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Oligonucleotide, Therapy, and Applications 3.0

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

Deadline for manuscript submissions: closed (30 December 2022) | Viewed by 7486

Special Issue Editors


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Guest Editor
Pharmacogenetics Platform, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain
Interests: pharmacogenetics; genetic variants; non-viral vector; transfection; hydrodynamic transfection; ex vivo organ; therapeutic oligonucleotides; antisense oligonucleotides
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Pharmacogenetic Unit, Instituto de Investigación Sanitaria La Fe, Gene Therapy Group, Universitat de València, Valencia, Spain
Interests: gene therapy; non viral; oligonucleotides; vaccines; pharmacogenetic
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Oligonucleotides (ON) constitute a new group of molecular agents, an object of significant interest due to their potential value as drugs for diagnostic and therapeutic applications. The special interest in ONs derives from their intrinsic characteristics: a) ONs are informative agents, a property that derives from the order in which the nucleotides of each particular ON are arranged. b) ONs can act as ligands (ASO, TFO, aptamers, G-quadruplex, etc.) of complementary nucleic acid sequences (DNA or RNA) due to their high capacity to hybridize (by means of Watson and Crick or Hoogsteen links) with other nucleotide sequences, resulting in specific gene modulatory effects. However, nonspecific sequences may also be of interest, as is the case with repetitive nucleotide sequences (CpG) with adjuvant effects of vaccines. c) ONs can also rapidly evolve to achieve specific advantages of utility (targeting, stability, efficacy, toxicity, etc.) or high-sensitivity diagnostic technology (markers, analyzes, biosensors, FISH, microarrays, etc.) by chemical modification of nucleotides in any of their atoms. These properties show that ONs are first-order molecules due to their potential usefulness in practice.

In this collection of research articles and review papers, we aim to highlight their therapeutic, diagnostic and technological applications as drugs.

Prof. Dr. Salvador Aliño
Dr. Luis Sendra
Guest Editors

Manuscript Submission Information

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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.

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Keywords

  • oligonucleotide
  • antisense
  • silencing
  • splicing
  • aptamer
  • gapmer
  • siRNA
  • CpG
  • editing
  • targeting
  • delivery
  • release
  • analysis
  • bioassay
  • biosensor
  • array
  • disease
  • diagnostics
  • FISH
  • beacons
  • vaccine
  • adjuvant
  • immunomodulation

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Published Papers (2 papers)

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Research

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16 pages, 1731 KiB  
Article
Investigating SH-SY5Y Neuroblastoma Cell Surfaceome as a Model for Neuronal-Targeted Novel Therapeutic Modalities
by Pooja Gangras, Valentina Gelfanova, Graham D. Williams, Samuel K. Handelman, Ryan M. Smith and Marjoke F. Debets
Int. J. Mol. Sci. 2022, 23(23), 15062; https://doi.org/10.3390/ijms232315062 - 1 Dec 2022
Cited by 5 | Viewed by 2352
Abstract
The SH-SY5Y neuroblastoma cells are a widely used in vitro model approximating neurons for testing the target engagement of therapeutics designed for neurodegenerative diseases and pain disorders. However, their potential as a model for receptor-mediated delivery and uptake of novel modalities, such as [...] Read more.
The SH-SY5Y neuroblastoma cells are a widely used in vitro model approximating neurons for testing the target engagement of therapeutics designed for neurodegenerative diseases and pain disorders. However, their potential as a model for receptor-mediated delivery and uptake of novel modalities, such as antibody-drug conjugates, remains understudied. Investigation of the SH-SY5Y cell surfaceome will aid in greater in vitro to in vivo correlation of delivery and uptake, thereby accelerating drug discovery. So far, the majority of studies have focused on total cell proteomics from undifferentiated and differentiated SH-SY5Y cells. While some studies have investigated the expression of specific proteins in neuroblastoma tissue, a global approach for comparison of neuroblastoma cell surfaceome to the brain and dorsal root ganglion (DRG) neurons remains uninvestigated. Furthermore, an isoform-specific evaluation of cell surface proteins expressed on neuroblastoma cells remains unexplored. In this study, we define a bioinformatic workflow for the identification of high-confidence surface proteins expressed on brain and DRG neurons using tissue proteomic and transcriptomic data. We then delineate the SH-SY5Y cell surfaceome by surface proteomics and show that it significantly overlaps with the human brain and DRG neuronal surface proteome. We find that, for 32% of common surface proteins, SH-SY5Y-specific major isoforms are alternatively spliced, maintaining their protein-coding ability, and are predicted to localize to the cell surface. Validation of these isoforms using surface proteomics confirms a SH-SY5Y-specific alternative NRCAM (neuron-glia related cell adhesion molecule) isoform, which is absent in typical brain neurons, but present in neuroblastomas, making it a receptor of interest for neuroblastoma-specific therapeutics. Full article
(This article belongs to the Special Issue Oligonucleotide, Therapy, and Applications 3.0)
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Review

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22 pages, 19443 KiB  
Review
Structural Modifications of siRNA Improve Its Performance In Vivo
by Ivan V. Chernikov, Ulyana A. Ponomareva and Elena L. Chernolovskaya
Int. J. Mol. Sci. 2023, 24(2), 956; https://doi.org/10.3390/ijms24020956 - 4 Jan 2023
Cited by 5 | Viewed by 4535
Abstract
The use of small interfering RNA (siRNA) in the clinic gives a wide range of possibilities for the treatment of previously incurable diseases. However, the main limitation for biomedical applications is their delivery to target cells and organs. Currently, delivery of siRNA to [...] Read more.
The use of small interfering RNA (siRNA) in the clinic gives a wide range of possibilities for the treatment of previously incurable diseases. However, the main limitation for biomedical applications is their delivery to target cells and organs. Currently, delivery of siRNA to liver cells is a solved problem due to the bioconjugation of siRNA with N-acetylgalactosamine; other organs remain challenging for siRNA delivery to them. Despite the important role of the ligand in the composition of the bioconjugate, the structure and molecular weight of siRNA also play an important role in the delivery of siRNA. The basic principle is that siRNAs with smaller molecular weights are more efficient at entering cells, whereas siRNAs with larger molecular weights have advantages at the organism level. Here we review the relationships between siRNA structure and its biodistribution and activity to find new strategies for improving siRNA performance. Full article
(This article belongs to the Special Issue Oligonucleotide, Therapy, and Applications 3.0)
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