysis showed that these DEGs were mainly involved in the TNF signaling pathway, IL-17 signaling pathway, Rheumatoid arthritis, Cytokine-cytokine receptor interaction. The PPI network was constructed with 146 nodes and 276 edges, and 3 significant modules are selected. Finally, top 10 hub genes were identified from the PPI network. The results revealed that extracellular matrix remodeling and immune inflammatory response could be the key links of keratoconus, TNF, IL6, IL1A, IL1B, CCL3, MMP3, MMP9, MMP1, and TGFB1 may be potential crucial genes, and TNF signaling pathway and IL-17 signaling pathway were the potential pathways accounting for pathogenesis and development of keratoconus.
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Affiliation(s)
- Di Hu
- Department of Ophthalmology, Children's Hospital of Fudan University, No.399 Wanyuan Road, Shanghai, 201102, China
| | - Zenan Lin
- Department of Ophthalmology, Shanghai First People's Hospital, Shanghai Jiao Tong University School of Medicine, No.100 Haining Road, Shanghai, 200080, China
| | - Pan Li
- Department of Ophthalmology, First Hospital of Xi'an, Institute of Ophthalmology, Key Lab of Ophthalmology, Clinical Center for Ophthalmology, Xi'an, 710002, China
| | - Zhehuan Zhang
- Department of Ophthalmology, Children's Hospital of Fudan University, No.399 Wanyuan Road, Shanghai, 201102, China
| | - Junhong Jiang
- Department of Ophthalmology, Shanghai First People's Hospital, Shanghai Jiao Tong University School of Medicine, No.100 Haining Road, Shanghai, 200080, China.
| | - Chenhao Yang
- Department of Ophthalmology, Children's Hospital of Fudan University, No.399 Wanyuan Road, Shanghai, 201102, China.
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25
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Tan HY, Wu YF, Wang CY, Lin SJ, Ma YH, Young TH. The cellular responses of corneal fibroblasts to cyclic stretching loads. Exp Eye Res 2023; 237:109696. [PMID: 37890758 DOI: 10.1016/j.exer.2023.109696] [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: 07/21/2023] [Revised: 09/28/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
Mechanical signaling plays a crucial role in maintaining extracellular matrix (ECM) homeostasis in various structures. In this study, we investigated the responses of corneal fibroblasts to cyclic stretching loads using an in vitro cell culture system. Bovine corneal fibroblasts were cultured and subjected to equibiaxial cyclic strain of 15% for 72 h at a frequency of 0.25 Hz, with bovine skin fibroblasts used as a comparison. We explored various cellular behaviors, including morphological changes, cell proliferation, and metabolism in response to mechanical stretching loads. The expression of genes, protein secretion, and enzymatic activity for several major metalloproteinases was also determined through Q-PCR, Western blot, and gel zymography. Additionally, we investigated the involvement of mitogen-activated protein kinases (MAPKs) signaling pathways in the corneal fibroblasts when subjected to mechanical stimuli. Our findings revealed that, compared to skin fibroblasts, corneal fibroblasts were reluctant to morphological changes in response to a prolonged (72 h) and high-amplitude (15% of strain) cyclic stretching load. However, cyclic stretching loads stimulated the upregulation of MMP-2 expression in corneal fibroblasts via the MAPK signaling pathways involving extracellular signal-regulated kinase and p38. Together with a lack of upregulation in type I collagen expression, our results indicate the induction of the ECM degradation process in corneal fibroblasts in response to cyclic stretching. These findings emphasize the mechanoresponsive nature of corneal fibroblasts and shed light on the potential impact of intense mechanical stress on the cornea in both normal and pathological conditions such as keratoconus, providing valuable insights for understanding corneal mechanobiology.
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Affiliation(s)
- Hsin-Yuan Tan
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan; Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yueh-Feng Wu
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
| | - Chia-Yi Wang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Sung-Jan Lin
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan; Department of Dermatology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yunn-Hwa Ma
- Department of Physiology and Pharmacology and Healthy Aging Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Tai-Horng Young
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan.
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26
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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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27
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Kauppila M, Mörö A, Valle-Delgado JJ, Ihalainen T, Sukki L, Puistola P, Kallio P, Ilmarinen T, Österberg M, Skottman H. Toward Corneal Limbus In Vitro Model: Regulation of hPSC-LSC Phenotype by Matrix Stiffness and Topography During Cell Differentiation Process. Adv Healthc Mater 2023; 12:e2301396. [PMID: 37449943 DOI: 10.1002/adhm.202301396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
A functional limbal epithelial stem cells (LSC) niche is a vital element in the regular renewal of the corneal epithelium by LSCs and maintenance of good vision. However, little is known about its unique structure and mechanical properties on LSC regulation, creating a significant gap in development of LSC-based therapies. Herein, the effect of mechanical and architectural elements of the niche on human pluripotent derived LSCs (hPSC-LSC) phenotype and growth is investigated in vitro. Specifically, three formulations of polyacrylamide gels with different controlled stiffnesses are used for culture and characterization of hPSC-LSCs from different stages of differentiation. In addition, limbal mimicking topography in polydimethylsiloxane is utilized for culturing hPSC-LSCs at early time point of differentiation. For comparison, the expression of selected key proteins of the corneal cells is analyzed in their native environment through whole mount staining of human donor corneas. The results suggest that mechanical response and substrate preference of the cells is highly dependent on their developmental stage. In addition, data indicate that cells may carry possible mechanical memory from previous culture matrix, both highlighting the importance of mechanical design of a functional in vitro limbus model.
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Affiliation(s)
- Maija Kauppila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Anni Mörö
- Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Juan José Valle-Delgado
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, 02150, Finland
| | - Teemu Ihalainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Lassi Sukki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Paula Puistola
- Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Pasi Kallio
- Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Tanja Ilmarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Monika Österberg
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, 02150, Finland
| | - Heli Skottman
- Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
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28
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Wolf J, Rasmussen DK, Sun YJ, Vu JT, Wang E, Espinosa C, Bigini F, Chang RT, Montague AA, Tang PH, Mruthyunjaya P, Aghaeepour N, Dufour A, Bassuk AG, Mahajan VB. Liquid-biopsy proteomics combined with AI identifies cellular drivers of eye aging and disease in vivo. Cell 2023; 186:4868-4884.e12. [PMID: 37863056 PMCID: PMC10720485 DOI: 10.1016/j.cell.2023.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/26/2023] [Accepted: 09/13/2023] [Indexed: 10/22/2023]
Abstract
Single-cell analysis in living humans is essential for understanding disease mechanisms, but it is impractical in non-regenerative organs, such as the eye and brain, because tissue biopsies would cause serious damage. We resolve this problem by integrating proteomics of liquid biopsies with single-cell transcriptomics from all known ocular cell types to trace the cellular origin of 5,953 proteins detected in the aqueous humor. We identified hundreds of cell-specific protein markers, including for individual retinal cell types. Surprisingly, our results reveal that retinal degeneration occurs in Parkinson's disease, and the cells driving diabetic retinopathy switch with disease stage. Finally, we developed artificial intelligence (AI) models to assess individual cellular aging and found that many eye diseases not associated with chronological age undergo accelerated molecular aging of disease-specific cell types. Our approach, which can be applied to other organ systems, has the potential to transform molecular diagnostics and prognostics while uncovering new cellular disease and aging mechanisms.
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Affiliation(s)
- Julian Wolf
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Ditte K Rasmussen
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA; Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Young Joo Sun
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Jennifer T Vu
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Elena Wang
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Fabio Bigini
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Robert T Chang
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Artis A Montague
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Peter H Tang
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; Retina Consultants of Minnesota, Edina, MN 55435, USA
| | - Prithvi Mruthyunjaya
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Antoine Dufour
- Departments of Physiology and Pharmacology & Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Alexander G Bassuk
- Departments of Pediatrics and Neurology, The Iowa Neuroscience Institute (INI), University of Iowa, Iowa City, IA 52242, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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29
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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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Moreno IY, Parsaie A, Gesteira TF, Coulson-Thomas VJ. Characterization of the Limbal Epithelial Stem Cell Niche. Invest Ophthalmol Vis Sci 2023; 64:48. [PMID: 37906057 PMCID: PMC10619699 DOI: 10.1167/iovs.64.13.48] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023] Open
Abstract
Purpose Limbal epithelial stem cells (LESCs) reside within a LSC niche (LSCN). We recently identified that hyaluronan (HA) is a major constituent of the LSCN, and that HA is necessary for maintaining LESCs in the "stem cell" state, both in vitro and in vivo. Herein, we characterized the LSCN to identify key components of the HA-specific LSCN. Methods The cornea and limbal rim were dissected from mouse corneas, subjected to mRNA extraction, and sequenced using a NextSeq 500 (Illumina) and data processed using CLC Genomics Workbench 20 (Qiagen) and the STRING database to identify key components of the LSCN. Their expression was confirmed by real-time PCR, Western blotting, and immunohistochemistry. Furthermore, the differential expression of key compounds in different corneal cell types were determined with single-cell RNA sequencing. Results We identified that the hyaladherins inter-alpha-inhibitor (IαI), TSG-6 and versican are highly expressed in the limbus. Specifically, HA/HC complexes are present in the LSCN, in the stroma underlying the limbal epithelium, and surrounding the limbal vasculature. For IαI, heavy chains 5 and 2 (HC5 and HC2) were found to be the most highly expressed HCs in the mouse and human limbus and were associate with HA-forming HA/HC-specific matrices. Conclusions The LSCN contains HA/HC complexes, which have been previously correlated with stem cell niches. The identification of HA/HC complexes in the LSCN could serve as a new therapeutic avenue for treating corneal pathology. Additionally, HA/HC complexes could be used as a substrate for culturing LESCs before LESC transplantation.
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Affiliation(s)
- Isabel Y. Moreno
- College of Optometry, University of Houston, Houston, Texas, United States
| | - Arian Parsaie
- College of Optometry, University of Houston, Houston, Texas, United States
- College of Natural Science and Mathematics, University of Houston, Houston, Texas, United States
| | - Tarsis F. Gesteira
- College of Optometry, University of Houston, Houston, Texas, United States
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31
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Smits JGA, Cunha DL, Amini M, Bertolin M, Laberthonnière C, Qu J, Owen N, Latta L, Seitz B, Roux LN, Stachon T, Ferrari S, Moosajee M, Aberdam D, Szentmary N, van Heeringen SJ, Zhou H. Identification of the regulatory circuit governing corneal epithelial fate determination and disease. PLoS Biol 2023; 21:e3002336. [PMID: 37856539 PMCID: PMC10586658 DOI: 10.1371/journal.pbio.3002336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/14/2023] [Indexed: 10/21/2023] Open
Abstract
The transparent corneal epithelium in the eye is maintained through the homeostasis regulated by limbal stem cells (LSCs), while the nontransparent epidermis relies on epidermal keratinocytes for renewal. Despite their cellular similarities, the precise cell fates of these two types of epithelial stem cells, which give rise to functionally distinct epithelia, remain unknown. We performed a multi-omics analysis of human LSCs from the cornea and keratinocytes from the epidermis and characterized their molecular signatures, highlighting their similarities and differences. Through gene regulatory network analyses, we identified shared and cell type-specific transcription factors (TFs) that define specific cell fates and established their regulatory hierarchy. Single-cell RNA-seq (scRNA-seq) analyses of the cornea and the epidermis confirmed these shared and cell type-specific TFs. Notably, the shared and LSC-specific TFs can cooperatively target genes associated with corneal opacity. Importantly, we discovered that FOSL2, a direct PAX6 target gene, is a novel candidate associated with corneal opacity, and it regulates genes implicated in corneal diseases. By characterizing molecular signatures, our study unveils the regulatory circuitry governing the LSC fate and its association with corneal opacity.
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Affiliation(s)
- Jos G. A. Smits
- Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Dulce Lima Cunha
- Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Maryam Amini
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg/Saar, Germany
| | | | - Camille Laberthonnière
- Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Jieqiong Qu
- Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Nicholas Owen
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, United Kingdom
| | - Lorenz Latta
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg/Saar, Germany
- Department of Ophthalmology, Saarland University Medical Center, UKS, Homburg, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, UKS, Homburg, Germany
| | | | - Tanja Stachon
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg/Saar, Germany
| | | | - Mariya Moosajee
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, United Kingdom
- Department of Genetics, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
| | - Daniel Aberdam
- INSERM U976, Paris, France
- Université de Paris, INSERM U1138, Centre des Cordeliers, Paris, France
| | - Nora Szentmary
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg/Saar, Germany
| | - Simon J. van Heeringen
- Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Huiqing Zhou
- Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
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Català P, Vivensang F, van Beek D, Adriaens ME, Dickman MM, LaPointe VLS, Kutmon M. Elucidating the Corneal Endothelial Cell Proliferation Capacity through an Interspecies Transcriptome Comparison. Adv Biol (Weinh) 2023; 7:e2300065. [PMID: 37062753 DOI: 10.1002/adbi.202300065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/20/2023] [Indexed: 04/18/2023]
Abstract
The regenerative capacity of corneal endothelial cells (CECs) differs between species; in bigger mammals, CECs are arrested in a non-proliferative state. Damage to these cells can compromise their function causing corneal opacity. Corneal transplantation is the current treatment for the recovery of clear eyesight, but the donor tissue demand is higher than the availability and there is a need to develop novel treatments. Interestingly, rabbit CECs retain a high proliferative profile and can repopulate the endothelium. There is a lack of fundamental knowledge to explain these differences. Gaining information on their transcriptomic variances could allow the identification of CEC proliferation drivers. In this study, human, sheep, and rabbit CECs are analyzed at the transcriptomic level. To understand the differences across each species, a pipeline for the analysis of pathways with different activities is generated. The results reveal that 52 pathways have different activity when comparing species with non-proliferative CECs (human and sheep) to species with proliferative CECs (rabbit). The results show that Notch and TGF-β pathways have increased activity in species with non-proliferative CECs, which might be associated with their low proliferation. Overall, this study illustrates transcriptomic pathway-level differences that can provide leads to develop novel therapies to regenerate the corneal endothelium.
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Affiliation(s)
- Pere Català
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht, 6229ER, The Netherlands
- University Eye Clinic Maastricht, Maastricht University Medical Center+, Maastricht, 6229HX, The Netherlands
| | - Flora Vivensang
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht, 6229ER, The Netherlands
| | - Daan van Beek
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229EN, The Netherlands
| | - Michiel E Adriaens
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229EN, The Netherlands
| | - Mor M Dickman
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht, 6229ER, The Netherlands
- University Eye Clinic Maastricht, Maastricht University Medical Center+, Maastricht, 6229HX, The Netherlands
| | - Vanessa L S LaPointe
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht, 6229ER, The Netherlands
| | - Martina Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229EN, The Netherlands
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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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Martínez-Carrasco R, Argüeso P. Characterization of Cell Surface Glycan Profiles in Human and Mouse Corneas Using Lectin Microarrays. Cells 2023; 12:2356. [PMID: 37830569 PMCID: PMC10572028 DOI: 10.3390/cells12192356] [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: 08/04/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023] Open
Abstract
The advent of high-throughput sequencing technologies has facilitated the profiling of glycosylation genes at a single-cell level in complex biological systems, but the significance of these gene signatures to the composition of the glycocalyx remains ambiguous. Here, we used lectin microarrays to characterize the composition of cell surface glycans in human and mouse corneas and determine its relationship to single-cell transcriptomic data. Our results identify a series of cell surface glycan signatures that are unique to the different cell types of the human cornea and that correlate, to a certain extent, with the transcriptional expression of glycosylation genes. These include pathways involved in the biosynthesis of O-glycans in epithelial cells and core fucose on stromal and endothelial cell surfaces. Moreover, we show that human and mouse corneas display some structural differences in terms of cell surface glycan composition. These results could provide insights into the specialized function of individual cell types in the cornea and foster the identification of novel cornea-specific biomarkers.
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Affiliation(s)
| | - Pablo Argüeso
- Department of Ophthalmology, Tufts Medical Center, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02114, USA
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Bonnet C, González S, Deng SX, Zheng JJ. Wnt activation as a potential therapeutic approach to treat partial limbal stem cell deficiency. Sci Rep 2023; 13:15670. [PMID: 37735479 PMCID: PMC10514048 DOI: 10.1038/s41598-023-42794-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
Limbal epithelial stem/progenitor cells (LSCs) are adult stem cells located at the limbus, tightly regulated by their niche involving numerous signaling pathways, such as Wnt. Wnt proteins are secreted morphogens that play critical roles in embryonic development, stem cell proliferation, self-renewal, tissue regeneration, and remodeling in adults. It has been shown that a small molecule Wnt mimic could improve LSCs expansion ex vivo. Damage to the LSCs and/or their niche can lead to limbal stem cell deficiency (LSCD), a condition that can cause corneal blindness and is difficult to treat. This study explored if repopulating residual LSCs in partial LSCD through Wnt activation could be a novel therapeutic approach. To mimic LSCD due to a chemical injury, single cultured LSCs were exposed to various concentrations of sodium hydroxide. A progressive loss of the LSCs phenotype was observed: the percentage of p63bright cells and cytokeratin (K)14+ cells decreased while the percentage of K12+ increased. Wnt activation was attained by treating the LSCs with lithium chloride (LiCl) and a small-molecule Wnt mimic, respectively. After 18 h of treatment, LSCs proliferation was increased, and the LSCs phenotype was recovered, while the untreated cells did not proliferate and lost their phenotype. The percentage of p63bright cells was significantly higher in the Wnt mimic-treated cells compared with untreated cells, while the percentage of K12+ cells was significantly lower. These findings suggest that local Wnt activation may rescue LSCs upon alkaline injury.
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Affiliation(s)
- Clémence Bonnet
- Department of Ophthalmology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, 100 Stein Plaza, Los Angeles, CA, 90095, USA
- INSERM, UMRS1138, Team 17, From Physiopathology of Ocular Diseases to Clinical Development, Cordeliers Research Center, Ophthalmology Department, Cochin Hospital, AP-HP, Université Paris Cité, 75005, Paris, France
| | - Sheyla González
- Department of Ophthalmology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, 100 Stein Plaza, Los Angeles, CA, 90095, USA
| | - Sophie X Deng
- Department of Ophthalmology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, 100 Stein Plaza, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
| | - Jie J Zheng
- Department of Ophthalmology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, 100 Stein Plaza, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
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36
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Madadi Y, Monavarfeshani A, Chen H, Stamer WD, Williams RW, Yousefi S. Artificial Intelligence Models for Cell Type and Subtype Identification Based on Single-Cell RNA Sequencing Data in Vision Science. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2837-2852. [PMID: 37294649 PMCID: PMC10631573 DOI: 10.1109/tcbb.2023.3284795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) provides a high throughput, quantitative and unbiased framework for scientists in many research fields to identify and characterize cell types within heterogeneous cell populations from various tissues. However, scRNA-seq based identification of discrete cell-types is still labor intensive and depends on prior molecular knowledge. Artificial intelligence has provided faster, more accurate, and user-friendly approaches for cell-type identification. In this review, we discuss recent advances in cell-type identification methods using artificial intelligence techniques based on single-cell and single-nucleus RNA sequencing data in vision science. The main purpose of this review paper is to assist vision scientists not only to select suitable datasets for their problems, but also to be aware of the appropriate computational tools to perform their analysis. Developing novel methods for scRNA-seq data analysis remains to be addressed in future studies.
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37
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Swamy VS, Batz ZA, McGaughey DM. PLAE Web App Enables Powerful Searching and Multiple Visualizations Across One Million Unified Single-Cell Ocular Transcriptomes. Transl Vis Sci Technol 2023; 12:18. [PMID: 37747415 PMCID: PMC10578359 DOI: 10.1167/tvst.12.9.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 07/02/2023] [Indexed: 09/26/2023] Open
Abstract
Purpose To create a high-performance reactive web application to query single-cell gene expression data across cell type, species, study, and other factors. Methods We updated the content and structure of the underlying data (single cell Eye in a Disk [scEiaD]) and wrote the web application PLAE (https://plae.nei.nih.gov) to visualize and explore the data. Results The new portal provides quick visualization of over a million individual cells from vertebrate eye and body transcriptomes encompassing four species, 60 cell types, six ocular tissues, and 23 body tissues across 35 publications. To demonstrate the value of this unified pan-eye dataset, we replicated known neurogenic and cone macula markers in addition to proposing six new cone human region markers. Conclusions The PLAE web application offers the eye community a powerful and quick means to test hypotheses related to gene expression across a highly diverse, community-derived database. Translational Relevance The PLAE resource enables any researcher or clinician to study and research gene expression patterning across a wide variety of curated ocular cell types with a responsive web app.
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Affiliation(s)
- Vinay S Swamy
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Zachary A Batz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - David M McGaughey
- Bioinformatics Group, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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Ujiie N, Norden PR, Fang R, Beckmann L, Cai Z, Kweon J, Liu T, Tan C, Kuhn MS, Stamer WD, Aoto K, Quaggin SE, Zhang HF, Kume T. Differential roles of FOXC2 in the trabecular meshwork and Schlemm's canal in glaucomatous pathology. Life Sci Alliance 2023; 6:e202201721. [PMID: 37414529 PMCID: PMC10326420 DOI: 10.26508/lsa.202201721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
Impaired development and maintenance of Schlemm's canal (SC) are associated with perturbed aqueous humor outflow and intraocular pressure. The angiopoietin (ANGPT)/TIE2 signaling pathway regulates SC development and maintenance, whereas the molecular mechanisms of crosstalk between SC and the neural crest (NC)-derived neighboring tissue, the trabecular meshwork (TM), are poorly understood. Here, we show NC-specific forkhead box (Fox)c2 deletion in mice results in impaired SC morphogenesis, loss of SC identity, and elevated intraocular pressure. Visible-light optical coherence tomography analysis further demonstrated functional impairment of the SC in response to changes in intraocular pressure in NC-Foxc2 -/- mice, suggesting altered TM biomechanics. Single-cell RNA-sequencing analysis identified that this phenotype is predominately characterized by transcriptional changes associated with extracellular matrix organization and stiffness in TM cell clusters, including increased matrix metalloproteinase expression, which can cleave the TIE2 ectodomain to produce soluble TIE2. Moreover, endothelial-specific Foxc2 deletion impaired SC morphogenesis because of reduced TIE2 expression, which was rescued by deleting the TIE2 phosphatase VE-PTP. Thus, Foxc2 is critical in maintaining SC identity and morphogenesis via TM-SC crosstalk.
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Affiliation(s)
- Naoto Ujiie
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Pieter R Norden
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Raymond Fang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Lisa Beckmann
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Zhen Cai
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Junghun Kweon
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Ting Liu
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Can Tan
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Megan S Kuhn
- Duke Eye Center, Duke University, Durham, NC, USA
| | | | - Kazushi Aoto
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Susan E Quaggin
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Department of Ophthalmology, Northwestern University, Chicago, IL, USA
| | - Tsutomu Kume
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Ophthalmology, Northwestern University, Chicago, IL, USA
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Yam GHF, Pi S, Du Y, Mehta JS. Posterior corneoscleral limbus: Architecture, stem cells, and clinical implications. Prog Retin Eye Res 2023; 96:101192. [PMID: 37392960 DOI: 10.1016/j.preteyeres.2023.101192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/03/2023]
Abstract
The limbus is a transition from the cornea to conjunctiva and sclera. In human eyes, this thin strip has a rich variation of tissue structures and composition, typifying a change from scleral irregularity and opacity to corneal regularity and transparency; a variation from richly vascularized conjunctiva and sclera to avascular cornea; the neural passage and drainage of aqueous humor. The limbal stroma is enriched with circular fibres running parallel to the corneal circumference, giving its unique role in absorbing small pressure changes to maintain corneal curvature and refractivity. It contains specific niches housing different types of stem cells for the corneal epithelium, stromal keratocytes, corneal endothelium, and trabecular meshwork. This truly reflects the important roles of the limbus in ocular physiology, and the limbal functionality is crucial for corneal health and the entire visual system. Since the anterior limbus containing epithelial structures and limbal epithelial stem cells has been extensively reviewed, this article is focused on the posterior limbus. We have discussed the structural organization and cellular components of the region beneath the limbal epithelium, the characteristics of stem cell types: namely corneal stromal stem cells, endothelial progenitors and trabecular meshwork stem cells, and recent advances leading to the emergence of potential cell therapy options to replenish their respective mature cell types and to correct defects causing corneal abnormalities. We have reviewed different clinical disorders associated with defects of the posterior limbus and summarized the available preclinical and clinical evidence about the developing topic of cell-based therapy for corneal disorders.
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Affiliation(s)
- Gary Hin-Fai Yam
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore; McGowan Institute for Regenerative Medicine, Pittsburgh, PA, USA.
| | - Shaohua Pi
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yiqin Du
- Department of Ophthalmology, University of South Florida, Tampa, FL, USA
| | - Jodhbir S Mehta
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore; Department of Cornea and External Eye Disease, Singapore National Eye Centre, Singapore; Ophthalmology and Visual Sciences Academic Clinical Program, Duke-National University of Singapore (NUS) Medical School, Singapore.
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Monavarfeshani A, Yan W, Pappas C, Odenigbo KA, He Z, Segrè AV, van Zyl T, Hageman GS, Sanes JR. Transcriptomic analysis of the ocular posterior segment completes a cell atlas of the human eye. Proc Natl Acad Sci U S A 2023; 120:e2306153120. [PMID: 37566633 PMCID: PMC10450437 DOI: 10.1073/pnas.2306153120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/29/2023] [Indexed: 08/13/2023] Open
Abstract
Although the visual system extends through the brain, most vision loss originates from defects in the eye. Its central element is the neural retina, which senses light, processes visual signals, and transmits them to the rest of the brain through the optic nerve (ON). Surrounding the retina are numerous other structures, conventionally divided into anterior and posterior segments. Here, we used high-throughput single-nucleus RNA sequencing (snRNA-seq) to classify and characterize cells in six extraretinal components of the posterior segment: ON, optic nerve head (ONH), peripheral sclera, peripapillary sclera (PPS), choroid, and retinal pigment epithelium (RPE). Defects in each of these tissues are associated with blinding diseases-for example, glaucoma (ONH and PPS), optic neuritis (ON), retinitis pigmentosa (RPE), and age-related macular degeneration (RPE and choroid). From ~151,000 single nuclei, we identified 37 transcriptomically distinct cell types, including multiple types of astrocytes, oligodendrocytes, fibroblasts, and vascular endothelial cells. Our analyses revealed a differential distribution of many cell types among distinct structures. Together with our previous analyses of the anterior segment and retina, the data presented here complete a "Version 1" cell atlas of the human eye. We used this atlas to map the expression of >180 genes associated with the risk of developing glaucoma, which is known to involve ocular tissues in both anterior and posterior segments as well as the neural retina. Similar methods can be used to investigate numerous additional ocular diseases, many of which are currently untreatable.
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Affiliation(s)
- Aboozar Monavarfeshani
- Center for Brain Science, Harvard University, Cambridge, MA02138
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA02115
| | - Wenjun Yan
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
| | - Christian Pappas
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT84132
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT84132
| | - Kenechukwu A. Odenigbo
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA02115
| | - Ayellet V. Segrè
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA02114
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA02142
| | - Tavé van Zyl
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA02114
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT065101
| | - Gregory S. Hageman
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT84132
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT84132
| | - Joshua R. Sanes
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
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Jurkunas UV, Yin J, Johns LK, Li S, Negre H, Shaw KL, Samarakoon L, Ayala AR, Kheirkhah A, Katikireddy K, Gauthier A, Ong Tone S, Kaufman AR, Ellender S, Hernandez Rodriguez DE, Daley H, Dana R, Armant M, Ritz J. Cultivated autologous limbal epithelial cell (CALEC) transplantation: Development of manufacturing process and clinical evaluation of feasibility and safety. SCIENCE ADVANCES 2023; 9:eadg6470. [PMID: 37595035 PMCID: PMC10438443 DOI: 10.1126/sciadv.adg6470] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023]
Abstract
To treat unilateral limbal stem cell (LSC) deficiency, we developed cultivated autologous limbal epithelial cells (CALEC) using an innovative xenobiotic-free, serum-free, antibiotic-free, two-step manufacturing process for LSC isolation and expansion onto human amniotic membrane with rigorous quality control in a good manufacturing practices facility. Limbal biopsies were used to generate CALEC constructs, and final grafts were evaluated by noninvasive scanning microscopy and tested for viability and sterility. Cultivated cells maintained epithelial cell phenotype with colony-forming and proliferative capacities. Analysis of LSC biomarkers showed preservation of "stemness." After preclinical development, a phase 1 clinical trial enrolled five patients with unilateral LSC deficiency. Four of these patients received CALEC transplants, establishing preliminary feasibility. Clinical case histories are reported, with no primary safety events. On the basis of these results, a second recruitment phase of the trial was opened to provide longer term safety and efficacy data on more patients.
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Affiliation(s)
- Ula V. Jurkunas
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Jia Yin
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Lynette K. Johns
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Sanming Li
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Helene Negre
- Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kit L. Shaw
- Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Ahmad Kheirkhah
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Kishore Katikireddy
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Alex Gauthier
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Stephan Ong Tone
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Aaron R. Kaufman
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Stacey Ellender
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | | | - Heather Daley
- Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Reza Dana
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Myriam Armant
- TransLab, Translational Research Program, Boston Children’s Hospital, Boston, MA, USA
| | - Jerome Ritz
- Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Jiang X, Boutin T, Vitart V. Colocalization of corneal resistance factor GWAS loci with GTEx e/sQTLs highlights plausible candidate causal genes for keratoconus postnatal corneal stroma weakening. Front Genet 2023; 14:1171217. [PMID: 37621707 PMCID: PMC10445647 DOI: 10.3389/fgene.2023.1171217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/17/2023] [Indexed: 08/26/2023] Open
Abstract
Background: Genome-wide association studies (GWAS) for corneal resistance factor (CRF) have identified 100s of loci and proved useful to uncover genetic determinants for keratoconus, a corneal ectasia of early-adulthood onset and common indication of corneal transplantation. In the current absence of studies to probe the impact of candidate causal variants in the cornea, we aimed to fill some of this knowledge gap by leveraging tissue-shared genetic effects. Methods: 181 CRF signals were examined for evidence of colocalization with genetic signals affecting steady-state gene transcription and splicing in adult, non-eye, tissues of the Genotype-Tissue Expression (GTEx) project. Expression of candidate causal genes thus nominated was evaluated in single cell transcriptomes from adult cornea, limbus and conjunctiva. Fine-mapping and colocalization of CRF and keratoconus GWAS signals was also deployed to support their sharing causal variants. Results and discussion: 26.5% of CRF causal signals colocalized with GTEx v8 signals and nominated genes enriched in genes with high and specific expression in corneal stromal cells amongst tissues examined. Enrichment analyses carried out with nearest genes to all 181 CRF GWAS signals indicated that stromal cells of the limbus could be susceptible to signals that did not colocalize with GTEx's. These cells might not be well represented in GTEx and/or the genetic associations might have context specific effects. The causal signals shared with GTEx provide new insights into mediation of CRF genetic effects, including modulation of splicing events. Functionally relevant roles for several implicated genes' products in providing tensile strength, mechano-sensing and signaling make the corresponding genes and regulatory variants prime candidates to be validated and their roles and effects across tissues elucidated. Colocalization of CRF and keratoconus GWAS signals strengthened support for shared causal variants but also highlighted many ways into which likely true shared signals could be missed when using readily available GWAS summary statistics.
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Affiliation(s)
- Xinyi Jiang
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Genetics and Molecular Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Thibaud Boutin
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
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Kitao M, Hayashi R, Nomi K, Kobayashi R, Katayama T, Takayanagi H, Oguchi A, Murakawa Y, Nishida K. Identification of BST2 as a conjunctival epithelial stem/progenitor cell marker. iScience 2023; 26:107016. [PMID: 37389178 PMCID: PMC10300367 DOI: 10.1016/j.isci.2023.107016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/25/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023] Open
Abstract
The conjunctival epithelium consists of conjunctival epithelial cells and goblet cells derived from conjunctival epithelial stem/progenitor cells. However, the source of these cells is not well known because no specific markers for conjunctival epithelial stem/progenitor cells have been discovered. Therefore, to identify conjunctival epithelial stem/progenitor cell markers, we performed single-cell RNA sequencing of a conjunctival epithelial cell population derived from human-induced pluripotent stem cells (hiPSCs). The following conjunctival epithelial markers were identified: BST2, SLC2A3, AGR2, TMEM54, OLR1, and TRIM29. Notably, BST2 was strongly positive in the basal conjunctival epithelium, which is thought to be rich in stem/progenitor cells. Moreover, BST2 was able to sort conjunctival epithelial stem/progenitor cells from hiPSC-derived ocular surface epithelial cell populations. BST2-positive cells were highly proliferative and capable of successfully generating conjunctival epithelial sheets containing goblet cells. In conclusion, BST2 has been identified as a specific marker of conjunctival epithelial stem/progenitor cells.
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Affiliation(s)
- Masahiro Kitao
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Ryuhei Hayashi
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
- Department of Stem Cells and Applied Medicine, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kimihito Nomi
- Business Strategy Office, ROHTO Pharmaceutical, Osaka, Osaka 544-0012, Japan
| | - Reiko Kobayashi
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Tomohiko Katayama
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Hiroshi Takayanagi
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
- Department of Stem Cells and Applied Medicine, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Akiko Oguchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Kohji Nishida
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka 565-0871, Japan
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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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45
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Jaskiewicz K, Maleszka-Kurpiel M, Kabza M, Karolak JA, Gajecka M. Sequence variants contributing to dysregulated inflammatory responses across keratoconic cone surface in adolescent patients with keratoconus. Front Immunol 2023; 14:1197054. [PMID: 37483635 PMCID: PMC10359427 DOI: 10.3389/fimmu.2023.1197054] [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: 03/30/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023] Open
Abstract
Background Keratoconus (KTCN) is the most common corneal ectasia resulting in a conical shape of the cornea. Here, genomic variation in the corneal epithelium (CE) across the keratoconic cone surface in patients with KTCN and its relevance in the functioning of the immune system were assessed. Methods Samples from four unrelated adolescent patients with KTCN and two control individuals were obtained during the CXL and PRK procedures, respectively. Three topographic regions, central, middle, and peripheral, were separated towards the whole-genome sequencing (WGS) study embracing a total of 18 experimental samples. The coding and non-coding sequence variation, including structural variation, was assessed and then evaluated together with the previously reported transcriptomic outcomes for the same CE samples and full-thickness corneas. Results First, pathway enrichment analysis of genes with identified coding variants pointed to "Antigen presentation" and "Interferon alpha/beta signaling" as the most overrepresented pathways, indicating the involvement of inflammatory responses in KTCN. Both coding and non-coding sequence variants were found in genes (or in their close proximity) linked to the previously revealed KTCN-specific cellular components, namely, "Actin cytoskeleton", "Extracellular matrix", "Collagen-containing extracellular matrix", "Focal adhesion", "Hippo signaling pathway", and "Wnt signaling" pathways. No genomic heterogeneity across the corneal surface was found comparing the assessed topographic regions. Thirty-five chromosomal regions enriched in both coding and non-coding KTCN-specific sequence variants were revealed, with a most representative 5q locus previously recognized as involved in KTCN. Conclusion The identified genomic features indicate the involvement of innate and adaptive immune system responses in KTCN pathogenesis.
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Affiliation(s)
| | - Magdalena Maleszka-Kurpiel
- Optegra Eye Health Care Clinic in Poznan, Poznan, Poland
- Chair of Ophthalmology and Optometry, Poznan University of Medical Sciences, Poznan, Poland
| | - Michał Kabza
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marzena Gajecka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
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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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47
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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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48
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Lewinsohn DP, Vigh-Conrad KA, Conrad DF, Scott CB. Consensus label propagation with graph convolutional networks for single-cell RNA sequencing cell type annotation. Bioinformatics 2023; 39:btad360. [PMID: 37267208 PMCID: PMC10272704 DOI: 10.1093/bioinformatics/btad360] [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: 12/05/2022] [Revised: 05/02/2023] [Accepted: 06/01/2023] [Indexed: 06/04/2023] Open
Abstract
MOTIVATION Single-cell RNA sequencing (scRNA-seq) data, annotated by cell type, is useful in a variety of downstream biological applications, such as profiling gene expression at the single-cell level. However, manually assigning these annotations with known marker genes is both time-consuming and subjective. RESULTS We present a Graph Convolutional Network (GCN)-based approach to automate the annotation process. Our process builds upon existing labeling approaches, using state-of-the-art tools to find cells with highly confident label assignments through consensus and spreading these confident labels with a semi-supervised GCN. Using simulated data and two scRNA-seq datasets from different tissues, we show that our method improves accuracy over a simple consensus algorithm and the average of the underlying tools. We also compare our method to a nonparametric neighbor majority approach, showing comparable results. We then demonstrate that our GCN method allows for feature interpretation, identifying important genes for cell type classification. We present our completed pipeline, written in PyTorch, as an end-to-end tool for automating and interpreting the classification of scRNA-seq data. AVAILABILITY AND IMPLEMENTATION Our code for conducting the experiments in this paper and using our model is available at https://github.com/lewinsohndp/scSHARP.
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Affiliation(s)
- Daniel P Lewinsohn
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, United States
- Department of Mathematics and Computer Science, Colorado College, Colorado Springs, CO 80903, United States
| | - Katinka A Vigh-Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, United States
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, United States
| | - Cory B Scott
- Department of Mathematics and Computer Science, Colorado College, Colorado Springs, CO 80903, United States
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Sun D, Shi WY, Dou SQ. Single-cell RNA sequencing in cornea research: Insights into limbal stem cells and their niche regulation. World J Stem Cells 2023; 15:466-475. [PMID: 37342216 PMCID: PMC10277966 DOI: 10.4252/wjsc.v15.i5.466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/28/2023] [Accepted: 04/17/2023] [Indexed: 05/26/2023] Open
Abstract
The corneal epithelium is composed of stratified squamous epithelial cells on the outer surface of the eye, which acts as a protective barrier and is critical for clear and stable vision. Its continuous renewal or wound healing depends on the proliferation and differentiation of limbal stem cells (LSCs), a cell population that resides at the limbus in a highly regulated niche. Dysfunction of LSCs or their niche can cause limbal stem cell deficiency, a disease that is manifested by failed epithelial wound healing or even blindness. Nevertheless, compared to stem cells in other tissues, little is known about the LSCs and their niche. With the advent of single-cell RNA sequencing, our understanding of LSC characteristics and their microenvironment has grown considerably. In this review, we summarized the current findings from single-cell studies in the field of cornea research and focused on important advancements driven by this technology, including the heterogeneity of the LSC population, novel LSC markers and regulation of the LSC niche, which will provide a reference for clinical issues such as corneal epithelial wound healing, ocular surface reconstruction and interventions for related diseases.
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Affiliation(s)
- Di Sun
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao 266000, Shandong Province, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266000, Shandong Province, China
| | - Wei-Yun Shi
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao 266000, Shandong Province, China
- Eye Hospital of Shandong First Medical University, Jinan 250000, Shandong Province, China
- School of Ophthalmology, Shandong First Medical University, Qingdao 266000, Shandong Province, China
| | - Sheng-Qian Dou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao 266000, Shandong Province, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266000, Shandong Province, China
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Dhull A, Yu C, Wilmoth AH, Chen M, Sharma A, Yiu S. Dendrimers in Corneal Drug Delivery: Recent Developments and Translational Opportunities. Pharmaceutics 2023; 15:1591. [PMID: 37376040 DOI: 10.3390/pharmaceutics15061591] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Dendrimers are biocompatible organic nanomaterials with unique physicochemical properties, making them the focus of recent research in drug delivery. The cornea of the human eye presents a challenge for drug transit due to its inherently impenetrable nature, requiring nanocarrier-mediated targeted drug delivery. This review intends to examine recent advancements in the use of dendrimers for corneal drug delivery, including their properties and their potential for treating various ocular diseases. The review will also highlight the benefit of the novel technologies that have been developed and applied in the field, such as corneal targeting, drug release kinetics, treatments for dry eye disease, antibacterial drug delivery, corneal inflammation, and corneal tissue engineering. The review seeks to provide a comprehensive overview of the current state of research in this field, along with the translational developments in the field of dendrimer-based therapeutics and imaging agents and inspire the potential for future developments and translational opportunities in dendrimers based corneal drug delivery.
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Affiliation(s)
- Anubhav Dhull
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Carson Yu
- Center for Nanomedicine, Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Cornea Division, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alex Hunter Wilmoth
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Minjie Chen
- Center for Nanomedicine, Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Cornea Division, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Anjali Sharma
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Samuel Yiu
- Center for Nanomedicine, Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Cornea Division, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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