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Raen R, Islam MM, Islam R, Islam MR, Jarin T. Functional characterization and structural prediction of hypothetical proteins in monkeypox virus and identification of potential inhibitors. Mol Divers 2024:10.1007/s11030-024-10935-4. [PMID: 39043911 DOI: 10.1007/s11030-024-10935-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/10/2024] [Indexed: 07/25/2024]
Abstract
The excessive activation of the monkeypox virus (MPXV-Congo_8-156) is linked to various skin and respiratory disorders such as rashes, fluid-filled blisters, swollen lymph nodes and encephalitis (inflammation of the brain), highlighting MPXV-Congo_8-156 as a promising target for drug intervention. Despite the effectiveness of Cidofovir, in inhibiting MPXV activity, its limited ability to penetrate the skin and its strong side effects restrict its application. To address this challenge, we screened 500 compounds capable of penetrating the skin and gastrointestinal tract to identify potent MPXV inhibitors. Various characterization schemes and structural models of MPXV-Congo_8-156 were explored with bioinformatics tools like PROTPARAM, SOPMA, SWISS-MODEL and PROCHECK. Using molecular docking in PyRx, we evaluated the binding affinities of these compounds with MPXV-Congo_8-156 and identified the top five candidates ranging from - 9.2 to - 8.8 kcal/mol. ADMET analysis indicated that all five compounds were safer alternatives, showing no AMES toxicity or carcinogenicity in toxicological assessments. Molecular dynamics (MD) simulations, conducted for 100 ns each, confirmed the docking interactions of the top five compounds alongside the control (Cidofovir), validating their potential as MPXV inhibitors. The compounds with PubChem CID numbers 4061636, 4422538, 3583576, 4856107 and 4800629 demonstrated strong support in terms of root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA) value, hydrogen bond analysis, and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) analysis. Thus, our investigation identified these five compounds as promising inhibitors of MPXV, offering potential therapeutic avenues. However, further in vivo studies are necessary to validate our findings.
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Affiliation(s)
- Reana Raen
- Department of Biomedical Engineering, Khulna University of Engineering & Technology, Khulna, Bangladesh.
- Department of Biomedical Engineering, Chittagong University of Engineering & Technology, Chittagong, Bangladesh.
| | - Muhammad Muinul Islam
- Department of Biomedical Engineering, Khulna University of Engineering & Technology, Khulna, Bangladesh
| | - Redwanul Islam
- Department of Biomedical Engineering, Khulna University of Engineering & Technology, Khulna, Bangladesh
| | - Md Rabiul Islam
- Department of Electrical and Electronic Engineering, Jashore University of Science & Technology, Jashore, Bangladesh
| | - Tanima Jarin
- Department of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
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Heo JI, Ryu J. Exosomal noncoding RNA: A potential therapy for retinal vascular diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102128. [PMID: 38356865 PMCID: PMC10865410 DOI: 10.1016/j.omtn.2024.102128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Exosomes are extracellular vesicles that can contain DNA, RNA, proteins, and metabolites. They are secreted by cells and play a regulatory role in various biological responses by mediating cell-to-cell communication. Moreover, exosomes are of interest in developing therapies for retinal vascular disorders because they can deliver various substances to cellular targets. According to recent research, exosomes can be used as a strategy for managing retinal vascular diseases, and they are being investigated for therapeutic purposes in eye conditions, including glaucoma, dry eye syndrome, retinal ischemia, diabetic retinopathy, and age-related macular degeneration. However, the role of exosomal noncoding RNA in retinal vascular diseases is not fully understood. Here, we reviewed the latest research on the biological role of exosomal noncoding RNA in treating retinal vascular diseases. Research has shown that noncoding RNAs, including microRNAs, circular RNAs, and long noncoding RNAs play a significant role in the regulation of retinal vascular diseases. Furthermore, through exosome engineering, the expression of relevant noncoding RNAs in exosomes can be controlled to regulate retinal vascular diseases. Therefore, this review suggests that exosomal noncoding RNA could be considered as a biomarker for diagnosis and as a therapeutic target for treating retinal vascular disease.
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Affiliation(s)
- Jong-Ik Heo
- Vessel-Organ Interaction Research Center, College of Pharmacy, Kyungpook National University, Daegu, South Korea
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, South Korea
| | - Juhee Ryu
- Vessel-Organ Interaction Research Center, College of Pharmacy, Kyungpook National University, Daegu, South Korea
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, South Korea
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Shwani T, Zhang C, Owen LA, Shakoor A, Vitale AT, Lillvis JH, Barr JL, Cromwell P, Finley R, Husami N, Au E, Zavala RA, Graves EC, Zhang SX, Farkas MH, Ammar DA, Allison KM, Tawfik A, Sherva RM, Li M, Stambolian D, Kim IK, Farrer LA, DeAngelis MM. Patterns of Gene Expression, Splicing, and Allele-Specific Expression Vary among Macular Tissues and Clinical Stages of Age-Related Macular Degeneration. Cells 2023; 12:2668. [PMID: 38067097 PMCID: PMC10705168 DOI: 10.3390/cells12232668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/05/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of blindness, and elucidating its underlying disease mechanisms is vital to the development of appropriate therapeutics. We identified differentially expressed genes (DEGs) and differentially spliced genes (DSGs) across the clinical stages of AMD in disease-affected tissue, the macular retina pigment epithelium (RPE)/choroid and the macular neural retina within the same eye. We utilized 27 deeply phenotyped donor eyes (recovered within a 6 h postmortem interval time) from Caucasian donors (60-94 years) using a standardized published protocol. Significant findings were then validated in an independent set of well-characterized donor eyes (n = 85). There was limited overlap between DEGs and DSGs, suggesting distinct mechanisms at play in AMD pathophysiology. A greater number of previously reported AMD loci overlapped with DSGs compared to DEGs between disease states, and no DEG overlap with previously reported loci was found in the macular retina between disease states. Additionally, we explored allele-specific expression (ASE) in coding regions of previously reported AMD risk loci, uncovering a significant imbalance in C3 rs2230199 and CFH rs1061170 in the macular RPE/choroid for normal eyes and intermediate AMD (iAMD), and for CFH rs1061147 in the macular RPE/choroid for normal eyes and iAMD, and separately neovascular AMD (NEO). Only significant DEGs/DSGs from the macular RPE/choroid were found to overlap between disease states. STAT1, validated between the iAMD vs. normal comparison, and AGTPBP1, BBS5, CERKL, FGFBP2, KIFC3, RORα, and ZNF292, validated between the NEO vs. normal comparison, revealed an intricate regulatory network with transcription factors and miRNAs identifying potential upstream and downstream regulators. Findings regarding the complement genes C3 and CFH suggest that coding variants at these loci may influence AMD development via an imbalance of gene expression in a tissue-specific manner. Our study provides crucial insights into the multifaceted genomic underpinnings of AMD (i.e., tissue-specific gene expression changes, potential splice variation, and allelic imbalance), which may open new avenues for AMD diagnostics and therapies specific to iAMD and NEO.
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Affiliation(s)
- Treefa Shwani
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Charles Zhang
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Leah A. Owen
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA; (A.S.); (A.T.V.)
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
| | - Akbar Shakoor
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA; (A.S.); (A.T.V.)
| | - Albert T. Vitale
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA; (A.S.); (A.T.V.)
| | - John H. Lillvis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
| | - Julie L. Barr
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Parker Cromwell
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Robert Finley
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Nadine Husami
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Elizabeth Au
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Rylee A. Zavala
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Elijah C. Graves
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Sarah X. Zhang
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Michael H. Farkas
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - David A. Ammar
- Lion’s Eye Institute for Transplant & Research, Tampa, FL 33605, USA;
| | - Karen M. Allison
- Department of Ophthalmology, Flaum Eye Institute, University of Rochester, Rochester, NY 14642, USA;
| | - Amany Tawfik
- Department of Foundational Medical Studies and Eye Research Center, Oakland University William Beaumont School of Medicine, Rochester, MI 48309, USA;
- Eye Research Institute, Oakland University, Rochester, MI 48309, USA
| | - Richard M. Sherva
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; (R.M.S.); (L.A.F.)
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Dwight Stambolian
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Ivana K. Kim
- Retina Service, Massachusetts Eye & Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA;
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; (R.M.S.); (L.A.F.)
| | - Margaret M. DeAngelis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA; (A.S.); (A.T.V.)
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
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Acar IE, Galesloot TE, Luhmann UFO, Fauser S, Gayán J, den Hollander AI, Nogoceke E. Whole Genome Sequencing Identifies Novel Common and Low-Frequency Variants Associated With Age-Related Macular Degeneration. Invest Ophthalmol Vis Sci 2023; 64:24. [PMID: 37975850 PMCID: PMC10664724 DOI: 10.1167/iovs.64.14.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 10/22/2023] [Indexed: 11/19/2023] Open
Abstract
Purpose To identify associations of common, low-frequency, and rare variants with advanced age-related macular degeneration (AMD) using whole genome sequencing (WGS). Methods WGS data were obtained for 2123 advanced AMD patients (participants of clinical trials for advanced AMD) and 2704 controls (participants of clinical trials for asthma [N = 2518] and Alzheimer's disease [N = 186]), and joint genotype calling was performed, followed by quality control of the dataset. Single variant association analyses were performed for all identified common, low-frequency, and rare variants. Gene-based tests were executed for rare and low-frequency variants using SKAT-O and three groups of variants based on putative impact information: (1) all variants, (2) modifier impact variants, and (3) high- and moderate-impact variants. To ascertain independence of the identified associations from previously reported AMD and asthma loci, conditional analyses were performed. Results Previously identified AMD variants at the CFH, ARMS2/HTRA1, APOE, and C3 loci were associated with AMD at a genome-wide significance level. We identified new single variant associations for common variants near the PARK7 gene and in the long non-coding RNA AC103876.1, and for a rare variant near the TENM3 gene. In addition, gene-based association analyses identified a burden of modifier variants in eight intergenic and gene-spanning regions and of high- and moderate-impact variants in the C3, CFHR5, SLC16A8, and CFI genes. Conclusions We describe the largest WGS study in AMD to date. We confirmed previously identified associations and identified several novel associations that are worth exploring in further follow-up studies.
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Affiliation(s)
- Ilhan E. Acar
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tessel E. Galesloot
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department for Health Evidence, Nijmegen, The Netherlands
| | - Ulrich F. O. Luhmann
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Sascha Fauser
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Javier Gayán
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Anneke I. den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Everson Nogoceke
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
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Dähmcke M, Busch M, Pfeil JM, Brauckmann T, Schulz D, Omran W, Morawiec-Kisiel E, Wähler F, Paul S, Tayar A, Bründer MC, Grundel B, Stahl A. Circulating MicroRNAs as Biomarker for Vessel-Associated Retinal Diseases. Ophthalmologica 2023; 246:227-237. [PMID: 37721532 DOI: 10.1159/000533481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/04/2023] [Indexed: 09/19/2023]
Abstract
INTRODUCTION Vessel-associated retinal diseases are a major cause of blindness and severe visual impairment. The identification of appropriate biomarkers is of great importance to better anticipate disease progression and establish more targeted treatment options. MicroRNAs (miRNAs) are short, single-stranded, noncoding ribonucleic acids that are involved in the posttranscriptional regulation of gene expression through hybridization with messenger RNA. The expression of certain miRNAs can be different in patients with pathological processes and can be used for the detection and differentiation of various diseases. In this study, we investigate to what extent previously in vitro identified miRNAs are present as cell-free circulating miRNAs in the serum and vitreous of human patients with and without vessel-associated retinal diseases. METHODS Relative quantification by quantitative real-time polymerase chain reaction was used to analyze miRNA expression in patients with vessel-associated retinal diseases such as age-related macular degeneration (AMD), diabetic retinopathy (DR), and retinal vein occlusion compared with control patients. RESULTS In serum samples, miR-29a-3p and miR-192-5p showed increased expression in patients with neovascular AMD relative to control patients. Similarly, miR-335-5p, miR-192-5p, and miR-194-5p showed increased expression in serum from patients with proliferative DR. In vitreous samples, miR-100-5p was decreased in patients with proliferative DR. Differentially expressed miRNAs showed good diagnostic accuracy in receiver operating characteristic (ROC) and area under the ROC curve analysis. CONCLUSION The miRNAs investigated in this study may have the potential to serve as biomarkers for vessel-associated retinal diseases. Combining multiple miRNAs may enhance the predictive power of the analysis.
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Affiliation(s)
- Merlin Dähmcke
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Martin Busch
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Johanna M Pfeil
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Tara Brauckmann
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Daniel Schulz
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Wael Omran
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Ewa Morawiec-Kisiel
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Fabienne Wähler
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Sebastian Paul
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Allam Tayar
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | | | - Bastian Grundel
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Andreas Stahl
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
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Markitantova Y, Simirskii V. Endogenous and Exogenous Regulation of Redox Homeostasis in Retinal Pigment Epithelium Cells: An Updated Antioxidant Perspective. Int J Mol Sci 2023; 24:10776. [PMID: 37445953 DOI: 10.3390/ijms241310776] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
The retinal pigment epithelium (RPE) performs a range of necessary functions within the neural layers of the retina and helps ensure vision. The regulation of pro-oxidative and antioxidant processes is the basis for maintaining RPE homeostasis and preventing retinal degenerative processes. Long-term stable changes in the redox balance under the influence of endogenous or exogenous factors can lead to oxidative stress (OS) and the development of a number of retinal pathologies associated with RPE dysfunction, and can eventually lead to vision loss. Reparative autophagy, ubiquitin-proteasome utilization, the repair of damaged proteins, and the maintenance of their conformational structure are important interrelated mechanisms of the endogenous defense system that protects against oxidative damage. Antioxidant protection of RPE cells is realized as a result of the activity of specific transcription factors, a large group of enzymes, chaperone proteins, etc., which form many signaling pathways in the RPE and the retina. Here, we discuss the role of the key components of the antioxidant defense system (ADS) in the cellular response of the RPE against OS. Understanding the role and interactions of OS mediators and the components of the ADS contributes to the formation of ideas about the subtle mechanisms in the regulation of RPE cellular functions and prospects for experimental approaches to restore RPE functions.
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Affiliation(s)
- Yuliya Markitantova
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Vladimir Simirskii
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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7
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Orozco LD, Owen LA, Hofmann J, Stockwell AD, Tao J, Haller S, Mukundan VT, Clarke C, Lund J, Sridhar A, Mayba O, Barr JL, Zavala RA, Graves EC, Zhang C, Husami N, Finley R, Au E, Lillvis JH, Farkas MH, Shakoor A, Sherva R, Kim IK, Kaminker JS, Townsend MJ, Farrer LA, Yaspan BL, Chen HH, DeAngelis MM. A systems biology approach uncovers novel disease mechanisms in age-related macular degeneration. CELL GENOMICS 2023; 3:100302. [PMID: 37388919 PMCID: PMC10300496 DOI: 10.1016/j.xgen.2023.100302] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/21/2023] [Accepted: 03/22/2023] [Indexed: 07/01/2023]
Abstract
Age-related macular degeneration (AMD) is a leading cause of blindness, affecting 200 million people worldwide. To identify genes that could be targeted for treatment, we created a molecular atlas at different stages of AMD. Our resource is comprised of RNA sequencing (RNA-seq) and DNA methylation microarrays from bulk macular retinal pigment epithelium (RPE)/choroid of clinically phenotyped normal and AMD donor eyes (n = 85), single-nucleus RNA-seq (164,399 cells), and single-nucleus assay for transposase-accessible chromatin (ATAC)-seq (125,822 cells) from the retina, RPE, and choroid of 6 AMD and 7 control donors. We identified 23 genome-wide significant loci differentially methylated in AMD, over 1,000 differentially expressed genes across different disease stages, and an AMD Müller state distinct from normal or gliosis. Chromatin accessibility peaks in genome-wide association study (GWAS) loci revealed putative causal genes for AMD, including HTRA1 and C6orf223. Our systems biology approach uncovered molecular mechanisms underlying AMD, including regulators of WNT signaling, FRZB and TLE2, as mechanistic players in disease.
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Affiliation(s)
- Luz D. Orozco
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Leah A. Owen
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Jeffrey Hofmann
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Amy D. Stockwell
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Jianhua Tao
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Susan Haller
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Vineeth T. Mukundan
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Christine Clarke
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Jessica Lund
- Departments of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Akshayalakshmi Sridhar
- Department of Human Pathobiology & OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Oleg Mayba
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Julie L. Barr
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Rylee A. Zavala
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Elijah C. Graves
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Charles Zhang
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Nadine Husami
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Robert Finley
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Elizabeth Au
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - John H. Lillvis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
| | - Michael H. Farkas
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
| | - Akbar Shakoor
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
| | - Richard Sherva
- Department of Medicine, Biomedical Genetics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ivana K. Kim
- Retina Service, Massachusetts Eye & Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Joshua S. Kaminker
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Michael J. Townsend
- Department of Human Pathobiology & OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Lindsay A. Farrer
- Department of Medicine, Biomedical Genetics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Brian L. Yaspan
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Hsu-Hsin Chen
- Department of Human Pathobiology & OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Margaret M. DeAngelis
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
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Hyttinen JMT, Blasiak J, Kaarniranta K. Non-Coding RNAs Regulating Mitochondrial Functions and the Oxidative Stress Response as Putative Targets against Age-Related Macular Degeneration (AMD). Int J Mol Sci 2023; 24:ijms24032636. [PMID: 36768958 PMCID: PMC9917342 DOI: 10.3390/ijms24032636] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Age-related macular degeneration (AMD) is an ever-increasing, insidious disease which reduces the quality of life of millions of elderly people around the world. AMD is characterised by damage to the retinal pigment epithelium (RPE) in the macula region of the retina. The origins of this multi-factorial disease are complex and still not fully understood. Oxidative stress and mitochondrial imbalance in the RPE are believed to be important factors in the development of AMD. In this review, the regulation of the mitochondrial function and antioxidant stress response by non-coding RNAs (ncRNAs), newly emerged epigenetic factors, is discussed. These molecules include microRNAs, long non-coding RNAs, and circular non-coding RNAs. They act mainly as mRNA suppressors, controllers of other ncRNAs, or by interacting with proteins. We include here examples of these RNA molecules which affect various mitochondrial processes and antioxidant signaling of the cell. As a future prospect, the possibility to manipulate these ncRNAs to strengthen mitochondrial and antioxidant response functions is discussed. Non-coding RNAs could be used as potential diagnostic markers for AMD, and in the future, also as therapeutic targets, either by suppressing or increasing their expression. In addition to AMD, it is possible that non-coding RNAs could be regulators in other oxidative stress-related degenerative diseases.
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Affiliation(s)
- Juha M. T. Hyttinen
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
- Correspondence:
| | - Janusz Blasiak
- Department of Molecular Genetics, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Kai Kaarniranta
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
- Department of Ophthalmology, Kuopio University Hospital, P.O. Box 100, FI-70029 Kuopio, Finland
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