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Non-coding RNA (ncRNA) in Cancer 2.0

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

Deadline for manuscript submissions: 31 October 2024 | Viewed by 3714

Special Issue Editors


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Guest Editor
Department of Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
Interests: molecular medicine; novel diagnostic approaches; genetic diseases; cancer; next generation sequencing; mutation detection; non-coding RNAs as biomarkers
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Guest Editor
Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
Interests: regulation of gene expretion through epigenetics and non-coding RNAs; genetic polymorphysms and mutations; non coding RNAs (miRNAs, lncRNAs, circRNAs) as circulating biomarkers in diseases of neurodegeneration and cancer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the last three decades, researchers have discovered multiple types of RNA, including non-coding RNAs (ncRNAs) that are in general not involved in the production of proteins. ncRNAs include small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), guide RNAs (gRNAs), RNaseP RNAs, transfer RNAs (tRNAs), ribosome RNAs (rRNAs), transfer messenger RNAs (tmRNAs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), piwi interaction RNAs (piRNAs), circular RNAs (circRNAs), and Y RNA (YRNA).

ncRNAs constitute almost 60% of the transcriptome of human cells, and are involved in the regulation of cellular processes and pathways in health and disease. The field of non-coding RNA research in cancer started in 2002, only two years after the discovery of the first human miRNA (let-7). In patients with B-cell chronic lymphocytic leukemia, two miRNA genes, mir-15a and mir-16-1, were identified within chromosomal region 13q14. Both miRNAs were either deleted or downregulated, suggesting their potential role as tumor suppressors. Since then, the ncRNA research field has grown exponentially. More recently, two classes of ncRNAs, long non-coding RNA (lncRNA), defined by RNA transcripts longer than 200 nucleotides, and circular RNA (circRNA), defined as endogenous ncRNA that has a non-polyadenylated, closed, single-stranded, and continuous loop structure, have been shown to have a functional role in cancer.

Novel RNA sequencing technologies and bioinformatics approaches have revealed not only novel types of ncRNAs but also elucidated the role of many ncRNAs in carcinogenesis. Usually, different ncRNAs interact with each other and form a highly complex regulatory network that controls important cellular programs. Disturbances to these programs lead to widespread changes in the fate of cells and contribute to development of cancer. A vast amount of data on ncRNAs has been generated, collected, and organized using computational approaches.

In this Special Issue, we will cover recent advances in any of the roles of ncRNA in cancer, such as function, mechanism of action, mode of interaction, as well as clinical studies. We welcome contributions in the form of original research articles and reviews.

Prof. Dr. Damjan Glavač
Prof. Dr. Metka Ravnik-Glavač
Guest Editors

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Keywords

  • non-coding RNA (ncRNA)
  • cancer
  • oncogenes
  • tumor suppressor genes
  • microRNA
  • lncRNA
  • circRNA
  • cancer biomarkers

Published Papers (3 papers)

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Research

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15 pages, 5800 KiB  
Article
Small Non-Coding RNAs and Their Role in Locoregional Metastasis and Outcomes in Early-Stage Breast Cancer Patients
by Daniel Escuin, Olga Bell, Bárbara García-Valdecasas, Montserrat Clos, Itziar Larrañaga, Laura López-Vilaró, Josefina Mora, Marta Andrés, Cristina Arqueros and Agustí Barnadas
Int. J. Mol. Sci. 2024, 25(7), 3982; https://doi.org/10.3390/ijms25073982 - 3 Apr 2024
Viewed by 612
Abstract
Deregulation of small non-coding RNAs (sncRNAs) has been associated with the onset of metastasis. We evaluated the expression of sncRNAs in patients with early-stage breast cancer, performing RNA sequencing in 60 patients for whom tumor and sentinel lymph node (SLN) samples were available, [...] Read more.
Deregulation of small non-coding RNAs (sncRNAs) has been associated with the onset of metastasis. We evaluated the expression of sncRNAs in patients with early-stage breast cancer, performing RNA sequencing in 60 patients for whom tumor and sentinel lymph node (SLN) samples were available, and conducting differential expression, gene ontology, enrichment and survival analyses. Sequencing annotation classified most of the sncRNAs into small nucleolar RNA (snoRNAs, 70%) and small nuclear RNA (snRNA, 13%). Our results showed no significant differences in sncRNA expression between tumor or SLNs obtained from the same patient. Differential expression analysis showed down-regulation (n = 21) sncRNAs and up-regulation (n = 2) sncRNAs in patients with locoregional metastasis. The expression of SNHG5, SNORD90, SCARNA2 and SNORD78 differentiated luminal A from luminal B tumors, whereas SNORD124 up-regulation was associated with luminal B HER2+ tumors. Discriminating analysis and receiver-operating curve analysis revealed a signature of six snoRNAs (SNORD93, SNORA16A, SNORD113-6, SNORA7A, SNORA57 and SNORA18A) that distinguished patients with locoregional metastasis and predicted patient outcome. Gene ontology and Reactome pathway analysis showed an enrichment of biological processes associated with translation initiation, protein targeting to specific cell locations, and positive regulation of Wnt and NOTCH signaling pathways, commonly involved in the promotion of metastases. Our results point to the potential of several sncRNAs as surrogate markers of lymph node metastases and patient outcome in early-stage breast cancer patients. Further preclinical and clinical studies are required to understand the biological significance of the most significant sncRNAs and to validate our results in a larger cohort of patients. Full article
(This article belongs to the Special Issue Non-coding RNA (ncRNA) in Cancer 2.0)
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16 pages, 2394 KiB  
Article
SNHG15-Mediated Localization of Nucleolin at the Cell Protrusions Regulates CDH2 mRNA Expression and Cell Invasion
by Shaoying Chen, Yanchun Zhou, Pei Peng, Liqun Xu, Quandong Tang, Weibin Chen and Wei Gu
Int. J. Mol. Sci. 2023, 24(21), 15600; https://doi.org/10.3390/ijms242115600 - 26 Oct 2023
Cited by 1 | Viewed by 879
Abstract
LncRNAs are emerging as important regulators of gene expression by controlling transcription in the nucleus and by modulating mRNA translation in the cytoplasm. In this study, we reveal a novel function of lncRNA SNHG15 in mediating breast cancer cell invasion through regulating the [...] Read more.
LncRNAs are emerging as important regulators of gene expression by controlling transcription in the nucleus and by modulating mRNA translation in the cytoplasm. In this study, we reveal a novel function of lncRNA SNHG15 in mediating breast cancer cell invasion through regulating the local translation of CDH2 mRNA. We show that SNHG15 preferentially localizes at the cellular protrusions or cell leading edge and that this localization is directed by IMP1, a multifunctional protein involved in many aspects of RNA regulation. We demonstrate that SNHG15 also forms a complex with nucleolin, allowing nucleolin to be co-transported with SNHG15 to the cell protrusions, where the accumulated nucleolin is able to bind to CDH2 mRNA. Interaction with nucleolin stabilizes local CDH2 mRNA and regulates its translation, thus promoting cell invasive potential. Our findings reveal an underlying mechanism by which lncRNA could serve as a carrier to transport a protein regulator into a specific cell compartment to enhance target mRNA expression. Full article
(This article belongs to the Special Issue Non-coding RNA (ncRNA) in Cancer 2.0)
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Review

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37 pages, 2463 KiB  
Review
Breast Cancer Chemoresistance: Insights into the Regulatory Role of lncRNA
by Seyedeh Tayebeh Ahmadpour, Charlotte Orre, Priscila Silvana Bertevello, Delphine Mirebeau-Prunier, Jean-François Dumas and Valérie Desquiret-Dumas
Int. J. Mol. Sci. 2023, 24(21), 15897; https://doi.org/10.3390/ijms242115897 - 2 Nov 2023
Cited by 2 | Viewed by 1793
Abstract
Long noncoding RNAs (lncRNAs) are a subclass of noncoding RNAs composed of more than 200 nucleotides without the ability to encode functional proteins. Given their involvement in critical cellular processes such as gene expression regulation, transcription, and translation, lncRNAs play a significant role [...] Read more.
Long noncoding RNAs (lncRNAs) are a subclass of noncoding RNAs composed of more than 200 nucleotides without the ability to encode functional proteins. Given their involvement in critical cellular processes such as gene expression regulation, transcription, and translation, lncRNAs play a significant role in organism homeostasis. Breast cancer (BC) is the second most common cancer worldwide and evidence has shown a relationship between aberrant lncRNA expression and BC development. One of the main obstacles in BC control is multidrug chemoresistance, which is associated with the deregulation of multiple mechanisms such as efflux transporter activity, mitochondrial metabolism reprogramming, and epigenetic regulation as well as apoptosis and autophagy. Studies have shown the involvement of a large number of lncRNAs in the regulation of such pathways. However, the underlying mechanism is not clearly elucidated. In this review, we present the principal mechanisms associated with BC chemoresistance that can be directly or indirectly regulated by lncRNA, highlighting the importance of lncRNA in controlling BC chemoresistance. Understanding these mechanisms in deep detail may interest the clinical outcome of BC patients and could be used as therapeutic targets to overcome BC therapy resistance. Full article
(This article belongs to the Special Issue Non-coding RNA (ncRNA) in Cancer 2.0)
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