RNA Biology: From Genome to Therapeutic Targets

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

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 3752

Special Issue Editors


E-Mail Website
Guest Editor
Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
Interests: biological data analysis (scRNA, RNA-Bulk); genomics; proteomics; transcriptomics; NGS data analysis; machine learning; computational drug design; in-silico pharmacokinetic studies; biological database development
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Co-Guest Editor
School of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94115, USA
Interests: computational genomics; machine learning; immunology; cancer

E-Mail Website
Co-Guest Editor
National Cancer Institute (NCI), Rockville, MD, USA
Interests: gene regulatory network; cellular heterogeneity; RNA-Seq

Special Issue Information

Dear Colleagues,

Biological data analysis of RNA (ribonucleic acid) is a crucial aspect of modern molecular biology research, as RNA plays key roles in gene expression and regulation. The analysis of RNA data aims to understand gene expression patterns, detect changes in gene expression levels, and identify novel RNA species and post-transcriptional modifications.

Advances in high-throughput sequencing technologies have greatly expanded the body of RNA data available for analysis, providing a wealth of information about the transcriptomes. However, analysing this large body of data can be challenging, as it requires the development of sophisticated computational tools and algorithms. The current frontiers of RNA data analysis include the development of methods for the detection of differential gene expressions and the identification and characterization of novel RNA species, including non-coding RNAs, long non-coding RNAs, and circular RNA, additionally enabling the detection of new microbiome species using 16sRNA. New techniques, such as single-cell RNA sequencing, have enabled the analysis of gene expression on the single-cell level, providing a more detailed and accurate picture of gene expression patterns, with single-cell RNA sequencing being most recent technology to be widely used in cancer studies (not limited) to explore the microenvironments of tumour cells.

Overall, the analysis of RNA data is a rapidly evolving field, with new techniques and methods being developed in order to better understand gene expression and regulation. The results of these studies have important implications for our understanding of biological processes, the development of new therapies, and the diagnosis and treatment of diseases.

For this Special Issue, we invite authors to submit original research and review manuscripts aiming to present the most recent advances in RNA biological data analysis.

Dr. Yogesh Kumar
Dr. Sugandh Kumar
Dr. Bharati Mehani
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. 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.

Keywords

  • RNA
  • decoding
  • single-cell RNA
  • non-coding RNA
  • SiRNA
  • 16sRNA
  • RNA data analysis
  • microbiome

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (2 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

16 pages, 9353 KiB  
Article
A Comprehensive Analysis of the Effect of A>I(G) RNA-Editing Sites on Genotoxic Drug Response and Progression in Breast Cancer
by Yanara A. Bernal, Alejandro Blanco, Eduardo A. Sagredo, Karen Oróstica, Ivan Alfaro, Katherine Marcelain and Ricardo Armisén
Biomedicines 2024, 12(4), 728; https://doi.org/10.3390/biomedicines12040728 - 25 Mar 2024
Cited by 2 | Viewed by 1562
Abstract
Dysregulated A>I(G) RNA editing, which is mainly catalyzed by ADAR1 and is a type of post-transcriptional modification, has been linked to cancer. A low response to therapy in breast cancer (BC) is a significant contributor to mortality. However, it remains unclear if there [...] Read more.
Dysregulated A>I(G) RNA editing, which is mainly catalyzed by ADAR1 and is a type of post-transcriptional modification, has been linked to cancer. A low response to therapy in breast cancer (BC) is a significant contributor to mortality. However, it remains unclear if there is an association between A>I(G) RNA-edited sites and sensitivity to genotoxic drugs. To address this issue, we employed a stringent bioinformatics approach to identify differentially RNA-edited sites (DESs) associated with low or high sensitivity (FDR 0.1, log2 fold change 2.5) according to the IC50 of PARP inhibitors, anthracyclines, and alkylating agents using WGS/RNA-seq data in BC cell lines. We then validated these findings in patients with basal subtype BC. These DESs are mainly located in non-coding regions, but a lesser proportion in coding regions showed predicted deleterious consequences. Notably, some of these DESs are previously reported as oncogenic variants, and in genes related to DNA damage repair, drug metabolism, gene regulation, the cell cycle, and immune response. In patients with BC, we uncovered DESs predominantly in immune response genes, and a subset with a significant association (log-rank test p < 0.05) between RNA editing level in LSR, SMPDL3B, HTRA4, and LL22NC03-80A10.6 genes, and progression-free survival. Our findings provide a landscape of RNA-edited sites that may be involved in drug response mechanisms, highlighting the value of A>I(G) RNA editing in clinical outcomes for BC. Full article
(This article belongs to the Special Issue RNA Biology: From Genome to Therapeutic Targets)
Show Figures

Graphical abstract

Review

Jump to: Research

25 pages, 3902 KiB  
Review
Plasma Circular RNAs as Biomarkers for Breast Cancer
by Domenico Tierno, Gabriele Grassi, Fabrizio Zanconati, Barbara Dapas and Bruna Scaggiante
Biomedicines 2024, 12(4), 875; https://doi.org/10.3390/biomedicines12040875 - 16 Apr 2024
Viewed by 1427
Abstract
Breast cancer (BC) is currently the most common neoplasm, the second leading cause of cancer death in women worldwide, and is a major health problem. The discovery of new biomarkers is crucial to improve our knowledge of breast cancer and strengthen our clinical [...] Read more.
Breast cancer (BC) is currently the most common neoplasm, the second leading cause of cancer death in women worldwide, and is a major health problem. The discovery of new biomarkers is crucial to improve our knowledge of breast cancer and strengthen our clinical approaches to diagnosis, prognosis, and follow-up. In recent decades, there has been increasing interest in circulating RNA (circRNA) as modulators of gene expression involved in tumor development and progression. The study of circulating circRNAs (ccircRNAs) in plasma may provide new non-invasive diagnostic, prognostic, and predictive biomarkers for BC. This review describes the latest findings on BC-associated ccircRNAs in plasma and their clinical utility. Several ccircRNAs in plasma have shown great potential as BC biomarkers, especially from a diagnostic point of view. Mechanistically, most of the reported BC-associated ccircRNAs are involved in the regulation of cell survival, proliferation, and invasion, mainly via MAPK/AKT signaling pathways. However, the study of circRNAs is a relatively new area of research, and a larger number of studies will be crucial to confirm their potential as plasma biomarkers and to understand their involvement in BC. Full article
(This article belongs to the Special Issue RNA Biology: From Genome to Therapeutic Targets)
Show Figures

Figure 1

Back to TopTop