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Molecules
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Circulating RNA Molecules: A New Class of Potential Biomarkers
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Circulating RNA Molecules: A New Class of Potential Biomarkers

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (31 May 2020) | Viewed by 7622

Special Issue Editors

Prof. Dr. Leonidas A. Phylactou

E-Mail Website
Guest Editor
Chief Executive Officer and Medical Director, The Cyprus Institute of Neurology & Genetics, PO Box 23462, Nicosia 1683, Cyprus
Interests: RNA biology; regulatory RNA molecules; extracellular vesicles; identification of genetic defects in inherited diseases
Special Issues, Collections and Topics in MDPI journals
Dr. Andrie Koutsoulidou

E-Mail Website
Co-Guest Editor
Department of Molecular Genetics, The Cyprus Institute of Neurology& Genetics, PO Box 23462, Nicosia 1683, Cyprus
Interests: muscular dystrophies; gene therapy; biomarkers; miRNAs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biomarkers are measurable indicators of normal or pathogenic conditions or pharmacological responses to a therapeutic intervention. Different types of biomarkers have been defined and classified based on their use. More specifically, diagnostic, monitoring, prognostic, and pharmacodynamic/response biomarkers have been recorded. Diagnostic biomarkers are used to identify individuals with a disease or condition of interest, or to define a subset of the disease. Prognostic biomarkers are used to detect the possibility of a clinical symptom, disease recurrence, or disease progression. Monitoring biomarkers are used to regularly screen the patients for a change in the degree or extent of disease. Pharmacodynamic/response biomarkers are used to evaluate the response of the patient to a therapeutic intervention. In blood, circulating biomarkers can exist in the form of DNA, RNA, protein, metabolites, or other molecules. In current years, because of the new high-throughput technologies, RNA circulating biomarkers have gained interest, and hold great promise for their potential use in clinical practise.

The focus of this Special Issue is on the RNA molecules in blood circulation, and their potential use as biomarkers. This Special Issue will include original research articles and review articles on all of the types of RNA molecules circulating in blood, their correlation with a disease state, their classification as specific types of biomarkers, evaluation studies, and new advances in technologies for their identification and evaluation.

Prof. Dr. Leonidas A. Phylactou
Dr. Andrie Koutsoulidou
Guest Editors

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. Molecules 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

  • RNA
  • MiRNA
  • Long-non coding RNA
  • Circular RNA
  • mRNA
  • Extracellular RNA
  • Exosomal RNA

Published Papers (2 papers)

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Research

14 pages, 1821 KiB  
Article
Association of mRNA Levels of IL6, MMP-8, GSS in Saliva and Pyelonephritis in Children
by Sirma Angelova, Ayshe Salim, Yoana Kiselova-Kaneva, Diana Ivanova and Stefan Peev
Molecules 2020, 25(1), 85; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25010085 - 25 Dec 2019
Cited by 3 | Viewed by 2533
Abstract
Nowadays, saliva is a subject of growing scientific interest because of its definite advantages as diagnostic medium. The aim of our study was to investigate the diagnostic potential and reliability of messenger RNAs (mRNAs) of selected genes—interleukin-6 (IL-6), matrix metalloproteinase-8 (MMP-8) and glutathione [...] Read more.
Nowadays, saliva is a subject of growing scientific interest because of its definite advantages as diagnostic medium. The aim of our study was to investigate the diagnostic potential and reliability of messenger RNAs (mRNAs) of selected genes—interleukin-6 (IL-6), matrix metalloproteinase-8 (MMP-8) and glutathione synthetase (GSS)—as salivary markers in children with diagnosed pyelonephritis and to correlate their levels with typical urine para-clinical indicators of the disease. Analysis of the mRNA levels for IL-6, MMP-8 and GSS in 28 children hospitalized with the diagnosis of pyelonephritis was conducted applying the method of quantitative reverse transcription polymerase chain reaction (RT-qPCR). In the study group (n = 28), IL-6 mRNA levels demonstrated 64-fold increase (p < 0.001). MMP-8 and GSS mRNA levels were increased in 12 samples in patients with pyelonephritis 3.27 (p < 0.01) and 1.94 (p < 0.001) times, respectively. We found a strong and significant correlation (p < 0.001) between the investigated mRNA for IL-6 and MMP-8, IL-6 and GSS, MMP-8 and GSS. Moderate degree of correlation was established between IL-6 and the typical para-clinical indicator of leucocytes (0.43, p < 0.05) and between GSS and leucocytes (0.54, p < 0.01). Salivary IL-6, MMP-8 and GSS mRNA levels in combination with urine test analysis could be useful diagnostic tool for the very distributed disorder of pyelonephritis in childhood. Full article
(This article belongs to the Special Issue Circulating RNA Molecules: A New Class of Potential Biomarkers)
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13 pages, 1383 KiB  
Article
Identifying Cancer-Specific circRNA–RBP Binding Sites Based on Deep Learning
by Zhengfeng Wang, Xiujuan Lei and Fang-Xiang Wu
Molecules 2019, 24(22), 4035; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24224035 - 07 Nov 2019
Cited by 53 | Viewed by 4656
Abstract
Circular RNAs (circRNAs) are extensively expressed in cells and tissues, and play crucial roles in human diseases and biological processes. Recent studies have reported that circRNAs could function as RNA binding protein (RBP) sponges, meanwhile RBPs can also be involved in back-splicing. The [...] Read more.
Circular RNAs (circRNAs) are extensively expressed in cells and tissues, and play crucial roles in human diseases and biological processes. Recent studies have reported that circRNAs could function as RNA binding protein (RBP) sponges, meanwhile RBPs can also be involved in back-splicing. The interaction with RBPs is also considered an important factor for investigating the function of circRNAs. Hence, it is necessary to understand the interaction mechanisms of circRNAs and RBPs, especially in human cancers. Here, we present a novel method based on deep learning to identify cancer-specific circRNA–RBP binding sites (CSCRSites), only using the nucleotide sequences as the input. In CSCRSites, an architecture with multiple convolution layers is utilized to detect the features of the raw circRNA sequence fragments, and further identify the binding sites through a fully connected layer with the softmax output. The experimental results show that CSCRSites outperform the conventional machine learning classifiers and some representative deep learning methods on the benchmark data. In addition, the features learnt by CSCRSites are converted to sequence motifs, some of which can match to human known RNA motifs involved in human diseases, especially cancer. Therefore, as a deep learning-based tool, CSCRSites could significantly contribute to the function analysis of cancer-associated circRNAs. Full article
(This article belongs to the Special Issue Circulating RNA Molecules: A New Class of Potential Biomarkers)
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