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Meng F, Ren S. Identification of hub genes and molecular pathways in keratoconus by integrating bioinformatics and literature mining at the RNA level. Int Ophthalmol 2024; 44:244. [PMID: 38904678 DOI: 10.1007/s10792-024-03071-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/16/2024] [Indexed: 06/22/2024]
Abstract
OBJECTIVE Keratoconus (KC) is a condition characterized by progressive corneal steepening and thinning. However, its pathophysiological mechanism remains vague. We mainly performed literature mining to extract bioinformatic and related data on KC at the RNA level. The objective of this study was to explore the potential pathological mechanisms of KC by identifying hub genes and key molecular pathways at the RNA level. METHODS We performed an exhaustive search of the PubMed database and identified studies that pertained to gene transcripts derived from diverse corneal layers in patients with KC. The identified differentially expressed genes were intersected, and overlapping genes were extracted for further analyses. Significantly enriched genes were screened using "Gene Ontology" (GO) and "Kyoto Encyclopedia of Genes and Genomes" (KEGG) analysis with the "Database for Annotation, Visualization, and Integrated Discovery" (DAVID) database. A protein-protein interaction (PPI) network was constructed for the significantly enriched genes using the STRING database. The PPI network was visualized using the Cytoscape software, and hub genes were screened via betweenness centrality values. Pathways that play a critical role in the pathophysiology of KC were discovered using the GO and KEGG analyses of the hub genes. RESULTS 68 overlapping genes were obtained. Fifty genes were significantly enriched in 67 biological processes, and 16 genes were identified in 7 KEGG pathways. Moreover, 14 nodes and 32 edges were identified via the PPI network constructed using the STRING database. Multiple analyses identified 4 hub genes, 12 enriched biological processes, and 6 KEGG pathways. GO enrichment analysis showed that the hub genes are mainly involved in the positive regulation of apoptotic process, and KEGG analysis showed that the hub genes are primarily associated with the interleukin-17 (IL-17) and tumor necrosis factor (TNF) pathways. Overall, the matrix metalloproteinase 9, IL-6, estrogen receptor 1, and prostaglandin-endoperoxide synthase 2 were the potential important genes associated with KC. CONCLUSION Four genes, matrix metalloproteinase 9, IL-6, estrogen receptor 1, and prostaglandin endoperoxide synthase 2, as well as IL-17 and TNF pathways, are critical in the development of KC. Inflammation and apoptosis may contribute to the pathogenesis of KC.
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Affiliation(s)
- Feiying Meng
- Henan Eye Hospital, Henan Provincial People's Hospital/People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
- Eye Institute, Henan Academy of Innovations in Medical Science, Zhengzhou, China
| | - Shengwei Ren
- Henan Eye Hospital, Henan Provincial People's Hospital/People's Hospital of Zhengzhou University, Zhengzhou, 450003, China.
- Eye Institute, Henan Academy of Innovations in Medical Science, Zhengzhou, China.
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Thomasy SM, Leonard BC, Greiner MA, Skeie JM, Raghunathan VK. Squishy matters - Corneal mechanobiology in health and disease. Prog Retin Eye Res 2024; 99:101234. [PMID: 38176611 PMCID: PMC11193890 DOI: 10.1016/j.preteyeres.2023.101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024]
Abstract
The cornea, as a dynamic and responsive tissue, constantly interacts with mechanical forces in order to maintain its structural integrity, barrier function, transparency and refractive power. Cells within the cornea sense and respond to various mechanical forces that fundamentally regulate their morphology and fate in development, homeostasis and pathophysiology. Corneal cells also dynamically regulate their extracellular matrix (ECM) with ensuing cell-ECM crosstalk as the matrix serves as a dynamic signaling reservoir providing biophysical and biochemical cues to corneal cells. Here we provide an overview of mechanotransduction signaling pathways then delve into the recent advances in corneal mechanobiology, focusing on the interplay between mechanical forces and responses of the corneal epithelial, stromal, and endothelial cells. We also identify species-specific differences in corneal biomechanics and mechanotransduction to facilitate identification of optimal animal models to study corneal wound healing, disease, and novel therapeutic interventions. Finally, we identify key knowledge gaps and therapeutic opportunities in corneal mechanobiology that are pressing for the research community to address especially pertinent within the domains of limbal stem cell deficiency, keratoconus and Fuchs' endothelial corneal dystrophy. By furthering our understanding corneal mechanobiology, we can contextualize discoveries regarding corneal diseases as well as innovative treatments for them.
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Affiliation(s)
- Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California - Davis, Davis, CA, United States; Department of Ophthalmology & Vision Science, School of Medicine, University of California - Davis, Davis, CA, United States; California National Primate Research Center, Davis, CA, United States.
| | - Brian C Leonard
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California - Davis, Davis, CA, United States; Department of Ophthalmology & Vision Science, School of Medicine, University of California - Davis, Davis, CA, United States
| | - Mark A Greiner
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, United States; Iowa Lions Eye Bank, Coralville, IA, United States
| | - Jessica M Skeie
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, United States; Iowa Lions Eye Bank, Coralville, IA, United States
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Loiseau A, Raîche-Marcoux G, Maranda C, Bertrand N, Boisselier E. Animal Models in Eye Research: Focus on Corneal Pathologies. Int J Mol Sci 2023; 24:16661. [PMID: 38068983 PMCID: PMC10706114 DOI: 10.3390/ijms242316661] [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: 09/15/2023] [Revised: 09/27/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
The eye is a complex sensory organ that enables visual perception of the world. The dysfunction of any of these tissues can impair vision. Conduction studies on laboratory animals are essential to ensure the safety of therapeutic products directly applied or injected into the eye to treat ocular diseases before eventually proceeding to clinical trials. Among these tissues, the cornea has unique homeostatic and regenerative mechanisms for maintaining transparency and refraction of external light, which are essential for vision. However, being the outermost tissue of the eye and directly exposed to the external environment, the cornea is particularly susceptible to injury and diseases. This review highlights the evidence for selecting appropriate animals to better understand and treat corneal diseases, which rank as the fifth leading cause of blindness worldwide. The development of reliable and human-relevant animal models is, therefore, a valuable research tool for understanding and translating fundamental mechanistic findings, as well as for assessing therapeutic potential in humans. First, this review emphasizes the unique characteristics of animal models used in ocular research. Subsequently, it discusses current animal models associated with human corneal pathologies, their utility in understanding ocular disease mechanisms, and their role as translational models for patients.
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Affiliation(s)
- Alexis Loiseau
- Faculty of Medicine, Department of Ophthalmology and Otolaryngology—Head and Neck Surgery, CHU de Québec Research Center, Université Laval, Québec, QC G1S 4L8, Canada; (G.R.-M.); (C.M.)
| | - Gabrielle Raîche-Marcoux
- Faculty of Medicine, Department of Ophthalmology and Otolaryngology—Head and Neck Surgery, CHU de Québec Research Center, Université Laval, Québec, QC G1S 4L8, Canada; (G.R.-M.); (C.M.)
| | - Cloé Maranda
- Faculty of Medicine, Department of Ophthalmology and Otolaryngology—Head and Neck Surgery, CHU de Québec Research Center, Université Laval, Québec, QC G1S 4L8, Canada; (G.R.-M.); (C.M.)
| | - Nicolas Bertrand
- Faculty of Pharmacy, CHU de Quebec Research Center, Université Laval, Québec, QC G1V 4G2, Canada;
| | - Elodie Boisselier
- Faculty of Medicine, Department of Ophthalmology and Otolaryngology—Head and Neck Surgery, CHU de Québec Research Center, Université Laval, Québec, QC G1S 4L8, Canada; (G.R.-M.); (C.M.)
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Shetty R, Mahendran K, Joshi PD, Jeyabalan N, Jayadev C, Das D. Corneal stromal regeneration-keratoconus cell therapy: a review. Graefes Arch Clin Exp Ophthalmol 2023; 261:3051-3065. [PMID: 37074409 DOI: 10.1007/s00417-023-06064-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/28/2023] [Accepted: 04/05/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Keratoconus is a corneal ectatic disease caused by stromal thinning leading to astigmatism and progressive loss of vision. Loss of the keratocytes and excessive degradation of collagen fibres by matrix metalloproteinases are the molecular signatures of the disease. Despite several limitations, corneal collagen cross-linking and keratoplasty are the most widely used treatment options for keratoconus. In the pursuit of alternative treatment modalities, clinician scientists have explored cell therapy paradigms for treating the condition. METHODS Articles pertaining to keratoconus cell therapy with relevant key words were used to search in PubMed, Researchgate, and Google Scholar. The articles were selected based on their relevance, reliability, publication year, published journal, and accessibility. RESULTS Various cellular abnormalities have been reported in keratoconus. Diverse cell types such as mesenchymal stromal cells, dental pulp cells, bone marrow stem cells, haematopoietic stem cells, adipose-derived stem cells apart from embryonic and induced pluripotent stem cells can be used for keratoconus cell therapy. The results obtained show that there is a potential for these cells from various sources as a viable treatment option. CONCLUSION There is a need for consensus with respect to the source of cells, mode of delivery, stage of disease, and duration of follow-up, to establish a standard operating protocol. This would eventually widen the cell therapy options for corneal ectatic diseases beyond keratoconus.
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Affiliation(s)
- Rohit Shetty
- Department of Cornea and Refractive Surgery, Narayana Nethralaya Eye Hospital, Bangalore, India
| | - Krithikaa Mahendran
- Stem Cell Research Lab, GROW Lab, Narayana Nethralaya Foundation, Narayana Nethralaya, Bangalore, India
| | - Parth D Joshi
- Stem Cell Research Lab, GROW Lab, Narayana Nethralaya Foundation, Narayana Nethralaya, Bangalore, India
| | | | - Chaitra Jayadev
- Department of Vitreo-Retina, Narayana Nethralaya Eye Hospital, Bangalore, India
| | - Debashish Das
- Stem Cell Research Lab, GROW Lab, Narayana Nethralaya Foundation, Narayana Nethralaya, Bangalore, India.
- Stem Cell Lab, GROW Lab, Narayana Nethralaya Foundation, Narayana Nethralaya Eye Hospital, Narayana Health City, 258/A Bommasandra Industrial Area, Bangalore, 560099, Karnataka, India.
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Hadvina R, Lotfy Khaled M, Akoto T, Zhi W, Karamichos D, Liu Y. Exosomes and their miRNA/protein profile in keratoconus-derived corneal stromal cells. Exp Eye Res 2023; 236:109642. [PMID: 37714423 PMCID: PMC10842962 DOI: 10.1016/j.exer.2023.109642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023]
Abstract
Keratoconus (KC) is a corneal thinning disorder and a leading cause of corneal transplantation worldwide. Exosomes are small, secreted extracellular vesicles (30-150 nm) that mediate cellular communication via their protein, lipid, and nucleic acid content. We aimed to characterize the exosomes secreted by primary corneal fibroblasts from subjects with or without KC. Using human keratoconus stromal fibroblast cells (HKC, n = 4) and healthy stromal fibroblasts (HCF, n = 4), we collected and isolated exosomes using serial ultracentrifugation. Using nanoparticle tracking analysis (NTA) with ZetaView®, we compared the size and concentration of isolated exosomes. Different exosomal markers were identified and quantified using a transmission electron microscope (TEM) (CD81) and Western blot (CD9 and CD63). Exosomal miRNA profiles were determined by qRT-PCR using Exiqon Human panel I miRNA assays of 368 pre-selected miRNAs. Proteomic profiles were determined using a label-free spectral counting method with mass spectrometry. Differential expression analysis for miRNAs and proteins was done using student's t-test with a significance cutoff of p-value ≤0.05. We successfully characterized exosomes isolated from HCFs using several complementary techniques. We found no significant differences in the size, quantity, or morphology between exosomes secreted by HCFs with or without KC. Expression of CD81 was confirmed by immuno-EM, and expression of CD63 and CD9 with western blots in all exosome samples. We detected the expression of 72-144 miRNAs (threshold cycle Ct < 36) in all exosome samples. In HKC-derived exosome samples, miR-328-3p, miR-532-5p, miR-345-5p, and miR-424-5p showed unique expression, while let-7c-5p and miR-665 have increased expression. Protein profiling identified 157 proteins in at least half of the exosome samples, with 38 known exosomal proteins. We identified 12 up- and 2 down-regulated proteins in HKC-derived exosomes. The proteins are involved in membrane-bounded vesicles, cytoskeletal, calcium binding, and nucleotide binding. These proteins are predicted to be regulated by NRF2, miR-205, and TGF-β1, which are involved in KC pathogenesis. We successfully characterized the HKC-derived exosomes and profiled their miRNA and protein contents, suggesting their potential role in KC development. Further studies are necessary to determine if and how these exosomes with differential protein/miRNA profiles contribute to the pathogenesis of KC.
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Affiliation(s)
- Rachel Hadvina
- Department of Cellular Biology & Anatomy, Augusta University, Augusta, GA, 30912, USA; Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Mariam Lotfy Khaled
- Department of Cellular Biology & Anatomy, Augusta University, Augusta, GA, 30912, USA; Department of Biochemistry, Cairo University, Egypt
| | - Theresa Akoto
- Department of Cellular Biology & Anatomy, Augusta University, Augusta, GA, 30912, USA
| | - Wenbo Zhi
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Dimitrios Karamichos
- North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA; Department of Pharmaceutical Sciences, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA; Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.
| | - Yutao Liu
- Department of Cellular Biology & Anatomy, Augusta University, Augusta, GA, 30912, USA; Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA; James & Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
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Jeon KI, Kumar A, Callan CL, DeMagistris M, MacRae S, Nehrke K, Huxlin KR. Blocking Mitochondrial Pyruvate Transport Alters Corneal Myofibroblast Phenotype: A New Target for Treating Fibrosis. Invest Ophthalmol Vis Sci 2023; 64:36. [PMID: 37870848 PMCID: PMC10599161 DOI: 10.1167/iovs.64.13.36] [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: 06/12/2023] [Accepted: 09/21/2023] [Indexed: 10/24/2023] Open
Abstract
Purpose The purpose of this study was to critically test the hypothesis that mitochondrial pyruvate carrier (MPC) function is essential for maintenance of the corneal myofibroblast phenotype in vitro and in vivo. Methods Protein and mRNA for canonical profibrotic markers were assessed in cultured cat corneal myofibroblasts generated via transforming growth factor (TGF)-β1 stimulation and treated with either the thiazolidinedione (TZD) troglitazone or the MPC inhibitor alpha-cyano-beta-(1-phenylindol-3-yl) acrylate (UK-5099). RNA sequencing was used to gain insight into signaling modules related to instructive, permissive, or corollary changes in gene expression following treatment. A feline photorefractive keratectomy (PRK) model of corneal wounding was used to test the efficacy of topical troglitazone at reducing α-smooth muscle actin (SMA)-positive staining when applied 2 to 4 weeks postoperatively, during peak fibrosis. Results Troglitazone caused cultured myofibroblasts to adopt a fibroblast-like phenotype through a noncanonical, peroxisome proliferator-activated receptor (PPAR)-γ-independent mechanism. Direct MPC inhibition using UK-5099 recapitulated this effect, but classic inhibitors of oxidative phosphorylation (OXPHOS) did not. Gene Set Enrichment Analysis (GSEA) of RNA sequencing data converged on energy substrate utilization and the Mitochondrial Permeability Transition pore as key players in myofibroblast maintenance. Finally, troglitazone applied onto an established zone of active fibrosis post-PRK significantly reduced stromal α-SMA expression. Conclusions Our results provide empirical evidence that metabolic remodeling in myofibroblasts creates selective vulnerabilities beyond simply mitochondrial energy production, and that these are critical for maintenance of the myofibroblast phenotype. For the first time, we provide proof-of-concept data showing that this remodeling can be exploited to treat existing corneal fibrosis via inhibition of the MPC.
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Affiliation(s)
- Kye-Im Jeon
- Department of Ophthalmology, Flaum Eye Institute and Center for Visual Science, University of Rochester, Rochester, New York, United States
| | - Ankita Kumar
- Department of Ophthalmology, Flaum Eye Institute and Center for Visual Science, University of Rochester, Rochester, New York, United States
| | - Christine L Callan
- Department of Ophthalmology, Flaum Eye Institute and Center for Visual Science, University of Rochester, Rochester, New York, United States
| | - Margaret DeMagistris
- Department of Ophthalmology, Flaum Eye Institute and Center for Visual Science, University of Rochester, Rochester, New York, United States
| | - Scott MacRae
- Department of Ophthalmology, Flaum Eye Institute and Center for Visual Science, University of Rochester, Rochester, New York, United States
| | - Keith Nehrke
- Department of Medicine-Nephrology Division, University of Rochester, Rochester, New York, United States
| | - Krystel R Huxlin
- Department of Ophthalmology, Flaum Eye Institute and Center for Visual Science, University of Rochester, Rochester, New York, United States
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Akoto T, Cai J, Nicholas S, McCord H, Estes AJ, Xu H, Karamichos D, Liu Y. Unravelling the Impact of Cyclic Mechanical Stretch in Keratoconus-A Transcriptomic Profiling Study. Int J Mol Sci 2023; 24:7437. [PMID: 37108600 PMCID: PMC10139219 DOI: 10.3390/ijms24087437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/04/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Biomechanical and molecular stresses may contribute to the pathogenesis of keratoconus (KC). We aimed to profile the transcriptomic changes in healthy primary human corneal (HCF) and KC-derived cells (HKC) combined with TGFβ1 treatment and cyclic mechanical stretch (CMS), mimicking the pathophysiological condition in KC. HCFs (n = 4) and HKCs (n = 4) were cultured in flexible-bottom collagen-coated 6-well plates treated with 0, 5, and 10 ng/mL of TGFβ1 with or without 15% CMS (1 cycle/s, 24 h) using a computer-controlled Flexcell FX-6000T Tension system. We used stranded total RNA-Seq to profile expression changes in 48 HCF/HKC samples (100 bp PE, 70-90 million reads per sample), followed by bioinformatics analysis using an established pipeline with Partek Flow software. A multi-factor ANOVA model, including KC, TGFβ1 treatment, and CMS, was used to identify differentially expressed genes (DEGs, |fold change| ≥ 1.5, FDR ≤ 0.1, CPM ≥ 10 in ≥1 sample) in HKCs (n = 24) vs. HCFs (n = 24) and those responsive to TGFβ1 and/or CMS. PANTHER classification system and the DAVID bioinformatics resources were used to identify significantly enriched pathways (FDR ≤ 0.05). Using multi-factorial ANOVA analyses, 479 DEGs were identified in HKCs vs. HCFs including TGFβ1 treatment and CMS as cofactors. Among these DEGs, 199 KC-altered genes were responsive to TGFβ1, thirteen were responsive to CMS, and six were responsive to TGFβ1 and CMS. Pathway analyses using PANTHER and DAVID indicated the enrichment of genes involved in numerous KC-relevant functions, including but not limited to degradation of extracellular matrix, inflammatory response, apoptotic processes, WNT signaling, collagen fibril organization, and cytoskeletal structure organization. TGFβ1-responsive KC DEGs were also enriched in these. CMS-responsive KC-altered genes such as OBSCN, CLU, HDAC5, AK4, ITGA10, and F2RL1 were identified. Some KC-altered genes, such as CLU and F2RL1, were identified to be responsive to both TGFβ1 and CMS. For the first time, our multi-factorial RNA-Seq study has identified many KC-relevant genes and pathways in HKCs with TGFβ1 treatment under CMS, suggesting a potential role of TGFβ1 and biomechanical stretch in KC development.
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Affiliation(s)
- Theresa Akoto
- Department of Cellular Biology & Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Jingwen Cai
- Department of Cellular Biology & Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Sarah Nicholas
- North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Department of Pharmaceutical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Hayden McCord
- Department of Cellular Biology & Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Amy J. Estes
- Department of Ophthalmology, Augusta University, Augusta, GA 30912, USA
- James & Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Hongyan Xu
- Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Dimitrios Karamichos
- North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Department of Pharmaceutical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Yutao Liu
- Department of Cellular Biology & Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- James & Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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MAPK Pathways in Ocular Pathophysiology: Potential Therapeutic Drugs and Challenges. Cells 2023; 12:cells12040617. [PMID: 36831285 PMCID: PMC9954064 DOI: 10.3390/cells12040617] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) pathways represent ubiquitous cellular signal transduction pathways that regulate all aspects of life and are frequently altered in disease. Once activated through phosphorylation, these MAPKs in turn phosphorylate and activate transcription factors present either in the cytoplasm or in the nucleus, leading to the expression of target genes and, as a consequence, they elicit various biological responses. The aim of this work is to provide a comprehensive review focusing on the roles of MAPK signaling pathways in ocular pathophysiology and the potential to influence these for the treatment of eye diseases. We summarize the current knowledge of identified MAPK-targeting compounds in the context of ocular diseases such as macular degeneration, cataract, glaucoma and keratopathy, but also in rare ocular diseases where the cell differentiation, proliferation or migration are defective. Potential therapeutic interventions are also discussed. Additionally, we discuss challenges in overcoming the reported eye toxicity of some MAPK inhibitors.
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Shrestha P, Whelchel AE, Nicholas SE, Liang W, Ma JX, Karamichos D. Monocarboxylate Transporters: Role and Regulation in Corneal Diabetes. Anal Cell Pathol (Amst) 2022; 2022:6718566. [PMID: 36340268 PMCID: PMC9629935 DOI: 10.1155/2022/6718566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/01/2022] [Indexed: 03/23/2024] Open
Abstract
Diabetes mellitus (DM) is a group of metabolic diseases that is known to cause structural and functional ocular complications. In the human cornea, DM-related complications affect the epithelium, stroma, and nerves. Monocarboxylate transporters (MCTs) are a family of proton-linked plasma membrane transporters that carry monocarboxylates across plasma membranes. In the context of corneal health and disease, their role, presence, and function are largely undetermined and solely focused on the most common MCT isoforms, 1 through 4. In this study, we investigated the regulation of MCT1, 2, 4, 5, 8, and 10, in corneal DM, using established 3D self-assembled extracellular matrix (ECM) in vitro models. Primary stromal corneal fibroblasts were isolated from healthy (HCFs), type I (T1DMs), and type II (T2DMs) DM donors. Monoculture 3D constructs were created by stimulating stromal cells on transwells with stable vitamin C for two or four weeks. Coculture 3D constructs were created by adding SH-SY5Y neurons at two different densities, 12 k and 500 k, on top of the monocultures. Our data showed significant upregulation of MCT1 at 4 weeks for HCF, T1DM, and T2DM monocultures, as well as the 500 k nerve cocultures. MCT8 was significantly upregulated in HCF and T1DM monocultures and all of the 500 k nerve cocultures. Further, MCT10 was only expressed at 4 weeks for all cocultures and was limited to HCFs and T1DMs in monocultures. Immunofluorescence analysis showed cytoplasmic MCT expression for all cell types and significant downregulation of both MCT2 and MCT4 in HCFs, when compared to T1DMs and T2DMs. Herein, we reveal the existence and modulation of MCTs in the human diabetic cornea in vitro. Changes appeared dependent on neuronal density, suggesting that MCTs are very likely critical to the neuronal defects observed in diabetic keratopathy/neuropathy. Further studies are warranted in order to fully delineate the role of MCTs in corneal diabetes.
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Affiliation(s)
- Pawan Shrestha
- North Texas Eye Research Institute, University of North Texas Health Science Center, 3430 Camp Bowie Blvd, Fort Worth, TX 76107, USA
- Department of Pharmaceutical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - Amy E. Whelchel
- Department of Physiology, University of Oklahoma Health Sciences Center, 940 Stanton L Young Blvd, Oklahoma City, OK 73104, USA
| | - Sarah E. Nicholas
- North Texas Eye Research Institute, University of North Texas Health Science Center, 3430 Camp Bowie Blvd, Fort Worth, TX 76107, USA
- Department of Pharmaceutical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - Wentao Liang
- Department of Physiology, University of Oklahoma Health Sciences Center, 940 Stanton L Young Blvd, Oklahoma City, OK 73104, USA
- Department of Biochemistry, Wake Forest University School of Medicine, 575 N Patterson Ave, Winston-Salem, NC 27101, USA
| | - Jian-Xing Ma
- Department of Biochemistry, Wake Forest University School of Medicine, 575 N Patterson Ave, Winston-Salem, NC 27101, USA
| | - Dimitrios Karamichos
- North Texas Eye Research Institute, University of North Texas Health Science Center, 3430 Camp Bowie Blvd, Fort Worth, TX 76107, USA
- Department of Pharmaceutical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
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Lozano V, Martín C, Blanco N, Alcalde I, Fernandez-Vega Cueto L, Merayo-Lloves J, Quirós LM. Exosomes Released by Corneal Stromal Cells Show Molecular Alterations in Keratoconus Patients and Induce Different Cellular Behavior. Biomedicines 2022; 10:biomedicines10102348. [PMID: 36289615 PMCID: PMC9598276 DOI: 10.3390/biomedicines10102348] [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: 06/02/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 11/23/2022] Open
Abstract
Exosomes have been related to various disorders, but their study in relation to ocular pathologies has been limited. In this article, we analyze exosomes produced by corneal stromal cells from healthy individuals and from patients with keratoconus. The proteomic study allowed for the identification of 14 new proteins with altered expression, related to molecules previously associated with the pathology. miRNA analysis detected 16 altered species, including miR-184, responsible for familial severe keratoconus. The prediction of its potential biological targets identified 1121 genes, including some related to this pathology. Exosomes produced by keratoconic cells induced a marked increase in the migration of stromal cells and corneal epithelium, while those produced by healthy cells had no effect on stromal cells. Both types of nanovesicles reduced the proliferation of stromal and corneal cells, but those produced by healthy cells had less effect. Exosomes produced by healthy cells had concentration-dependent effects on the transcription of genes encoding proteoglycans by keratoconus cells, with a relative normalization observed at concentrations of 240 µg/mL. These results show the alteration of stromal exosomes in keratoconus and suggest an influence on the development of the pathology, although the use of healthy exosomes could also have therapeutic potential.
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Affiliation(s)
- Víctor Lozano
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Spain; (V.L.); (C.M.); (N.B.)
- Instituto Universitario Fernández-Vega, Fundación de Investigación Oftalmológica, University of Oviedo, 33012 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Carla Martín
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Spain; (V.L.); (C.M.); (N.B.)
- Instituto Universitario Fernández-Vega, Fundación de Investigación Oftalmológica, University of Oviedo, 33012 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Noelia Blanco
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Spain; (V.L.); (C.M.); (N.B.)
- Instituto Universitario Fernández-Vega, Fundación de Investigación Oftalmológica, University of Oviedo, 33012 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Ignacio Alcalde
- Instituto Universitario Fernández-Vega, Fundación de Investigación Oftalmológica, University of Oviedo, 33012 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Luis Fernandez-Vega Cueto
- Instituto Universitario Fernández-Vega, Fundación de Investigación Oftalmológica, University of Oviedo, 33012 Oviedo, Spain;
- Correspondence: (L.F.-V.C.); (J.M.-L.); (L.M.Q.); Tel.: +34-985240141 (L.F.-V.C.); +34-985240141 (J.M.-L.); +34-985103560 (L.M.Q.)
| | - Jesús Merayo-Lloves
- Instituto Universitario Fernández-Vega, Fundación de Investigación Oftalmológica, University of Oviedo, 33012 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Correspondence: (L.F.-V.C.); (J.M.-L.); (L.M.Q.); Tel.: +34-985240141 (L.F.-V.C.); +34-985240141 (J.M.-L.); +34-985103560 (L.M.Q.)
| | - Luis M. Quirós
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Spain; (V.L.); (C.M.); (N.B.)
- Instituto Universitario Fernández-Vega, Fundación de Investigación Oftalmológica, University of Oviedo, 33012 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Correspondence: (L.F.-V.C.); (J.M.-L.); (L.M.Q.); Tel.: +34-985240141 (L.F.-V.C.); +34-985240141 (J.M.-L.); +34-985103560 (L.M.Q.)
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11
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Xu L, Yang K, Yin S, Gu Y, Fan Q, Wang Y, Zhao D, Ren S. Family-based exome sequencing identifies candidate genes related to keratoconus in Chinese families. Front Genet 2022; 13:988620. [PMID: 36118869 PMCID: PMC9478549 DOI: 10.3389/fgene.2022.988620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Keratoconus (KC) is a complex corneal disorder with a strong genetic component. The present study aimed to identify candidate genes related to KC in Chinese families.Methods: Family-based exome sequencing was performed in ten patients suffering from KC who belong to five families with two affected members in each. The candidate rare variants were identified with multi-step bioinformatics analysis. The STRING website was used to perform the protein interaction of the identified genes.Results: Our analyses identified 32 candidate rare variants in 13 genes by family-based exome sequencing. The molecular analyses of identified genes showed that EPCAM directly interacted with CTNNB1 of the Hippo signaling pathway and focal adhesion pathway, and directly interacted with CTNNB1, CDH1 of the WNT signaling pathway. SHROOM3 directly interacted with ROCK2, ROCK1 of the focal adhesion pathway. SYNE1 directly interacted with MUSK of the extracellular matrix organization pathway. TEK directly interacted with VEGFA, SHC1, PIK3R1, GRB2 of the focal adhesion pathway. TTN directly interacted with CAPN3 of the extracellular matrix organization pathway.Conclusion: The EPCAM, SHROOM3, SYNE1, TEK, and TTN genes were potential high-risk candidate pathogenic genes of familial KC. The findings might significantly improve our understanding of the genetic etiology of the disease, providing novel insights on KC pathogenesis.
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Affiliation(s)
- Liyan Xu
- Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Kaili Yang
- Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Shanshan Yin
- Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institution, Zhengzhou, China
| | - Yuwei Gu
- Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Qi Fan
- Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Yawen Wang
- Henan University People’s Hospital, Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, Zhengzhou, China
| | - Dongqing Zhao
- Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Shengwei Ren
- Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
- *Correspondence: Shengwei Ren,
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12
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Stachon T, Nastaranpour M, Seitz B, Meese E, Latta L, Taneri S, Ardjomand N, Szentmáry N, Ludwig N. Altered Regulation of mRNA and miRNA Expression in Epithelial and Stromal Tissue of Keratoconus Corneas. Invest Ophthalmol Vis Sci 2022; 63:7. [PMID: 35816043 PMCID: PMC9284461 DOI: 10.1167/iovs.63.8.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Evaluation of mRNA and microRNA (miRNA) expression in epithelium and stroma of patients with keratoconus. Methods The epithelium and stroma of eight corneas of eight patients with keratoconus and eight corneas of eight non-keratoconus healthy controls were studied separately. RNA was extracted, and mRNA and miRNA analyses were performed using microarrays. Differentially expressed mRNAs and miRNAs in epithelial and stromal keratoconus samples compared to healthy controls were identified. Selected genes and miRNAs were further validated using RT-qPCR. Results We discovered 170 epithelial and 1498 stromal deregulated protein-coding mRNAs in KC samples. In addition, in epithelial samples 180 miRNAs and in stromal samples 379 miRNAs were significantly deregulated more than twofold compared to controls. Pathway analysis revealed enrichment of metabolic and axon guidance pathways for epithelial cells and enrichment of metabolic, mitogen-activated protein kinase (MAPK), and focal adhesion pathways for stromal cells. Conclusions This study demonstrates significant differences in the expression and regulation of mRNAs and miRNAs in the epithelium and stroma of Patients with KC. Also, in addition to the well-known target candidates, we were able to identify further genes and miRNAs that may be associated with keratoconus. Signaling pathways influencing metabolic changes and cell contacts are affected in epithelial and stromal cells of patients with keratoconus.
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Affiliation(s)
- Tanja Stachon
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Homburg (Saar), Germany
| | - Mahsa Nastaranpour
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Homburg (Saar), Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, Homburg (Saar), Germany
| | - Eckart Meese
- Department of Human Genetics and Center for Human and Molecular Biology, Saarland University, Homburg (Saar), Germany
| | - Lorenz Latta
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Homburg (Saar), Germany
| | - Suphi Taneri
- Center for Refractive Surgery, Eye Department at St. Francis Hospital, Muenster, Germany
| | | | - Nóra Szentmáry
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Homburg (Saar), Germany.,Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Nicole Ludwig
- Department of Human Genetics and Center for Human and Molecular Biology, Saarland University, Homburg (Saar), Germany
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13
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Hao XD, Gao H, Xu WH, Shan C, Liu Y, Zhou ZX, Wang K, Li PF. Systematically Displaying the Pathogenesis of Keratoconus via Multi-Level Related Gene Enrichment-Based Review. Front Med (Lausanne) 2022; 8:770138. [PMID: 35141241 PMCID: PMC8818795 DOI: 10.3389/fmed.2021.770138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/31/2021] [Indexed: 01/20/2023] Open
Abstract
Keratoconus (KC) is an etiologically heterogeneous corneal ectatic disorder. To systematically display the pathogenesis of keratoconus (KC), this study reviewed all the reported genes involved in KC, and performed an enrichment analysis of genes identified at the genome, transcription, and protein levels respectively. Combined analysis of multi-level results revealed their shared genes, gene ontology (GO), and pathway terms, to explore the possible pathogenesis of KC. After an initial search, 80 candidate genes, 2,933 transcriptional differential genes, and 947 differential proteins were collected. The candidate genes were significantly enriched in extracellular matrix (ECM) related terms, Wnt signaling pathway and cytokine activities. The enriched GO/pathway terms of transcription and protein levels highlight the importance of ECM, cell adhesion, and inflammatory once again. Combined analysis of multi-levels identified 13 genes, 43 GOs, and 12 pathways. The pathogenic relationships among these overlapping factors maybe as follows. The gene mutations/variants caused insufficient protein dosage or abnormal function, together with environmental stimulation, leading to the related functions and pathways changes in the corneal cells. These included response to the glucocorticoid and reactive oxygen species; regulation of various signaling (P13K-AKT, MAPK and NF-kappaB), apoptosis and aging; upregulation of cytokines and collagen-related enzymes; and downregulation of collagen and other ECM-related proteins. These undoubtedly lead to a reduction of extracellular components and induction of cell apoptosis, resulting in the loosening and thinning of corneal tissue structure. This study, in addition to providing information about the genes involved, also provides an integrated insight into the gene-based etiology and pathogenesis of KC.
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Affiliation(s)
- Xiao-Dan Hao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- *Correspondence: Xiao-Dan Hao
| | - Hua Gao
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, China
- Shandong Eye Hospital, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Wen-Hua Xu
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, China
| | - Chan Shan
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Ying Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Zhi-Xia Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- Kun Wang
| | - Pei-Feng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- Pei-Feng Li
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14
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Stachon T, Latta L, Seitz B, Szentmáry N. Different mRNA expression patterns in keratoglobus and pellucid marginal degeneration keratocytes. Exp Eye Res 2021; 213:108804. [PMID: 34756941 DOI: 10.1016/j.exer.2021.108804] [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: 04/20/2021] [Revised: 10/07/2021] [Accepted: 10/20/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE Alike keratoconus (KC), keratoglobus (KG) and pellucid marginal degeneration (PMD) belong to ectatic corneal diseases. While there are numerous studies on keratoconus pathophysiology, there is no exact knowledge on genetic and pathophysiological background of KG and PMD, so far. It is not yet clarified, whether KG and PMD are independent clinical entities or represent different stages of the same disease. Our purpose was to investigate key parameters concerning collagen synthesis, intracellular LOX expression and inflammation in corneal stromal cells of KG and PMD subjects, in vitro. METHODS Normal human keratocytes of corneas from the LIONS Cornea Bank Saar-Lor-Lux, Trier/Westpfalz and human keratocytes of KG and PMD patients were isolated and cultured as keratocytes. To examine Collagen I and V (Col I, Col V), heat shock protein 47 (Hsp47), Lysyl Oxidase (LOX), nuclear factor kappa B (NF-κB) mRNA and protein expression in all cell types, quantitative PCR and Western blot analysis has been performed. RESULTS Col5A1 mRNA expression was significantly lower in KG and PMD keratocytes and LOX mRNA expression was significantly higher in KG-keratocytes, compared to controls. Col1A1, Hsp47 and NF-κB mRNA expression and the analyzed protein expressions did not differ from controls, in KG or PMD. CONCLUSIONS Col5A1 mRNA expression is decreased in KG and PMD and LOX mRNA expression is increased in KG. Therefore, the pathophysiology of KG and PMD differs from KC and these seem to be from KC independent entities. The explanation of the peripheral corneal thinning in KG and PMD must be investigated in further studies.
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Affiliation(s)
- Tanja Stachon
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Homburg/Saar, Germany.
| | - Lorenz Latta
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Homburg/Saar, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Nóra Szentmáry
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Homburg/Saar, Germany; Department of Ophthalmology, Semmelweis University, Budapest, Hungary
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15
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Ligocki AJ, Fury W, Gutierrez C, Adler C, Yang T, Ni M, Bai Y, Wei Y, Lehmann GL, Romano C. Molecular characteristics and spatial distribution of adult human corneal cell subtypes. Sci Rep 2021; 11:16323. [PMID: 34381080 PMCID: PMC8357950 DOI: 10.1038/s41598-021-94933-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/19/2021] [Indexed: 12/13/2022] Open
Abstract
Bulk RNA sequencing of a tissue captures the gene expression profile from all cell types combined. Single-cell RNA sequencing identifies discrete cell-signatures based on transcriptomic identities. Six adult human corneas were processed for single-cell RNAseq and 16 cell clusters were bioinformatically identified. Based on their transcriptomic signatures and RNAscope results using representative cluster marker genes on human cornea cross-sections, these clusters were confirmed to be stromal keratocytes, endothelium, several subtypes of corneal epithelium, conjunctival epithelium, and supportive cells in the limbal stem cell niche. The complexity of the epithelial cell layer was captured by eight distinct corneal clusters and three conjunctival clusters. These were further characterized by enriched biological pathways and molecular characteristics which revealed novel groupings related to development, function, and location within the epithelial layer. Moreover, epithelial subtypes were found to reflect their initial generation in the limbal region, differentiation, and migration through to mature epithelial cells. The single-cell map of the human cornea deepens the knowledge of the cellular subsets of the cornea on a whole genome transcriptional level. This information can be applied to better understand normal corneal biology, serve as a reference to understand corneal disease pathology, and provide potential insights into therapeutic approaches.
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Affiliation(s)
- Ann J Ligocki
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Wen Fury
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | | | - Tao Yang
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Min Ni
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Yu Bai
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Yi Wei
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | - Carmelo Romano
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA.
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Abstract
Purpose of Review To summarize the recent advances in transcriptomics and proteomics studies of keratoconus using advanced genome-wide gene and protein expression profiling techniques. Recent Findings Second-generation sequencing including RNA sequencing has been widely used to characterize the genome-wide gene expression in corneal tissues or cells affected by keratoconus. Due to different sample types, sequencing platforms, and analysis pipeline, different lists of genes have been identified to be differentially expressed in KC-affected samples. Gene ontology and pathway/network analyses have indicated the involvement of genes related with extracellular matrix, WNT-signaling, TGFβ pathway, and NRF2-regulated network. High throughput proteomics studies using mass spectrometry have uncovered many KC-related protein molecules in pathways related with cytoskeleton, cell matrix, TGFβ signaling, and extracellular matrix remodeling, consistent with gene expression profiling. Summary Both transcriptomics and proteomics studies using genome-wide gene/protein expression profiling techniques have identified significant genes/proteins that may contribute to the pathogenesis of keratoconus. These molecules may be involved in functional categories related with extracellular matrix and TGFβ signaling. It is necessary to perform comprehensive gene/protein expression studies using larger sample size, same type of samples, up-to-date platform and bioinformatics tools.
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17
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Bykhovskaya Y, Rabinowitz YS. Update on the genetics of keratoconus. Exp Eye Res 2020; 202:108398. [PMID: 33316263 DOI: 10.1016/j.exer.2020.108398] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023]
Abstract
In the past few years we have seen a great acceleration of discoveries in the field of keratoconus including new treatments, diagnostic tools, genomic and molecular determinants of disease risk. Recent genome-wide association studies (GWAS) of keratoconus cases and population wide studies of variation in central corneal thickness and in corneal biomechanical properties confirmed already identified genes and found many new susceptibility variants and biological pathways. Recent findings in genetic determinants of familial keratoconus revealed functionally important variants and established first mouse model of keratoconus. Latest transcriptomic and expression studies started assessing novel non-coding RNA targets in addition to identifying tissue specific effects of coding genes. First genomic insights into better prediction of treatment outcomes are bringing the advent of genomic medicine into keratoconus clinical practice.
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Affiliation(s)
- Yelena Bykhovskaya
- Cornea Genetic Eye Institute, Department of Surgery and Board of the Governors Regenerative Medicine Institute, Beverly Hills, Cedars-Sinai, Los Angeles, CA, United States.
| | - Yaron S Rabinowitz
- Cornea Genetic Eye Institute, Department of Surgery and Board of the Governors Regenerative Medicine Institute, Beverly Hills, Cedars-Sinai, Los Angeles, CA, United States
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18
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Hao XD, Chen XN, Zhang YY, Chen P, Wei C, Shi WY, Gao H. Multi-level consistent changes of the ECM pathway identified in a typical keratoconus twin's family by multi-omics analysis. Orphanet J Rare Dis 2020; 15:227. [PMID: 32867823 PMCID: PMC7457807 DOI: 10.1186/s13023-020-01512-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/13/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Keratoconus (KC) is a common, degenerative disorder of the cornea, and genetic factors play a key role in its development. However, the genetic etiology of KC is still unclear. This study used the family of twins as material, using, for the first time, multi-omics analysis, to systematically display the changes in KC candidate factors in patients at the DNA, RNA, and protein levels. These can evaluate candidate pathogenic factors in depth and lock onto pathogenic targets. RESULTS The twins in this study presented classic phenotypes, clear diagnoses, complete case data, and clinical samples, which are excellent materials for genetically studying KC. Whole-exome sequencing was conducted on both the twins and their parents. Transcriptome sequencing was conducted on proband's and health individual's primary human corneal fibroblast cells. Quantitative Real-time PCR and western blot were used to validate the differential gene expressions between the proband and controls. By integrating genomics, transcriptome, and protein level data, multiple consecutive events of KC were systematically analyzed to help better understand the molecular mechanism and genetic basis of KC. The results showed that the accumulation of rare, micro-effect risk variants was the pathogenic factor in this Chinese KC family. Consistent changes in extracellular matrices (ECMs) at the DNA and RNA levels suggested that ECM related changes play a key role in KC pathogenesis. The major gene variants (WNT16, CD248, COL6A2, COL4A3 and ADAMTS3) may affect the expression of related collagens or ECM proteins, thus reducing the amount of ECM in corneas and resulting in KC. CONCLUSIONS This study, the first to explore the genetic etiology of KC via multi-omics analysis under the polygenetic model, has provided new insights into the genetic mechanisms underlying KC and an effective strategy for studying KC pathogenesis in the future.
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Affiliation(s)
- Xiao-Dan Hao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China.,State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, 266071, China
| | - Xiu-Nian Chen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China.,State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, 266071, China
| | - Yang-Yang Zhang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, 266071, China
| | - Peng Chen
- Department of Human Anatomy, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Chao Wei
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, 266071, China
| | - Wei-Yun Shi
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, 266071, China.,Shandong Eye Hospital, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250021, China
| | - Hua Gao
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, 266071, China. .,Shandong Eye Hospital, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250021, China.
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Karolak JA, Ginter-Matuszewska B, Tomela K, Kabza M, Nowak-Malczewska DM, Rydzanicz M, Polakowski P, Szaflik JP, Gajecka M. Further evaluation of differential expression of keratoconus candidate genes in human corneas. PeerJ 2020; 8:e9793. [PMID: 32879808 PMCID: PMC7443321 DOI: 10.7717/peerj.9793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/31/2020] [Indexed: 12/26/2022] Open
Abstract
Background Keratoconus (KTCN) is a progressive eye disease, characterized by changes in the shape and thickness of the cornea that results in loss of visual acuity. While numerous KTCN candidate genes have been identified, the genetic etiology of the disease remains undetermined. To further investigate and verify the contribution of particular genetic factors to KTCN, we assessed 45 candidate genes previously indicated as involved in KTCN etiology based on transcriptomic and genomic data. Methods The RealTime ready Custom Panel, covering 45 KTCN candidate genes and two reference transcripts, has been designed. Then, the expression profiles have been assessed using the RT-qPCR assay in six KTCN and six non-KTCN human corneas, obtained from individuals undergoing a penetrating keratoplasty procedure. Results In total, 35 genes exhibiting differential expression between KTCN and non-KTCN corneas have been identified. Among these genes were ones linked to the extracellular matrix formation, including collagen synthesis or the TGF-β, Hippo, and Wnt signaling pathways. The most downregulated transcripts in KTCN corneas were CTGF, TGFB3, ZNF469, COL5A2, SMAD7, and SPARC, while TGFBI and SLC4A11 were the most upregulated ones. Hierarchical clustering of expression profiles demonstrated almost clear separation between KTCN and non-KTCN corneas. The gene expression levels determined using RT-qPCR showed a strong correlation with previous RNA sequencing (RNA-Seq) results. Conclusions A strong correlation between RT-qPCR and earlier RNA-Seq data confirms the possible involvement of genes from collagen synthesis and the TGF-β, Hippo, and Wnt signaling pathways in KTCN etiology. Our data also revealed altered expression of several genes, such as LOX, SPARC, and ZNF469, in which single nucleotide variants have been frequently identified in KTCN. These findings further highlight the heterogeneous nature of KTCN.
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Affiliation(s)
- Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Barbara Ginter-Matuszewska
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Katarzyna Tomela
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Michal Kabza
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Dorota M Nowak-Malczewska
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Piotr Polakowski
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Jacek P Szaflik
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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Karolak JA, Gambin T, Rydzanicz M, Polakowski P, Ploski R, Szaflik JP, Gajecka M. Accumulation of sequence variants in genes of Wnt signaling and focal adhesion pathways in human corneas further explains their involvement in keratoconus. PeerJ 2020; 8:e8982. [PMID: 32328353 PMCID: PMC7164425 DOI: 10.7717/peerj.8982] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Background Keratoconus (KTCN) is a protrusion and thinning of the cornea, resulting in loss of visual acuity. The etiology of KTCN remains unclear. The purpose of this study was to assess the potential involvement of new genetic variants in KTCN etiology based on both the genomic and transcriptomic findings recognized in the same corneal tissues. Methods Corneal tissues derived from five unrelated Polish individuals with KTCN were examined using exome sequencing (ES), followed by enrichment analyses. For comparison purposes, the datasets comprising ES data of five randomly selected Polish individuals without ocular abnormalities and five Polish patients with high myopia were used. Expression levels of selected genes from the overrepresented pathways were obtained from the previous RNA-Seq study. Results Exome capture discovered 117 potentially relevant variants that were further narrowed by gene overrepresentation analyses. In each of five patients, the assessment of functional interactions revealed rare (MAF ≤ 0.01) DNA variants in at least one gene from Wnt signaling (VANGL1, WNT1, PPP3CC, LRP6, FZD2) and focal adhesion (BIRC2, PAK6, COL4A4, PPP1R12A, PTK6) pathways. No genes involved in pathways enriched in KTCN corneas were overrepresented in our control sample sets. Conclusions The results of this first pilot ES profiling of human KTCN corneas emphasized that accumulation of sequence variants in several genes from Wnt signaling and/or focal adhesion pathways might cause the phenotypic effect and further points to a complex etiology of KTCN.
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Affiliation(s)
- Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Piotr Polakowski
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Jacek P Szaflik
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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