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Biomedicines
Special Issues
Next-Generation Sequencing and Proteomics Research for Retinal Diseases
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Next-Generation Sequencing and Proteomics Research for Retinal Diseases

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular and Translational Medicine".

Deadline for manuscript submissions: closed (16 February 2025) | Viewed by 3864

Special Issue Editor

Dr. Jayshree Advani

E-Mail Website
Guest Editor
Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MA, USA
Interests: age-related macular degeneration; inherited retinal diseases; gene regulation; quantitative trait loci; multi-omics

Special Issue Information

Dear Colleagues,

The retina is considered our window to the outside world. It captures, integrates, and processes visual information. The dysfunction or death of retinal photoreceptors is the major cause of vision loss, leading to several retinal diseases including age-related macular degeneration (AMD), glaucoma, and retinitis pigmentosa (RP). In recent years, Next-Generation Sequencing (NGS) and proteomics technologies have enabled various diseases to be characterized at the molecular level to identify new targets and biomarkers to monitor disease progression and treatment efficacy. The analysis of several retinal diseases using NGS and proteomics methods represents a unique opportunity to understand the pathophysiological mechanisms of such diseases and to develop new therapeutic approaches. This Biomedicines Special Issue invites contributions dealing with the identification and characterization of new genes and proteins, and recent advances in the discovery and development of methods in NGS, proteomics, and translation, and their clinical application to retinal diseases. This Special Issue also welcomes articles on transcriptomics research on retinal disease. 

Dr. Jayshree Advan
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. Biomedicines 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.

Publisher’s Notice

At the request of the Guest Editor, this Special Issue has been closed ahead of the originally planned submission deadline. The deadline has been updated accordingly, and no further submissions will be accepted.

Keywords

  • genomics
  • proteomics
  • biomarker
  • variant interpretation
  • single-molecule sequencing
  • epigenome
  • retinal degeneration
  • genetics

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Published Papers (2 papers)

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Research

17 pages, 2501 KiB  
Article
Age-Related Choroidal Involution Is Associated with the Senescence of Endothelial Progenitor Cells in the Choroid
by Ali Riza Nazari, Loraine Gresseau, Tiffany Habelrih, Aliabbas Zia, Isabelle Lahaie, Yosra Er-Reguyeg, France Coté, Borhane Annabi, Alain Rivard, Sylvain Chemtob and Michel Desjarlais
Biomedicines 2024, 12(12), 2669; https://doi.org/10.3390/biomedicines12122669 - 22 Nov 2024
Cited by 1 | Viewed by 1072
Abstract
Background: Choroidal involution is a common feature of age-related ischemic retinopathies such as age-related macular degeneration (AMD). It is now well recognized that endothelial progenitor cells (EPCs) are essential to endothelial repair processes and in maintaining vascular integrity. However, the contribution of EPCs [...] Read more.
Background: Choroidal involution is a common feature of age-related ischemic retinopathies such as age-related macular degeneration (AMD). It is now well recognized that endothelial progenitor cells (EPCs) are essential to endothelial repair processes and in maintaining vascular integrity. However, the contribution of EPCs and the role of senescence in age-related choroidal vascular degeneration remain to be investigated. In this study, we compared the senescent phenotype of EPCs in the choroid and performed whole-genome profiling of EPCs derived from young versus old rats. Methods and Results: We isolated and compared the retinas of young (6-weeks-old) and old (16–18-month-old) rats. The thickness of the choroid and outer nuclear layer (ONL), along with local quantification of CD34+ EPCs, was performed. Compared to young rats, older rats displayed a significant reduction in choroidal and ONL thickness associated with markedly fewer choroid-localized EPCs; this was attested by lower expression of several EPC markers (CXCR4, CD34, CD117, CD133, and KLF-2). Choroid and choroid-localized EPCs displayed abundant senescence as revealed by increased β-gal and P53 expression and decreased Lamin-B1 (immunostaining and RT-qPCR). Concordantly, choroidal cells and EPCs isolated from older rats were unable to form vascular networks ex vivo. To better understand the potential mechanisms associated with the dysfunctional EPCs linked to age-related choroidal involution, we performed whole-genome profiling (mRNA and miRNA) of EPCs derived from old and young rats using next-generation sequencing (NGS); 802 genes were significantly modulated in old vs. young EPCs, corresponding to ~2% of total genes expressed. Using a bioinformatic algorithm, the KEGG pathways suggested that these genes participate in the modulation of several key signaling processes including inflammation, G protein-coupled receptors, and hematopoietic cell lineages. Moreover, we identified 13 miRNAs involved in the regulation of immune system processes, cell cycle arrest and senescence, which are significantly modulated in EPCs from old rats compared to young ones. Conclusions: Our results suggest that age-related choroidal involution is associated with fewer EPCs, albeit displaying a senescence-like phenotype. One would be tempted to propose that biological modification of native EPCs (such as with senolytic agents) could potentially provide a new strategy to preserve the vascular integrity of the aged choroid, and evade progression to degenerative maculopathies. Full article
(This article belongs to the Special Issue Next-Generation Sequencing and Proteomics Research for Retinal Diseases)
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19 pages, 2660 KiB  
Article
Optimised, Broad NGS Panel for Inherited Eye Diseases to Diagnose 1000 Patients in Poland
by Ewa Matczyńska, Marta Beć-Gajowniczek, Larysa Sivitskaya, Elżbieta Gregorczyk, Przemysław Łyszkiewicz, Robert Szymańczak, Maria Jędrzejowska, Edward Wylęgała, Maciej R. Krawczyński, Sławomir Teper and Anna Boguszewska-Chachulska
Biomedicines 2024, 12(6), 1355; https://doi.org/10.3390/biomedicines12061355 - 18 Jun 2024
Cited by 3 | Viewed by 2017
Abstract
Advances in gene therapy and genome editing give hope that new treatments will soon be available for inherited eye diseases that together affect a significant proportion of the adult population. New solutions are needed to make genetic diagnosis fast and affordable. This is [...] Read more.
Advances in gene therapy and genome editing give hope that new treatments will soon be available for inherited eye diseases that together affect a significant proportion of the adult population. New solutions are needed to make genetic diagnosis fast and affordable. This is the first study of such a large group of patients with inherited retinal dystrophies (IRD) and inherited optic neuropathies (ION) in the Polish population. It is based on four years of diagnostic analysis using a broad, targeted NGS approach. The results include the most common pathogenic variants, as well as 91 novel causative variants, including frameshifts in the cumbersome RPGR ORF15 region. The high frequency of the ABCA4 complex haplotype p.(Leu541Pro;Ala1038Val) was confirmed. Additionally, a deletion of exons 22–24 in USH2A, probably specific to the Polish population, was uncovered as the most frequent copy number variation. The diagnostic yield of the broad NGS panel reached 64.3% and is comparable to the results reported for genetic studies of IRD and ION performed for other populations with more extensive WES or WGS methods. A combined approach to identify genetic causes of all known diseases manifesting in the posterior eye segment appears to be the optimal choice given the currently available treatment options and advanced clinical trials. Full article
(This article belongs to the Special Issue Next-Generation Sequencing and Proteomics Research for Retinal Diseases)
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