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Dos Santos FM, Ciordia S, Mesquita J, de Sousa JPC, Paradela A, Tomaz CT, Passarinha LAP. Vitreous humor proteome: unraveling the molecular mechanisms underlying proliferative and neovascular vitreoretinal diseases. Cell Mol Life Sci 2022; 80:22. [PMID: 36585968 PMCID: PMC11072707 DOI: 10.1007/s00018-022-04670-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 11/09/2022] [Accepted: 12/12/2022] [Indexed: 01/01/2023]
Abstract
Proliferative diabetic retinopathy (PDR), proliferative vitreoretinopathy (PVR), and neovascular age-related macular degeneration (nAMD) are among the leading causes of blindness. Due to the multifactorial nature of these vitreoretinal diseases, omics approaches are essential for a deeper understanding of the pathophysiologic processes underlying the evolution to a proliferative or neovascular etiology, in which patients suffer from an abrupt loss of vision. For many years, it was thought that the function of the vitreous was merely structural, supporting and protecting the surrounding ocular tissues. Proteomics studies proved that vitreous is more complex and biologically active than initially thought, and its changes reflect the physiological and pathological state of the eye. The vitreous is the scenario of a complex interplay between inflammation, fibrosis, oxidative stress, neurodegeneration, and extracellular matrix remodeling. Vitreous proteome not only reflects the pathological events that occur in the retina, but the changes in the vitreous itself play a central role in the onset and progression of vitreoretinal diseases. Therefore, this review offers an overview of the studies on the vitreous proteome that could help to elucidate some of the pathological mechanisms underlying proliferative and/or neovascular vitreoretinal diseases and to find new potential pharmaceutical targets.
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Affiliation(s)
- Fátima Milhano Dos Santos
- Health Sciences Research Centre (CICS-UBI), Universidade da Beira Interior, 6201-001, Covilhã, Portugal.
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB-CSIC), Unidad de Proteomica, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Sergio Ciordia
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB-CSIC), Unidad de Proteomica, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Joana Mesquita
- Health Sciences Research Centre (CICS-UBI), Universidade da Beira Interior, 6201-001, Covilhã, Portugal
| | - João Paulo Castro de Sousa
- Health Sciences Research Centre (CICS-UBI), Universidade da Beira Interior, 6201-001, Covilhã, Portugal
- Department of Ophthalmology, Centro Hospitalar de Leiria, 2410-197, Leiria, Portugal
| | - Alberto Paradela
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB-CSIC), Unidad de Proteomica, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Cândida Teixeira Tomaz
- Health Sciences Research Centre (CICS-UBI), Universidade da Beira Interior, 6201-001, Covilhã, Portugal
- C4-UBI, Cloud Computing Competence Centre, University of Beira Interior, 6200-501, Covilhã, Portugal
- Chemistry Department, Faculty of Sciences, Universidade da Beira Interior, 6201-001, Covilhã, Portugal
| | - Luís António Paulino Passarinha
- Health Sciences Research Centre (CICS-UBI), Universidade da Beira Interior, 6201-001, Covilhã, Portugal.
- Associate Laboratory i4HB, Faculdade de Ciências e Tecnologia, Institute for Health and Bioeconomy, Universidade NOVA, 2819-516, Caparica, Portugal.
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
- Pharmaco-Toxicology Laboratory, UBIMedical, Universidade da Beira Interior, 6200-000, Covilhã, Portugal.
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2
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Parra MM, Spoth E, Ronquillo CC, Henderson R, Hartnett ME. Multimodal Retinal Imaging Findings in Two Cousins With VCAN-Related Vitreoretinopathy or Wagner Disease. Ophthalmic Surg Lasers Imaging Retina 2022; 53:639-643. [PMID: 36378611 DOI: 10.3928/23258160-20221026-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Wagner disease is a rare, nonsyndromic vitreoretinopathy caused by autosomal dominant variants in the versican (VCAN) gene. It is associated with abnormalities of the vitreoretinal interface that can lead to peripheral traction and retinal detachments, which also occur in other vitreoretinopathies such as X-linked retinoschisis (XLRS), familial exudative vitreoretinopathy (FEVR) and Stickler syndrome. There is variability in the clinical phenotype in Wagner disease potentially due to variants in VCAN gene variants. In this article, we report a family harboring the VCAN c.9265+1G>C variant and describe the clinical and retinal findings in two members. [Ophthalmic Surg Lasers Imaging Retina 2022;53:639-643.].
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Al-Moujahed A, Velez G, Vu JT, Lima de Carvalho JR, Levi SR, Bassuk AG, Sepah YJ, Tsang SH, Mahajan VB. Proteomic analysis of autoimmune retinopathy implicates NrCAM as a potential biomarker. OPHTHALMOLOGY SCIENCE 2022; 2:100131. [PMID: 35529077 PMCID: PMC9075676 DOI: 10.1016/j.xops.2022.100131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 11/26/2022]
Abstract
Purpose To identify vitreous molecular biomarkers associated with autoimmune retinopathy (AIR). Design Case-control study. Participants We analyzed six eyes from four patients diagnosed with AIR and eight comparative controls diagnosed with idiopathic macular holes and epiretinal membranes. Methods Vitreous biopsies were collected from the participants and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) or multiplex ELISA. Outcome Measures Protein expression changes were evaluated by 1-way ANOVA (significant p-value <0.05), hierarchical clustering, and pathway analysis to identify candidate protein biomarkers. Results There were 16 significantly upregulated and 17 significantly downregulated proteins in the vitreous of three AIR patients compared to controls. The most significantly upregulated proteins included lysozyme C (LYSC), zinc-alpha-2-glycoprotein (ZA2G), complement factor D (CFAD), transforming growth factor-beta induced protein (BGH3), beta-crystallin B2, and alpha-crystallin A chain. The most significantly downregulated proteins included disco-interacting protein 2 homolog (DIP2C), retbindin (RTBDN), and amyloid beta precursor like protein 2 (APLP2). Pathway analysis revealed that vascular endothelial growth factor (VEGF) signaling was a top represented pathway in the vitreous of AIR patients compared to controls. In comparison to a different cohort of three AIR patients analyzed by multiplex ELISA, a commonly differentially expressed protein was neuronal cell adhesion molecule (NrCAM) with p-values of 0.027 in the LC-MS/MS dataset and 0.035 in the ELISA dataset. Conclusion Protein biomarkers such as NrCAM in the vitreous may eventually help diagnose AIR.
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Key Words
- autoimmune retinopathy
- nrcam
- proteomics
- retina
- vitreous
- air, autoimmune retinopathy
- elisa, enzyme-linked immunosorbent assay
- erm, epiretinal membrane
- il, interleukin
- imh, idiopathic macular hole
- lc-ms/ms, liquid chromatography-tandem mass spectrometry
- nrcam, neuronal cell adhesion molecule
- rgc, retinal ganglion cell
- rnfl, retinal nerve fiber layer
- tgf-ß, transforming growth factor beta
- vegf, vascular endothelial growth factor
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Affiliation(s)
- Ahmad Al-Moujahed
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California
| | - Gabriel Velez
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California
- Medical Scientist Training Program, University of Iowa, Iowa City, Iowa
| | - Jennifer T. Vu
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California
| | | | - Sarah R. Levi
- Department of Ophthalmology, Columbia University, New York, New York
| | | | - Yasir J. Sepah
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California
| | - Stephen H. Tsang
- Department of Ophthalmology, Columbia University, New York, New York
| | - Vinit B. Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California
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4
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Rousseau G, Chao de la Barca JM, Rougé-Maillart C, Teresiński G, Chabrun F, Dieu X, Drevin G, Mirebeau-Prunier D, Simard G, Reynier P, Palmiere C. Preliminary Metabolomic Profiling of the Vitreous Humor from Hypothermia Fatalities. J Proteome Res 2021; 20:2390-2396. [PMID: 33818108 DOI: 10.1021/acs.jproteome.0c00901] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The postmortem diagnosis of hypothermia fatalities is often complex due to the absence of pathognomonic lesions and biomarkers. In this study, potential novel biomarkers of hypothermia fatalities were searched in the vitreous humor of known cases of hypothermia fatalities (n = 20) compared to control cases (n = 16), using a targeted metabolomics approach allowing quantitative detection of 188 metabolites. A robust discriminant model with good predictivity was obtained with the supervised OPLS-DA multivariate analysis, showing a distinct separation between the hypothermia and control groups. This signature was characterized by the decreased concentrations of five metabolites (methionine sulfoxide, tryptophan, phenylalanine, alanine, and ornithine) and the increased concentration of 28 metabolites (21 phosphatidylcholines, 3 sphingomyelins, spermine, citrulline, acetylcarnitine, and hydroxybutyrylcarnitine) in hypothermia fatalities compared to controls. The signature shows similarities with already identified features in serum such as the altered concentrations of tryptophan, acylcarnitines, and unsaturated phosphatidylcholines, revealing a highly significant increased activity of methionine sulfoxide reductase, attested by a low methionine sulfoxide-to-methionine ratio. Our results show a preliminary metabolomics signature of hypothermia fatalities in the vitreous humor, highlighting an increased methionine sulfoxide reductase activity.
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Affiliation(s)
- Guillaume Rousseau
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers, France.,Unité Mixte de Recherche MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U-1083, Université d'Angers, 49000 Angers, France
| | - Juan Manuel Chao de la Barca
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers, France.,Unité Mixte de Recherche MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U-1083, Université d'Angers, 49000 Angers, France
| | - Clotilde Rougé-Maillart
- GEROM-LHEA, IRIS-IBS Institut de Biologie en Santé, Centre Hospitalier Universitaire d'Angers, 49933 Angers, France
| | - Grzegorz Teresiński
- Department of Forensic Medicine, Medical University of Lublin, 20-090 Lublin, Poland
| | - Floris Chabrun
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers, France.,Unité Mixte de Recherche MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U-1083, Université d'Angers, 49000 Angers, France
| | - Xavier Dieu
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers, France.,Unité Mixte de Recherche MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U-1083, Université d'Angers, 49000 Angers, France
| | - Guillaume Drevin
- Service de Pharmacologie et Toxicologie, Centre Hospitalier Universitaire d'Angers, 49933 Angers, France
| | - Delphine Mirebeau-Prunier
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers, France.,Unité Mixte de Recherche MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U-1083, Université d'Angers, 49000 Angers, France
| | - Gilles Simard
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers, France
| | - Pascal Reynier
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers, France.,Unité Mixte de Recherche MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U-1083, Université d'Angers, 49000 Angers, France
| | - Cristian Palmiere
- Centre Universitaire Romand de Médecine Légale, Hôpital Universitaire de Lausanne, 1000 Lausanne 25, Switzerland
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Robinson R, Youngblood H, Iyer H, Bloom J, Lee TJ, Chang L, Lukowski Z, Zhi W, Sharma A, Sharma S. Diabetes Induced Alterations in Murine Vitreous Proteome Are Mitigated by IL-6 Trans-Signaling Inhibition. Invest Ophthalmol Vis Sci 2021; 61:2. [PMID: 32870245 PMCID: PMC7476668 DOI: 10.1167/iovs.61.11.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Purpose Diabetic retinopathy (DR) is a microvascular complication caused by prolonged hyperglycemia and characterized by leaky retinal vasculature and ischemia-induced angiogenesis. Vitreous humor is a gel-like biofluid in the posterior segment of the eye between the lens and the retina. Disease-related changes are observed in the biochemical constituents of the vitreous, including proteins and macromolecules. Recently, we found that IL-6 trans-signaling plays a significant role in the vascular leakage and retinal pathology associated with DR. Therefore, in this study, comprehensive proteomic profiling of the murine vitreous was performed to identify diabetes-induced alterations and to determine effects of IL-6 trans-signaling inhibition on these changes. Methods Vitreous samples from mice were collected by evisceration, and proteomic analyses were performed using liquid chromatography–tandem mass spectrometry (LC-MS/MS). Results A total of 154 proteins were identified with high confidence in control mice and were considered to be characteristic of healthy murine vitreous fluid. The levels of 72 vitreous proteins were significantly altered in diabetic mice, including several members of heat shock proteins, 14-3-3 proteins, and tubulins. Alterations in 52 out of 72 proteins in diabetic mice were mitigated by IL-6 trans-signaling inhibition. Conclusions Proteomic analysis of murine vitreous fluid performed in this study provides important information about the changes caused by diabetes in the ocular microenvironment. These diabetes-induced alterations in the murine vitreous proteome were mitigated by IL-6 trans-signaling inhibition. These findings further support that IL-6 trans-signaling may be an important therapeutic target for the treatment of DR.
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Affiliation(s)
- Rebekah Robinson
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
| | - Hannah Youngblood
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
| | - Hersha Iyer
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
| | - Justin Bloom
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
| | - Tae Jin Lee
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
| | - Luke Chang
- Department of Ophthalmology, Augusta University, Augusta, Georgia, United States
| | - Zachary Lukowski
- Department of Ophthalmology, Augusta University, Augusta, Georgia, United States
| | - Wenbo Zhi
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States.,Department of Ophthalmology, Augusta University, Augusta, Georgia, United States.,Department of Population Health Sciences, Augusta University, Augusta, Georgia, United States.,Culver Vision Discovery Institute, Augusta University, Augusta, Georgia, United States
| | - Shruti Sharma
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States.,Department of Ophthalmology, Augusta University, Augusta, Georgia, United States.,Culver Vision Discovery Institute, Augusta University, Augusta, Georgia, United States
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6
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Murenu E, Kostidis S, Lahiri S, Geserich AS, Imhof A, Giera M, Michalakis S. Metabolic Analysis of Vitreous/Lens and Retina in Wild Type and Retinal Degeneration Mice. Int J Mol Sci 2021; 22:ijms22052345. [PMID: 33652907 PMCID: PMC7956175 DOI: 10.3390/ijms22052345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023] Open
Abstract
Photoreceptors are the light-sensing cells of the retina and the major cell type affected in most inherited retinal degenerations. Different metabolic pathways sustain their high energetic demand in physiological conditions, particularly aerobic glycolysis. The principal metabolome of the mature retina has been studied, but only limited information is available on metabolic adaptations in response to key developmental events, such as eye opening. Moreover, dynamic metabolic changes due to retinal degeneration are not well understood. Here, we aimed to explore and map the ocular metabolic dynamics induced by eye opening in healthy (wild type) or Pde6b-mutant (retinal degeneration 1, Rd1) mice, in which photoreceptors degenerate shortly after eye opening. To unravel metabolic differences emerging before and after eye opening under physiological and pathophysiological conditions, we performed nuclear magnetic resonance (NMR) spectroscopy-based metabolome analysis of wild type and Rd1 retina and vitreous/lens. We show that eye opening is accompanied by changes in the concentration of selected metabolites in the retina and by alterations in the vitreous/lens composition only in the retinal degeneration context. As such, we identify NAcetylaspartate as a potential novel vitreous/lens marker reflecting progressive retinal degeneration. Thus, our data can help elucidating mechanisms underlying key events in retinal physiology and reveal changes occurring in pathology, while highlighting the importance of the vitreous/lens in the characterization of retinal diseases.
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Affiliation(s)
- Elisa Murenu
- Department of Ophthalmology, Ludwig-Maximilians-Universität München, Mathildenstraße 8, 80336 Munich, Germany;
- Department of Pharmacy, Ludwig-Maximilians Universität München, Butenandtstr. 7, 81377 Munich, Germany;
| | - Sarantos Kostidis
- Leiden University Medical Center, Center for Proteomics & Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands; (S.K.); (M.G.)
| | - Shibojyoti Lahiri
- Biomedical Center Munich-Molecular Biology, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany; (S.L.); (A.I.)
| | - Anna S. Geserich
- Department of Pharmacy, Ludwig-Maximilians Universität München, Butenandtstr. 7, 81377 Munich, Germany;
| | - Axel Imhof
- Biomedical Center Munich-Molecular Biology, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany; (S.L.); (A.I.)
| | - Martin Giera
- Leiden University Medical Center, Center for Proteomics & Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands; (S.K.); (M.G.)
| | - Stylianos Michalakis
- Department of Ophthalmology, Ludwig-Maximilians-Universität München, Mathildenstraße 8, 80336 Munich, Germany;
- Department of Pharmacy, Ludwig-Maximilians Universität München, Butenandtstr. 7, 81377 Munich, Germany;
- Correspondence: ; Tel.: +49-89-2180-77325
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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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8
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Velez G, Mahajan VB. Molecular Surgery: Proteomics of a Rare Genetic Disease Gives Insight into Common Causes of Blindness. iScience 2020; 23:101667. [PMID: 33134897 PMCID: PMC7586135 DOI: 10.1016/j.isci.2020.101667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Rare diseases are an emerging global health priority. Although individually rare, the prevalence of rare "orphan" diseases is high, affecting approximately 300 million people worldwide. Treatments for these conditions are often inadequate, leaving the disease to progress unabated. Here, we review the clinical features and pathophysiology of neovascular inflammatory vitreoretinopathy (NIV), a rare inflammatory retinal disease caused by mutations in the CAPN5 gene. Although the prevalence of NIV is low (1 in 1,000,000 people), the disease mimics more common causes of blindness (e.g. uveitis, retinitis pigmentosa, proliferative diabetic retinopathy, and proliferative vitreoretinopathy) at distinct clinical stages. There is no cure for NIV to date. We highlight how personalized proteomics helped identify potential stage-specific biomarkers and drug targets in liquid vitreous biopsies. The NIV vitreous proteome revealed enrichment of molecular pathways associated with common retinal pathologies and implicated superior targets for therapeutic drug repositioning. In addition, we review our pipeline for collecting, storing, and analyzing ophthalmic surgical samples. This approach can be adapted to treat a variety of rare genetic diseases.
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Affiliation(s)
- Gabriel Velez
- Omics Laboratory, Stanford University, Palo Alto, CA, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Vinit B. Mahajan
- Omics Laboratory, Stanford University, Palo Alto, CA, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
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9
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Hurley JB, Chao JR. Retinal disease: How to use proteomics to speed up diagnosis and metabolomics to slow down degeneration. EBioMedicine 2020; 53:102687. [PMID: 32113163 PMCID: PMC7047175 DOI: 10.1016/j.ebiom.2020.102687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/09/2020] [Accepted: 02/09/2020] [Indexed: 01/07/2023] Open
Affiliation(s)
- James B Hurley
- Department of Biochemistry, University of Washington, Seattle, WA 98195, United States; Department of Ophthalmology, University of Washington, Seattle, WA 98109, United States.
| | - Jennifer R Chao
- Department of Ophthalmology, University of Washington, Seattle, WA 98109, United States
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10
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Metabolite therapy guided by liquid biopsy proteomics delays retinal neurodegeneration. EBioMedicine 2020; 52:102636. [PMID: 32028070 PMCID: PMC7005447 DOI: 10.1016/j.ebiom.2020.102636] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/26/2019] [Accepted: 01/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background Neurodegenerative diseases are incurable disorders caused by progressive neuronal cell death. Retinitis pigmentosa (RP) is a blinding neurodegenerative disease that results in photoreceptor death and progresses to the loss of the entire retinal network. We previously found that proteomic analysis of the adjacent vitreous served as way to indirectly biopsy the retina and identify changes in the retinal proteome. Methods We analyzed protein expression in liquid vitreous biopsies from autosomal recessive (ar)RP patients with PDE6A mutations and arRP mice with Pde6ɑ mutations. Proteomic analysis of retina and vitreous samples identified molecular pathways affected at the onset of photoreceptor death. Based on affected molecular pathways, arRP mice were treated with a ketogenic diet or metabolites involved in fatty-acid synthesis, oxidative phosphorylation, and the tricarboxylic acid (TCA) cycle. Findings Dietary supplementation of a single metabolite, ɑ-ketoglutarate, increased docosahexaeonic acid levels, provided neuroprotection, and enhanced visual function in arRP mice. A ketogenic diet delayed photoreceptor cell loss, while vitamin B supplementation had a limited effect. Finally, desorption electrospray ionization mass spectrometry imaging (DESI-MSI) on ɑ-ketoglutarate-treated mice revealed restoration of metabolites that correlated with our proteomic findings: uridine, dihydrouridine, and thymidine (pyrimidine and purine metabolism), glutamine and glutamate (glutamine/glutamate conversion), and succinic and aconitic acid (TCA cycle). Interpretation This study demonstrates that replenishing TCA cycle metabolites via oral supplementation prolongs retinal function and provides a neuroprotective effect on the photoreceptor cells and inner retinal network. Funding NIH grants [R01EY026682, R01EY024665, R01EY025225, R01EY024698, R21AG050437, P30EY026877, 5P30EY019007, R01EY018213, F30EYE027986, T32GM007337, 5P30CA013696], NSF grant CHE-1734082.
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11
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Proteomic Biomarkers of Retinal Inflammation in Diabetic Retinopathy. Int J Mol Sci 2019; 20:ijms20194755. [PMID: 31557880 PMCID: PMC6801709 DOI: 10.3390/ijms20194755] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
Diabetic retinopathy (DR), a sight-threatening neurovasculopathy, is the leading cause of irreversible blindness in the developed world. DR arises as the result of prolonged hyperglycemia and is characterized by leaky retinal vasculature, retinal ischemia, retinal inflammation, angiogenesis, and neovascularization. The number of DR patients is growing with an increase in the elderly population, and therapeutic approaches are limited, therefore, new therapies to prevent retinal injury and enhance repair are a critical unmet need. Besides vascular endothelial growth factor (VEGF)-induced vascular proliferation, several other mechanisms are important in the pathogenesis of diabetic retinopathy, including vascular inflammation. Thus, combining anti-VEGF therapy with other new therapies targeting these pathophysiological pathways of DR may further optimize treatment outcomes. Technological advancements have allowed for high-throughput proteomic studies examining biofluids such as aqueous humor, vitreous humor, tear, and serum. Many DR biomarkers have been identified, especially proteins involved in retinal inflammatory processes. This review attempts to summarize the proteomic biomarkers of DR-associated retinal inflammation identified over the last several years.
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Pulley JM, Rhoads JP, Jerome RN, Challa AP, Erreger KB, Joly MM, Lavieri RR, Perry KE, Zaleski NM, Shirey-Rice JK, Aronoff DM. Using What We Already Have: Uncovering New Drug Repurposing Strategies in Existing Omics Data. Annu Rev Pharmacol Toxicol 2019; 60:333-352. [PMID: 31337270 DOI: 10.1146/annurev-pharmtox-010919-023537] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The promise of drug repurposing is to accelerate the translation of knowledge to treatment of human disease, bypassing common challenges associated with drug development to be more time- and cost-efficient. Repurposing has an increased chance of success due to the previous validation of drug safety and allows for the incorporation of omics. Hypothesis-generating omics processes inform drug repurposing decision-making methods on drug efficacy and toxicity. This review summarizes drug repurposing strategies and methodologies in the context of the following omics fields: genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, phenomics, pregomics, and personomics. While each omics field has specific strengths and limitations, incorporating omics into the drug repurposing landscape is integral to its success.
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Affiliation(s)
- Jill M Pulley
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Jillian P Rhoads
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Rebecca N Jerome
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Anup P Challa
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Kevin B Erreger
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Meghan M Joly
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Robert R Lavieri
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Kelly E Perry
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Nicole M Zaleski
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Jana K Shirey-Rice
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - David M Aronoff
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.,Departments of Obstetrics and Gynecology, and Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA;
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13
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Refinement of two-dimensional electrophoresis for vitreous proteome profiling using an artificial neural network. Anal Bioanal Chem 2019; 411:5115-5126. [DOI: 10.1007/s00216-019-01887-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/18/2019] [Accepted: 04/30/2019] [Indexed: 01/07/2023]
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14
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Proteomic insight into the pathogenesis of CAPN5-vitreoretinopathy. Sci Rep 2019; 9:7608. [PMID: 31110225 PMCID: PMC6527583 DOI: 10.1038/s41598-019-44031-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/07/2019] [Indexed: 02/07/2023] Open
Abstract
CAPN5 Neovascular Inflammatory Vitreoretinopathy (CAPN5-NIV; OMIM 193235) is a poorly-understood rare, progressive inflammatory intraocular disease with limited therapeutic options. To profile disease effector proteins in CAPN5-NIV patient vitreous, liquid vitreous biopsies were collected from two groups: eyes from control subjects (n = 4) with idiopathic macular holes (IMH) and eyes from test subjects (n = 12) with different stages of CAPN5-NIV. Samples were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein expression changes were evaluated by principal component analysis, 1-way ANOVA (significant p-value < 0.05), hierarchical clustering, gene ontology, and pathway representation. There were 216 differentially-expressed proteins (between CAPN5-NIV and control vitreous), including those unique to and abundant in each clinical stage. Gene ontology analysis revealed decreased synaptic signaling proteins in CAPN5-NIV vitreous compared to controls. Pathway analysis revealed that inflammatory mediators of the acute phase response and the complement cascade were highly-represented. The CAPN5-NIV vitreous proteome displayed characteristic enrichment of proteins and pathways previously-associated with non-infectious posterior uveitis, rhegmatogenous retinal detachment (RRD), age-related macular degeneration (AMD), proliferative diabetic retinopathy (PDR), and proliferative vitreoretinopathy (PVR). This study expands our knowledge of affected molecular pathways in CAPN5-NIV using unbiased, shotgun proteomic analysis rather than targeted detection platforms. The high-levels and representation of acute phase response proteins suggests a functional role for the innate immune system in CAPN5-NIV pathogenesis.
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15
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Chen X, Rao J, Zheng Z, Yu Y, Lou S, Liu L, He Q, Wu L, Sun X. Integrated Tear Proteome and Metabolome Reveal Panels of Inflammatory-Related Molecules via Key Regulatory Pathways in Dry Eye Syndrome. J Proteome Res 2019; 18:2321-2330. [PMID: 30966751 DOI: 10.1021/acs.jproteome.9b00149] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Dry eye syndrome (DES) is a growing public health concern with a high global prevalence; however, the fundamental processes involved in its pathogenic mechanisms remain poorly understood. In the present study, we applied nanoscale liquid chromatography and quadrupole time-of-flight tandem mass spectrometry (nanoLC/Q-TOF-MS/MS) and ultraperformance LC/Q-TOF-MS/MS technologies on tear samples obtained from 18 dry eye patients and 19 healthy controls for integrated proteomic and metabolomic analyses. Overall, 1031 tear proteins were detected, while 190 proteins were determined to be significantly expressed in dry eye patients. Further functional analysis suggested that various biological processes were highly expressed and involved in the pathogenesis of DES, especially immune and inflammatory processes. In total, 156 named metabolites were identified, among which 34 were found to be significantly changed in dry eye patients. The results highlighted the key elements, especially inflammatory-related proteins and metabolites that played important roles in the development of DES. Further, the regulatory roles of primary pathways, including complement and coagulation cascades, glycolysis/gluconeogenesis, and amino acid metabolism, were also identified as processes involved in DES. Collectively, our work not only provided insight into the potential biomarkers of DES for diagnostic and prognostic purposes but extended our knowledge of the physiopathology of this syndrome.
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Affiliation(s)
- Xueli Chen
- Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College , Fudan University , Shanghai , China
| | - Jun Rao
- Jiangxi Provincial Key Laboratory of Translational Medicine and Oncology , Jiangxi Cancer Hospital, Jiangxi Cancer Center , Nanchang , 330029 , People's Republic of China
| | - Zhi Zheng
- Jiangxi Provincial Key Laboratory of Translational Medicine and Oncology , Jiangxi Cancer Hospital, Jiangxi Cancer Center , Nanchang , 330029 , People's Republic of China
| | - Yan Yu
- Jiangxi Provincial Key Laboratory of Translational Medicine and Oncology , Jiangxi Cancer Hospital, Jiangxi Cancer Center , Nanchang , 330029 , People's Republic of China
| | - Shang Lou
- Jiangxi Provincial Key Laboratory of Translational Medicine and Oncology , Jiangxi Cancer Hospital, Jiangxi Cancer Center , Nanchang , 330029 , People's Republic of China
| | - Liping Liu
- Jiangxi Provincial Key Laboratory of Translational Medicine and Oncology , Jiangxi Cancer Hospital, Jiangxi Cancer Center , Nanchang , 330029 , People's Republic of China
| | - Qinsi He
- Jiangxi Provincial Key Laboratory of Translational Medicine and Oncology , Jiangxi Cancer Hospital, Jiangxi Cancer Center , Nanchang , 330029 , People's Republic of China
| | - Luhua Wu
- Department of Ophthalmology , The Third Affiliated Hospital of Beijing University of Chinese Medicine , Beijing 100029 , China
| | - Xinghuai Sun
- Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College , Fudan University , Shanghai , China
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16
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Kasudhan KS, Sarkar S, Gupta V, Gupta A, Chakraborti A. Identification of unique proteins in vitreous fluid of patients with noninfectious uveitis. Acta Ophthalmol 2018; 96:e989-e1003. [PMID: 30146788 DOI: 10.1111/aos.13801] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/01/2018] [Indexed: 12/25/2022]
Abstract
PURPOSE Uveitis is a cause for concern in the developing countries like India. Its poor diagnosis and lack of proper therapeutics often cause blindness in children and young adults. Moreover, the exact mechanism of pathogenesis of different types of uveitis is still elusive. Modern proteomic techniques are found to be advantageous for an in-depth understanding of the ocular physiology using proteomic diversity. Our aim was to identify unique proteins involved in the pathogenesis of autoimmune or noninfectious uveitis. METHODS Vitreous fluid samples (n = 90) were obtained from infectious (N = 34) and noninfectious (N = 56) uveitis patients, and their protein profiles were compared by analysing sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and 2D electrophoresis. Unique proteins were identified through matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and further studied for pathway analysis. RESULTS Protein spots having different molecular weights were observed in noninfectious vitreous fluid samples. Enzymatic digestion of these spots after MALDI-TOF MS analysis revealed different proteins. We identified 25 different proteins through SDS-PAGE and 22 through 2D electrophoresis. 50% of the proteins from SDS-PAGE were associated with heterotrimeric G-protein signalling pathway-rod outer segment phototransduction. 50% proteins from SDS-PAGE and 20% from 2D electrophoresis revealed association with de novo purine biosynthesis. Carbonic anhydrase 1 and serpin B3 were found to be common in both analyses. CONCLUSION High-throughput proteomic and pathway analyses have exposed the potential association of these proteins with autoimmune pathogenesis in uveitis. The exact role of most of the proteins in autoimmune uveitis is yet to be unfurled.
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Affiliation(s)
| | - Subendu Sarkar
- Department of Experimental Medicine and Biotechnology; Chandigarh India
| | - Vishali Gupta
- Advance Eye Center; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Amod Gupta
- Advance Eye Center; Postgraduate Institute of Medical Education and Research; Chandigarh India
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Machlab DA, Velez G, Bassuk AG, Mahajan VB. ProSave: an application for restoring quantitative data to manipulated subsets of protein lists. SOURCE CODE FOR BIOLOGY AND MEDICINE 2018; 13:3. [PMID: 30459825 PMCID: PMC6233572 DOI: 10.1186/s13029-018-0070-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 11/01/2018] [Indexed: 12/21/2022]
Abstract
Background In proteomics studies, liquid chromatography tandem mass spectrometry data (LC-MS/MS) is quantified by spectral counts or by some measure of ion abundance. Downstream comparative analysis of protein content (e.g. Venn diagrams and network analysis) typically does not include this quantitative data and critical information is often lost. To avoid loss of spectral count data in comparative proteomic analyses, it is critical to implement a tool that can rapidly retrieve this information. Results We developed ProSave, a free and user-friendly Java-based program that retrieves spectral count data from a curated list of proteins in a large proteomics dataset. ProSave allows for the management of LC-MS/MS datasets and rapidly retrieves spectral count information for a desired list of proteins. Conclusions ProSave is open source and freely available at https://github.com/MahajanLab/ProSave. The user manual, implementation notes, and description of methodology and examples are available on the site.
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Affiliation(s)
| | - Gabriel Velez
- 1Omics Laboratory, Stanford University, Palo Alto, CA USA.,2Department of Ophthalmology, Byers Eye Institute, Stanford University, 1651 Page Mill Road, Palo Alto, CA 94304 USA.,3Medical Scientist Training Program, University of Iowa, Iowa City, IA USA
| | | | - Vinit B Mahajan
- 1Omics Laboratory, Stanford University, Palo Alto, CA USA.,2Department of Ophthalmology, Byers Eye Institute, Stanford University, 1651 Page Mill Road, Palo Alto, CA 94304 USA.,Palo Alto Veterans Administration, Palo Alto, CA USA
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18
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Velez G, Tang PH, Cabral T, Cho GY, Machlab DA, Tsang SH, Bassuk AG, Mahajan VB. Personalized Proteomics for Precision Health: Identifying Biomarkers of Vitreoretinal Disease. Transl Vis Sci Technol 2018; 7:12. [PMID: 30271679 PMCID: PMC6159735 DOI: 10.1167/tvst.7.5.12] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/30/2018] [Indexed: 12/14/2022] Open
Abstract
Proteomic analysis is an attractive and powerful tool for characterizing the molecular profiles of diseased tissues, such as the vitreous. The complexity of data available for analysis ranges from single (e.g., enzyme-linked immunosorbent assay [ELISA]) to thousands (e.g., mass spectrometry) of proteins, and unlike genomic analysis, which is limited to denoting risk, proteomic methods take snapshots of a diseased vitreous to evaluate ongoing molecular processes in real time. The proteome of diseased ocular tissues was recently characterized, uncovering numerous biomarkers for vitreoretinal diseases and identifying protein targets for approved drugs, allowing for drug repositioning. These biomarkers merit more attention regarding their therapeutic potential and prospective validation, as well as their value as reproducible, sensitive, and specific diagnostic markers. TRANSLATIONAL RELEVANCE Personalized proteomics offers many advantages over alternative precision-health platforms for the diagnosis and treatment of vitreoretinal diseases, including identification of molecular constituents in the diseased tissue that can be targeted by available drugs.
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Affiliation(s)
- Gabriel Velez
- Omics Laboratory, Stanford University, Palo Alto, CA, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Peter H. Tang
- Omics Laboratory, Stanford University, Palo Alto, CA, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Thiago Cabral
- Department of Specialized Medicine, CCS, Federal University of Espírito Santo (UFES), Vitória, Brazil
- Vision Center Unit, Ophthalmology, EBSERH, HUCAM-UFES, Vitória, Brazil
- Department of Ophthalmology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Galaxy Y. Cho
- Frank H. Netter MD School of Medicine, Quinnipiac University, North Haven, CT, USA
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine and Bernard & Shirlee Brown Glaucoma Laboratory, Columbia University, New York, NY, USA
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Daniel A. Machlab
- Omics Laboratory, Stanford University, Palo Alto, CA, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
| | - Stephen H. Tsang
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine and Bernard & Shirlee Brown Glaucoma Laboratory, Columbia University, New York, NY, USA
- Department of Ophthalmology, Columbia University, New York, NY, USA
- Department of Pathology & Cell Biology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | | | - Vinit B. Mahajan
- Omics Laboratory, Stanford University, Palo Alto, CA, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
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19
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Evans LP, Newell EA, Mahajan M, Tsang SH, Ferguson PJ, Mahoney J, Hue CD, Vogel EW, Morrison B, Arancio O, Nichols R, Bassuk AG, Mahajan VB. Acute vitreoretinal trauma and inflammation after traumatic brain injury in mice. Ann Clin Transl Neurol 2018; 5:240-251. [PMID: 29560370 PMCID: PMC5846452 DOI: 10.1002/acn3.523] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/16/2022] Open
Abstract
Objective Limited attention has been given to ocular injuries associated with traumatic brain injury (TBI). The retina is an extension of the central nervous system and evaluation of ocular damage may offer a less‐invasive approach to gauge TBI severity and response to treatment. We aim to characterize acute changes in the mouse eye after exposure to two different models of TBI to assess the utility of eye damage as a surrogate to brain injury. Methods A model of blast TBI (bTBI) using a shock tube was compared to a lateral fluid percussion injury model (LFPI) using fluid pressure applied directly to the brain. Whole eyes were collected from mice 3 days post LFPI and 24 days post bTBI and were evaluated histologically using a hematoxylin and eosin stain. Results bTBI mice showed evidence of vitreous detachment in the posterior chamber in addition to vitreous hemorrhage with inflammatory cells. Subretinal hemorrhage, photoreceptor degeneration, and decreased cellularity in the retinal ganglion cell layer was also seen in bTBI mice. In contrast, eyes of LFPI mice showed evidence of anterior uveitis and subcapsular cataracts. Interpretation We demonstrated that variations in the type of TBI can result in drastically different phenotypic changes within the eye. As such, molecular and phenotypic changes in the eye following TBI may provide valuable information regarding the mechanism, severity, and ongoing pathophysiology of brain injury. Because vitreous samples are easily obtained, molecular changes within the eye could be utilized as biomarkers of TBI in human patients.
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Affiliation(s)
- Lucy P Evans
- Medical Scientist Training Program University of Iowa Iowa City Iowa.,Department of Pediatrics University of Iowa Iowa City Iowa
| | | | - MaryAnn Mahajan
- Omics Laboratory Department of Ophthalmology Stanford University Palo Alto California
| | - Stephen H Tsang
- Bernard and Shirlee Brown Glaucoma Laboratory and Barbara Donald Jonas Laboratory of Regenerative Medicine Columbia University New York New York.,Edward S. Harkness Eye Institute Columbia University New York New York.,Departments of Ophthalmology, Pathology & Cell Biology Institute of Human Nutrition Columbia University New York New York
| | | | | | - Christopher D Hue
- Department of Biomedical Engineering Columbia University New York New York
| | - Edward W Vogel
- Department of Biomedical Engineering Columbia University New York New York
| | - Barclay Morrison
- Department of Biomedical Engineering Columbia University New York New York
| | - Ottavio Arancio
- Department of Pathology & Cell Biology Taub Institute Columbia University New York New York
| | - Russell Nichols
- Department of Pathology & Cell Biology Taub Institute Columbia University New York New York
| | | | - Vinit B Mahajan
- Omics Laboratory Department of Ophthalmology Stanford University Palo Alto California.,Palo Alto Veterans Administration Palo Alto California
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20
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Velez G, Machlab DA, Tang PH, Sun Y, Tsang SH, Bassuk AG, Mahajan VB. Proteomic analysis of the human retina reveals region-specific susceptibilities to metabolic- and oxidative stress-related diseases. PLoS One 2018; 13:e0193250. [PMID: 29466423 PMCID: PMC5821407 DOI: 10.1371/journal.pone.0193250] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/07/2018] [Indexed: 12/14/2022] Open
Abstract
Differences in regional protein expression within the human retina may explain molecular predisposition of specific regions to ophthalmic diseases like age-related macular degeneration, cystoid macular edema, retinitis pigmentosa, and diabetic retinopathy. To quantify protein levels in the human retina and identify patterns of differentially-expressed proteins, we collected foveomacular, juxta-macular, and peripheral retina punch biopsies from healthy donor eyes and analyzed protein content by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein expression was analyzed with 1-way ANOVA, gene ontology, pathway representation, and network analysis. We identified a mean of 1,974 proteins in the foveomacular retina, 1,999 in the juxta-macular retina, and 1,779 in the peripheral retina. Six hundred ninety-seven differentially-expressed proteins included those unique to and abundant in each anatomic region. Proteins with higher expression in each region include: heat-shock protein 90-alpha (HSP90AA1), and pyruvate kinase (PKM) in the foveomacular retina; vimentin (VIM) and fructose-bisphosphate aldolase C (ALDOC); and guanine nucleotide-binding protein subunit beta-1 (GNB1) and guanine nucleotide-binding protein subunit alpha-1 (GNAT1) in the peripheral retina. Pathway analysis identified downstream mediators of the integrin signaling pathway to be highly represented in the foveomacular region (P = 6.48 e-06). Metabolic pathways were differentially expressed among all retinal regions. Gene ontology analysis showed that proteins related to antioxidant activity were higher in the juxta-macular and the peripheral retina, but present in lower amounts in the foveomacular retina. Our proteomic analysis suggests that certain retinal regions are susceptible to different forms of metabolic and oxidative stress. The findings give mechanistic insight into retina function, reveal important molecular processes, and prioritize new pathways for therapeutic targeting.
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Affiliation(s)
- Gabriel Velez
- Omics Laboratory, Stanford University, Palo Alto, California, United States of America
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, United States of America
- Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, United States of America
| | - Daniel A. Machlab
- Omics Laboratory, Stanford University, Palo Alto, California, United States of America
| | - Peter H. Tang
- Omics Laboratory, Stanford University, Palo Alto, California, United States of America
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, United States of America
- Palo Alto Veterans Administration, Palo Alto, California, United States of America
| | - Yang Sun
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, United States of America
- Palo Alto Veterans Administration, Palo Alto, California, United States of America
| | - Stephen H. Tsang
- Jonas Children’s Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Columbia Stem Cell Initiative, Departments of Ophthalmology, Pathology & Cell Biology, Institute of Human Nutrition, Columbia University, New York, New York, United States of America
- Department of Pathology & Cell Biology, College of Physicians & Surgeons, Columbia University, New York, New York, United States of America
| | - Alexander G. Bassuk
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Vinit B. Mahajan
- Omics Laboratory, Stanford University, Palo Alto, California, United States of America
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, United States of America
- Palo Alto Veterans Administration, Palo Alto, California, United States of America
- * E-mail:
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21
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Velez G, Bassuk AG, Colgan D, Tsang SH, Mahajan VB. Therapeutic drug repositioning using personalized proteomics of liquid biopsies. JCI Insight 2017; 2:97818. [PMID: 29263305 DOI: 10.1172/jci.insight.97818] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/08/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND In patients with limited response to conventional therapeutics, repositioning of already approved drugs can bring new, more effective options. Current drug repositioning methods, however, frequently rely on retrospective computational analyses and genetic testing - time consuming methods that delay application of repositioned drugs. Here, we show how proteomic analysis of liquid biopsies successfully guided treatment of neovascular inflammatory vitreoretinopathy (NIV), an inherited autoinflammatory disease with otherwise poor clinical outcomes. METHODS Vitreous biopsies from NIV patients were profiled by an antibody array for expression of 200 cytokine-signaling proteins. Non-NIV controls were compared with NIV samples from various stages of disease progression. Patterns were identified by 1-way ANOVA, hierarchical clustering, and pathway analysis. Subjects treated with repositioned therapies were followed longitudinally. RESULTS Proteomic profiles revealed molecular pathways in NIV pathologies and implicated superior and inferior targets for therapy. Anti-VEGF injections resolved vitreous hemorrhages without the need for vitrectomy surgery. Methotrexate injections reversed inflammatory cell reactions without the side effects of corticosteroids. Anti-IL-6 therapy prevented recurrent fibrosis and retinal detachment where all prior antiinflammatory interventions had failed. The cytokine array also showed that TNF-α levels were normal and that corticosteroid-sensitive pathways were absent in fibrotic NIV, helping explain prior failure of these conventional therapeutic approaches. CONCLUSIONS Personalized proteomics can uncover highly personalized therapies for autoinflammatory disease that can be timed with specific pathologic activities. This precision medicine strategy can also help prevent delivery of ineffective drugs. Importantly, proteomic profiling of liquid biopsies offers an endpoint analysis that can directly guide treatment using available drugs.
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Affiliation(s)
- Gabriel Velez
- Omics Laboratory, Stanford University, Palo Alto, California, USA.,Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, USA.,Medical Scientist Training Program, and
| | | | - Diana Colgan
- Omics Laboratory, Stanford University, Palo Alto, California, USA.,Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, USA
| | - Stephen H Tsang
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine and Bernard & Shirlee Brown Glaucoma Laboratory, Edward S. Harkness Eye Institute, and.,Department of Pathology & Cell Biology, College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Vinit B Mahajan
- Omics Laboratory, Stanford University, Palo Alto, California, USA.,Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, USA.,Palo Alto Veterans Administration, Palo Alto, California, USA
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22
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Velez G, Tsang SH, Tsai YT, Hsu CW, Gore A, Abdelhakim AH, Mahajan M, Silverman RH, Sparrow JR, Bassuk AG, Mahajan VB. Gene Therapy Restores Mfrp and Corrects Axial Eye Length. Sci Rep 2017; 7:16151. [PMID: 29170418 PMCID: PMC5701072 DOI: 10.1038/s41598-017-16275-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/09/2017] [Indexed: 01/07/2023] Open
Abstract
Hyperopia (farsightedness) is a common and significant cause of visual impairment, and extreme hyperopia (nanophthalmos) is a consequence of loss-of-function MFRP mutations. MFRP deficiency causes abnormal eye growth along the visual axis and significant visual comorbidities, such as angle closure glaucoma, cystic macular edema, and exudative retinal detachment. The Mfrp rd6 /Mfrp rd6 mouse is used as a pre-clinical animal model of retinal degeneration, and we found it was also hyperopic. To test the effect of restoring Mfrp expression, we delivered a wild-type Mfrp to the retinal pigmented epithelium (RPE) of Mfrp rd6 /Mfrp rd6 mice via adeno-associated viral (AAV) gene therapy. Phenotypic rescue was evaluated using non-invasive, human clinical testing, including fundus auto-fluorescence, optical coherence tomography, electroretinography, and ultrasound. These analyses showed gene therapy restored retinal function and normalized axial length. Proteomic analysis of RPE tissue revealed rescue of specific proteins associated with eye growth and normal retinal and RPE function. The favorable response to gene therapy in Mfrp rd6 /Mfrp rd6 mice suggests hyperopia and associated refractive errors may be amenable to AAV gene therapy.
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Affiliation(s)
- Gabriel Velez
- Omics Laboratory, Stanford University, Palo Alto, CA, USA
- Byers Eye Institute, Department of Ophthalmology, Stanford University, Palo Alto, CA, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Stephen H Tsang
- Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Institute of Human Nutrition, Columbia University, New York, NY, USA.
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA.
| | - Yi-Ting Tsai
- Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Institute of Human Nutrition, Columbia University, New York, NY, USA
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Chun-Wei Hsu
- Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Institute of Human Nutrition, Columbia University, New York, NY, USA
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Anuradha Gore
- Omics Laboratory, Stanford University, Palo Alto, CA, USA
| | - Aliaa H Abdelhakim
- Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Institute of Human Nutrition, Columbia University, New York, NY, USA
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | | | - Ronald H Silverman
- Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Institute of Human Nutrition, Columbia University, New York, NY, USA
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Janet R Sparrow
- Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Institute of Human Nutrition, Columbia University, New York, NY, USA
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Alexander G Bassuk
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA.
- Department of Neurology, University of Iowa, Iowa City, IA, USA.
- Palo Alto Veterans Administration, Palo Alto, CA, USA.
| | - Vinit B Mahajan
- Omics Laboratory, Stanford University, Palo Alto, CA, USA.
- Byers Eye Institute, Department of Ophthalmology, Stanford University, Palo Alto, CA, USA.
- Department of Neurology, University of Iowa, Iowa City, IA, USA.
- Palo Alto Veterans Administration, Palo Alto, CA, USA.
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Cabral T, Toral MA, Velez G, DiCarlo JE, Gore AM, Mahajan M, Tsang SH, Bassuk AG, Mahajan VB. Dissection of Human Retina and RPE-Choroid for Proteomic Analysis. J Vis Exp 2017. [PMID: 29155757 DOI: 10.3791/56203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The human retina is composed of the sensory neuroretina and the underlying retinal pigmented epithelium (RPE), which is firmly complexed to the vascular choroid layer. Different regions of the retina are anatomically and molecularly distinct, facilitating unique functions and demonstrating differential susceptibility to disease. Proteomic analysis of each of these regions and layers can provide vital insights into the molecular process of many diseases, including Age-Related Macular Degeneration (AMD), diabetes mellitus, and glaucoma. However, separation of retinal regions and layers is essential before quantitative proteomic analysis can be accomplished. Here, we describe a method for dissection and collection of the foveal, macular, and peripheral retinal regions and underlying RPE-choroid complex, involving regional punch biopsies and manual removal of tissue layers from a human eye.One-dimensional SDS-PAGE as well as downstream proteomic analysis, such as liquid chromatography-tandem mass spectrometry (LC-MS/MS), can be used to identify proteins in each dissected retinal layer, revealing molecular biomarkers for retinal disease.
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Affiliation(s)
- Thiago Cabral
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Pathology & Cell Biology, Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University; Edward S. Harkness Eye Institute, New York-Presbyterian Hospital; Department of Ophthalmology, Federal University of Sao Paulo (UNIFESP); Department of Ophthalmology, Federal University of EspÍrito Santo (UFES)
| | - Marcus A Toral
- Omics Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University; Medical Scientist Training Program, University of Iowa
| | - Gabriel Velez
- Omics Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University; Medical Scientist Training Program, University of Iowa
| | - James E DiCarlo
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Pathology & Cell Biology, Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University; Edward S. Harkness Eye Institute, New York-Presbyterian Hospital
| | - Anuradha M Gore
- Omics Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University
| | - MaryAnn Mahajan
- Omics Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University
| | - Stephen H Tsang
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Pathology & Cell Biology, Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University; Edward S. Harkness Eye Institute, New York-Presbyterian Hospital
| | - Alexander G Bassuk
- Department of Pediatrics, University of Iowa; Department of Neurology, University of Iowa
| | - Vinit B Mahajan
- Omics Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University; Palo Alto Veterans Administration, Palo Alto, CA;
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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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Velez G, Roybal CN, Binkley E, Bassuk AG, Tsang SH, Mahajan VB. Proteomic Analysis of Elevated Intraocular Pressure with Retinal Detachment. Am J Ophthalmol Case Rep 2017; 5:107-110. [PMID: 28825049 PMCID: PMC5560621 DOI: 10.1016/j.ajoc.2016.12.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To report a case of elevated intraocular pressure with retinal detachment. Observations Liquid chromatography and tandem mass spectrometry was performed on the patient aqueous biopsy. Protein levels were analyzed with 1-way analysis of variance (ANOVA) and unbiased clustering. High levels of rod outer segment proteins were not detected, suggesting that this was not a case of Schwartz-Matsuo syndrome. Instead, elevated levels of Hepcidin (HEPC) and Cystatin C (CYTC; candidate biomarkers for primary open angle glaucoma) were detected, suggesting a different, unknown etiology. Conclusions and importance Molecular diagnoses can differentiate between clinical diagnoses and point to common biomarkers or disease mechanisms.
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Affiliation(s)
- Gabriel Velez
- Omics Laboratory, University of Iowa, Iowa City, IA.,Departments of Ophthalmology, University of Iowa, Iowa City, IA.,Medical Scientist Training Program, University of Iowa, Iowa City, IA
| | - C Nathaniel Roybal
- Omics Laboratory, University of Iowa, Iowa City, IA.,Departments of Ophthalmology, University of Iowa, Iowa City, IA
| | - Elaine Binkley
- Departments of Ophthalmology, University of Iowa, Iowa City, IA
| | - Alexander G Bassuk
- Department of Pediatrics, University of Iowa, Iowa City, IA.,Department of Neurology, University of Iowa, Iowa City, IA
| | - Stephen H Tsang
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Pathology & Cell Biology, Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY 10032
| | - Vinit B Mahajan
- Omics Laboratory, University of Iowa, Iowa City, IA.,Departments of Ophthalmology, University of Iowa, Iowa City, IA
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26
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Velez G, Roybal CN, Colgan D, Tsang SH, Bassuk AG, Mahajan VB. Precision Medicine: Personalized Proteomics for the Diagnosis and Treatment of Idiopathic Inflammatory Disease. JAMA Ophthalmol 2016; 134:444-8. [PMID: 26848019 DOI: 10.1001/jamaophthalmol.2015.5934] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
IMPORTANCE To better characterize posterior uveitis, vitreous samples from 15 patients were subjected to antibody arrays, and the expression levels of 200 human cytokines were evaluated. Expression was analyzed by 1-way analysis of variance (significance at P < .01), unsupervised cluster algorithm, and pathway analysis. OBSERVATIONS Unbiased clustering of patients, based on their cytokine expression profile, suggested that particular protein networks and molecular pathways are altered in various forms of uveitis. Expression of interleukin 23 (IL-23), IL-1 receptor I (IL-1RI), IL-17R, tissue inhibitors of metalloproteinase 1 and 2 (TIMP-1 and TIMP-2), insulinlike growth factor-binding protein 2 (IGFBP-2), nerve growth factor (b-NGF), platelet-derived growth factor receptor β polypeptide (PDGFRb), bone morphogenic protein 4 (BMP-4), and stem cell factor (SCF) constituted a common cytokine signature in the vitreous of patients with uveitis. In 1 patient with progressive, idiopathic visual loss, this last-line analysis implicated retinal autoimmunity, a diagnosis that was validated when her serum sample was found to contain antibodies to S-arrestin, a retinal protein and potent cause of autoimmune retinal degeneration. CONCLUSIONS AND RELEVANCE The analysis identifies a common cytokine signature for posterior uveitis and guides the diagnosis of a patient with idiopathic uveitis. Personalized treatment reversed the visual loss, illustrating how proteomic tools may individualize therapy.
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Affiliation(s)
- Gabriel Velez
- Omics Laboratory, University of Iowa Carver College of Medicine, Iowa City2Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City3Medical Scientist Training Program, University of Iowa Carver College of M
| | - C Nathaniel Roybal
- Omics Laboratory, University of Iowa Carver College of Medicine, Iowa City2Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City
| | - Diana Colgan
- Omics Laboratory, University of Iowa Carver College of Medicine, Iowa City2Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City
| | - Stephen H Tsang
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine and Bernard and Shirlee Brown Glaucoma Laboratory, Edward S. Harkness Eye Institute, Columbia University, New York, New York5Department of Pathology and Cell Biology, College of P
| | - Alexander G Bassuk
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City
| | - Vinit B Mahajan
- Omics Laboratory, University of Iowa Carver College of Medicine, Iowa City2Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City
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27
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Wert KJ, Mahajan VB, Zhang L, Yan Y, Li Y, Tosi J, Hsu CW, Nagasaki T, Janisch KM, Grant MB, Mahajan M, Bassuk AG, Tsang SH. Neuroretinal hypoxic signaling in a new preclinical murine model for proliferative diabetic retinopathy. Signal Transduct Target Ther 2016; 1. [PMID: 27195131 PMCID: PMC4868361 DOI: 10.1038/sigtrans.2016.5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Diabetic retinopathy (DR) affects approximately one-third of diabetic patients and, if left untreated, progresses to proliferative DR (PDR) with associated vitreous hemorrhage, retinal detachment, iris neovascularization, glaucoma and irreversible blindness. In vitreous samples of human patients with PDR, we found elevated levels of hypoxia inducible factor 1 alpha (HIF1α). HIFs are transcription factors that promote hypoxia adaptation and have important functional roles in a wide range of ischemic and inflammatory diseases. To recreate the human PDR phenotype for a preclinical animal model, we generated a mouse with neuroretinal-specific loss of the von Hippel Lindau tumor suppressor protein, a protein that targets HIF1α for ubiquitination. We found that the neuroretinal cells in these mice overexpressed HIF1α and developed severe, irreversible ischemic retinopathy that has features of human PDR. Rapid progression of retinopathy in these mutant mice should facilitate the evaluation of therapeutic agents for ischemic and inflammatory blinding disorders. In addition, this model system can be used to manipulate the modulation of the hypoxia signaling pathways, for the treatment of non-ocular ischemic and inflammatory disorders.
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Affiliation(s)
- Katherine J Wert
- Bernard and Shirlee Brown Glaucoma Laboratory and Barbara & Donald Jonas Laboratory of Regenerative Medicine, Columbia University, New York, NY, USA; Edward S. Harkness Eye Institute, Columbia University, New York, NY, USA; Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Vinit B Mahajan
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA; Omics Laboratory, University of Iowa, Iowa City, IA, USA
| | - Lijuan Zhang
- Bernard and Shirlee Brown Glaucoma Laboratory and Barbara & Donald Jonas Laboratory of Regenerative Medicine, Columbia University, New York, NY, USA; Edward S. Harkness Eye Institute, Columbia University, New York, NY, USA
| | - Yuanqing Yan
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - Yao Li
- Bernard and Shirlee Brown Glaucoma Laboratory and Barbara & Donald Jonas Laboratory of Regenerative Medicine, Columbia University, New York, NY, USA; Edward S. Harkness Eye Institute, Columbia University, New York, NY, USA
| | - Joaquin Tosi
- Bernard and Shirlee Brown Glaucoma Laboratory and Barbara & Donald Jonas Laboratory of Regenerative Medicine, Columbia University, New York, NY, USA; Edward S. Harkness Eye Institute, Columbia University, New York, NY, USA
| | - Chun Wei Hsu
- Bernard and Shirlee Brown Glaucoma Laboratory and Barbara & Donald Jonas Laboratory of Regenerative Medicine, Columbia University, New York, NY, USA; Edward S. Harkness Eye Institute, Columbia University, New York, NY, USA
| | - Takayuki Nagasaki
- Edward S. Harkness Eye Institute, Columbia University, New York, NY, USA
| | - Kerstin M Janisch
- Bernard and Shirlee Brown Glaucoma Laboratory and Barbara & Donald Jonas Laboratory of Regenerative Medicine, Columbia University, New York, NY, USA; Edward S. Harkness Eye Institute, Columbia University, New York, NY, USA
| | - Maria B Grant
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - MaryAnn Mahajan
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA; Omics Laboratory, University of Iowa, Iowa City, IA, USA
| | | | - Stephen H Tsang
- Bernard and Shirlee Brown Glaucoma Laboratory and Barbara & Donald Jonas Laboratory of Regenerative Medicine, Columbia University, New York, NY, USA; Edward S. Harkness Eye Institute, Columbia University, New York, NY, USA; Institute of Human Nutrition, Columbia University, New York, NY, USA; New York Presbyterian Hospital/Columbia University Medical Center, New York, NY, USA; Department of Pathology and Cellular Biology, Columbia University, New York, NY, USA
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Proteomic Analysis of the Vitreous following Experimental Retinal Detachment in Rabbits. J Ophthalmol 2015; 2015:583040. [PMID: 26664739 PMCID: PMC4667062 DOI: 10.1155/2015/583040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 10/17/2015] [Accepted: 10/19/2015] [Indexed: 01/04/2023] Open
Abstract
Purpose. The pathogenesis of rhegmatogenous retinal detachment (RRD) remains incompletely understood, with no clinically effective treatment for potentially severe complications such as photoreceptor cell death and proliferative vitreoretinopathy. Here we investigate the protein profile of the vitreous following experimental retinal detachment using a comparative proteomic based approach. Materials and Methods. Retinal detachment was created in the right eyes of six New Zealand red pigmented rabbits. Sham surgery was undertaken in five other rabbits that were used as controls. After seven days the eyes were enucleated and the vitreous was removed. The vitreous samples were evaluated with two-dimensional polyacrylamide gel electrophoresis and the differentially expressed proteins were identified with tandem mass spectrometry. Results. Ten protein spots were found to be at least twofold differentially expressed when comparing the vitreous samples of the sham and retinal detachment surgery groups. Protein spots that were upregulated in the vitreous following retinal detachment were identified as albumin fragments, and those downregulated were found to be peroxiredoxin 2, collagen-Iα1 fragment, and α-1-antiproteinase F. Conclusions. Proteomic investigation of the rabbit vitreous has identified a set of proteins that help further our understanding of the pathogenesis of rhegmatogenous retinal detachment and its complications.
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Abstract
Current proteomic technologies can effectively be used to study the proteins of the vitreous body and retina in health and disease. The use of appropriate samples, analytical platform and bioinformatic method are essential factors to consider when undertaking such studies. Certain proteins may hinder the detection and evaluation of more relevant proteins associated with pathological processes if not carefully considered, particularly in the sample preparation and data analysis stages. The utilization of more than one quantification technique and database search program to expand the level of proteome coverage and analysis will help to generate more robust and worthwhile results. This review discusses important aspects of sample processing and the use of label and label-free quantitative proteomics strategies applied to the vitreous and retina.
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30
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Skeie JM, Roybal CN, Mahajan VB. Proteomic insight into the molecular function of the vitreous. PLoS One 2015; 10:e0127567. [PMID: 26020955 PMCID: PMC4447289 DOI: 10.1371/journal.pone.0127567] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/16/2015] [Indexed: 02/06/2023] Open
Abstract
The human vitreous contains primarily water, but also contains proteins which have yet to be fully characterized. To gain insight into the four vitreous substructures and their potential functions, we isolated and analyzed the vitreous protein profiles of three non-diseased human eyes. The four analyzed substructures were the anterior hyaloid, the vitreous cortex, the vitreous core, and the vitreous base. Proteins were separated by multidimensional liquid chromatography and identified by tandem mass spectrometry. Bioinformatics tools then extracted the expression profiles, signaling pathways, and interactomes unique to each tissue. From each substructure, a mean of 2,062 unique proteins were identified, with many being differentially expressed in a specific substructure: 278 proteins were unique to the anterior hyaloid, 322 to the vitreous cortex, 128 to the vitreous base, and 136 to the vitreous core. When the identified proteins were organized according to relevant functional pathways and networks, key patterns appeared. The blood coagulation pathway and extracellular matrix turnover networks were highly represented. Oxidative stress regulation and energy metabolism proteins were distributed throughout the vitreous. Immune functions were represented by high levels of immunoglobulin, the complement pathway, damage-associated molecular patterns (DAMPs), and evolutionarily conserved antimicrobial proteins. The majority of vitreous proteins detected were intracellular proteins, some of which originate from the retina, including rhodopsin (RHO), phosphodiesterase 6 (PDE6), and glial fibrillary acidic protein (GFAP). This comprehensive analysis uncovers a picture of the vitreous as a biologically active tissue, where proteins localize to distinct substructures to protect the intraocular tissues from infection, oxidative stress, and energy disequilibrium. It also reveals the retina as a potential source of inflammatory mediators. The vitreous proteome catalogues the dynamic interactions between the vitreous and surrounding tissues. It therefore could be an indirect and effective method for surveying vitreoretinal disease for specific biomarkers.
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Affiliation(s)
- Jessica M. Skeie
- Omics Laboratory, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States of America
| | - C. Nathaniel Roybal
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States of America
| | - Vinit B. Mahajan
- Omics Laboratory, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States of America
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States of America
- * E-mail:
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32
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Monteiro JP, Santos FM, Rocha AS, Castro-de-Sousa JP, Queiroz JA, Passarinha LA, Tomaz CT. Vitreous humor in the pathologic scope: insights from proteomic approaches. Proteomics Clin Appl 2015; 9:187-202. [PMID: 25523418 DOI: 10.1002/prca.201400133] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/11/2014] [Accepted: 12/15/2014] [Indexed: 12/22/2022]
Abstract
The vitreous humor (VH) is the largest component of the eye. It is a colorless, gelatinous, highly hydrated matrix that fills the posterior segment of the eye between the lens and retina in vertebrates. In VH, a diversity of proteins that can influence retinal physiology is present, including growth factors, hormones, proteins with transporter activity, and enzymes. More importantly, the protein composition of VH has been described as being altered in a number of disease states. Therefore, attempts aiming at establishing a map of VH proteins and detecting putative biomarkers for ocular illness or protein fluctuations with putative physiologic significance were conducted over the last two decades, using proteomic approaches. Proteomic strategies often involve gel-based or LC techniques as sample fractioning approaches, subsequently coupled with MS procedures. This set of studies resulted in the proteomic characterization of a range of ocular disease samples, with particular incidence on diabetic retinopathy. However, practical therapeutic applications arising from these studies are scarce at the moment. A pertinent example of therapeutic targets arising from VH proteomics has emerged concerning vasoproliferative factors present in the vitreous, which should be involved in neovascularization and subsequent fibrovascular proliferation of the retina, in ocular disease context. Therefore, this review attempts to sum up the information acquired from the proteomic approaches to ocular disease conducted in VH samples, highlighting its clinical potential for disclosing ocular disease mechanisms and engendering pharmacological therapeutic treatments.
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Affiliation(s)
- João P Monteiro
- CICS-UBI Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
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