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Biomolecules
Special Issues
ncRNA in Cancer and Tissue Regeneration
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ncRNA in Cancer and Tissue Regeneration

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Genetics".

Deadline for manuscript submissions: closed (15 April 2022) | Viewed by 16254

Special Issue Editors

Dr. Jaqueline Carvalho De Oliveira

E-Mail Website
Guest Editor
Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81530-000, PR, Brazil
Interests: gene regulation; non-coding RNAs; cancer pathways; molecular biomarkers
Dr. Daniela Fiori Gradia

E-Mail Website
Guest Editor
Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81530-000, PR, Brazil
Interests: post transcriptinal regulation; ncRNAs; RNA binding proteins; molecular biology of cancer
Dr. Maria Ines Almeida

E-Mail Website
Guest Editor
ICBAS/i3S, University of Porto, R. Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
Interests: non-coding RNAs; Regenerative Medicine; Cancer; Molecular Biology; Mesenchymal Stem Cells; Osteoarticular diseases

Special Issue Information

Dear Colleagues,

Non-coding RNAs are a large class of transcripts that can be classified according to their size, comprising small and long RNAs. Rapid technological advances in high-throughput sequencing revealed several novel non-coding RNAs to be associated with distinct diseases. Non-coding RNAs can control multiple cellular functions and, among their roles, they act on gene regulation at transcriptional and/or posttranscriptional levels. Non-coding RNAs are involved in numerous biological processes and are associated with multifactorial diseases, although most of them are still underexplored.

The role of non-coding RNA in carcinogenesis is a promising and fascinating research field that has attracted a lot of attention. Although most cancer molecular markers are based on coding genome regions, an increasing number of studies show the suitability of non-coding regions, such as non-coding RNAs. On the other hand, non-coding RNAs are emerging as potential tools for tissue regeneration and repair.

There are still a lot of questions to be solved and many new non-coding RNA candidates to be explored. Thus, it is expected that this Special Issue will shed attractive and stimulating new light on various aspects of non-coding RNA mechanisms in carcinogenesis and in tissue regeneration/repair. Additionally, their potential as diagnosis and prognosis markers will also be explored."

Dr. Jaqueline Carvalho De Oliveira
Dr. Daniela Fiori Gradia
Dr. Maria Ines Almeida 
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. Biomolecules 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 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

  • Cancer
  • microRNA
  • lncRNA
  • circRNA
  • ncRNA
  • Carcionogenesis
  • Molecular markers
  • Cell biology
  • Apoptosis
  • Proliferation
  • Cell cycle
  • Invasion
  • Migration
  • Regenerative Medicine
  • Molecular Biology
  • Mesenchymal Stem Cells
  • Stem Cells
  • Osteoarticular diseases

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Published Papers (5 papers)

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Research

13 pages, 1046 KiB  
Article
Plasma Exosome-Derived microRNAs as Potential Diagnostic and Prognostic Biomarkers in Brazilian Pancreatic Cancer Patients
by Anelis Maria Marin, Sibelle Botogosque Mattar, Rafaela Ferreira Amatuzzi, Roger Chammas, Miyuki Uno, Dalila Luciola Zanette and Mateus Nóbrega Aoki
Biomolecules 2022, 12(6), 769; https://doi.org/10.3390/biom12060769 - 31 May 2022
Cited by 20 | Viewed by 3077
Abstract
Pancreatic cancer represents one of the leading causes of oncological death worldwide. A combination of pancreatic cancer aggressiveness and late diagnosis are key factors leading to a low survival rate and treatment inefficiency, and early diagnosis is pursued as a critical factor for [...] Read more.
Pancreatic cancer represents one of the leading causes of oncological death worldwide. A combination of pancreatic cancer aggressiveness and late diagnosis are key factors leading to a low survival rate and treatment inefficiency, and early diagnosis is pursued as a critical factor for pancreatic cancer. In this context, plasma microRNAs are emerging as promising players due to their non-invasive and practical usage in oncological diagnosis and prognosis. Recent studies have showed some miRNAs associated with pancreatic cancer subtypes, or with stages of the disease. Here we demonstrate plasma exosome-derived microRNA expression in pancreatic cancer patients and healthy individuals from Brazilian patients. Using plasma of 65 pancreatic cancer patients and 78 healthy controls, plasma exosomes were isolated and miRNAs miR-27b, miR-125b-3p, miR-122-5p, miR-21-5p, miR-221-3p, miR-19b, and miR-205-5p were quantified by RT-qPCR. We found that miR-125b-3p, miR-122-5p, and miR-205-5p were statistically overexpressed in the plasma exosomes of pancreatic cancer patients compared to healthy controls. Moreover, miR-205-5p was significantly overexpressed in European descendants, in patients with tumor progression and in those who died from the disease, and diagnostic ability by ROC curve was 0.86. Therefore, we demonstrate that these three microRNAs are potential plasma exosome-derived non-invasive biomarkers for the diagnosis and prognosis of Brazilian pancreatic cancer, demonstrating the importance of different populations and epidemiological bias. Full article
(This article belongs to the Special Issue ncRNA in Cancer and Tissue Regeneration)
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19 pages, 6129 KiB  
Article
Decrease in RNase HII and Accumulation of lncRNAs/DNA Hybrids: A Causal Implication in Psoriasis?
by Ecmel Mehmetbeyoglu, Leila Kianmehr, Murat Borlu, Zeynep Yilmaz, Seyma Basar Kılıc, Hassan Rajabi-Maham, Serpil Taheri and Minoo Rassoulzadegan
Biomolecules 2022, 12(3), 368; https://doi.org/10.3390/biom12030368 - 25 Feb 2022
Cited by 5 | Viewed by 2938
Abstract
Functional long non-coding RNAs (lncRNAs) have been in the limelight in aging research because short telomeres are associated with higher levels of TERRA (Telomeric Repeat containing RNA). The genomic instability, which leads to short telomeres, is a mechanism observed in cell aging and [...] Read more.
Functional long non-coding RNAs (lncRNAs) have been in the limelight in aging research because short telomeres are associated with higher levels of TERRA (Telomeric Repeat containing RNA). The genomic instability, which leads to short telomeres, is a mechanism observed in cell aging and in a class of cancer cells. Psoriasis, a skin disease, is a disorder of epidermal keratinocytes, with altered telomerase activity. Research on the fraction of nascent RNAs in hybrid with DNA offers avenues for new strategies. Skin and blood samples from patients were fractionated to obtain the RNA associated with DNA as a R-loop structure. The higher amount of TERRA levels attached with each chromosome end was found with psoriasis patients in blood and skin. In addition to telomeric TERRA, we evidenced accumulation of others non-coding RNA, such as non-telomeric TERRA and centromeric transcripts. Increased levels of non-coding RNAs attached to DNA correlates with a decreased in Ribonuclease HII (RNase-HII) transcript which means that overall unresolved DNA–RNA hybrids can ultimately weaken DNA and cause skin lesions. Since the genome is actively transcribed, cellular RNase-HII is essential for removing RNA from the DNA–RNA hybrid in controls of genome stability and epigenome shaping and can be used as a causal prognostic marker in patients with psoriasis. Full article
(This article belongs to the Special Issue ncRNA in Cancer and Tissue Regeneration)
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16 pages, 2542 KiB  
Article
Transcribed Ultraconserved Regions Are Associated with Clinicopathological Features in Breast Cancer
by Erika Pereira Zambalde, Douglas Adamoski, Daniela Fiori Gradia, Iris Rabinovich, Ana Carolina Rodrigues, Cristina Ivan, Enilze M. S. F. Ribeiro, George Adrian Calin and Jaqueline Carvalho de Oliveira
Biomolecules 2022, 12(2), 214; https://doi.org/10.3390/biom12020214 - 26 Jan 2022
Cited by 2 | Viewed by 2573
Abstract
Ultraconserved regions (UCRs) are 481 genome segments, with length longer than 200 bp, that are 100% conserved among humans, mice, and rats. The majority of UCRs are transcriptionally active (T-UCRs) as many of them produce non-coding RNAs. In a previous study, we evaluated [...] Read more.
Ultraconserved regions (UCRs) are 481 genome segments, with length longer than 200 bp, that are 100% conserved among humans, mice, and rats. The majority of UCRs are transcriptionally active (T-UCRs) as many of them produce non-coding RNAs. In a previous study, we evaluated the expression level of T-UCRs in breast cancer (BC) patients and found that 63% of transcripts correlated with some clinical and/or molecular parameter of BC. In this study, we delved into the expression levels of 12 T-UCRs and correlated them with clinicopathological parameters, immunohistochemical markers, and overall survival in two breast cancer cohorts: TCGA and Brazilian patients. We found that uc.268 is more expressed in TCGA patients under 40 years of age, associated with progesterone receptor (PR) and estrogen receptor (ER), and its high expression is found in luminal A. Lower uc.84 and uc.376 were respectively observed in metastatic and stage IV tumors associated with good prognostic in luminal B. Moreover, uc.84 was only related to the HER2+, while uc.376 was related to ER+ and PR+, and HER2+. A panel composed of uc.147, uc.271, and uc.427 distinguished luminal A from triple negative patients with an AUC of 0.9531 (sensitivity 92.19% and specificity 86.76%). These results highlight the potential role of T-UCRs in BC and provide insights into the potential application of T-UCRs as biomarkers. Full article
(This article belongs to the Special Issue ncRNA in Cancer and Tissue Regeneration)
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17 pages, 2846 KiB  
Article
MiR-182-5p Modulates Prostate Cancer Aggressive Phenotypes by Targeting EMT Associated Pathways
by Marilesia Ferreira Souza, Ilce Mara Syllos Cólus, Aline Simoneti Fonseca, Valquíria Casanova Antunes, Deepak Kumar and Luciane Regina Cavalli
Biomolecules 2022, 12(2), 187; https://doi.org/10.3390/biom12020187 - 22 Jan 2022
Cited by 13 | Viewed by 3402
Abstract
Prostate cancer (PCa) is a clinically heterogeneous disease, where deregulation of epigenetic events, such as miRNA expression alterations, are determinants for its development and progression. MiR-182-5p, a member of the miR-183 family, when overexpressed has been associated with PCa tumor progression and decreased [...] Read more.
Prostate cancer (PCa) is a clinically heterogeneous disease, where deregulation of epigenetic events, such as miRNA expression alterations, are determinants for its development and progression. MiR-182-5p, a member of the miR-183 family, when overexpressed has been associated with PCa tumor progression and decreased patients’ survival rates. In this study, we determined the regulatory role of miR-182-5p in modulating aggressive tumor phenotypes in androgen-refractory PCa cell lines (PC3 and DU-145). The transient transfection of the cell lines with miR-182-5p inhibitor and mimic systems, significantly affected cell proliferation, adhesion, migration, and the viability of the cells to the chemotherapeutic agents, docetaxel, and abiraterone. It also affected the protein expression levels of the tumor progression marker pAKT. These changes, however, were differentially observed in the cell lines studied. A comprehensive biological and functional enrichment analysis and miRNA/mRNA interaction revealed its strong involvement in the epithelial-mesenchymal transition (EMT) process; expression analysis of EMT markers in the PCa transfected cells directly or indirectly modulated the analyzed tumor phenotypes. In conclusion, miR-182-5p differentially impacts tumorigenesis in androgen-refractory PCa cells, in a compatible oncomiR mode of action by targeting EMT-associated pathways. Full article
(This article belongs to the Special Issue ncRNA in Cancer and Tissue Regeneration)
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17 pages, 2790 KiB  
Article
Long Non-Coding RNAs Associated with Ribosomes in Human Adipose-Derived Stem Cells: From RNAs to Microproteins
by Bernardo Bonilauri, Fabiola Barbieri Holetz and Bruno Dallagiovanna
Biomolecules 2021, 11(11), 1673; https://doi.org/10.3390/biom11111673 - 11 Nov 2021
Cited by 9 | Viewed by 3299
Abstract
Ribosome profiling reveals the translational dynamics of mRNAs by capturing a ribosomal footprint snapshot. Growing evidence shows that several long non-coding RNAs (lncRNAs) contain small open reading frames (smORFs) that are translated into functional peptides. The difficulty in identifying bona-fide translated smORFs is [...] Read more.
Ribosome profiling reveals the translational dynamics of mRNAs by capturing a ribosomal footprint snapshot. Growing evidence shows that several long non-coding RNAs (lncRNAs) contain small open reading frames (smORFs) that are translated into functional peptides. The difficulty in identifying bona-fide translated smORFs is a constant challenge in experimental and bioinformatics fields due to their unconventional characteristics. This motivated us to isolate human adipose-derived stem cells (hASC) from adipose tissue and perform a ribosome profiling followed by bioinformatics analysis of transcriptome, translatome, and ribosome-protected fragments of lncRNAs. Here, we demonstrated that 222 lncRNAs were associated with the translational machinery in hASC, including the already demonstrated lncRNAs coding microproteins. The ribosomal occupancy of some transcripts was consistent with the translation of smORFs. In conclusion, we were able to identify a subset of 15 lncRNAs containing 35 smORFs that likely encode functional microproteins, including four previously demonstrated smORF-derived microproteins, suggesting a possible dual role of these lncRNAs in hASC self-renewal. Full article
(This article belongs to the Special Issue ncRNA in Cancer and Tissue Regeneration)
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