MicroRNA: Mechanisms of Action, Physio-Pathological Implications, and Disease Biomarkers, 3rd Edition

Topic Information

Dear Colleagues,

MicroRNAs (miRNAs) are known to be one of the most widespread non-coding RNAs, contributing to a wide range of biological processes including disease development. Thus, it is critically important to understand the mechanisms by which various miRNAs mediate the post-transcriptional regulation of gene expression. miRNA functions have been extensively investigated in experiments and clinical studies. The exploration of miRNA disease or diagnosis biomarkers has become a popular research topic in recent years. In addition to investigating miRNA biomarkers and miRNA mechanisms, miRNA-based therapeutics such as treatment targeting miRNAs or miRNA drug discovery present potentially challenging tasks for researchers. Diagnosis using miRNA biomarkers and treatment targeting miRNAs are useful strategies in the development of personalized medicine. Moreover, the sequence of many miRNAs is found to be conserved among different organisms. The exploration of miRNA conservation may be beneficial for developing antivirus therapy for variant viruses such as those of coronavirus.

This Topic invites submissions of reviews and original papers that cover any type of innovative miRNA research, including the study of miRNA functionality via both biological and computational methods, clinical studies addressing miRNA biomarkers and miRNA evolution, and the study of other related subjects. First Version: https://www.mdpi.com/topics/microRNA, Second Version: https://www.mdpi.com/topics/2RQC1YG7QD.

Prof. Dr. Hsiuying Wang
Prof. Dr. Y-h. Taguchi
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Biomolecules biomolecules	4.8	9.4	2011	18.4 Days	CHF 2700	Submit
Cells cells	5.1	9.9	2012	17 Days	CHF 2700	Submit
Genes genes	2.8	5.2	2010	14.9 Days	CHF 2600	Submit
Non-Coding RNA ncrna	3.6	6.7	2015	26.8 Days	CHF 1800	Submit
International Journal of Molecular Sciences ijms	4.9	8.1	2000	16.8 Days	CHF 2900	Submit

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Published Papers (4 papers)

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All Biomolecules Cells Genes ncRNA IJMS

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26 pages, 2988 KiB  

Open AccessArticle

A Multi-Input Neural Network Model for Accurate MicroRNA Target Site Detection

by Mohammad Mohebbi, Amirhossein Manzourolajdad, Ethan Bennett and Phillip Williams

Non-Coding RNA 2025, 11(2), 23; https://doi.org/10.3390/ncrna11020023 - 7 Mar 2025

Viewed by 540

Abstract

(1) Background: MicroRNAs are non-coding RNA sequences that regulate cellular functions by targeting messenger RNAs and inhibiting protein synthesis. Identifying their target sites is vital to understanding their roles. However, it is challenging due to the high cost and time demands of experimental [...] Read more.

(1) Background: MicroRNAs are non-coding RNA sequences that regulate cellular functions by targeting messenger RNAs and inhibiting protein synthesis. Identifying their target sites is vital to understanding their roles. However, it is challenging due to the high cost and time demands of experimental methods and the high false-positive rates of computational approaches. (2) Methods: We introduce a Multi-Input Neural Network (MINN) algorithm that integrates diverse biologically relevant features, including the microRNA duplex structure, substructures, minimum free energy, and base-pairing probabilities. For each feature derived from a microRNA target-site duplex, we create a corresponding image. These images are processed in parallel by the MINN algorithm, allowing it to learn a comprehensive and precise representation of the underlying biological mechanisms. (3) Results: Our method, on an experimentally validated test set, detects target sites with an AUPRC of 0.9373, Precision of 0.8725, and Recall of 0.8703 and outperforms several commonly used computational methods of microRNA target-site predictions. (4) Conclusions: Incorporating diverse biologically explainable features, such as duplex structure, substructures, their MFEs, and binding probabilities, enables our model to perform well on experimentally validated test data. These features, rather than nucleotide sequences, enhance our model to generalize beyond specific sequence contexts and perform well on sequentially distant samples. Full article

(This article belongs to the Topic MicroRNA: Mechanisms of Action, Physio-Pathological Implications, and Disease Biomarkers, 3rd Edition)

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13 pages, 2242 KiB  

Open AccessArticle

Small G Protein Regulates Virus Infection via MiRNA and Autophagy in Shrimp

by Yaodong He, Yiqi Hu and Ting Ye

Biomolecules 2025, 15(2), 277; https://doi.org/10.3390/biom15020277 - 13 Feb 2025

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Abstract

Recently, there has been a burgeoning scholarly interest in elucidating the functional significance and regulatory mechanisms underlying the involvement of small G proteins, such as Rab, in the antiviral immune response of crustaceans. Rab is a member of the small G protein family [...] Read more.

Recently, there has been a burgeoning scholarly interest in elucidating the functional significance and regulatory mechanisms underlying the involvement of small G proteins, such as Rab, in the antiviral immune response of crustaceans. Rab is a member of the small G protein family and plays a crucial role in the transport of cell membranes within eukaryotic cells. It is involved in the movement of cell membranes both within the cell and on its surface, aiding in the entry of effector proteins into specific membrane subregions. While previous research has highlighted the importance of Rab in phagosome formation and maturation, as well as the clearance of innate immune pathogens by phagocytes, its role in regulating autophagy and the antiviral mechanism remains unclear. This study focused on Rab10 and its role in the autophagy pathway within shrimp, as it pertains to defending against viral infections. MiRNA targeting Rab10 was analyzed and verified by bioinformatic methods. It was found that inhibition of miR-2c could enhance the shrimp’s ability to combat viral infections. This discovery suggests a potential new strategy for screening antiviral drugs. In summation, this investigation augments our comprehension of the antiviral mechanism associated with Rab10, illuminating its significance in the antiviral immune response of shrimp. Full article

(This article belongs to the Topic MicroRNA: Mechanisms of Action, Physio-Pathological Implications, and Disease Biomarkers, 3rd Edition)

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14 pages, 1508 KiB  

Open AccessArticle

New Insights on the miRNA Role in Diabetic Tendinopathy: Adipose-Derived Mesenchymal Stem Cell Conditioned Medium as a Potential Innovative Epigenetic-Based Therapy for Tendon Healing

by Marina Russo, Caterina Claudia Lepre, Gianluca Conza, Nicoletta Tangredi, Giovanbattista D’Amico, Adriano Braile, Antimo Moretti, Umberto Tarantino, Francesca Gimigliano, Michele D’Amico, Maria Consiglia Trotta and Giuseppe Toro

Biomolecules 2025, 15(2), 264; https://doi.org/10.3390/biom15020264 - 11 Feb 2025

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Abstract

Background: Adipose-derived mesenchymal stem cell conditioned medium (ASC-CM) improved the viability and wound closure of human tenocytes (HTCN) exposed to high glucose (HG) by activating the transforming growth factor beta 1 (TGF-β1) pathway. Objectives: Since ASC-CM can also modulate microRNAs (miRNAs) in recipient [...] Read more.

Background: Adipose-derived mesenchymal stem cell conditioned medium (ASC-CM) improved the viability and wound closure of human tenocytes (HTCN) exposed to high glucose (HG) by activating the transforming growth factor beta 1 (TGF-β1) pathway. Objectives: Since ASC-CM can also modulate microRNAs (miRNAs) in recipient cells, this study investigated the effects of ASC-CM on the miRNAs regulating tendon repair (miR-29a-3p, miR-210-3p and miR-21-5p) in HG-HTNC. Methods: ASC-CM was obtained by ASCs isolated from the abdominal fat tissue of seven non-diabetic patients. HTNC were cultured in HG for 20 days, then scratched and exposed for 24 h to ASC-CM. qRT-PCR and ELISAs assessed miRNA and target levels. Results: HG-HTNC exhibited a significant downregulation of miRNAs. ASC-CM restored the levels of miRNAs and their related targets involved in tendon repair. Conclusions: The epigenetic modulation observed in HG-HTNC exposed to ASC-CM could be an innovative option in the management of diabetic tendinopathy. Full article

(This article belongs to the Topic MicroRNA: Mechanisms of Action, Physio-Pathological Implications, and Disease Biomarkers, 3rd Edition)

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17 pages, 1920 KiB  

Open AccessReview

The Role of microRNA in the Regulation of Differentiation and the Functionality of Osteoblasts, Osteoclasts, and Their Precursors in Osteoporosis

by Bulat I. Yalaev, Elena I. Kaletnik, Yulia S. Karpova, Zhanna E. Belaya, Ildar R. Minniakhmetov, Natalia G. Mokrysheva and Rita I. Khusainova

Non-Coding RNA 2025, 11(1), 14; https://doi.org/10.3390/ncrna11010014 - 8 Feb 2025

Viewed by 879

Abstract

Osteoporosis is a complex disease that is affected by a variety of factors, including genetic and epigenetic influences. While DNA markers for osteoporosis have been identified, they do not fully explain the hereditary basis of the disease. Epigenetic factors, such as small microRNAs [...] Read more.

Osteoporosis is a complex disease that is affected by a variety of factors, including genetic and epigenetic influences. While DNA markers for osteoporosis have been identified, they do not fully explain the hereditary basis of the disease. Epigenetic factors, such as small microRNAs (miRNAs), may provide a missing link in understanding the molecular mechanisms underlying osteoporosis. miRNAs are a class of non-coding RNAs that play a role in the epigenetic regulation of gene expression. They are known to be involved in various biological processes, including bone formation and remodelling. Differential expression of miRNAs has been linked to the pathological decrease in bone mineral density associated with osteoporosis. It has been shown that an abnormal miRNA expression pattern leads to a decrease in osteoblast activity and an increase in osteoclast activity. Further research into the role of miRNAs in osteoporosis may help to better understand this disease and identify potential therapeutic targets for treatment. Based on these assumptions, the study of miRNA expression patterns in osteoblasts, osteoclasts, and their precursors under normal and osteoporotic conditions is a rapidly growing field of scientific research. Although the results of this research are still incomplete and sometimes contradictory, they require additional scientific analysis to better understand the complex mechanisms involved. The purpose of this paper is to review the current research on miRNAs specifically expressed in osteoblasts and osteoclasts under both normal and pathological conditions. We will also discuss the potential applications of these miRNAs as biomarkers for osteoporosis diagnosis and as targets for osteoporosis treatment. Full article

(This article belongs to the Topic MicroRNA: Mechanisms of Action, Physio-Pathological Implications, and Disease Biomarkers, 3rd Edition)

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