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Genome Stability in Visual Sciences
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Genome Stability in Visual Sciences

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 5155

Special Issue Editor

Dr. Wai Kit Chu

E-Mail Website
Guest Editor
Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
Interests: visual sciences; retinoblastoma; ocular inflammation; pterygium; thyroid-associated orbitopathy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genetic information is stored in the base-pairing of double stranded DNA. However, the genome of all living organisms is under constant threat from extrinsic mutagens, such as γ-irradiation, or intrinsic problems of DNA metabolism, such as DNA replication fork collapse. The roles of genome stability have been mainly studied in cancer biology in the past. Recently, genome stability has been identified associating with many eye diseases.

This issue will focus on genome stability in ophthalmology and visual sciences. We seek high quality manuscripts describing the role of genomic alterations in mediating the initiation, progression and treatment responses in various eye diseases.

We specifically encourage the submission of manuscripts presenting innovative approaches exploiting the genome stability concept in an attempt to identify novel strategies to improve the visual outcome.

Dr. Wai Kit Chu
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • ophthalmology
  • visual sciences
  • genome stability
  • DNA metabolism
  • eye diseases
  • genomic alterations

Published Papers (2 papers)

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Research

17 pages, 3024 KiB  
Article
Single-Cell Transcriptomic Profiling in Inherited Retinal Degeneration Reveals Distinct Metabolic Pathways in Rod and Cone Photoreceptors
by Yiyi Chen, Yujie Dong, Jie Yan, Lan Wang, Shirley Yu, Kangwei Jiao and François Paquet-Durand
Int. J. Mol. Sci. 2022, 23(20), 12170; https://doi.org/10.3390/ijms232012170 - 12 Oct 2022
Cited by 4 | Viewed by 2066
Abstract
The cellular mechanisms underlying hereditary photoreceptor degeneration are still poorly understood. The aim of this study was to systematically map the transcriptional changes that occur in the degenerating mouse retina at the single cell level. To this end, we employed single-cell RNA-sequencing (scRNA-seq) [...] Read more.
The cellular mechanisms underlying hereditary photoreceptor degeneration are still poorly understood. The aim of this study was to systematically map the transcriptional changes that occur in the degenerating mouse retina at the single cell level. To this end, we employed single-cell RNA-sequencing (scRNA-seq) and retinal degeneration-1 (rd1) mice to profile the impact of the disease mutation on the diverse retinal cell types during early post-natal development. The transcriptome data allowed to annotate 43,979 individual cells grouped into 20 distinct clusters. We further characterized cluster-specific metabolic and biological changes in individual cell types. Our results highlight Ca2+-signaling as relevant to hereditary photoreceptor degeneration. Although metabolic reprogramming in retina, known as the ‘Warburg effect’, has been documented, further metabolic changes were noticed in rd1 mice. Such metabolic changes in rd1 mutation was likely regulated through mitogen-activated protein kinase (MAPK) pathway. By combining single-cell transcriptomes and immunofluorescence staining, our study revealed cell type-specific changes in gene expression, as well as interplay between Ca2+-induced cell death and metabolic pathways. Full article
(This article belongs to the Special Issue Genome Stability in Visual Sciences)
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11 pages, 973 KiB  
Article
Potential of Aqueous Humor as a Liquid Biopsy for Uveal Melanoma
by Deborah H. Im, Chen-Ching Peng, Liya Xu, Mary E. Kim, Dejerianne Ostrow, Venkata Yellapantula, Moiz Bootwalla, Jaclyn A. Biegel, Xiaowu Gai, Rishvanth K. Prabakar, Peter Kuhn, James Hicks and Jesse L. Berry
Int. J. Mol. Sci. 2022, 23(11), 6226; https://doi.org/10.3390/ijms23116226 - 02 Jun 2022
Cited by 12 | Viewed by 2576
Abstract
Tumor biopsy can identify prognostic biomarkers for metastatic uveal melanoma (UM), however aqueous humor (AH) liquid biopsy may serve as an adjunct. This study investigated whether the AH of UM eyes has sufficient circulating tumor DNA (ctDNA) to perform genetic analysis. This is [...] Read more.
Tumor biopsy can identify prognostic biomarkers for metastatic uveal melanoma (UM), however aqueous humor (AH) liquid biopsy may serve as an adjunct. This study investigated whether the AH of UM eyes has sufficient circulating tumor DNA (ctDNA) to perform genetic analysis. This is a case series of 37 AH samples, taken before or after radiation, and one tumor wash sample, from 12 choroidal and 8 ciliary body (CB) melanoma eyes. AH was analyzed for nucleic acid concentrations. AH DNA and one tumor wash sample underwent shallow whole-genome sequencing followed by Illumina sequencing to detect somatic copy number alterations (SCNAs). Four post-radiation AH underwent targeted sequencing of BAP1 and GNAQ genes. Post-radiation AH had significantly higher DNA and miRNA concentrations than paired pre-radiation samples. Highly recurrent UM SCNAs were identified in 0/11 post-radiation choroidal and 6/8 post-radiation CB AH. SCNAs were highly concordant in a CB post-radiation AH with its matched tumor (r = 0.978). BAP1 or GNAQ variants were detected in 3/4 post-radiation AH samples. AH is a source of ctDNA in UM eyes, particularly in post-radiation CB eyes. For the first time, UM SCNAs and mutations were identified in AH-derived ctDNA. Suggesting that AH can serve as a liquid biopsy for UM. Full article
(This article belongs to the Special Issue Genome Stability in Visual Sciences)
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