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Bonnet C, González S, Roberts JS, Robertson SYT, Ruiz M, Zheng J, Deng SX. Human limbal epithelial stem cell regulation, bioengineering and function. Prog Retin Eye Res 2021; 85:100956. [PMID: 33676006 PMCID: PMC8428188 DOI: 10.1016/j.preteyeres.2021.100956] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/21/2021] [Accepted: 02/26/2021] [Indexed: 12/13/2022]
Abstract
The corneal epithelium is continuously renewed by limbal stem/progenitor cells (LSCs), a cell population harbored in a highly regulated niche located at the limbus. Dysfunction and/or loss of LSCs and their niche cause limbal stem cell deficiency (LSCD), a disease that is marked by invasion of conjunctival epithelium into the cornea and results in failure of epithelial wound healing. Corneal opacity, pain, loss of vision, and blindness are the consequences of LSCD. Successful treatment of LSCD depends on accurate diagnosis and staging of the disease and requires restoration of functional LSCs and their niche. This review highlights the major advances in the identification of potential LSC biomarkers and components of the LSC niche, understanding of LSC regulation, methods and regulatory standards in bioengineering of LSCs, and diagnosis and staging of LSCD. Overall, this review presents key points for researchers and clinicians alike to consider in deepening the understanding of LSC biology and improving LSCD therapies.
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Affiliation(s)
- Clémence Bonnet
- Cornea Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA; Cornea Department, Paris University, Cochin Hospital, AP-HP, F-75014, Paris, France
| | - Sheyla González
- Cornea Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA
| | - JoAnn S Roberts
- Cornea Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA
| | - Sarah Y T Robertson
- Cornea Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA
| | - Maxime Ruiz
- Cornea Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA
| | - Jie Zheng
- Basic Science Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA
| | - Sophie X Deng
- Cornea Division, Stein Eye Institute, University of California, Los Angeles, CA, 90095, USA.
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Ali D, Alhattab D, Jafar H, Alzubide M, Sharar N, Bdour S, Awidi A. Differential Marker Expression between Keratinocyte Stem Cells and Their Progeny Generated from a Single Colony. Int J Mol Sci 2021; 22:ijms221910810. [PMID: 34639148 PMCID: PMC8509450 DOI: 10.3390/ijms221910810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 01/31/2023] Open
Abstract
The stemness in keratinocyte stem cells (KSCs) is determined by their gene expression patterns. KSCs are crucial in maintaining epidermal homeostasis and wound repair and are widely used candidates for therapeutic applications. Although several studies have reported their positive identifiers, unique biomarkers for KSCs remain elusive. Here, we aim to identify potential candidate stem cell markers. Human epidermal keratinocytes (HEKs) from neonatal foreskin tissues were isolated and cultured. Single-cell clonal analysis identified and characterized three types of cells: KSCs (holoclones), transient amplifying cells (TACs; meroclones), and differentiated cells (DSCs; paraclones). The clonogenic potential of KSCs demonstrated the highest proliferation potential of KSCs, followed by TACs and DSCs, respectively. Whole-transcriptome analysis using microarray technology unraveled the molecular signatures of these cells. These results were validated by quantitative real-time polymerase chain reaction and flow cytometry analysis. A total of 301 signature upregulated and 149 downregulated differentially expressed genes (DEGs) were identified in the KSCs, compared to TACs and DSCs. Furthermore, DEG analyses revealed new sets of genes related to cell proliferation, cell adhesion, surface makers, and regulatory factors. In conclusion, this study provides a useful source of information for the identification of potential SC-specific candidate markers.
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Affiliation(s)
- Dema Ali
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; (D.A.); (D.A.); (H.J.); (M.A.); (N.S.)
- Department of Biological Sciences, Faculty of Science, The University of Jordan, Amman 11942, Jordan
| | - Dana Alhattab
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; (D.A.); (D.A.); (H.J.); (M.A.); (N.S.)
- Laboratory for Nanomedicine, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Hanan Jafar
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; (D.A.); (D.A.); (H.J.); (M.A.); (N.S.)
- Department of Anatomy and Histology, School of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Malak Alzubide
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; (D.A.); (D.A.); (H.J.); (M.A.); (N.S.)
| | - Nour Sharar
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; (D.A.); (D.A.); (H.J.); (M.A.); (N.S.)
| | - Salwa Bdour
- Department of Clinical Laboratory Sciences, Faculty of Science, The University of Jordan, Amman 11942, Jordan
- Correspondence: (S.B.); (A.A.)
| | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; (D.A.); (D.A.); (H.J.); (M.A.); (N.S.)
- Department of Hematology and Oncology, Faculty of Medicine, The University of Jordan, Amman 11942, Jordan
- Correspondence: (S.B.); (A.A.)
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Kapoor D, Khan A, O'Donnell MJ, Kolosov D. Novel mechanisms of epithelial ion transport: insights from the cryptonephridial system of lepidopteran larvae. CURRENT OPINION IN INSECT SCIENCE 2021; 47:53-61. [PMID: 33866042 DOI: 10.1016/j.cois.2021.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Lepidopterans are among the most widespread and easily recognized insects. Whereas adult lepidopterans are known for their beauty and ecological importance as pollinators and sources of food for other animals, larvae are economically important pests of forests and agricultural crops. In the larval body, rapid growth while feeding on plant-based diet is associated with extreme alkalinity (up to pH = 11) of the midgut lumen that helps digest plant proteins. Additionally, the presence of plant secondary metabolites which serve as anti-herbivory agents requires uninterrupted excretory function, accomplished primarily by the Malpighian tubules (MTs). The so-called cryptonephridial condition, along with extreme regional heterogeneity of the MTs, and the ability to rapidly and reversibly alter the direction of epithelial ion transport are features that allow uninterrupted MT functioning and recycling of base equivalents. Studies of MTs in lepidopteran larvae have revealed that rapid adjustments in epithelial ion transport include unexpected roles for voltage-gated, ligand-gated and mechanosensitive ion channels, as well as gap junctions. These molecular components are present in epithelia of a variety of vertebrates and invertebrates and thus are likely to constitute a universal epithelial toolkit for rapid autonomous regulation of epithelial function.
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Affiliation(s)
| | - Aliyyah Khan
- Department of Biology, McMaster University, Hamilton, Canada
| | | | - Dennis Kolosov
- Department of Biological Sciences, California State University San Marcos, San Marcos, USA.
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Ligocki AJ, Fury W, Gutierrez C, Adler C, Yang T, Ni M, Bai Y, Wei Y, Lehmann GL, Romano C. Molecular characteristics and spatial distribution of adult human corneal cell subtypes. Sci Rep 2021; 11:16323. [PMID: 34381080 PMCID: PMC8357950 DOI: 10.1038/s41598-021-94933-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/19/2021] [Indexed: 12/13/2022] Open
Abstract
Bulk RNA sequencing of a tissue captures the gene expression profile from all cell types combined. Single-cell RNA sequencing identifies discrete cell-signatures based on transcriptomic identities. Six adult human corneas were processed for single-cell RNAseq and 16 cell clusters were bioinformatically identified. Based on their transcriptomic signatures and RNAscope results using representative cluster marker genes on human cornea cross-sections, these clusters were confirmed to be stromal keratocytes, endothelium, several subtypes of corneal epithelium, conjunctival epithelium, and supportive cells in the limbal stem cell niche. The complexity of the epithelial cell layer was captured by eight distinct corneal clusters and three conjunctival clusters. These were further characterized by enriched biological pathways and molecular characteristics which revealed novel groupings related to development, function, and location within the epithelial layer. Moreover, epithelial subtypes were found to reflect their initial generation in the limbal region, differentiation, and migration through to mature epithelial cells. The single-cell map of the human cornea deepens the knowledge of the cellular subsets of the cornea on a whole genome transcriptional level. This information can be applied to better understand normal corneal biology, serve as a reference to understand corneal disease pathology, and provide potential insights into therapeutic approaches.
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Affiliation(s)
- Ann J Ligocki
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Wen Fury
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | | | - Tao Yang
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Min Ni
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Yu Bai
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Yi Wei
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | - Carmelo Romano
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA.
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Di Girolamo N. "Eyeing" corneal stem cell identity, dynamics, and compartmentalization. Cell Stem Cell 2021; 28:1181-1183. [PMID: 34214435 DOI: 10.1016/j.stem.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The mammalian cornea is maintained by the lifelong self-replenishing activity of its stem cells. In this issue of Cell Stem Cell, Altshuler et al. (2021) and Farrelly et al. (2021) identify two stem cell populations with diverse function and genetic signature, one "active" and one "quiescent," that support corneal health.
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Affiliation(s)
- Nick Di Girolamo
- Mechanisms of Disease and Translational Research, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
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Li JM, Kim S, Zhang Y, Bian F, Hu J, Lu R, Pflugfelder SC, Chen R, Li DQ. Single-Cell Transcriptomics Identifies a Unique Entity and Signature Markers of Transit-Amplifying Cells in Human Corneal Limbus. Invest Ophthalmol Vis Sci 2021; 62:36. [PMID: 34297801 PMCID: PMC8300054 DOI: 10.1167/iovs.62.9.36] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Purpose Differentiated from adult stem cells (ASCs), transit-amplifying cells (TACs) play an important role in tissue homeostasis, development, and regeneration. This study aimed to characterize the gene expression profile of a candidate TAC population in limbal basal epithelial cells using single-cell RNA sequencing (scRNA-seq). Methods Single cells isolated from the basal corneal limbus were subjected to scRNA-seq using the 10x Genomics platform. Cell types were clustered by graph-based visualization methods and unbiased computational analysis. BrdU proliferation assays, immunofluorescent staining, and real-time reverse transcription quantitative polymerase chain reaction were performed using multiple culture models of primary human limbal epithelial cells to characterize the TAC pool. Results Single-cell transcriptomics of 16,360 limbal basal cells revealed 12 cell clusters. A unique cluster (3.21% of total cells) was identified as a TAC entity, based on its less differentiated progenitor status and enriched exclusive proliferation marker genes, with 98.1% cells in S and G2/M phases. The cell cycle-dependent genes were revealed to be largely enriched by the TAC population. The top genes were characterized morphologically and functionally at protein and mRNA levels. The specific expression patterns of RRM2, TK1, CENPF, NUSAP1, UBE2C, and CDC20 were well correlated in a time- and cycle-dependent manner with proliferation stages in the cell growth and regeneration models. Conclusions For the first time, to the best of our knowledge, we have identified a unique TAC entity and uncovered a group of cell cycle-dependent genes that serve as TAC signature markers. The findings provide insight into ASCs and TACs and lay the foundation for understanding corneal homeostasis and diseases.
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Affiliation(s)
- Jin-Miao Li
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Sangbae Kim
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Yun Zhang
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
| | - Fang Bian
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
| | - Jiaoyue Hu
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
| | - Rong Lu
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Stephen C Pflugfelder
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
| | - Rui Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - De-Quan Li
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
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Abstract
It has been known for over a century that the basic organization of the retina is conserved across vertebrates. It has been equally clear that retinal cells can be classified into numerous types, but only recently have methods been devised to explore this diversity in unbiased, scalable, and comprehensive ways. Advances in high-throughput single-cell RNA-sequencing (scRNA-seq) have played a pivotal role in this effort. In this article, we outline the experimental and computational components of scRNA-seq and review studies that have used them to generate retinal atlases of cell types in several vertebrate species. These atlases have enabled studies of retinal development, responses of retinal cells to injury, expression patterns of genes implicated in retinal disease, and the evolution of cell types. Recently, the inquiry has expanded to include the entire eye and visual centers in the brain. These studies have enhanced our understanding of retinal function and dysfunction and provided tools and insights for exploring neural diversity throughout the brain. Expected final online publication date for the Annual Review of Vision Science, Volume 7 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Karthik Shekhar
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; and California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, USA;
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cell Biology, Harvard University, Cambridge, Massachusetts 02138, USA;
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Lavker RM, Kaplan N, McMahon KM, Calvert AE, Henrich SE, Onay UV, Lu KQ, Peng H, Thaxton CS. Synthetic high-density lipoprotein nanoparticles: Good things in small packages. Ocul Surf 2021; 21:19-26. [PMID: 33894397 PMCID: PMC8328934 DOI: 10.1016/j.jtos.2021.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/26/2021] [Accepted: 03/06/2021] [Indexed: 12/26/2022]
Abstract
Medicine has been a great beneficiary of the nanotechnology revolution. Nanotechnology involves the synthesis of functional materials with at least one size dimension between 1 and 100 nm. Advances in the field have enabled the synthesis of bio-nanoparticles that can interface with physiological systems to modulate fundamental cellular processes. One example of a diverse acting nanoparticle-based therapeutic is synthetic high-density lipoprotein (HDL) nanoparticles (NP), which have great potential for treating diseases of the ocular surface. Our group has developed a spherical HDL NP using a gold nanoparticle core. HDL NPs: (i) closely mimic the physical and chemical features of natural HDLs; (ii) contain apoA-I; (iii) bind with high-affinity to SR-B1, which is the major receptor through which HDL modulates cell cholesterol metabolism and controls the selective uptake of HDL cargo into cells; (iv) are non-toxic to cells and tissues; and (v) can be chemically engineered to display nearly any surface or core composition desired. With respect to the ocular surface, topical application of HDL NPs accelerates re-epithelization of the cornea following wounding, attenuates inflammation resulting from chemical burns and/or other stresses, and effectively delivers microRNAs with biological activity to corneal cells and tissues. HDL NPs will be the foundation of a new class of topical eye drops with great translational potential and exemplify the impact that nanoparticles can have in medicine.
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Affiliation(s)
- Robert M Lavker
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Nihal Kaplan
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Kaylin M McMahon
- Department of Dermatology Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Andrea E Calvert
- Department of Dermatology Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Stephen E Henrich
- Department of Dermatology Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ummiye V Onay
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Kurt Q Lu
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Han Peng
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - C Shad Thaxton
- Department of Dermatology Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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Kaplan N, Wang S, Wang J, Yang W, Ventrella R, Majekodunmi A, Perez White BE, Getsios S, Mitchell BJ, Peng H, Lavker RM. Ciliogenesis and autophagy are coordinately regulated by EphA2 in the cornea to maintain proper epithelial architecture. Ocul Surf 2021; 21:193-205. [PMID: 34119713 DOI: 10.1016/j.jtos.2021.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 11/25/2022]
Abstract
PURPOSE To understand the relationship between ciliogenesis and autophagy in the corneal epithelium. METHODS siRNAs for EphA2 or PLD1 were used to inhibit protein expression in vitro. Morpholino-anti-EphA2 was used to knockdown EphA2 in Xenopus skin. An EphA2 knockout mouse was used to conduct loss of function studies. Autophagic vacuoles were visualized by contrast light microscopy. Autophagy flux, was measured by LC3 turnover and p62 protein levels. Immunostaining and confocal microscopy were conducted to visualize cilia in cultured cells and in vivo. RESULTS Loss of EphA2 (i) increased corneal epithelial thickness by elevating proliferative potential in wing cells, (ii) reduced the number of ciliated cells, (iii) increased large hollow vacuoles, that could be rescued by BafA1; (iv) inhibited autophagy flux and (v) increased GFP-LC3 puncta in the mouse corneal epithelium. This indicated a role for EphA2 in stratified epithelial assembly via regulation of proliferation as well as a positive role in both ciliogenesis and end-stage autophagy. Inhibition of PLD1, an EphA2 interacting protein that is a critical regulator of end-stage autophagy, reversed the accumulation of vacuoles, and the reduction in the number of ciliated cells due to EphA2 depletion, suggesting EphA2 regulation of both end-stage autophagy and ciliogenesis via PLD1. PLD1 mediated rescue of ciliogenesis by EphA2 depletion was blocked by BafA1, placing autophagy between EphA2 signaling and regulation of ciliogenesis. CONCLUSION Our findings demonstrate a novel role for EphA2 in regulating both autophagy and ciliogenesis, processes that are essential for proper corneal epithelial homeostasis.
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Affiliation(s)
- Nihal Kaplan
- Department of Dermatology, Northwestern University, Chicago, IL, 60611, USA
| | - Sijia Wang
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Junyi Wang
- Department of Dermatology, Northwestern University, Chicago, IL, 60611, USA; Department of Ophthalmology, The Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Wending Yang
- Department of Dermatology, Northwestern University, Chicago, IL, 60611, USA
| | - Rosa Ventrella
- Cell and Developmental Biology, Northwestern University, Chicago, IL 60611, USA
| | - Ahmed Majekodunmi
- Department of Neurology, Northwestern University, Chicago, IL, 60611, USA
| | | | | | - Brian J Mitchell
- Cell and Developmental Biology, Northwestern University, Chicago, IL 60611, USA
| | - Han Peng
- Department of Dermatology, Northwestern University, Chicago, IL, 60611, USA.
| | - Robert M Lavker
- Department of Dermatology, Northwestern University, Chicago, IL, 60611, USA.
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Farrelly O, Suzuki-Horiuchi Y, Brewster M, Kuri P, Huang S, Rice G, Bae H, Xu J, Dentchev T, Lee V, Rompolas P. Two-photon live imaging of single corneal stem cells reveals compartmentalized organization of the limbal niche. Cell Stem Cell 2021; 28:1233-1247.e4. [PMID: 33984283 DOI: 10.1016/j.stem.2021.02.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/18/2020] [Accepted: 02/16/2021] [Indexed: 12/11/2022]
Abstract
The functional heterogeneity of resident stem cells that support adult organs is incompletely understood. Here, we directly visualize the corneal limbus in the eyes of live mice and identify discrete stem cell niche compartments. By recording the life cycle of individual stem cells and their progeny, we directly analyze their fates and show that their location within the tissue can predict their differentiation status. Stem cells in the inner limbus undergo mostly symmetric divisions and are required to sustain the population of transient progenitors that support corneal homeostasis. Using in situ photolabeling, we captured their progeny exiting the niche before moving centripetally in unison. The long-implicated slow-cycling stem cells are functionally distinct and display local clonal dynamics during homeostasis but can contribute to corneal regeneration after injury. This study demonstrates how the compartmentalized organization of functionally diverse stem cell populations supports the maintenance and regeneration of an adult organ.
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Affiliation(s)
- Olivia Farrelly
- Department of Dermatology, Department of Cell and Developmental Biology, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yoko Suzuki-Horiuchi
- Department of Dermatology, Department of Cell and Developmental Biology, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Megan Brewster
- Department of Dermatology, Department of Cell and Developmental Biology, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Paola Kuri
- Department of Dermatology, Department of Cell and Developmental Biology, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sixia Huang
- Department of Dermatology, Department of Cell and Developmental Biology, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Gabriella Rice
- Department of Dermatology, Department of Cell and Developmental Biology, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hyunjin Bae
- Department of Dermatology, Department of Cell and Developmental Biology, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jianming Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tzvete Dentchev
- Department of Dermatology, Department of Cell and Developmental Biology, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Vivian Lee
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Panteleimon Rompolas
- Department of Dermatology, Department of Cell and Developmental Biology, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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Dou S, Wang Q, Qi X, Zhang B, Jiang H, Chen S, Duan H, Lu Y, Dong J, Cao Y, Xie L, Zhou Q, Shi W. Molecular identity of human limbal heterogeneity involved in corneal homeostasis and privilege. Ocul Surf 2021; 21:206-220. [PMID: 33964410 DOI: 10.1016/j.jtos.2021.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/10/2021] [Accepted: 04/24/2021] [Indexed: 12/20/2022]
Abstract
PURPOSE The corneal limbus maintains the homeostasis, immune and angiogenic privilege of cornea. This study aimed to depict the landscape of human limbal tissues by single-cell RNA sequencing (scRNA-seq). METHODS Single cells of human limbus collected from donor corneas were subjected to 10x scRNA-seq, followed by clustering cell types through the t-distributed stochastic neighbor embedding (t-SNE) and unbiased computational informatic analysis. Immunofluorescent staining was performed using human corneas to validate the analysis results. RESULTS 47,627 cells acquired from six human limbal tissues were collected and subjected to scRNA-seq. 14 distinct clusters were identified and 8 cell types were annotated with representative markers. In-depth dissection revealed three limbal epithelial cell subtypes and refined the X-Y-Z hypothesis of corneal epithelial maintenance. We further unveiled two cell states with higher stemness (TP63+ and CCL20+ cells), and two other differentiated cell states (GPHA2+ and KRT6B + cells) in homeostatic limbal stem/progenitor cells (LSPCs) that differ in transcriptional profiles. Cell-cell communication analysis revealed the central role of LSPCs and their bidirectional regulation with various niche cells. Moreover, comparative analysis between limbus and skin deciphered the pivotal contribution of limbal immune cells, vascular and lymphatic endothelial cells to corneal immune and angiogenic privilege. CONCLUSIONS The human limbus atlas provided valuable resources and foundations for understanding corneal biology, disease and potential interventions.
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Affiliation(s)
- Shengqian Dou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 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, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Xia Qi
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Bin Zhang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Hui Jiang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Shengwen Chen
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Haoyun Duan
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Yao Lu
- OE Biotech Co., Ltd, Shanghai, Shanghai, China
| | | | - Yihai Cao
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Lixin Xie
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 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, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China.
| | - Weiyun Shi
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China; Eye Hospital of Shandong First Medical University, Jinan, China.
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Yamada Y, Takai S, Watanabe Y, Osaki A, Kawabata Y, Oike A, Hirayama A, Iwata S, Sanematsu K, Tabata S, Shigemura N. Gene expression profiling of α-gustducin-expressing taste cells in mouse fungiform and circumvallate papillae. Biochem Biophys Res Commun 2021; 557:206-212. [PMID: 33872990 DOI: 10.1016/j.bbrc.2021.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/08/2021] [Indexed: 11/27/2022]
Abstract
Taste buds are complex sensory organs embedded in the epithelium of fungiform papillae (FP) and circumvallate papillae (CV). The sweet, bitter, and umami tastes are sensed by type II taste cells that express taste receptors (Tas1rs and Tas2rs) coupled with the taste G-protein α-gustducin. Recent studies revealed that the taste response profiles of α-gustducin-expressing cells are different between FP and CV, but which genes could generate such distinctive cell characteristics are still largely unknown. We performed a comprehensive transcriptome analysis on α-gustducin-expressing cells in mouse FP and CV by single-cell RNA sequencing combined with fluorescence-activated cell sorting. Transcriptome profiles of the α-gustducin-expressing cells showed various expression patterns of taste receptors. Our clustering analysis defined the specific cell populations derived from FP or CV based on their distinct gene expression. Immunohistochemistry confirmed the specific expression of galectin-3, encoded by Lgals3, which was recognized as a differentially expressed gene in the transcriptome analysis. Our work provides fundamental knowledge toward understanding the genetic heterogeneity of type II cells, potentially revealing differential characterization of FP and CV taste bud cells.
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Affiliation(s)
- Yu Yamada
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Laboratory of Functional Anatomy, Graduate School of Biosource and Bioenvironmental Science, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka-city, Fukuoka, 819-0395, Japan
| | - Shingo Takai
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan.
| | - Yu Watanabe
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Section of Implant and Rehabilitative Dentistry, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan
| | - Ayana Osaki
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Section of Interdisciplinary Dentistry, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, 812-8582, Fukuoka, Japan
| | - Yuko Kawabata
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan
| | - Asami Oike
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Section of Interdisciplinary Dentistry, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, 812-8582, Fukuoka, Japan
| | - Ayaka Hirayama
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Section of Orthodontics and Dentofacial Orthopedics, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan
| | - Shusuke Iwata
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Research and Development Center for Five-Sense Devices Taste and Odor Sensing, Kyushu University, 744, Nishi-ku, Fukuoka-city, Fukuoka, 819-0395, Japan
| | - Keisuke Sanematsu
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; OBT Research Center, Graduate School of Dental Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Research and Development Center for Five-Sense Devices Taste and Odor Sensing, Kyushu University, 744, Nishi-ku, Fukuoka-city, Fukuoka, 819-0395, Japan
| | - Shoji Tabata
- Laboratory of Functional Anatomy, Graduate School of Biosource and Bioenvironmental Science, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka-city, Fukuoka, 819-0395, Japan
| | - Noriatsu Shigemura
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Research and Development Center for Five-Sense Devices Taste and Odor Sensing, Kyushu University, 744, Nishi-ku, Fukuoka-city, Fukuoka, 819-0395, Japan.
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63
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Collin J, Queen R, Zerti D, Bojic S, Dorgau B, Moyse N, Molina MM, Yang C, Dey S, Reynolds G, Hussain R, Coxhead JM, Lisgo S, Henderson D, Joseph A, Rooney P, Ghosh S, Clarke L, Connon C, Haniffa M, Figueiredo F, Armstrong L, Lako M. A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells. Ocul Surf 2021; 21:279-298. [PMID: 33865984 PMCID: PMC8343164 DOI: 10.1016/j.jtos.2021.03.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/05/2021] [Accepted: 03/25/2021] [Indexed: 02/08/2023]
Abstract
Purpose Single cell (sc) analyses of key embryonic, fetal and adult stages were performed to generate a comprehensive single cell atlas of all the corneal and adjacent conjunctival cell types from development to adulthood. Methods Four human adult and seventeen embryonic and fetal corneas from 10 to 21 post conception week (PCW) specimens were dissociated to single cells and subjected to scRNA- and/or ATAC-Seq using the 10x Genomics platform. These were embedded using Uniform Manifold Approximation and Projection (UMAP) and clustered using Seurat graph-based clustering. Cluster identification was performed based on marker gene expression, bioinformatic data mining and immunofluorescence (IF) analysis. RNA interference, IF, colony forming efficiency and clonal assays were performed on cultured limbal epithelial cells (LECs). Results scRNA-Seq analysis of 21,343 cells from four adult human corneas and adjacent conjunctivas revealed the presence of 21 cell clusters, representing the progenitor and differentiated cells in all layers of cornea and conjunctiva as well as immune cells, melanocytes, fibroblasts, and blood/lymphatic vessels. A small cell cluster with high expression of limbal progenitor cell (LPC) markers was identified and shown via pseudotime analysis to give rise to five other cell types representing all the subtypes of differentiated limbal and corneal epithelial cells. A novel putative LPCs surface marker, GPHA2, expressed on the surface of 0.41% ± 0.21 of the cultured LECs, was identified, based on predominant expression in the limbal crypts of adult and developing cornea and RNAi validation in cultured LECs. Combining scRNA- and ATAC-Seq analyses, we identified multiple upstream regulators for LPCs and demonstrated a close interaction between the immune cells and limbal progenitor cells. RNA-Seq analysis indicated the loss of GPHA2 expression and acquisition of proliferative limbal basal epithelial cell markers during ex vivo LEC expansion, independently of the culture method used. Extending the single cell analyses to keratoconus, we were able to reveal activation of collagenase in the corneal stroma and a reduced pool of limbal suprabasal cells as two key changes underlying the disease phenotype. Single cell RNA-Seq of 89,897 cells obtained from embryonic and fetal cornea indicated that during development, the conjunctival epithelium is the first to be specified from the ocular surface epithelium, followed by the corneal epithelium and the establishment of LPCs, which predate the formation of limbal niche by a few weeks. Conclusions Our scRNA-and ATAC-Seq data of developing and adult cornea in steady state and disease conditions provide a unique resource for defining genes/pathways that can lead to improvement in ex vivo LPCs expansion, stem cell differentiation methods and better understanding and treatment of ocular surface disorders.
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Affiliation(s)
- Joseph Collin
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Rachel Queen
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Darin Zerti
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Sanja Bojic
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Birthe Dorgau
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Nicky Moyse
- Newcastle Cellular Therapies Facility, Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, UK
| | - Marina Moya Molina
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Chunbo Yang
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Sunanda Dey
- Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Israel
| | - Gary Reynolds
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Rafiqul Hussain
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Jonathan M Coxhead
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Steven Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Deborah Henderson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Agatha Joseph
- NHS Blood and Transplant Tissue and Eye Services, Liverpool, UK
| | - Paul Rooney
- NHS Blood and Transplant Tissue and Eye Services, Liverpool, UK
| | - Saurabh Ghosh
- Sunderland Eye Infirmary, South Tyneside and Sunderland NHS Foundation Trust, Sunderland, UK
| | - Lucy Clarke
- UK Department of Ophthalmology, Royal Victoria Infirmary and Newcastle University, Newcastle, UK
| | - Che Connon
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Muzlifah Haniffa
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Francisco Figueiredo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK; UK Department of Ophthalmology, Royal Victoria Infirmary and Newcastle University, Newcastle, UK
| | - Lyle Armstrong
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK.
| | - Majlinda Lako
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK.
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Abstract
Purpose of Review To summarize the recent advances in transcriptomics and proteomics studies of keratoconus using advanced genome-wide gene and protein expression profiling techniques. Recent Findings Second-generation sequencing including RNA sequencing has been widely used to characterize the genome-wide gene expression in corneal tissues or cells affected by keratoconus. Due to different sample types, sequencing platforms, and analysis pipeline, different lists of genes have been identified to be differentially expressed in KC-affected samples. Gene ontology and pathway/network analyses have indicated the involvement of genes related with extracellular matrix, WNT-signaling, TGFβ pathway, and NRF2-regulated network. High throughput proteomics studies using mass spectrometry have uncovered many KC-related protein molecules in pathways related with cytoskeleton, cell matrix, TGFβ signaling, and extracellular matrix remodeling, consistent with gene expression profiling. Summary Both transcriptomics and proteomics studies using genome-wide gene/protein expression profiling techniques have identified significant genes/proteins that may contribute to the pathogenesis of keratoconus. These molecules may be involved in functional categories related with extracellular matrix and TGFβ signaling. It is necessary to perform comprehensive gene/protein expression studies using larger sample size, same type of samples, up-to-date platform and bioinformatics tools.
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Bargagna‐Mohan P, Schultz G, Rheaume B, Trakhtenberg EF, Robson P, Pal‐Ghosh S, Stepp MA, Given KS, Macklin WB, Mohan R. Corneal nonmyelinating Schwann cells illuminated by single-cell transcriptomics and visualized by protein biomarkers. J Neurosci Res 2021; 99:731-749. [PMID: 33197966 PMCID: PMC7894186 DOI: 10.1002/jnr.24757] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 10/05/2020] [Accepted: 10/25/2020] [Indexed: 12/23/2022]
Abstract
The cornea is the most innervated tissue in the human body. Myelinated axons upon inserting into the peripheral corneal stroma lose their myelin sheaths and continue into the central cornea wrapped by only nonmyelinating corneal Schwann cells (nm-cSCs). This anatomical organization is believed to be important for central vision. Here we employed single-cell RNA sequencing (scRNA-seq), microscopy, and transgenics to characterize these nm-cSCs of the central cornea. Using principal component analysis, uniform manifold approximation and projection, and unsupervised hierarchal cell clustering of scRNA-seq data derived from central corneal cells of male rabbits, we successfully identified several clusters representing different corneal cell types, including a unique cell cluster representing nm-cSCs. To confirm protein expression of cSC genes, we performed cross-species validation, employing corneal whole-mount immunostaining with confocal microscopy in mouse corneas. The expression of several representative proteins of nm-cSCs were validated. As the proteolipid protein 1 (PLP1) gene was also expressed in nm-cSCs, we explored the Plp1-eGFP transgenic reporter mouse line to visualize cSCs. Specific and efficient eGFP expression was observed in cSCs in adult mice of different ages. Of several putative cornea-specific SC genes identified, Dickkopf-related protein 1 was shown to be present in nm-cSCs. Taken together, our findings, for the first time, identify important insights and tools toward the study nm-cSCs in isolated tissue and adult animals. We expect that our results will advance the future study of nm-cSCs in applications of nerve repair, and provide a resource for the study of corneal sensory function.
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Affiliation(s)
- Paola Bargagna‐Mohan
- Department of NeuroscienceUniversity of Connecticut Health CenterFarmingtonCTUSA
| | - Gwendolyn Schultz
- Department of NeuroscienceUniversity of Connecticut Health CenterFarmingtonCTUSA
| | - Bruce Rheaume
- Department of NeuroscienceUniversity of Connecticut Health CenterFarmingtonCTUSA
| | | | - Paul Robson
- Department of Genetics & Genome SciencesUniversity of Connecticut Health CenterFarmingtonCTUSA
- The Jackson Laboratory for Genomic MedicineFarmingtonCTUSA
| | - Sonali Pal‐Ghosh
- Department of Anatomy and Regenerative BiologyGeorge Washington University Medical SchoolWashingtonDCUSA
| | - Mary Ann Stepp
- Department of Anatomy and Regenerative BiologyGeorge Washington University Medical SchoolWashingtonDCUSA
| | - Katherine S. Given
- Department of Cell and Developmental BiologyUniversity of Colorado School of MedicineAuroraCOUSA
| | - Wendy B. Macklin
- Department of Cell and Developmental BiologyUniversity of Colorado School of MedicineAuroraCOUSA
| | - Royce Mohan
- Department of NeuroscienceUniversity of Connecticut Health CenterFarmingtonCTUSA
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Sun C, Wang H, Ma Q, Chen C, Yue J, Li B, Zhang X. Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells. Cell Biosci 2021; 11:24. [PMID: 33485387 PMCID: PMC7824938 DOI: 10.1186/s13578-021-00541-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/15/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Human pluripotent stem cell-derived limbal stem cells (hPSC-derived LSCs) provide a promising cell source for corneal transplants and ocular surface reconstruction. Although recent efforts in the identification of LSC markers have increased our understanding of the biology of LSCs, much more remains to be characterized in the developmental origin, cell fate determination, and identity of human LSCs. The lack of knowledge hindered the establishment of efficient differentiation protocols for generating hPSC-derived LSCs and held back their clinical application. RESULTS Here, we performed a time-course single-cell RNA-seq to investigate transcriptional heterogeneity and expression changes of LSCs derived from human embryonic stem cells (hESCs). Based on current protocol, expression heterogeneity of reported LSC markers were identified in subpopulations of differentiated cells. EMT has been shown to occur during differentiation process, which could possibly result in generation of untargeted cells. Pseudotime trajectory analysis revealed transcriptional changes and signatures of commitment of hESCs-derived LSCs and their progeny-the transit amplifying cells. CONCLUSION Single-cell RNA-seq revealed time-course expression changes and significant transcriptional heterogeneity during hESC-derived LSC differentiation in vitro. Our results demonstrated candidate developmental trajectory and several new candidate markers for LSCs, which could facilitate elucidating the identity and developmental origin of human LSCs in vivo.
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Affiliation(s)
- Changbin Sun
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China
| | - Hailun Wang
- Department of Radiation Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Qiwang Ma
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China
| | - Chao Chen
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China
| | - Jianhui Yue
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China.,Section of Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bo Li
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China.
| | - Xi Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China.
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Single-cell transcriptomics identifies limbal stem cell population and cell types mapping its differentiation trajectory in limbal basal epithelium of human cornea. Ocul Surf 2021; 20:20-32. [PMID: 33388438 DOI: 10.1016/j.jtos.2020.12.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/17/2020] [Accepted: 12/27/2020] [Indexed: 12/15/2022]
Abstract
PURPOSE This study aimed to uncover novel cell types in heterogenous basal limbus of human cornea for identifying LSC at single cell resolution. METHODS Single cells of human limbal basal epithelium were isolated from young donor corneas. Single-cell RNA-Sequencing was performed using 10x Genomics platform, followed by clustering cell types through the graph-based visualization method UMAP and unbiased computational informatic analysis. Tissue RNA in situ hybridization with RNAscope, immunofluorescent staining and multiple functional assays were performed using human corneas and limbal epithelial culture models. RESULTS Single-cell transcriptomics of 16,360 limbal basal cells revealed 12 cell clusters belonging to three lineages. A smallest cluster (0.4% of total cells) was identified as LSCs based on their quiescent and undifferentiated states with enriched marker genes for putative epithelial stem cells. TSPAN7 and SOX17 are discovered and validated as new LSC markers based on their exclusive expression pattern and spatial localization in limbal basal epithelium by RNAscope and immunostaining, and functional role in cell growth and tissue regeneration models with RNA interference in cultures. Interestingly, five cell types/states mapping a developmental trajectory of LSC from quiescence to proliferation and differentiation are uncovered by Monocle3 and CytoTRACE pseudotime analysis. The transcription factor networks linking novel signaling pathways are revealed to maintain LSC stemness. CONCLUSIONS This human corneal scRNA-Seq identifies the LSC population and uncovers novel cell types mapping the differentiation trajectory in heterogenous limbal basal epithelium. The findings provide insight into LSC concept and lay the foundation for understanding the corneal homeostasis and diseases.
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68
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Ishii R, Yanagisawa H, Sada A. Defining compartmentalized stem cell populations with distinct cell division dynamics in the ocular surface epithelium. Development 2020; 147:dev197590. [PMID: 33199446 PMCID: PMC7758628 DOI: 10.1242/dev.197590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022]
Abstract
Adult tissues contain label-retaining cells (LRCs), which are relatively slow-cycling and considered to represent a property of tissue stem cells (SCs). In the ocular surface epithelium, LRCs are present in the limbus and conjunctival fornix; however, the character of these LRCs remains unclear, owing to lack of appropriate molecular markers. Using three CreER transgenic mouse lines, we demonstrate that the ocular surface epithelium accommodates spatially distinct populations with different cell division dynamics. In the limbus, long-lived Slc1a3CreER-labeled SCs either migrate centripetally toward the central cornea or slowly expand their clones laterally within the limbal region. In the central cornea, non-LRCs labeled with Dlx1CreER and K14CreER behave as short-lived progenitor cells. The conjunctival epithelium in the bulbar, fornix and palpebral compartment is regenerated by regionally unique SC populations. Severe damage to the cornea leads to the cancellation of SC compartments and conjunctivalization, whereas milder limbal injury induces a rapid increase of laterally expanding clones in the limbus. Taken together, our work defines compartmentalized multiple SC/progenitor populations of the mouse eye in homeostasis and their behavioral changes in response to injury.
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Affiliation(s)
- Ryutaro Ishii
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8577, Japan
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Hiromi Yanagisawa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8577, Japan
- Faculty of Medicine, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Aiko Sada
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8577, Japan
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto 860-0811, Japan
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69
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Wang J, Calvert AE, Kaplan N, McMahon KM, Yang W, Lu KQ, Peng H, Thaxton CS, Lavker RM. HDL nanoparticles have wound healing and anti-inflammatory properties and can topically deliver miRNAs. ADVANCED THERAPEUTICS 2020; 3. [PMID: 33709017 DOI: 10.1002/adtp.202000138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
microRNAs regulate numerous biological processes, making them potential therapeutic agents. Problems with delivery and stability of these molecules have limited their usefulness as treatments. We demonstrate that synthetic high-density lipoprotein nanoparticles (HDL NPs) topically applied to the intact ocular surface are taken up by epithelial and stromal cells. microRNAs complexed to HDL NPs (miR-HDL NPs) are similarly taken up by cells and tissues and retain biological activity. Topical treatment of diabetic mice with either HDL NPs or miR-HDL NPs significantly improved corneal re-epithelialization following wounding compared with controls. Mouse corneas with alkali burn-induced inflammation, topically treated with HDL NPs, displayed clinical, morphological and immunological improvement. These results should yield a novel HDL NP-based eye drop for patients with compromised wound healing ability (diabetics) and/or corneal inflammatory diseases (e.g. dry eye).
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Affiliation(s)
- Junyi Wang
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL.,Department of Ophthalmology, The Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Andrea E Calvert
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Nihal Kaplan
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Kaylin M McMahon
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Wending Yang
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Kurt Q Lu
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Han Peng
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - C Shad Thaxton
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Robert M Lavker
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
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Lavker RM, Kaplan N, Wang J, Peng H. Corneal epithelial biology: Lessons stemming from old to new. Exp Eye Res 2020; 198:108094. [PMID: 32697979 DOI: 10.1016/j.exer.2020.108094] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
The anterior surface of the eye functions as a barrier to the external environment and protects the delicate underlying tissues from injury. Central to this protection are the corneal, limbal and conjunctival epithelia. The corneal epithelium is a self-renewing stratified squamous epithelium that protects the underlying delicate structures of the eye, supports a tear film and maintains transparency so that light can be transmitted to the interior of the eye (Basu et al., 2014; Cotsarelis et al., 1989; Funderburgh et al., 2016; Lehrer et al., 1998; Pajoohesh-Ganji and Stepp, 2005; Parfitt et al., 2015; Peng et al., 2012b; Stepp and Zieske, 2005). In this review, dedicated to James Funderburgh and his contributions to visual science, in particular the limbal niche, corneal stroma and corneal stromal stem cells, we will focus on recent data on the identification of novel regulators in corneal epithelial cell biology, their roles in stem cell homeostasis, wound healing, limbal/corneal boundary maintenance and the utility of single cell RNA sequencing (scRNA-seq) in vision biology studies.
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Affiliation(s)
- Robert M Lavker
- Departments of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Nihal Kaplan
- Departments of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Junyi Wang
- Departments of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Ophthalmology, The First Center of the PLA General Hospital, Haidian District, Beijing, China
| | - Han Peng
- Departments of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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Wang J, Kaplan N, Wang S, Yang W, Wang L, He C, Peng H. Autophagy plays a positive role in induction of epidermal proliferation. FASEB J 2020; 34:10657-10667. [PMID: 32598088 DOI: 10.1096/fj.202000770rr] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/12/2020] [Accepted: 05/29/2020] [Indexed: 12/09/2022]
Abstract
Autophagy is a multistage catabolic process that mediates stress responses. However, the role of autophagy in epidermal proliferation, particularly under conditions when the epidermis becomes "activated" (hyperproliferative), remains unclear. We have shown that inhibition of Beclin 1, a key activator in the initiation phase of autophagy, attenuates imiquimod (IMQ)-induced epidermal hyperplasia in adult mice as well as naturally occurring hyperproliferation in neonatal mouse epidermis. Inhibition of Beclin 1 did not change the levels of several key inflammatory molecules or the numbers of immune cells in lesional skins. This indicates that autophagy does not affect inflammatory regulators in IMQ-treated mouse skin. Bioinformatic analysis combined with gene expression quantitative assays, revealed that a deficiency in autophagy decreases the expression of PDZ Binding Kinase (PBK), a regulator of the cell cycle, in mouse epidermis and human epidermal keratinocytes (HEKs). Interestingly, the decrease in PBK results in inhibition of proliferation in HEKs and such reduced proliferation can be rescued by activation of p38, the downstream signaling of PBK. Collectively, autophagy plays a positive role in epidermal proliferation, which is in part via regulating PBK expression.
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Affiliation(s)
- Junyi Wang
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States.,Department of Ophthalmology, The First Center of the PLA General Hospital, Beijing, China
| | - Nihal Kaplan
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Sijia Wang
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wending Yang
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Liqiang Wang
- Department of Ophthalmology, The First Center of the PLA General Hospital, Beijing, China
| | - Congcong He
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Han Peng
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
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Seyed-Safi AG, Daniels JT. The limbus: Structure and function. Exp Eye Res 2020; 197:108074. [PMID: 32502532 DOI: 10.1016/j.exer.2020.108074] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/14/2020] [Accepted: 05/17/2020] [Indexed: 12/12/2022]
Abstract
Limbal function is a key determinant of corneal epithelial integrity. Lineage tracing studies in mice have highlighted that the centripetal movement of epithelial progenitors from the limbus drives both the steady-state maintenance of the corneal epithelium and its regeneration following injury. It is well established that this is facilitated by a population of limbal epithelial stem cells within the limbus. It is becoming increasingly apparent that the behaviour of these stem cells and their ability to respond to the needs of the tissue are closely linked to their immediate microenvironment - the stem cell niche. Increasing understanding of the structural features of this niche and the signalling networks that they coordinate is required to enhance the therapeutic application of these cells in the treatment of limbal stem cell deficiency. Importantly, an improved characterisation of the hierarchy of limbal epithelial progenitors using both new and old putative markers will enable a greater appreciation for the effects of many of these limbal niche factors on stem cell fate.
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Molecular taxonomy of human ocular outflow tissues defined by single-cell transcriptomics. Proc Natl Acad Sci U S A 2020; 117:12856-12867. [PMID: 32439707 PMCID: PMC7293718 DOI: 10.1073/pnas.2001896117] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ocular hypertension is the primary and only modifiable risk factor for glaucoma, the leading cause of irreversible blindness. Intraocular pressure is regulated homeostatically by resistance to aqueous humor outflow through an architecturally complex tissue, the conventional/trabecular pathway. In this study, we generated a comprehensive cell atlas of the human trabecular meshwork and neighboring tissues using single-cell RNA sequencing. We identified 12 distinct cell types and mapped region-specific expression of candidate genes. The utility of our atlas was demonstrated by mapping glaucoma-relevant genes to conventional outflow cell types. Our study provides a comprehensive molecular and cellular classification of tissue structures responsible for intraocular pressure homeostasis in health and dysregulation in disease. The conventional outflow pathway is a complex tissue responsible for maintaining intraocular pressure (IOP) homeostasis. The coordinated effort of multiple cells with differing responsibilities ensures healthy outflow function and IOP maintenance. Dysfunction of one or more resident cell types results in ocular hypertension and risk for glaucoma, a leading cause of blindness. In this study, single-cell RNA sequencing was performed to generate a comprehensive cell atlas of human conventional outflow tissues. We obtained expression profiles of 17,757 genes from 8,758 cells from eight eyes of human donors representing the outflow cell transcriptome. Upon clustering analysis, 12 distinct cell types were identified, and region-specific expression of candidate genes was mapped in human tissues. Significantly, we identified two distinct expression patterns (myofibroblast- and fibroblast-like) from cells located in the trabecular meshwork (TM), the primary structural component of the conventional outflow pathway. We also located Schwann cell and macrophage signatures in the TM. The second primary component structure, Schlemm’s canal, displayed a unique combination of lymphatic/blood vascular gene expression. Other expression clusters corresponded to cells from neighboring tissues, predominantly in the ciliary muscle/scleral spur, which together correspond to the uveoscleral outflow pathway. Importantly, the utility of our atlas was demonstrated by mapping glaucoma-relevant genes to outflow cell clusters. Our study provides a comprehensive molecular and cellular classification of conventional and unconventional outflow pathway structures responsible for IOP homeostasis.
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