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Biomedicines
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Role of Non-coding RNAs in Cancer: Markers in Disease Progression...
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Role of Non-coding RNAs in Cancer: Markers in Disease Progression and Therapeutics

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Gene and Cell Therapy".

Deadline for manuscript submissions: closed (15 March 2022) | Viewed by 10314

Special Issue Editor

Dr. Balaji Krishnamachary

E-Mail Website
Guest Editor
Postdoctoral Research Fellow, University of Kansas Medical Center, Kansas City, KS 66160, USA
Interests: extracellular vesicles; colon cancer; non-coding RNAs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Long non-coding RNAs (lncRNAs) are a novel class of non-coding RNAs which are longer than 200 bp and do not have protein-coding ability. The literature suggests that lncRNAs are important regulators of various fundamental cellular processes and have been highlighted as important potential therapeutic targets. The Special Issue would like to focus on the following topics:

  1. Role of circulating non-coding RNAs in cancer diagnosis and progression;
  2. Potential role of lncRNA–miRNA–mRNA and their interactions in cancer diagnosis and therapeutics;
  3. Creating a database of regulatory lncRNAs and its miRNA targets in cancer progression and therapeutics.

Dr. Balaji Krishnamachary
Guest Editor

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

  • lncRNA
  • miRNA
  • m-RNA
  • cancer

Published Papers (5 papers)

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Research

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17 pages, 3774 KiB  
Article
LncRNA SNHG4 Modulates EMT Signal and Antitumor Effects in Endometrial Cancer through Transcription Factor SP-1
by Lee Kyung Kim, Sun-Ae Park, Eun Ji Nam, Young Tae Kim, Tae-Hwe Heo and Hee Jung Kim
Biomedicines 2023, 11(4), 1018; https://doi.org/10.3390/biomedicines11041018 - 27 Mar 2023
Cited by 2 | Viewed by 1248
Abstract
Long non-coding RNAs (lncRNAs) are implicated in the initiation and progression of a variety of tumors, including endometrial cancer. However, the mechanisms of lncRNA in endometrial cancer formation and progression remain largely unknown. In this study, we confirmed that the lncRNA SNHG4 is [...] Read more.
Long non-coding RNAs (lncRNAs) are implicated in the initiation and progression of a variety of tumors, including endometrial cancer. However, the mechanisms of lncRNA in endometrial cancer formation and progression remain largely unknown. In this study, we confirmed that the lncRNA SNHG4 is upregulated in endometrial cancer and correlates with lower survival rates in endometrial cancer patients. Knock-down of SNHG4 significantly reduced cell proliferation, colonization, migration, and invasion in vitro, as well as modulating the cell cycle and reduced tumor growth of endometrial cancer in vivo. In addition, the effect of SNHG4 by the transcription factor SP-1 was confirmed in vitro. We found in this study that SNHG4/SP-1 plays an important role in endometrial cancer progression and may be used as a potential therapeutic and prognostic biomarker for endometrial cancer. Full article
(This article belongs to the Special Issue Role of Non-coding RNAs in Cancer: Markers in Disease Progression and Therapeutics)
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29 pages, 7291 KiB  
Article
The Impact of YRNAs on HNSCC and HPV Infection
by Kacper Guglas, Tomasz Kolenda, Joanna Kozłowska-Masłoń, Patricia Severino, Anna Teresiak, Renata Bliźniak and Katarzyna Lamperska
Biomedicines 2023, 11(3), 681; https://doi.org/10.3390/biomedicines11030681 - 23 Feb 2023
Cited by 2 | Viewed by 1338
Abstract
HPV infection is one of the most important risk factors for head and neck squamous cell carcinoma among younger patients. YRNAs are short non-coding RNAs involved in DNA replication. YRNAs have been found to be dysregulated in many cancers, including head and neck [...] Read more.
HPV infection is one of the most important risk factors for head and neck squamous cell carcinoma among younger patients. YRNAs are short non-coding RNAs involved in DNA replication. YRNAs have been found to be dysregulated in many cancers, including head and neck squamous cell carcinoma (HNSCC). In this study, we investigated the role of YRNAs in HPV-positive HNSCC using publicly available gene expression datasets from HNSCC tissue, where expression patterns of YRNAs in HPV(+) and HPV(−) HNSCC samples significantly differed. Additionally, HNSCC cell lines were treated with YRNA1-overexpressing plasmid and RNA derived from these cell lines was used to perform a NGS analysis. Additionally, a deconvolution analysis was performed to determine YRNA1’s impact on immune cells. YRNA expression levels varied according to cancer pathological and clinical stages, and correlated with more aggressive subtypes. YRNAs were mostly associated with more advanced cancer stages in the HPV(+) group, and YRNA3 and YRNA1 expression levels were found to be correlated with more advanced clinical stages despite HPV infection status, showing that they may function as potential biomarkers of more advanced stages of the disease. YRNA5 was associated with less-advanced cancer stages in the HPV(−) group. Overall survival and progression-free survival analyses showed opposite results between the HPV groups. The expression of YRNAs, especially YRNA1, correlated with a vast number of proteins and cellular processes associated with viral infections and immunologic responses to viruses. HNSCC-derived cell lines overexpressing YRNA1 were then used to determine the correlation of YRNA1 and the expression of genes associated with HPV infections. Taken together, our results highlight the potential of YRNAs as possible HNSCC biomarkers and new molecular targets. Full article
(This article belongs to the Special Issue Role of Non-coding RNAs in Cancer: Markers in Disease Progression and Therapeutics)
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21 pages, 5263 KiB  
Article
Circulating lncRNA- and miRNA-Associated ceRNA Network as a Potential Prognostic Biomarker for Non-Hodgkin Lymphoma: A Bioinformatics Analysis and a Pilot Study
by Mara Fernandes, Herlander Marques, Ana Luísa Teixeira and Rui Medeiros
Biomedicines 2022, 10(6), 1322; https://doi.org/10.3390/biomedicines10061322 - 04 Jun 2022
Cited by 2 | Viewed by 1906
Abstract
Non-Hodgkin lymphoma (NHL) is characterized by a great variability in patient outcomes, resulting in the critical need for identifying new molecular prognostic biomarkers. This study aimed to identify novel circulating prognostic biomarkers based on an miRNA/lncRNA-associated ceRNA network for NHL. Using bioinformatic analysis, [...] Read more.
Non-Hodgkin lymphoma (NHL) is characterized by a great variability in patient outcomes, resulting in the critical need for identifying new molecular prognostic biomarkers. This study aimed to identify novel circulating prognostic biomarkers based on an miRNA/lncRNA-associated ceRNA network for NHL. Using bioinformatic analysis, we identified the miRNA-lncRNA pairs, and using RT-qPCR, we analyzed their plasma levels in a cohort of 113 NHL patients to assess their prognostic value. Bioinformatic analysis identified SNHG16 and SNHG6 as hsa-miR-20a-5p and hsa-miR-181a-5p sponges, respectively. Plasma levels of hsa-miR-20a-5p/SNHG16 and hsa-miR-181a-5p/SNG6 were significantly associated with more aggressive disease and IPI/FLIPI scores. Moreover, we found that patients with risk expression profiles of hsa-miR-20a-5p/SNHG16 and hsa-miR-181a-5p/SNHG6 presented a higher risk of positive bone marrow involvement. Moreover, hsa-miR-20a-5p/SNHG16 and hsa-miR-181a-5p/SNHG6 pairs’ plasma levels were associated with overall survival and progression-free survival of NHL patients, being independent prognostic factors in a multivariate Cox analysis. The prediction models incorporating the ceRNA network expression analysis improved the predictive capacity compared to the model, which only considered the clinicopathological variables. There are still few studies on using the ceRNA network as a potential prognostic biomarker, particularly in NHL, which may permit the implementation of a more personalized management of these patients. Full article
(This article belongs to the Special Issue Role of Non-coding RNAs in Cancer: Markers in Disease Progression and Therapeutics)
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26 pages, 7646 KiB  
Article
miR-154 Influences HNSCC Development and Progression through Regulation of the Epithelial-to-Mesenchymal Transition Process and Could Be Used as a Potential Biomarker
by Weronika Tomaszewska, Joanna Kozłowska-Masłoń, Dawid Baranowski, Anna Perkowska, Sandra Szałkowska, Urszula Kazimierczak, Patricia Severino, Katarzyna Lamperska and Tomasz Kolenda
Biomedicines 2021, 9(12), 1894; https://doi.org/10.3390/biomedicines9121894 - 13 Dec 2021
Cited by 4 | Viewed by 2448
Abstract
MicroRNAs and their role in cancer have been extensively studied for the past decade. Here, we analyzed the biological role and diagnostic potential of miR-154-5p and miR-154-3p in head and neck squamous cell carcinoma (HNSCC). miRNA expression analyses were performed using The Cancer [...] Read more.
MicroRNAs and their role in cancer have been extensively studied for the past decade. Here, we analyzed the biological role and diagnostic potential of miR-154-5p and miR-154-3p in head and neck squamous cell carcinoma (HNSCC). miRNA expression analyses were performed using The Cancer Genome Atlas (TCGA) data accessed from cBioPortal, UALCAN, Santa Cruz University, and Gene Expression Omnibus (GEO). The expression data were correlated with clinicopathological parameters. The functional enrichment was assessed with Gene Set Enrichment Analysis (GSEA). The immunological profiles were assessed using the ESTIMATE tool and RNAseq data from TCGA. All statistical analyses were performed with GraphPad Prism and Statistica. The study showed that both miR-154-5p and miR-154-3p were downregulated in the HNSCC samples and their expression levels correlated with tumor localization, overall survival, cancer stage, tumor grade, and HPV p16 status. GSEA indicated that individuals with the increased levels of miR-154 had upregulated AKT-MTOR, CYCLIN D1, KRAS, EIF4E, RB, ATM, and EMT gene sets. Finally, the elevated miR-154 expression correlated with better immune response. This study showed that miR-154 is highly involved in HNSCC pathogenesis, invasion, and immune response. The implementation of miR-154 as a biomarker may improve the effectiveness of HNSCC treatment. Full article
(This article belongs to the Special Issue Role of Non-coding RNAs in Cancer: Markers in Disease Progression and Therapeutics)
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Review

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13 pages, 772 KiB  
Review
Clinical Implications of Circulating Circular RNAs in Lung Cancer
by Sae Seul Choi, Sae Eun Kim, Seon Young Oh and Young-Ho Ahn
Biomedicines 2022, 10(4), 871; https://doi.org/10.3390/biomedicines10040871 - 08 Apr 2022
Cited by 3 | Viewed by 2376
Abstract
Circular RNAs (circRNAs) are single-stranded RNAs with a covalently closed-loop structure that increases their stability; thus, they are more advantageous to use as liquid biopsy markers than linear RNAs. circRNAs are thought to be generated by back-splicing of pre-mRNA transcripts, which can be [...] Read more.
Circular RNAs (circRNAs) are single-stranded RNAs with a covalently closed-loop structure that increases their stability; thus, they are more advantageous to use as liquid biopsy markers than linear RNAs. circRNAs are thought to be generated by back-splicing of pre-mRNA transcripts, which can be facilitated by reverse complementary sequences in the flanking introns and trans-acting factors, such as splicing regulatory factors and RNA-binding factors. circRNAs function as miRNA sponges, interact with target proteins, regulate the stability and translatability of other mRNAs, regulate gene expression, and produce microproteins. circRNAs are also found in the body fluids of cancer patients, including plasma, saliva, urine, and cerebrospinal fluid, and these “circulating circRNAs” can be used as cancer biomarkers. In lung cancer, some circulating circRNAs have been reported to regulate cancer progression and drug resistance. Circulating circRNAs have significant diagnostic value and are associated with the prognosis of lung cancer patients. Owing to their functional versatility, heightened stability, and practical applicability, circulating circRNAs represent promising biomarkers for lung cancer diagnosis, prognosis, and treatment monitoring. Full article
(This article belongs to the Special Issue Role of Non-coding RNAs in Cancer: Markers in Disease Progression and Therapeutics)
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