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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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Lammers S, Barrera V, Brennecke P, Miller C, Yoon J, Balolong J, Anderson MS, Ho Sui S, Steinmetz LM, von Andrian UH, Rattay K. Ehf and Fezf2 regulate late medullary thymic epithelial cell and thymic tuft cell development. Front Immunol 2024; 14:1277365. [PMID: 38420512 PMCID: PMC10901246 DOI: 10.3389/fimmu.2023.1277365] [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: 08/14/2023] [Accepted: 12/29/2023] [Indexed: 03/02/2024] Open
Abstract
Thymic epithelial cells are indispensable for T cell maturation and selection and the induction of central immune tolerance. The self-peptide repertoire expressed by medullary thymic epithelial cells is in part regulated by the transcriptional regulator Aire (Autoimmune regulator) and the transcription factor Fezf2. Due to the high complexity of mTEC maturation stages (i.e., post-Aire, Krt10+ mTECs, and Dclk1+ Tuft mTECs) and the heterogeneity in their gene expression profiles (i.e., mosaic expression patterns), it has been challenging to identify the additional factors complementing the transcriptional regulation. We aimed to identify the transcriptional regulators involved in the regulation of mTEC development and self-peptide expression in an unbiased and genome-wide manner. We used ATAC footprinting analysis as an indirect approach to identify transcription factors involved in the gene expression regulation in mTECs, which we validated by ChIP sequencing. This study identifies Fezf2 as a regulator of the recently described thymic Tuft cells (i.e., Tuft mTECs). Furthermore, we identify that transcriptional regulators of the ELF, ESE, ERF, and PEA3 subfamily of the ETS transcription factor family and members of the Krüppel-like family of transcription factors play a role in the transcriptional regulation of genes involved in late mTEC development and promiscuous gene expression.
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Affiliation(s)
- Sören Lammers
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Victor Barrera
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Philip Brennecke
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, United States
- Stanford Genome Technology Center, Stanford University, Stanford, CA, United States
| | - Corey Miller
- Diabetes Center, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Joon Yoon
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Jared Balolong
- Diabetes Center, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Mark S. Anderson
- Diabetes Center, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Shannan Ho Sui
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Lars M. Steinmetz
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, United States
- Stanford Genome Technology Center, Stanford University, Stanford, CA, United States
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Ulrich H. von Andrian
- Department of Immunology & HMS Center for Immune Imaging, Harvard Medical School, Boston, MA, United States
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
| | - Kristin Rattay
- Department of Immunology & HMS Center for Immune Imaging, Harvard Medical School, Boston, MA, United States
- Pharmacological Institute, Biochemical Pharmacological Center, University of Marburg, Marburg, Germany
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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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Selvarajah K, Tan JJ, Shaharuddin B. Corneal Epithelial Development and the Role of Induced Pluripotent Stem Cells for Regeneration. Curr Stem Cell Res Ther 2024; 19:292-306. [PMID: 36915985 DOI: 10.2174/1574888x18666230313094121] [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: 07/15/2022] [Revised: 12/02/2022] [Accepted: 01/02/2023] [Indexed: 03/16/2023]
Abstract
Severe corneal disorders due to infective aetiologies, trauma, chemical injuries, and chronic cicatricial inflammations, are among vision-threatening pathologies leading to permanent corneal scarring. The whole cornea or lamellar corneal transplantation is often used as a last resort to restore vision. However, limited autologous tissue sources and potential adverse post-allotransplantation sequalae urge the need for more robust and strategic alternatives. Contemporary management using cultivated corneal epithelial transplantation has paved the way for utilizing stem cells as a regenerative potential. Humaninduced pluripotent stem cells (hiPSCs) can generate ectodermal progenitors and potentially be used for ocular surface regeneration. This review summarizes the process of corneal morphogenesis and the signaling pathways underlying the development of corneal epithelium, which is key to translating the maturation and differentiation process of hiPSCs in vitro. The current state of knowledge and methodology for driving efficient corneal epithelial cell differentiation from pluripotent stem cells are highlighted.
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Affiliation(s)
- Komathi Selvarajah
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
- Department of Microbiology, Faculty of Medicine, Asian Institute of Medical Sciences and Technology (AIMST) University, Kedah, Malaysia
| | - Jun Jie Tan
- Department of Microbiology, Faculty of Medicine, Asian Institute of Medical Sciences and Technology (AIMST) University, Kedah, Malaysia
| | - Bakiah Shaharuddin
- Department of Microbiology, Faculty of Medicine, Asian Institute of Medical Sciences and Technology (AIMST) University, Kedah, Malaysia
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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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Kaur S, Sohnen P, Swamynathan S, Du Y, Espana EM, Swamynathan SK. Molecular nature of ocular surface barrier function, diseases that affect it, and its relevance for ocular drug delivery. Ocul Surf 2023; 30:3-13. [PMID: 37543173 PMCID: PMC10837323 DOI: 10.1016/j.jtos.2023.08.001] [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: 06/29/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/07/2023]
Abstract
The structural and functional integrity of the ocular surface, a continuous epithelial structure comprised of the cornea, the conjunctiva, and the ductal surface of the lacrimal as well as meibomian glands, is crucial for proper vision. The ocular surface barrier function (OSBF), sum of the different types of protective mechanisms that exist at the ocular surface, is essential to protect the rest of the eye from vision-threatening physical, chemical, and biological insults. OSBF helps maintain the immune privileged nature of the cornea and the aqueous humor by preventing entry of infectious agents, allergens, and noxious chemicals. Disruption of OSBF exposes the dense nerve endings of the cornea to these stimuli, resulting in discomfort and pain. This review summarizes the status of our knowledge related to the molecular nature of OSBF, describes the effect of different ocular surface disorders on OSBF, and examines the relevance of this knowledge for ocular drug delivery.
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Affiliation(s)
- Satinder Kaur
- Department of Ophthalmology, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., Room 2114, Tampa, FL 33612. USA
| | - Peri Sohnen
- Department of Ophthalmology, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., Room 2114, Tampa, FL 33612. USA
| | - Sudha Swamynathan
- Department of Ophthalmology, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., Room 2114, Tampa, FL 33612. USA
| | - Yiqin Du
- Department of Ophthalmology, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., Room 2114, Tampa, FL 33612. USA
| | - Edgar M Espana
- Department of Ophthalmology, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., Room 2114, Tampa, FL 33612. USA
| | - Shivalingappa K Swamynathan
- Department of Ophthalmology, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., Room 2114, Tampa, FL 33612. USA.
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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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Lu ZJ, Ye JG, Wang DL, Li MK, Zhang QK, Liu Z, Huang YJ, Pan CN, Lin YH, Shi ZX, Zheng YF. Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Mouse Corneal Epithelial Cells. Invest Ophthalmol Vis Sci 2023; 64:30. [PMID: 36943152 PMCID: PMC10043503 DOI: 10.1167/iovs.64.3.30] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Purpose Corneal epithelial homeostasis is maintained by coordinated gene expression across distinct cell populations, but the gene regulatory programs underlying this cellular diversity remain to be characterized. Here we applied single-cell multi-omics analysis to delineate the gene regulatory profile of mouse corneal epithelial cells under normal homeostasis. Methods Single cells isolated from the cornea epithelium (with marginal conjunctiva) of adult mice were subjected to scRNA-seq and scATAC-seq using the 10×Genomics platform. Cell types were clustered by the graph-based visualization method uniform manifold approximation and projection and unbiased computational informatics analysis. The scRNA-seq and scATAC-seq datasets were integrated following the integration pipeline described in ArchR and Seurat. Results We characterized diverse corneal epithelial cell types based on gene expression signatures and chromatin accessibility. We found that cell type-specific accessibility regions were mainly located at distal regions, suggesting essential roles of distal regulatory elements in determining corneal epithelial cell diversity. Trajectory analyses revealed a continuum of cell state transition and higher coordination between transcription factor (TF) motif accessibility and gene expression during corneal epithelial cell differentiation. By integrating transcriptomic and chromatin accessibility analysis, we identified cell type-specific and shared gene regulation programs. We also uncovered critical TFs driving corneal epithelial cell differentiation, such as nuclear factor I (NFI) family members, Rarg, Elf3. We found that nuclear factor-κB (NF-κB) family members were positive TFs in limbal cells and some superficial cells, but they were involved in regulating distinct biological processes. Conclusions Our study presents a comprehensive gene regulatory landscape of mouse cornea epithelial cells, and provides valuable foundations for future investigation of corneal epithelial homeostasis in the context of cornea pathologies and regenerative medicine.
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Affiliation(s)
- Zhao-Jing Lu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, China
| | - Jin-Guo Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Dong-Liang Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Meng-Ke Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qi-Kai Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhong Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yan-Jing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Cai-Neng Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yu-Heng Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhuo-Xing Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Ying-Feng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, China
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Koudouna E, Young RD, Quantock AJ, Ralphs JR. Developmental Changes in Patterns of Distribution of Fibronectin and Tenascin-C in the Chicken Cornea: Evidence for Distinct and Independent Functions during Corneal Development and Morphogenesis. Int J Mol Sci 2023; 24:ijms24043555. [PMID: 36834965 PMCID: PMC9964472 DOI: 10.3390/ijms24043555] [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: 11/28/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
The cornea forms the tough and transparent anterior part of the eye and by accurate shaping forms the major refractive element for vision. Its largest component is the stroma, a dense collagenous connective tissue positioned between the epithelium and the endothelium. In chicken embryos, the stroma initially develops as the primary stroma secreted by the epithelium, which is then invaded by migratory neural crest cells. These cells secrete an organised multi-lamellar collagenous extracellular matrix (ECM), becoming keratocytes. Within individual lamellae, collagen fibrils are parallel and orientated approximately orthogonally in adjacent lamellae. In addition to collagens and associated small proteoglycans, the ECM contains the multifunctional adhesive glycoproteins fibronectin and tenascin-C. We show in embryonic chicken corneas that fibronectin is present but is essentially unstructured in the primary stroma before cell migration and develops as strands linking migrating cells as they enter, maintaining their relative positions as they populate the stroma. Fibronectin also becomes prominent in the epithelial basement membrane, from which fibronectin strings penetrate into the stromal lamellar ECM at right angles. These are present throughout embryonic development but are absent in adults. Stromal cells associate with the strings. Since the epithelial basement membrane is the anterior stromal boundary, strings may be used by stromal cells to determine their relative anterior-posterior positions. Tenascin-C is organised differently, initially as an amorphous layer above the endothelium and subsequently extending anteriorly and organising into a 3D mesh when the stromal cells arrive, enclosing them. It continues to shift anteriorly in development, disappearing posteriorly, and finally becoming prominent in Bowman's layer beneath the epithelium. The similarity of tenascin-C and collagen organisation suggests that it may link cells to collagen, allowing cells to control and organise the developing ECM architecture. Fibronectin and tenascin-C have complementary roles in cell migration, with the former being adhesive and the latter being antiadhesive and able to displace cells from their adhesion to fibronectin. Thus, in addition to the potential for associations between cells and the ECM, the two could be involved in controlling migration and adhesion and subsequent keratocyte differentiation. Despite the similarities in structure and binding capabilities of the two glycoproteins and the fact that they occupy similar regions of the developing stroma, there is little colocalisation, demonstrating their distinctive roles.
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Affiliation(s)
- Elena Koudouna
- Structural Biophysics Group, School of Optometry & Vision Sciences, Cardiff University, Maindy Road, Cathays, Cardiff CF24 4HQ, UK
| | - Robert D. Young
- Structural Biophysics Group, School of Optometry & Vision Sciences, Cardiff University, Maindy Road, Cathays, Cardiff CF24 4HQ, UK
| | - Andrew J. Quantock
- Structural Biophysics Group, School of Optometry & Vision Sciences, Cardiff University, Maindy Road, Cathays, Cardiff CF24 4HQ, UK
| | - James R. Ralphs
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
- Correspondence:
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10
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Wang B, Guo H, Liu D, Wu S, Liu J, Lan X, Huang H, An F, Zhu J, Ji J, Wang L, Ouyang H, Li M. ETS1-HMGA2 Axis Promotes Human Limbal Epithelial Stem Cell Proliferation. Invest Ophthalmol Vis Sci 2023; 64:12. [PMID: 36652264 PMCID: PMC9855287 DOI: 10.1167/iovs.64.1.12] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Purpose This study aimed to investigate the role and molecular mechanism of ETS1 in the proliferation and differentiation of human limbal epithelial stem cells (LESCs). Methods RNA-seq and quantitative real-time PCR were used to determine gene expression changes when ETS1 and HMGA2 was knocked down using short-hairpin RNAs or overexpressed by lentivirus. Immunofluorescence and flow cytometry experiments were performed to assess the roles of ETS1 and HMGA2 in LESC proliferation. ETS1-bound cis-regulatory elements and target genes in LESCs were identified using chromatin immunoprecipitation sequencing. The epigenetic features of ETS1-binding sites were assessed by the published histone modification and chromatin accessibility profiles. Results ETS1 was robustly expressed in LESCs but dramatically reduced on differentiation into corneal epithelial cells (CECs). ETS1 knockdown in LESCs inhibited cellular proliferation and activated CEC markers (KRT3, KRT12, CLU, and ALDH3A1). When ETS1 was overexpressed during CEC differentiation, LESC-associated genes were upregulated while CEC-associated genes were downregulated. The genome-wide binding profile of ETS1 was identified in LESCs. ETS1 occupied H3K4me3-marked promoters and H3K27ac/H3K4me1-marked enhancers. ETS1-binding sites were also enriched for chromatin accessibility signal. HMGA2 showed a consistent expression pattern with ETS1. ETS1 activates HMAG2 by binding to its promoter. Knockdown and overexpression experiments suggested that HMGA2 can promote LESC proliferation and inhibits its differentiation. Conclusions ETS1 promotes LESC proliferation and inhibits its differentiation via activating HMGA2.
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Affiliation(s)
- Bofeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Huizhen Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Dongmei Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Siqi Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jiafeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xihong Lan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Huaxing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Fengjiao An
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jin Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jianping Ji
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Hong Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Mingsen Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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11
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Sonam S, Bangru S, Perry KJ, Chembazhi UV, Kalsotra A, Henry JJ. Cellular and molecular profiles of larval and adult Xenopus corneal epithelia resolved at the single-cell level. Dev Biol 2022; 491:13-30. [PMID: 36049533 PMCID: PMC10241109 DOI: 10.1016/j.ydbio.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022]
Abstract
Corneal Epithelial Stem Cells (CESCs) and their proliferative progeny, the Transit Amplifying Cells (TACs), are responsible for homeostasis and maintaining corneal transparency. Owing to our limited knowledge of cell fates and gene activity within the cornea, the search for unique markers to identify and isolate these cells remains crucial for ocular surface reconstruction. We performed single-cell RNA sequencing of corneal cells from larval and adult stages of Xenopus. Our results indicate that as the cornea develops and matures, there is an increase in cellular diversity, which is accompanied by a substantial shift in transcriptional profile, gene regulatory network and cell-cell communication dynamics. Our data also reveals several novel genes expressed in corneal cells and changes in gene expression during corneal differentiation at both developmental time-points. Importantly, we identify specific basal cell clusters in both the larval and adult cornea that comprise a relatively undifferentiated cell type and express distinct stem cell markers, which we propose are the putative larval and adult CESCs, respectively. This study offers a detailed atlas of single-cell transcriptomes in the frog cornea. In the future, this work will be useful to elucidate the function of novel genes in corneal epithelial homeostasis, wound healing and regeneration.
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Affiliation(s)
- Surabhi Sonam
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA; Cancer Center@Illinois, University of Illinois, Urbana-Champaign, IL, USA
| | - Kimberly J Perry
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL, USA
| | - Ullas V Chembazhi
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, USA; Cancer Center@Illinois, University of Illinois, Urbana-Champaign, IL, USA.
| | - Jonathan J Henry
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL, USA.
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12
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Di Girolamo N, Park M. Cell identity changes in ocular surface Epithelia. Prog Retin Eye Res 2022:101148. [DOI: 10.1016/j.preteyeres.2022.101148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/13/2022] [Accepted: 11/09/2022] [Indexed: 11/21/2022]
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13
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Sunny SS, Lachova J, Dupacova N, Kozmik Z. Multiple roles of Pax6 in postnatal cornea development. Dev Biol 2022; 491:1-12. [PMID: 36049534 DOI: 10.1016/j.ydbio.2022.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
Abstract
Mammalian corneal development is a multistep process, including formation of the corneal epithelium (CE), endothelium and stroma during embryogenesis, followed by postnatal stratification of the epithelial layers and continuous renewal of the epithelium to replace the outermost corneal cells. Here, we employed the Cre-loxP system to conditionally deplete Pax6 proteins in two domains of ocular cells, i.e., the ocular surface epithelium (cornea, limbus and conjunctiva) (OSE) or postnatal CE via K14-cre or Aldh3-cre, respectively. Earlier and broader inactivation of Pax6 in the OSE resulted in thickened OSE with CE and limbal cells adopting the conjunctival keratin expression pattern. More restricted depletion of Pax6 in postnatal CE resulted in an abnormal cornea marked by reduced epithelial thickness despite increased epithelial cell proliferation. Immunofluorescence studies revealed loss of intermediate filament Cytokeratin 12 and diffused expression of adherens junction components, together with reduced tight junction protein, Zonula occludens-1. Furthermore, the expression of Cytokeratin 14, a basal cell marker in apical layers, indicates impaired differentiation of CE cells. Collectively, our data demonstrate that Pax6 is essential for maintaining proper differentiation and strong intercellular adhesion in postnatal CE cells, whereas limbal Pax6 is required to prevent the outgrowth of conjunctival cells to the cornea.
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Affiliation(s)
- Sweetu Susan Sunny
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, Praha 4, 142 20, Czech Republic
| | - Jitka Lachova
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, Praha 4, 142 20, Czech Republic
| | - Naoko Dupacova
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, Praha 4, 142 20, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, Praha 4, 142 20, Czech Republic.
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14
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Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity. Nat Commun 2022; 13:1293. [PMID: 35277509 PMCID: PMC8917218 DOI: 10.1038/s41467-022-28966-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/21/2022] [Indexed: 11/24/2022] Open
Abstract
The insights into how genome topology couples with epigenetic states to govern the function and identity of the corneal epithelium are poorly understood. Here, we generate a high-resolution Hi-C interaction map of human limbal stem/progenitor cells (LSCs) and show that chromatin multi-hierarchical organisation is coupled to gene expression. By integrating Hi-C, epigenome and transcriptome data, we characterize the comprehensive 3D epigenomic landscapes of LSCs. We find that super-silencers mediate gene repression associated with corneal development, differentiation and disease via chromatin looping and/or proximity. Super-enhancer (SE) interaction analysis identified a set of SE interactive hubs that contribute to LSC-specific gene activation. These active and inactive element-anchored loop networks occur within the cohesin-occupied CTCF-CTCF loops. We further reveal a coordinated regulatory network of core transcription factors based on SE-promoter interactions. Our results provide detailed insights into the genome organization principle for epigenetic regulation of gene expression in stratified epithelia. Genome topology provides a structural basis for epigenome-mediated transcriptional regulation in eukaryotes. Here the authors characterized the 3D genome of stratified squamous epithelia. They generated a Hi-C map of human limbal stem/progenitor cells (LSCs) and integrated these data with epigenomics, transcription factor binding maps, and transcriptome data.
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15
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Swamynathan S, Campbell G, Tiwari A, Swamynathan SK. Secreted Ly-6/uPAR-related protein-1 (SLURP1) is a pro-differentiation factor that stalls G1-S transition during corneal epithelial cell cycle progression. Ocul Surf 2021; 24:1-11. [PMID: 34923162 DOI: 10.1016/j.jtos.2021.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE Previously we demonstrated that the secreted Ly-6/uPAR related protein-1 (SLURP1), abundantly expressed in the corneal epithelium (CE) and secreted into the tear fluid, serves as an anti-inflammatory and anti-angiogenic molecule. Here we describe the Slurp1-null (Slurp1X-/-) mouse corneal phenotype for the first time. METHODS We compared the 10-week-old wild type (WT) and Slurp1X-/- mouse corneal (i) histology by hematoxylin-eosin and periodic acid-Schiff's reagent staining, (ii) cell proliferation by immunostaining for Ki67, (iii) cell adhesion molecules by immunostaining for desmosomal and tight junction proteins, (iv) barrier function by fluorescein staining and (v) wound-healing by epithelial debridement. Effect of SLURP1 on cell cycle was quantified in human corneal limbal epithelial (HCLE) cells engineered to express SLURP1 (HCLE-SLURP1). RESULTS WT and Slurp1X-/- corneal histology was largely comparable, other than a few loosely attached superficial cells in Slurp1X-/- corneas. Compared with the WT, Slurp1X-/- corneas displayed (i) increase in Ki67+ cells, (ii) altered expression and/or localization of tight junction proteins Tjp1 and Pard3, and desmosomal Dsp, (iii) increased superficial fragility and (iv) slower CE wound healing. HCLE-SLURP1 cells displayed (i) decrease in Ki67+ cells, (ii) increased cell number doubling time, (iii) stalling in G1-S phase transition during cell cycle, and (iv) downregulation of cyclins CCNE and CCND1/D2, cyclin-dependent kinases CDK4 and CDK6, and upregulation of CDK inhibitor p15/CDKN2B. CONCLUSIONS Collectively, these results elucidate that Slurp1X-/- CE cell homeostasis is altered and suggest that SLURP1 is a pro-differentiation factor that stalls G1-S transition during cell cycle progression by downregulating cyclins and upregulating p15/CDKN2B.
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Affiliation(s)
- Sudha Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Gregory Campbell
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Anil Tiwari
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Shivalingappa K Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, USA; McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, USA; Fox Center for Vision Restoration, University of Pittsburgh, Pittsburgh, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, USA.
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16
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Transcriptome Analysis of Pterygium and Pinguecula Reveals Evidence of Genomic Instability Associated with Chronic Inflammation. Int J Mol Sci 2021; 22:ijms222112090. [PMID: 34769520 PMCID: PMC8584501 DOI: 10.3390/ijms222112090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 12/24/2022] Open
Abstract
Solar damage due to ultraviolet radiation (UVR) is implicated in the development of two proliferative lesions of the ocular surface: pterygium and pinguecula. Pterygium and pinguecula specimens were collected, along with adjacent healthy conjunctiva specimens. RNA was extracted and sequenced. Pairwise comparisons were made of differentially expressed genes (DEGs). Computational methods were used for analysis. Transcripts from 18,630 genes were identified. Comparison of two subgroups of pterygium specimens uncovered evidence of genomic instability associated with inflammation and the immune response; these changes were also observed in pinguecula, but to a lesser extent. Among the top DEGs were four genes encoding tumor suppressors that were downregulated in pterygium: C10orf90, RARRES1, DMBT1 and SCGB3A1; C10orf90 and RARRES1 were also downregulated in pinguecula. Ingenuity Pathway Analysis overwhelmingly linked DEGs to cancer for both lesions; however, both lesions are clearly still benign, as evidenced by the expression of other genes indicating their well-differentiated and non-invasive character. Pathways for epithelial cell proliferation were identified that distinguish the two lesions, as well as genes encoding specific pathway components. Upregulated DEGs common to both lesions, including KRT9 and TRPV3, provide a further insight into pathophysiology. Our findings suggest that pterygium and pinguecula, while benign lesions, are both on the pathological pathway towards neoplastic transformation.
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17
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Seese SE, Deml B, Muheisen S, Sorokina E, Semina EV. Genetic disruption of zebrafish mab21l1 reveals a conserved role in eye development and affected pathways. Dev Dyn 2021; 250:1056-1073. [PMID: 33570754 PMCID: PMC8349561 DOI: 10.1002/dvdy.312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The male-abnormal 21 like (MAB21L) genes are important in human ocular development. Homozygous loss of MAB21L1 leads to corneal dystrophy in all affected individuals along with cataracts and buphthalmos in some. The molecular function and downstream pathways of MAB21L factors are largely undefined. RESULTS We generated the first mab21l1 zebrafish mutant carrying a putative loss-of-function allele, c.107delA p.(Lys36Argfs*7). At the final stages of embryonic development, homozygous mab21l1c.107delA fish displayed enlarged anterior chambers and corneal thinning which progressed with age. Additional studies revealed increased cell death in the mutant corneas, transformation of the cornea into a skin-like epithelium, and progressive lens degeneration with development of fibrous masses in the anterior chamber. RNA-seq of wild-type and mutant ocular transcriptomes revealed significant changes in expression of several genes, including irf1a and b, stat1, elf3, krt17, tlr9, and loxa associated with immunity and/or corneal function. Abnormal expression of lysyl oxidases have been previously linked with corneal thinning, fibrosis, and lens defects in mammals, suggesting a role for loxa misexpression in the progressive mab21l1c.107delA eye phenotype. CONCLUSIONS Zebrafish mab21l1 is essential for normal corneal development, similar to human MAB21L1. The identified molecular changes in mab21l1c.107delA mutants provide the first clues about possible affected pathways.
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Affiliation(s)
- Sarah E. Seese
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Brett Deml
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin
- PreventionGenetics, Marshfield, Wisconsin
| | - Sanaa Muheisen
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Elena Sorokina
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Elena V. Semina
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Children's of Wisconsin, Milwaukee, Wisconsin
- Children's Research Institute, Medical College of Wisconsin, Children's of Wisconsin, Milwaukee, Wisconsin
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18
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Reehorst CM, Nightingale R, Luk IY, Jenkins L, Koentgen F, Williams DS, Darido C, Tan F, Anderton H, Chopin M, Schoffer K, Eissmann MF, Buchert M, Mouradov D, Sieber OM, Ernst M, Dhillon AS, Mariadason JM. EHF is essential for epidermal and colonic epithelial homeostasis, and suppresses Apc-initiated colonic tumorigenesis. Development 2021; 148:269265. [PMID: 34180969 DOI: 10.1242/dev.199542] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/19/2021] [Indexed: 01/01/2023]
Abstract
Ets homologous factor (EHF) is a member of the epithelial-specific Ets (ESE) family of transcription factors. To investigate its role in development and epithelial homeostasis, we generated a series of novel mouse strains in which the Ets DNA-binding domain of Ehf was deleted in all tissues (Ehf-/-) or specifically in the gut epithelium. Ehf-/- mice were born at the expected Mendelian ratio, but showed reduced body weight gain, and developed a series of pathologies requiring most Ehf-/- mice to reach an ethical endpoint before reaching 1 year of age. These included papillomas in the facial skin, abscesses in the preputial glands (males) or vulvae (females), and corneal ulcers. Ehf-/-mice also displayed increased susceptibility to experimentally induced colitis, which was confirmed in intestinal-specific Ehf knockout mice. Gut-specific Ehf deletion also impaired goblet cell differentiation, induced extensive transcriptional reprogramming in the colonic epithelium and enhanced Apc-initiated adenoma development. The Ets DNA-binding domain of EHF is therefore essential for postnatal homeostasis of the epidermis and colonic epithelium, and its loss promotes colonic tumour development.
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Affiliation(s)
- Camilla M Reehorst
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, 3084Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, 3084Australia
| | - Rebecca Nightingale
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, 3084Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, 3084Australia
| | - Ian Y Luk
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, 3084Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, 3084Australia
| | - Laura Jenkins
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, 3084Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, 3084Australia
| | | | - David S Williams
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, 3084Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, 3084Australia
| | - Charbel Darido
- Peter MacCallum Cancer Centre, Melbourne, 3000Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3010Australia
| | - Fiona Tan
- Peter MacCallum Cancer Centre, Melbourne, 3000Australia
| | - Holly Anderton
- Walter and Eliza Hall Institute, Melbourne, 3052Australia
| | - Michael Chopin
- Walter and Eliza Hall Institute, Melbourne, 3052Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010Australia
| | - Kael Schoffer
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, 3084Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, 3084Australia
| | - Moritz F Eissmann
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, 3084Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, 3084Australia
| | - Michael Buchert
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, 3084Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, 3084Australia
| | | | - Oliver M Sieber
- Walter and Eliza Hall Institute, Melbourne, 3052Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010Australia.,Department of Surgery, The University of Melbourne, Parkville, Victoria, 3010Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, 3084Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, 3084Australia
| | - Amardeep S Dhillon
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, Victoria, 3216Australia
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, 3084Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, 3084Australia.,Department of Medicine, University of Melbourne, Parkville, Victoria, 3010Australia
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19
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Hardcastle AJ, Liskova P, Bykhovskaya Y, McComish BJ, Davidson AE, Inglehearn CF, Li X, Choquet H, Habeeb M, Lucas SEM, Sahebjada S, Pontikos N, Lopez KER, Khawaja AP, Ali M, Dudakova L, Skalicka P, Van Dooren BTH, Geerards AJM, Haudum CW, Faro VL, Tenen A, Simcoe MJ, Patasova K, Yarrand D, Yin J, Siddiqui S, Rice A, Farraj LA, Chen YDI, Rahi JS, Krauss RM, Theusch E, Charlesworth JC, Szczotka-Flynn L, Toomes C, Meester-Smoor MA, Richardson AJ, Mitchell PA, Taylor KD, Melles RB, Aldave AJ, Mills RA, Cao K, Chan E, Daniell MD, Wang JJ, Rotter JI, Hewitt AW, MacGregor S, Klaver CCW, Ramdas WD, Craig JE, Iyengar SK, O'Brart D, Jorgenson E, Baird PN, Rabinowitz YS, Burdon KP, Hammond CJ, Tuft SJ, Hysi PG. A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus. Commun Biol 2021; 4:266. [PMID: 33649486 PMCID: PMC7921564 DOI: 10.1038/s42003-021-01784-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
Keratoconus is characterised by reduced rigidity of the cornea with distortion and focal thinning that causes blurred vision, however, the pathogenetic mechanisms are unknown. It can lead to severe visual morbidity in children and young adults and is a common indication for corneal transplantation worldwide. Here we report the first large scale genome-wide association study of keratoconus including 4,669 cases and 116,547 controls. We have identified significant association with 36 genomic loci that, for the first time, implicate both dysregulation of corneal collagen matrix integrity and cell differentiation pathways as primary disease-causing mechanisms. The results also suggest pleiotropy, with some disease mechanisms shared with other corneal diseases, such as Fuchs endothelial corneal dystrophy. The common variants associated with keratoconus explain 12.5% of the genetic variance, which shows potential for the future development of a diagnostic test to detect susceptibility to disease.
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Affiliation(s)
- Alison J Hardcastle
- UCL Institute of Ophthalmology, London, UK.
- Moorfields Eye Hospital, NHS Foundation Trust, London, UK.
| | - Petra Liskova
- UCL Institute of Ophthalmology, London, UK
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Yelena Bykhovskaya
- The Cornea Eye Institute, Beverly Hills, CA, USA
- Department of Surgery and Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bennet J McComish
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | | | - Chris F Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Xiaohui Li
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Mahmoud Habeeb
- Department of Ophthalmology, Erasmus Medical Center GD, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center GD, Rotterdam, The Netherlands
| | - Sionne E M Lucas
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Srujana Sahebjada
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
- Department of Surgery, Ophthalmology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | | | | | - Anthony P Khawaja
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital, NHS Foundation Trust, London, UK
- NIHR Biomedical Research Centre, Moorfields Eye Hospital, London, UK
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Lubica Dudakova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Pavlina Skalicka
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Bart T H Van Dooren
- Department of Ophthalmology, Erasmus Medical Center GD, Rotterdam, The Netherlands
- Amphia Hospital, Breda, The Netherlands
| | | | - Christoph W Haudum
- Division of Endocrinology and Diabetology, Endocrinology Lab Platform, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Valeria Lo Faro
- Department of Ophthalmology, University Medical Center Groningen (UMCG), Groningen, the Netherlands
- Department of Ophthalmology, Academic Medical Center, Amsterdam, The Netherlands
| | - Abi Tenen
- Vision Eye Institute, Melbourne, VIC, Australia
- School of Primary and Allied Health Care, Monash University, Melbourne, VIC, Australia
- Melbourne Stem Cell Centre, Melbourne, VIC, 3800, Australia
| | - Mark J Simcoe
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Karina Patasova
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Darioush Yarrand
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jie Yin
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Salina Siddiqui
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Department of Ophthalmology, St James's University Hospital, Leeds, UK
| | - Aine Rice
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Layal Abi Farraj
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jugnoo S Rahi
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | | | | | - Jac C Charlesworth
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | | | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Magda A Meester-Smoor
- Department of Ophthalmology, Erasmus Medical Center GD, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center GD, Rotterdam, The Netherlands
| | - Andrea J Richardson
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Paul A Mitchell
- Centre for Vision Research, Department of Ophthalmology, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ronald B Melles
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Anthony J Aldave
- The Jules Stein Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Richard A Mills
- Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Ke Cao
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
- Department of Surgery, Ophthalmology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Elsie Chan
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
- Department of Surgery, Ophthalmology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Mark D Daniell
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
- Department of Surgery, Ophthalmology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Jie Jin Wang
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Vision Eye Institute, Melbourne, VIC, Australia
- School of Primary and Allied Health Care, Monash University, Melbourne, VIC, Australia
- Melbourne Stem Cell Centre, Melbourne, VIC, 3800, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center GD, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center GD, Rotterdam, The Netherlands
| | - Wishal D Ramdas
- Department of Ophthalmology, Erasmus Medical Center GD, Rotterdam, The Netherlands
| | - Jamie E Craig
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Sudha K Iyengar
- Department of Ophthalmology, Case Western Reserve University, Cleveland, OH, USA
| | - David O'Brart
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK
- St Thomas Hospital, Guy's and St. Thomas NHS Trust, London, London, UK
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Paul N Baird
- Department of Surgery, Ophthalmology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Yaron S Rabinowitz
- The Cornea Eye Institute, Beverly Hills, CA, USA
- Department of Surgery and Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Chris J Hammond
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- St Thomas Hospital, Guy's and St. Thomas NHS Trust, London, London, UK
| | - Stephen J Tuft
- UCL Institute of Ophthalmology, London, UK.
- Moorfields Eye Hospital, NHS Foundation Trust, London, UK.
| | - Pirro G Hysi
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK.
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK.
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20
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Chauhan BK, Medsinge A, Scanga HL, Chu CT, Nischal KK. Transcriptome from opaque cornea of Fanconi anemia patient uncovers fibrosis and two connected players. Mol Genet Metab Rep 2021; 26:100712. [PMID: 33552906 PMCID: PMC7846932 DOI: 10.1016/j.ymgmr.2021.100712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 11/28/2022] Open
Abstract
Congenital corneal opacities (CCO) are a group of blinding corneal disorders, where the underlying molecular mechanisms are poorly understood. Phenotyping through specialized imaging and histopathology analysis, together with assessment of key transcriptomic changes (including glycosaminoglycan metabolic enzymes) in cornea(s) with CCO from a case of Fanconi anemia is the approach taken in this study to identify causal mechanisms. Based on our findings, we propose a novel mechanism and two key players contributing to CCO.
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Affiliation(s)
- Bharesh K Chauhan
- UPMC Eye Center, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.,Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Anagha Medsinge
- UPMC Eye Center, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Hannah L Scanga
- UPMC Eye Center, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Charleen T Chu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ken K Nischal
- UPMC Eye Center, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.,Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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21
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Loss of FOXC1 contributes to the corneal epithelial fate switch and pathogenesis. Signal Transduct Target Ther 2021; 6:5. [PMID: 33414365 PMCID: PMC7791103 DOI: 10.1038/s41392-020-00378-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/01/2020] [Accepted: 07/31/2020] [Indexed: 11/08/2022] Open
Abstract
Forkhead box C1 (FOXC1) is required for neural crest and ocular development, and mutations in FOXC1 lead to inherited Axenfeld-Rieger syndrome. Here, we find that FOXC1 and paired box 6 (PAX6) are co-expressed in the human limbus and central corneal epithelium. Deficiency of FOXC1 and alternation in epithelial features occur in patients with corneal ulcers. FOXC1 governs the fate of the corneal epithelium by directly binding to lineage-specific open promoters or enhancers marked by H3K4me2. FOXC1 depletion not only activates the keratinization pathway and reprograms corneal epithelial cells into skin-like epithelial cells, but also disrupts the collagen metabolic process and interferon signaling pathways. Loss of interferon regulatory factor 1 and PAX6 induced by FOXC1 dysfunction is linked to the corneal ulcer. Collectively, our results reveal a FOXC1-mediated regulatory network responsible for corneal epithelial homeostasis and provide a potential therapeutic target for corneal ulcer.
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22
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Tiwari A, Swamynathan S, Campbell G, Jhanji V, Swamynathan SK. BMP6 Regulates Corneal Epithelial Cell Stratification by Coordinating Their Proliferation and Differentiation and Is Upregulated in Pterygium. Invest Ophthalmol Vis Sci 2021; 61:46. [PMID: 32845956 PMCID: PMC7452852 DOI: 10.1167/iovs.61.10.46] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Purpose Proper balance between cell proliferation and differentiation is essential for corneal epithelial (CE) stratification and homeostasis. Although bone morphogenetic protein-6 (BMP6) is known to be expressed in the CE for over 25 years, its function in this tissue remains unknown. Here, we test the hypothesis that BMP6 promotes CE cell stratification and homeostasis by regulating their proliferation and differentiation. Methods We employed postnatal day-12 (PN-12), PN-14, PN-20, and PN-90 mouse eyes; human corneal limbal epithelial (HCLE) cells; and ocular surface fibrovascular disease pterygium tissues to evaluate the role of BMP6 in CE proliferation, differentiation, and pathology by RT-qPCR, immunoblots, and/or immunofluorescent staining. Cell proliferation was quantified by immunostaining for Ki67. Results Coincident with the mouse CE stratification between PN-12 and PN-20, BMP6 was significantly upregulated and the BMP6 antagonist Noggin downregulated. Mature CE retained high BMP6 and low Noggin expression at PN-90. BMP6 and its receptors BMPR1A and BMPR2 were upregulated during in vitro stratification of HCLE cells. Consistent with its anti-proliferative role, exogenous BMP6 suppressed HCLE cell proliferation, downregulated cyclin-D1 and cyclin-D2, and upregulated cell-cycle inhibitors Krüppel-like factor 4 (KLF4) and p21. BMP6 also upregulated the desmosomal cadherins desmoplakin and desmoglein in HCLE cells, consistent with its pro-differentiation role. Human pterygium displayed significant upregulation of BMP6 coupled with downregulation of Noggin and cell-cycle suppressors KLF4 and p21. Conclusions BMP6 coordinates CE stratification and homeostasis by regulating their proliferation and differentiation. BMP6 is significantly upregulated in human pterygium concurrent with downregulation of Noggin, KLF4, and p21.
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Affiliation(s)
- Anil Tiwari
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Sudha Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Gregory Campbell
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Vishal Jhanji
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Shivalingappa K Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States.,Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States.,Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States.,McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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23
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Tiwari A, Swamynathan S, Jhanji V, Swamynathan SK. KLF4 Coordinates Corneal Epithelial Apical-Basal Polarity and Plane of Cell Division and Is Downregulated in Ocular Surface Squamous Neoplasia. Invest Ophthalmol Vis Sci 2020; 61:15. [PMID: 32396634 PMCID: PMC7409308 DOI: 10.1167/iovs.61.5.15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose Previously, we demonstrated that Krüppel-like factor 4 (KLF4) promotes corneal epithelial (CE) homeostasis by suppressing epithelial-mesenchymal transition (EMT) and TGF-β signaling. As TGF-β affects epithelial apicobasal polarity (ABP) and plane of division, we investigated the role of KLF4 in these processes. Methods Klf4 was ablated in adult ternary transgenic Klf4Δ/ΔCE (Klf4LoxP/LoxP/Krt12rtTA/rtTA/Tet-O-Cre) mouse CE using doxycycline chow. ABP and plane of division markers’ expression in Klf4Δ/ΔCE and human ocular surface squamous neoplasia (OSSN) tissues relative to controls was evaluated by quantitative PCR, immunoblots, and/or immunofluorescent staining. Results Klf4Δ/ΔCE CE cells displayed downregulation of apical Pals1 and Crumbs1, apicolateral Par3, and basolateral Scribble, as well as upregulation of Rho family GTPase Cdc42, suggesting disruption of ABP. Phalloidin staining revealed that the Klf4Δ/ΔCE CE actin cytoskeleton is disrupted. Klf4Δ/ΔCE cells favored vertical plane of division within 67.5° to 90° of the CE basement membrane (39% and 47% of the dividing cells relative to 23% and 26% in the control based on phospho-histone-H3 and survivin, respectively), resulting in more dividing cells within the Klf4Δ/ΔCE CE as reported previously. KLF4 was downregulated in human OSSN tissues that displayed EMT and downregulation of PAR3, PALS1, and SCRIB, consistent with a protective role for KLF4. Conclusions By demonstrating that Klf4 ablation affects CE expression of ABP markers and Cdc42, cytoskeletal actin organization, and the plane of cell division and that KLF4 is downregulated in OSSN tissues that display EMT and lack ABP, these results elucidate the key integrative role of KLF4 in coordinating CE cell polarity and plane of division, loss of which results in OSSN.
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24
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Wang L, Ai M, Nie M, Zhao L, Deng G, Hu S, Han Y, Zeng W, Wang Y, Yang M, Wang S. EHF promotes colorectal carcinoma progression by activating TGF-β1 transcription and canonical TGF-β signaling. Cancer Sci 2020; 111:2310-2324. [PMID: 32372436 PMCID: PMC7385339 DOI: 10.1111/cas.14444] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/27/2020] [Accepted: 05/01/2020] [Indexed: 12/16/2022] Open
Abstract
ETS homologous factor (EHF) plays a critical function in epithelial cell differentiation and proliferation. However, the roles of EHF in cancer remain largely unknown. In the present study, we investigated the expression levels, precise function and mechanism of EHF in colorectal carcinoma (CRC). We observed significantly elevated EHF expression in CRC cell lines and tissues. EHF overexpression correlated positively with poor differentiation, advanced T stage, and shorter overall survival of CRC patients. Function experiments revealed that EHF overexpression promoted CRC cell proliferation, migration, and invasion in vitro and in vivo. Mechanistically, EHF could directly upregulate transforming growth factor β1 (TGF-β1) expression at the transcription level, thereby activating canonical TGF-β signaling. Our findings provide novel insights into the mechanisms of EHF in tumorigenesis, invasion, and metastasis of CRC, which may help to provide new therapeutic targets for CRC intervention.
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Affiliation(s)
- Lan Wang
- Department of PathologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Department of PathologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Meiling Ai
- Department of PathologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Department of PathologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Miaoting Nie
- Department of PathologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Department of PathologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Li Zhao
- Department of PathologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Guangxu Deng
- Department of General SurgeryNanfang Hospital, Southern Medical UniversityGuangzhouChina
| | - Shasha Hu
- Department of PathologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Department of PathologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Yue Han
- Department of PathologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Department of PathologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Weiting Zeng
- Department of PathologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Department of PathologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Yiqing Wang
- Department of PathologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Department of PathologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Minhui Yang
- Department of PathologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Department of PathologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Shuang Wang
- Department of PathologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Department of PathologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
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25
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Ten Kate CA, Brouwer RWW, van Bever Y, Martens VK, Brands T, van Beelen NWG, Brooks AS, Huigh D, van der Helm RM, Eussen BHFMM, van IJcken WFJ, IJsselstijn H, Tibboel D, Wijnen RMH, de Klein A, Hofstra RMW, Brosens E. Infantile hypertrophic pyloric stenosis in patients with esophageal atresia. Birth Defects Res 2020; 112:670-687. [PMID: 32298054 DOI: 10.1002/bdr2.1683] [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: 02/12/2020] [Revised: 03/25/2020] [Accepted: 04/02/2020] [Indexed: 11/07/2022]
Abstract
BACKGROUND Patients born with esophageal atresia (EA) have a higher incidence of infantile hypertrophic pyloric stenosis (IHPS), suggestive of a relationship. A shared etiology makes sense from a developmental perspective as both affected structures are foregut derived. A genetic component has been described for both conditions as single entities and EA and IHPS are variable components in several monogenetic syndromes. We hypothesized that defects disturbing foregut morphogenesis are responsible for this combination of malformations. METHODS We investigated the genetic variation of 15 patients with both EA and IHPS with unaffected parents using exome sequencing and SNP array-based genotyping, and compared the results to mouse transcriptome data of the developing foregut. RESULTS We did not identify putatively deleterious de novo mutations or recessive variants. However, we detected rare inherited variants in EA or IHPS disease genes or in genes important in foregut morphogenesis, expressed at the proper developmental time-points. Two pathways were significantly enriched (p < 1 × 10-5 ): proliferation and differentiation of smooth muscle cells and self-renewal of satellite cells. CONCLUSIONS None of our findings could fully explain the combination of abnormalities on its own, which makes complex inheritance the most plausible genetic explanation, most likely in combination with mechanical and/or environmental factors. As we did not find one defining monogenetic cause for the EA/IHPS phenotype, the impact of the corrective surgery could should be further investigated.
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Affiliation(s)
- Chantal A Ten Kate
- Department of Pediatric Surgery and Intensive Care Children, Erasmus University Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Vera K Martens
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tom Brands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nicole W G van Beelen
- Department of Pediatric Surgery and Intensive Care Children, Erasmus University Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Daphne Huigh
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert M van der Helm
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bert H F M M Eussen
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Hanneke IJsselstijn
- Department of Pediatric Surgery and Intensive Care Children, Erasmus University Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery and Intensive Care Children, Erasmus University Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Rene M H Wijnen
- Department of Pediatric Surgery and Intensive Care Children, Erasmus University Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert M W Hofstra
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
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26
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Phillips MA, Cánovas A, Rea MA, Islas-Trejo A, Medrano JF, Durbin-Johnson B, Rocke DM, Rice RH. Deducing signaling pathways from parallel actions of arsenite and antimonite in human epidermal keratinocytes. Sci Rep 2020; 10:2890. [PMID: 32076005 PMCID: PMC7031270 DOI: 10.1038/s41598-020-59577-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/29/2020] [Indexed: 11/09/2022] Open
Abstract
Inorganic arsenic oxides have been identified as carcinogens in several human tissues, including epidermis. Due to the chemical similarity between trivalent inorganic arsenic (arsenite) and antimony (antimonite), we hypothesized that common intracellular targets lead to similarities in cellular responses. Indeed, transcriptional and proteomic profiling revealed remarkable similarities in differentially expressed genes and proteins resulting from exposure of cultured human epidermal keratinocytes to arsenite and antimonite in contrast to comparisons of arsenite with other metal compounds. These data were analyzed to predict upstream regulators and affected signaling pathways following arsenite and antimonite treatments. A majority of the top findings in each category were identical after treatment with either compound. Inspection of the predicted upstream regulators led to previously unsuspected roles for oncostatin M, corticosteroids and ephrins in mediating cellular response. The influence of these predicted mediators was then experimentally verified. Together with predictions of transcription factor effects more generally, the analysis has led to model signaling networks largely accounting for arsenite and antimonite action. The striking parallels between responses to arsenite and antimonite indicate the skin carcinogenic risk of exposure to antimonite merits close scrutiny.
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Affiliation(s)
- Marjorie A Phillips
- Department of Environmental Toxicology, University of California, Davis, CA, USA
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Miguel A Rea
- Department of Chemistry, Universidad Autónoma Querétaro, Querétaro, Mexico
| | - Alma Islas-Trejo
- Department of Animal Science, University of California, Davis, CA, USA
| | - Juan F Medrano
- Department of Animal Science, University of California, Davis, CA, USA
| | - Blythe Durbin-Johnson
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California, Davis, CA, USA
| | - David M Rocke
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California, Davis, CA, USA
| | - Robert H Rice
- Department of Environmental Toxicology, University of California, Davis, CA, USA.
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27
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Binder RL, Freedman MA, Sharma KB, Farage MA, Wang Y, Combs C, Moore D, Tiesman JP, Bascom CC, Isfort RJ, Warren R. Histological and Gene Expression Analysis of the Effects of Menopause Status and Hormone Therapy on the Vaginal Introitus and Labia Majora. J Clin Med Res 2019; 11:745-759. [PMID: 31803317 PMCID: PMC6879024 DOI: 10.14740/jocmr4006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/27/2019] [Indexed: 12/19/2022] Open
Abstract
Background The study aimed to determine the effect of menopausal status and hormone therapy on the introitus and labia majora at the levels of histology and gene expression. Methods Three cohorts of 10 women each (pre-menopause, post-menopause and post-menopause + hormone therapy) were selected based on the presentation of clinical atrophy and vaginal pH. Biopsies were obtained from the introitus (fourchette) and labia majora and processed for histology and gene expression analyses with microarrays. Other data collected included self-assessed symptoms, serum estradiol, testosterone, serum hormone binding globulin and the pH of the vagina and labia majora. Results The introitus appears exquisitely sensitive to hormone status. Dramatic changes were observed in histology including a thinning of the epithelium in post-menopausal subjects with vaginal atrophy. Furthermore, there was differential expression of many genes that may contribute to tissue remodeling in the atrophic introitus. Levels of expression of genes associated with wound healing, angiogenesis, cell migration/locomotion, dermal structure, apoptosis, inflammation, epithelial cell differentiation, fatty acid, carbohydrate and steroid metabolism were significantly different in the cohort exhibiting atrophy of the introitus. While changes were also observed at the labia, that site was considerably less sensitive to hormone status. The gene expression changes observed at the introitus in this study were very similar to those reported previously in the atrophic vagina providing further evidence that these changes are associated with atrophy. Conclusions The histological and gene expression changes occurring within the introitus after menopause may contribute to the constellation of symptoms that constitute the genitourinary syndrome of menopause.
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Affiliation(s)
| | - Murray A Freedman
- Obstetrics & Gynecology, Medical College of Georgia, Augusta, GA, USA
| | - Kailash B Sharma
- Obstetrics & Gynecology, Medical College of Georgia, Augusta, GA, USA
| | | | - Yu Wang
- The Procter & Gamble Company, Cincinnati, OH, USA
| | | | - David Moore
- The Procter & Gamble Company, Cincinnati, OH, USA
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28
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Li L, Rispoli R, Patient R, Ciau-Uitz A, Porcher C. Etv6 activates vegfa expression through positive and negative transcriptional regulatory networks in Xenopus embryos. Nat Commun 2019; 10:1083. [PMID: 30842454 PMCID: PMC6403364 DOI: 10.1038/s41467-019-09050-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 02/15/2019] [Indexed: 01/09/2023] Open
Abstract
VEGFA signaling controls physiological and pathological angiogenesis and hematopoiesis. Although many context-dependent signaling pathways downstream of VEGFA have been uncovered, vegfa transcriptional regulation in vivo remains unclear. Here, we show that the ETS transcription factor, Etv6, positively regulates vegfa expression during Xenopus blood stem cell development through multiple transcriptional inputs. In agreement with its established repressive functions, Etv6 directly inhibits expression of the repressor foxo3, to prevent Foxo3 from binding to and repressing the vegfa promoter. Etv6 also directly activates expression of the activator klf4; reflecting a genome-wide paucity in ETS-binding motifs in Etv6 genomic targets, Klf4 then recruits Etv6 to the vegfa promoter to activate its expression. These two mechanisms (double negative gate and feed-forward loop) are classic features of gene regulatory networks specifying cell fates. Thus, Etv6's dual function, as a transcriptional repressor and activator, controls a major signaling pathway involved in endothelial and blood development in vivo.
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Affiliation(s)
- Lei Li
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Rossella Rispoli
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Division of Genetics and Molecular Medicine, NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, SE1 9RT, UK
| | - Roger Patient
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Aldo Ciau-Uitz
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Catherine Porcher
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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29
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Zeng F, Liu H, Lu D, Liu Q, Chen H, Zheng F. Integrated analysis of gene expression profiles identifies transcription factors potentially involved in psoriasis pathogenesis. J Cell Biochem 2019; 120:12582-12594. [PMID: 30825251 DOI: 10.1002/jcb.28525] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 01/03/2019] [Accepted: 02/07/2019] [Indexed: 02/04/2023]
Abstract
Psoriasis is a common inflammatory skin disease mediated by cells and molecules in both the innate and adaptive immune systems. Recently, gene expression profile analysis revealed a large set of immune-related differentially expressed genes (DEGs) in psoriasis. However, the associations between these DEGs and their transcriptional regulation mechanisms have not been completely elucidated. In this study, several psoriasis Gene Expression Omnibus data sets were systematically analyzed using bioinformatics tools to uncover important transcription factors (TFs) that regulate the expression of immune-related DEGs and further enhance our understanding of psoriasis pathogenesis. Common DEGs encoding chemokines, cytokines, antimicrobial peptides, and keratins were identified in psoriasis, and extensive correlations existed among these DEGs. Several common TFs that bind the promoters of the DEGs, including the well-known signal transducer and activator of transcription 1 (STAT1), STAT3, and nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) as well as ETS homologous factor (EHF), Fos-like antigen 1 (FOSL1), and Forkhead box C1 (FOXC1), which are rarely studied in psoriasis, were also identified. STAT1, EHF, FOSL1, STAT3, and NFKB1 were positively correlated with these DEGs in psoriasis lesions, whereas FOXC1 was negatively correlated with most DEGs. The decreased expression of the DEGs was accompanied by the downregulation of STAT1, EHF, FOSL1, STAT3, and NFKB1 and the upregulation of FOXC1 upon blocking interleukin 17 (IL-17) or tumor necrosis factor α signaling in psoriasis. Additionally, the downregulation of IL37 in psoriasis was negatively correlated with STAT1 and CXCL10, which are associated with Th1 responses. These results suggest that TFs play an important role in the pathogenesis of psoriasis, and interfering with the activity of key TFs may be a promising therapeutic strategy for psoriasis.
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Affiliation(s)
- Fanfan Zeng
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China.,Department of Clinical Medicine, Lingui Clinical Medical College, Guilin Medical University, Guilin, China
| | - Di Lu
- Department of Clinical Medicine, Lingui Clinical Medical College, Guilin Medical University, Guilin, China
| | - Qianqian Liu
- Department of Clinical Medicine, Lingui Clinical Medical College, Guilin Medical University, Guilin, China
| | - Huoying Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China.,Department of Clinical Medicine, Lingui Clinical Medical College, Guilin Medical University, Guilin, China
| | - Fang Zheng
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Organ Transplantation, Ministry of Education, Chinese Academy of Medical Sciences, Wuhan, China.,NHC Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China.,Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
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30
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Madison BJ, Clark KA, Bhachech N, Hollenhorst PC, Graves BJ, Currie SL. Electrostatic repulsion causes anticooperative DNA binding between tumor suppressor ETS transcription factors and JUN-FOS at composite DNA sites. J Biol Chem 2018; 293:18624-18635. [PMID: 30315111 DOI: 10.1074/jbc.ra118.003352] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/02/2018] [Indexed: 12/22/2022] Open
Abstract
Many different transcription factors (TFs) regulate gene expression in a combinatorial fashion, often by binding in close proximity to each other on composite cis-regulatory DNA elements. Here, we investigated how ETS TFs bind with the AP1 TFs JUN-FOS at composite DNA-binding sites. DNA-binding ability with JUN-FOS correlated with the phenotype of ETS proteins in prostate cancer. We found that the oncogenic ETS-related gene (ERG) and ETS variant (ETV) 1/4/5 subfamilies co-occupy ETS-AP1 sites with JUN-FOS in vitro, whereas JUN-FOS robustly inhibited DNA binding by the tumor suppressors ETS homologous factor (EHF) and SAM pointed domain-containing ETS TF (SPDEF). EHF bound ETS-AP1 DNA with tighter affinity than ERG in the absence of JUN-FOS, possibly enabling EHF to compete with ERG and JUN-FOS for binding to ETS-AP1 sites. Genome-wide mapping of EHF- and ERG-binding sites in prostate epithelial cells revealed that EHF is preferentially excluded from closely spaced ETS-AP1 DNA sequences. Structural modeling and mutational analyses indicated that adjacent positively charged surfaces from EHF and JUN-FOS use electrostatic repulsion to disfavor simultaneous DNA binding. Conservation of positive residues on the JUN-FOS interface identified E74-like ETS TF 1 (ELF1) as an additional ETS TF exhibiting anticooperative DNA binding with JUN-FOS, and we found that ELF1 is frequently down-regulated in prostate cancer. In summary, divergent electrostatic features of ETS TFs at their JUN-FOS interface enable distinct binding events at ETS-AP1 DNA sites, which may drive specific targeting of ETS TFs to facilitate distinct transcriptional programs.
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Affiliation(s)
- Bethany J Madison
- From the Department of Oncological Sciences and.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Kathleen A Clark
- From the Department of Oncological Sciences and.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Niraja Bhachech
- From the Department of Oncological Sciences and.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Peter C Hollenhorst
- the Medical Sciences program, Indiana University School of Medicine, Bloomington, Indiana 47405, and
| | - Barbara J Graves
- From the Department of Oncological Sciences and .,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112.,the Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
| | - Simon L Currie
- From the Department of Oncological Sciences and.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112
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31
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A transcription factor network represses CFTR gene expression in airway epithelial cells. Biochem J 2018; 475:1323-1334. [PMID: 29572268 DOI: 10.1042/bcj20180044] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/19/2018] [Accepted: 03/22/2018] [Indexed: 02/06/2023]
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause the inherited disorder cystic fibrosis (CF). Lung disease is the major cause of CF morbidity, though CFTR expression levels are substantially lower in the airway epithelium than in pancreatic duct and intestinal epithelia, which also show compromised function in CF. Recently developed small molecule therapeutics for CF are highly successful for one specific CFTR mutation and have a positive impact on others. However, the low abundance of CFTR transcripts in the airway limits the opportunity for drugs to correct the defective substrate. Elucidation of the transcriptional mechanisms for the CFTR locus has largely focused on intragenic and intergenic tissue-specific enhancers and their activating trans-factors. Here, we investigate whether the low CFTR levels in the airway epithelium result from the recruitment of repressive proteins directly to the locus. Using an siRNA screen to deplete ∼1500 transcription factors (TFs) and associated regulatory proteins in Calu-3 lung epithelial cells, we identified nearly 40 factors that upon depletion elevated CFTR mRNA levels more than 2-fold. A subset of these TFs was validated in primary human bronchial epithelial cells. Among the strongest repressors of airway expression of CFTR were Krüppel-like factor 5 and Ets homologous factor, both of which have pivotal roles in the airway epithelium. Depletion of these factors, which are both recruited to an airway-selective cis-regulatory element at -35 kb from the CFTR promoter, improved CFTR production and function, thus defining novel therapeutic targets for enhancement of CFTR.
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32
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Pellacani D, Bilenky M, Kannan N, Heravi-Moussavi A, Knapp DJHF, Gakkhar S, Moksa M, Carles A, Moore R, Mungall AJ, Marra MA, Jones SJM, Aparicio S, Hirst M, Eaves CJ. Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks. Cell Rep 2017; 17:2060-2074. [PMID: 27851968 DOI: 10.1016/j.celrep.2016.10.058] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 08/10/2016] [Accepted: 09/30/2016] [Indexed: 01/06/2023] Open
Abstract
The normal adult human mammary gland is a continuous bilayered epithelial system. Bipotent and myoepithelial progenitors are prominent and unique components of the outer (basal) layer. The inner (luminal) layer includes both luminal-restricted progenitors and a phenotypically separable fraction that lacks progenitor activity. We now report an epigenomic comparison of these three subsets with one another, with their associated stromal cells, and with three immortalized, non-tumorigenic human mammary cell lines. Each genome-wide analysis contains profiles for six histone marks, methylated DNA, and RNA transcripts. Analysis of these datasets shows that each cell type has unique features, primarily within genomic regulatory regions, and that the cell lines group together. Analyses of the promoter and enhancer profiles place the luminal progenitors in between the basal cells and the non-progenitor luminal subset. Integrative analysis reveals networks of subset-specific transcription factors.
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Affiliation(s)
- Davide Pellacani
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Misha Bilenky
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Nagarajan Kannan
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Alireza Heravi-Moussavi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - David J H F Knapp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Sitanshu Gakkhar
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Michelle Moksa
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Annaick Carles
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Connie J Eaves
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
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33
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Loughner CL, Tiwari A, Kenchegowda D, Swamynathan S, Swamynathan SK. Spatiotemporally Controlled Ablation of Klf5 Results in Dysregulated Epithelial Homeostasis in Adult Mouse Corneas. Invest Ophthalmol Vis Sci 2017; 58:4683-4693. [PMID: 28910443 PMCID: PMC5598321 DOI: 10.1167/iovs.17-22498] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Purpose Corneal epithelial (CE) homeostasis requires coordination between proliferation and differentiation. Here we examine the role of cell proliferation regulator Krüppel-like factor 5 (Klf5) in adult mouse CE homeostasis. Methods Klf5 was ablated in a spatiotemporally restricted manner by inducing Cre expression in 8-week-old ternary transgenic Klf5LoxP/LoxP/Krt12rtTA/rtTA/Tet-O-Cre (Klf5Δ/ΔCE) mouse CE by administering doxycycline via chow. Normal chow-fed ternary transgenic siblings served as controls. The control and Klf5Δ/ΔCE corneal (1) histology, (2) cell proliferation, and (3) Klf5-target gene expression were examined using (1) periodic acid Schiff reagent-stained sections, (2) Ki67 expression, and (3) quantitative PCR and immunostaining, respectively. The effect of KLF4, KLF5, and OCT1 on gastrokine-1 (GKN1) promoter activity was determined by transient transfection in human skin keratinocyte NCTC-2544 cells. Results Klf5 expression was decreased to 23% of the controls in Klf5Δ/ΔCE corneas, which displayed increased fluorescein uptake, downregulation of tight junction proteins Tjp1 and Gkn1, desmosomal Dsg1a, and basement membrane Lama3 and Lamb1, suggesting defective permeability barrier. In transient transfection assays, KLF5 and OCT1 synergistically stimulated GKN1 promoter activity. Klf5Δ/ΔCE CE displayed significantly fewer cell layers and Ki67+ proliferative cells coupled with significantly decreased cyclin-D1, and elevated phospho(Ser-10) p27/Kip1 expression. Expression of Krt12, E-cadherin, and β-catenin remained unaltered in Klf5Δ/ΔCE corneas. Conclusions Klf5 contributes to adult mouse CE homeostasis by promoting (1) permeability barrier function through upregulation of Tjp1, Gkn1, Dsg1a, Lama3, and Lamb1, and (2) basal cell proliferation through upregulation of cyclin-D1 and suppression of phospho(Ser-10) p27/Kip1, without significantly affecting the expression of epithelial markers Krt12, E-cadherin, and β-catenin.
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Affiliation(s)
- Chelsea L Loughner
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Anil Tiwari
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Doreswamy Kenchegowda
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Sudha Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Shivalingappa K Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, United States.,McGowan Institute of Regenerative Medicine, University of Pittsburgh, United States.,Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States.,Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, United States
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34
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Klein RH, Hu W, Kashgari G, Lin Z, Nguyen T, Doan M, Andersen B. Characterization of enhancers and the role of the transcription factor KLF7 in regulating corneal epithelial differentiation. J Biol Chem 2017; 292:18937-18950. [PMID: 28916725 DOI: 10.1074/jbc.m117.793117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 09/11/2017] [Indexed: 02/01/2023] Open
Abstract
During tissue development, transcription factors bind regulatory DNA regions called enhancers, often located at great distances from the genes they regulate, to control gene expression. The enhancer landscape during embryonic stem cell differentiation has been well characterized. By contrast, little is known about the shared and unique enhancer regulatory mechanisms in different ectodermally derived epithelial cells. Here we use ChIP sequencing (ChIP-seq) to identify domains enriched for the histone marks histone H3 lysine 4 trimethylation, histone H3 lysine 4 monomethylation, and histone H3 lysine 27 acetylation (H3K4me3, H3K4me1, and H3K27ac) and define, for the first time, the super enhancers and typical enhancers active in primary human corneal epithelial cells. We show that regulatory regions are often shared between cell types of the ectodermal lineage and that corneal epithelial super enhancers are already marked as potential regulatory domains in embryonic stem cells. Kruppel-like factor (KLF) motifs were enriched in corneal epithelial enhancers, consistent with the important roles of KLF4 and KLF5 in promoting corneal epithelial differentiation. We now show that the Kruppel family member KLF7 promotes the corneal progenitor cell state; on many genes, KLF7 antagonized the corneal differentiation-promoting KLF4. Furthermore, we found that two SNPs linked previously to corneal diseases, astigmatism, and Stevens-Johnson syndrome fall within corneal epithelial enhancers and alter their activity by disrupting transcription factor motifs that overlap these SNPs. Taken together, our work defines regulatory enhancers in corneal epithelial cells, highlights global gene-regulatory relationships shared among different epithelial cells, identifies a role for KLF7 as a KLF4 antagonist in corneal epithelial cell differentiation, and explains how two SNPs may contribute to corneal diseases.
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Affiliation(s)
- Rachel Herndon Klein
- From the Departments of Biological Chemistry and.,Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697
| | - William Hu
- From the Departments of Biological Chemistry and
| | | | - Ziguang Lin
- From the Departments of Biological Chemistry and
| | - Tuyen Nguyen
- From the Departments of Biological Chemistry and.,Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697
| | - Michael Doan
- From the Departments of Biological Chemistry and
| | - Bogi Andersen
- From the Departments of Biological Chemistry and .,Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697.,Medicine, Division of Endocrinology, and
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35
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Gong YC, Ren GL, Liu B, Li F, Zhao HP, Chen JB, Li YP, Yu HH. miR‑206 inhibits cancer initiating cells by targeting EHF in gastric cancer. Oncol Rep 2017; 38:1688-1694. [PMID: 28714026 DOI: 10.3892/or.2017.5794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 06/08/2017] [Indexed: 11/05/2022] Open
Abstract
Cancer initiating cells (CIC) are defined as the unique subpopulation in the tumors that possess the ability to initiate tumor growth and sustain self-renewal as well as metastatic potential. In this study, we found that EHF overexpression promoted formation of CIC traits and silencing it inhibited the traits in gastric cancer NCI‑N87 cells. Overexpressing EHF downregulated the antitumor effect of 5-fluorouracil (5-FU) in NCI‑N87 cells. We found that miR‑206 downregulated EHF protein expression by targeting its 3'UTR in NCI‑N87 cells and GES-1 cells. Overexpressing miR‑206 inhibited formation of CIC in NCI‑N87 cells. In gastric cancer tissues, EHF protein expression was upregulated and miR‑206 was downregulated. We identified a negative correlation between EHF protein and miR‑206 expression in gastric cancer tissues. Thus, we concluded that miR‑206 inhibits formation of CICs by targeting EHF in gastric cancer.
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Affiliation(s)
- Yan-Cui Gong
- Health Management Center, Linyi Central Hospital, Linyi, Shandong 276400, P.R. China
| | - Guo-Liang Ren
- Intensive Care Unit (ICU), Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Bo Liu
- Department of Gastrointestinal Surgery, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| | - Feng Li
- Department of Gastrointestinal Surgery, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| | - Hong-Peng Zhao
- Department of Gastrointestinal Surgery, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| | - Jing-Bo Chen
- Department of Gastrointestinal Surgery, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| | - Yu-Peng Li
- Department of Gastrointestinal Surgery, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| | - Hai-Hua Yu
- Department of Gastrointestinal Surgery, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
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36
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Tiwari A, Loughner CL, Swamynathan S, Swamynathan SK. KLF4 Plays an Essential Role in Corneal Epithelial Homeostasis by Promoting Epithelial Cell Fate and Suppressing Epithelial-Mesenchymal Transition. Invest Ophthalmol Vis Sci 2017; 58:2785-2795. [PMID: 28549095 PMCID: PMC5455171 DOI: 10.1167/iovs.17-21826] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Purpose The purpose of this study was to test the hypothesis that KLF4 promotes corneal epithelial (CE) cell fate by suppressing the epithelial–mesenchymal transition (EMT), using spatiotemporally regulated CE-specific ablation of Klf4 in Klf4Δ/ΔCE (Klf4LoxP/LoxP/Krt12rtTA/rtTA/Tet-O-Cre) mice. Methods CE-specific ablation of Klf4 was achieved by feeding Klf4Δ/ΔCE mice with doxycycline chow. The wild-type (WT; normal chow-fed littermates) and the Klf4Δ/ΔCE histology was compared by hematoxylin and eosin–stained sections; EMT marker expression was quantified by quantitative PCR, immunoblots, and immunofluorescent staining; and wound healing rate was measured by CE debridement using Algerbrush. KLF4 and EMT markers were quantified in human corneal limbal epithelial (HCLE) cells undergoing TGF-β1–induced EMT by quantitative PCR, immunoblots, and immunofluorescent staining. Results The epithelial markers E-cadherin, Krt12, claudin-3, and claudin-4 were down-regulated, whereas the mesenchymal markers vimentin, β-catenin, survivin, and cyclin-D1 and the EMT transcription factors Snail, Slug, Twist1, Twist2, Zeb1, and Zeb2 were up-regulated in the Klf4Δ/ΔCE corneas. The Klf4Δ/ΔCE cells migrated faster, filling 93% of the debrided area within 16 hours compared with 61% in the WT. After 7 days of wounding, the Klf4Δ/ΔCE cells that filled the gap failed to regain epithelial characteristics, as they displayed abnormal stratification; down-regulation of E-cadherin and Krt12; up-regulation of β-catenin, survivin, and cyclin-D1; and a 2.5-fold increase in the number of proliferative Ki67+ cells. WT CE cells at the migrating edge and the HCLE cells undergoing TGF-β1–induced EMT displayed significant down-regulation of KLF4. Conclusions Collectively, these results reveal that KLF4 plays an essential role in CE homeostasis by promoting epithelial cell fate and suppressing EMT.
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Affiliation(s)
- Anil Tiwari
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Chelsea L Loughner
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Sudha Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Shivalingappa K Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States 2McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States 3Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States 4Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
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Fossum SL, Mutolo MJ, Tugores A, Ghosh S, Randell SH, Jones LC, Leir SH, Harris A. Ets homologous factor (EHF) has critical roles in epithelial dysfunction in airway disease. J Biol Chem 2017; 292:10938-10949. [PMID: 28461336 DOI: 10.1074/jbc.m117.775304] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 04/27/2017] [Indexed: 12/16/2022] Open
Abstract
The airway epithelium forms a barrier between the internal and external environments. Epithelial dysfunction is critical in the pathology of many respiratory diseases, including cystic fibrosis. Ets homologous factor (EHF) is a key member of the transcription factor network that regulates gene expression in the airway epithelium in response to endogenous and exogenous stimuli. EHF, which has altered expression in inflammatory states, maps to the 5' end of an intergenic region on Chr11p13 that is implicated as a modifier of cystic fibrosis airway disease. Here we determine the functions of EHF in primary human bronchial epithelial (HBE) cells and relevant airway cell lines. Using EHF ChIP followed by deep sequencing (ChIP-seq) and RNA sequencing after EHF depletion, we show that EHF targets in HBE cells are enriched for genes involved in inflammation and wound repair. Furthermore, changes in gene expression impact cell phenotype because EHF depletion alters epithelial secretion of a neutrophil chemokine and slows wound closure in HBE cells. EHF activates expression of the SAM pointed domain-containing ETS transcription factor, which contributes to goblet cell hyperplasia. Our data reveal a critical role for EHF in regulating epithelial function in lung disease.
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Affiliation(s)
- Sara L Fossum
- From the Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois 60614.,the Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Michael J Mutolo
- From the Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois 60614.,the Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Antonio Tugores
- the Unidad de Investigación, Complejo Hospitalario Universitario Insular Materno Infantil, 35016 Las Palmas de Gran Canaria, Spain
| | - Sujana Ghosh
- From the Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois 60614.,the Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Scott H Randell
- the Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599, and
| | - Lisa C Jones
- the Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599, and
| | - Shih-Hsing Leir
- From the Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois 60614.,the Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611.,the Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44016
| | - Ann Harris
- From the Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois 60614, .,the Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611.,the Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44016
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Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation, and Homeostasis by PTF1A. Mol Cell Biol 2016; 36:3033-3047. [PMID: 27697859 DOI: 10.1128/mcb.00358-16] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/23/2016] [Indexed: 12/17/2022] Open
Abstract
Maintenance of cell type identity is crucial for health, yet little is known of the regulation that sustains the long-term stability of differentiated phenotypes. To investigate the roles that key transcriptional regulators play in adult differentiated cells, we examined the effects of depletion of the developmental master regulator PTF1A on the specialized phenotype of the adult pancreatic acinar cell in vivo Transcriptome sequencing and chromatin immunoprecipitation sequencing results showed that PTF1A maintains the expression of genes for all cellular processes dedicated to the production of the secretory digestive enzymes, a highly attuned surveillance of unfolded proteins, and a heightened unfolded protein response (UPR). Control by PTF1A is direct on target genes and indirect through a ten-member transcription factor network. Depletion of PTF1A causes an imbalance that overwhelms the UPR, induces cellular injury, and provokes acinar metaplasia. Compromised cellular identity occurs by derepression of characteristic stomach genes, some of which are also associated with pancreatic ductal cells. The loss of acinar cell homeostasis, differentiation, and identity is directly relevant to the pathologies of pancreatitis and pancreatic adenocarcinoma.
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Increased expression of EHF via gene amplification contributes to the activation of HER family signaling and associates with poor survival in gastric cancer. Cell Death Dis 2016; 7:e2442. [PMID: 27787520 PMCID: PMC5134001 DOI: 10.1038/cddis.2016.346] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 09/04/2016] [Accepted: 09/26/2016] [Indexed: 01/29/2023]
Abstract
The biological function of E26 transformation-specific (ETS) transcription factor EHF/ESE-3 in human cancers remains largely unknown, particularly gastric cancer. The aim of this study was to explore the role of EHF in tumorigenesis and its potential as a therapeutic target in gastric cancer. By using quantitative RT-PCR (qRT-PCR), immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) assays, we investigated the expression and copy number of EHF in a cohort of gastric cancers and control subjects. Specific EHF siRNAs was used to determine the biologic impacts and mechanisms of altered EHF expression in vitro and in vivo. Dual-luciferase reporter, chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assay (EMSA) assays were performed to identify its downstream targets. Our results demonstrated that EHF was significantly upregulated and frequently amplified in gastric cancer tissues as compared with control subjects. Moreover, EHF amplification was positively correlated with its overexpression and significantly associated with poor clinical outcomes of gastric cancer patients. We also found that EHF knockdown notably inhibited gastric cancer cell proliferation, colony formation, migration, invasion and tumorigenic potential in nude mice and induced cell cycle arrest and apoptosis. Importantly, we identified EHF as a new HER2 transcription factor and the modulator of HER3 and HER4 in gastric cancer. Collectively, our findings suggest that EHF is a novel functional oncogene in gastric cancer by regulating the human epidermal growth factor receptor (HER) family of receptor tyrosine kinases and may represent a potential prognostic marker and therapeutic target for this cancer.
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Novel variation at chr11p13 associated with cystic fibrosis lung disease severity. Hum Genome Var 2016; 3:16020. [PMID: 27408752 PMCID: PMC4935763 DOI: 10.1038/hgv.2016.20] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 12/28/2022] Open
Abstract
Published genome-wide association studies (GWASs) identified an intergenic region with regulatory features on chr11p13 associated with cystic fibrosis (CF) lung disease severity. Targeted resequencing in n=377, followed by imputation to n=6,365 CF subjects, was used to identify unrecognized genetic variants (including indels and microsatellite repeats) associated with phenotype. Highly significant associations were in strong linkage disequilibrium and were seen only in Phe508del homozygous CF subjects, indicating a CFTR genotype-specific mechanism.
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Klein RH, Stephens DN, Ho H, Chen JK, Salmans ML, Wang W, Yu Z, Andersen B. Cofactors of LIM Domains Associate with Estrogen Receptor α to Regulate the Expression of Noncoding RNA H19 and Corneal Epithelial Progenitor Cell Function. J Biol Chem 2016; 291:13271-85. [PMID: 27129775 DOI: 10.1074/jbc.m115.709386] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Indexed: 11/06/2022] Open
Abstract
Cofactors of LIM domain proteins, CLIM1 and CLIM2, are widely expressed transcriptional cofactors that are recruited to gene regulatory regions by DNA-binding proteins, including LIM domain transcription factors. In the cornea, epithelium-specific expression of a dominant negative (DN) CLIM under the keratin 14 (K14) promoter causes blistering, wounding, inflammation, epithelial hyperplasia, and neovascularization followed by epithelial thinning and subsequent epidermal-like differentiation of the corneal epithelium. The defects in corneal epithelial differentiation and cell fate determination suggest that CLIM may regulate corneal progenitor cells and the transition to differentiation. Consistent with this notion, the K14-DN-Clim corneal epithelium first exhibits increased proliferation followed by fewer progenitor cells with decreased proliferative potential. In vivo ChIP-sequencing experiments with corneal epithelium show that CLIM binds to and regulates numerous genes involved in cell adhesion and proliferation, including limbally enriched genes. Intriguingly, CLIM associates primarily with non-LIM homeodomain motifs in corneal epithelial cells, including that of estrogen receptor α. Among CLIM targets is the noncoding RNA H19 whose deregulation is associated with Silver-Russell and Beckwith-Wiedemann syndromes. We demonstrate here that H19 negatively regulates corneal epithelial proliferation. In addition to cell cycle regulators, H19 affects the expression of multiple cell adhesion genes. CLIM interacts with estrogen receptor α at the H19 locus, potentially explaining the higher expression of H19 in female than male corneas. Together, our results demonstrate an important role for CLIM in regulating the proliferative potential of corneal epithelial progenitors and identify CLIM downstream target H19 as a regulator of corneal epithelial proliferation and adhesion.
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Affiliation(s)
- Rachel Herndon Klein
- From the Departments of Biological Chemistry and Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697 and
| | | | | | | | - Michael L Salmans
- From the Departments of Biological Chemistry and Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697 and
| | - Winnie Wang
- From the Departments of Biological Chemistry and
| | - Zhengquan Yu
- From the Departments of Biological Chemistry and State Key Laboratories for AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Bogi Andersen
- From the Departments of Biological Chemistry and Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697 and Medicine and
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Swamynathan S, Delp EE, Harvey SAK, Loughner CL, Raju L, Swamynathan SK. Corneal Expression of SLURP-1 by Age, Sex, Genetic Strain, and Ocular Surface Health. Invest Ophthalmol Vis Sci 2016; 56:7888-96. [PMID: 26670825 DOI: 10.1167/iovs.15-18206] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Although secreted Ly6/urokinase-type plasminogen activator receptor-related protein-1 (Slurp1) transcript is highly abundant in the mouse cornea, corresponding protein expression remains uncharacterized. Also, SLURP1 was undetected in previous tear proteomics studies, resulting in ambiguity about its baseline levels. Here, we examine mouse corneal Slurp1 expression in different sexes, age groups, strains, and health conditions, and quantify SLURP1 in human tears from healthy or inflamed ocular surfaces. METHODS Expression of Slurp1 in embryonic day-13 (E13), E16, postnatal day-1 (PN1), PN10, PN20, and PN70 Balb/C, FVBN, C57Bl/6, and DBA/2J mouse corneas, Klf4Δ/ΔCE corneas with corneal epithelial-specific ablation of Klf4, migrating cells in wild-type corneal epithelial wound edge, and in corneas exposed to pathogen-associated molecular patterns (PAMPs) poly(I:C), zymosan-A, or Pam3Csk4 was examined by QPCR, immunoblots, and immunofluorescent staining. Human SLURP1 levels were quantified by ELISA in tears from 34 men and women aged 18 to 80 years. RESULTS Expression of Slurp1, comparable in different strains and sexes, was low in E13, E16, PN1, and PN10 mouse corneas, and increased rapidly after eyelid opening in a Klf4-dependent manner. We found Slurp1 was downregulated in corneas exposed to PAMPs, and in migrating cells at the wound edge. Human SLURP1 expression, comparable in different sexes and age groups, was significantly decreased in tears from inflamed ocular surfaces (0.34%) than those from healthy individuals (0.77%). CONCLUSIONS These data describe the influence of age, sex, genetic background, and ocular surface health on mouse corneal expression of Slurp1, establish the baseline for human tear SLURP1 expression, and identify SLURP1 as a useful diagnostic and/or therapeutic target for inflammatory ocular surface disorders.
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Affiliation(s)
- Sudha Swamynathan
- Department of Ophthalmology University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Emili E Delp
- Department of Ophthalmology University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Stephen A K Harvey
- Department of Ophthalmology University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Chelsea L Loughner
- Department of Ophthalmology University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Leela Raju
- Department of Ophthalmology University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Shivalingappa K Swamynathan
- Department of Ophthalmology University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States 2McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States 3Department of Cell Biology, Un
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Delp EE, Swamynathan S, Kao WW, Swamynathan SK. Spatiotemporally Regulated Ablation of Klf4 in Adult Mouse Corneal Epithelial Cells Results in Altered Epithelial Cell Identity and Disrupted Homeostasis. Invest Ophthalmol Vis Sci 2015; 56:3549-58. [PMID: 26047041 DOI: 10.1167/iovs.15-16463] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
PURPOSE In previous studies, conditional disruption of Klf4 in the developing mouse ocular surface from embryonic day 10 resulted in corneal epithelial fragility, stromal edema, and loss of conjunctival goblet cells, revealing the importance of Klf4 in ocular surface maturation. Here, we use spatiotemporally regulated ablation of Klf4 to investigate its functions in maintenance of adult corneal epithelial homeostasis. METHODS Expression of Cre was induced in ternary transgenic (Klf4(LoxP/LoxP)/Krt12(rtTA/rtTA)/Tet-O-Cre) mouse corneal epithelium by doxycycline administered through intraperitoneal injections and drinking water, to generate corneal epithelium-specific deletion of Klf4 (Klf4(Δ/ΔCE)). Corneal epithelial barrier function was tested by fluorescein staining. Expression of selected Klf4-target genes was determined by quantitative PCR (QPCR), immunoblotting, and immunofluorescent staining. RESULTS Klf4 was efficiently ablated within 5 days of doxycycline administration in adult Klf4(Δ/ΔCE) corneal epithelium. The Klf4(Δ/ΔCE) corneal epithelial barrier function was disrupted, and the basal cells were swollen and rounded after 15 days of doxycycline treatment. Increased numbers of cell layers and Ki67-positive proliferating cells suggested deregulated Klf4(Δ/ΔCE) corneal epithelial homeostasis. Expression of tight junction proteins ZO-1 and occludin, desmosomal Dsg and Dsp, basement membrane laminin-332, and corneal epithelial-specific keratin-12 was decreased, while that of matrix metalloproteinase Mmp9 and noncorneal keratin-17 increased, suggesting altered Klf4(Δ/ΔCE) corneal epithelial cell identity. CONCLUSIONS Ablation of Klf4 in the adult mouse corneas resulted in the absence of characteristic corneal epithelial cell differentiation, disrupted barrier function, and squamous metaplasia, revealing that Klf4 is essential for maintenance of the adult corneal epithelial cell identity and homeostasis.
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Affiliation(s)
- Emili E Delp
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Sudha Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Winston W Kao
- Department of Ophthalmology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
| | - Shivalingappa K Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States 3McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States 4Department of Cell Biology, U
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Yamazaki S, Nakano N, Honjo A, Hara M, Maeda K, Nishiyama C, Kitaura J, Ohtsuka Y, Okumura K, Ogawa H, Shimizu T. The Transcription Factor Ehf Is Involved in TGF-β–Induced Suppression of FcεRI and c-Kit Expression and FcεRI-Mediated Activation in Mast Cells. THE JOURNAL OF IMMUNOLOGY 2015; 195:3427-35. [DOI: 10.4049/jimmunol.1402856] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 07/28/2015] [Indexed: 01/21/2023]
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Swindell WR, Sarkar MK, Stuart PE, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE. Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites. Clin Transl Med 2015; 4:13. [PMID: 25883770 PMCID: PMC4392043 DOI: 10.1186/s40169-015-0054-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/26/2015] [Indexed: 12/22/2022] Open
Abstract
Background Psoriasis is a cytokine-mediated skin disease that can be treated effectively with immunosuppressive biologic agents. These medications, however, are not equally effective in all patients and are poorly suited for treating mild psoriasis. To develop more targeted therapies, interfering with transcription factor (TF) activity is a promising strategy. Methods Meta-analysis was used to identify differentially expressed genes (DEGs) in the lesional skin from psoriasis patients (n = 237). We compiled a dictionary of 2935 binding sites representing empirically-determined binding affinities of TFs and unconventional DNA-binding proteins (uDBPs). This dictionary was screened to identify “psoriasis response elements” (PREs) overrepresented in sequences upstream of psoriasis DEGs. Results PREs are recognized by IRF1, ISGF3, NF-kappaB and multiple TFs with helix-turn-helix (homeo) or other all-alpha-helical (high-mobility group) DNA-binding domains. We identified a limited set of DEGs that encode proteins interacting with PRE motifs, including TFs (GATA3, EHF, FOXM1, SOX5) and uDBPs (AVEN, RBM8A, GPAM, WISP2). PREs were prominent within enhancer regions near cytokine-encoding DEGs (IL17A, IL19 and IL1B), suggesting that PREs might be incorporated into complex decoy oligonucleotides (cdODNs). To illustrate this idea, we designed a cdODN to concomitantly target psoriasis-activated TFs (i.e., FOXM1, ISGF3, IRF1 and NF-kappaB). Finally, we screened psoriasis-associated SNPs to identify risk alleles that disrupt or engender PRE motifs. This identified possible sites of allele-specific TF/uDBP binding and showed that PREs are disproportionately disrupted by psoriasis risk alleles. Conclusions We identified new TF/uDBP candidates and developed an approach that (i) connects transcriptome informatics to cdODN drug development and (ii) enhances our ability to interpret GWAS findings. Disruption of PRE motifs by psoriasis risk alleles may contribute to disease susceptibility. Electronic supplementary material The online version of this article (doi:10.1186/s40169-015-0054-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William R Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Mrinal K Sarkar
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - James T Elder
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Andrew Johnston
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
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Fossum SL, Mutolo MJ, Yang R, Dang H, O'Neal WK, Knowles MR, Leir SH, Harris A. Ets homologous factor regulates pathways controlling response to injury in airway epithelial cells. Nucleic Acids Res 2014; 42:13588-98. [PMID: 25414352 PMCID: PMC4267623 DOI: 10.1093/nar/gku1146] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Ets homologous factor (EHF) is an Ets family transcription factor expressed in many epithelial cell types including those lining the respiratory system. Disruption of the airway epithelium is central to many lung diseases, and a network of transcription factors coordinates its normal function. EHF can act as a transcriptional activator or a repressor, though its targets in lung epithelial cells are largely uncharacterized. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq), showed that the majority of EHF binding sites in lung epithelial cells are intergenic or intronic and coincide with putative enhancers, marked by specific histone modifications. EHF occupies many genomic sites that are close to genes involved in intercellular and cell–matrix adhesion. RNA-seq after EHF depletion or overexpression showed significant alterations in the expression of genes involved in response to wounding. EHF knockdown also targeted genes in pathways of epithelial development and differentiation and locomotory behavior. These changes in gene expression coincided with alterations in cellular phenotype including slowed wound closure and increased transepithelial resistance. Our data suggest that EHF regulates gene pathways critical for epithelial response to injury, including those involved in maintenance of barrier function, inflammation and efficient wound repair.
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Affiliation(s)
- Sara L Fossum
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Michael J Mutolo
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
| | - Rui Yang
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wanda K O'Neal
- Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael R Knowles
- Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shih-Hsing Leir
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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