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Pan J, Wang M, Zhu J, Huang Y, Zhang F, Li E, Qin J, Chen L, Wang X. Quantitative proteomic and metabolomic profiling reveals different osmoregulation mechanisms of tilapia cells coping with different hyperosmotic stress. J Proteomics 2024; 296:105113. [PMID: 38346667 DOI: 10.1016/j.jprot.2024.105113] [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: 08/10/2023] [Revised: 01/13/2024] [Accepted: 02/03/2024] [Indexed: 02/18/2024]
Abstract
This study aimed to investigate the different regulatory mechanisms of euryhaline fish under regular hyperosmotic and extreme hyperosmotic stress. The OmB (Oreochromis mossambicus brain) cells were exposed to three treatments: control, regular hyperosmotic stress and extreme hyperosmotic stress. After 12 h exposure, proteomics, metabolomics analyses and integrative analyses were explored. Both kinds of stress lead to lowering cell growth and morphology changes, while under regular hyperosmotic stress, the up-regulated processes related with compatible organic osmolytes synthesis are crucial strategy for the euryhaline fish cell line to survive; On the other hand, under extreme hyperosmotic stress, the processes related with cell apoptosis and cell cycle arrest are dominant. Furthermore, down-regulated pyrimidine metabolism and several ribosomal proteins partially participated in the lowered cell metabolism and increased cell death under both kinds of hyperosmotic stress. The PI3K-Akt and p53 signaling pathways were involved in the stagnant stage of cell cycles and induction of cell apoptosis under both kinds of hyperosmotic stress. However, HIF-1, FoxO, JAK-STAT and Hippo signaling pathways mainly contribute to disrupting the cell cycle, metabolism and induction of cell apoptosis under extreme hyperosmotic stress. SIGNIFICANCE: In the past, the research on fish osmoregulation mainly focused on the transcription factors and ion transporters of osmoregulation, the processes between osmotic sensing and signal transduction, and the associations between signaling pathways and regulation processes have been poorly understood. Investigating fish cell osmoregulation and potential signal transduction pathways is necessary. With the advancements in omics research, it is now feasible to investigate the relationship between environmental stress and molecular responses. In this study, we aimed to explore the signaling pathways and substance metabolism mode during hyper-osmoregulation in OmB cell line, to reveal the key factors that are critical to cell osmoregulation.
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Affiliation(s)
- Jingyu Pan
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Minxu Wang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiahua Zhu
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yuxing Huang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Fan Zhang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Erchao Li
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jianguang Qin
- College of Science and Engineering, Flinders University, Adelaide, SA 5001, Australia
| | - Liqiao Chen
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xiaodan Wang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai 200241, China.
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2
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Martins TGDS, Sipahi AM, Mendes MA, Fowler SB, Schor P. Metaboloma use in ophthalmology. REVISTA BRASILEIRA DE OFTALMOLOGIA 2022. [DOI: 10.37039/1982.8551.20220056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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3
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Modulation of photosynthesis and other proteins during water-stress. Mol Biol Rep 2021; 48:3681-3693. [PMID: 33856605 DOI: 10.1007/s11033-021-06329-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/31/2021] [Indexed: 10/25/2022]
Abstract
Protein changes under drought or water stress conditions have been widely investigated. These investigations have given us enormous understanding of how drought is manifested in plants and how plants respond and adopt to such conditions. Chlorophyll fluoroescence, gas exchange, OMICS, biochemical and molecular analyses have shed light on regulation of physiology and photosynthesis of plants under drought. Use of proteomics has greatly increased the repertoire of drought-associated proteins which nevertheless, need to be investigated for their mechanistic and functional roles. Roles of such proteins have been succinctly discussed in various review articles, however more information on their functional role in countering drought is needed. In this review, recent developments in the field, alterations in the abundance of plant proteins in response to drought, monitored through numerous proteomic and immuno-blot analyses, and how these could affect plants growth and development, are discussed.
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Lipidomic analysis of epithelial corneal cells following hyperosmolarity and benzalkonium chloride exposure: New insights in dry eye disease. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158728. [DOI: 10.1016/j.bbalip.2020.158728] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/20/2020] [Accepted: 04/22/2020] [Indexed: 02/06/2023]
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Nazifova-Tasinova N, Radeva M, Galunska B, Grupcheva C. Metabolomic analysis in ophthalmology. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2020; 164:236-246. [PMID: 32690974 DOI: 10.5507/bp.2020.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022] Open
Abstract
Modern science takes into account phenotype complexity and establishes approaches to track changes on every possible level. Many "omics" studies have been developed over the last decade. Metabolomic analysis enables dynamic measurement of the metabolic response of a living system to a variety of stimuli or genetic modifications. Important targets of metabolomics is biomarker development and translation to the clinic for personalized diagnosis and a greater understanding of disease pathogenesis. The current review highlights the major aspects of metabolomic analysis and its applications for the identification of relevant predictive, diagnostic and prognostic biomarkers for some ocular diseases including dry eye, keratoconus, retinal diseases, macular degeneration, and glaucoma. To date, possible biomarker candidates for dry eye disease are lipid metabolites and androgens, for keratoconus cytokeratins, urea, citrate cycle, and oxidative stress metabolites. Palmitoylcarnitine, sphingolipids, vitamin D related metabolites, and steroid precursors may be used for distinguishing glaucoma patients from healthy controls. Dysregulation of amino acid and carnitine metabolism is critical in the development and progression of diabetic retinopathy. Further work is needed to discover and validate metabolic biomarkers as a powerful tool for understanding the molecular mechanisms of ocular diseases, to provide knowledge on their etiology and pathophysiology and opportunities for personalized clinical intervention at an early stage.
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Affiliation(s)
- Neshe Nazifova-Tasinova
- Department of Biochemistry, Molecular medicine and Nutrigenomics, Faculty of Pharmacy, Medical University of Varna, 84 Tzar Osvoboditel street, 9000 Varna, Bulgaria
| | - Mladena Radeva
- Department of Ophthalmology and Visual Sciences, Faculty of Medicine, Medical University of Varna, 15 Doyran street, 9000 Varna, Bulgaria
| | - Bistra Galunska
- Department of Biochemistry, Molecular medicine and Nutrigenomics, Faculty of Pharmacy, Medical University of Varna, 84 Tzar Osvoboditel street, 9000 Varna, Bulgaria
| | - Christina Grupcheva
- Department of Ophthalmology and Visual Sciences, Faculty of Medicine, Medical University of Varna, 15 Doyran street, 9000 Varna, Bulgaria
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6
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Benítez Del Castillo JM, Pinazo-Duran MD, Sanz-González SM, Muñoz-Hernández AM, Garcia-Medina JJ, Zanón-Moreno V. Tear 1H Nuclear Magnetic Resonance-Based Metabolomics Application to the Molecular Diagnosis of Aqueous Tear Deficiency and Meibomian Gland Dysfunction. Ophthalmic Res 2020; 64:297-309. [PMID: 32674101 DOI: 10.1159/000510211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/11/2020] [Indexed: 11/19/2022]
Abstract
PURPOSE Meibomian gland dysfunction (MGD) is a major cause of signs and symptoms related to dry eyes (DE) and eyelid inflammation. We investigated the composition of human tears by metabolomic approaches in patients with aqueous tear deficiency and MGD. METHODS Participants in this prospective, case-control pilot study were split into patients with aqueous tear deficiency and MGD (DE-MGD [n = 15]) and healthy controls (CG; n = 20). Personal interviews, ocular surface disease index (OSDI), and ophthalmic examinations were performed. Reflex tears collected by capillarity were processed to 1H nuclear magnetic resonance (NMR) spectroscopy and quantitative data analysis to identify molecules by spectra comparison to library entries of purified standards and/or unknown entities. Statistical analyses were made by the SPSS 22.0 program. RESULTS Chemometric analysis and 1H NMR spectra comparison revealed the presence of 60 metabolites in tears. Differentiating features were evident in the NMR spectra of the 2 clinical groups, characterized by significant upregulation of phenylalanine, glycerol, and isoleucine, and downregulation of glycoproteins, leucine, and -CH3 lipids, as compared to the CG. The 1H NMR metabolomic analyses of human tears confirmed the applicability of this platform with high predictive accuracy/reliability. CONCLUSIONS Our key distinctive findings support that DE-MGD induces tear metabolomics profile changes. Metabolites contributing to a higher separation from the CG can presumably be used, in the foreseeable future, as DE-MGD biomarkers for better managing the diagnosis and therapy of this disease.
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Affiliation(s)
- José Manuel Benítez Del Castillo
- Department of Ophthalmology, San Carlos Clinic Hospital, Madrid, Spain.,Spanish Net of Ophthalmic Pathology (OFTARED) of the Institute of Health Carlos III, Madrid, Spain
| | - Maria Dolores Pinazo-Duran
- Spanish Net of Ophthalmic Pathology (OFTARED) of the Institute of Health Carlos III, Madrid, Spain.,Ophthalmic Research Unit "Santiago Grisolía"/FISABIO, Valencia, Spain.,Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery (Ophthalmology), Faculty of Medicine and Odontology, University of Valencia, Valencia, Spain
| | - Silvia M Sanz-González
- Spanish Net of Ophthalmic Pathology (OFTARED) of the Institute of Health Carlos III, Madrid, Spain.,Ophthalmic Research Unit "Santiago Grisolía"/FISABIO, Valencia, Spain.,Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery (Ophthalmology), Faculty of Medicine and Odontology, University of Valencia, Valencia, Spain
| | - Ana M Muñoz-Hernández
- Department of Ophthalmology, San Carlos Clinic Hospital, Madrid, Spain.,Spanish Net of Ophthalmic Pathology (OFTARED) of the Institute of Health Carlos III, Madrid, Spain
| | - Jose J Garcia-Medina
- Spanish Net of Ophthalmic Pathology (OFTARED) of the Institute of Health Carlos III, Madrid, Spain.,Ophthalmic Research Unit "Santiago Grisolía"/FISABIO, Valencia, Spain.,Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery (Ophthalmology), Faculty of Medicine and Odontology, University of Valencia, Valencia, Spain.,Department of Ophthalmology, University Hospital Morales Meseguer, Murcia, Spain
| | - Vicente Zanón-Moreno
- Spanish Net of Ophthalmic Pathology (OFTARED) of the Institute of Health Carlos III, Madrid, Spain, .,Ophthalmic Research Unit "Santiago Grisolía"/FISABIO, Valencia, Spain, .,Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery (Ophthalmology), Faculty of Medicine and Odontology, University of Valencia, Valencia, Spain, .,International University of Valencia, Valencia, Spain,
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Heidari M, Noorizadeh F, Wu K, Inomata T, Mashaghi A. Dry Eye Disease: Emerging Approaches to Disease Analysis and Therapy. J Clin Med 2019; 8:jcm8091439. [PMID: 31514344 PMCID: PMC6780511 DOI: 10.3390/jcm8091439] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/01/2019] [Accepted: 09/06/2019] [Indexed: 12/11/2022] Open
Abstract
Dry eye disease (DED) is among the most common ocular disorders affecting tens of millions of individuals worldwide; however, the condition remains incompletely understood and treated. Valuable insights have emerged from multidisciplinary approaches, including immunometabolic analyses, microbiome analyses, and bioengineering. Furthermore, we have seen new developments in clinical assessment approaches and treatment strategies in the recent past. Here, we review the emerging frontiers in the pathobiology and clinical management of DED.
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Affiliation(s)
- Mostafa Heidari
- Basir Eye Health Research Center, Tehran 1418643561, Iran.
- Farabi Eye Hospital, Department of Ophthalmology and Eye Research Center, Tehran University of Medical Sciences, Tehran 133661635, Iran.
| | | | - Kevin Wu
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, Ophthalmic Consultation Service, New York, NY 10029, USA
- New York Eye and Ear Infirmary of Mount Sinai, New York, NY 10003, USA
| | - Takenori Inomata
- Department of Ophthalmology, Juntendo University Faculty of Medicine, Tokyo 1130033, Japan.
- Department of Strategic Operating Room Management and Improvement, Juntendo University Faculty of Medicine, Tokyo 1130033, Japan.
| | - Alireza Mashaghi
- Systems Biomedicine and Pharmacology Division, Leiden Academic Centre for Drug Research, Leiden University, 2333CC Leiden, The Netherlands.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
- Department of Ophthalmology, Shanghai Medical College, Fudan University, Shanghai 200000, China.
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Yazdani M, Elgstøen KBP, Rootwelt H, Shahdadfar A, Utheim ØA, Utheim TP. Tear Metabolomics in Dry Eye Disease: A Review. Int J Mol Sci 2019; 20:E3755. [PMID: 31374809 PMCID: PMC6695908 DOI: 10.3390/ijms20153755] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022] Open
Abstract
Dry eye disease (DED) is a multifactorial syndrome that can be caused by alteration in the quality or quantity of the precorneal tear film. It is considered one of the most common ocular conditions leading patients to seek eye care. The current method for diagnostic evaluations and follow-up examinations of DED is a combination of clinical signs and symptoms determined by clinical tests and questionnaires, respectively. The application of powerful omics technologies has opened new avenues toward analysis of subjects in health and disease. Metabolomics is a new emerging and complementary research discipline to all modern omics in the comprehensive analysis of biological systems. The identification of distinct metabolites and integrated metabolic profiles in patients can potentially inform clinicians at an early stage or during monitoring of disease progression, enhancing diagnosis, prognosis, and the choice of therapy. In ophthalmology, metabolomics has gained considerable attention over the past decade but very limited such studies have been reported on DED. This paper aims to review the application of tear metabolomics in DED.
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Affiliation(s)
- Mazyar Yazdani
- Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway.
- Center for Eye Research, Department of Ophthalmology, Oslo University Hospital, Ullevål, 0450 Oslo, Norway.
- The Norwegian Dry Eye Clinic, 0366 Oslo, Norway.
| | | | - Helge Rootwelt
- Department of Medical Biochemistry, Oslo University Hospital, 0027 Oslo, Norway
| | - Aboulghassem Shahdadfar
- Center for Eye Research, Department of Ophthalmology, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | | | - Tor Paaske Utheim
- Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
- The Norwegian Dry Eye Clinic, 0366 Oslo, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, 0450 Oslo, Norway
- Department of Maxillofacial Surgery, Oslo University Hospital, 0450 Oslo, Norway
- Department of Ophthalmology, Vestre Viken Hospital Trust, 3019 Drammen, Norway
- Department of Ophthalmology, Stavanger University Hospital, 4011 Stavanger, Norway
- Department of Clinical Medicine, Faculty of Medicine, University of Bergen, 5020 Bergen, Norway
- Department of Ophthalmology, Sørlandet Hospital Arendal, 4604 Arendal, Norway
- Department of Life Sciences and Health, Oslo Metropolitan University, 0130 Oslo, Norway
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9
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Narasimhan M, Kannan S, Chawade A, Bhattacharjee A, Govekar R. Clinical biomarker discovery by SWATH-MS based label-free quantitative proteomics: impact of criteria for identification of differentiators and data normalization method. J Transl Med 2019; 17:184. [PMID: 31151397 PMCID: PMC6545036 DOI: 10.1186/s12967-019-1937-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/24/2019] [Indexed: 02/06/2023] Open
Abstract
Background SWATH-MS has emerged as the strategy of choice for biomarker discovery due to the proteome coverage achieved in acquisition and provision to re-interrogate the data. However, in quantitative analysis using SWATH, each sample from the comparison group is run individually in mass spectrometer and the resulting inter-run variation may influence relative quantification and identification of biomarkers. Normalization of data to diminish this variation thereby becomes an essential step in SWATH data processing. In most reported studies, data normalization methods used are those provided in instrument-based data analysis software or those used for microarray data. This study, for the first time provides an experimental evidence for selection of normalization method optimal for biomarker identification. Methods The efficiency of 12 normalization methods to normalize SWATH-MS data was evaluated based on statistical criteria in ‘Normalyzer’—a tool which provides comparative evaluation of normalization by different methods. Further, the suitability of normalized data for biomarker discovery was assessed by evaluating the clustering efficiency of differentiators, identified from the normalized data based on p-value, fold change and both, by hierarchical clustering in Genesis software v.1.8.1. Results Conventional statistical criteria identified VSN-G as the optimal method for normalization of SWATH data. However, differentiators identified from VSN-G normalized data failed to segregate test and control groups. We thus assessed data normalized by eleven other methods for their ability to yield differentiators which segregate the study groups. Datasets in our study demonstrated that differentiators identified based on p-value from data normalized with Loess-R stratified the study groups optimally. Conclusion This is the first report of experimentally tested strategy for SWATH-MS data processing with an emphasis on identification of clinically relevant biomarkers. Normalization of SWATH-MS data by Loess-R method and identification of differentiators based on p-value were found to be optimal for biomarker discovery in this study. The study also demonstrates the need to base the choice of normalization method on the application of the data. Electronic supplementary material The online version of this article (10.1186/s12967-019-1937-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mythreyi Narasimhan
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.,BARC Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Sadhana Kannan
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Atanu Bhattacharjee
- Section of Biostatistics, Centre for Cancer Epidemiology, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
| | - Rukmini Govekar
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India. .,BARC Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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10
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Differential epithelial and stromal protein profiles in cone and non-cone regions of keratoconus corneas. Sci Rep 2019; 9:2965. [PMID: 30814630 PMCID: PMC6393548 DOI: 10.1038/s41598-019-39182-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/18/2019] [Indexed: 12/14/2022] Open
Abstract
Keratoconus (KC) is an ectatic corneal disease characterized by progressive thinning and irregular astigmatism, and a leading indication for corneal transplantation. KC-associated changes have been demonstrated for the entire cornea, but the pathological thinning and mechanical weakening is usually localized. We performed quantitative proteomics using Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectrometry (SWATH-MS) to analyze epithelial and stromal changes between the topographically-abnormal cone and topographically-normal non-cone regions of advanced KC corneas, compared to age-matched normal corneas. Expression of 20 epithelial and 14 stromal proteins was significantly altered (≥2 or ≤0.5-fold) between cone and non-cone in all 4 KC samples. Ingenuity pathway analysis illustrated developmental and metabolic disorders for the altered epithelial proteome with mitochondrion as the significant gene ontology (GO) term. The differential stromal proteome was related to cellular assembly, tissue organization and connective tissue disorders with endoplasmic reticulum protein folding as the significant GO term. Validation of selected protein expression was performed on archived KC, non-KC and normal corneal specimens by immunohistochemistry. This is the first time to show that KC-associated proteome changes were not limited to the topographically-thinner and mechanically-weakened cone but also non-cone region with normal topography, indicating a peripheral involvement in KC development.
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Picart-Armada S, Fernández-Albert F, Vinaixa M, Yanes O, Perera-Lluna A. FELLA: an R package to enrich metabolomics data. BMC Bioinformatics 2018; 19:538. [PMID: 30577788 PMCID: PMC6303911 DOI: 10.1186/s12859-018-2487-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 11/12/2018] [Indexed: 12/27/2022] Open
Abstract
Background Pathway enrichment techniques are useful for understanding experimental metabolomics data. Their purpose is to give context to the affected metabolites in terms of the prior knowledge contained in metabolic pathways. However, the interpretation of a prioritized pathway list is still challenging, as pathways show overlap and cross talk effects. Results We introduce FELLA, an R package to perform a network-based enrichment of a list of affected metabolites. FELLA builds a hierarchical representation of an organism biochemistry from the Kyoto Encyclopedia of Genes and Genomes (KEGG), containing pathways, modules, enzymes, reactions and metabolites. In addition to providing a list of pathways, FELLA reports intermediate entities (modules, enzymes, reactions) that link the input metabolites to them. This sheds light on pathway cross talk and potential enzymes or metabolites as targets for the condition under study. FELLA has been applied to six public datasets –three from Homo sapiens, two from Danio rerio and one from Mus musculus– and has reproduced findings from the original studies and from independent literature. Conclusions The R package FELLA offers an innovative enrichment concept starting from a list of metabolites, based on a knowledge graph representation of the KEGG database that focuses on interpretability. Besides reporting a list of pathways, FELLA suggests intermediate entities that are of interest per se. Its usefulness has been shown at several molecular levels on six public datasets, including human and animal models. The user can run the enrichment analysis through a simple interactive graphical interface or programmatically. FELLA is publicly available in Bioconductor under the GPL-3 license. Electronic supplementary material The online version of this article (10.1186/s12859-018-2487-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sergio Picart-Armada
- B2SLab, Departament d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, Barcelona, 08028, Spain. .,Networking Biomedical Research Centre in the subject area of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain. .,Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, 08950, Spain.
| | - Francesc Fernández-Albert
- B2SLab, Departament d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, Barcelona, 08028, Spain.,Networking Biomedical Research Centre in the subject area of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain.,Takeda Cambridge Ltd, Cambridge, CB4 0PZ, UK
| | - Maria Vinaixa
- Metabolomics Platform, IISPV, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, 43003, Spain.,CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, 28029, Spain
| | - Oscar Yanes
- Metabolomics Platform, IISPV, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, 43003, Spain.,CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, 28029, Spain
| | - Alexandre Perera-Lluna
- B2SLab, Departament d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, Barcelona, 08028, Spain.,Networking Biomedical Research Centre in the subject area of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain.,Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, 08950, Spain
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12
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Zou W, Zhou Q, Zhang X, Mu L, Hu X. Characterization of the effects of trace concentrations of graphene oxide on zebrafish larvae through proteomic and standard methods. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 159:221-231. [PMID: 29753824 DOI: 10.1016/j.ecoenv.2018.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 05/01/2018] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
The effects of graphene oxide (GO) carbon nanomaterials on ecosystems have been well characterized, but the toxicity of GO at predicted environmental concentrations to living organisms at the protein level remain largely unknown. In the present work, the adverse effects and mechanisms of GO at predicted environmental concentrations were evaluated by integrating proteomics and standard analyses for the first time. The abundances of 243 proteins, including proteins involved in endocytosis (e.g., cltcb, arf6, capzb and dnm1a), oxidative stress (e.g., gpx4b, sod2, and prdx1), cytoskeleton assembly (e.g., krt8, krt94, lmna and vim), mitochondrial function (e.g., ndufa10, ndufa8, cox5aa, and cox6b1), Ca2+ handling (e.g., atp1b2a, atp1b1a, atp6v0a1b and ncx4a) and cardiac function (e.g., tpm4a, tpm2, tnni2a.1 and tnnt3b), were found to be notably altered in response to exposure 100 μg/L GO. The results revealed that GO caused malformation and mortality, likely through the downregulation of proteins related to actin filaments and formation of the cytoskeleton, and induced oxidative stress and mitochondrial disorders by altering the levels of antioxidant enzymes and proteins associated with the mitochondrial membrane respiratory chain. Exposure to GO also increased the heart rate of zebrafish larvae and induced pericardial edema, likely by changing the expression of proteins related to Ca2+ balance and cardiac function. This study provides new proteomic-level insights into GO toxicity against aquatic organisms, which will greatly benefit our understanding of the bio-safety of GO and its toxicity at predicted environmental concentrations.
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Affiliation(s)
- Wei Zou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Xingli Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Li Mu
- Tianjin Key Laboratory of Agro-environment and Safe-product, Key Laboratory for Environmental Factors Control of Agro-product Quality Safety (Ministry of Agriculture), Institute of Agro-environmental Protection, Ministry of Agriculture, Tianjin 300191, China.
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China.
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Recent advances in the applications of metabolomics in eye research. Anal Chim Acta 2018; 1037:28-40. [PMID: 30292303 DOI: 10.1016/j.aca.2018.01.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 11/21/2022]
Abstract
Metabolomics, the identification and quantitation of metabolites in a system, have been applied to identify new biomarkers or elucidate disease mechanism. In this review, we discussed the application of metabolomics in several ocular diseases and recent developments in metabolomics regarding tear fluids analysis, data acquisition and processing.
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14
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Li J, Tan G, Ding X, Wang Y, Wu A, Yang Q, Ye L, Shao Y. A mouse dry eye model induced by topical administration of the air pollutant particulate matter 10. Biomed Pharmacother 2017; 96:524-534. [PMID: 29032336 DOI: 10.1016/j.biopha.2017.10.032] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 10/03/2017] [Accepted: 10/09/2017] [Indexed: 12/11/2022] Open
Abstract
AIM To introduce a novel dry eye mouse model induced by topical administration of the air pollutant particulate matter 10 (PM10). METHOD A total of 60 male BALB/c mice were used in this study and divided into two groups: group A (PBS eye drops, n=30) and group B (PM10 eye drop group, n=30). Each treatment was dosed four times a day, every time 50ul with the concentration of 5mg/ml PM10, for 14 consecutive days in the right eye. The clinical manifestations of dry eye were measured before therapy and 4, 7 and 14days post-treatment respectively, which included the tear volume, tear break-up (BUT) time, corneal fluorescein staining, rose bengal staining, Lissamine Green staining and inflammatory index. Eye samples were collected on D14 and examined by histologic light microscopy, transmission electron microscopy (TEM) and scanning electron microscopy (SEM), corneal cytokeration 10 (K10) immunnostaining, and tumor necrosis factor-α (TNF-α), NF-κB-p65 and NF-κB Western Blot analysis. RESULTS At 0d, 7d and 14d, there were no statistical changes in tear volume, BUT after treatment (P>0.05) with PBS in group A. In group B, all items showed statistical differences at each time point (P<0.05). At 14d after therapy, the fluorescein staining score of group B was higher than group A (P<0.05). The score of rose bengal staining and Lissamine Green staining in group B was also higher than that in group A (P<0.05). The number of mean layers of corneal epithelial cells in the group A was significantly lower than that in the group B (P<0.05). TEM and SEM revealed that the number of corneal epithelial microvilli were drastically reduced in group B. The number of corneal chondriosome/desmosomes was also reduced in group B by TEM. PM10 induced apoptosis in the superficial and basal corneal epithelium, and leaded to abnormal differentiation and proliferation of the ocular surface with higher expression levels of K10 and reduced number of goblet cells in the conjunctival fornix in group B. PM10 significantly increased the levels of TNF-α, NF-κB-p65 and NF-κB in the cornea. CONCLUSION PM10 can damage the tear film function and cause the destruction of the structural organization of ocular surface in mice. Topical administration of PM10 in mice induces ocular surface changes that are similar to those of dry eye in humans, representing a novel model of DES.
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Affiliation(s)
- Juan Li
- Department of Ophthalmology, the Fourth Hospital of Xi'an, Xi'an 710004, Shaanxi Province, China
| | - Gang Tan
- Department of Ophthalmology, the First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China; Department of Ophthalmology, the First Affiliated Hospital of University of South China, Henyang 421000, Hunan Province, China
| | - Xiaoyan Ding
- Department of Ophthalmology, the Second Hospital of Xi'an, Xi'an 710003, Shaanxi Province, China
| | - Yahong Wang
- Environmental Monitoring Station of Xi'an City, Xi'an 710054, Shaanxi Province, China
| | - Anhua Wu
- Department of Ophthalmology, the First Affiliated Hospital of University of South China, Henyang 421000, Hunan Province, China
| | - Qichen Yang
- Eye Institute of Xiamen University, Xiamen 361102, Fujian Province, China
| | - Lei Ye
- Department of Ophthalmology, the First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Yi Shao
- Department of Ophthalmology, the First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China.
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Bron AJ, de Paiva CS, Chauhan SK, Bonini S, Gabison EE, Jain S, Knop E, Markoulli M, Ogawa Y, Perez V, Uchino Y, Yokoi N, Zoukhri D, Sullivan DA. TFOS DEWS II pathophysiology report. Ocul Surf 2017; 15:438-510. [PMID: 28736340 DOI: 10.1016/j.jtos.2017.05.011] [Citation(s) in RCA: 965] [Impact Index Per Article: 137.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 12/18/2022]
Abstract
The TFOS DEWS II Pathophysiology Subcommittee reviewed the mechanisms involved in the initiation and perpetuation of dry eye disease. Its central mechanism is evaporative water loss leading to hyperosmolar tissue damage. Research in human disease and in animal models has shown that this, either directly or by inducing inflammation, causes a loss of both epithelial and goblet cells. The consequent decrease in surface wettability leads to early tear film breakup and amplifies hyperosmolarity via a Vicious Circle. Pain in dry eye is caused by tear hyperosmolarity, loss of lubrication, inflammatory mediators and neurosensory factors, while visual symptoms arise from tear and ocular surface irregularity. Increased friction targets damage to the lids and ocular surface, resulting in characteristic punctate epithelial keratitis, superior limbic keratoconjunctivitis, filamentary keratitis, lid parallel conjunctival folds, and lid wiper epitheliopathy. Hybrid dry eye disease, with features of both aqueous deficiency and increased evaporation, is common and efforts should be made to determine the relative contribution of each form to the total picture. To this end, practical methods are needed to measure tear evaporation in the clinic, and similarly, methods are needed to measure osmolarity at the tissue level across the ocular surface, to better determine the severity of dry eye. Areas for future research include the role of genetic mechanisms in non-Sjögren syndrome dry eye, the targeting of the terminal duct in meibomian gland disease and the influence of gaze dynamics and the closed eye state on tear stability and ocular surface inflammation.
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Affiliation(s)
- Anthony J Bron
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Vision and Eye Research Unit, Anglia Ruskin University, Cambridge, UK.
| | - Cintia S de Paiva
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, USA
| | - Sunil K Chauhan
- Schepens Eye Research Institute & Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Stefano Bonini
- Department of Ophthalmology, University Campus Biomedico, Rome, Italy
| | - Eric E Gabison
- Department of Ophthalmology, Fondation Ophtalmologique Rothschild & Hôpital Bichat Claude Bernard, Paris, France
| | - Sandeep Jain
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Erich Knop
- Departments of Cell and Neurobiology and Ocular Surface Center Berlin, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Maria Markoulli
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Yoko Ogawa
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Victor Perez
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA
| | - Yuichi Uchino
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Norihiko Yokoi
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Driss Zoukhri
- Tufts University School of Dental Medicine, Boston, MA, USA
| | - David A Sullivan
- Schepens Eye Research Institute & Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
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16
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Dick JM. Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. PeerJ 2017; 5:e3421. [PMID: 28603672 PMCID: PMC5463988 DOI: 10.7717/peerj.3421] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/16/2017] [Indexed: 12/19/2022] Open
Abstract
The changes of protein expression that are monitored in proteomic experiments are a type of biological transformation that also involves changes in chemical composition. Accompanying the myriad molecular-level interactions that underlie any proteomic transformation, there is an overall thermodynamic potential that is sensitive to microenvironmental conditions, including local oxidation and hydration potential. Here, up- and down-expressed proteins identified in 71 comparative proteomics studies were analyzed using the average oxidation state of carbon (ZC) and water demand per residue (\documentclass[12pt]{minimal}
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}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O), calculated using elemental abundances and stoichiometric reactions to form proteins from basis species. Experimental lowering of oxygen availability (hypoxia) or water activity (hyperosmotic stress) generally results in decreased ZC or \documentclass[12pt]{minimal}
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}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O of up-expressed compared to down-expressed proteins. This correspondence of chemical composition with experimental conditions provides evidence for attraction of the proteomes to a low-energy state. An opposite compositional change, toward higher average oxidation or hydration state, is found for proteomic transformations in colorectal and pancreatic cancer, and in two experiments for adipose-derived stem cells. Calculations of chemical affinity were used to estimate the thermodynamic potentials for proteomic transformations as a function of fugacity of O2 and activity of H2O, which serve as scales of oxidation and hydration potential. Diagrams summarizing the relative potential for formation of up- and down-expressed proteins have predicted equipotential lines that cluster around particular values of oxygen fugacity and water activity for similar datasets. The changes in chemical composition of proteomes are likely linked with reactions among other cellular molecules. A redox balance calculation indicates that an increase in the lipid to protein ratio in cancer cells by 20% over hypoxic cells would generate a large enough electron sink for oxidation of the cancer proteomes. The datasets and computer code used here are made available in a new R package, canprot.
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Anjo SI, Santa C, Manadas B. SWATH-MS as a tool for biomarker discovery: From basic research to clinical applications. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600278] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/05/2017] [Accepted: 01/23/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Sandra Isabel Anjo
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Faculty of Sciences and Technology; University of Coimbra; Coimbra Portugal
| | - Cátia Santa
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Institute for Interdisciplinary Research (III); University of Coimbra; Coimbra Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
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18
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Lawson TN, Weber RJM, Jones MR, Chetwynd AJ, Rodrı́guez-Blanco G, Di Guida R, Viant MR, Dunn WB. msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry-Based Fragmentation in Metabolomics. Anal Chem 2017; 89:2432-2439. [DOI: 10.1021/acs.analchem.6b04358] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Thomas N. Lawson
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Ralf J. M. Weber
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Martin R. Jones
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Andrew J. Chetwynd
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Giovanny Rodrı́guez-Blanco
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Riccardo Di Guida
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Mark R. Viant
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Warwick B. Dunn
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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A Metabolome-Wide Study of Dry Eye Disease Reveals Serum Androgens as Biomarkers. Ophthalmology 2017; 124:505-511. [PMID: 28139245 PMCID: PMC5375174 DOI: 10.1016/j.ophtha.2016.12.011] [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] [Received: 08/30/2016] [Revised: 11/28/2016] [Accepted: 12/08/2016] [Indexed: 01/24/2023] Open
Abstract
PURPOSE To test the association between serum metabolites and dry eye disease (DED) using a hypothesis-free metabolomics approach. DESIGN Cross-sectional association study. PARTICIPANTS A total of 2819 subjects from the population-representative TwinsUK cohort in the United Kingdom, with a mean age of 57 years (range, 17-82 years). METHODS We tested associations between 222 known serum metabolites and DED. All subjects underwent nontargeted metabolomic analysis of plasma samples using gas and liquid chromatography in combination with mass spectrometry (Metabolon Inc., Durham, NC). Dry eye disease was defined from the validated Short Questionnaire for Dry Eye Syndrome (SQDES) as a previous diagnosis of DED by a clinician or "often" or "constant" symptoms of dryness and irritation. Analyses were performed with linear mixed effect models that included age, BMI, and sex as covariates, corrected for multiple testing. MAIN OUTCOME MEASURES Primary outcome was DED as defined by the SQDES, and secondary outcomes were symptom score of DED and a clinical diagnosis of DED. RESULTS Prevalence of DED as defined by the SQDES was 15.5% (n = 436). A strong and metabolome-wide significant association with DED was found with decreased levels of the metabolites androsterone sulfate (P = 0.00030) and epiandrosterone sulfate (P = 0.00036). Three other metabolites involved in androgen metabolism, 4-androsten-3beta,17beta-diol disulfate 1 and 2, and dehydroepiandrosterone sulfate, were the next most strongly associated of the 222 metabolites, but did not reach metabolome-wide significance. Dryness and irritation symptoms, as opposed to a clinical diagnosis, were particularly strongly associated with decreased androgen steroid metabolites, with all reaching metabolome-wide significance (androsterone sulfate, P = 0.000000029; epiandrosterone sulfate, P = 0.0000040; 4-androsten-3beta,17beta-diol disulfate 1, P = 0.000016; 4-androsten-3beta,17beta-diol disulfate 2, P = 0.000064; and dehydroepiandrosterone sulfate, P = 0.00011). Of these 5 androgens, epiandrosterone sulfate (P = 0.0076) was most associated with 2-year incidence of clinician-diagnosed DED. In addition, we found decreased glycerophosphocholines to be associated with DED, although not at metabolome-wide significance. CONCLUSIONS This hypothesis-free metabolomic approach found decreased serum androgens to be highly associated with DED and adds important evidence to the growing body of research that links androgens to ocular surface disease and DED.
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Warcoin E, Baudouin C, Gard C, Brignole-Baudouin F. In Vitro Inhibition of NFAT5-Mediated Induction of CCL2 in Hyperosmotic Conditions by Cyclosporine and Dexamethasone on Human HeLa-Modified Conjunctiva-Derived Cells. PLoS One 2016; 11:e0159983. [PMID: 27486749 PMCID: PMC4972436 DOI: 10.1371/journal.pone.0159983] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 07/12/2016] [Indexed: 01/13/2023] Open
Abstract
Purpose To investigate the pro-inflammatory intracellular mechanisms induced by an in vitro model of dry eye disease (DED) on a Hela-modified conjunctiva-derived cells in hyperosmolarity (HO) stress conditions. This study focused on CCL2 induction and explored the implications of the nuclear factor of activated T-cells 5 (NFAT5) as well as mitogen-activated protein kinases (MAPK) and nuclear factor kappa B (NFĸB). This work was completed by an analysis of the effects of cyclosporine A (CsA), dexamethasone (Dex) and doxycycline (Dox) on HO-induced CCL2 and NFAT5 induction. Methods A human HeLa-modified conjunctiva-derived cell line was cultured in NaCl-hyperosmolar medium for various exposure times. Cellular viability, CCL2 secretion, NFAT5 and CCL2 gene expression, and intracytoplasmic NFAT5 were assessed using the Cell Titer Blue® assay, enzyme-linked immunosorbent assay (ELISA), RT-qPCR and immunostaining, respectively. In selected experiments, inhibitors of MAPKs or NFκB, therapeutic agents or NFAT5 siRNAs were added before the hyperosmolar stimulations. Results HO induced CCL2 secretion and expression as well as NFAT5 gene expression and translocation. Adding NFAT5-siRNA before hyperosmolar stimulation led to a complete inhibition of CCL2 induction and to a decrease in cellular viability. p38 MAPK (p38), c-Jun NH2-terminal kinase (JNK) and NFĸB inhibitors, CsA and Dex induced a partial inhibition of HO-induced CCL2, while Dox and extracellular signal-regulated kinase (ERK) inhibitor did not. Dex also induced a partial inhibition of HO-induced NFAT5 gene expression but not CsA or Dox. Conclusions These in vitro results suggest a potential role of CCL2 in DED and highlight the crucial role of NFAT5 in the pro-inflammatory effect of HO on HeLa-modified conjunctiva-derived cells, a rarely studied cellular type. This inflammatory pathway involving NFAT5 and CCL2 could offer a promising target for developing new therapies to treat DED, warranting further investigations to fully grasp the complete intracellular mechanisms.
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Affiliation(s)
- Elise Warcoin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
- CHNO des Quinze-Vingts, Service Pharmacie, Paris, France
- * E-mail: (EW); (FB)
| | - Christophe Baudouin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
- CHNO des Quinze-Vingts, Service III, Paris, France
| | | | - Françoise Brignole-Baudouin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
- Faculté de Pharmacie de Paris, Univ Paris Descartes, Sorbonne Paris Cité, Paris, France
- * E-mail: (EW); (FB)
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