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Hammid A, Honkakoski P. Ocular Drug-Metabolizing Enzymes: Focus on Esterases. Drug Metab Rev 2024:1-23. [PMID: 38888291 DOI: 10.1080/03602532.2024.2368247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Affiliation(s)
- Anam Hammid
- School of Pharmacy, University of Eastern Finland, Yliopistonrinne3, FI-70210 Kuopio, Finland
| | - Paavo Honkakoski
- School of Pharmacy, University of Eastern Finland, Yliopistonrinne3, FI-70210 Kuopio, Finland
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2
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Jiang J, Kong K, Fang X, Wang D, Zhang Y, Wang P, Yang Z, Zhang Y, Liu X, Aung T, Li F, Yu-Wai-Man P, Zhang X. CRISPR-Cas9-mediated deletion of carbonic anhydrase 2 in the ciliary body to treat glaucoma. Cell Rep Med 2024; 5:101524. [PMID: 38670096 PMCID: PMC11148640 DOI: 10.1016/j.xcrm.2024.101524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/27/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024]
Abstract
The carbonic anhydrase 2 (Car2) gene encodes the primary isoenzyme responsible for aqueous humor (AH) production and plays a major role in the regulation of intraocular pressure (IOP). The CRISPR-Cas9 system, based on the ShH10 adenovirus-associated virus, can efficiently disrupt the Car2 gene in the ciliary body. With a single intravitreal injection, Car2 knockout can significantly and sustainably reduce IOP in both normal mice and glaucoma models by inhibiting AH production. Furthermore, it effectively delays and even halts glaucomatous damage induced by prolonged high IOP in a chronic ocular hypertension model, surpassing the efficacy of clinically available carbonic anhydrase inhibitors such as brinzolamide. The clinical application of CRISPR-Cas9 based disruption of Car2 is an attractive therapeutic strategy that could bring additional benefits to patients with glaucoma.
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Affiliation(s)
- Jiaxuan Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Disease, Guangzhou 510060, China
| | - Kangjie Kong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Disease, Guangzhou 510060, China
| | - Xiuli Fang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Disease, Guangzhou 510060, China
| | - Deming Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Disease, Guangzhou 510060, China
| | - Yinhang Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Disease, Guangzhou 510060, China
| | - Peiyuan Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Disease, Guangzhou 510060, China
| | - Zefeng Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Disease, Guangzhou 510060, China
| | - Yuwei Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Disease, Guangzhou 510060, China
| | - Xiaoyi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Disease, Guangzhou 510060, China
| | - Tin Aung
- Singapore Eye Research Institute and Singapore National Eye Centre, Singapore, Singapore; National University of Singapore, Singapore, Singapore
| | - Fei Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Disease, Guangzhou 510060, China.
| | - Patrick Yu-Wai-Man
- Cambridge Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK; Moorfields Eye Hospital, London, UK; UCL Institute of Ophthalmology, University College London, London, UK.
| | - Xiulan Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Disease, Guangzhou 510060, China.
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3
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He T, Liu Y, Zhou Y, Li L, Wang H, Chen S, Gao J, Jiang W, Yu Y, Ge W, Chang HY, Fan Z, Nesvizhskii AI, Guo T, Sun Y. Comparative Evaluation of Proteome Discoverer and FragPipe for the TMT-Based Proteome Quantification. J Proteome Res 2022; 21:3007-3015. [PMID: 36315902 DOI: 10.1021/acs.jproteome.2c00390] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Isobaric labeling-based proteomics is widely applied in deep proteome quantification. Among the platforms for isobaric labeled proteomic data analysis, the commercial software Proteome Discoverer (PD) is widely used, incorporating the search engine CHIMERYS, while FragPipe (FP) is relatively new, free for noncommercial purposes, and integrates the engine MSFragger. Here, we compared PD and FP over three public proteomic data sets labeled using 6plex, 10plex, and 16plex tandem mass tags. Our results showed the protein abundances generated by the two software are highly correlated. PD quantified more proteins (10.02%, 15.44%, 8.19%) than FP with comparable NA ratios (0.00% vs. 0.00%, 0.85% vs. 0.38%, and 11.74% vs. 10.52%) in the three data sets. Using the 16plex data set, PD and FP outputs showed high consistency in quantifying technical replicates, batch effects, and functional enrichment in differentially expressed proteins. However, FP saved 93.93%, 96.65%, and 96.41% of processing time compared to PD for analyzing the three data sets, respectively. In conclusion, while PD is a well-maintained commercial software integrating various additional functions and can quantify more proteins, FP is freely available and achieves similar output with a shorter computational time. Our results will guide users in choosing the most suitable quantification software for their needs.
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Affiliation(s)
- Tianen He
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, No.18 Shilongshan Road, Hangzhou 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, No.18 Shilongshan Road, Hangzhou 310024, China.,Research Center for Industries of the Future, Westlake University, No.600 Dunyu Road, Hangzhou 310030, China.,School of Life Sciences, Peking University, No.5 Yiheyuan Road, Beijing 100871, China
| | - Youqi Liu
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., No.1 Yunmeng Road, Hangzhou 310024, China
| | - Yan Zhou
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, No.18 Shilongshan Road, Hangzhou 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, No.18 Shilongshan Road, Hangzhou 310024, China.,Research Center for Industries of the Future, Westlake University, No.600 Dunyu Road, Hangzhou 310030, China
| | - Lu Li
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, No.18 Shilongshan Road, Hangzhou 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, No.18 Shilongshan Road, Hangzhou 310024, China.,Research Center for Industries of the Future, Westlake University, No.600 Dunyu Road, Hangzhou 310030, China
| | - He Wang
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, No.18 Shilongshan Road, Hangzhou 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, No.18 Shilongshan Road, Hangzhou 310024, China.,Research Center for Industries of the Future, Westlake University, No.600 Dunyu Road, Hangzhou 310030, China
| | - Shanjun Chen
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., No.1 Yunmeng Road, Hangzhou 310024, China
| | - Jinlong Gao
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, No.18 Shilongshan Road, Hangzhou 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, No.18 Shilongshan Road, Hangzhou 310024, China.,Research Center for Industries of the Future, Westlake University, No.600 Dunyu Road, Hangzhou 310030, China
| | - Wenhao Jiang
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, No.18 Shilongshan Road, Hangzhou 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, No.18 Shilongshan Road, Hangzhou 310024, China.,Research Center for Industries of the Future, Westlake University, No.600 Dunyu Road, Hangzhou 310030, China
| | - Yi Yu
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., No.1 Yunmeng Road, Hangzhou 310024, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., No.1 Yunmeng Road, Hangzhou 310024, China
| | - Hui-Yin Chang
- Department of Pathology; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Biomedical Sciences and Engineering, National Central University, Taoyuan City 320317, Taiwan
| | - Ziquan Fan
- Thermo Fisher Scientific, No.2517 Jinke Road, Shanghai 201203, China
| | - Alexey I Nesvizhskii
- Department of Pathology; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tiannan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, No.18 Shilongshan Road, Hangzhou 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, No.18 Shilongshan Road, Hangzhou 310024, China.,Research Center for Industries of the Future, Westlake University, No.600 Dunyu Road, Hangzhou 310030, China
| | - Yaoting Sun
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, No.18 Shilongshan Road, Hangzhou 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, No.18 Shilongshan Road, Hangzhou 310024, China.,Research Center for Industries of the Future, Westlake University, No.600 Dunyu Road, Hangzhou 310030, China
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4
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Grigoryan EN. Pigment Epithelia of the Eye: Cell-Type Conversion in Regeneration and Disease. Life (Basel) 2022; 12:life12030382. [PMID: 35330132 PMCID: PMC8955580 DOI: 10.3390/life12030382] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 12/17/2022] Open
Abstract
Pigment epithelial cells (PECs) of the retina (RPE), ciliary body, and iris (IPE) are capable of altering their phenotype. The main pathway of phenotypic switching of eye PECs in vertebrates and humans in vivo and/or in vitro is neural/retinal. Besides, cells of amphibian IPE give rise to the lens and its derivatives, while mammalian and human RPE can be converted along the mesenchymal pathway. The PECs’ capability of conversion in vivo underlies the lens and retinal regeneration in lower vertebrates and retinal diseases such as proliferative vitreoretinopathy and fibrosis in mammals and humans. The present review considers these processes studied in vitro and in vivo in animal models and in humans. The molecular basis of conversion strategies in PECs is elucidated. Being predetermined onto- and phylogenetically, it includes a species-specific molecular context, differential expression of transcription factors, signaling pathways, and epigenomic changes. The accumulated knowledge regarding the mechanisms of PECs phenotypic switching allows the development of approaches to specified conversion for many purposes: obtaining cells for transplantation, creating conditions to stimulate natural regeneration of the retina and the lens, blocking undesirable conversions associated with eye pathology, and finding molecular markers of pathology to be targets of therapy.
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Affiliation(s)
- Eleonora N Grigoryan
- Kol'tsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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5
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Proteomic Analysis of Leishmania donovani Membrane Components Reveals the Role of Activated Protein C Kinase in Host-Parasite Interaction. Pathogens 2021; 10:pathogens10091194. [PMID: 34578226 PMCID: PMC8465321 DOI: 10.3390/pathogens10091194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 12/05/2022] Open
Abstract
Visceral leishmaniasis (VL), mainly caused by the Leishmania donovani parasitic infection, constitutes a potentially fatal disease, for which treatment is primarily dependent on chemotherapy. The emergence of a resistant parasite towards current antileishmanial agents and increasing reports of relapses are the major concerns. Detailed research on the molecular interaction at the host-parasite interface may provide the identification of the parasite and the host-related factors operating during disease development. Genomic and proteomic studies highlighted several essential secretory and cytosolic proteins that play vital roles during Leishmania pathogenesis. The aim of this study was to identify membrane proteins from the Leishmania donovani parasite and the host macrophage that interact with each other using 2-DE/MALDI-TOF/MS. We identified membrane proteins including activated protein C kinase, peroxidoxin, small myristoylated protein 1 (SMP-1), and cytochrome C oxidase from the parasite, while identifying filamin A interacting protein 1(FILIP1) and β-actin from macrophages. We further investigated parasite replication and persistence within macrophages following the macrophage-amastigote model in the presence or absence of withaferin (WA), an inhibitor of activated C kinase. WA significantly reduced Leishmania donovani replication within host macrophages. This study sheds light on the important interacting proteins for parasite proliferation and virulence, and the establishment of infection within host cells, which can be targeted further to develop a strategy for chemotherapeutic intervention.
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6
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Abstract
The diseases affecting the retina or uvea (iris, ciliary body, or choroid) generate changes in the biochemical or protein composition of ocular fluids/tissues due to disruption of blood-retinal barrier. Ocular infections and inflammations are sight-threatening diseases associated with various infectious and non-infectious etiologies. Several etiological entities cause uveitis, a complex intraocular inflammatory disease. These causes of uveitis differ in different populations due to geographical, racial, and socioeconomic variations. While clinical appearance is sufficiently diagnostic in many diseases, some of the uveitic entities manifest nonspecific or atypical clinical presentation. Identification of biomarkers in such diseases is an important aid in their diagnostic armamentarium. Different diseases and their different severity states release varying concentrations of proteins, which can serve as biomarkers. Proteomics is a high throughput technology and a powerful screening tool for serum biomarkers in various diseases that identifies proteins by mass spectrometry and helps to improve the understanding of pathogenesis of a disease. Proteins determine the biological state of a cell. Once identified as biomarkers, they serve as future diagnostic and pharmaceutical targets. With a potential to redirect the diagnosis of idiopathic uveitis, ocular proteomics provide a new insight into the pathophysiology and therapeutics of various ocular inflammatory diseases. Tears, aqueous and vitreous humor represent potential repositories for proteomic biomarkers discovery in uveitis. With an extensive proteomics work done on animal models of uveitis, various types of human uveitis are being subjected to proteome analysis for biomarker discovery in different ocular fluids (vitreous, aqueous, or tears).
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Affiliation(s)
- Reema Bansal
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Amod Gupta
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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7
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Killer HE, Pircher A. What is the optimal glaucoma treatment: reducing aqueous humour production or facilitating its outflow? Eye (Lond) 2020; 34:1719-1721. [PMID: 32415188 PMCID: PMC7608181 DOI: 10.1038/s41433-020-0862-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/24/2020] [Indexed: 12/02/2022] Open
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8
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Grigoryan EN. Potential Endogenous Cell Sources for Retinal Regeneration in Vertebrates and Humans: Progenitor Traits and Specialization. Biomedicines 2020; 8:E208. [PMID: 32664635 PMCID: PMC7400588 DOI: 10.3390/biomedicines8070208] [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: 06/05/2020] [Revised: 07/04/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022] Open
Abstract
Retinal diseases often cause the loss of photoreceptor cells and, consequently, impairment of vision. To date, several cell populations are known as potential endogenous retinal regeneration cell sources (RRCSs): the eye ciliary zone, the retinal pigment epithelium, the iris, and Müller glia. Factors that can activate the regenerative responses of RRCSs are currently under investigation. The present review considers accumulated data on the relationship between the progenitor properties of RRCSs and the features determining their differentiation. Specialized RRCSs (all except the ciliary zone in low vertebrates), despite their differences, appear to be partially "prepared" to exhibit their plasticity and be reprogrammed into retinal neurons due to the specific gene expression and epigenetic landscape. The "developmental" characteristics of RRCS gene expression are predefined by the pathway by which these cell populations form during eye morphogenesis; the epigenetic features responsible for chromatin organization in RRCSs are under intracellular regulation. Such genetic and epigenetic readiness is manifested in vivo in lower vertebrates and in vitro in higher ones under conditions permissive for cell phenotype transformation. Current studies on gene expression in RRCSs and changes in their epigenetic landscape help find experimental approaches to replacing dead cells through recruiting cells from endogenous resources in vertebrates and humans.
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Affiliation(s)
- Eleonora N Grigoryan
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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9
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Roy S, Goel R, Aggarwal S, Asthana S, Yadav AK, Awasthi A. Proteome analysis revealed the essential functions of protein phosphatase PP2A in the induction of Th9 cells. Sci Rep 2020; 10:10992. [PMID: 32620893 PMCID: PMC7335106 DOI: 10.1038/s41598-020-67845-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 06/11/2020] [Indexed: 12/25/2022] Open
Abstract
Proteomic analysis identifies post-translational functions of proteins, which remains obscure in transcriptomics. Given the important functions of Th9 cells in anti-tumor immunity, we performed proteome analysis of Th9 cells to understand the involvement of proteins that might be crucial for the anti-tumor functions of Th9 cells. Here we performed a comprehensive proteomic analysis of murine Th0 and Th9 cells, and identified proteins that are enriched in Th9 cells. Pathway analysis identified an abundance of phosphoproteins in the proteome of Th9 cells as compared to Th0 cells. Among upregulated phosphoproteins, Ppp2ca (catalytic subunit of protein phosphatase, PP2A) was found to be highly enriched in Th9 cells. Although the role of PP2A has been shown to regulate the differentiation and functions of Th1, Th2, Th17 and Tregs, its role in the differentiation and functions of Th9 cells is not identified yet. Here we found that PP2A is required for the induction of Th9 cells, as PP2A inhibition leads to the suppression of IL-9 and expression of key transcription factors of Th9 cells. PP2A inhibition abrogates Th9 cell-mediated anti-tumor immune response in B16-OVA melanoma tumor model. Thus, we report that PP2A is essential for the differentiation and anti-tumor functions of Th9 cells.
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Affiliation(s)
- Suyasha Roy
- Immuno-Biology Laboratory, Translational Health Science and Technology Institute (THSTI), 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad, Haryana, 121 001, India
| | - Renu Goel
- Drug Discovery Research Centre, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Suruchi Aggarwal
- Drug Discovery Research Centre, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Shailendra Asthana
- Drug Discovery Research Centre, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Kumar Yadav
- Drug Discovery Research Centre, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Awasthi
- Immuno-Biology Laboratory, Translational Health Science and Technology Institute (THSTI), 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad, Haryana, 121 001, India.
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10
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Taunk K, Kalita B, Kale V, Chanukuppa V, Naiya T, Zingde SM, Rapole S. The development and clinical applications of proteomics: an Indian perspective. Expert Rev Proteomics 2020; 17:433-451. [PMID: 32576061 DOI: 10.1080/14789450.2020.1787157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Proteomic research has been extensively used to identify potential biomarkers or targets for various diseases. Advances in mass spectrometry along with data analytics have led proteomics to become a powerful tool for exploring the critical molecular players associated with diseases, thereby, playing a significant role in the development of proteomic applications for the clinic. AREAS COVERED This review presents recent advances in the development and clinical applications of proteomics in India toward understanding various diseases including cancer, metabolic diseases, and reproductive diseases. Keywords combined with 'clinical proteomics in India' 'proteomic research in India' and 'mass spectrometry' were used to search PubMed. EXPERT OPINION The past decade has seen a significant increase in research in clinical proteomics in India. This approach has resulted in the development of proteomics-based marker technologies for disease management in the country. The majority of these investigations are still in the discovery phase and efforts have to be made to address the intended clinical use so that the identified potential biomarkers reach the clinic. To move toward this necessity, there is a pressing need to establish some key infrastructure requirements and meaningful collaborations between the clinicians and scientists which will enable more effective solutions to address health issues specific to India.
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Affiliation(s)
- Khushman Taunk
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India.,Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal , Haringhata, West Bengal, India
| | - Bhargab Kalita
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
| | - Vaikhari Kale
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
| | | | - Tufan Naiya
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal , Haringhata, West Bengal, India
| | - Surekha M Zingde
- CH3-53, Kendriya Vihar, Sector 11, Kharghar , Navi Mumbai, Maharashtra, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
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11
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Mohanty V, Pinto SM, Subbannayya Y, Najar MA, Murthy KB, Prasad TSK, Murthy KR. Digging Deeper for the Eye Proteome in Vitreous Substructures: A High-Resolution Proteome Map of the Normal Human Vitreous Base. ACTA ACUST UNITED AC 2020; 24:379-389. [DOI: 10.1089/omi.2020.0020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sneha M. Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Mohd. Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Kalpana Babu Murthy
- Department of vitreo retina, Vittala International Institute of Ophthalmology, Bangalore, India
- Department of vitreo retina, Prabha Eye Clinic and Research Centre, Bangalore, India
| | | | - Krishna R. Murthy
- Department of vitreo retina, Vittala International Institute of Ophthalmology, Bangalore, India
- Department of vitreo retina, Prabha Eye Clinic and Research Centre, Bangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, India
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12
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CPAMD8 loss-of-function underlies non-dominant congenital glaucoma with variable anterior segment dysgenesis and abnormal extracellular matrix. Hum Genet 2020; 139:1209-1231. [PMID: 32274568 DOI: 10.1007/s00439-020-02164-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/03/2020] [Indexed: 01/08/2023]
Abstract
Abnormal development of the ocular anterior segment may lead to a spectrum of clinical phenotypes ranging from primary congenital glaucoma (PCG) to variable anterior segment dysgenesis (ASD). The main objective of this study was to identify the genetic alterations underlying recessive congenital glaucoma with ASD (CG-ASD). Next-generation DNA sequencing identified rare biallelic CPAMD8 variants in four patients with CG-ASD and in one case with PCG. CPAMD8 is a gene of unknown function and recently associated with ASD. Bioinformatic and in vitro functional evaluation of the variants using quantitative reverse transcription PCR and minigene analysis supported a loss-of-function pathogenic mechanism. Optical and electron microscopy of the trabeculectomy specimen from one of the CG-ASD cases revealed an abnormal anterior chamber angle, with altered extracellular matrix, and apoptotic trabecular meshwork cells. The CPAMD8 protein was immunodetected in adult human ocular fluids and anterior segment tissues involved in glaucoma and ASD (i.e., aqueous humor, non-pigmented ciliary epithelium, and iris muscles), as well as in periocular mesenchyme-like cells of zebrafish embryos. CRISPR/Cas9 disruption of this gene in F0 zebrafish embryos (96 hpf) resulted in varying degrees of gross developmental abnormalities, including microphthalmia, pharyngeal maldevelopment, and pericardial and periocular edemas. Optical and electron microscopy examination of these embryos showed iridocorneal angle hypoplasia (characterized by altered iris stroma cells, reduced anterior chamber, and collagen disorganized corneal stroma extracellular matrix), recapitulating some patients' features. Our data support the notion that CPAMD8 loss-of-function underlies a spectrum of recessive CG-ASD phenotypes associated with extracellular matrix disorganization and provide new insights into the normal and disease roles of this gene.
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13
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Subbannayya Y, Pinto SM, Mohanty V, Dagamajalu S, Prasad TSK, Murthy KR. What Makes Cornea Immunologically Unique and Privileged? Mechanistic Clues from a High-Resolution Proteomic Landscape of the Human Cornea. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:129-139. [PMID: 32125911 DOI: 10.1089/omi.2019.0190] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Success rates of corneal transplantation are particularly high owing to its unique, innate immune privilege derived from a phenomenon known as Anterior Chamber-Associated Immune Deviation (ACAID). Of note, cornea is a transparent, avascular structure that acts as a barrier along with sclera to protect the eye and contributes to optical power. Molecular and systems biology mechanisms underlying ACAID and the immunologically unique and privileged status of cornea are not well known. We report here a global unbiased proteomic profiling of the human cornea and the identification of 4824 proteins, the largest catalog of human corneal proteins identified to date. Moreover, signaling pathway analysis revealed enrichment of spliceosome, phagosome, lysosome, and focal adhesion pathways, thereby demonstrating the protective functions of corneal proteins. We observed an enrichment of neutrophil-mediated immune response processes in the cornea as well as proteins belonging to the complement and ER-Phagosome pathways that are suggestive of active immune and inflammatory surveillance response. This study provides a key expression map of the corneal proteome repertoire that should enable future translational medicine studies on the pathological conditions of the cornea and the mechanisms by which cornea immunology are governed. Molecular mechanisms of corneal immune privilege have broad relevance to understand and anticipate graft rejection in the field of organ transplantation.
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Affiliation(s)
- Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | | | - Krishna R Murthy
- Vittala International Institute of Ophthalmology, Bangalore, India.,Prabha Eye Clinic and Research Centre, Bangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
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14
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Choudhary J, Singh S, Tiwari R, Goel R, Nain L. An iTRAQ Based Comparative Proteomic Profiling of Thermotolerant Saccharomyces cerevisiae JRC6 in Response to High Temperature Fermentation. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164616666190131145217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Bioethanol derived from lignocellulosic biomass can supplement the ethanol
supplies in a sustainable manner. However, the bioethanol production process is still not cost effective
and researchers are looking for novel strategies like simultaneous saccharification fermentation to cut
down the production cost. Thermotolerant yeast Saccharomyces cerevisiae JRC6 is reported to improve
the fermentation efficiency under SSF. However, the mechanism of thermotolerance of the
strain is unknown which is important for developing more robust yeast strains for simultaneous saccharification
and fermentation.
Objective:
To identify proteomic changes responsible for imparting thermotolerance by iTRAQ based
profiling of Saccharomyces cerevisiae JRC6 by growing at optimum (30°C) and high temperature (40°C).
Methods: iTRAQ labeling followed by electrospray ionization based tandem mass spectrometry using
SCIEX 5600 Triple-TOF Mass Spectrometer (MS).
Methods:
iTRAQ labeling followed by electrospray ionization based tandem mass spectrometry using
SCIEX 5600 Triple-TOF Mass Spectrometer (MS).
Results:
A total of 582 proteins involved in heat shock, metabolism, biosynthesis, transport of biomolecules,
cell division, etc. were identified. Cells grown at 40°C showed many-fold increase in the
expression for many proteins involved in different functions specially biosynthesis, heat stress and metabolism.
At 40°C heat shock proteins (78), prefoldin subunit (6), DNA binding protein SNT1, J type
co-chaperone JAC1, elongation factor 1-β, glutathione synthase, malate synthase (2), purine biosynthesis
protein ADE17, SSD1 protein, alcohol dehydrogenase 1, 3, 60S ribosomal protein L35-B, mitochondrial
import protein MAS5 and many other proteins were significantly upregulated.
Conclusion:
The iTRAQ analysis revealed many heat shock proteins and heat stable alcohol dehydrogenases
which can be exploited to develop a more robust yeast strain suitable for simultaneous saccharification
and fermentation or consolidated bioprocessing.
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Affiliation(s)
- Jairam Choudhary
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
| | - Surender Singh
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
| | - Rameshwar Tiwari
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
| | - Renu Goel
- Drug Discovery Research Centre (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad - 121001, India
| | - Lata Nain
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
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15
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Suri F, Yazdani S, Chapi M, Safari I, Rasooli P, Daftarian N, Jafarinasab MR, Ghasemi Firouzabadi S, Alehabib E, Darvish H, Klotzle B, Fan JB, Turk C, Elahi E. COL18A1 is a candidate eye iridocorneal angle-closure gene in humans. Hum Mol Genet 2019; 27:3772-3786. [PMID: 30007336 DOI: 10.1093/hmg/ddy256] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 07/05/2018] [Indexed: 01/09/2023] Open
Abstract
Primary angle-closure glaucoma (PACG) is a common form of glaucoma in the Far East. Its defining feature is iridocorneal angle closure. In addition to PACG, indications of angle closure are included in the diagnostic criteria of related conditions primary angle-closure suspect (PACS) and primary angle closure (PAC). To the best of our knowledge, a causative gene for iridocorneal angle closure in humans has not been identified. This study aimed to identify the genetic cause of iridocorneal angle closure in a pedigree with at least 10 individuals diagnosed with PACS, PAC or PACG. Results of linkage analysis, segregation analysis of 44 novel variations, whole exome sequencing of 10 individuals, screenings of controls and bioinformatics predictions identified a mutation in COL18A1 that encodes collagen type XVIII as the most likely cause of angle closure in the pedigree. The role of COL18A1 in the etiology of Knobloch syndrome (KS) that is consistently accompanied by optic anomalies, available functional data on the encoded protein and the recognized role of collagens and the extracellular matrix in glaucoma pathogenesis supported the proposed role of the COL18A1 mutation in the pedigree. Subsequent identification of other COL18A1 mutations in PACS affected individuals of two unrelated families further supported that COL18A1 may affect angle closure. These PACS individuals were parents and grandparents of KS-affected children. In conclusion, a gene that affects angle closure in humans, a critical feature of PACG, has been identified. The findings also reinforce the importance of collagens in eye features and functions.
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Affiliation(s)
- Fatemeh Suri
- Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,School of Biology, University College of Science, University of Tehran, Tehran, Iran
| | - Shahin Yazdani
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marjan Chapi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Iman Safari
- School of Biology, University College of Science, University of Tehran, Tehran, Iran
| | - Paniz Rasooli
- School of Biology, University College of Science, University of Tehran, Tehran, Iran
| | - Narsis Daftarian
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Jafarinasab
- Ophthalmic Epidemiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Elham Alehabib
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Darvish
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | | | | | | | - Elahe Elahi
- School of Biology, University College of Science, University of Tehran, Tehran, Iran.,Department of Biotechnology, University College of Science, University of Tehran, Tehran, Iran
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16
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Ahmad MT, Zhang P, Dufresne C, Ferrucci L, Semba RD. The Human Eye Proteome Project: Updates on an Emerging Proteome. Proteomics 2019; 18:e1700394. [PMID: 29356342 DOI: 10.1002/pmic.201700394] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/08/2018] [Indexed: 01/05/2023]
Abstract
The human eye is a complex organ consisting of multiple compartments with unique and specialized properties that reflect their varied functions. Although there have been advancements in ocular imaging and therapeutics over the past decade, the pathogenesis of many common eye diseases remains poorly understood. Proteomics is an invaluable tool to gain insight into pathogenesis, diagnosis, and treatment of eye diseases. By 2013, when the Human Eye Proteome Project (also known as the EyeOme) was founded, there were 4842 nonredundant proteins identified in the human eye. Twenty-three recent papers on the human eye proteome were identified in PubMed searches. These papers were used to compile an updated resource of 9782 nonredundant proteins in the human eye. This updated catalogue sheds light on the molecular makeup of previously undescribed proteomes within the human eye, including optic nerve, sclera, iris, and ciliary body, while adding additional proteins to previously characterized proteomes such as aqueous humor, lens, vitreous, retina, and retinal pigment epithelium/choroid. Although considerable advances have been made to characterize the complete proteome of the human eye, additional high-quality data are needed to confirm and quantify previously discovered eye proteins in both health and disease.
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Affiliation(s)
- Meleha T Ahmad
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pingbo Zhang
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Richard D Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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17
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Mohanty V, Subbannayya Y, Najar MA, Pinto SM, Kasaragod S, Karuppiah H, Sreeramulu B, Singh KK, Dalal S, Manikkoth S, Arunachalam C, Prasad TSK, Murthy KR. Proteomics and Visual Health Research: Proteome of the Human Sclera Using High-Resolution Mass Spectrometry. ACTA ACUST UNITED AC 2019; 23:98-110. [DOI: 10.1089/omi.2018.0185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Mohammed Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sneha M. Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sandeep Kasaragod
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Hilda Karuppiah
- Department of Zoology, University of Madras, Guindy Campus, Chennai, India
| | | | - Kunal Kumar Singh
- Department of Clinical Biochemistry, Pondicherry University, Puducherry, India
| | - Sunita Dalal
- Department of Biotechnology, Kurukshetra University, Kurukshetra, India
| | - Shyamjith Manikkoth
- Department of Pharmacology, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangalore, India
| | - Cynthia Arunachalam
- Department of Ophthalmology, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangalore, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Krishna R. Murthy
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Vittala International Institute of Ophthalmology, Bangalore, India
- Manipal Academy of Higher Education, Manipal, India
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18
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Karthikkeyan G, Subbannayya Y, Najar MA, Mohanty V, Pinto SM, Arunachalam C, Prasad TSK, Murthy KR. Human Optic Nerve: An Enhanced Proteomic Expression Profile. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 22:642-652. [PMID: 30346883 DOI: 10.1089/omi.2018.0130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Ophthalmology and visual health are new frontiers for postgenomic research and technologies such as proteomics. In this context, the optic nerve and retina extend as the outgrowth of the brain, wherein the latter receives the optical input and the former relays the information for processing. While efforts to understand the optic nerve proteome have been made earlier, there exists a lacuna in its biochemical composition and molecular functions. We report, in this study, a high-resolution mass spectrometry-based approach using an Orbitrap Fusion Tribrid mass spectrometer to elucidate the human optic nerve proteomic profile. Raw spectra were searched against NCBI Human RefSeq 75 database using SEQUEST HT and MASCOT algorithms. We identified nearly 35,000 peptides in human optic nerve samples, corresponding to 5682 proteins, of which 3222 proteins are being reported for the first time. Label-free quantification using spectral abundance pointed out to neuronal structural proteins such as myelin basic protein, glial fibrillary acidic protein, and proteolipid protein 1 as the most abundant proteins. We also identified several neurotransmitter receptors and postsynaptic density synaptosomal scaffold proteins. Pathway analysis revealed that a majority of the proteins are structural proteins and have catalytic and binding activity. This study is one of the largest proteomic profiles of the human optic nerve and offers the research community an initial baseline optic nerve proteome for further studies. This will also help understand the protein dynamics of the human optic nerve under normal conditions.
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Affiliation(s)
- Gayathree Karthikkeyan
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Yashwanth Subbannayya
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Mohd Altaf Najar
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Varshasnata Mohanty
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Sneha M Pinto
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Cynthia Arunachalam
- 2 Department of Ophthalmology, Yenepoya Medical College, Yenepoya (Deemed to be University) , Mangalore, India
| | - Thottethodi Subrahmanya Keshava Prasad
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India .,3 Institute of Bioinformatics , International Tech Park, Bangalore, Karnataka, India
| | - Krishna R Murthy
- 3 Institute of Bioinformatics , International Tech Park, Bangalore, Karnataka, India .,4 Vittala International Institute of Ophthalmology , Bangalore, Karnataka, India .,5 Manipal Academy of Higher Education , Manipal, Karnataka, India
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19
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Drewry MD, Challa P, Kuchtey JG, Navarro I, Helwa I, Hu Y, Mu H, Stamer WD, Kuchtey RW, Liu Y. Differentially expressed microRNAs in the aqueous humor of patients with exfoliation glaucoma or primary open-angle glaucoma. Hum Mol Genet 2018; 27:1263-1275. [PMID: 29401312 PMCID: PMC6048986 DOI: 10.1093/hmg/ddy040] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/27/2017] [Accepted: 01/16/2018] [Indexed: 12/16/2022] Open
Abstract
Both exfoliation glaucoma (XFG) and primary open-angle glaucoma (POAG) have been linked to decreased conventional outflow of aqueous humor (AH). To better understand the molecular changes in the AH content under such conditions, we analyzed the miRNA profiles of AH samples from patients with POAG and XFG compared to non-glaucoma controls. Individual AH samples (n = 76) were collected from POAG and XFG patients and age-matched controls during surgical procedure. After RNA extraction, the miRNA profiles were individually determined in 12 POAG, 12 XFG and 11 control samples. We identified 205, 295 and 195 miRNAs in the POAG, XFG and control samples, respectively. Our differential expression analysis identified three miRNAs (miR-125b-5p, miR-302d-3p and miR-451a) significantly different between POAG and controls, five miRNAs (miR-122-5p, miR-3144-3p, miR-320a, miR-320e and miR-630) between XFG and controls and one miRNA (miR-302d-3p) between POAG and XFG. While none of these miRNAs have been previously linked to glaucoma, miR-122-5p may target three glaucoma-associated genes: OPTN, TMCO1 and TGF-ß1. Pathway analysis revealed that these miRNAs are involved in potential glaucoma pathways, including focal adhesion, tight junctions, and TGF-ß signaling. Comparison of the miRNA profile in AH to unrelated human serum (n = 12) exposed potential relationships between these two fluids, although they were not significantly correlated. In summary, we have successfully profiled the miRNA expression without amplification in individual human AH samples and identified several POAG or XFG-associated miRNAs. These miRNAs may play a role in pathways previously implicated in glaucoma and act as biomarkers for disease pathogenesis.
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Affiliation(s)
- Michelle D Drewry
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta, GA, USA
| | - Pratap Challa
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | - John G Kuchtey
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Iris Navarro
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | - Inas Helwa
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta, GA, USA
| | - Yanzhong Hu
- Department of Cell Biology and Genetics, Henan University School of Medicine, Kaifeng, Henan, China
| | - Hongmei Mu
- Kaifeng Key Lab of Cataract and Myopia, Institute of Eye Diseases, Kaifeng Centre Hospital, Kaifeng, Henan, China
| | - W Daniel Stamer
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | - Rachel W Kuchtey
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta, GA, USA
- James and Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, USA
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA, USA
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20
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Salamanca D, Gómez-Chaparro JL, Hidalgo A, Labella F. Differential expression of proteome in aqueous humor in patients with and without glaucoma. ARCHIVOS DE LA SOCIEDAD ESPANOLA DE OFTALMOLOGIA 2018; 93:160-168. [PMID: 29439810 DOI: 10.1016/j.oftal.2017.12.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/20/2017] [Accepted: 12/06/2017] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To determine quantitative and qualitative differences of aqueous humor proteome in patients with and without glaucoma. METHOD Observational, descriptive and cross-sectional study of 12 patients (8 men; 4 women) with and without glaucoma. There are 3 groups of minority proteins with serum equimolar contribution of each of the patients. Specimens were obtained during cataract surgery from patients without glaucoma (performed with retrobulbar anaesthesia [cataract retrobulbar patient -CRP-;n=4] or topical [cataract topical patient -CTP-; n=4]), or from patients with glaucoma (performed with retrobulbar anaesthesia [glaucoma retrobulbar patient -GRP-; n=4]). The humor proteome samples were frozen at -80°C until processing by trypsin digestion to obtain tryptic peptides, and then performing liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) to obtain the proteome and its differential expression between groups. Statistical analysis was performed using the SPSS v.17 program. RESULTS The study included 12 patients, aged (mean±standard deviation) 74.50±9.53 years. Concentrations obtained: 0.48±0.25μg/μl for CRP, 0.28±0.04μg/μl for CTP, and 0.35±0.16μg/μl for GRP. A total of 309 proteins were identified, of which 205, 210, and 182 were in CRP, CTP, and GRP, respectively. A total of 114 proteins were common to all three groups, 50 were exclusive to CRP, 58 to CTP, and 27 to GRP. CONCLUSIONS In this pilot study, a quantitative difference was found in the protein expression of humor among patients with glaucoma, there being 27 proteins unique to patients with glaucomatous disease.
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Affiliation(s)
- D Salamanca
- Universidad de Córdoba (UCO), Córdoba, España.
| | - J L Gómez-Chaparro
- Distrito Córdoba-Guadalquivir (SAS), Córdoba, España; Instituto de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, España
| | - A Hidalgo
- Departamento de Neuro-Oftalmología, Uveítis, Inmunología y Glaucoma, Hospital La Arruzafa, Córdoba, España
| | - F Labella
- Universidad de Córdoba (UCO), Córdoba, España
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21
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Margolis MJ, Martinez M, Valencia J, Lee RK, Bhattacharya SK. Phospholipid secretions of organ cultured ciliary body. J Cell Biochem 2017; 119:2556-2566. [PMID: 28981155 DOI: 10.1002/jcb.26419] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/03/2017] [Indexed: 12/24/2022]
Abstract
Homeostasis of intraocular pressure (IOP) is important for the maintenance of anterior eye anatomic integrity, minimizing pressure-associated damage to the optic nerve, and maintaining a pressure gradient for blood flow to the eye. IOP is regulated by equilibrium between aqueous humor (AH) production and its outflow. The ciliary body (CB) is thought to actively secrete AH. However, whether AH composition and in particular, its phospholipids are entirely due to CB secretion remains uncertain. Comparison of phospholipids released by cultured CB, phospholipids present within CB tissue, within AH, and within blood and serum are consistent with release of most phospholipids into the AH by the CB. Treatment of CB in culture with timolol, a non-specific beta-adrenergic antagonist, alters the release of phospholipids by CB into the media. However, dorzalamide, a carbonic anhydrase inhibitor that reduces production of AH, does not affect phospholipid release thereby suggesting timolol, which also decreases IOP through decreased AH outflow, affects other physiological homeostatic mechanisms regulating aqueous outflow. These outflow changes also affect the composition of secreted phospholipids. We present evidence that release of lipids by the CB has a prolonged survival effect on cultured primary TM cells and TM tissue.
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Affiliation(s)
- Michael J Margolis
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Mitchell Martinez
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Jeffrey Valencia
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Richard K Lee
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Sanjoy K Bhattacharya
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
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22
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Seo YM, Park SJ, Lee HK, Park JC. Copine-7 binds to the cell surface receptor, nucleolin, and regulates ciliogenesis and Dspp expression during odontoblast differentiation. Sci Rep 2017; 7:11283. [PMID: 28900213 PMCID: PMC5595916 DOI: 10.1038/s41598-017-11641-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/25/2017] [Indexed: 12/30/2022] Open
Abstract
Tooth development is a progressive process regulated by interactions between epithelial and mesenchymal tissues. Our previous studies showed that copine-7 (Cpne7), a dental epithelium-derived protein, is a signalling molecule that is secreted by preameloblasts and regulates the differentiation of preodontoblasts into odontoblasts. However, the mechanisms involved in the translocation of Cpne7 from preameloblasts to preodontoblasts and the functions of Cpne7 during odontogenesis are poorly understood. Here, we showed that the internalization of Cpne7 was mediated primarily by caveolae. This process was initiated by Cpne7 binding to the cell surface protein, nucleolin. Treatment with recombinant Cpne7 protein (rCpne7) in human dental pulp cells (hDPCs) caused an increase in the number of ciliated cells. The expression level of cilium components, Ift88 and Kif3a, and Dspp were increased by rCpne7. Treatment with Ift88 siRNA in hDPCs and MDPC-23 cells significantly down-regulated the expression of Dspp, an odontoblastic differentiation marker gene. Furthermore, the treatment with nucleolin siRNA in MDPC-23 cells decreased the expression of Dmp1, Dspp, and cilium components. Our findings suggested that the binding of Cpne7 with its receptor, nucleolin, has an important function involving Cpne7 internalization into preodontoblasts and regulation of Dspp expression through ciliogenesis during odontoblast differentiation.
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Affiliation(s)
- You-Mi Seo
- Department of Oral Histology-Developmental Biology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Su-Jin Park
- Department of Oral Histology-Developmental Biology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Hye-Kyung Lee
- Department of Oral Histology-Developmental Biology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Joo-Cheol Park
- Department of Oral Histology-Developmental Biology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea.
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23
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Hollmann AK, Dammann I, Wemheuer WM, Wemheuer WE, Chilla A, Tipold A, Schulz-Schaeffer WJ, Beck J, Schütz E, Brenig B. Morgagnian cataract resulting from a naturally occurring nonsense mutation elucidates a role of CPAMD8 in mammalian lens development. PLoS One 2017; 12:e0180665. [PMID: 28683140 PMCID: PMC5500361 DOI: 10.1371/journal.pone.0180665] [Citation(s) in RCA: 16] [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: 03/28/2017] [Accepted: 06/19/2017] [Indexed: 11/23/2022] Open
Abstract
To investigate the genetic basis of hereditary lens opacities we analyzed 31 cases of bilateral congenital cataract in Red Holstein Friesian cattle. A genome-wide association study revealed a significant association on bovine chromosome 7 at positions 6,166,179 and 12,429,691. Whole genome re-sequencing of one case and four relatives showed a nonsense mutation (g.5995966C>T) in the PZP-like, alpha-2-macroglobulin domain containing 8 (CPAMD8) gene leading to a premature stop codon (CPAMD8 p.Gln74*) associated with cataract development in cattle. With immunohistochemistry we confirmed a physiological expression of CPAMD8 in the ciliary body epithelium of the eye in unaffected cattle, while the protein was not detectable in the ciliary body of cattle with cataracts. RNA expression of CPAMD8 was detected in healthy adult, fetal and cataractous lenses.
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Affiliation(s)
- Anne K. Hollmann
- University of Goettingen, Institute of Veterinary Medicine, Goettingen, Germany
| | - Insa Dammann
- University Medical Center Goettingen, Department of Neuropathology, Prion and Dementia Research Unit, Goettingen, Germany
| | - Wiebke M. Wemheuer
- University of the Saarland, Institute of Neuropathology, Homburg, Germany
| | - Wilhelm E. Wemheuer
- University of Goettingen, Institute of Veterinary Medicine, Goettingen, Germany
| | - Almuth Chilla
- University of Goettingen, Institute of Veterinary Medicine, Goettingen, Germany
| | - Andrea Tipold
- University of Veterinary Medicine Hannover, Foundation, Department of Small Animal Medicine and Surgery, Hannover, Germany
| | | | | | - Ekkehard Schütz
- University of Goettingen, Institute of Veterinary Medicine, Goettingen, Germany
| | - Bertram Brenig
- University of Goettingen, Institute of Veterinary Medicine, Goettingen, Germany
- * E-mail:
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24
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Funke S, Perumal N, Bell K, Pfeiffer N, Grus FH. The potential impact of recent insights into proteomic changes associated with glaucoma. Expert Rev Proteomics 2017; 14:311-334. [PMID: 28271721 DOI: 10.1080/14789450.2017.1298448] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
INTRODUCTION Glaucoma, a major ocular neuropathy, is still far from being understood on a molecular scale. Proteomic workflows revealed glaucoma associated alterations in different eye components. By using state-of-the-art mass spectrometric (MS) based discovery approaches large proteome datasets providing important information about glaucoma related proteins and pathways could be generated. Corresponding proteomic information could be retrieved from various ocular sample species derived from glaucoma experimental models or from original human material (e.g. optic nerve head or aqueous humor). However, particular eye tissues with the potential for understanding the disease's molecular pathomechanism remains underrepresented. Areas covered: The present review provides an overview of the analysis depth achieved for the glaucomatous eye proteome. With respect to different eye regions and biofluids, proteomics related literature was found using PubMed, Scholar and UniProtKB. Thereby, the review explores the potential of clinical proteomics for glaucoma research. Expert commentary: Proteomics will provide important contributions to understanding the molecular processes associated with glaucoma. Sensitive discovery and targeted MS approaches will assist understanding of the molecular interplay of different eye components and biofluids in glaucoma. Proteomic results will drive the comprehension of glaucoma, allowing a more stringent disease hypothesis within the coming years.
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Affiliation(s)
- Sebastian Funke
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
| | - Natarajan Perumal
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
| | - Katharina Bell
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
| | - Norbert Pfeiffer
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
| | - Franz H Grus
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
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25
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Chen HY, Chou HC, Chang SJ, Liao EC, Tsai YT, Wei YS, Li JM, Lin LH, Lin MW, Chen YJ, Chen YS, Lin CC, Wang YS, Ko ML, Chan HL. Proteomic Analysis of Various Rat Ocular Tissues after Ischemia-Reperfusion Injury and Possible Relevance to Acute Glaucoma. Int J Mol Sci 2017; 18:ijms18020334. [PMID: 28165428 PMCID: PMC5343869 DOI: 10.3390/ijms18020334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 12/21/2022] Open
Abstract
Glaucoma is a group of eye diseases that can cause vision loss and optical nerve damage. To investigate the protein expression alterations in various intraocular tissues (i.e., the cornea, conjunctiva, uvea, retina, and sclera) during ischemia–reperfusion (IR) injury, this study performed a proteomic analysis to qualitatively investigate such alterations resulting from acute glaucoma. The IR injury model combined with the proteomic analysis approach of two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to monitor the protein expression alterations in two groups of specimens (an IR injury group and a control group). The analysis results revealed 221 unique differentially expressed proteins of a total of 1481 proteins in the cornea between the two groups. In addition, 97 of 1206 conjunctival proteins, 90 of 1354 uveal proteins, 61 of 1180 scleral proteins, and 37 of 1204 retinal proteins were differentially expressed. These findings imply that different ocular tissues have different tolerances against IR injury. To sum up, this study utilized the acute glaucoma model combined with 2D-DIGE and MALDI-TOF MS to investigate the IR injury affected protein expression on various ocular tissues, and based on the ratio of protein expression alterations, the alterations in the ocular tissues were in the following order: the cornea, conjunctiva, uvea, sclera, and retina.
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Affiliation(s)
- Hsin-Yi Chen
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Hsiu-Chuan Chou
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
- Center for Teacher Education, National Tsing Hua University, Hsinchu 300, Taiwan.
- Department of Applied Science, National Hsinchu University of Education, Hsinchu 300, Taiwan.
| | - Shing-Jyh Chang
- Gynecologic Oncology Section Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu 300, Taiwan.
| | - En-Chi Liao
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Yi-Ting Tsai
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Yu-Shan Wei
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Ji-Min Li
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Li-Hsun Lin
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Meng-Wei Lin
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Ying-Jen Chen
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Yu-Sheng Chen
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Chih-Chun Lin
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Yi-Shiuan Wang
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Mei-Lan Ko
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
- Department of Ophthalmology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu 300, Taiwan.
| | - Hong-Lin Chan
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
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26
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Dammalli M, Murthy KR, Pinto SM, Murthy KB, Nirujogi RS, Madugundu AK, Dey G, Nair B, Gowda H, Keshava Prasad TS. Toward Postgenomics Ophthalmology: A Proteomic Map of the Human Choroid–Retinal Pigment Epithelium Tissue. ACTA ACUST UNITED AC 2017; 21:114-122. [DOI: 10.1089/omi.2016.0170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Manjunath Dammalli
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, India
| | - Krishna R. Murthy
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Amrita School of Biotechnology, Amrita VishwaVidyapeetham, Kollam, India
- Vittala International Institute of Ophthalmology, Bangalore, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | | | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Anil K. Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Department of Biotechnology, Manipal University, Manipal, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita VishwaVidyapeetham, Kollam, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
- NIMHANS-IOB Bioinformatics and Proteomics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, India
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27
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Murthy KR, Dammalli M, Pinto SM, Murthy KB, Nirujogi RS, Madugundu AK, Dey G, Subbannayya Y, Mishra UK, Nair B, Gowda H, Prasad TK. A Comprehensive Proteomics Analysis of the Human Iris Tissue: Ready to Embrace Postgenomics Precision Medicine in Ophthalmology? OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:510-9. [DOI: 10.1089/omi.2016.0100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Krishna R. Murthy
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Amrita School of Biotechnology, Amrita VishwaVidyapeetham, Kollam, India
- Vittala International Institute of Ophthalmology, Bangalore, India
| | - Manjunath Dammalli
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | | | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Anil K. Madugundu
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Gourav Dey
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Manipal, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | | | - Bipin Nair
- Amrita School of Biotechnology, Amrita VishwaVidyapeetham, Kollam, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - T.S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
- NIMHANS-IOB Bioinformatics and Proteomics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, India
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28
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Zhang P, Kirby D, Dufresne C, Chen Y, Turner R, Ferri S, Edward DP, Van Eyk JE, Semba RD. Defining the proteome of human iris, ciliary body, retinal pigment epithelium, and choroid. Proteomics 2016; 16:1146-53. [PMID: 26834087 DOI: 10.1002/pmic.201500188] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 11/19/2015] [Accepted: 01/25/2016] [Indexed: 11/09/2022]
Abstract
The iris is a fine structure that controls the amount of light that enters the eye. The ciliary body controls the shape of the lens and produces aqueous humor. The retinal pigment epithelium and choroid (RPE/choroid) are essential in supporting the retina and absorbing light energy that enters the eye. Proteins were extracted from iris, ciliary body, and RPE/choroid tissues of eyes from five individuals and fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed using LC-MS/MS on an Orbitrap Elite mass spectrometer. In iris, ciliary body, and RPE/choroid, we identified 2959, 2867, and 2755 nonredundant proteins with peptide and protein false-positive rates of <0.1% and <1%, respectively. Forty-three unambiguous protein isoforms were identified in iris, ciliary body, and RPE/choroid. Four "missing proteins" were identified in ciliary body based on ≥2 proteotypic peptides. The mass spectrometric proteome database of the human iris, ciliary body, and RPE/choroid may serve as a valuable resource for future investigations of the eye in health and disease. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001424 and PXD002194.
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Affiliation(s)
- Pingbo Zhang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Kirby
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Yan Chen
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Randi Turner
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sara Ferri
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Deepak P Edward
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,King Khaled Eye Specialist Hospital, Riyadh, Kingdom of Saudi Arabia
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Medicine, The Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Richard D Semba
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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29
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Murthy KR, Rajagopalan P, Pinto SM, Advani J, Murthy PR, Goel R, Subbannayya Y, Balakrishnan L, Dash M, Anil AK, Manda SS, Nirujogi RS, Kelkar DS, Sathe GJ, Dey G, Chatterjee A, Gowda H, Chakravarti S, Shankar S, Sahasrabuddhe NA, Nair B, Somani BL, Prasad TSK, Pandey A. Proteomics of Human Aqueous Humor. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:283-93. [DOI: 10.1089/omi.2015.0029] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Krishna R. Murthy
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
- Vittala International Institute of Ophthalmology, Bangalore, India
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
| | | | - Renu Goel
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Rajiv Gandhi University of Health Sciences, Bangalore, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Department of Biotechnology, Kuvempu University, Shankaraghatta, India
| | - Mahashweta Dash
- Department of Internal Medicine, Armed Forces Medical College, Pune, India
| | - Abhijith K. Anil
- Department of Internal Medicine, Armed Forces Medical College, Pune, India
| | - Srikanth S. Manda
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | | | - Gajanan J. Sathe
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
| | - Gourav Dey
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Shukti Chakravarti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Subramanian Shankar
- Department of Rheumatology, Medical Division, Command Hospital (Air Force), Bangalore, India
| | | | - Bipin Nair
- Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Babu Lal Somani
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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30
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Reddy PJ, Ray S, Srivastava S. The Quest of the Human Proteome and the Missing Proteins: Digging Deeper. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:276-82. [DOI: 10.1089/omi.2015.0035] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Panga Jaipal Reddy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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31
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32
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Murthy KR, Goel R, Subbannayya Y, Jacob HK, Murthy PR, Manda SS, Patil AH, Sharma R, Sahasrabuddhe NA, Parashar A, Nair BG, Krishna V, Prasad TK, Gowda H, Pandey A. Proteomic analysis of human vitreous humor. Clin Proteomics 2014; 11:29. [PMID: 25097467 PMCID: PMC4106660 DOI: 10.1186/1559-0275-11-29] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/16/2014] [Indexed: 12/11/2022] Open
Abstract
Background The vitreous humor is a transparent, gelatinous mass whose main constituent is water. It plays an important role in providing metabolic nutrient requirements of the lens, coordinating eye growth and providing support to the retina. It is in close proximity to the retina and reflects many of the changes occurring in this tissue. The biochemical changes occurring in the vitreous could provide a better understanding about the pathophysiological processes that occur in vitreoretinopathy. In this study, we investigated the proteome of normal human vitreous humor using high resolution Fourier transform mass spectrometry. Results The vitreous humor was subjected to multiple fractionation techniques followed by LC-MS/MS analysis. We identified 1,205 proteins, 682 of which have not been described previously in the vitreous humor. Most proteins were localized to the extracellular space (24%), cytoplasm (20%) or plasma membrane (14%). Classification based on molecular function showed that 27% had catalytic activity, 10% structural activity, 10% binding activity, 4% cell and 4% transporter activity. Categorization for biological processes showed 28% participate in metabolism, 20% in cell communication and 13% in cell growth. The data have been deposited to the ProteomeXchange with identifier PXD000957. Conclusion This large catalog of vitreous proteins should facilitate biomedical research into pathological conditions of the eye including diabetic retinopathy, retinal detachment and cataract.
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Affiliation(s)
- Krishna R Murthy
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690 525, India.,Vittala International Institute Of Ophthalmology, Bangalore, Karnataka 560085, India
| | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka 577 451, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Harrys Kc Jacob
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Praveen R Murthy
- Vittala International Institute Of Ophthalmology, Bangalore, Karnataka 560085, India
| | - Srikanth Srinivas Manda
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Centre of Excellence in Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - Arun H Patil
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Rakesh Sharma
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore 560 006, India
| | | | | | - Bipin G Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690 525, India
| | | | - Ts Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690 525, India.,Centre of Excellence in Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Akhilesh Pandey
- Department of Biological Chemistry, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA.,Department of Oncology and Pathology, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
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33
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Chatterjee A, Villarreal G, Rhee DJ. Matricellular proteins in the trabecular meshwork: review and update. J Ocul Pharmacol Ther 2014; 30:447-63. [PMID: 24901502 DOI: 10.1089/jop.2014.0013] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Abstract Primary open-angle glaucoma (POAG) is a leading cause of blindness worldwide, and intraocular pressure (IOP) is an important modifiable risk factor. IOP is a function of aqueous humor production and aqueous humor outflow, and it is thought that prolonged IOP elevation leads to optic nerve damage over time. Within the trabecular meshwork (TM), the eye's primary drainage system for aqueous humor, matricellular proteins generally allow cells to modulate their attachments with and alter the characteristics of their surrounding extracellular matrix (ECM). It is now well established that ECM turnover in the TM affects outflow facility, and matricellular proteins are emerging as significant players in IOP regulation. The formalized study of matricellular proteins in TM has gained increased attention. Secreted protein acidic and rich in cysteine (SPARC), myocilin, connective tissue growth factor (CTGF), and thrombospondin-1 and -2 (TSP-1 and -2) have been localized to the TM, and a growing body of evidence suggests that these matricellular proteins play an important role in IOP regulation and possibly the pathophysiology of POAG. As evidence continues to emerge, these proteins are now seen as potential therapeutic targets. Further study is warranted to assess their utility in treating glaucoma in humans.
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Affiliation(s)
- Ayan Chatterjee
- Department of Ophthalmology and Visual Sciences, University Hospitals Eye Institute, Case Western Reserve University School of Medicine , Cleveland, Ohio
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34
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Elsobky S, Crane AM, Margolis M, Carreon TA, Bhattacharya SK. Review of application of mass spectrometry for analyses of anterior eye proteome. World J Biol Chem 2014; 5:106-114. [PMID: 24921002 PMCID: PMC4050106 DOI: 10.4331/wjbc.v5.i2.106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/16/2014] [Accepted: 03/04/2014] [Indexed: 02/05/2023] Open
Abstract
Proteins have important functional roles in the body, which can be altered in disease states. The eye is a complex organ rich in proteins; in particular, the anterior eye is very sophisticated in function and is most commonly involved in ophthalmic diseases. Proteomics, the large scale study of proteins, has greatly impacted our knowledge and understanding of gene function in the post-genomic period. The most significant breakthrough in proteomics has been mass spectrometric identification of proteins, which extends analysis far beyond the mere display of proteins that classical techniques provide. Mass spectrometry functions as a “mass analyzer” which simplifies the identification and quantification of proteins extracted from biological tissue. Mass spectrometric analysis of the anterior eye proteome provides a differential display for protein comparison of normal and diseased tissue. In this article we present the key proteomic findings in the recent literature related to the cornea, aqueous humor, trabecular meshwork, iris, ciliary body and lens. Through this we identified unique proteins specific to diseases related to the anterior eye.
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