Special Issue "Regulatory microRNA"

A special issue of Cells (ISSN 2073-4409).

Deadline for manuscript submissions: 31 October 2018

Special Issue Editors

Guest Editor
Prof. Dr. Y-h. Taguchi

Department of Physics, Chuo University, Tokyo, Japan
Website | E-Mail
Phone: +81 3 3817 1791
Fax: +81 3 3817 1792
Interests: gene expression analysis; microRNA regulation of target genes; multivariate analysis; feature extraction
Guest Editor
Prof. Hsiuying Wang

Institute of Statistics, National Chiao Tung University, Hsinchu,Taiwan
Website | E-Mail
Interests: microRNA; phylogenetic tree; anti-NMDA receptor encephalitis

Special Issue Information

Dear Colleagues,

MicroRNAs (miRNAs), short non-coding RNAs, have been shown to be involved in the pathogenesis of many human disorders, ranging from cancers to autoimmune diseases. However, the role of microRNA in its detailed mechanisms about the initiation and progression of these diseases is still quite uncharacterized. Therefore, researches describe their mechanisms of actions, expression patterns and cellular pathways are especially important. This Special Issue seeks reviews and original papers covering a wide range of topics related to microRNA biology, such as miRNA therapeutics, miRNA regulation in various disorders (cancer, metabolism, autoimmunity or others), function of interactions between microRNAs and target genes, pathway analysis, and other related interesting topics.

Prof. Y-h. Taguchi
Prof. Hsiuying Wang
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 papers will be 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. Cells 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 1000 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

  • miRNA regulation
  • biomarker
  • pathway analysis
  • cancer, metabolism and diabetes, autoimmunity, aging
  • target genes
  • expression patterns

Published Papers (6 papers)

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Research

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Open AccessArticle Relationship between Altered miRNA Expression and DNA Methylation of the DLK1-DIO3 Region in Azacitidine-Treated Patients with Myelodysplastic Syndromes and Acute Myeloid Leukemia with Myelodysplasia-Related Changes
Received: 14 August 2018 / Revised: 5 September 2018 / Accepted: 11 September 2018 / Published: 14 September 2018
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Abstract
The DLK1–DIO3 region contains a large miRNA cluster, the overexpression of which has previously been associated with myelodysplastic syndromes (MDS). To reveal whether this overexpression is epigenetically regulated, we performed an integrative analysis of miRNA/mRNA expression and DNA methylation of the regulatory sequences
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The DLK1–DIO3 region contains a large miRNA cluster, the overexpression of which has previously been associated with myelodysplastic syndromes (MDS). To reveal whether this overexpression is epigenetically regulated, we performed an integrative analysis of miRNA/mRNA expression and DNA methylation of the regulatory sequences in the region (promoter of the MEG3 gene) in CD34+ bone marrow cells from the patients with higher-risk MDS and acute myeloid leukemia with myelodysplasia-related changes (AML-MRC), before and during hypomethylating therapy with azacytidine (AZA). Before treatment, 50% of patients showed significant miRNA/mRNA overexpression in conjunction with a diagnosis of AML-MRC. Importantly, increased level of MEG3 was associated with poor outcome. After AZA treatment, the expression levels were reduced and were closer to those seen in the healthy controls. In half of the patients, we observed significant hypermethylation in a region preceding the MEG3 gene that negatively correlated with expression. Interestingly, this hypermethylation (when found before treatment) was associated with longer progression-free survival after therapy initiation. However, neither expression nor methylation status were associated with future responsiveness to AZA treatment. In conclusion, we correlated expression and methylation changes in the DLK1–DIO3 region, and we propose a complex model for regulation of this region in myelodysplasia. Full article
(This article belongs to the Special Issue Regulatory microRNA)
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Open AccessArticle Integration of miRNA and mRNA Co-Expression Reveals Potential Regulatory Roles of miRNAs in Developmental and Immunological Processes in Calf Ileum during Early Growth
Received: 13 August 2018 / Revised: 3 September 2018 / Accepted: 5 September 2018 / Published: 11 September 2018
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Abstract
This study aimed to investigate the potential regulatory roles of miRNAs in calf ileum developmental transition from the pre- to the post-weaning period. For this purpose, ileum tissues were collected from eight calves at the pre-weaning period and another eight calves at the
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This study aimed to investigate the potential regulatory roles of miRNAs in calf ileum developmental transition from the pre- to the post-weaning period. For this purpose, ileum tissues were collected from eight calves at the pre-weaning period and another eight calves at the post-weaning period and miRNA expression characterized by miRNA sequencing, followed by functional analyses. A total of 388 miRNAs, including 81 novel miRNAs, were identified. A total of 220 miRNAs were differentially expressed (DE) between the two periods. The potential functions of DE miRNAs in ileum development were supported by significant enrichment of their target genes in gene ontology terms related to metabolic processes and transcription factor activities or pathways related to metabolism (peroxisomes), vitamin digestion and absorption, lipid and protein metabolism, as well as intracellular signaling. Integration of DE miRNAs and DE mRNAs revealed several DE miRNA-mRNA pairs with crucial roles in ileum development (bta-miR-374a—FBXO18, bta-miR-374a—GTPBP3, bta-miR-374a—GNB2) and immune function (bta-miR-15b—IKBKB). This is the first integrated miRNA-mRNA analysis exploring the potential roles of miRNAs in calf ileum growth and development during early life. Full article
(This article belongs to the Special Issue Regulatory microRNA)
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Open AccessArticle Predicting MicroRNA Mediated Gene Regulation between Human and Viruses
Received: 26 June 2018 / Revised: 2 August 2018 / Accepted: 6 August 2018 / Published: 8 August 2018
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Abstract
MicroRNAs (miRNAs) mediate various biological processes by actively fine-tuning gene expression at the post-transcriptional level. With the identification of numerous human and viral miRNAs, growing evidence has indicated a common role of miRNAs in mediating the interactions between humans and viruses. However, there
[...] Read more.
MicroRNAs (miRNAs) mediate various biological processes by actively fine-tuning gene expression at the post-transcriptional level. With the identification of numerous human and viral miRNAs, growing evidence has indicated a common role of miRNAs in mediating the interactions between humans and viruses. However, there is only limited information about Cross-Kingdom miRNA target sites from studies. To facilitate an extensive investigation on the interplay among the gene regulatory networks of humans and viruses, we designed a prediction pipeline, mirTarP, that is suitable for miRNA target screening on the genome scale. By applying mirTarP, we constructed the database mirTar, which is a comprehensive miRNA target repository of bidirectional interspecies regulation between viruses and humans. To provide convenient downloading for users from both the molecular biology field and medical field, mirTar classifies viruses according to “ICTV viral category” and the “medical microbiology classification” on the web page. The mirTar database and mirTarP tool are freely available online. Full article
(This article belongs to the Special Issue Regulatory microRNA)
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Open AccessFeature PaperArticle Tensor Decomposition-Based Unsupervised Feature Extraction Can Identify the Universal Nature of Sequence-Nonspecific Off-Target Regulation of mRNA Mediated by MicroRNA Transfection
Received: 3 May 2018 / Revised: 28 May 2018 / Accepted: 31 May 2018 / Published: 4 June 2018
Cited by 1 | PDF Full-text (597 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
MicroRNA (miRNA) transfection is known to degrade target mRNAs and to decrease mRNA expression. In contrast to the notion that most of the gene expression alterations caused by miRNA transfection involve downregulation, they often involve both up- and downregulation; this phenomenon is thought
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MicroRNA (miRNA) transfection is known to degrade target mRNAs and to decrease mRNA expression. In contrast to the notion that most of the gene expression alterations caused by miRNA transfection involve downregulation, they often involve both up- and downregulation; this phenomenon is thought to be, at least partially, mediated by sequence-nonspecific off-target effects. In this study, I used tensor decomposition-based unsupervised feature extraction to identify genes whose expression is likely to be altered by miRNA transfection. These gene sets turned out to largely overlap with one another regardless of the type of miRNA or cell lines used in the experiments. These gene sets also overlap with the gene set associated with altered expression induced by a Dicer knockout. This result suggests that the off-target effect is at least as important as the canonical function of miRNAs that suppress translation. The off-target effect is also suggested to consist of competition for the protein machinery between transfected miRNAs and miRNAs in the cell. Because the identified genes are enriched in various biological terms, these genes are likely to play critical roles in diverse biological processes. Full article
(This article belongs to the Special Issue Regulatory microRNA)
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Review

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Open AccessReview MicroRNAs in Cardiac Autophagy: Small Molecules and Big Role
Received: 5 July 2018 / Revised: 8 August 2018 / Accepted: 9 August 2018 / Published: 11 August 2018
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Abstract
Autophagy, which is an evolutionarily conserved process according to the lysosomal degradation of cellular components, plays a critical role in maintaining cell homeostasis. Autophagy and mitochondria autophagy (mitophagy) contribute to the preservation of cardiac homeostasis in physiological settings. However, impaired or excessive autophagy
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Autophagy, which is an evolutionarily conserved process according to the lysosomal degradation of cellular components, plays a critical role in maintaining cell homeostasis. Autophagy and mitochondria autophagy (mitophagy) contribute to the preservation of cardiac homeostasis in physiological settings. However, impaired or excessive autophagy is related to a variety of diseases. Recently, a close link between autophagy and cardiac disorders, including myocardial infarction, cardiac hypertrophy, cardiomyopathy, cardiac fibrosis, and heart failure, has been demonstrated. MicroRNAs (miRNAs) are a class of small non-coding RNAs with a length of approximately 21–22 nucleotides (nt), which are distributed widely in viruses, plants, protists, and animals. They function in mediating the post-transcriptional gene silencing. A growing number of studies have demonstrated that miRNAs regulate cardiac autophagy by suppressing the expression of autophagy-related genes in a targeted manner, which are involved in the pathogenesis of heart diseases. This review summarizes the role of microRNAs in cardiac autophagy and related cardiac disorders. Furthermore, we mainly focused on the autophagy regulation pathways, which consisted of miRNAs and their targeted genes. Full article
(This article belongs to the Special Issue Regulatory microRNA)
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Open AccessReview The Role of Extracellular Vesicles in Cancer: Cargo, Function, and Therapeutic Implications
Received: 9 July 2018 / Revised: 27 July 2018 / Accepted: 29 July 2018 / Published: 1 August 2018
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Abstract
Extracellular vesicles (EVs) are a heterogeneous collection of membrane-bound structures that play key roles in intercellular communication. EVs are potent regulators of tumorigenesis and function largely via the shuttling of cargo molecules (RNA, DNA, protein, etc.) among cancer cells and the cells of
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Extracellular vesicles (EVs) are a heterogeneous collection of membrane-bound structures that play key roles in intercellular communication. EVs are potent regulators of tumorigenesis and function largely via the shuttling of cargo molecules (RNA, DNA, protein, etc.) among cancer cells and the cells of the tumor stroma. EV-based crosstalk can promote proliferation, shape the tumor microenvironment, enhance metastasis, and allow tumor cells to evade immune destruction. In many cases these functions have been linked to the presence of specific cargo molecules. Herein we will review various types of EV cargo molecule and their functional impacts in the context of oncology. Full article
(This article belongs to the Special Issue Regulatory microRNA)
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