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RNA Modifications in Disease and Development
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RNA Modifications in Disease and Development

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (15 July 2022) | Viewed by 6215

Special Issue Editors

Dr. Ludmila K. Savinkova

E-Mail Website
Guest Editor
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
Interests: TATA binding protein; TATA box; SNP; disease; gene expression; RNA Polymerase I
Prof. Dr. Nikolay A. Kolchanov

E-Mail Website
Guest Editor
Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
Interests: bioinformatics; systems biology; genetics; genomics; gene networks
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Currently, more than 170 different types of chemical modifications of RNA are known. RNA modifications are critical post-transcriptional regulatory mechanisms for gene expression. Modifications of messenger RNA (mRNA) regulate various aspects of mRNA metabolism, and thus the expression of mammalian genes. For example, N-6-methyladenosine (m6A) affects the translation and stability of modified transcripts, providing a mechanism for the coordinated regulation of transcript groups during cell state preservation. mRNA modifications also contribute to the survival and growth of tumor cells, highlighting their importance in regulating cell fate determination. Some modifications in transport RNAs are needed to maintain RNA structure and function, and others to adapt protein synthesis and gene-specific translation in response to external signals. Complex human pathologies such as cancer, type 2 diabetes, neurological disorders and mitochondrial disorders are associated with tRNA modifications. There is increasing evidence that microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) are closely associated with the occurrence and development of various diseases, including inflammatory and metabolic diseases and cancer. microRNAs from regulatory non-coding RNAs cause gene silencing by mRNA degradation or translation repression through RNA interference. Various mechanisms are involved in gene regulation mediated by long non-coding RNAs (lncRNAs), which is explained by their ability to interact with DNA, RNA or protein. Thus, different RNAs can play a critical role in various biological functions and disease processes, including cancer.

Dr. Ludmila K. Savinkova
Prof. Dr. Nikolay Kolchanov
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. 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

  • RNA
  • RNA modifications
  • mRNAs
  • tRNAs
  • miRNAs
  • lncRNAs
  • ncRNAs
  • peptide
  • protein
  • circRNAs
  • expression profiles
  • cell fate
  • inflammatory and metabolic diseases
  • cancer

Published Papers (2 papers)

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Research

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10 pages, 826 KiB  
Article
RNADSN: Transfer-Learning 5-Methyluridine (m5U) Modification on mRNAs from Common Features of tRNA
by Zhirou Li, Jinge Mao, Daiyun Huang, Bowen Song and Jia Meng
Int. J. Mol. Sci. 2022, 23(21), 13493; https://doi.org/10.3390/ijms232113493 - 4 Nov 2022
Cited by 6 | Viewed by 2601
Abstract
One of the most abundant non-canonical bases widely occurring on various RNA molecules is 5-methyluridine (m5U). Recent studies have revealed its influences on the development of breast cancer, systemic lupus erythematosus, and the regulation of stress responses. The accurate identification of m5 [...] Read more.
One of the most abundant non-canonical bases widely occurring on various RNA molecules is 5-methyluridine (m5U). Recent studies have revealed its influences on the development of breast cancer, systemic lupus erythematosus, and the regulation of stress responses. The accurate identification of m5U sites is crucial for understanding their biological functions. We propose RNADSN, the first transfer learning deep neural network that learns common features between tRNA m5U and mRNA m5U to enhance the prediction of mRNA m5U. Without seeing the experimentally detected mRNA m5U sites, RNADSN has already outperformed the state-of-the-art method, m5UPred. Using mRNA m5U classification as an additional layer of supervision, our model achieved another distinct improvement and presented an average area under the receiver operating characteristic curve (AUC) of 0.9422 and an average precision (AP) of 0.7855. The robust performance of RNADSN was also verified by cross-technical and cross-cellular validation. The interpretation of RNADSN also revealed the sequence motif of common features. Therefore, RNADSN should be a useful tool for studying m5U modification. Full article
(This article belongs to the Special Issue RNA Modifications in Disease and Development)
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Review

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45 pages, 1401 KiB  
Review
Promising Biomarkers in Head and Neck Cancer: The Most Clinically Important miRNAs
by Arsinoe C. Thomaidou, Panagiota Batsaki, Maria Adamaki, Maria Goulielmaki, Constantin N. Baxevanis, Vassilis Zoumpourlis and Sotirios P. Fortis
Int. J. Mol. Sci. 2022, 23(15), 8257; https://doi.org/10.3390/ijms23158257 - 26 Jul 2022
Cited by 10 | Viewed by 3394
Abstract
Head and neck cancers (HNCs) comprise a heterogeneous group of tumors that extend from the oral cavity to the upper gastrointestinal tract. The principal etiologic factors for oral tumors include tobacco smoking and alcohol consumption, while human papillomavirus (HPV) infections have been accused [...] Read more.
Head and neck cancers (HNCs) comprise a heterogeneous group of tumors that extend from the oral cavity to the upper gastrointestinal tract. The principal etiologic factors for oral tumors include tobacco smoking and alcohol consumption, while human papillomavirus (HPV) infections have been accused of a high incidence of pharyngeal tumors. Accordingly, HPV detection has been extensively used to categorize carcinomas of the head and neck. The diverse nature of HNC highlights the necessity for novel, sensitive, and precise biomarkers for the prompt diagnosis of the disease, its successful monitoring, and the timely prognosis of patient clinical outcomes. In this context, the identification of certain microRNAs (miRNAs) and/or the detection of alterations in their expression patterns, in a variety of somatic fluids and tissues, could serve as valuable biomarkers for precision oncology. In the present review, we summarize some of the most frequently studied miRNAs (including miR-21, -375, -99, -34a, -200, -31, -125a/b, -196a/b, -9, -181a, -155, -146a, -23a, -16, -29, and let-7), their role as biomarkers, and their implication in HNC pathogenesis. Moreover, we designate the potential of given miRNAs and miRNA signatures as novel diagnostic and prognostic tools for successful patient stratification. Finally, we discuss the currently ongoing clinical trials that aim to identify the diagnostic, prognostic, or therapeutic utility of miRNAs in HNC. Full article
(This article belongs to the Special Issue RNA Modifications in Disease and Development)
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