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Vergouwen DPC, van Beek AA, de Hoog J, de Boer JH, Los LI, Gijs M, Erckens RJ, Verdijk RM, Haasnoot GW, Roelen DL, Rothova A, Rönnelid J, Ten Berge JC, Schreurs MWJ. The enigma of sclera-specific autoimmunity in scleritis. J Autoimmun 2024; 144:103178. [PMID: 38368769 DOI: 10.1016/j.jaut.2024.103178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/29/2023] [Accepted: 02/08/2024] [Indexed: 02/20/2024]
Abstract
Scleritis is a severe and painful ophthalmic disorder, in which a pathogenic role for collagen-directed autoimmunity was repeatedly suggested. We evaluated the presence of sclera-specific antibodies in a large cohort of patients with non-infectious scleritis. Therefore, we prospectively collected serum samples from 121 patients with non-infectious scleritis in a multicenter cohort study in the Netherlands. In addition, healthy (n = 39) and uveitis controls (n = 48) were included. Serum samples were tested for anti-native human type II collagen antibodies using a validated enzyme-linked immunosorbent assay (ELISA). Further, sclera-specific antibodies were determined using indirect immunofluorescence (IIF) on primate retinal/scleral cryosections. Lastly, human leukocyte antigen (HLA) typing was performed in 111 patients with scleritis. Anti-type II collagen antibodies were found in 13% of scleritis patients, in 10% of healthy controls and in 11% of uveitis controls (p = 0.91). A specific reaction to scleral nerve tissue on IIF was observed in 33% of patients with scleritis, which was higher than in healthy controls (11%; p = 0.01), but similar to uveitis controls (25%; p = 0.36). Reactivity to the scleral nerve tissue was significantly associated with earlier onset of scleritis (48 versus 56 years; p < 0.001), bilateral involvement (65% versus 42%; p = 0.01), and less frequent development of scleral necrosis (5% versus 22%; p = 0.02). HLA-B27 was found to be twice as prevalent in patients with scleritis (15.3%) compared to a healthy population (7.2%). In conclusion, scleral nerve autoantibody reactivity was more common in scleritis and uveitis patients in contrast to healthy controls. Further research is needed to characterize these scleral-nerve directed antibodies and assess their clinical value.
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Affiliation(s)
- Daphne P C Vergouwen
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Adriaan A van Beek
- Department of Immunology, HLA laboratory, Leiden University Medical Center, Leiden, the Netherlands
| | - Joeri de Hoog
- Department of Ophthalmology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Joke H de Boer
- Department of Ophthalmology, UMC Utrecht, Utrecht, the Netherlands
| | - Leonoor I Los
- Department of Ophthalmology, UMC Groningen, Groningen, the Netherlands
| | - Marlies Gijs
- University Eye Clinic, Maastricht UMC+, Maastricht, the Netherlands
| | - Roel J Erckens
- University Eye Clinic, Maastricht UMC+, Maastricht, the Netherlands
| | - Rob M Verdijk
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Geert W Haasnoot
- Eurotransplant Reference Laboratory, Leiden University Medical Center, Leiden, the Netherlands
| | - Dave L Roelen
- Department of Immunology, HLA laboratory, Leiden University Medical Center, Leiden, the Netherlands
| | - Aniki Rothova
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Johan Rönnelid
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Josianne C Ten Berge
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marco W J Schreurs
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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Vergouwen DP, Kolijn PM, de Hoog J, de Boer JH, Los LI, Gijs M, Erckens RJ, de Jong PH, Rothova A, Ten Berge JC, Schreurs MW. Potential Biomarkers for Noninfectious Scleritis Identified by Serum and Tear Fluid Proteomics. OPHTHALMOLOGY SCIENCE 2024; 4:100407. [PMID: 38054106 PMCID: PMC10694766 DOI: 10.1016/j.xops.2023.100407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 12/07/2023]
Abstract
Purpose Scleritis is an extremely painful and potentially blinding inflammation of the sclera with unknown pathogenesis and unpredictable course. To gain insight in its disease process and identify biomarker candidates, we performed extensive proteomics in serum and tear fluid. Design Prospective multicenter cohort study. Participants A total of 121 patients with noninfectious scleritis (of which 39 active cases), 30 healthy controls, and 23 disease controls (uveitis and rheumatoid arthritis) were enrolled in the Netherlands from 2020 to 2022. Methods Serum, tear fluid of both eyes, and clinical data were gathered. The level of 368 inflammatory proteins was measured using proximity extension assays. Results were validated in an independent cohort of 15 patients with scleritis, and using addressable laser bead immunoassay, or enzyme-linked immunoassays. In addition, we studied an extended panel of matrix metalloproteinases in tear fluid of necrotizing scleritis with addressable laser bead immunoassay. Main Outcome Measures Statistically significant differences in the level of inflammatory proteins between patients with scleritis and control groups. Results Proteomics revealed 18 significantly upregulated or downregulated serum proteins in active scleritis cases compared with all control groups in both the discovery cohort and the validation cohort. The most upregulated protein was nuclear migration protein nudC (NudC; P = 0.0032), a protein involved in neurogenesis. The other significant hits included proteins involved in T-cell activation, apoptosis, epithelial barrier maintenance, and angiogenesis. Our tear fluid analysis showed matrix metalloproteinase 9 (MMP9) to be upregulated in the tear fluid of patients with scleral necrosis. Conclusions The results of our proteomics analysis suggest a role for neurogenesis, T-cell activation, disruption of epithelial barrier, and angiogenesis in the pathogenesis of scleritis, and highlight MMP9 and NudC as biomarkers with potential clinical relevance. Funding Disclosures The authors have no proprietary or commercial interest in any materials discussed in this article.
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Affiliation(s)
- Daphne P.C. Vergouwen
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - P. Martijn Kolijn
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joeri de Hoog
- Department of Ophthalmology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Joke H. de Boer
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leonoor I. Los
- Department of Ophthalmology, University Medical Center Groningen, Groningen, The Netherlands
| | - Marlies Gijs
- University Eye Clinic, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Roel J. Erckens
- University Eye Clinic, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Pascal H.P. de Jong
- Department of Rheumatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Aniki Rothova
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Josianne C. Ten Berge
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marco W.J. Schreurs
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
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A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. iScience 2022; 25:104580. [PMID: 35789843 PMCID: PMC9250027 DOI: 10.1016/j.isci.2022.104580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 12/17/2022] Open
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Hayes AJ, Melrose J. Neural Tissue Homeostasis and Repair Is Regulated via CS and DS Proteoglycan Motifs. Front Cell Dev Biol 2021; 9:696640. [PMID: 34409033 PMCID: PMC8365427 DOI: 10.3389/fcell.2021.696640] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/13/2021] [Indexed: 01/04/2023] Open
Abstract
Chondroitin sulfate (CS) is the most abundant and widely distributed glycosaminoglycan (GAG) in the human body. As a component of proteoglycans (PGs) it has numerous roles in matrix stabilization and cellular regulation. This chapter highlights the roles of CS and CS-PGs in the central and peripheral nervous systems (CNS/PNS). CS has specific cell regulatory roles that control tissue function and homeostasis. The CNS/PNS contains a diverse range of CS-PGs which direct the development of embryonic neural axonal networks, and the responses of neural cell populations in mature tissues to traumatic injury. Following brain trauma and spinal cord injury, a stabilizing CS-PG-rich scar tissue is laid down at the defect site to protect neural tissues, which are amongst the softest tissues of the human body. Unfortunately, the CS concentrated in gliotic scars also inhibits neural outgrowth and functional recovery. CS has well known inhibitory properties over neural behavior, and animal models of CNS/PNS injury have demonstrated that selective degradation of CS using chondroitinase improves neuronal functional recovery. CS-PGs are present diffusely in the CNS but also form denser regions of extracellular matrix termed perineuronal nets which surround neurons. Hyaluronan is immobilized in hyalectan CS-PG aggregates in these perineural structures, which provide neural protection, synapse, and neural plasticity, and have roles in memory and cognitive learning. Despite the generally inhibitory cues delivered by CS-A and CS-C, some CS-PGs containing highly charged CS disaccharides (CS-D, CS-E) or dermatan sulfate (DS) disaccharides that promote neural outgrowth and functional recovery. CS/DS thus has varied cell regulatory properties and structural ECM supportive roles in the CNS/PNS depending on the glycoform present and its location in tissue niches and specific cellular contexts. Studies on the fruit fly, Drosophila melanogaster and the nematode Caenorhabditis elegans have provided insightful information on neural interconnectivity and the role of the ECM and its PGs in neural development and in tissue morphogenesis in a whole organism environment.
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Affiliation(s)
- Anthony J. Hayes
- Bioimaging Research Hub, Cardiff School of Biosciences, Cardiff University, Wales, United Kingdom
| | - James Melrose
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, Australia
- Raymond Purves Bone and Joint Research Laboratories, Kolling Institute of Medical Research, Royal North Shore Hospital and The Faculty of Medicine and Health, The University of Sydney, St. Leonard’s, NSW, Australia
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da Silva EMG, Santos LGC, de Oliveira FS, Freitas FCDP, Parreira VDSC, dos Santos HG, Tavares R, Carvalho PC, Neves-Ferreira AGDC, Haibara AS, de Araujo-Souza PS, Dias AAM, Passetti F. Proteogenomics Reveals Orthologous Alternatively Spliced Proteoforms in the Same Human and Mouse Brain Regions with Differential Abundance in an Alzheimer's Disease Mouse Model. Cells 2021; 10:1583. [PMID: 34201730 PMCID: PMC8303486 DOI: 10.3390/cells10071583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/12/2021] [Accepted: 06/18/2021] [Indexed: 01/19/2023] Open
Abstract
Alternative splicing (AS) may increase the number of proteoforms produced by a gene. Alzheimer's disease (AD) is a neurodegenerative disease with well-characterized AS proteoforms. In this study, we used a proteogenomics strategy to build a customized protein sequence database and identify orthologous AS proteoforms between humans and mice on publicly available shotgun proteomics (MS/MS) data of the corpus callosum (CC) and olfactory bulb (OB). Identical proteotypic peptides of six orthologous AS proteoforms were found in both species: PKM1 (gene PKM/Pkm), STXBP1a (gene STXBP1/Stxbp1), Isoform 3 (gene HNRNPK/Hnrnpk), LCRMP-1 (gene CRMP1/Crmp1), SP3 (gene CADM1/Cadm1), and PKCβII (gene PRKCB/Prkcb). These AS variants were also detected at the transcript level by publicly available RNA-Seq data and experimentally validated by RT-qPCR. Additionally, PKM1 and STXBP1a were detected at higher abundances in a publicly available MS/MS dataset of the AD mouse model APP/PS1 than its wild type. These data corroborate other reports, which suggest that PKM1 and STXBP1a AS proteoforms might play a role in amyloid-like aggregate formation. To the best of our knowledge, this report is the first to describe PKM1 and STXBP1a overexpression in the OB of an AD mouse model. We hope that our strategy may be of use in future human neurodegenerative studies using mouse models.
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Affiliation(s)
- Esdras Matheus Gomes da Silva
- Instituto Carlos Chagas, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba, PR 81310-020, Brazil; (E.M.G.d.S.); (L.G.C.S.); (F.C.d.P.F.); (V.d.S.C.P.); (H.G.d.S.); (P.C.C.)
- Laboratory of Toxinology, Oswaldo Cruz Institute (FIOCRUZ), Av. Brazil 4365, Manguinhos, Rio de Janeiro, RJ 21040-900, Brazil;
| | - Letícia Graziela Costa Santos
- Instituto Carlos Chagas, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba, PR 81310-020, Brazil; (E.M.G.d.S.); (L.G.C.S.); (F.C.d.P.F.); (V.d.S.C.P.); (H.G.d.S.); (P.C.C.)
| | - Flávia Santiago de Oliveira
- Laboratório de Inflamação e Câncer, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Avenida Presidente Antônio Carlos 6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil; (F.S.d.O.); (A.A.M.D.)
| | - Flávia Cristina de Paula Freitas
- Instituto Carlos Chagas, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba, PR 81310-020, Brazil; (E.M.G.d.S.); (L.G.C.S.); (F.C.d.P.F.); (V.d.S.C.P.); (H.G.d.S.); (P.C.C.)
| | - Vinícius da Silva Coutinho Parreira
- Instituto Carlos Chagas, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba, PR 81310-020, Brazil; (E.M.G.d.S.); (L.G.C.S.); (F.C.d.P.F.); (V.d.S.C.P.); (H.G.d.S.); (P.C.C.)
| | - Hellen Geremias dos Santos
- Instituto Carlos Chagas, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba, PR 81310-020, Brazil; (E.M.G.d.S.); (L.G.C.S.); (F.C.d.P.F.); (V.d.S.C.P.); (H.G.d.S.); (P.C.C.)
| | - Raphael Tavares
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Avenida Presidente Antônio Carlos 6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil;
| | - Paulo Costa Carvalho
- Instituto Carlos Chagas, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba, PR 81310-020, Brazil; (E.M.G.d.S.); (L.G.C.S.); (F.C.d.P.F.); (V.d.S.C.P.); (H.G.d.S.); (P.C.C.)
| | | | - Andrea Siqueira Haibara
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Avenida Presidente Antônio Carlos 6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil;
| | - Patrícia Savio de Araujo-Souza
- Laboratory of Immunogenetics and Histocompatibility, Department of Genetics, Universidade Federal do Paraná, Av. Cel. Francisco H. dos Santos 100, Jardim das Américas, Curitiba, PR 81530-980, Brazil;
| | - Adriana Abalen Martins Dias
- Laboratório de Inflamação e Câncer, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Avenida Presidente Antônio Carlos 6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil; (F.S.d.O.); (A.A.M.D.)
| | - Fabio Passetti
- Instituto Carlos Chagas, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba, PR 81310-020, Brazil; (E.M.G.d.S.); (L.G.C.S.); (F.C.d.P.F.); (V.d.S.C.P.); (H.G.d.S.); (P.C.C.)
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Wu J, Zhao Y, Fu Y, Li S, Zhang X. Effects of lumican expression on the apoptosis of scleral fibroblasts: In vivo and in vitro experiments. Exp Ther Med 2021; 21:495. [PMID: 33791004 PMCID: PMC8005674 DOI: 10.3892/etm.2021.9926] [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: 02/12/2020] [Accepted: 09/15/2020] [Indexed: 11/16/2022] Open
Abstract
Lumican serves an important role in the maintenance of sclera biomechanical properties. However, whether lumican expression is altered in myopia and the mechanisms of action involved are unknown. In the present study, the expression of lumican in cultured scleral fibroblasts and in the scleral tissue of a rat model of form-deprivation myopia was assessed. It was confirmed that diopter was decreased, whereas axial length was increased in modeled eyes relative to normal control eyes, indicating that the model of myopia was successfully established. These pathologic changes were accompanied by the upregulation of lumican and tissue inhibitor of metalloproteinases (TIMP)-2, as well as the downregulation of matrix metalloproteinase (MMP)-2 and MMP-14. The same trends in TIMP-2, MMP-2 and MMP-14 expression were observed when lumican was overexpressed in cultured scleral fibroblasts. Additionally, cell proliferation decreased whereas apoptosis increased compared with those of control cells. Inhibiting lumican expression had no effect on cell proliferation or apoptosis, but stimulated the expression of MMP-2 and MMP-14 while decreasing that of TIMP-2. The results suggested that lumican overexpression contributed to myopia by promoting apoptosis in scleral fibroblasts via the modulation of TIMP-2, MMP-2 and MMP-14 expression.
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Affiliation(s)
- Jinsong Wu
- Department of Pediatric Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yanzhi Zhao
- The First Clinical Medical College, Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Yanmei Fu
- Department of Pediatric Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Shurong Li
- Department of Pediatric Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Xu Zhang
- The Affiliated Eye Hospital, Nanchang University, Nanchang, Jiangxi 330000, P.R. China
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Hao J, Kohler C, van den Dorpel H, Scholl HPN, Meyer P, Killer HE, Neutzner A. The extracellular matrix composition of the optic nerve subarachnoid space. Exp Eye Res 2020; 200:108250. [PMID: 32956686 DOI: 10.1016/j.exer.2020.108250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/20/2020] [Accepted: 09/12/2020] [Indexed: 10/23/2022]
Abstract
The meninges not only surround the brain and the spinal cord but also the optic nerve. Meningeal-derived extracellular matrix (ECM) is a crucial component of the pial basement membrane, glia limitans and important for maintenance of optic nerve axon integrity, homeostasis and retinal ganglion cell health. To get closer insight into optic nerve meningeal-derived ECM composition, we performed proteomic analysis of the sheep optic nerve subarachnoid space (SAS). Candidate components were confirmed in cultures of primary human meningothelial cells (phMECs) and human optic nerve samples. Sheep optic nerve SAS samples were analysed by LC-MS, identified proteins were matched to their human orthologs and filtered using gene lists representing all major ECM components. To validate these findings digital droplet PCR (ddPCR) to evaluate mRNA expression of all candidate components identified was performed on cultures of phMECs. In addition, one protein per major ECM group was stained on human optic nerve sections and on phMEC cultures. Employing LC-MS, 1273 proteins were identified and subjected to bioinformatic analysis. Gene ontology analysis revealed six out of forty-four collagen types (1A1, 1A2, 3A1, 6A2, 6A3 and 14A1), three out of eleven laminin subunits (A4, B2, C1) and six out of twenty-seven hyaluronan binding proteins (CD44, versican (VCAN), C1q binding protein, neurocan (NCAN), brevican (BCAN) and hyalaluronan proteoglycan link protein 2 (HAPLN2)) were present in our cohort. DdPCR in phMEC cell culture confirmed presence of all candidate components except NCAN, BCAN and HAPLN2. Immunohistochemistry (IHC) staining on human optic nerve sections and immunofluorescence (IF) staining on in vitro cultured phMECs showed strong immunopositivity for collagen-typeI-α1 (COL1A1), lamininγ1 (LAMC1), and VCAN. Fibronectin (FN1) was exclusively present in cultures of phMECs. Using a combined bioinformatics and immunohistological approach, we describe the ECM composition of the optic nerve subarachnoid space. As this space plays an important role in maintaining optic nerve function, a better understanding of ECM composition in this delicate environment might be key to further pathophysiological insight into optic nerve degeneration and associated disorders.
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Affiliation(s)
- Jie Hao
- Department of Biomedicine, University Hospital Basel & University Basel, Hebelstr.20, 4031, Basel, Switzerland; Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China.
| | - Corina Kohler
- Department of Biomedicine, University Hospital Basel & University Basel, Hebelstr.20, 4031, Basel, Switzerland; Department of Ophthalmology, University Hospital Basel & University Basel, Mittlere Str.91, 4056, Basel, Switzerland.
| | - Hubrecht van den Dorpel
- Department of Biomedicine, University Hospital Basel & University Basel, Hebelstr.20, 4031, Basel, Switzerland; Department of Ophthalmology, University Hospital Basel & University Basel, Mittlere Str.91, 4056, Basel, Switzerland.
| | - Hendrik P N Scholl
- Department of Biomedicine, University Hospital Basel & University Basel, Hebelstr.20, 4031, Basel, Switzerland; Department of Ophthalmology, University Hospital Basel & University Basel, Mittlere Str.91, 4056, Basel, Switzerland; Institute of Molecular and Clinical Ophthalmology, Mittlere Str.91, 4056, Basel, Switzerland.
| | - Peter Meyer
- Department of Ophthalmology, University Hospital Basel & University Basel, Mittlere Str.91, 4056, Basel, Switzerland.
| | - Hanspeter E Killer
- Department of Biomedicine, University Hospital Basel & University Basel, Hebelstr.20, 4031, Basel, Switzerland; Department of Ophthalmology, Kantonsspital Aarau, Herzogstrasse 15, 5000, Aarau, Switzerland.
| | - Albert Neutzner
- Department of Biomedicine, University Hospital Basel & University Basel, Hebelstr.20, 4031, Basel, Switzerland; Department of Ophthalmology, University Hospital Basel & University Basel, Mittlere Str.91, 4056, Basel, Switzerland.
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Yeung J, Gadjeva M, Geddes-McAlister J. Label-Free Quantitative Proteomics Distinguishes General and Site-Specific Host Responses to Pseudomonas aeruginosa Infection at the Ocular Surface. Proteomics 2020; 20:e1900290. [PMID: 31874121 PMCID: PMC7079286 DOI: 10.1002/pmic.201900290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 12/07/2019] [Indexed: 01/01/2023]
Abstract
Mass spectrometry-based proteomics enables the unbiased and sensitive profiling of cellular proteomes and extracellular environments. Recent technological and bioinformatic advances permit identifying dual biological systems in a single experiment, supporting investigation of infection from both the host and pathogen perspectives. At the ocular surface, Pseudomonas aeruginosa is commonly associated with biofilm formation and inflammation of the ocular tissues, causing damage to the eye. The interaction between P. aeruginosa and the immune system at the site of infection describes limitations in clearance of infection and enhanced pathogenesis. Here, the extracellular environment (eye wash) of murine ocular surfaces infected with a clinical isolate of P. aeruginosa is profiled and neutrophil marker proteins are detected, indicating neutrophil recruitment to the site of infection. The first potential diagnostic markers of P. aeruginosa-associated keratitis are also identified. In addition, the deepest murine corneal proteome to date is defined and proteins, categories, and networks critical to the host response are detected. Moreover, the first identification of bacterial proteins attached to the ocular surface is reported. The findings are validated through in silico comparisons and enzymatic profiling. Overall, the work provides comprehensive profiling of the host-pathogen interface and uncovers differences between general and site-specific host responses to infection.
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Affiliation(s)
- J. Yeung
- Molecular and Cellular Biology Department, University of Guelph, Guelph, Ontario, Canada
| | - M. Gadjeva
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - J. Geddes-McAlister
- Molecular and Cellular Biology Department, University of Guelph, Guelph, Ontario, Canada
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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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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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Amit C, Muralikumar S, Janaki S, Lakshmipathy M, Therese KL, Umashankar V, Padmanabhan P, Narayanan J. Designing and enhancing the antifungal activity of corneal specific cell penetrating peptide using gelatin hydrogel delivery system. Int J Nanomedicine 2019; 14:605-622. [PMID: 30697045 PMCID: PMC6339655 DOI: 10.2147/ijn.s184911] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Fungal keratitis is a major cause of corneal blindness accounting for more than one-third of microbiologically proven cases. The management of fungal keratitis is through topical or systemic antifungal medications alone or in combination with surgical treatment. Topical medications such as natamycin and voriconazole pose major challenges due to poor penetration across the corneal epithelium. To address the issue various carrier molecules like nanoparticles, lipid vesicles, and cell penetrating peptides were explored. But the major drawback such as non-specificity and lack of bioavailability remains. Purpose In this study, we have attempted to design corneal specific cell penetrating peptide using subtractive proteomic approach from the published literature and tried to improve its bioavailability through gelatin hydrogel delivery system. Material and Methods Using subtractive proteomic approach two peptides VRF005 and VRF007 were identified on the basis of solubility, cell permeability and amphipathicity. The peptides were modeled for three-dimensional structure and simulated for membrane penetration. The peptides were characterized using circular dichroism spectroscopy, dynamic light scattering and native polyacrylamide gel electrophoresis. Further uptake studies were performed on primary corneal epithelial cells and the stability was analyzed in corneal epithelial tissue lysates. Insilico prediction of peptides showed it to have antifungal activity which was further validated using colony forming assay and time killing kinetics. The duration of antifungal activity of peptide was improved using gelatin hydrogel through sustained delivery. Results VRF005 and VRF007 showed α-helical structure and was within the allowed region of Ramachandran plot. The simulation study showed their membrane penetration. The peptide uptake was found to be specific to corneal epithelial cells and also showed intracellular localization in Candida albicans and Fusarium solani. Peptides were found to be stable up to 2 hours when incubated with corneal epithelial tissue lysate. Dynamic light scattering, and native polyacrylamide gel electrophoresis revealed aggregation of peptides. VRF007 showed antifungal activity up to 24 hour whereas VRF005 showed activity up to 4 hours. Hence gelatin hydrogel-based delivery system was used to improve the activity. Actin staining of corneal epithelial cells showed that the cells were attached on gelatin hydrogel. Conclusion We have designed corneal specific cell penetrating peptides using subtractive proteomic approach. Bioavailability and delivery of peptide was enhanced using gelatin hydrogel system.
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Affiliation(s)
- Chatterjee Amit
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya campus, Chennai, Tamil Nadu, India, .,School of Chemical and Biotechnology, SASTRA University, Tanjore, Tamil Nadu, India
| | - Shalini Muralikumar
- Centre for Bioinformatics, Vision Research Foundation, Sankara Nethralaya campus, Chennai, Tamil Nadu, India
| | - Sargunam Janaki
- L&T Microbiology Research Centre, Vision Research Foundation, Sankara Nethralaya campus, Chennai, Tamil Nadu, India
| | - Meena Lakshmipathy
- Department of Cornea, Medical Research Foundation, Sankara Nethralaya campus, Chennai, Tamil Nadu, India
| | - Kulandai Lily Therese
- L&T Microbiology Research Centre, Vision Research Foundation, Sankara Nethralaya campus, Chennai, Tamil Nadu, India
| | - Vetrivel Umashankar
- Centre for Bioinformatics, Vision Research Foundation, Sankara Nethralaya campus, Chennai, Tamil Nadu, India
| | - Prema Padmanabhan
- Department of Cornea, Medical Research Foundation, Sankara Nethralaya campus, Chennai, Tamil Nadu, India
| | - Janakiraman Narayanan
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya campus, Chennai, Tamil Nadu, India,
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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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13
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Sudha D, Kohansal-Nodehi M, Kovuri P, Manda SS, Neriyanuri S, Gopal L, Bhende P, Chidambaram S, Arunachalam JP. Proteomic profiling of human intraschisis cavity fluid. Clin Proteomics 2017; 14:13. [PMID: 28450823 PMCID: PMC5404285 DOI: 10.1186/s12014-017-9148-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/07/2017] [Indexed: 12/24/2022] Open
Abstract
Background X-linked retinoschisis (XLRS) is a vitreoretinal degenerative disorder causing vision deterioration, due to structural defects in retina. The hallmark of this disease includes radial streaks arising from the fovea and splitting of inner retinal layers (schisis). Although these retinal changes are attributed to mutations in the retinoschisin gene, schisis is also observed in patients who do not carry mutations. In addition, the origin of intraschisis fluid, the triggering point of schisis formation and its progression are largely unknown still. So far, there is no report on the complete proteomic analysis of this fluid. Schisis fluid proteome could reflect biochemical changes in the disease condition, helping in better understanding and management of retinoschisis. Therefore it was of interest to investigate the intraschisis fluid proteome using high-resolution mass spectrometry. Methods Two male XLRS patients (aged 4 and 40 years) underwent clinical and genetic evaluation followed by surgical extraction of intraschisis fluids. The two fluid samples were resolved on a SDS-PAGE and the processed peptides were analyzed by Q-Exactive plus hybrid quadrupole-Orbitrap mass spectrometry. Functional annotation of the identified proteins was performed using Ingenuity pathway analysis software. Results Mass spectrometry analysis detected 770 nonredundant proteins in the intraschisis fluid. Retinol dehydrogenase 14 was found to be abundant in the schisis fluid. Gene ontology based analysis indicated that 19% of the intraschisis fluid proteins were localized to the extracellular matrix and 15% of the proteins were involved in signal transduction. Functional annotation identified three primary canonical pathways to be associated with the schisis fluid proteome viz., LXR/RXR activation, complement system and acute phase response signalling, which are involved in immune and inflammatory responses. Collectively, our results show that intraschisis fluid comprises specific inflammatory proteins which highly reflect the disease environment. Conclusion Based on our study, it is suggested that inflammation might play a key role in the pathogenesis of XLRS. To our knowledge, this is the first report describing the complete proteome of intraschisis fluid, which could serve as a template for future research and facilitate the development of therapeutic modalities for XLRS. Electronic supplementary material The online version of this article (doi:10.1186/s12014-017-9148-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dhandayuthapani Sudha
- SN ONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India.,School of Biotechnology, SASTRA University, Thanjavur, India
| | | | - Purnima Kovuri
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, India
| | | | - Srividya Neriyanuri
- Elite School of Optometry, Unit of Medical Research Foundation, Chennai, India
| | - Lingam Gopal
- Shri Bhagwan Mahavir Vitreo-Retinal Services, Medical Research Foundation, Chennai, India
| | - Pramod Bhende
- Shri Bhagwan Mahavir Vitreo-Retinal Services, Medical Research Foundation, Chennai, India
| | | | - Jayamuruga Pandian Arunachalam
- SN ONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India.,Central Inter-Disciplinary Research Facility (CIDRF), Sri Balaji Vidyapeeth Medical University, Mahatma Gandhi Medical College and Research Institute Campus, Puducherry, India
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Omenn GS. The proteomes of the human eye, a highly compartmentalized organ. Proteomics 2016; 17. [PMID: 27860232 DOI: 10.1002/pmic.201600340] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 01/12/2023]
Abstract
Proteomics has now published a series of Dataset Briefs on the EyeOme from the HUPO Human Proteome Project with high-quality analyses of the proteomes of these compartments of the human eye: retina, iris, ciliary body, retinal pigment epithelium/choroid, retrobulbar optic nerve, and sclera, with 3436, 2929, 2867, 2755, 2711, and 1945 proteins, respectively. These proteomics resources represent a useful starting point for a broad range of research aimed at developing preventive and therapeutic interventions for the various causes of blindness.
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Affiliation(s)
- Gilbert S Omenn
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
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