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Introduction: Keratoconus (KTCN) is a corneal ectasia, characterized by a progressive thinning and protrusion of the cornea, with a complex etiology involving genetic, behavioral, lifestyle, and environmental factors. Previous studies indicated that microRNAs (miRNAs) could be involved in KTCN pathogenesis. This in silico study aimed to identify precursor microRNAs (premiRNAs) differentially expressed in KTCN corneas and to characterize mature miRNAs and their target genes. Materials and methods: Expression levels of pre-miRNAs were retrieved from our previously obtained RNA sequencing data of 25 KTCN and 25 non-KTCN human corneas (PMID:28145428, PMID:30994860). Differential expression with FDR =0.01 and =1.5-fold changes were considered significant. Lists of target genes (target score =90) of mature miRNAs were obtained from miRDB. Revealed up-/downregulated miRNAs and their target genes were assessed in databases and literature. Enrichment analyses were completed applying the DAVID database. Results: From a total of 47 pre-miRNAs, six were remarkably upregulated (MIR184, MIR548I1, MIR200A, MIR6728, MIR429, MIR1299) and four downregulated (MIR6081, MIR27B, MIR23B, MIR23A) in KTCN corneas. Out of the 1,409 target genes, 220 genes with decreased and 57 genes with increased expression levels in KTCN samples vs non-KTCN samples were found. The extracellular matrix (ECM) organization, response to mechanical stimulus, regulation of cell shape, and signal transduction processes/pathways were identified as distinctive in enrichment analyses. Also, processes associated with the regulation of transcription and DNA binding were listed. Conclusion: Indicated miRNAs and their target genes might be involved in KTCN pathogenesis via disruption of crucial molecular processes, including ECM organization and signal transduction. [ABSTRACT FROM AUTHOR]

Introduction: Keratoconus (KTCN) is a corneal ectasia, characterized by a progressive thinning and protrusion of the cornea, with a complex etiology involving genetic, behavioral, lifestyle, and environmental factors. Previous studies indicated that microRNAs (miRNAs) could be involved in KTCN pathogenesis. This in silico study aimed to identify precursor microRNAs (pre-miRNAs) differentially expressed in KTCN corneas and to characterize mature miRNAs and their target genes.Materials and methods: Expression levels of pre-miRNAs were retrieved from our previously obtained RNA sequencing data of 25 KTCN and 25 non-KTCN human corneas (PMID:28145428, PMID:30994860). Differential expression with FDR ≤0.01 and ≥1.5-fold changes were considered significant. Lists of target genes (target score ≥90) of mature miRNAs were obtained from miRDB. Revealed up-/downregulated miRNAs and their target genes were assessed in databases and literature. Enrichment analyses were completed applying the DAVID database.Results: From a total of 47 pre-miRNAs, six were remarkably upregulated (MIR184, MIR548I1, MIR200A, MIR6728, MIR429, MIR1299) and four downregulated (MIR6081, MIR27B, MIR23B, MIR23A) in KTCN corneas. Out of the 1,409 target genes, 220 genes with decreased and 57 genes with increased expression levels in KTCN samples vs non-KTCN samples were found. The extracellular matrix (ECM) organization, response to mechanical stimulus, regulation of cell shape, and signal transduction processes/pathways were identified as distinctive in enrichment analyses. Also, processes associated with the regulation of transcription and DNA binding were listed.Conclusion: Indicated miRNAs and their target genes might be involved in KTCN pathogenesis via disruption of crucial molecular processes, including ECM organization and signal transduction.

(1) Background: MicroRNAs are involved in the expression of the gene encoding the chloride channel CFTR (Cystic Fibrosis Transmembrane Conductance Regulator); the objective of this short report is to study the effects of the treatment of bronchial epithelial Calu-3 cells with molecules mimicking the activity of pre-miR-145-5p, pre-miR-335-5p, and pre-miR-101-3p, and to discuss possible translational applications of these molecules in pre-clinical studies focusing on the development of protocols of possible interest in therapy; (2) Methods: CFTR mRNA was quantified by Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR). The production of the CFTR protein was assessed by Western blotting; (3) Results: The treatment of Calu-3 cells with agomiR-145-5p caused the highest inhibition of CFTR mRNA accumulation and CFTR production; (4) Conclusions: The treatment of target cells with the agomiR pre-miR-145-5p should be considered when CFTR gene expression should be inhibited in pathological conditions, such as polycystic kidney disease (PKD), some types of cancer, cholera, and SARS-CoV-2 infection. [ABSTRACT FROM AUTHOR]

The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has been recently found responsible for the pandemic outbreak of a novel coronavirus disease (COVID-19). In this work, a novel approach based on deep learning is proposed for identifying precursors of small active RNA molecules named microRNA (miRNA) in the genome of the novel coronavirus. Viral miRNA-like molecules have shown to modulate the host transcriptome during the infection progression, thus their identification is crucial for helping the diagnosis or medical treatment of the disease. The existence of the mature miRNAs derived from computationally predicted miRNA precursors (pre-miRNAs) in the novel coronavirus was validated with small RNA-seq data from SARS-CoV-2-infected human cells. The results demonstrate that computational models can provide accurate and useful predictions of pre-miRNAs in the SARS-CoV-2 genome, underscoring the relevance of machine learning in the response to a global sanitary emergency. Moreover, the interpretability of our model shed light on the molecular mechanisms underlying the viral infection, thus contributing to the fight against the COVID-19 pandemic and the fast development of new treatments. Our study shows how recent advances in machine learning can be used, effectively, in response to public health emergencies. The approach developed in this work could be of great help in future similar emergencies to accelerate the understanding of the singularities of any viral agent and for the development of novel therapies. Data and source code available at: https://sourceforge.net/projects/sourcesinc/files/aicovid/.

Inflammation is a complex biological process which alters the normal physiological function of the immune system resulting in an abnormal microenvironment that leads to several clinical complications. The process of inflammation is mediated through various intracellular signaling factors inside the cells. Apoptosis signal–regulating kinase 1 (ASK1) is an inflammation-derived kinase that controls the activation of other family of kinases such as p38 mitogen–activated protein kinases (p38 MAPKs), which mediates various the inflammatory processes. In this study, we cultured THP-1 macrophage cells to undergo inflammatory proliferation with LPS (1 μg/ml) and TNFα (10 ng/ml) stimulation. Initial in silico analysis was utilized to predict novel microRNAs (miRNAs) that target ASK1 signaling and its expression levels in LPS and TNFα stimulated THP-1 cells were estimated. Among the miRNAs, miR-532-3p showcased the highest binding affinity towards ASK1 kinase. We witnessed that transient transfection of miR-532-3p diminished the levels of ASK1 and downstream phosphorylation/translocation of p38 MAPK. Furthermore, direct targeting of ASK1 resulted in regulation of uncontrolled release of cytokines (TNFα, IL-6, and IL-23) and chemokines (GM-CSF and MIP-2α). Overall, we suggest that miR-532-3p attenuates the pro-inflammatory nature of macrophages by targeting ASK1/p38 MAPK signaling pathway and can be used as a molecular intervention for treating inflammatory diseases. [ABSTRACT FROM AUTHOR]

Abstract Background The central tenet of ‘genome content’ has been that the ‘non-coding’ parts are highly enriched with ‘microsatellites’ or ‘Simple Sequence Repeats’ (SSRs). We presume that the presence and change in number of repeat unit (n) of SSRs in different genomic locations may or may not become beneficial, depending on the position of SSRs in a gene. Very few studies have looked into the existence of SSRs in the hair-pin precursors of miRNAs (pre-miRNAs). The interplay between SSRs and miRNAs is not yet clearly understood. Results Considering the potential significance of SSRs in pre-miRNAs, we analysed the miRNA hair-pin precursors of 171 organisms, which revealed a noticeable (29.8%) existence of SSRs in their pre-miRNAs. The maintenance of SSRs in pre-miRNAs even in the complex, highly evolved phyla like Chordata and Magnoliophyta shed light upon its diverse functions. Putative effects of SSRs in either regulating the biogenesis or function of miRNAs were more underlined based on computational and experimental analysis. A preliminary computational analysis to explore the relevance of such SSRs maintained in pre-miRNA sequences led to the detection of splicing regulatory elements (SREs) either in or near to the SSRs. The absence of SSRs correspondingly decreased the detection of SREs. Conclusion The present study is the first implication for the possible involvement of SSRs in shaping the SREs to undergo Alternative Splicing events to produce miRNA isoforms in accordance with different stress environments. This part of work well demonstrates the importance of studying such consistently maintained SSRs residing in pre-miRNAs and can enhance more and more research towards deciphering the exact function of SSRs in the near future.

OBJECTIVE: microRNAs (miRNAs) play important roles in the pathogenesis of asthma. Single-nucleotide polymorphisms (SNPs) in the promotor regions of miRNAs or pre-miRNAs are involved in the alteration of miRNA expression levels or their maturation process and can contribute to asthma pathogenesis. PATIENTS AND METHODS: A total of 591 asthma cases and 621 controls were recruited for this study to evaluate the genetic effects of the following five single nucleotide polymorphisms (SNPs) on the development of asthma: rs8089787 and rs9948906 in the promoter region of mir-133a-1, pre-mir-499 rs37464444, premir-152 rs1707, pre-mir-155 rs5186. The genotypes were determined using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). RESULTS: Logistic regression analysis revealed that the CT and CT+TT genotypes in the mir-133a-1 rs8089787 (CT vs. CC, OR = 0.413, 95% CI: 0.315-0.541; CT+TT vs. CC, OR = 0.443, 95% CI: 0.342-0.574, respectively) were significantly associated with a decreased risk for asthma in sample of the Chinese Han population, compared with CC genotype. Similarly, the CT and CT+TT genotypes in the mir-133a-1 rs9948906 (CT vs. CC, OR = 0.398, 95% CI: 0.300-0.528; CT+TT vs. CC, OR = 0.403, 95% CI: 0.306-0.532, respectively) were associated with a decreased risk of asthma. However, the C alleles of both mir-133a-1 rs8089787 (C vs. T, OR = 1.867, 95% CI: 1.486-2.345) and rs9948906 (C vs. T, OR = 2 .177, 9 5% C I: 1 .690-2.804) were significantly associated with an increased risk for asthma. The CT genotype frequencies of pre-mir-152 rs1707 (CT vs. TT, OR = 4.730, 95% CI: 2.425-9.223) were significantly associated with an increased risk for asthma in a Chinese Han population (p < 0.001). The C allele frequencies of pre-mir-152 rs1707 (C vs. T, OR = 6.671, 95% CI: 3.146-14.147) was also significantly associated with an increased risk of asthma in a Chinese Han population (p < 0.001). However, the genotype and allele frequencies of rs5186, located in pre-miR-155, did not significantly differ between the cases and the controls; as well as those of rs3746444 in pre-miR-499. CONCLUSIONS: Our study provided evidence that polymorphisms of rs8089787 and rs9948906 in the promotor region of mir-133a-1 and premir-152 rs1707 may contribute to the risk of asthma in a Chinese Han population. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally. MicroRNAs target about 80% of the protein-coding mRNAs and therefore can be considered master regulators of multiple cellular pathways, contributing to the fine-tuning the cell's most important processes, like the ones involved in cellular growth and proliferation. Deregulation of miRNAs plays a fundamental role in the onset, progression and dissemination of many cancers; therefore impairment of miRNA biosynthesis is an important event in the tumorigenic cascade. MicroRNA synthesis is a multistep regulated process that requires transport of RNA molecules from the nucleus to the cytoplasm. The immature miRNA species that are produced in the nucleus are exported through the nuclear pore complexes via mobile export receptors. Small RNAs such as precursors of miRNAs (pre-miRNAs) are transported out of the nucleus by a specific nuclear transport receptor, exportin-5 (XPO5). Pre-miRNA nuclear export is a fundamental step in miRNAs biosynthesis and its deregulation through inactivating mutations in the XPO5 gene can lead to pre-miRNA nuclear accumulation and disturbance of mature miRNA expression. In addition, it is becoming increasingly evident that mature miRNAs also function as gene regulators in the nuclear compartment. In this review, we will discuss the export of miRNA precursors and its impairment in human cancer as well as the recently described nuclear functions of miRNAs. [ABSTRACT FROM AUTHOR]

Abstract: In recent years, various biological processes have been found to be regulated by miRNA-mediated gene silencing. A small molecule that modulate the miRNA pathway will provide the biological tool for elucidating mechanisms of miRNA-mediated gene regulation, and can be the drug lead for miRNA related diseases. In this study, we demonstrated that an aminoalkoxy-substituted thioxanthone derivative interferes Dicer-mediated processing of pre-miRNA. Information about the interaction between these xanthone derivatives and pre-miRNAs will enable us to design and develop new small molecule-based inhibitors for miRNA pathway. [Copyright &y& Elsevier]

Neuroblastoma is one of the most common malignancy in childhood, which originates from the developing sympathetic nervous system. Single nucleotide polymorphisms (SNPs) in primary miRNA (pri-miRNA) have shown to associate with cancer susceptibility, including neuroblastoma. Three precursor miRNA (pre-miRNA) SNPs ( pre-miR-146a rs2910164, pre-miR-149 rs2292832 and pre-miR-196a2 rs11614913) were found to contribute to pathogenesis of various diseases. Here, to evaluate the association among these three pre-miRNA SNPs and neuroblastoma susceptibility in Eastern Chinese children, we carried out a three-center case-control study involving 312 neuroblastoma cases and 762 healthy controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the association of these three polymorphisms with neuroblastoma risk. However, no significant association was observed among these three SNPs and neuroblastoma susceptibility, in either overall or subgroups analysis by tumor sites, gender and age. Further larger studies consisting of diverse ethnic populations are required to clarify the associations among these three pre-miRNAs polymorphisms and neuroblastoma risk., (© 2019 The Author(s).)

Background: The central tenet of 'genome content' has been that the 'non-coding' parts are highly enriched with 'microsatellites' or 'Simple Sequence Repeats' (SSRs). We presume that the presence and change in number of repeat unit (n) of SSRs in different genomic locations may or may not become beneficial, depending on the position of SSRs in a gene. Very few studies have looked into the existence of SSRs in the hair-pin precursors of miRNAs (pre-miRNAs). The interplay between SSRs and miRNAs is not yet clearly understood. Results: Considering the potential significance of SSRs in pre-miRNAs, we analysed the miRNA hair-pin precursors of 171 organisms, which revealed a noticeable (29.8%) existence of SSRs in their pre-miRNAs. The maintenance of SSRs in pre-miRNAs even in the complex, highly evolved phyla like Chordata and Magnoliophyta shed light upon its diverse functions. Putative effects of SSRs in either regulating the biogenesis or function of miRNAs were more underlined based on computational and experimental analysis. A preliminary computational analysis to explore the relevance of such SSRs maintained in pre-miRNA sequences led to the detection of splicing regulatory elements (SREs) either in or near to the SSRs. The absence of SSRs correspondingly decreased the detection of SREs. Conclusion: The present study is the first implication for the possible involvement of SSRs in shaping the SREs to undergo Alternative Splicing events to produce miRNA isoforms in accordance with different stress environments. This part of work well demonstrates the importance of studying such consistently maintained SSRs residing in pre-miRNAs and can enhance more and more research towards deciphering the exact function of SSRs in the near future. [ABSTRACT FROM AUTHOR]

Long intergenic non-coding RNAs (lincRNAs) are a new type of non-coding RNAs and are closely related with the occurrence and development of diseases. In previous studies, most lincRNAs have been identified through next-generation sequencing. Because lincRNAs exhibit tissue-specific expression, the reproducibility of lincRNA discovery in different studies is very poor. In this study, not including lincRNA expression, we used the sequence, structural and protein-coding potential features as potential features to construct a classifier that can be used to distinguish lincRNAs from non-lincRNAs. The GA-SVM algorithm was performed to extract the optimized feature subset. Compared with several feature subsets, the five-fold cross validation results showed that this optimized feature subset exhibited the best performance for the identification of human lincRNAs. Moreover, the LincRNA Classifier based on Selected Features (linc-SF) was constructed by support vector machine (SVM) based on the optimized feature subset. The performance of this classifier was further evaluated by predicting lincRNAs from two independent lincRNA sets. Because the recognition rates for the two lincRNA sets were 100% and 99.8%, the linc-SF was found to be effective for the prediction of human lincRNAs., (© 2013 Elsevier B.V. All rights reserved.)

MicroRNAs (miRNAs), a family of small nonprotein-coding RNAs, play a critical role in posttranscriptional gene regulation by acting as adaptors for the miRNA-induced silencing complex to inhibit gene expression by targeting mRNAs for translational repression and/or cleavage. miR-155-5p and miR-155-3p are processed from the B-cell Integration Cluster (BIC) gene (now designated, MIR155 host gene or MIR155HG). MiR-155-5p is highly expressed in both activated B- and T-cells and in monocytes/macrophages. MiR-155-5p is one of the best characterized miRNAs and recent data indicate that miR-155-5p plays a critical role in various physiological and pathological processes such as hematopoietic lineage differentiation, immunity, inflammation, viral infections, cancer, cardiovascular disease, and Down syndrome. In this review we summarize the mechanisms by which MIR155HG expression can be regulated. Given that the pathologies mediated by miR-155-5p result from the over-expression of this miRNA it may be possible to therapeutically attenuate miR-155-5p levels in the treatment of several pathological processes., (© 2013 Elsevier B.V. All rights reserved.)

In various human malignancies, widespread dysregulation of microRNA (miRNA) expression is reported to occur and affects various cell growth programs. Recent studies suggest that the expression levels of miRNAs that act as tumor suppressors are frequently reduced in cancers because of chromosome deletions, epigenetical changes, aberrant transcription, and disturbances in miRNA processing. MiR-143 and -145 are well-recognized miRNAs that are highly expressed in several tissues, but down-regulated in most types of cancers. However, the mechanism of this down-regulation has not been investigated in detail. Here, we show that DEAD-box RNA helicase 6, DDX6 (p54/RCK), post-transcriptionally down-regulated miR-143/145 expression by prompting the degradation of its host gene product, NCR143/145 RNA. In human gastric cancer cell line MKN45, DDX6 protein was abundantly expressed and accumulated in processing bodies (P-bodies). DDX6 preferentially increased the instability of non-coding RNA, NCR143/145, which encompasses the miR-143/145 cluster, and down-regulated the expression of mature miR-143/145. In human monocytic cell line THP-1, lipopolysaccharide treatment promoted the assembly of P-bodies and down-regulated the expression of NCR143/145 and its miR-143/145 rapidly. In these cells, cycloheximide treatment led to a loss of P-bodies and to an increase in NCR143/145 RNA stability, thus resulting in up-regulation of miR-143/145 expression. These data demonstrate that DDX6 contributed to the control of NCR143/145 RNA stability in P-bodies and post-transcriptionally regulated miR-143/145 expression in cancer cells., (© 2013.)