The Role of Small RNAs as Cancer Biomarkers: Biology and Clinical Potential Application

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Medical Research".

Deadline for manuscript submissions: closed (26 May 2023) | Viewed by 4281

Special Issue Editors


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Guest Editor
Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 04107 Leipzig, Germany
Interests: cancer; non-coding RNAs; bioinformatics; sequence analysis; expression analysis; network analysis

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Guest Editor
Canadian Food Inspection Agency, Township Road 9-1, Postal Box 640, Lethbridge, AB T1J 3Z4, Canada
Interests: bioinformatics; genomics; transcriptomics; liquid biopsy; oncology; proteomics; computational biology; sequencing

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Guest Editor
Department of Biological Sciences, University at Albany, State University of New York (SUNY), Albany, NY 12222, USA
Interests: non-coding RNAs; muscle degenerative diseases
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Special Issue Information

Dear Colleagues,

Small RNA molecules include all types of RNA that are transcribed from a gene that can reach up to 35–40 nucleotides and are not translated. These include many molecular subtypes, such as miRNAs, piRNAs, siRNAs, snRNAs, and snoRNAs. In addition to these subtypes, some recent works have also reported small RNAs derived from longer molecules such as tRNAs, mRNAs, lncRNAs, and vault RNAs. These molecules play an important role in regulating cellular processes such as growth, differentiation, apoptosis, migration, and other metabolic functions. 

Therefore, the abnormal expression, sequence alteration, or molecular modification of different small RNAs have been used as potential new biomarkers for diagnosis, prognosis, and even drug targets for known challenging human diseases such as cancer. These small molecules are very important for the regulation of multiple systems, and new publications show new associations with tumor growth, metastasis, apoptosis resistance, the promotion/avoidance of immune response, or drug resistance. 

In addition, it was already shown that anomalies in small ncRNAs are not only found in tumors but also in liquid-derived samples, such as milk (for breast tumors), urine (for prostate tumors), and plasma (for other types of tumors). Many small RNA types have more molecular stability when outside of the cell, and therefore they may be better biomarkers in these types of liquid samples compared to larger RNAs.

Although most publications with small RNAs associate miRNAs to biomarker discovery in tumors, there is more evidence of other small RNA types involved in this human disease with multiple challenges in diagnosis, prognosis, and treatment target. There is a great deal of room for new research aiming to better understand tumors.

This Special Issue aims to publish novel research articles and reviews regarding any or multiple types of small RNAs associated with potential biomarkers in cancer research for diagnosis, prognosis, or treatment target. We welcome original research papers using molecular biology, bioinformatics, genetics, cell biology and general medical sciences in order to help patients with the disease to have a better life expectancy.  

Dr. Natasha de Nogueira Jorge
Dr. Gabriel Wajnberg
Dr. Bijan Dey
Guest Editors

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Keywords

  • small RNA
  • miRNA
  • cancer
  • molecular biology
  • sequencing
  • transcriptomics

Published Papers (2 papers)

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Research

19 pages, 1528 KiB  
Article
Alteration in Levels of Specific miRNAs and Their Potential Protein Targets between Human Pancreatic Cancer Samples, Adjacent Normal Tissue, and Xenografts Derived from These Tumors
by Fiona O’Neill, Taylor-Jade Allen-Coyle, Sandra Roche, Justine Meiller, Neil T. Conlon, Niall Swan, Robert M. Straubinger, Justin Geoghegan, Ninfa L. Straubinger, Kevin Conlon, Ray McDermott, Finbarr O’Sullivan, Michael Henry, Paula Meleady, Gerard McVey, Robert O’Connor, Michael Moriarty and Martin Clynes
Life 2023, 13(3), 608; https://doi.org/10.3390/life13030608 - 22 Feb 2023
Cited by 1 | Viewed by 1890
Abstract
Herein, we describe the global comparison of miRNAs in human pancreatic cancer tumors, adjacent normal tissue, and matched patient-derived xenograft models using microarray screening. RNA was extracted from seven tumor, five adjacent normal, and eight FI PDX tumor samples and analyzed by Affymetrix [...] Read more.
Herein, we describe the global comparison of miRNAs in human pancreatic cancer tumors, adjacent normal tissue, and matched patient-derived xenograft models using microarray screening. RNA was extracted from seven tumor, five adjacent normal, and eight FI PDX tumor samples and analyzed by Affymetrix GeneChip miRNA 4.0 array. A transcriptome analysis console (TAC) was used to generate comparative lists of up- and downregulated miRNAs for the comparisons, tumor vs. normal and F1 PDX vs. tumor. Particular attention was paid to miRNAs that were changed in the same direction in both comparisons. We identified the involvement in pancreatic tumor tissue of several miRNAs, including miR4534, miR3154, and miR4742, not previously highlighted as being involved in this type of cancer. Investigation in the parallel mRNA and protein lists from the same samples allowed the elimination of proteins where altered expression correlated with corresponding mRNA levels and was thus less likely to be miRNA regulated. Using the remaining differential expression protein lists for proteins predicted to be targeted for differentially expressed miRNA on our list, we were able to tentatively ascribe specific protein changes to individual miRNA. Particularly interesting target proteins for miRs 615-3p, 2467-3p, 4742-5p, 509-5p, and 605-3p were identified. Prominent among the protein targets are enzymes involved in aldehyde metabolism and membrane transport and trafficking. These results may help to uncover vulnerabilities that could enable novel approaches to treating pancreatic cancer. Full article
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15 pages, 2023 KiB  
Article
Lipid Handling Protein Gene Expression in Colorectal Cancer: CD36 and Targeting miRNAs
by Andrei Marian Niculae, Maria Dobre, Vlad Herlea, Florina Vasilescu, Laura Cristina Ceafalan, Bogdan Trandafir, Elena Milanesi and Mihail Eugen Hinescu
Life 2022, 12(12), 2127; https://doi.org/10.3390/life12122127 - 16 Dec 2022
Cited by 1 | Viewed by 1790
Abstract
The reprogramming of lipid metabolism has been highlighted in colorectal cancer (CRC) studies, suggesting a critical role for the scavenger receptor CD36 and fatty acid synthase (FASN) in this malignancy. In this study, we analyzed the gene expression levels of CD36, FASN, the [...] Read more.
The reprogramming of lipid metabolism has been highlighted in colorectal cancer (CRC) studies, suggesting a critical role for the scavenger receptor CD36 and fatty acid synthase (FASN) in this malignancy. In this study, we analyzed the gene expression levels of CD36, FASN, the cell surface glypican 4 (GPC4), and the two transporters SLC27A3 and SLC27A4 in 39 paired tumoral and peritumoral tissues from patients with CRC compared with 18 normal colonic mucosae. Moreover, the levels of seven miRNAs targeting CD36 and most of the analyzed genes were evaluated. We found a significant impairment of the expression of all the analyzed genes except GPC4 as well as the differential expression of miR-16-5p, miR-26b-5p, miR-107, miR-195-5p, and miR-27a-3p in the colonic mucosa of CRC patients. Interestingly, CD36 and miR-27a-3p were downregulated and upregulated, respectively, in tumoral tissues compared to peritumoral and control tissues, with a significant negative correlation in the group of patients developing lymph node metastasis. Our results sustain the relationship between CRC and fatty acid metabolism and emphasize the importance of related miRNAs in developing new therapeutic strategies. Full article
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