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Ophthalmic Genetics, Epigenetics, and Disease
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Ophthalmic Genetics, Epigenetics, and Disease

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Epigenomics".

Deadline for manuscript submissions: closed (20 March 2024) | Viewed by 17892

Special Issue Editors

Prof. Dr. Lian-Wang Guo

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Guest Editor
Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
Interests: retinal degeneration; vascular biology; epigenetics; nanomedicine
Dr. Wenbo Zhang

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Guest Editor
Department of Ophthalmology, University of Texas Medical Branch, Galveston, TX 77555, USA
Interests: retinal neuronal injury; vascular injury; pathological angiogenesis; mechanisms; animal models
Dr. Bikash Pattnaik

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Guest Editor
Department of Pediatrics, Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
Interests: vision physiology; electrophysiology; cellular signaling; channelopathy; stem cells
Prof. Dr. Akihiro Ikeda

E-Mail Website
Guest Editor
Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
Interests: aging; age-related disease; retina; mouse genetics

Special Issue Information

Dear Colleagues,

This Special Issue presents the exciting advances in basic and translational sciences and potential new clinical options pertaining to ophthalmic genetics, epigenetics, and diseases. Potential topics include, but are not limited to: human genetics, animal models, DNA and histone modifications, miRNAs and other non-coding RNAs, metabolic regulations, signaling, human pathology and biomarkers, gene therapy and cell therapy, pharmacological interventions, and bioengineered therapeutic approaches.

Prof. Dr. Lian-Wang Guo
Dr. Wenbo Zhang
Dr. Bikash Pattnaik
Prof. Dr. Akihiro Ikeda
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genetics and epigenetics
  • disease mechanisms
  • signaling
  • histone and dna modifiers
  • non-coding rnas
  • metabolism
  • cell death
  • regeneration
  • diagnostic biomarkers
  • translational research
  • pharmacology

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Published Papers (7 papers)

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Research

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12 pages, 284 KiB  
Article
Inflammation and Oxidative Stress Gene Variability in Retinal Detachment Patients with and without Proliferative Vitreoretinopathy
by Xhevat Lumi, Filippo Confalonieri, Metka Ravnik-Glavač, Katja Goričar, Tanja Blagus, Vita Dolžan, Goran Petrovski, Marko Hawlina and Damjan Glavač
Genes 2023, 14(4), 804; https://doi.org/10.3390/genes14040804 - 27 Mar 2023
Cited by 2 | Viewed by 1712
Abstract
This study investigated the association between certain genetic variations and the risk of developing proliferative vitreoretinopathy (PVR) after surgery. The study was conducted on 192 patients with primary rhegmatogenous retinal detachment (RRD) who underwent 3-port pars plana vitrectomy (PPV). The distribution of single [...] Read more.
This study investigated the association between certain genetic variations and the risk of developing proliferative vitreoretinopathy (PVR) after surgery. The study was conducted on 192 patients with primary rhegmatogenous retinal detachment (RRD) who underwent 3-port pars plana vitrectomy (PPV). The distribution of single nucleotide polymorphisms (SNPs) located in genes involved in inflammation and oxidative stress associated with PVR pathways were analyzed among patients with and without postoperative PVR grade C1 or higher. A total of 7 defined SNPs of 5 genes were selected for genotyping: rs4880 (SOD2); rs1001179 (CAT); rs1050450 (GPX1); rs1143623, rs16944, rs1071676 (IL1B); rs2910164 (MIR146A) using competitive allele-specific polymerase chain reaction. The association of SNPs with PVR risk was evaluated using logistic regression. Furthermore, the possible association of SNPs with postoperative clinical parameters was evaluated using non-parametric tests. The difference between two genotype frequencies between patients with or without PVR grade C1 or higher was found to be statistically significant: SOD2 rs4880 and IL1B rs1071676. Carriers of at least one polymorphic IL1B rs1071676 GG allele appeared to have better postoperative best-corrected visual acuity only in patients without PVR (p = 0.070). Our study suggests that certain genetic variations may play a role in the development of PVR after surgery. These findings may have important implications for identifying patients at higher risk for PVR and developing new treatments. Full article
(This article belongs to the Special Issue Ophthalmic Genetics, Epigenetics, and Disease)
15 pages, 4942 KiB  
Article
Reduced OPA1, Mitochondrial Fragmentation and Increased Susceptibility to Apoptosis in Granular Corneal Dystrophy Type 2 Corneal Fibroblasts
by Seung-Il Choi, Ga-Hyun Lee, Jong-Hwan Woo, Ikhyun Jun and Eung Kweon Kim
Genes 2023, 14(3), 566; https://doi.org/10.3390/genes14030566 - 24 Feb 2023
Cited by 1 | Viewed by 2300
Abstract
The progressive degeneration of granular corneal dystrophy type 2 (GCD2) corneal fibroblasts is associated with altered mitochondrial function, but the underlying mechanisms are incompletely understood. We investigated whether an imbalance of mitochondrial dynamics contributes to mitochondrial dysfunction of GCD2 corneal fibroblasts. Transmission electron [...] Read more.
The progressive degeneration of granular corneal dystrophy type 2 (GCD2) corneal fibroblasts is associated with altered mitochondrial function, but the underlying mechanisms are incompletely understood. We investigated whether an imbalance of mitochondrial dynamics contributes to mitochondrial dysfunction of GCD2 corneal fibroblasts. Transmission electron microscopy revealed several small, structurally abnormal mitochondria with altered cristae morphology in GCD2 corneal fibroblasts. Confocal microscopy showed enhanced mitochondrial fission and fragmented mitochondrial tubular networks. Western blotting revealed higher levels of MFN1, MFN2, and pDRP1 and decreased levels of OPA1 and FIS1 in GCD2. OPA1 reduction by short hairpin RNA (shRNA) resulted in fragmented mitochondrial tubular networks and increased susceptibility to mitochondrial stress-induced apoptosis. A decrease in the mitochondrial biogenesis-related transcription factors NRF1 and PGC1α was observed, while there was an increase in the mitochondrial membrane proteins TOM20 and TIM23. Additionally, reduced levels of mitochondrial DNA (mtDNA) were exhibited in GCD2 corneal fibroblasts. These observations suggest that altered mitochondrial fission/fusion and biogenesis are the critical molecular mechanisms that cause mitochondrial dysfunction contributing to the degeneration of GCD2 corneal fibroblasts. Full article
(This article belongs to the Special Issue Ophthalmic Genetics, Epigenetics, and Disease)
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11 pages, 1283 KiB  
Article
Genetic Modifiers of Non-Penetrance and RNA Expression Levels in PRPF31-Associated Retinitis Pigmentosa in a Danish Cohort
by Kristian Lisbjerg, Karen Grønskov, Mette Bertelsen, Lisbeth Birk Møller and Line Kessel
Genes 2023, 14(2), 435; https://doi.org/10.3390/genes14020435 - 8 Feb 2023
Cited by 4 | Viewed by 1925
Abstract
(1) Background/aims: To examine potential genetic modifiers of disease penetrance in PRPF31-associated retinitis pigmentosa 11 (RP11). (2) Methods: Blood samples from individuals (n = 37) with PRPF31 variants believed to be disease-causing were used for molecular genetic testing and, in some cases [...] Read more.
(1) Background/aims: To examine potential genetic modifiers of disease penetrance in PRPF31-associated retinitis pigmentosa 11 (RP11). (2) Methods: Blood samples from individuals (n = 37) with PRPF31 variants believed to be disease-causing were used for molecular genetic testing and, in some cases (n = 23), also for mRNA expression analyses. Medical charts were used to establish if individuals were symptomatic (RP) or asymptomatic non-penetrant carriers (NPC). RNA expression levels of PRPF31 and CNOT3 were measured on peripheral whole blood using quantitative real-time PCR normalized to GAPDH. Copy number variation of minisatellite repeat element 1 (MSR1) was performed with DNA fragment analysis. (3) Results: mRNA expression analyses on 22 individuals (17 with RP and 5 non-penetrant carriers) revealed no statistically significant differences in PRPF31 or CNOT3 mRNA expression levels between individuals with RP and non-penetrant carriers. Among 37 individuals, we found that all three carriers of a 4-copy MSR1 sequence on their wild-type (WT) allele were non-penetrant carriers. However, copy number variation of MSR1 is not the sole determinant factor of non-penetrance, as not all non-penetrant carriers carried a 4-copy WT allele. A 4-copy MSR1 mutant allele was not associated with non-penetrance. (4) Conclusions: In this Danish cohort, a 4-copy MSR1 WT allele was associated with non-penetrance of retinitis pigmentosa caused by PRPF31 variants. The level of PRPF31 mRNA expression in peripheral whole blood was not a useful indicator of disease status. Full article
(This article belongs to the Special Issue Ophthalmic Genetics, Epigenetics, and Disease)
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Review

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14 pages, 316 KiB  
Review
Uncovering the Genetics and Physiology behind Optic Neuritis
by Ilaria Del Negro, Giada Pauletto, Lorenzo Verriello, Leopoldo Spadea, Carlo Salati, Tamara Ius and Marco Zeppieri
Genes 2023, 14(12), 2192; https://doi.org/10.3390/genes14122192 - 9 Dec 2023
Cited by 2 | Viewed by 2732
Abstract
Optic neuritis (ON) is an inflammatory condition affecting the optic nerve, leading to vision impairment and potential vision loss. This manuscript aims to provide a comprehensive review of the current understanding of ON, including its definition, epidemiology, physiology, genetics, molecular pathways, therapy, ongoing [...] Read more.
Optic neuritis (ON) is an inflammatory condition affecting the optic nerve, leading to vision impairment and potential vision loss. This manuscript aims to provide a comprehensive review of the current understanding of ON, including its definition, epidemiology, physiology, genetics, molecular pathways, therapy, ongoing clinical studies, and future perspectives. ON is characterized by inflammation of the optic nerve, often resulting from an autoimmune response. Epidemiological studies have shown a higher incidence in females and an association with certain genetic factors. The physiology of ON involves an immune-mediated attack on the myelin sheath surrounding the optic nerve, leading to demyelination and subsequent impairment of nerve signal transmission. This inflammatory process involves various molecular pathways, including the activation of immune cells and the release of pro-inflammatory cytokines. Genetic factors play a significant role in the susceptibility to ON. Several genes involved in immune regulation and myelin maintenance have been implicated in the disease pathogenesis. Understanding the genetic basis can provide insights into disease mechanisms and potential therapeutic targets. Therapy for ON focuses on reducing inflammation and promoting nerve regeneration. Future perspectives involve personalized medicine approaches based on genetic profiling, regenerative therapies to repair damaged myelin, and the development of neuroprotective strategies. Advancements in understanding molecular pathways, genetics, and diagnostic tools offer new opportunities for targeted therapies and improved patient outcomes in the future. Full article
(This article belongs to the Special Issue Ophthalmic Genetics, Epigenetics, and Disease)
12 pages, 256 KiB  
Review
Advances in Ophthalmic Epigenetics and Implications for Epigenetic Therapies: A Review
by Spencer M. Moore and John B. Christoforidis
Genes 2023, 14(2), 417; https://doi.org/10.3390/genes14020417 - 5 Feb 2023
Cited by 2 | Viewed by 3265
Abstract
The epigenome represents a vast molecular apparatus that writes, reads, and erases chemical modifications to the DNA and histone code without changing the DNA base-pair sequence itself. Recent advances in molecular sequencing technology have revealed that epigenetic chromatin marks directly mediate critical events [...] Read more.
The epigenome represents a vast molecular apparatus that writes, reads, and erases chemical modifications to the DNA and histone code without changing the DNA base-pair sequence itself. Recent advances in molecular sequencing technology have revealed that epigenetic chromatin marks directly mediate critical events in retinal development, aging, and degeneration. Epigenetic signaling regulates retinal progenitor (RPC) cell cycle exit during retinal laminar development, giving rise to retinal ganglion cells (RGCs), amacrine cells, horizontal cells, bipolar cells, photoreceptors, and Müller glia. Age-related epigenetic changes such as DNA methylation in the retina and optic nerve are accelerated in pathogenic conditions such as glaucoma and macular degeneration, but reversing these epigenetic marks may represent a novel therapeutic target. Epigenetic writers also integrate environmental signals such as hypoxia, inflammation, and hyperglycemia in complex retinal conditions such as diabetic retinopathy (DR) and choroidal neovascularization (CNV). Histone deacetylase (HDAC) inhibitors protect against apoptosis and photoreceptor degeneration in animal models of retinitis pigmentosa (RP). The epigenome represents an intriguing therapeutic target for age-, genetic-, and neovascular-related retinal diseases, though more work is needed before advancement to clinical trials. Full article
(This article belongs to the Special Issue Ophthalmic Genetics, Epigenetics, and Disease)
14 pages, 1099 KiB  
Review
MicroRNA of Epithelial to Mesenchymal Transition in Fuchs’ Endothelial Corneal Dystrophy
by Spela Stunf Pukl
Genes 2022, 13(10), 1711; https://doi.org/10.3390/genes13101711 - 23 Sep 2022
Cited by 2 | Viewed by 2504
Abstract
Aim: a review of miRNA expression connected to epithelial mesenchymal transition studies in Fuchs’ endothelial corneal dystrophy (FECD). Methods: literature search strategy—PubMed central database, using “miRNA” or “microRNA” and “epithelial mesenchymal transition” or “EMT” and “Fuchs’ endothelial corneal dystrophy” or “FECD” as keywords. [...] Read more.
Aim: a review of miRNA expression connected to epithelial mesenchymal transition studies in Fuchs’ endothelial corneal dystrophy (FECD). Methods: literature search strategy—PubMed central database, using “miRNA” or “microRNA” and “epithelial mesenchymal transition” or “EMT” and “Fuchs’ endothelial corneal dystrophy” or “FECD” as keywords. Experimental or clinical studies on humans published in English regarding miRNA profiles of epithelial mesenchymal transition in Fuchs’ endothelial corneal dystrophy published between 2009 and 2022 were included. Conclusion: The publications regarding the miRNA profiles of epithelial mesenchymal transition in Fuchs’ endothelial corneal dystrophy are scarce but provide some valuable information about the potential biomarkers differentiating aging changes from early disease stages characterized by epithelial mesenchymal transition. In the corneal tissue of FECD patients, miRNA-184 seed-region mutation as well as unidirectional downregulation of total miRNA expression led by the miRNA-29 were demonstrated. For early diagnostics the miRNA of epithelial mesenchymal transition in aqueous humor should be analyzed and used as biomarkers. Full article
(This article belongs to the Special Issue Ophthalmic Genetics, Epigenetics, and Disease)
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Other

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11 pages, 1717 KiB  
Brief Report
Retinal Photoreceptor Protection in an AMD-Related Mouse Model by Selective Sigma-1 or Sigma-2 Receptor Modulation
by Timur A. Mavlyutov, Jing Li, Xinying Liu, Hongtao Shen, Huan Yang, Christopher R. McCurdy, Bikash Pattnaik and Lian-Wang Guo
Genes 2022, 13(12), 2386; https://doi.org/10.3390/genes13122386 - 16 Dec 2022
Cited by 5 | Viewed by 2453
Abstract
The structurally and genetically distinct sigma-1 receptor (S1R) and sigma-2 receptor (S2R) comprise a unique class of drug binding sites. Their alleles are associated with human diseases involving neuronal systems, such as age-related macular degeneration (AMD) characterized by photoreceptor and retinal pigment epithelium [...] Read more.
The structurally and genetically distinct sigma-1 receptor (S1R) and sigma-2 receptor (S2R) comprise a unique class of drug binding sites. Their alleles are associated with human diseases involving neuronal systems, such as age-related macular degeneration (AMD) characterized by photoreceptor and retinal pigment epithelium (RPE) atrophy. Previous studies have suggested neuroprotective benefits for the brain and retina from pharmacological modulation of S1R and/or S2R. However, the effect of such modulation on AMD pathology remains underexplored. Here, we evaluated S1R- or S2R-selective modulation in an AMD-related model of Abca4−/−Rdh8−/− mice with a disrupted visual cycle that predisposes RPE and photoreceptors to illumination-induced damage. For S1R modulation, we used (+)-pentazocine, which is a high-affinity S1R-selective drug. For S2R modulation, we chose CM398, a high-affinity and highly S2R-selective ligand with drug-like properties. Abca4−/−Rdh8−/− mice received a single i.p. injection of (+)-pentazocine or CM398 or vehicle 30 min before illumination. Pretreatment with (+)-pentazocine improved electroretinogram a- and b-waves compared to that with vehicle. Consistently, in another AMD-related mouse model induced by tail-vein injected NaIO3, S1R genetic ablation aggravated photoreceptor loss. In Abca4−/−Rdh8−/− mice, pretreatment with CM398 appeared to partially avert illumination-induced photoreceptor loss and autofluorescent granule formation that signals RPE damage, as revealed by optical coherence tomography. Thus, this study using AMD-related models provides evidence of photoreceptor protection afforded by selective modulation of S1R or S2R. Full article
(This article belongs to the Special Issue Ophthalmic Genetics, Epigenetics, and Disease)
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