Potential Biomarkers of miR-371–373 Gene Cluster in Tumorigenesis

microRNAs (miRNAs) are small non-coding RNA transcripts (20–24 nucleotides) that bind to their complementary sequences in the 3′-untranslated regions (3′-UTR) of targeted genes to negatively or positively regulate their expression. miRNAs affect the expression of genes in cells, thereby contributing to several important biological processes, including tumorigenesis. Identifying the miRNA cluster as a human embryonic stem cell (hESC)-specific miRNAs initially led to the identification of miR-371, miR-372, miR-373, and miR-373*, which can ultimately be translated into mature miRNAs. Recent evidence suggests that miR-371–373 genes are abnormally expressed in various cancers and act either as oncogenes or tumor suppressors, indicating they may be suitable as molecular biomarkers for cancer diagnosis and prevention. In this article, we summarize recent studies linking miR-371–373 functions to tumorigenesis and speculate on the potential applications of miR-371–373 as biomarkers for cancer diagnosis and treatment.

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MicroRNAs in Obesity and Related Metabolic Disorders

Cells ◽

10.3390/cells8080859 ◽

2019 ◽

Vol 8 (8) ◽

pp. 859 ◽

Cited By ~ 28

Author(s):

Jean-François Landrier ◽

Adel Derghal ◽

Lourdes Mounien

Keyword(s):

Metabolic Disease ◽

Metabolic Disorders ◽

Molecular Mechanisms ◽

Metabolic Diseases ◽

Untranslated Regions ◽

Rna Molecules ◽

Expression Of Genes ◽

Non Coding Rna ◽

Micro Rnas

Metabolic disorders are characterized by the inability to properly use and/or store energy. The burdens of metabolic disease, such as obesity or diabetes, are believed to arise through a complex interplay between genetics and epigenetics predisposition, environment and nutrition. Therefore, understanding the molecular mechanisms for the onset of metabolic disease will provide new insights for prevention and treatment. There is growing concern about the dysregulation of micro-RNAs (miRNAs) in metabolic diseases. MiRNAs are short non-coding RNA molecules that post-transcriptionally repress the expression of genes by binding to untranslated regions and coding sequences of the target mRNAs. This review aims to provide recent data about the potential involvement of miRNAs in metabolic diseases, particularly obesity and type 2 diabetes.

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MicroRNA-934 is a novel primate-specific small non-coding RNA with neurogenic function during early development

eLife ◽

10.7554/elife.50561 ◽

2020 ◽

Vol 9 ◽

Author(s):

Kanella Prodromidou ◽

Ioannis S Vlachos ◽

Maria Gaitanou ◽

Georgia Kouroupi ◽

Artemis G Hatzigeorgiou ◽

...

Keyword(s):

Embryonic Stem ◽

Neurite Growth ◽

Specific Expression ◽

Expression Of Genes ◽

Non Coding Rna ◽

Neuronal Lineage ◽

Newborn Neurons ◽

Specific Expression Pattern ◽

Species Specific ◽

Early Human

Integrating differential RNA and miRNA expression during neuronal lineage induction of human embryonic stem cells we identified miR-934, a primate-specific miRNA that displays a stage-specific expression pattern during progenitor expansion and early neuron generation. We demonstrate the biological relevance of this finding by comparison with data from early to mid-gestation human cortical tissue. Further we find that miR-934 directly controls progenitor to neuroblast transition and impacts on neurite growth of newborn neurons. In agreement, miR-934 targets are involved in progenitor proliferation and neuronal differentiation whilst miR-934 inhibition results in profound global transcriptome changes associated with neurogenesis, axonogenesis, neuronal migration and neurotransmission. Interestingly, miR-934 inhibition affects the expression of genes associated with the subplate zone, a transient compartment most prominent in primates that emerges during early corticogenesis. Our data suggest that mir-934 is a novel regulator of early human neurogenesis with potential implications for a species-specific evolutionary role in brain function.

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Transforming Growth Factor-β and Long Non-coding RNA in Renal Inflammation and Fibrosis

Frontiers in Physiology ◽

10.3389/fphys.2021.684236 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yue-Yu Gu ◽

Jing-Yun Dou ◽

Xiao-Ru Huang ◽

Xu-Sheng Liu ◽

Hui-Yao Lan

Keyword(s):

Growth Factor ◽

Renal Fibrosis ◽

Transforming Growth Factor ◽

Kidney Diseases ◽

Therapeutic Targets ◽

Transforming Growth Factor Β ◽

Renal Inflammation ◽

Rna Transcripts ◽

Non Coding Rna ◽

Potential Applications

Renal fibrosis is one of the most characterized pathological features in chronic kidney disease (CKD). Progressive fibrosis eventually leads to renal failure, leaving dialysis or allograft transplantation the only clinical option for CKD patients. Transforming growth factor-β (TGF-β) is the key mediator in renal fibrosis and is an essential regulator for renal inflammation. Therefore, the general blockade of the pro-fibrotic TGF-β may reduce fibrosis but may risk promoting renal inflammation and other side effects due to the diverse role of TGF-β in kidney diseases. Long non-coding RNAs (lncRNAs) are RNA transcripts with more than 200 nucleotides and have been regarded as promising therapeutic targets for many diseases. This review focuses on the importance of TGF-β and lncRNAs in renal inflammation, fibrogenesis, and the potential applications of TGF-β and lncRNAs as the therapeutic targets and biomarkers in renal fibrosis and CKD are highlighted.

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The Role of Extracellular Vesicles as Shuttles of RNA and Their Clinical Significance as Biomarkers in Hepatocellular Carcinoma

Genes ◽

10.3390/genes12060902 ◽

2021 ◽

Vol 12 (6) ◽

pp. 902

Author(s):

Eva Costanzi ◽

Carolina Simioni ◽

Gabriele Varano ◽

Cinzia Brenna ◽

Ilaria Conti ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Extracellular Vesicles ◽

Tumor Metastasis ◽

Biological Processes ◽

Rna Molecules ◽

Expression Of Genes ◽

Non Coding Rna ◽

Donor Cells ◽

Relevant Role

Extracellular vesicles (EVs) have attracted interest as mediators of intercellular communication following the discovery that EVs contain RNA molecules, including non-coding RNA (ncRNA). Growing evidence for the enrichment of peculiar RNA species in specific EV subtypes has been demonstrated. ncRNAs, transferred from donor cells to recipient cells, confer to EVs the feature to regulate the expression of genes involved in differentiation, proliferation, apoptosis, and other biological processes. These multiple actions require accuracy in the isolation of RNA content from EVs and the methodologies used play a relevant role. In liver, EVs play a crucial role in regulating cell–cell communications and several pathophysiological events in the heterogeneous liver class of cells via horizontal transfer of their cargo. This review aims to discuss the rising role of EVs and their ncRNAs content in regulating specific aspects of hepatocellular carcinoma development, including tumorigenesis, angiogenesis, and tumor metastasis. We analyze the progress in EV-ncRNAs’ potential clinical applications as important diagnostic and prognostic biomarkers for liver conditions.

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Identification of sex differentiation-related microRNA and long non-coding RNA in Takifugu rubripes gonads

Scientific Reports ◽

10.1038/s41598-021-83891-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hongwei Yan ◽

Qi Liu ◽

Jieming Jiang ◽

Xufang Shen ◽

Lei Zhang ◽

...

Keyword(s):

Sex Determination ◽

High Throughput Sequencing ◽

Sex Differentiation ◽

Mature Mirnas ◽

Takifugu Rubripes ◽

Sequencing Technology ◽

Non Coding Rna ◽

Differentially Expressed Mirnas ◽

Tiger Pufferfish ◽

Long Non Coding Rna

AbstractAlthough sex determination and differentiation are key developmental processes in animals, the involvement of non-coding RNA in the regulation of this process is still not clarified. The tiger pufferfish (Takifugu rubripes) is one of the most economically important marine cultured species in Asia, but analyses of miRNA and long non-coding RNA (lncRNA) at early sex differentiation stages have not been conducted yet. In our study, high-throughput sequencing technology was used to sequence transcriptome libraries from undifferentiated gonads of T. rubripes. In total, 231 (107 conserved, and 124 novel) miRNAs were obtained, while 2774 (523 conserved, and 2251 novel) lncRNAs were identified. Of these, several miRNAs and lncRNAs were predicted to be the regulators of the expression of sex-related genes (including fru-miR-15b/foxl2, novel-167, novel-318, and novel-538/dmrt1, novel-548/amh, lnc_000338, lnc_000690, lnc_000370, XLOC_021951, and XR_965485.1/gsdf). Analysis of differentially expressed miRNAs and lncRNAs showed that three mature miRNAs up-regulated and five mature miRNAs were down-regulated in male gonads compared to female gonads, while 79 lncRNAs were up-regulated and 51 were down-regulated. These findings could highlight a group of interesting miRNAs and lncRNAs for future studies and may reveal new insights into the function of miRNAs and lncRNAs in sex determination and differentiation.

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Identification of the conserved long non-coding RNAs in myogenesis

BMC Genomics ◽

10.1186/s12864-021-07615-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Anupam Bhattacharya ◽

Simang Champramary ◽

Tanya Tripathi ◽

Debajit Thakur ◽

Ilya Ioshikhes ◽

...

Keyword(s):

Gene Regulation ◽

Muscle Development ◽

Three Dimensional ◽

C2c12 Cells ◽

Mouse Muscle ◽

Rna Molecules ◽

Expression Of Genes ◽

Novel Approach ◽

Non Coding Rna ◽

Topologically Associated Domains

Abstract Background Our understanding of genome regulation is ever-evolving with the continuous discovery of new modes of gene regulation, and transcriptomic studies of mammalian genomes have revealed the presence of a considerable population of non-coding RNA molecules among the transcripts expressed. One such non-coding RNA molecule is long non-coding RNA (lncRNA). However, the function of lncRNAs in gene regulation is not well understood; moreover, finding conserved lncRNA across species is a challenging task. Therefore, we propose a novel approach to identify conserved lncRNAs and functionally annotate these molecules. Results In this study, we exploited existing myogenic transcriptome data and identified conserved lncRNAs in mice and humans. We identified the lncRNAs expressing differentially between the early and later stages of muscle development. Differential expression of these lncRNAs was confirmed experimentally in cultured mouse muscle C2C12 cells. We utilized the three-dimensional architecture of the genome and identified topologically associated domains for these lncRNAs. Additionally, we correlated the expression of genes in domains for functional annotation of these trans-lncRNAs in myogenesis. Using this approach, we identified conserved lncRNAs in myogenesis and functionally annotated them. Conclusions With this novel approach, we identified the conserved lncRNAs in myogenesis in humans and mice and functionally annotated them. The method identified a large number of lncRNAs are involved in myogenesis. Further studies are required to investigate the reason for the conservation of the lncRNAs in human and mouse while their sequences are dissimilar. Our approach can be used to identify novel lncRNAs conserved in different species and functionally annotated them.

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6S RNA regulation of relA alters ppGpp levels in early stationary phase

Microbiology ◽

10.1099/mic.0.043992-0 ◽

2010 ◽

Vol 156 (12) ◽

pp. 3791-3800 ◽

Cited By ~ 21

Author(s):

Amy T. Cavanagh ◽

Pete Chandrangsu ◽

Karen M. Wassarman

Keyword(s):

Amino Acid ◽

Stationary Phase ◽

Regulation Of Transcription ◽

Early Stationary Phase ◽

Rna Regulation ◽

Global Regulators ◽

Expression Of Genes ◽

Non Coding Rna ◽

6S Rna ◽

Altered Regulation

6S RNA is a small, non-coding RNA that interacts directly with σ 70-RNA polymerase and regulates transcription at many σ 70-dependent promoters. Here, we demonstrate that 6S RNA regulates transcription of relA, which encodes a ppGpp synthase. The 6S RNA-dependent regulation of relA expression results in increased ppGpp levels during early stationary phase in cells lacking 6S RNA. These changes in ppGpp levels, although modest, are sufficient to result in altered regulation of transcription from σ 70-dependent promoters sensitive to ppGpp, including those promoting expression of genes involved in amino acid biosynthesis and rRNA. These data place 6S RNA as another player in maintaining appropriate gene expression as cells transition into stationary phase. Independent of this ppGpp-mediated 6S RNA-dependent regulation, we also demonstrate that in later stationary phase, 6S RNA continues to downregulate transcription in general, and specifically at a subset of the amino acid promoters, but through a mechanism that is independent of ppGpp and which we hypothesize is through direct regulation. In addition, 6S RNA-dependent regulation of σ S activity is not mediated through observed changes in ppGpp levels. We suggest a role for 6S RNA in modulating transcription of several global regulators directly, including relA, to downregulate expression of key pathways in response to changing environmental conditions.

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