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MicroRNA for Cancer Diagnostic: Issues of Isolation, Quantification and Clinical Interpretation

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A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Pathology and Molecular Diagnostics".

Deadline for manuscript submissions: closed (30 April 2021) | Viewed by 24174

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Special Issue Editor

Dr. Anastasia Malek

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Guest Editor

Laboratory of Subcellular Technology, NN Petrov National Medical Research Center of Oncology, St. Petersburg, Russia
Interests: cancer; solid tumor; biopsy; liquid biopsy; miRNA; RT-PCR; thyroid cancer; cervical cancer

Special Issue Information

Dear Colleagues,

Since the discovery of the phenomenon of RNA interference in 1998, microRNA has been attracting a great amount of scientific interest as a natural mediator of this fundamental regulatory mechanism. MicroRNA is a class of short single-stranded RNA molecules that control stability and functionality of the messenger RNA pool and regulate many aspects of cellular biology. To date, more than four thousand miRNA molecules have been identified in human tissues. Cells of different types of tissues have a specific pattern of microRNAs, while their malignant transformation is associated with typical alteration of microRNA profiles. This indicates an option to use microRNA analysis with diagnostic purposes. Although cancer-relevant microRNA expression changes have been reported in a large number of scientific reports, microRNA-based diagnostic tests are still far from wide clinical application. Development of microRNA-based diagnostic tools is challenged by several issues. First, isolation of microRNA from biological material is hampered due to the small size of the molecules: The standard RNA purification protocols suppose large losses of these molecules. Second, the routine method of reverse transcription followed by PCR and sequencing is applicable for miRNA analysis but requires specific tricks overcoming the issues of the small size and the existence of similar and non-mature forms. Third, a robust method of normalization of microRNA expression data has still not been developed.

New approaches to implementing microRNA analysis in the clinical oncology are to be collected and presented in this Special Issue of Diagnostics. Various issues including fundamental aspects of microRNA involvement in certain cancer, methodological problems of microRNA analysis, and results interpretation are welcome to be addressed. Reports of advanced approaches of microRNA detection, such as enzyme-free and label-free platforms, are especially invited.

Dr. Anastasia Malek
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. Diagnostics is an international peer-reviewed open access semimonthly 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

Cancer
Diagnostics
microRNA profiling
microRNA detection
Clinical application

Published Papers (5 papers)

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Research

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17 pages, 598 KiB

Open AccessArticle

A Physically Active Status Affects the Circulating Profile of Cancer-Associated miRNAs

by Martina Faraldi, Laura Gerosa, Marta Gomarasca, Veronica Sansoni, Silvia Perego, Ewa Ziemann, Giuseppe Banfi and Giovanni Lombardi

Diagnostics 2021, 11(5), 820; https://doi.org/10.3390/diagnostics11050820 - 30 Apr 2021

Cited by 2 | Viewed by 1800

Abstract

Circulating miRNAs are ideal diagnostics and prognostics biomarkers in cancer since altered levels of specific miRNAs have been associated to development/progression of several cancers. Physical activity is a recognized preventive strategy against several cancers, but it may also modify the baseline levels of cancer-associated miRNAs and, hence, may act as a confounding pre-analytical variable. This study aimed at understanding whether physical activity-dependent changes in cancer-associated circulating miRNAs profile could act as a confounding variable. A panel comprising 179 miRNAs was assayed in plasma from 20 highly trained and 10 sedentary men. RT-qPCR data were analyzed with the 2^−2ΔΔCT methods and normalized on hsa-miR-320d, as determined by bioinformatics analysis. miRNAs associated with the diagnosis of the most prevalent cancers were considered. Only those miRNAs, relevantly associated with cancers, found ≥2-fold up- or downregulated in highly trained subjects compared to sedentary were disclosed. The results reveal that chronic physical activity determined modifications altering the baseline level of several cancer-associated miRNAs and, hence, their diagnostic and prognostic potential. In conclusion, based on our results, a physically active status emerges as an important pre-analytical variable able to alter the basal level of circulating miRNAs, and these alterations might be considered as potentially misleading the analytical output. Full article

(This article belongs to the Special Issue MicroRNA for Cancer Diagnostic: Issues of Isolation, Quantification and Clinical Interpretation)

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17 pages, 3232 KiB

Open AccessArticle

Identification of MicroRNAs as Diagnostic Biomarkers for Breast Cancer Based on the Cancer Genome Atlas

by Jungho Kim

Diagnostics 2021, 11(1), 107; https://doi.org/10.3390/diagnostics11010107 - 11 Jan 2021

Cited by 17 | Viewed by 3302

Abstract

Breast cancer is the most common cancer among women worldwide. MicroRNAs (miRNAs or miRs) play an important role in tumorigenesis, and thus, they have been identified as potential targets for translational research with diagnostic, prognostic, and therapeutic markers. This study aimed to identify differentially expressed (DE) miRNAs in breast cancer using the Cancer Genome Atlas. The miRNA profiles of 755 breast cancer tissues and 86 adjacent non-cancerous breast tissues were analyzed using Multi Experiment Viewer; miRNA–mRNA network analyses and constructed KEGG pathways with the predicted target genes were performed. The clinical relevance of miRNAs was investigated using area under the receiver operating characteristic curve (AUC) analysis, sensitivity, and specificity. The analysis identified 28 DE miRNAs in breast cancer tissues, including nine upregulated and 19 downregulated miRNAs, compared to non-cancerous breast tissues (p < 0.001). The AUC for each DE miRNA, miR-10b, miR-21, miR-96, miR-99a, miR-100, miR-125b-1, miR-125b-2, miR-139, miR-141, miR-145, miR-182, miR-183, miR-195, miR-200a, miR-337, miR-429, and let-7c, exceeded 0.9, indicating excellent diagnostic performance in breast cancer. Moreover, 1381 potential target genes were predicted using the prediction database tool, miRNet. These genes are related to PD-L1 expression and PD-1 checkpoint in cancer, MAPK signaling, apoptosis, and TNF pathways; hence, they regulate the development, progression, and immune escape of cancer. Thus, these 28 miRNAs can serve as prospective biomarkers for the diagnosis of breast cancer. Taken together, these results provide insight into the pathogenic mechanisms and potential therapies for breast cancer. Full article

(This article belongs to the Special Issue MicroRNA for Cancer Diagnostic: Issues of Isolation, Quantification and Clinical Interpretation)

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Review

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19 pages, 721 KiB

Open AccessReview

Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis

by Sarka Benesova, Mikael Kubista and Lukas Valihrach

Diagnostics 2021, 11(6), 964; https://doi.org/10.3390/diagnostics11060964 - 27 May 2021

Cited by 37 | Viewed by 9669

Abstract

MicroRNAs (miRNAs) are a class of small RNA molecules that have an important regulatory role in multiple physiological and pathological processes. Their disease-specific profiles and presence in biofluids are properties that enable miRNAs to be employed as non-invasive biomarkers. In the past decades, several methods have been developed for miRNA analysis, including small RNA sequencing (RNA-seq). Small RNA-seq enables genome-wide profiling and analysis of known, as well as novel, miRNA variants. Moreover, its high sensitivity allows for profiling of low input samples such as liquid biopsies, which have now found applications in diagnostics and prognostics. Still, due to technical bias and the limited ability to capture the true miRNA representation, its potential remains unfulfilled. The introduction of many new small RNA-seq approaches that tried to minimize this bias, has led to the existence of the many small RNA-seq protocols seen today. Here, we review all current approaches to cDNA library construction used during the small RNA-seq workflow, with particular focus on their implementation in commercially available protocols. We provide an overview of each protocol and discuss their applicability. We also review recent benchmarking studies comparing each protocol’s performance and summarize the major conclusions that can be gathered from their usage. The result documents variable performance of the protocols and highlights their different applications in miRNA research. Taken together, our review provides a comprehensive overview of all the current small RNA-seq approaches, summarizes their strengths and weaknesses, and provides guidelines for their applications in miRNA research. Full article

(This article belongs to the Special Issue MicroRNA for Cancer Diagnostic: Issues of Isolation, Quantification and Clinical Interpretation)

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17 pages, 570 KiB

Open AccessReview

Isolation of Cell-Free miRNA from Biological Fluids: Influencing Factors and Methods

by Olga Bryzgunova, Maria Konoshenko, Ivan Zaporozhchenko, Alexey Yakovlev and Pavel Laktionov

Diagnostics 2021, 11(5), 865; https://doi.org/10.3390/diagnostics11050865 - 11 May 2021

Cited by 23 | Viewed by 4699

Abstract

A vast wealth of recent research has seen attempts of using microRNA (miRNA) found in biological fluids in clinical research and medicine. One of the reasons behind this trend is the apparent their high stability of cell-free miRNA conferred by small size and packaging in supramolecular complexes. However, researchers in both basic and clinical settings often face the problem of selecting adequate methods to extract appropriate quality miRNA preparations for use in specific downstream analysis pipelines. This review outlines the variety of different methods of miRNA isolation from biofluids and examines the key determinants of their efficiency, including, but not limited to, the structural properties of miRNA and factors defining their stability in the extracellular environment. Full article

(This article belongs to the Special Issue MicroRNA for Cancer Diagnostic: Issues of Isolation, Quantification and Clinical Interpretation)

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16 pages, 1881 KiB

Open AccessReview

Clinico-Pathological Importance of miR-146a in Lung Cancer

by Javaid Ahmad Wani, Sabhiya Majid, Andleeb Khan, Azher Arafah, Ajaz Ahmad, Basit Latief Jan, Naveed Nazir Shah, Mohsin Kazi and Muneeb U. Rehman

Diagnostics 2021, 11(2), 274; https://doi.org/10.3390/diagnostics11020274 - 10 Feb 2021

Cited by 21 | Viewed by 3808

Abstract

Lung cancer is a well-known malignant tumor of the respiratory tract, which has caused a significant level of damage to human health in the 21st century. Micro-RNAs (miRNAs) are tiny, non-coding RNA stem-loop structures with a length of roughly 20–25 nucleotides that function as powerful modulators of mRNA and protein products of a gene. miRNAs may modulate many biological processes involving growth, differentiation, proliferation, and cell death and play a key role in the pathogenesis of various types of malignancies. Several accumulating pieces of evidence have proven that miRNA, especially miR-146a, are crucial modulators of innate immune response sequences. A novel and exciting cancer research field has involved miRNA for the detection and suppression of cancer. However, the actual mechanism which is adopted by these miRNA is still unclear. miRNAs have been used as a cancer-associated biomarker in several studies, suggesting their altered expression in various cancers compared to the normal cells. The amount of expression of miRNA can also be used to determine the stage of the disease, aiding in early detection. In breast, pancreatic, and hepatocellular carcinoma, and gastric cancer, cancer cell proliferation and metastasis has been suppressed by miR-146a. Changes in miR-146a expression levels have biomarker importance and possess a high potential as a therapeutic target in lung cancer. It retards epithelial-mesenchymal transition and promotes the therapeutic action of anticancer agents in lung cancer. Studies have also suggested that miR-146a affects gene expression through different signaling pathways viz. TNF-α, NF-κB and MEK-1/2, and JNK-1/2. Further research is required for understanding the molecular mechanisms of miR-146a in lung cancer. The potential role of miR-146a as a diagnostic marker of lung cancer must also be analyzed. This review summarizes the tumor-suppressing, anti-inflammatory, and antichemoresistive nature of miR-146a in lung cancer. Full article

(This article belongs to the Special Issue MicroRNA for Cancer Diagnostic: Issues of Isolation, Quantification and Clinical Interpretation)

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