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Latifi-Navid H, Barzegar Behrooz A, Jamehdor S, Davari M, Latifinavid M, Zolfaghari N, Piroozmand S, Taghizadeh S, Bourbour M, Shemshaki G, Latifi-Navid S, Arab SS, Soheili ZS, Ahmadieh H, Sheibani N. Construction of an Exudative Age-Related Macular Degeneration Diagnostic and Therapeutic Molecular Network Using Multi-Layer Network Analysis, a Fuzzy Logic Model, and Deep Learning Techniques: Are Retinal and Brain Neurodegenerative Disorders Related? Pharmaceuticals (Basel) 2023; 16:1555. [PMID: 38004422 PMCID: PMC10674956 DOI: 10.3390/ph16111555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Neovascular age-related macular degeneration (nAMD) is a leading cause of irreversible visual impairment in the elderly. The current management of nAMD is limited and involves regular intravitreal administration of anti-vascular endothelial growth factor (anti-VEGF). However, the effectiveness of these treatments is limited by overlapping and compensatory pathways leading to unresponsiveness to anti-VEGF treatments in a significant portion of nAMD patients. Therefore, a system view of pathways involved in pathophysiology of nAMD will have significant clinical value. The aim of this study was to identify proteins, miRNAs, long non-coding RNAs (lncRNAs), various metabolites, and single-nucleotide polymorphisms (SNPs) with a significant role in the pathogenesis of nAMD. To accomplish this goal, we conducted a multi-layer network analysis, which identified 30 key genes, six miRNAs, and four lncRNAs. We also found three key metabolites that are common with AMD, Alzheimer's disease (AD) and schizophrenia. Moreover, we identified nine key SNPs and their related genes that are common among AMD, AD, schizophrenia, multiple sclerosis (MS), and Parkinson's disease (PD). Thus, our findings suggest that there exists a connection between nAMD and the aforementioned neurodegenerative disorders. In addition, our study also demonstrates the effectiveness of using artificial intelligence, specifically the LSTM network, a fuzzy logic model, and genetic algorithms, to identify important metabolites in complex metabolic pathways to open new avenues for the design and/or repurposing of drugs for nAMD treatment.
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Affiliation(s)
- Hamid Latifi-Navid
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran; (H.L.-N.); (M.D.); (N.Z.); (S.P.); (S.T.); (Z.-S.S.)
- Departments of Ophthalmology and Visual Sciences and Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Amir Barzegar Behrooz
- Department of Human Anatomy and Cell Science, University of Manitoba College of Medicine, Winnipeg, MB R3T 2N2, Canada;
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran 1416634793, Iran
| | - Saleh Jamehdor
- Department of Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan 6517838636, Iran;
| | - Maliheh Davari
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran; (H.L.-N.); (M.D.); (N.Z.); (S.P.); (S.T.); (Z.-S.S.)
| | - Masoud Latifinavid
- Department of Mechatronic Engineering, University of Turkish Aeronautical Association, 06790 Ankara, Turkey;
| | - Narges Zolfaghari
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran; (H.L.-N.); (M.D.); (N.Z.); (S.P.); (S.T.); (Z.-S.S.)
| | - Somayeh Piroozmand
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran; (H.L.-N.); (M.D.); (N.Z.); (S.P.); (S.T.); (Z.-S.S.)
| | - Sepideh Taghizadeh
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran; (H.L.-N.); (M.D.); (N.Z.); (S.P.); (S.T.); (Z.-S.S.)
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Mahsa Bourbour
- Department of Biotechnology, Alzahra University, Tehran 1993893973, Iran;
| | - Golnaz Shemshaki
- Department of Studies in Zoology, University of Mysore, Manasagangothri, Mysore 570005, India;
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil 5619911367, Iran;
| | - Seyed Shahriar Arab
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran;
| | - Zahra-Soheila Soheili
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran; (H.L.-N.); (M.D.); (N.Z.); (S.P.); (S.T.); (Z.-S.S.)
| | - Hamid Ahmadieh
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran 1666673111, Iran;
| | - Nader Sheibani
- Departments of Ophthalmology and Visual Sciences and Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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Koster C, van den Hurk KT, ten Brink JB, Lewallen CF, Stanzel BV, Bharti K, Bergen AA. Sodium-Iodate Injection Can Replicate Retinal Degenerative Disease Stages in Pigmented Mice and Rats: Non-Invasive Follow-Up Using OCT and ERG. Int J Mol Sci 2022; 23:ijms23062918. [PMID: 35328338 PMCID: PMC8953416 DOI: 10.3390/ijms23062918] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 11/16/2022] Open
Abstract
Purpose: The lack of suitable animal models for (dry) age-related macular degeneration (AMD) has hampered therapeutic research into the disease, so far. In this study, pigmented rats and mice were systematically injected with various doses of sodium iodate (SI). After injection, the retinal structure and visual function were non-invasively characterized over time to obtain in-depth data on the suitability of these models for studying experimental therapies for retinal degenerative diseases, such as dry AMD. Methods: SI was injected into the tail vein (i.v.) using a series of doses (0–70 mg/kg) in adolescent C57BL/6J mice and Brown Norway rats. The retinal structure and function were assessed non-invasively at baseline (day 1) and at several time points (1–3, 5, and 10-weeks) post-injection by scanning laser ophthalmoscopy (SLO), optical coherence tomography (OCT), and electroretinography (ERG). Results: After the SI injection, retinal degeneration in mice and rats yielded similar results. The lowest dose (10 mg/kg) resulted in non-detectable structural or functional effects. An injection with 20 mg/kg SI did not result in an evident retinal degeneration as judged from the OCT data. In contrast, the ERG responses were temporarily decreased but returned to baseline within two-weeks. Higher doses (30, 40, 50, and 70 mg/kg) resulted in moderate to severe structural RPE and retinal injury and decreased the ERG amplitudes, indicating visual impairment in both mice and rat strains. Conclusions: After the SI injections, we observed dose-dependent structural and functional pathological effects on the retinal pigment epithelium (RPE) and retina in the pigmented mouse and rat strains that were used in this study. Similar effects were observed in both species. In particular, a dose of 30 mg/kg seems to be suitable for future studies on developing experimental therapies. These relatively easily induced non-inherited models may serve as useful tools for evaluating novel therapies for RPE-related retinal degenerations, such as AMD.
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Affiliation(s)
- Céline Koster
- Department of Human Genetics, Section Ophthalmogenetics, Amsterdam University Medical Centers (AUMC), University of Amsterdam (UvA), Location AMC, Meibergdreef, 1105 AZ Amsterdam, The Netherlands; (C.K.); (K.T.v.d.H.); (J.B.t.B.)
| | - Koen T. van den Hurk
- Department of Human Genetics, Section Ophthalmogenetics, Amsterdam University Medical Centers (AUMC), University of Amsterdam (UvA), Location AMC, Meibergdreef, 1105 AZ Amsterdam, The Netherlands; (C.K.); (K.T.v.d.H.); (J.B.t.B.)
| | - Jacoline B. ten Brink
- Department of Human Genetics, Section Ophthalmogenetics, Amsterdam University Medical Centers (AUMC), University of Amsterdam (UvA), Location AMC, Meibergdreef, 1105 AZ Amsterdam, The Netherlands; (C.K.); (K.T.v.d.H.); (J.B.t.B.)
| | - Colby F. Lewallen
- Georgia Institute of Technology, G.W. Woodruff School of Mechanical Engineering, Atlanta, GA 30332, USA;
| | - Boris V. Stanzel
- Eye Clinic Sulzbach, Knappschaft Hospital Saar, 66280 Sulzbach/Saar, Germany;
- Department of Ophthalmology, University of Bonn, 53113 Bonn, Germany
| | - Kapil Bharti
- Ocular and Stem Cell Research Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Arthur A. Bergen
- Department of Human Genetics, Section Ophthalmogenetics, Amsterdam University Medical Centers (AUMC), University of Amsterdam (UvA), Location AMC, Meibergdreef, 1105 AZ Amsterdam, The Netherlands; (C.K.); (K.T.v.d.H.); (J.B.t.B.)
- Department of Ophthalmology, AUMC, UvA, Location AMC, Meibergdreef, 1105 AZ Amsterdam, The Netherlands
- Correspondence:
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Cimaglia G, Votruba M, Morgan JE, André H, Williams PA. Potential Therapeutic Benefit of NAD + Supplementation for Glaucoma and Age-Related Macular Degeneration. Nutrients 2020; 12:nu12092871. [PMID: 32961812 PMCID: PMC7551676 DOI: 10.3390/nu12092871] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
Glaucoma and age-related macular degeneration are leading causes of irreversible blindness worldwide with significant health and societal burdens. To date, no clinical cures are available and treatments target only the manageable symptoms and risk factors (but do not remediate the underlying pathology of the disease). Both diseases are neurodegenerative in their pathology of the retina and as such many of the events that trigger cell dysfunction, degeneration, and eventual loss are due to mitochondrial dysfunction, inflammation, and oxidative stress. Here, we critically review how a decreased bioavailability of nicotinamide adenine dinucleotide (NAD; a crucial metabolite in healthy and disease states) may underpin many of these aberrant mechanisms. We propose how exogenous sources of NAD may become a therapeutic standard for the treatment of these conditions.
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Affiliation(s)
- Gloria Cimaglia
- Department of Clinical Neuroscience, Division of Eye and Vision, St. Erik Eye Hospital, Karolinska Institutet, 112 82 Stockholm, Sweden;
- School of Optometry and Vision Sciences, Cardiff University, Cardiff CF24 4HQ, Wales, UK; (M.V.); (J.E.M.)
| | - Marcela Votruba
- School of Optometry and Vision Sciences, Cardiff University, Cardiff CF24 4HQ, Wales, UK; (M.V.); (J.E.M.)
- Cardiff Eye Unit, University Hospital Wales, Cardiff CF14 4XW, Wales, UK
| | - James E. Morgan
- School of Optometry and Vision Sciences, Cardiff University, Cardiff CF24 4HQ, Wales, UK; (M.V.); (J.E.M.)
- School of Medicine, Cardiff University, Cardiff CF14 4YS, Wales, UK
| | - Helder André
- Department of Clinical Neuroscience, Division of Eye and Vision, St. Erik Eye Hospital, Karolinska Institutet, 112 82 Stockholm, Sweden;
- Correspondence: (H.A.); (P.A.W.)
| | - Pete A. Williams
- Department of Clinical Neuroscience, Division of Eye and Vision, St. Erik Eye Hospital, Karolinska Institutet, 112 82 Stockholm, Sweden;
- Correspondence: (H.A.); (P.A.W.)
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Implications of NAD + Metabolism in the Aging Retina and Retinal Degeneration. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:2692794. [PMID: 32454935 PMCID: PMC7238357 DOI: 10.1155/2020/2692794] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/17/2020] [Indexed: 12/19/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD+) plays an important role in various key biological processes including energy metabolism, DNA repair, and gene expression. Accumulating clinical and experimental evidence highlights an age-dependent decline in NAD+ levels and its association with the development and progression of several age-related diseases. This supports the establishment of NAD+ as a critical regulator of aging and longevity and, relatedly, a promising therapeutic target to counter adverse events associated with the normal process of aging and/or the development and progression of age-related disease. Relative to the above, the metabolism of NAD+ has been the subject of numerous investigations in various cells, tissues, and organ systems; however, interestingly, studies of NAD+ metabolism in the retina and its relevance to the regulation of visual health and function are comparatively few. This is surprising given the critical causative impact of mitochondrial oxidative damage and bioenergetic crises on the development and progression of degenerative disease of the retina. Hence, the role of NAD+ in this tissue, normally and aging and/or disease, should not be ignored. Herein, we discuss important findings in the field of NAD+ metabolism, with particular emphasis on the importance of the NAD+ biosynthesizing enzyme NAMPT, the related metabolism of NAD+ in the retina, and the consequences of NAMPT and NAD+ deficiency or depletion in this tissue in aging and disease. We discuss also the implications of potential therapeutic strategies that augment NAD+ levels on the preservation of retinal health and function in the above conditions. The overarching goal of this review is to emphasize the importance of NAD+ metabolism in normal, aging, and/or diseased retina and, by so doing, highlight the necessity of additional clinical studies dedicated to evaluating the therapeutic utility of strategies that enhance NAD+ levels in improving vision.
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