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What We Know about the Updated Information from Genes to...
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What We Know about the Updated Information from Genes to Eye Disease

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cellular Pathology".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 15263

Special Issue Editor

Dr. Shikun He

E-Mail Website
Guest Editor
Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
Interests: epigenetics; RNA methylation; fibrosis; angiogenesis; aging; retinal pigmental epithelium; age-related macular degeneration (AMD); proliferative vitreoretinopathy (PVR)

Special Issue Information

Dear Colleagues,

Genes control the basic functional processes of cells from DNA to proteins, while aberrant gene expression may contribute to the formation of pathologic conditions, including inflammatory, fibrotic, degenerative, angiogenic, senescent and traumatic eye disease. Genes related to the maintenance of normal vision functions and their roles in the pathogenesis of eye diseases are regulated by multilayers such epigenetic factors (DNA methylation, histone acetylation, non-coding RNA); RNA modification, more specifically N6-methyladenosine (m6A) modification; and numerous transcription and translation factors. This is especially true for complex eye diseases such as corneal degeneration, glaucoma, uveitis, diabetic retinopathy, age-related macular degeneration, proliferative vitreoretinopathy, ocular trauma and tumors. Thus, from aberrant gene expression to ocular diseases, pathological processes are regulated by networks involving genomics, epigenomics, transcriptomics, proteomics and metabolomics.

The pathogenesis of these complex eye diseases is still under investigation, and many questions remain to be answered; in particular, how do abnormal genes cause eye diseases? What is the link and pathways between genes and eye diseases? What roles do epigenomics, transcriptomics, proteomics, metabolomics play in complex eye diseases, and could the parameters of these omics be potential biomarkers and therapeutic approaches for the treatment of the eye diseases? Therefore, in this Special Issue, updated studies referring to ocular cell structures, cell function (proliferation, migration and differentiation), cell signaling, cell death, inflammation, fibrosis, angiogenesis, degeneration and regeneration based on aberrant gene expression or its relevance to the omics will be included. Studies including data from genomics, epigenomics, transcriptomics, proteomics and metabolomics are preferable. Original articles and review papers are welcome.

Dr. Shikun He
Guest Editor

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. Cells is an international peer-reviewed open access semimonthly 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 2700 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

  • eye diseases
  • ocular cells
  • genes expression
  • genomics
  • epigenomics
  • transcriptomics
  • proteomics
  • metabolomics
  • microbiomics
  • functional genomics

Published Papers (5 papers)

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Research

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15 pages, 1624 KiB  
Article
Novel Compound Heterozygous Variations in MPDZ Gene Caused Isolated Bilateral Macular Coloboma in a Chinese Family
by Shuang Zhang, Fangxia Zhang, Juan Wang, Shangying Yang, Yinghua Ren, Xue Rui, Xiaobo Xia and Xunlun Sheng
Cells 2022, 11(22), 3602; https://doi.org/10.3390/cells11223602 - 14 Nov 2022
Cited by 3 | Viewed by 1683
Abstract
Macular coloboma (MC) is a rare congenital retinochoroidal defect characterized by lesions of different sizes in the macular region. The pathological mechanism underlying congenital MC is unknown. Novel compound heterozygous variations, c.4301delA (p.Asp1434fs*3) and c.5255C>G (p.Ser1752Ter), in the multiple PDZ domain (MPDZ) proteins [...] Read more.
Macular coloboma (MC) is a rare congenital retinochoroidal defect characterized by lesions of different sizes in the macular region. The pathological mechanism underlying congenital MC is unknown. Novel compound heterozygous variations, c.4301delA (p.Asp1434fs*3) and c.5255C>G (p.Ser1752Ter), in the multiple PDZ domain (MPDZ) proteins were identified via whole-exome analysis on the proband with isolated bilateral macular coloboma in a Chinese family. Segregation analysis revealed that each of the unaffected parents was heterozygous for one of the two variants. The results of the in silico and bioinformatics analysis were aligned with the experimental data. The knockdown of MPDZ in zebrafish caused a decrease in the ellipsoid zone, a destruction of the outer limiting membrane, and the subsequent RPE degeneration. Overall, the loss of MPDZ in zebrafish contributed to retinal development failure. These results indicate that MPDZ plays an essential role in the occurrence and maintenance of the macula, and the novel compound heterozygous variations were responsible for an autosomal recessive macular deficiency in this Chinese family. Full article
(This article belongs to the Special Issue What We Know about the Updated Information from Genes to Eye Disease)
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Review

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25 pages, 2605 KiB  
Review
The Past and Present Lives of the Intraocular Transmembrane Protein CD36
by Rucui Yang, Qingping Liu and Mingzhi Zhang
Cells 2023, 12(1), 171; https://doi.org/10.3390/cells12010171 - 31 Dec 2022
Cited by 12 | Viewed by 2949
Abstract
Cluster of differentiation 36 (CD36) belongs to the B2 receptors of the scavenger receptor class B family, which is comprised of single-chain secondary transmembrane glycoproteins. It is present in a variety of cell types, including monocytes, macrophages, microvascular endothelial cells, adipocytes, hepatocytes, platelets, [...] Read more.
Cluster of differentiation 36 (CD36) belongs to the B2 receptors of the scavenger receptor class B family, which is comprised of single-chain secondary transmembrane glycoproteins. It is present in a variety of cell types, including monocytes, macrophages, microvascular endothelial cells, adipocytes, hepatocytes, platelets, skeletal muscle cells, kidney cells, cardiomyocytes, taste bud cells, and a variety of other cell types. CD36 can be localized on the cell surface, mitochondria, endoplasmic reticulum, and endosomes, playing a role in lipid accumulation, oxidative stress injury, apoptosis, and inflammatory signaling. Recent studies have found that CD36 is expressed in a variety of ocular cells, including retinal pigment epithelium (RPE), retinal microvascular endothelial cells, retinal ganglion cells (RGC), Müller cells, and photoreceptor cells, playing an important role in eye diseases, such as age-related macular degeneration (AMD), diabetic retinopathy (DR), and glaucoma. Therefore, a comprehensive understanding of CD36 function and downstream signaling pathways is of great significance for the prevention and treatment of eye diseases. This article reviews the molecular characteristics, distribution, and function of scavenger receptor CD36 and its role in ophthalmology in order to deepen the understanding of CD36 in eye diseases and provide new ideas for treatment strategies. Full article
(This article belongs to the Special Issue What We Know about the Updated Information from Genes to Eye Disease)
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23 pages, 981 KiB  
Review
Essential Role of Multi-Omics Approaches in the Study of Retinal Vascular Diseases
by Yi Lei, Ju Guo, Shikun He and Hua Yan
Cells 2023, 12(1), 103; https://doi.org/10.3390/cells12010103 - 26 Dec 2022
Cited by 1 | Viewed by 2031
Abstract
Retinal vascular disease is a highly prevalent vision-threatening ocular disease in the global population; however, its exact mechanism remains unclear. The expansion of omics technologies has revolutionized a new medical research methodology that combines multiple omics data derived from the same patients to [...] Read more.
Retinal vascular disease is a highly prevalent vision-threatening ocular disease in the global population; however, its exact mechanism remains unclear. The expansion of omics technologies has revolutionized a new medical research methodology that combines multiple omics data derived from the same patients to generate multi-dimensional and multi-evidence-supported holistic inferences, providing unprecedented opportunities to elucidate the information flow of complex multi-factorial diseases. In this review, we summarize the applications of multi-omics technology to further elucidate the pathogenesis and complex molecular mechanisms underlying retinal vascular diseases. Moreover, we proposed multi-omics-based biomarker and therapeutic strategy discovery methodologies to optimize clinical and basic medicinal research approaches to retinal vascular diseases. Finally, the opportunities, current challenges, and future prospects of multi-omics analyses in retinal vascular disease studies are discussed in detail. Full article
(This article belongs to the Special Issue What We Know about the Updated Information from Genes to Eye Disease)
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29 pages, 1786 KiB  
Review
Diabetic Macular Edema: Current Understanding, Molecular Mechanisms and Therapeutic Implications
by Jingfa Zhang, Jingxiang Zhang, Chaoyang Zhang, Jingting Zhang, Limin Gu, Dawei Luo and Qinghua Qiu
Cells 2022, 11(21), 3362; https://doi.org/10.3390/cells11213362 - 25 Oct 2022
Cited by 46 | Viewed by 6260
Abstract
Diabetic retinopathy (DR), with increasing incidence, is the major cause of vision loss and blindness worldwide in working-age adults. Diabetic macular edema (DME) remains the main cause of vision impairment in diabetic patients, with its pathogenesis still not completely elucidated. Vascular endothelial growth [...] Read more.
Diabetic retinopathy (DR), with increasing incidence, is the major cause of vision loss and blindness worldwide in working-age adults. Diabetic macular edema (DME) remains the main cause of vision impairment in diabetic patients, with its pathogenesis still not completely elucidated. Vascular endothelial growth factor (VEGF) plays a pivotal role in the pathogenesis of DR and DME. Currently, intravitreal injection of anti-VEGF agents remains as the first-line therapy in DME treatment due to the superior anatomic and functional outcomes. However, some patients do not respond satisfactorily to anti-VEGF injections. More than 30% patients still exist with persistent DME even after regular intravitreal injection for at least 4 injections within 24 weeks, suggesting other pathogenic factors, beyond VEGF, might contribute to the pathogenesis of DME. Recent advances showed nearly all the retinal cells are involved in DR and DME, including breakdown of blood-retinal barrier (BRB), drainage dysfunction of Müller glia and retinal pigment epithelium (RPE), involvement of inflammation, oxidative stress, and neurodegeneration, all complicating the pathogenesis of DME. The profound understanding of the changes in proteomics and metabolomics helps improve the elucidation of the pathogenesis of DR and DME and leads to the identification of novel targets, biomarkers and potential therapeutic strategies for DME treatment. The present review aimed to summarize the current understanding of DME, the involved molecular mechanisms, and the changes in proteomics and metabolomics, thus to propose the potential therapeutic recommendations for personalized treatment of DME. Full article
(This article belongs to the Special Issue What We Know about the Updated Information from Genes to Eye Disease)
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13 pages, 983 KiB  
Review
The Role of N6-Methyladenosine Modification in Microvascular Dysfunction
by Ye-Ran Zhang, Jiang-Dong Ji, Jia-Nan Wang, Ying Wang, Hong-Jing Zhu, Ru-Xu Sun, Qing-Huai Liu and Xue Chen
Cells 2022, 11(20), 3193; https://doi.org/10.3390/cells11203193 - 11 Oct 2022
Cited by 2 | Viewed by 1682
Abstract
Microvascular dysfunction (MVD) has long plagued the medical field despite improvements in its prevention, diagnosis, and intervention. Microvascular lesions from MVD increase with age and further lead to impaired microcirculation, target organ dysfunction, and a mass of microvascular complications, thus contributing to a [...] Read more.
Microvascular dysfunction (MVD) has long plagued the medical field despite improvements in its prevention, diagnosis, and intervention. Microvascular lesions from MVD increase with age and further lead to impaired microcirculation, target organ dysfunction, and a mass of microvascular complications, thus contributing to a heavy medical burden and rising disability rates. An up-to-date understanding of molecular mechanisms underlying MVD will facilitate discoveries of more effective therapeutic strategies. Recent advances in epigenetics have revealed that RNA methylation, an epigenetic modification, has a pivotal role in vascular events. The N6-methylation of adenosine (m6A) modification is the most prevalent internal RNA modification in eukaryotic cells, which regulates vascular transcripts through splicing, degradation, translation, as well as translocation, thus maintaining microvascular homeostasis. Conversely, the disruption of the m6A regulatory network will lead to MVD. Herein, we provide a review discussing how m6A methylation interacts with MVD. We also focus on alterations of the m6A regulatory network under pathological conditions. Finally, we highlight the value of m6A regulators as prognostic biomarkers and novel therapeutic targets, which might be a promising addition to clinical medicine. Full article
(This article belongs to the Special Issue What We Know about the Updated Information from Genes to Eye Disease)
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