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Matei IV, Paraoan L. Aging retinal pigmented epithelium: omics-based insights into vision decline. Aging (Albany NY) 2024; 16:205914. [PMID: 38870314 DOI: 10.18632/aging.205914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Affiliation(s)
- Ioan V Matei
- Faculty of Arts and Sciences, Edge Hill University, Ormskirk, Lancashire L39 4QP, UK
| | - Luminita Paraoan
- Faculty of Arts and Sciences, Edge Hill University, Ormskirk, Lancashire L39 4QP, UK
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2
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Luo S, Hu Q, Jiang B, Zhang Z, Sun D. Bioinformatics analysis for constructing a cellular senescence-related age-related macular degeneration diagnostic model and identifying relevant disease subtypes to guide treatment. Aging (Albany NY) 2024; 16:8044-8069. [PMID: 38742956 PMCID: PMC11131993 DOI: 10.18632/aging.205804] [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: 11/07/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Age-related macular degeneration (AMD) is a condition causing progressive central vision loss. Growing evidence suggests a link between cellular senescence and AMD. However, the exact mechanism by which cellular senescence leads to AMD remains unclear. Employing machine learning, we established an AMD diagnostic model. Through unsupervised clustering, two distinct AMD subtypes were identified. GO, KEGG, and GSVA analyses explored the diverse biological functions associated with the two subtypes. By WGCNA, we constructed a coexpression network of differential genes between the subtypes, revealing the regulatory role of hub genes at the level of transcription factors and miRNAs. We identified 5 genes associated with inflammation for the construction of the AMD diagnostic model. Additionally, we observed that the level of cellular senescence and pathways related to programmed cell death (PCD), such as ferroptosis, necroptosis, and pyroptosis, exhibited higher expression levels in subtype B than A. Immune microenvironments also differed between the subtypes, indicating potentially distinct pathogenic mechanisms and therapeutic targets. In summary, by leveraging cellular senescence-associated gene expression, we developed an AMD diagnostic model. Furthermore, we identified two subtypes with varying expression patterns of senescence genes, revealing their differential roles in programmed cell death, disease progression, and immune microenvironments within AMD.
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Affiliation(s)
- Shan Luo
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Qiang Hu
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Bo Jiang
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhongyu Zhang
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Dawei Sun
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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3
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Mullin NK, Voigt AP, Boese EA, Liu X, Stone EM, Tucker BA, Mullins RF. Transcriptomic and Chromatin Accessibility Analysis of the Human Macular and Peripheral Retinal Pigment Epithelium at the Single-Cell Level. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1750-1761. [PMID: 36775060 PMCID: PMC10616710 DOI: 10.1016/j.ajpath.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 02/12/2023]
Abstract
Some human retinal diseases are characterized by pathology that is restricted to specific cell types and to specific regions of the eye. Several disease entities either selectively affect or spare the macula, the retina region at the center of the posterior pole. Photoreceptor cells in the macula are involved in high-acuity vision and require metabolic support from non-neuronal cell types. Some macular diseases involve the retinal pigment epithelium (RPE), an epithelial cell layer with several metabolic-support functions essential for the overlying photoreceptors. In the current study, the ways in which RPE confers region-specific disease susceptibility were determined by examining heterogeneity within RPE tissue from human donors. RPE nuclei from the macular and peripheral retina were profiled using joint single-nucleus RNA and ATAC sequencing. The expression of several genes differed between macular and peripheral RPE. Region-specific ATAC peaks were found, suggesting regulatory elements used exclusively by macular or peripheral RPE. Across anatomic regions, subpopulations of RPE were identified that appeared to have differential levels of expression of visual cycle genes. Finally, loci associated with age-related macular degeneration were examined for a better understanding of RPE-specific disease phenotypes. These findings showed variations in the regulation of gene expression in the human RPE by region and subpopulation, and provide a source for a better understanding of the molecular basis of macular disease.
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Affiliation(s)
- Nathaniel K Mullin
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa; Medical Scientist Training Program, University of Iowa, Iowa City, Iowa
| | - Andrew P Voigt
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa; Medical Scientist Training Program, University of Iowa, Iowa City, Iowa
| | - Erin A Boese
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa
| | - Xiuying Liu
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa
| | - Edwin M Stone
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa
| | - Budd A Tucker
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa
| | - Robert F Mullins
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa.
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4
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Bohn T, Balbuena E, Ulus H, Iddir M, Wang G, Crook N, Eroglu A. Carotenoids in Health as Studied by Omics-Related Endpoints. Adv Nutr 2023; 14:1538-1578. [PMID: 37678712 PMCID: PMC10721521 DOI: 10.1016/j.advnut.2023.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023] Open
Abstract
Carotenoids have been associated with risk reduction for several chronic diseases, including the association of their dietary intake/circulating levels with reduced incidence of obesity, type 2 diabetes, certain types of cancer, and even lower total mortality. In addition to some carotenoids constituting vitamin A precursors, they are implicated in potential antioxidant effects and pathways related to inflammation and oxidative stress, including transcription factors such as nuclear factor κB and nuclear factor erythroid 2-related factor 2. Carotenoids and metabolites may also interact with nuclear receptors, mainly retinoic acid receptor/retinoid X receptor and peroxisome proliferator-activated receptors, which play a role in the immune system and cellular differentiation. Therefore, a large number of downstream targets are likely influenced by carotenoids, including but not limited to genes and proteins implicated in oxidative stress and inflammation, antioxidation, and cellular differentiation processes. Furthermore, recent studies also propose an association between carotenoid intake and gut microbiota. While all these endpoints could be individually assessed, a more complete/integrative way to determine a multitude of health-related aspects of carotenoids includes (multi)omics-related techniques, especially transcriptomics, proteomics, lipidomics, and metabolomics, as well as metagenomics, measured in a variety of biospecimens including plasma, urine, stool, white blood cells, or other tissue cellular extracts. In this review, we highlight the use of omics technologies to assess health-related effects of carotenoids in mammalian organisms and models.
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Affiliation(s)
- Torsten Bohn
- Nutrition and Health Research Group, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg.
| | - Emilio Balbuena
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States; Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, United States
| | - Hande Ulus
- Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, United States
| | - Mohammed Iddir
- Nutrition and Health Research Group, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Genan Wang
- Department of Chemical and Biomolecular Engineering, College of Engineering, North Carolina State University, Raleigh, NC, United States
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, College of Engineering, North Carolina State University, Raleigh, NC, United States
| | - Abdulkerim Eroglu
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States; Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, United States.
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5
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Matmat K, Conart JB, Graindorge PH, El Kouche S, Hassan Z, Siblini Y, Umoret R, Safar R, Baspinar O, Robert A, Alberto JM, Oussalah A, Coelho D, Guéant JL, Guéant-Rodriguez RM. A transgenic mice model of retinopathy of cblG-type inherited disorder of one-carbon metabolism highlights epigenome-wide alterations related to cone photoreceptor cells development and retinal metabolism. Clin Epigenetics 2023; 15:158. [PMID: 37798757 PMCID: PMC10557304 DOI: 10.1186/s13148-023-01567-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND MTR gene encodes the cytoplasmic enzyme methionine synthase, which plays a pivotal role in the methionine cycle of one-carbon metabolism. This cycle holds a significant importance in generating S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), the respective universal methyl donor and end-product of epigenetic transmethylation reactions. cblG type of inherited disorders of vitamin B12 metabolism due to mutations in MTR gene exhibits a wide spectrum of symptoms, including a retinopathy unresponsive to conventional therapies. METHODS To unveil the underlying epigenetic pathological mechanisms, we conducted a comprehensive study of epigenomic-wide alterations of DNA methylation by NGS of bisulfited retinal DNA in an original murine model with conditional Mtr deletion in retinal tissue. Our focus was on postnatal day 21, a critical developmental juncture for ocular structure refinement and functional maturation. RESULTS We observed delayed eye opening and impaired visual acuity and alterations in the one-carbon metabolomic profile, with a notable dramatic decline in SAM/SAH ratio predicted to impair DNA methylation. This metabolic disruption led to epigenome-wide changes in genes involved in eye development, synaptic plasticity, and retinoid metabolism, including promoter hypermethylation of Rarα, a regulator of Lrat expression. Consistently, we observed a decline in cone photoreceptor cells and reduced expression of Lrat, Rpe65, and Rdh5, three pivotal genes of eye retinoid metabolism. CONCLUSION We introduced an original in vivo model for studying cblG retinopathy, which highlighted the pivotal role of altered DNA methylation in eye development, cone differentiation, and retinoid metabolism. This model can be used for preclinical studies of novel therapeutic targets.
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Affiliation(s)
- Karim Matmat
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
| | - Jean-Baptiste Conart
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
- Department of Ophthalmology, University Regional Hospital Center of Nancy, 54000, Nancy, France
| | - Paul-Henri Graindorge
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
| | - Sandra El Kouche
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
| | - Ziad Hassan
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
| | - Youssef Siblini
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
| | - Rémy Umoret
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
| | - Ramia Safar
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
| | - Okan Baspinar
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
| | - Aurélie Robert
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
| | - Jean-Marc Alberto
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
| | - Abderrahim Oussalah
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
| | - David Coelho
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France
- National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, 54000, Nancy, France
| | - Jean-Louis Guéant
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France.
- National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, 54000, Nancy, France.
- Faculté de Médecine, Bâtiment C 2Ème Étage, 9 Avenue de La Forêt de Haye, 54505, Vandœuvre-lès-Nancy, France.
| | - Rosa-Maria Guéant-Rodriguez
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, 54500, Vandoeuvre-lès-Nancy, France.
- National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, 54000, Nancy, France.
- Faculté de Médecine, Bâtiment C 2Ème Étage, 9 Avenue de La Forêt de Haye, 54505, Vandœuvre-lès-Nancy, France.
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Tworak A, Kolesnikov AV, Hong JD, Choi EH, Luu JC, Palczewska G, Dong Z, Lewandowski D, Brooks MJ, Campello L, Swaroop A, Kiser PD, Kefalov VJ, Palczewski K. Rapid RGR-dependent visual pigment recycling is mediated by the RPE and specialized Müller glia. Cell Rep 2023; 42:112982. [PMID: 37585292 PMCID: PMC10530494 DOI: 10.1016/j.celrep.2023.112982] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/14/2023] [Accepted: 07/29/2023] [Indexed: 08/18/2023] Open
Abstract
In daylight, demand for visual chromophore (11-cis-retinal) exceeds supply by the classical visual cycle. This shortfall is compensated, in part, by the retinal G-protein-coupled receptor (RGR) photoisomerase, which is expressed in both the retinal pigment epithelium (RPE) and in Müller cells. The relative contributions of these two cellular pools of RGR to the maintenance of photoreceptor light responses are not known. Here, we use a cell-specific gene reactivation approach to elucidate the kinetics of RGR-mediated recovery of photoreceptor responses following light exposure. Electroretinographic measurements in mice with RGR expression limited to either cell type reveal that the RPE and a specialized subset of Müller glia contribute both to scotopic and photopic function. We demonstrate that 11-cis-retinal formed through photoisomerization is rapidly hydrolyzed, consistent with its role in a rapid visual pigment regeneration process. Our study shows that RGR provides a pan-retinal sink for all-trans-retinal released under sustained light conditions and supports rapid chromophore regeneration through the photic visual cycle.
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Affiliation(s)
- Aleksander Tworak
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA 92697, USA.
| | - Alexander V Kolesnikov
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA 92697, USA
| | - John D Hong
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA 92697, USA
| | - Elliot H Choi
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA 92697, USA
| | - Jennings C Luu
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA 92697, USA; Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Grazyna Palczewska
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA 92697, USA; Polgenix, Inc., Department of Medical Devices, Cleveland, OH 44106, USA
| | - Zhiqian Dong
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA 92697, USA
| | - Dominik Lewandowski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA 92697, USA
| | - Matthew J Brooks
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura Campello
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Philip D Kiser
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA 92697, USA; Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697, USA; Department of Clinical Pharmacy Practice, University of California, Irvine, Irvine, CA 92697, USA; Research Service, VA Long Beach Healthcare System, Long Beach, CA 90822, USA
| | - Vladimir J Kefalov
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA 92697, USA; Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA 92697, USA; Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA.
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7
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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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Dörschmann P, Akkurt H, Kopplin G, Mikkelsen MD, Meyer AS, Roider J, Klettner A. Establishment of specific age-related macular degeneration relevant gene expression panels using porcine retinal pigment epithelium for assessing fucoidan bioactivity. Exp Eye Res 2023; 231:109469. [PMID: 37037364 DOI: 10.1016/j.exer.2023.109469] [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: 11/11/2022] [Revised: 03/24/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023]
Abstract
PURPOSE Age-related macular degeneration (AMD) is the leading cause of severe vision loss in industrialized nations. Important factors in pathogenesis are oxidative stress, inflammation, and, in the wet form of AMD, angiogenesis. Fucoidans, sulfated polysaccharides from brown algae, may have antioxidant, anti-inflammatory, and antiangiogenic effects. In this study, we established specific gene expression panels for inflammation, oxidative stress and angiogenesis in porcine retinal pigment epithelium (RPE), and investigated the effect of fucoidans on gene expression under different noxious agents. METHODS Primary porcine RPE cells cultured for at least 14 days were used. Using viability assays with tetrazolium bromide and real-time polymerase chain reaction of marker genes, positive controls were established for appropriate concentrations and exposure times of selected noxious agents (lipopolysaccharide (LPS), H2O2, CoCl2). Three different AMD relevant gene panels specific for porcine RPE for inflammation, oxidative stress, and angiogenesis were established, and the influence of fucoidans (mainly Fucus vesiculosus; FV) on gene expression was investigated. RESULTS The following was shown by gene expression analyses: (1) Inflammation panel: Expression of 18 genes was affected under LPS (three days). Among them, LPS increased genes for interleukin 1 receptor 2, interleukin 8, cyclooxygenase-2 and vascular cell adhesion protein 1 expression which were diminished when FV was present. (2) Oxidative stress panel: Under stimulation of H2O2 (one day) and LPS (one day), expression of a total of 15 genes was affected. LPS induced increase in genes for superoxide dismutase-1, C-X-C motif chemokine 10, and CC chemokine ligand-5 expression was not detected when FV was present. (3) Angiogenesis panel: Under stimulation with CoCl2 (three days) expression of six genes was affected, with the increase of genes for angiopoietin 2, vascular endothelial growth factor receptor-1, and follistatin being diminished when FV was present. CONCLUSION Three specific gene expression panels for porcine RPE that map genes for three of the major pathological factors of AMD, inflammation, oxidative stress, and angiogenesis, were established. Further, we demonstrated that fucoidans can reduce stress related gene activation in all of these three major pathogenic pathways. This study is another indication that fucoidans can act on different pathomechanisms of AMD simultaneously, which provides further evidence for fucoidans as a possible drug for treatment and prevention of AMD.
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Affiliation(s)
- Philipp Dörschmann
- Kiel University, University Medical Center, Department of Ophthalmology, Arnold-Heller-Str. 3, Haus B2, 24105, Kiel, Germany.
| | - Hubeydullah Akkurt
- Kiel University, University Medical Center, Department of Ophthalmology, Arnold-Heller-Str. 3, Haus B2, 24105, Kiel, Germany
| | - Georg Kopplin
- Alginor ASA, Haraldsgata 162, 5525, Haugesund, Norway
| | | | - Anne S Meyer
- Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Johann Roider
- Kiel University, University Medical Center, Department of Ophthalmology, Arnold-Heller-Str. 3, Haus B2, 24105, Kiel, Germany
| | - Alexa Klettner
- Kiel University, University Medical Center, Department of Ophthalmology, Arnold-Heller-Str. 3, Haus B2, 24105, Kiel, Germany
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9
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Bian L, Nguyen VT, Tamaoki J, Endo Y, Dong G, Sato A, Kobayashi M. Genetic hyperactivation of Nrf2 causes larval lethality in Keap1a and Keap1b-double-knockout zebrafish. Redox Biol 2023; 62:102673. [PMID: 36934645 PMCID: PMC10031532 DOI: 10.1016/j.redox.2023.102673] [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: 01/19/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/15/2023] Open
Abstract
The Keap1-Nrf2 pathway is an evolutionarily conserved mechanism that protects cells from oxidative stress and electrophiles. Keap1 is a repressor of Nrf2 in normal cellular conditions but also a stress sensor for Nrf2 activation. Interestingly, fish and amphibians have two Keap1s (Keap1a and Keap1b), of which Keap1b is the ortholog of mammalian Keap1. Keap1a, on the other hand, is a gene found only in fish and amphibians, having been lost during the evolution to amniotes. We have previously shown that keap1b-knockout zebrafish have increased Nrf2 activity and reduced response to certain Nrf2-activating compounds but that they grow normally to adulthood. This may be because the remaining keap1a suppresses the hyperactivation of Nrf2, which is responsible for the post-natal lethality of Keap1-knockout mice. In this study, we analyzed keap1a;keap1b-double-knockout zebrafish to test this hypothesis. We found that keap1a;keap1b-double-knockout zebrafish, like Keap1-knockout mice, showed eating defects and were lethal within a week of hatching. Genetic introduction of the Nrf2 mutation rescued both the eating defects and the larval lethality, indicating that Nrf2 hyperactivation is the cause. However, unlike Keap1-knockout mice, keap1a;keap1b-double-knockout zebrafish showed no physical blockage of the food pathway; moreover, the cause of death was not directly related to eating defects. RNA-sequencing analysis revealed that keap1a;keap1b-double-knockout larvae showed extraordinarily high expression of known Nrf2-target genes as well as decreased expression of visual cycle genes. Finally, trigonelline or brusatol partially rescued the lethality of keap1a;keap1b-double-knockout larvae, suggesting that they can serve as an in vivo evaluation system for Nrf2-inhibiting compounds.
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Affiliation(s)
- Lixuan Bian
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Vu Thanh Nguyen
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan; Division of Aquaculture Biotechnology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Junya Tamaoki
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Yuka Endo
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Guilin Dong
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Ayaka Sato
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Makoto Kobayashi
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan.
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Emri E, Cappa O, Kelly C, Kortvely E, SanGiovanni JP, McKay BS, Bergen AA, Simpson DA, Lengyel I. Zinc Supplementation Induced Transcriptional Changes in Primary Human Retinal Pigment Epithelium: A Single-Cell RNA Sequencing Study to Understand Age-Related Macular Degeneration. Cells 2023; 12:773. [PMID: 36899910 PMCID: PMC10000409 DOI: 10.3390/cells12050773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Zinc supplementation has been shown to be beneficial to slow the progression of age-related macular degeneration (AMD). However, the molecular mechanism underpinning this benefit is not well understood. This study used single-cell RNA sequencing to identify transcriptomic changes induced by zinc supplementation. Human primary retinal pigment epithelial (RPE) cells could mature for up to 19 weeks. After 1 or 18 weeks in culture, we supplemented the culture medium with 125 µM added zinc for one week. RPE cells developed high transepithelial electrical resistance, extensive, but variable pigmentation, and deposited sub-RPE material similar to the hallmark lesions of AMD. Unsupervised cluster analysis of the combined transcriptome of the cells isolated after 2, 9, and 19 weeks in culture showed considerable heterogeneity. Clustering based on 234 pre-selected RPE-specific genes divided the cells into two distinct clusters, we defined as more and less differentiated cells. The proportion of more differentiated cells increased with time in culture, but appreciable numbers of cells remained less differentiated even at 19 weeks. Pseudotemporal ordering identified 537 genes that could be implicated in the dynamics of RPE cell differentiation (FDR < 0.05). Zinc treatment resulted in the differential expression of 281 of these genes (FDR < 0.05). These genes were associated with several biological pathways with modulation of ID1/ID3 transcriptional regulation. Overall, zinc had a multitude of effects on the RPE transcriptome, including several genes involved in pigmentation, complement regulation, mineralization, and cholesterol metabolism processes associated with AMD.
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Affiliation(s)
- Eszter Emri
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
- Section Ophthalmogenetics, Department of Human Genetics, Queen Emma Centre for Precision Medicine, Amsterdam UMC, Location AMC, 1105AZ Amsterdam, The Netherlands
| | - Oisin Cappa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
| | - Caoimhe Kelly
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
| | - Elod Kortvely
- Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - John Paul SanGiovanni
- Biosciences Research Laboratories, BIO5 Institute, University of Arizona, 1230 North Cherry Avenue, Tucson, AZ 85724, USA
| | - Brian S. McKay
- Department of Ophthalmology and Vision Science, University of Arizona, 1656 E. Mabel Street, Tucson, AZ 85724, USA
| | - Arthur A. Bergen
- Section Ophthalmogenetics, Department of Human Genetics, Queen Emma Centre for Precision Medicine, Amsterdam UMC, Location AMC, 1105AZ Amsterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN-KNAW), 1105AZ Amsterdam, The Netherlands
| | - David A. Simpson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
| | - Imre Lengyel
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
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11
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Analysis of Wild Type and Variant B Cystatin C Interactome in Retinal Pigment Epithelium Cells Reveals Variant B Interacting Mitochondrial Proteins. Cells 2023; 12:cells12050713. [PMID: 36899848 PMCID: PMC10001352 DOI: 10.3390/cells12050713] [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: 12/01/2022] [Revised: 02/09/2023] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
Cystatin C, a secreted cysteine protease inhibitor, is abundantly expressed in retinal pigment epithelium (RPE) cells. A mutation in the protein's leader sequence, corresponding to formation of an alternate variant B protein, has been linked with an increased risk for both age-related macular degeneration (AMD) and Alzheimer's disease (AD). Variant B cystatin C displays intracellular mistrafficking with partial mitochondrial association. We hypothesized that variant B cystatin C interacts with mitochondrial proteins and impacts mitochondrial function. We sought to determine how the interactome of the disease-related variant B cystatin C differs from that of the wild-type (WT) form. For this purpose, we expressed cystatin C Halo-tag fusion constructs in RPE cells to pull down proteins interacting with either the WT or variant B form, followed by identification and quantification by mass spectrometry. We identified a total of 28 interacting proteins, of which 8 were exclusively pulled down by variant B cystatin C. These included 18 kDa translocator protein (TSPO) and cytochrome B5 type B, both of which are localized to the mitochondrial outer membrane. Variant B cystatin C expression also affected RPE mitochondrial function with increased membrane potential and susceptibility to damage-induced ROS production. The findings help us to understand how variant B cystatin C differs functionally from the WT form and provide leads to RPE processes adversely affected by the variant B genotype.
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12
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Dhirachaikulpanich D, Lagger C, Chatsirisupachai K, de Magalhães JP, Paraoan L. Intercellular communication analysis of the human retinal pigment epithelial and choroidal cells predicts pathways associated with aging, cellular senescence and age-related macular degeneration. Front Aging Neurosci 2022; 14:1016293. [PMID: 36408112 PMCID: PMC9669800 DOI: 10.3389/fnagi.2022.1016293] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
The retinal pigment epithelium (RPE) and the choroid are ocular tissues with fundamental roles in supporting neuroretinal function. The pathogenesis of age-related macular degeneration (AMD), a leading cause of irreversible blindness for which aging is the highest risk factor is closely linked with progressive impairment of various functions of these tissues. Cellular senescence, marked by cell cycle arrest and secretion of proinflammatory factors, is known to be associated with aging and has been proposed as a potential driver of AMD. Here, we investigated the role played by intercellular communication in the RPE/choroid within the context of aging, senescence and AMD. We inferred cell–cell interactions in the RPE/choroid by applying CellChat and scDiffCom on a publicly available scRNA-seq dataset from three human donors with and without AMD. We identified age-regulated ligand and receptor genes by using limma on a separate publicly available bulk microarray dataset providing RPE/choroid samples at multiple time points. Cellular senescence was investigated by assigning a score to each cell and each sample of these scRNA-seq and microarray datasets, respectively, based on the expression of key signature genes determined by a previous senescence meta-analysis. We identified VEGF-, BMP-and tenascin-mediated pathways supporting some of the strongest cell–cell interactions between RPE cells, fibroblasts and choroidal endothelial cells and as strong intercellular communication pathways related to both aging and senescence. Their signaling strength was enhanced between subpopulations of cells having high senescence scores. Predominant ligands of these pathways were upregulated with age whereas predominant receptors were downregulated. Globally, we also observed that cells from AMD samples presented slightly bigger senescence scores than normal cells and that the senescence score positively correlated with age in bulk samples (R = 0.26, value of p < 0.01). Hence, our analysis provides novel information on RPE/choroid intercellular communication that gives insights into the connection between aging, senescence and AMD.
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Affiliation(s)
- Dhanach Dhirachaikulpanich
- Ocular Molecular Biology and Mechanisms of Disease Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
- Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Cyril Lagger
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
- *Correspondence: João Pedro de Magalhães,
| | - Luminita Paraoan
- Ocular Molecular Biology and Mechanisms of Disease Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
- Luminita Paraoan,
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13
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Subramanian R, Sahoo D. Boolean implication analysis of single-cell data predicts retinal cell type markers. BMC Bioinformatics 2022; 23:378. [PMID: 36114457 PMCID: PMC9482279 DOI: 10.1186/s12859-022-04915-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/25/2022] [Indexed: 11/15/2022] Open
Abstract
Background The retina is a complex tissue containing multiple cell types that are essential for vision. Understanding the gene expression patterns of various retinal cell types has potential applications in regenerative medicine. Retinal organoids (optic vesicles) derived from pluripotent stem cells have begun to yield insights into the transcriptomics of developing retinal cell types in humans through single cell RNA-sequencing studies. Previous methods of gene reporting have relied upon techniques in vivo using microarray data, or correlational and dimension reduction methods for analyzing single cell RNA-sequencing data computationally. We aimed to develop a state-of-the-art Boolean method that filtered out noise, could be applied to a wide variety of datasets and lent insight into gene expression over differentiation. Results Here, we present a bioinformatic approach using Boolean implication to discover genes which are retinal cell type-specific or involved in retinal cell fate. We apply this approach to previously published retina and retinal organoid datasets and improve upon previously published correlational methods. Our method improves the prediction accuracy of marker genes of retinal cell types and discovers several new high confidence cone and rod-specific genes. Conclusions The results of this study demonstrate the benefits of a Boolean approach that considers asymmetric relationships. We have shown a statistically significant improvement from correlational, symmetric methods in the prediction accuracy of retinal cell-type specific genes. Furthermore, our method contains no cell or tissue-specific tuning and hence could impact other areas of gene expression analyses in cancer and other human diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04915-4.
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14
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Hsu CC, Chuang HK, Hsiao YJ, Teng YC, Chiang PH, Wang YJ, Lin TY, Tsai PH, Weng CC, Lin TC, Hwang DK, Hsieh AR. Polygenic Risk Score Improves Cataract Prediction in East Asian Population. Biomedicines 2022; 10:biomedicines10081920. [PMID: 36009466 PMCID: PMC9406175 DOI: 10.3390/biomedicines10081920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 06/30/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Cataracts, characterized by crystalline lens opacities in human eyes, is the leading cause of blindness globally. Due to its multifactorial complexity, the molecular mechanisms remain poorly understood. Larger cohorts of genome-wide association studies (GWAS) are needed to investigate cataracts’ genetic basis. In this study, a GWAS was performed on the largest Han population to date, analyzing a total of 7079 patients and 13,256 controls from the Taiwan Biobank (TWB) 2.0 cohort. Two cataract-associated SNPs with an adjustment of p < 1 × 10−7 in the older groups and nine SNPs with an adjustment of p < 1 × 10−6 in the younger group were identified. Except for the reported AGMO in animal models, most variations, including rs74774546 in GJA1 and rs237885 in OXTR, were not identified before this study. Furthermore, a polygenic risk score (PRS) was created for the young and old populations to identify high-risk cataract individuals, with areas under the receiver operating curve (AUROCs) of 0.829 and 0.785, respectively, after covariate adjustments. Younger individuals had 17.45 times the risk while older people had 10.97 times the risk when comparing individuals in the highest and lowest PRS quantiles. Validation analysis on an independent TWB1.0 cohort revealed AUROCs of 0.744 and 0.659.
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Affiliation(s)
- Chih-Chien Hsu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112027, Taiwan
| | - Hao-Kai Chuang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112027, Taiwan
- Correspondence: (H.-K.C.); (D.-K.H.); (A.-R.H.); Tel.: +886-02-28757325 (D.-K.H.)
| | - Yu-Jer Hsiao
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112027, Taiwan
| | - Yuan-Chi Teng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112027, Taiwan
| | - Pin-Hsuan Chiang
- Department of Statistics, Tamkang University, New Taipei 251301, Taiwan
| | - Yu-Jun Wang
- Department of Statistics, Tamkang University, New Taipei 251301, Taiwan
| | - Ting-Yi Lin
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112027, Taiwan
| | - Ping-Hsing Tsai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112027, Taiwan
| | - Chang-Chi Weng
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112027, Taiwan
| | - Tai-Chi Lin
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112027, Taiwan
| | - De-Kuang Hwang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112027, Taiwan
- Correspondence: (H.-K.C.); (D.-K.H.); (A.-R.H.); Tel.: +886-02-28757325 (D.-K.H.)
| | - Ai-Ru Hsieh
- Department of Statistics, Tamkang University, New Taipei 251301, Taiwan
- Correspondence: (H.-K.C.); (D.-K.H.); (A.-R.H.); Tel.: +886-02-28757325 (D.-K.H.)
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15
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High-Fat Diet Alters the Retinal Pigment Epithelium and Choroidal Transcriptome in the Absence of Gut Microbiota. Cells 2022; 11:cells11132076. [PMID: 35805160 PMCID: PMC9266037 DOI: 10.3390/cells11132076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Relationships between retinal disease, diet, and the gut microbiome have started to emerge. In particular, high-fat diets (HFDs) are associated with the prevalence and progression of several retinal diseases, including age-related macular degeneration (AMD) and diabetic retinopathy (DR). These effects are thought to be partly mediated by the gut microbiome, which modulates interactions between diet and host homeostasis. Nevertheless, the effects of HFDs on the retina and adjacent retinal pigment epithelium (RPE) and choroid at the transcriptional level, independent of gut microbiota, are not well-understood. In this study, we performed the high-throughput RNA-sequencing of germ-free (GF) mice to explore the transcriptional changes induced by HFD in the RPE/choroid. After filtering and cleaning the data, 649 differentially expressed genes (DEGs) were identified, with 616 genes transcriptionally upregulated and 33 genes downregulated by HFD compared to a normal diet (ND). Enrichment analysis for gene ontology (GO) using the DEGs was performed to analyze over-represented biological processes in the RPE/choroid of GF-HFD mice relative to GF-ND mice. GO analysis revealed the upregulation of processes related to angiogenesis, immune response, and the inflammatory response. Additionally, molecular functions that were altered involved extracellular matrix (ECM) binding, ECM structural constituents, and heparin binding. This study demonstrates novel data showing that HFDs can alter RPE/choroid tissue transcription in the absence of the gut microbiome.
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16
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Tate PS, Marquioni-Ramella MD, Cerchiaro C, Suburo AM. Ilex paraguariensis Extracts Prevent Oxidative Damage in a Mouse Model of Age-Related Macular Degeneration. Mol Nutr Food Res 2022; 66:e2100807. [PMID: 35279946 DOI: 10.1002/mnfr.202100807] [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: 08/28/2021] [Revised: 02/23/2022] [Indexed: 11/11/2022]
Abstract
Age-related macular degeneration (AMD), a chronic disease of the retina, leads to severe visual loss. AMD affects the retinal pigment epithelium (RPE) and the visual cells (photoreceptors). RPE failure, the first step of this disease, is associated with oxidative stress. Since antioxidants can slow down AMD progression, the intake of foods and drinks rich in antioxidant compounds may reduce retinal damage. Ilex paraguariensis (yerba mate, YM) extracts reduce oxidative damage of RPE cells in vitro as shown in previous study. Here, the effects of YM drinking on RPE and photoreceptor survival after oxidative damage with sodium iodate (NaIO3; SI) in a murine AMD model are described. Funduscopy and histology show that YM treatment prevents RPE and photoreceptor damage. YM also increases the expression of NRF2, the master antioxidant gene, and its effectors HO-1 and SOD2. In mice receiving YM and SI, the antioxidant response is larger than in mice receiving YM or SI alone. The YM drink also increases expression of RPE65, a gene that is involved in the functionality and survival of photoreceptors and RPE cells. The results suggest YM can play an important role in the prevention of retinal damage associated with oxidative stress, such as AMD.
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Affiliation(s)
- Pablo S Tate
- Instituto de Investigaciones en Medicina Traslacional (IIMT, Universidad Austral-CONICET), Facultad de Ciencias Biomédicas, Universidad Austral, Pilar, Buenos Aires, B1629AHJ, Argentina
| | - Melisa D Marquioni-Ramella
- Instituto de Investigaciones en Medicina Traslacional (IIMT, Universidad Austral-CONICET), Facultad de Ciencias Biomédicas, Universidad Austral, Pilar, Buenos Aires, B1629AHJ, Argentina
| | - Constanza Cerchiaro
- Instituto de Investigaciones en Medicina Traslacional (IIMT, Universidad Austral-CONICET), Facultad de Ciencias Biomédicas, Universidad Austral, Pilar, Buenos Aires, B1629AHJ, Argentina
| | - Angela M Suburo
- Instituto de Investigaciones en Medicina Traslacional (IIMT, Universidad Austral-CONICET), Facultad de Ciencias Biomédicas, Universidad Austral, Pilar, Buenos Aires, B1629AHJ, Argentina
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17
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O’Connor C, Varshosaz P, Moise AR. Mechanisms of Feedback Regulation of Vitamin A Metabolism. Nutrients 2022; 14:nu14061312. [PMID: 35334970 PMCID: PMC8950952 DOI: 10.3390/nu14061312] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 02/06/2023] Open
Abstract
Vitamin A is an essential nutrient required throughout life. Through its various metabolites, vitamin A sustains fetal development, immunity, vision, and the maintenance, regulation, and repair of adult tissues. Abnormal tissue levels of the vitamin A metabolite, retinoic acid, can result in detrimental effects which can include congenital defects, immune deficiencies, proliferative defects, and toxicity. For this reason, intricate feedback mechanisms have evolved to allow tissues to generate appropriate levels of active retinoid metabolites despite variations in the level and format, or in the absorption and conversion efficiency of dietary vitamin A precursors. Here, we review basic mechanisms that govern vitamin A signaling and metabolism, and we focus on retinoic acid-controlled feedback mechanisms that contribute to vitamin A homeostasis. Several approaches to investigate mechanistic details of the vitamin A homeostatic regulation using genomic, gene editing, and chromatin capture technologies are also discussed.
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Affiliation(s)
- Catherine O’Connor
- MD Program, Northern Ontario School of Medicine, 317-MSE Bldg., 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada;
| | - Parisa Varshosaz
- Biology and Biomolecular Sciences Ph.D. Program, Northern Ontario School of Medicine, Laurentian University, Sudbury, ON P3E 2C6, Canada;
| | - Alexander R. Moise
- Medical Sciences Division, Northern Ontario School of Medicine, 317-MSE Bldg., 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada
- Department of Chemistry and Biochemistry, Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON P3E 2C6, Canada
- Correspondence: ; Tel.: +1-705-662-7253
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18
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Georgiou M, Yang C, Atkinson R, Pan K, Buskin A, Molina MM, Collin J, Al‐Aama J, Goertler F, Ludwig SEJ, Davey T, Lührmann R, Nagaraja‐Grellscheid S, Johnson CA, Ali R, Armstrong L, Korolchuk V, Urlaub H, Mozaffari‐Jovin S, Lako M. Activation of autophagy reverses progressive and deleterious protein aggregation in PRPF31 patient-induced pluripotent stem cell-derived retinal pigment epithelium cells. Clin Transl Med 2022; 12:e759. [PMID: 35297555 PMCID: PMC8926896 DOI: 10.1002/ctm2.759] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 01/18/2023] Open
Abstract
INTRODUCTION Mutations in pre-mRNA processing factor 31 (PRPF31), a core protein of the spliceosomal tri-snRNP complex, cause autosomal-dominant retinitis pigmentosa (adRP). It has remained an enigma why mutations in ubiquitously expressed tri-snRNP proteins result in retina-specific disorders, and so far, the underlying mechanism of splicing factors-related RP is poorly understood. METHODS We used the induced pluripotent stem cell (iPSC) technology to generate retinal organoids and RPE models from four patients with severe and very severe PRPF31-adRP, unaffected individuals and a CRISPR/Cas9 isogenic control. RESULTS To fully assess the impacts of PRPF31 mutations, quantitative proteomics analyses of retinal organoids and RPE cells were carried out showing RNA splicing, autophagy and lysosome, unfolded protein response (UPR) and visual cycle-related pathways to be significantly affected. Strikingly, the patient-derived RPE and retinal cells were characterised by the presence of large amounts of cytoplasmic aggregates containing the mutant PRPF31 and misfolded, ubiquitin-conjugated proteins including key visual cycle and other RP-linked tri-snRNP proteins, which accumulated progressively with time. The mutant PRPF31 variant was not incorporated into splicing complexes, but reduction of PRPF31 wild-type levels led to tri-snRNP assembly defects in Cajal bodies of PRPF31 patient retinal cells, altered morphology of nuclear speckles and reduced formation of active spliceosomes giving rise to global splicing dysregulation. Moreover, the impaired waste disposal mechanisms further exacerbated aggregate formation, and targeting these by activating the autophagy pathway using Rapamycin reduced cytoplasmic aggregates, leading to improved cell survival. CONCLUSIONS Our data demonstrate that it is the progressive aggregate accumulation that overburdens the waste disposal machinery rather than direct PRPF31-initiated mis-splicing, and thus relieving the RPE cells from insoluble cytoplasmic aggregates presents a novel therapeutic strategy that can be combined with gene therapy studies to fully restore RPE and retinal cell function in PRPF31-adRP patients.
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Affiliation(s)
- Maria Georgiou
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | - Chunbo Yang
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | - Robert Atkinson
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | - Kuan‐Ting Pan
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Adriana Buskin
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | | | - Joseph Collin
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | - Jumana Al‐Aama
- Faculty of MedicineKing Abdulaziz UniversitySaudi Arabia
| | | | | | - Tracey Davey
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | | | | | | | | | - Lyle Armstrong
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | | | - Henning Urlaub
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
- Bioanalytics, Department of Clinical ChemistryUniversity Medical CenterGoettingenGermany
| | - Sina Mozaffari‐Jovin
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
- Medical Genetics Research CenterMashhad University of Medical SciencesMashhadIran
- Department of Medical Genetics, Faculty of MedicineMashhad University of Medical SciencesMashhadIran
| | - Majlinda Lako
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
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19
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Butler JM, Supharattanasitthi W, Yang YC, Paraoan L. RNA-seq analysis of ageing human retinal pigment epithelium: Unexpected up-regulation of visual cycle gene transcription. J Cell Mol Med 2021; 25:5572-5585. [PMID: 33934486 PMCID: PMC8184696 DOI: 10.1111/jcmm.16569] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
Ageing presents adverse effects on the retina and is the primary risk factor for age‐related macular degeneration (AMD). We report the first RNA‐seq analysis of age‐related transcriptional changes in the human retinal pigment epithelium (RPE), the primary site of AMD pathogenesis. Whole transcriptome sequencing of RPE from human donors ranging in age from 31 to 93 reveals that ageing is associated with increasing transcription of main RPE‐associated visual cycle genes (including LRAT, RPE65, RDH5, RDH10, RDH11; pathway enrichment BH‐adjusted P = 4.6 × 10−6). This positive correlation is replicated in an independent set of 28 donors and a microarray dataset of 50 donors previously published. LRAT expression is positively regulated by retinoid by‐products of the visual cycle (A2E and all‐trans‐retinal) involving modulation by retinoic acid receptor alpha transcription factor. The results substantiate a novel age‐related positive feedback mechanism between accumulation of retinoid by‐products in the RPE and the up‐regulation of visual cycle genes.
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Affiliation(s)
- Joe M Butler
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Wasu Supharattanasitthi
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Yit C Yang
- Department of Ophthalmology, Wolverhampton Eye Infirmary, New Cross Hospital, Wolverhampton, UK
| | - Luminita Paraoan
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
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