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New Advances in Cellular and Molecular Mechanisms Involved in Retinal...
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New Advances in Cellular and Molecular Mechanisms Involved in Retinal Diseases

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

Deadline for manuscript submissions: closed (10 April 2022) | Viewed by 8556

Special Issue Editor

Dr. Takeshi Iwata

E-Mail Website
Guest Editor
Molecular and Cellular Biology Division, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1, Higashigaoka, Meguro-Ku, Tokyo 152-8902, Japan
Interests: molecular mechanisms of retinal diseases including inherited retinal diseases; inherited glaucoma; inherited optic neuropathy; age-related macular degeneration
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

Recent advances in DNA sequencing, gene editing, iPS cells, and AI have introduced powerful tools and materials to identify disease-causing variants and quickly pursue functional studies in vitro and in vivo to elucidate the molecular mechanisms of disease onset. These technologies were not available to most of us just one decade ago. This trend of advancement is continuing into the 2020s to assist in the deeper observation of disease onset. Over 270 genes have been identified for inherited retinal diseases and more are expected as patient genome analyses are performed in Southeast Asia, the Middle East, Africa, and South America. However, functional studies to confirm these variants in disease onset and to find seed information for the development of therapeutics have not successfully caught up. This is mainly due to the variety of proteins involved in retinal diseases. The approach to characterize an enzyme protein would be different from approaching transcription factors or other types of proteins.

The purpose of this Special Issue is to highlight recent findings and the techniques used to identify retinal disease causes, and different approaches taken to elucidate the molecular mechanisms of disease onset. The relevant retinal diseases include inherited retinal diseases, glaucoma, optic neuropathy, and age-related macular degeneration.

Dr. Takeshi Iwata
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

  • retina
  • genome
  • chromatin
  • non-coding RNA
  • enhancer
  • gene editing
  • iPS cells
  • animal models
  • single-cell analysis
  • proteomic
  • transcriptomic
  • epigenetics

Published Papers (3 papers)

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Research

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16 pages, 1785 KiB  
Article
Small Nucleolar RNAs in Pseudoexfoliation Glaucoma
by Karolina Gasińska, Marcin Czop, Ewa Kosior-Jarecka, Dominika Wróbel-Dudzińska, Janusz Kocki and Tomasz Żarnowski
Cells 2022, 11(17), 2738; https://doi.org/10.3390/cells11172738 - 02 Sep 2022
Cited by 5 | Viewed by 1596
Abstract
Small nucleolar RNAs (snoRNAs) are small non-coding regulatory RNAs that have been investigated extensively in recent years. However, the relationship between snoRNA and glaucoma is still unknown. This study aims to analyze the levels of snoRNA expression in the aqueous humor (AH) of [...] Read more.
Small nucleolar RNAs (snoRNAs) are small non-coding regulatory RNAs that have been investigated extensively in recent years. However, the relationship between snoRNA and glaucoma is still unknown. This study aims to analyze the levels of snoRNA expression in the aqueous humor (AH) of patients with pseudoexfoliation glaucoma (PEXG) compared to a control group and identify hypothetical snoRNA-dependent mechanisms contributing to PEXG. The AH was obtained from eighteen Caucasian patients, comprising nine PEXG and nine age-matched control patients. RNA was isolated, and a microarray system was used to determine the snoRNA expression profiles. Functional and enrichment analyses were performed. We identified seven snoRNAs, SNORD73B, SNORD58A, SNORD56, SNORA77, SNORA72, SNORA64, and SNORA32, in the AH of the PEXG and control group patients. Five snoRNAs showed statistically significantly lower expression in the PEXG group, and two snoRNAs had statistically significantly higher expression in the PEXG group compared to the control group. In addition, we identified two factors—CACNB3 for SNORA64 and TMEM63C for SNORA32, similar to PEX-related genes (CACNA1A and TMEM136). The enrichment analysis for four genes targeted by snoRNAs revealed possible mechanisms associated with glaucoma and/or PEX, but the direct role of snoRNAs in these biological processes was not proven. Full article
(This article belongs to the Special Issue New Advances in Cellular and Molecular Mechanisms Involved in Retinal Diseases)
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18 pages, 3527 KiB  
Article
Retinal Proteomic Alterations and Combined Transcriptomic-Proteomic Analysis in the Early Stages of Progression of a Mouse Model of X-Linked Retinoschisis
by Xiuxiu Jin, Xiaoli Zhang, Jingyang Liu, Weiping Wang, Meng Liu, Lin Yang, Guangming Liu, Ruiqi Qiu, Mingzhu Yang, Shun Yao and Bo Lei
Cells 2022, 11(14), 2150; https://doi.org/10.3390/cells11142150 - 08 Jul 2022
Cited by 3 | Viewed by 1992
Abstract
X-linked retinoschisis (XLRS) is among the most commonly inherited degenerative retinopathies. XLRS is caused by functional impairment of RS1. However, the molecular mechanisms underlying RS1 malfunction remain largely uncharacterized. Here, we performed a data-independent acquisition-mass spectrometry-based proteomic analysis in RS1-null mouse retina with [...] Read more.
X-linked retinoschisis (XLRS) is among the most commonly inherited degenerative retinopathies. XLRS is caused by functional impairment of RS1. However, the molecular mechanisms underlying RS1 malfunction remain largely uncharacterized. Here, we performed a data-independent acquisition-mass spectrometry-based proteomic analysis in RS1-null mouse retina with different postal days (Ps), including the onset (P15) and early progression stage (P56). Gene set enrichment analysis showed that type I interferon-mediated signaling was upregulated and photoreceptor proteins responsible for detection of light stimuli were downregulated at P15. Positive regulation of Tor signaling was downregulated and nuclear transcribed mRNA catabolic process nonsense-mediated decay was upregulated at P56. Moreover, the differentially expressed proteins at P15 were enriched in metabolism of RNA and RNA destabilization. A broader subcellular localization distribution and enriched proteins in visual perception and phototransduction were evident at P56. Combined transcriptomic-proteomic analysis revealed that functional impairments, including detection of visible light, visual perception, and visual phototransduction, occurred at P21 and continued until P56. Our work provides insights into the molecular mechanisms underlying the onset and progression of an XLRS mouse model during the early stages, thus enhancing the understanding of the mechanism of XLRS. Full article
(This article belongs to the Special Issue New Advances in Cellular and Molecular Mechanisms Involved in Retinal Diseases)
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Review

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50 pages, 21278 KiB  
Review
Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives
by Cristina Zibetti
Cells 2022, 11(5), 806; https://doi.org/10.3390/cells11050806 - 25 Feb 2022
Cited by 3 | Viewed by 4420
Abstract
Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes [...] Read more.
Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes to drive divergent retinal specification programs. Recent studies have furthered the understanding of the epigenetic contribution to the progression of age-related macular degeneration, a leading cause of blindness in the elderly. The knowledge of the epigenomic mechanisms that control the acquisition and stabilization of retinal cell fates and are evoked upon damage, holds the potential for the treatment of retinal degeneration. Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming. A pipeline is then reviewed to functionally interrogate the epigenetic and transcriptional networks underlying cell fate specification, relying on a truly unbiased screening of open chromatin states. The related work proposes an inferential model to identify gene regulatory networks, features the first footprinting analysis and the first tentative, systematic query of candidate pioneer factors in the retina ever conducted in any model organism, leading to the identification of previously uncharacterized master regulators of retinal cell identity, such as the nuclear factor I, NFI. This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context. Finally, challenges and limitations intrinsic to the current next-generation sequencing techniques are discussed, as well as recent advances in super-resolution imaging, enabling spatio-temporal resolution of the genome. Full article
(This article belongs to the Special Issue New Advances in Cellular and Molecular Mechanisms Involved in Retinal Diseases)
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