Approaches to microRNA discovery

Mix-and-Read Digital MicroRNA Analysis Based on Flow Cytometric Counting of Target-Clicked Nanobead Dimer

A one-step, enzyme-free, and highly sensitive digital microRNA (miRNA) assay is rationally devised based on flow cytometric counting of target miRNA-clicked nanobead dimers via a facile mix-and-read manner. In this strategy, highly efficient miRNA-sandwiched click chemical ligation of two DNA probes may remarkably stabilize and boost the dimer formation between two kinds of fluorescence-coded nanobeads, and the number of as-produced bead dimers will be target dose-responsive, particularly when the trace number of miRNA is much less than that of employed nanobeads. Finally, each fluorescence-coded bead dimer can be easily identified and digitally counted by a powerful flow cytometer (FCM) and accordingly, the amount of target miRNA can be accurately quantified in a digital way. This new digital miRNA assay can be accomplished with a facile mix-and-read operation just by simply mixing the target miRNA with two kinds of preprepared DNA probe-functionalized nanobeads, which do not require any nucleic acid amplification, purification, and complex operation procedures. In spite of the extremely simple one-step operation, benefiting from the low-background but high target-mediated click ligation efficiency, and the powerfully digital statistical capability of FCM, this strategy achieves high sensitivity with a quite low detection limit of 5.2 fM target miRNA as well as high specificity and good generality for miRNA analysis, pioneering a new direction for fabricating digital bioassays.

Regulatory role of RNA-binding proteins in microRNA biogenesis

MicroRNAs (miRNAs) are small non-coding RNAs that silence gene expression through their interaction with complementary sequences in the 3' untranslated regions (UTR) of target mRNAs. miRNAs undergo a series of steps during their processing and maturation, which are tightly regulated to fine-tune their abundance and ability to function in post-transcriptional gene silencing. miRNA biogenesis typically involves core catalytic proteins, namely, Drosha and Dicer, and several other RNA-binding proteins (RBPs) that recognize and interact with miRNA precursors and/or their intermediates, and mature miRNAs along with their interacting proteins. The series of RNA-protein and protein-protein interactions are critical to maintaining miRNA expression levels and their function, underlying a variety of cellular processes. Throughout this article, we review RBPs that play a role in miRNA biogenesis and focus on their association with components of the miRNA pathway with functional consequences in the processing and generation of mature miRNAs.

Exonuclease III-propelled DNAzyme walker: an electrochemical strategy for microRNA diagnostics

MicroRNA detection is crucial for early infectious disease diagnosis and rapid cancer screening. However, conventional techniques like reverse transcription-quantitative polymerase chain reaction, requiring specialized training and intricate procedures, are less suitable for point-of-care analyses. To address this, we've developed a straightforward amplifier based on an exonuclease III (exo III)-propelled DNAzyme walker for sensitive and selective microRNA detection. This amplifier employs a specially designed hairpin probe with two exposed segments for strand recognition. Once the target microRNA is identified by the hairpin's extended single-strand DNA, exo III initiates its digestion, allowing microRNA regeneration and subsequent hairpin probe digestion cycles. This cyclical process produces a significant amount of DNAzyme, leading to a marked reduction in electrochemical signals. The biosensor exhibits a detection range from 10 fM to 100 pM and achieves a detection limit of 5 fM (3σ criterion). Importantly, by integrating an "And logic gate," our system gains the capacity for simultaneous diagnosis of multiple microRNAs, enhancing its applicability in RNA-based disease diagnostics.

Tumor diagnosis using carbon-based quantum dots: Detection based on the hallmarks of cancer

Carbon-based quantum dots (CQDs) have been shown to have promising application value in tumor diagnosis. Their use, however, is severely hindered by the complicated nature of the nanostructures in the CQDs. Furthermore, it seems impossible to formulate the mechanisms involved using the inadequate theoretical frameworks that are currently available for CQDs. In this review, we re-consider the structure-property relationships of CQDs and summarize the current state of development of CQDs-based tumor diagnosis based on biological theories that are fully developed. The advantages and deficiencies of recent research on CQDs-based tumor diagnosis are thus explained in terms of the manifestation of nine essential changes in cell physiology. This review makes significant progress in addressing related problems encountered with other nanomaterials.

Identification of novel microRNAs in the embryonic mouse brain using deep sequencing

Many advances in small RNA-seq technology and bioinformatics pipelines have been made recently, permitting the discovery of novel miRNAs in the embryonic day 15.5 (E15.5) mouse brain. We aimed to improve miRNA discovery in this tissue to expand our knowledge of the regulatory networks that underpin normal neurodevelopment, find new candidates for neurodevelopmental disorder aetiology, and deepen our understanding of non-coding RNA evolution. A high-quality small RNA-seq dataset of 458 M reads was generated. An unbiased miRNA discovery pipeline identified fifty putative novel miRNAs, six of which were selected for further validation. A combination of conservation analysis and target functional prediction was used to determine the authenticity of novel miRNA candidates. These findings demonstrate that miRNAs remain to be discovered, particularly if they have the features of other small RNA species.

Application of Integrated Computational Approaches in Prediction of Plant Virus Encoded miRNAs and Their Targeted Plant Genes

This chapter presents a comprehensive approach to predict novel miRNAs encoded by plant viruses and identify their target plant genes, through integration of various ab initio computational approaches. The predictive process begins with the analysis of plant viral sequences using the VMir Analyzer software. VMir Viewer software is then used to extract primary hairpins from these sequences. To distinguish real miRNA precursors from pseudo miRNA precursors, MiPred web-based software is employed. Verified real pre-miRNA sequences with a minimum free energy of < -20 Kcal/mol, are further analyzed using the RNAshapes software. Validation of predictions involves comparing them with available Expressed Sequence Tags (ESTs) from the relevant plant using BlastN. Short sequences with lengths ranging from 19 to 25 nucleotides and exhibiting <5 mismatches are prioritized for miRNA prediction. The precise locations of these short sequences within pre-miRNA structures generated using RNAshapes are meticulously identified, with a focus on those situated on the 5' and 3' arms of the structures, indicating potential miRNAs. Sequences within the arms of pre-miRNA structures are used to predict target sites within the ESTs of the specific plant, facilitated by psRNA Target software, revealing genes with potential regulatory roles in the plant. To confirm the outcome of target prediction, results are individually submitted to the RNAhybrid web-based software. For practical demonstration, this approach is applied to analyze African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda (EACMV-UG) viruses, as well as the ESTs of Jatropha and cassava.

Liquid and Solid Hybridization Methods to Detect RNAs

Northern blotting (NB) has been a long-standing method for RNA detection. However, its labor-intensive nature, reliance on high-quality RNA, and use of radioactivity have diminished its appeal over time. Nevertheless, the emergence of microRNAs (miRNAs) has reignited the demand for sensitive and quantitative NB techniques. We have recently developed cost-effective and rapid protocols for RNA detection using solid and liquid hybridization (LH) techniques which exhibit high sensitivity without the need for radioactive or specialized reagents like locked nucleic acid (LNA) probes. Our assays incorporate biotinylated probes and improved techniques for probe hybridization, transfer, cross-linking, and signal enhancement. We demonstrate that while NB is sensitive in detecting mRNAs and small RNAs, our LH protocol efficiently detects these as well as miRNAs at lower amounts of RNA, achieving higher sensitivity comparable to radiolabeled probes. Compared to NB, LH offers benefits of speed, sensitivity, and specificity in detecting mRNAs, small RNAs, and miRNAs.

Rapid in situ RNA imaging based on Cas12a thrusting strand displacement reaction

RNA In situ imaging through DNA self-assembly is advantaged in illustrating its structures and functions with high-resolution, while the limited reaction efficiency and time-consuming operation hinder its clinical application. Here, we first proposed a new strand displacement reaction (SDR) model (Cas12a thrusting SDR, CtSDR), in which Cas12a could overcome the inherent reaction limitation and dramatically enhance efficiency through energy replenishment and by-product consumption. The target-initiated CtSDR amplification was established for RNA analysis, with order of magnitude lower limit of detection (LOD) than the Cas13a system. The CtSDR-based RNA in situ imaging strategy was developed to monitor intra-cellular microRNA expression change and delineate the landscape of oncogenic RNA in 66 clinic tissue samples, possessing a clear advantage over classic in situ hybridization (ISH) in terms of operation time (1 h versus 14 h) while showing comparable sensitivity and specificity. This work presents a promising approach to developing advanced molecular diagnostic tools.

The oncogene Musashi1 encodes novel miRNAs in breast cancer

RNA-binding protein Musashi1 (MSI1) shows an increased expression level in several cancers and has been introduced as a prognostic marker in some malignancies. It is expected that if any miRNA is encoded by this gene, it might have a role in cancer development or could be considered as a prognostic biomarker. Accordingly, in this study, we aimed to find novel miRNA(s) inside the intronic regions of the MSI1 gene. Here, we report two novel miRNAs within intron 4 of MSI1 gene, named MSM2 and MSM3, which were selected among several miRNA precursors predicted by bioinformatic studies. For experimental analysis, corresponding precursor miRNAs were transfected into HEK293T cells and exogenous expression of the mature miRNAs were detected. Two mature miRNAs, MSM3-3p and MSM3-5p were generated by MSM3 precursor and one, MSM2-5p was derived from MSM2. Besides, endogenous expression of MSM2-5p and MSM3-3p was detected in MCF-7 and SH-SY5Y cell lines. Expression of both mature miRNAs was also detected in clinical samples of breast cancer. Additionally, the interaction between the MSM3-3p and 3'UTR region of PDE11A was confirmed by dual luciferase assay. Overall, our data demonstrated that MSI1 gene encodes two novel miRNAs in breast cancer cells.

The role of clopidogrel resistance-related genetic and epigenetic factors in major adverse cardiovascular events among patients with acute coronary syndrome after percutaneous coronary intervention

Despite patients with acute coronary syndrome (ACS) undergoing percutaneous coronary intervention (PCI) and receiving clopidogrel therapy, some patients still experience major adverse cardiovascular events (MACEs). Clopidogrel resistance, which may be regulated by genetic and epigenetic factors, may play a role in MACEs. This study aimed to determine the association between genetic (CYP2C19 and P2Y12 polymorphisms) and epigenetic (DNA methylation of CYP2C19 and P2Y12 and miRNA-26a expression) factors and their effects on MACEs among post-PCI patients. Post-PCI patients who received a standard dosage of clopidogrel at Harapan Kita Hospital between September 2018 and June 2020 were included in this study. MACEs were observed in patients within 1 year after PCI. Platelet aggregation was assessed using light transmission aggregometry (LTA). DNA methylation of CYP2C19 and P2Y12 was assessed using the bisulfite conversion method. CYP2C19 and P2Y12 polymorphisms and miRNA-26a expression were evaluated using quantitative real-time polymerase chain reaction (qRT-PCR). Among a total of 201 subjects, 49.8% were clopidogrel-resistant, and 14.9% experienced MACEs within 1 year after PCI (death was 7.5%). Hypomethylation of CYP2C19 (p = 0.037) and miRNA-26a upregulation (p = 0.020) were associated with clopidogrel resistance. CYP2C19^*2/^*3 polymorphisms (p = 0.047) were associated with MACEs in 1 year. This study demonstrated that hypomethylation of CYP2C19 and miRNA-26a upregulation increased the risk of clopidogrel resistance in post-PCI patients, but there was no correlation between clopidogrel resistance and MACEs. However, CYP2C19^*2/^*3 polymorphisms were the factors that predicted MACEs within 1 year.

Combining non-negative matrix factorization with graph Laplacian regularization for predicting drug-miRNA associations based on multi-source information fusion

Increasing evidences suggest that miRNAs play a key role in the occurrence and progression of many complex human diseases. Therefore, targeting dysregulated miRNAs with small molecule drugs in the clinical has become a new treatment. Nevertheless, it is high cost and time-consuming for identifying miRNAs-targeted with drugs by biological experiments. Thus, more reliable computational method for identification associations of drugs with miRNAs urgently need to be developed. In this study, we proposed an efficient method, called GNMFDMA, to predict potential associations of drug with miRNA by combining graph Laplacian regularization with non-negative matrix factorization. We first calculated the overall similarity matrices of drugs and miRNAs according to the collected different biological information. Subsequently, the new drug-miRNA association adjacency matrix was reformulated based on the K nearest neighbor profiles so as to put right the false negative associations. Finally, graph Laplacian regularization collaborative non-negative matrix factorization was used to calculate the association scores of drugs with miRNAs. In the cross validation, GNMFDMA obtains AUC of 0.9193, which outperformed the existing methods. In addition, case studies on three common drugs (i.e., 5-Aza-CdR, 5-FU and Gemcitabine), 30, 31 and 34 of the top-50 associations inferred by GNMFDMA were verified. These results reveal that GNMFDMA is a reliable and efficient computational approach for identifying the potential drug-miRNA associations.

miR-146a-5p Promotes the Inflammatory Response in PBMCs Induced by Microcystin-Leucine-Arginine

Background

Microcystin-leucine-arginine (MC-LR) is the most abundant and most toxic variant of microcystin isomers. Various experiments have clearly shown that MC-LR has hepatotoxicity and carcinogenicity, but there are relatively few studies on its immune damage effect. In addition, numerous studies have shown that microRNAs (miRNAs) are involved in a wide range of biological processes. Do miRNAs also play a role in inflammatory response caused by microcystin exposure? This is the question to be answered in this study. Moreover, this study can also provides experimental evidence for the significance of miRNA applications.

Objective

To investigate the effect of MC-LR on the expressions of miR-146a and pro/anti-inflammatory cytokines in human peripheral blood mononuclear cells (PBMCs) and to further explore the role of miR-146a in the inflammatory responses caused by MC-LR.

Methods

Serum samples from 1789 medical examiners were collected and detect the concentrations of MCs, and 30 serum samples with concentrations of MCs around P₂₅, P₅₀, and p₇₅ were randomly selected for the detection of inflammatory factors. PBMCs from fresh peripheral blood extracted from these 90 medical examiners were subsequently tested for relative miR-146a expression. In vitro, the MC-LR were exposed to the PBMCs to detect the levels of inflammatory factors as well as the relative expression of miR-146a-5p. Then, a miRNA transfection assay was performed to verify the regulation of inflammatory factors by miR-146a-5p.

Results

In population samples, the expression of inflammatory factors and miR-146a-5p increased with increasing MCs concentration. In vitro experiments showed that the expression of inflammatory factors and miR-146a-5p in PBMCs increased with MC-LR exposure time or exposure dose too. In addition, inhibiting the expression of miR-146a-5p in PBMCs reduced inflammatory factor levels.

Conclusion

miR-146a-5p exerts a promoting effect on the MC-LR-induced inflammatory response by positively regulating inflammatory factor levels.

Analysis of MicroRNAs in Ferroptosis

MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that are involved in a wide range of biological processes, including development, differentiation, and disease. They function by binding to the 3' untranslated region (UTR) of target mRNAs, leading to mRNA degradation or translational repression. miRNAs are involved in the regulation of many cellular processes, including cell proliferation, apoptosis, and metabolism. MiRNAs have been shown to modulate ferroptosis in several ways. Some miRNAs have been shown to promote ferroptosis by increasing the expression of genes involved in lipid peroxidation. Other miRNAs have been shown to inhibit ferroptosis by decreasing the expression of genes involved in iron uptake. The role of miRNAs in ferroptosis is still being studied, but they play a significant role in this cell death pathway. miRNAs may be potential targets for therapeutic intervention in diseases associated with ferroptosis, such as cancer and neurodegenerative diseases. This chapter outlines several methods used to study the connection between miRNAs and ferroptosis through target discovery and validation.

The Role of miRNAs in the Prognosis of Triple-Negative Breast Cancer: A Systematic Review and Meta-Analysis

Breast cancer is one of the most common malignancies among women around the world. The basal or triple-negative subtype (TNBC) is a heterogeneous group of tumors, characterized by its aggressive and metastatic nature, with low survival and worse prognosis. Research on genetic biomarkers, such as microRNAs (miRs) in TNBC, demonstrate their relevance in the prognosis of the disease. Therefore, the objective of this research was to verify the role of miRs in the prognosis of TNBC. A search was carried out in the PubMed (MEDLINE), Web of Science, and Scopus databases, with articles in the English language from 2010 to 2022. Only articles that analyzed the role of miRNAs in the prognosis of TNBC and that met the criteria of the MOOSE method were included. For the preparation and planning of this systematic review, a PRISMA checklist and the MOOSE method were used. The Newcastle-Ottawa Scale was used to analyze the quality of the included studies. The excluded criteria considered were: (1) studies that presented duplication in the databases; (2) reviews of the literature, clinical case reports, meta-analyses, conference abstracts, letters to the editor, theses, dissertations, and book chapters; (3) studies that stratified only women diagnosed with other subtypes of breast cancer subtypes; (4) experiments without a control or comparison group. After the bibliographic survey of the 2.274 articles found, 43 articles met the inclusion criteria, totaling 5421 patients with TNBC analyzed for this review. Six miRs (miR-155, miR-21, miR-27a/b/, miR-374a/b, miR-30a/c/e, and miR-301a) were included in the meta-analysis. A low expression of miR-155 was associated with reduced overall survival (OS) (HR: 0.68, 95% CI: 0.58-0.81). A high expression of miR-21 was a predictor of OS reduction (HR: 2.56; 95% CI: 1.49-4.40). In addition, high levels of miR-27a/b and miR-301a/b were associated with lower OS, while the decreased expression levels of miR-30 and miR-374a/b were associated with worse relapse-free survival (RFS) and shorter disease-free survival (DFS), respectively. The present study revealed that miRs play essential roles in the development of metastases, in addition to acting as suppressors of the disease, thus improving the prognosis of TNBC. However, the clinical application of these findings has not yet been investigated.

ErbB4-encoded novel miRNAs act as tumor suppressors by regulating ErbB/PI3K signaling

BACKGROUND: ErbB/PI3K signaling is widely recognized as a critical modulator of malignancy and miRNAs have been found to play a crucial role in the regulation of this pathway. OBJECTIVE: This study aimed to identify novel miRNAs related to the ErbBs loci and investigate the functional effects of these miRNAs on ErbB/PI3K signaling in cancer progression. MATERIALS and METHODS: Bioinformatics tools and RNA-seq data were used to discover novel miRNAs in breast and colon cancer cells. Gene expression levels were determined using RT-qPCR. Western blotting and dual-luciferase assays were used to identify the regulatory mechanism between ErbB4-miR1/2 and related genes. The effects of ErbB4-miR1/2 on cell proliferation, viability, ROS production, and migration were assessed by PI-flow cytometry, colony formation, MTT, ROS, scratch, and transwell assays in SKBR3 and SW480 cells. RESULTS: MicroRNA prediction tools, RNA-seq data, RT-qPCR, and sequencing results identified ErbB4-miR1 and ErbB4-miR2 (ErbB4-miR1/2) as novel miRNAs encoded by ErbB4 gene. ErbB4-miR1/2 were downregulated in breast and colon tumor tissues and also in different cancerous cells. RT-qPCR and dual-luciferase assays revealed that ErbB2 and ErbB3 genes are regulated by ErbB4-miR1/2. Consistently, a decrease in the p-AKT/AKT protein ratio verified the suppressive effect of ErbB4-miR1/2 on ErbB/PI3K activity. Furthermore, ErbB4-miR1/2 overexpression suppressed cell proliferation, viability, and migration, and increased ROS production. CONCLUSIONS: ErbB4-miR1/2 are novel tumor suppressor miRNAs which attenuate ErbB/PI3K signaling in breast and colon cancer cells.

MicroRNA-769-3p Acts as a Prognostic Factor in Oral Squamous Cell Cancer by Modulating Stromal Genes

miR-769-3p expression is suppressed in the stromal subtype of head and neck squamous cell carcinoma (HNSCC); however, its role in stromal HNSCC has not been fully elucidated. To investigate the biological relevance of miR-769-3p in the stromal phenotype, we established oral squamous cell cancer (OSCC) cell lines, namely CAL27, HSC3, and YD8, overexpressing miR-769-3p. miR-769-3p expression was positively and negatively correlated with interferon-gamma-related genes and MYC target gene sets, respectively. miR-769-3p decreased OSCC cell migration and invasion as well as mesenchymal marker expression and increased epithelial marker expression. Moreover, miR-769-3p enhanced OSCC cell sensitivity to 5-fluorouracil. High miR-769-3p expression was associated with good prognosis of HNSCC patients. Collectively, these results suggest that miR-769-3p suppression enhances stromal gene expression and promotes the epithelial-to-mesenchymal transition. Therefore, miR-769-3p may be a potential biomarker of the miRNA phenotype in OSCC patients.

Intracellular miRNA Imaging Based on a Self-Powered and Self-Feedback Entropy-Driven Catalyst-DNAzyme Circuit

DNAzyme-based signal amplification circuits promote the advances in low-abundant miRNA imaging in living cells. However, due to the insufficient cofactor in living cells and unsustainable target utilization, self-powered and self-feedback DNAzyme amplification circuits have rarely been achieved. Here, a MnO₂ nanosheet-mediated self-powered and self-feedback entropy-driven catalyst (EDC)-DNAzyme nanoprobe (MnPFEDz) was demonstrated for sensitive imaging of intracellular microRNA (miRNA). In this strategy, MnPFEDz was formed by adsorbing EDC modules and substrate probes on MnO₂ nanosheets. The MnO₂ nanosheets acted not only as glutathione (GSH)-responsive nanocarriers for efficient delivery of DNA probes but also as a DNAzyme cofactor supplier to power the DNAzyme biocatalysis and promote signal transduction in a feedback way. When entering the cells, GSH could decompose MnO₂ nanosheets to generate numerous Mn²⁺ ion cofactors, leading to the release of DNA probes. Subsequently, the target miRNA initiated EDC cycles to generate amplified fluorescence signals and exposed the complete DNAzyme. Meanwhile, each of the exposed DNAzyme then cleaved the substrate probes with the help of Mn²⁺ ion cofactors and released a new trigger analogue for the next round of EDC cycles, initiating additional fluorescence signals in a feedback way. As a multiple signal amplification strategy, the MnPFEDz nanoprobe facilitated the effective detection of intracellular molecules with enhanced sensitivity and provided a versatile strategy for the construction of self-powered and self-feedback DNA circuits in living cells.

The negative regulation of gene expression by microRNAs as key driver of inducers and repressors of cardiomyocyte differentiation

Cardiac muscle damage-induced loss of cardiomyocytes (CMs) and dysfunction of the remaining ones leads to heart failure, which nowadays is the number one killer worldwide. Therapies fostering effective cardiac regeneration are the holy grail of cardiovascular research to stop the heart failure epidemic. The main goal of most myocardial regeneration protocols is the generation of new functional CMs through the differentiation of endogenous or exogenous cardiomyogenic cells. Understanding the cellular and molecular basis of cardiomyocyte commitment, specification, differentiation and maturation is needed to devise innovative approaches to replace the CMs lost after injury in the adult heart. The transcriptional regulation of CM differentiation is a highly conserved process that require sequential activation and/or repression of different genetic programs. Therefore, CM differentiation and specification have been depicted as a step-wise specific chemical and mechanical stimuli inducing complete myogenic commitment and cell-cycle exit. Yet, the demonstration that some microRNAs are sufficient to direct ESC differentiation into CMs and that four specific miRNAs reprogram fibroblasts into CMs show that CM differentiation must also involve negative regulatory instructions. Here, we review the mechanisms of CM differentiation during development and from regenerative stem cells with a focus on the involvement of microRNAs in the process, putting in perspective their negative gene regulation as a main modifier of effective CM regeneration in the adult heart.

A Novel miRNA Located in the HER2 Gene Shows an Inhibitory Effect on Wnt Signaling and Cell Cycle Progression

Human epidermal growth factor receptor 2 (HER2) is involved in the development of the majority of cancers. Therefore, it can be a potential target for cancer therapy. It was hypothesized that some of the broad effects of HER2 could be mediated by miRNAs that are probably embedded inside this gene. Here, we predicted and then empirically substantiated the processing and expression of a novel miRNA named HER2-miR1, located in the HER2 gene; transfection of a DNA fragment corresponding to HER2-miR1 precursor sequence (preHER2-miR1) resulted in ~4000-fold elevation of HER2-miR1 mature form in HEK293t cells. Also, the detection of HER2-miR1 in 5637, NT2, and HeLa cell lines confirmed its endogenous production. Following the HER2-miR1 overexpression, TOP/FOP flash assay and RT-qPCR results showed that Wnt signaling pathway was downregulated. Consistently, flow cytometry results revealed that overexpression of HER2-miR1 in Wnt⁺ cell lines (SW480 and HCT116) was ended in G1 arrest, unlike in Wnt⁻ cells (HEK293t). Taking everything into account, our results report the discovery of a novel miRNA that is located within the HER2 gene sequence and has a repressive impact on the Wnt signaling pathway.

Noncoding RNAs related to the hedgehog pathway in cancer: clinical implications and future perspectives

Cancer is a type of malignant affliction threatening human health worldwide; however, the molecular mechanism of cancer pathogenesis remains to be elusive. The oncogenic hedgehog (Hh) pathway is a highly evolutionarily conserved signaling pathway in which the hedgehog-Patched complex is internalized to cellular lysosomes for degradation, resulting in the release of Smoothened inhibition and producing downstream intracellular signals. Noncoding RNAs (ncRNAs) with diversified regulatory functions have the potency of controlling cellular processes. Compelling evidence reveals that Hh pathway, ncRNAs, or their crosstalk play complicated roles in the initiation, metastasis, apoptosis and drug resistance of cancer, allowing ncRNAs related to the Hh pathway to serve as clinical biomarkers for targeted cancer therapy. In this review, we attempt to depict the multiple patterns of ncRNAs in the progression of malignant tumors via interactions with the Hh crucial elements in order to better understand the complex regulatory mechanism, and focus on Hh associated ncRNA therapeutics aimed at boosting their application in the clinical setting.

Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations

Next generation sequencing of RNA molecules (RNA-seq) has become a common tool to characterize the expression profiles of RNAs and their regulations in normal physiological processes and diseases. Although increasingly accumulating RNA-seq data are widely available through publicly accessible sites, most of the data for short non-coding RNAs (sncRNAs) have been obtained for microRNA (miRNA) analyses by standard RNA-seq, which only capture the sncRNAs with 5'-phosphate (5'-P) and 3'-hydroxyl (3'-OH) ends. The sncRNAs with other terminal formations such as those with a 5'-hydroxyl end (5'-OH), a 3'-phosphate (3'-P) end, or a 2',3'-cyclic phosphate end (2',3'-cP) cannot be efficiently amplified and sequenced by standard RNA-seq. Due to the invisibility in standard RNA-seq data, these non-miRNA-sncRNAs have been a hidden component in the transcriptome. However, as the functional significances of these sncRNAs have become increasingly apparent, specific RNA-seq methods compatible with various terminal formations of sncRNAs have been developed and started shedding light on the previously unrecognized sncRNAs that lack 5'-P/3'-OH ends. In this review, we summarize the expanding world of sncRNAs with various terminal formations and the strategic approaches of specific RNA-seq methods to distinctively characterize their expression profiles.

Characterization of the first microRNA in human CDH1 that affects cell cycle and apoptosis and indicates breast cancers progression

The E-cadherin protein (Cadherin 1, gene: CDH1), a master regulator of the human epithelial homeostasis, contributes to the epithelial-mesenchymal transition (EMT) which confers cell migratory features to the cells. The EMT is central to many pathophysiological changes in cancer. Therefore, a better understanding of this regulatory scenario is beneficial for therapeutic regiments. The CDH1 gene is approximately 100 kbp long and consists of 16 exons with a relatively large second intron. Since none microRNA (miRNA) has been identified in CDH1 up to now we screened the CDH1 gene for promising miRNA hairpin structures in silico. Out of the 27 hairpin structures we identified, one stable RNA fold with a promising sequence motive was selected for experimental verification. The exogenous validation of the hairpin sequence was performed by transfection of HEK293T cells and the mature miRNA sequences could be verified by quantitative polymerase chain reaction. The endogenous expression of the mature miRNA provisionally named CDH1-i2-miR-1 could be confirmed in two normal (HEK293T, HUVEK) and five cancer cell lines (MCF7, MDA-MB-231, SW480, HT-29, A549). The functional characterization by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay showed a suppression of HEK293T cell proliferation. A flow cytometry-based approach showed the ability of CDH1-i2-miR-1 to arrest transfected cells on a G2/M state while annexin staining exemplified an apoptotic effect. BAX and PTEN expression levels were affected following the overexpression with the new miRNA. The in vivo expression level was assessed in 35 breast tumor tissues and their paired nonmalignant marginal part. A fourfold downregulation in the tumor specimens compared to their marginal controls could be observed. It can be concluded that the sequence of the hub gene CDH1 harbors at least one miRNA but eventually even more relevant for the pathophysiology of breast cancer.

Porcine Reproductive and Respiratory Syndrome Virus Evades Antiviral Innate Immunity via MicroRNAs Regulation

Porcine reproductive and respiratory syndrome (PRRS) is one of the most important diseases in pigs, leading to significant economic losses in the swine industry worldwide. MicroRNAs (miRNAs) are small single-stranded non-coding RNAs involved in regulating gene expressions at the post-transcriptional levels. A variety of host miRNAs are dysregulated and exploited by PRRSV to escape host antiviral surveillance and help virus infection. In addition, PRRSV might encode miRNAs. In this review, we will summarize current progress on how PRRSV utilizes miRNAs for immune evasions. Increasing knowledge of the role of miRNAs in immune evasion will improve our understanding of PRRSV pathogenesis and help us develop new treatments for PRRSV-associated diseases.

Machine learning meets omics: applications and perspectives

The innovation of biotechnologies has allowed the accumulation of omics data at an alarming rate, thus introducing the era of 'big data'. Extracting inherent valuable knowledge from various omics data remains a daunting problem in bioinformatics. Better solutions often need some kind of more innovative methods for efficient handlings and effective results. Recent advancements in integrated analysis and computational modeling of multi-omics data helped address such needs in an increasingly harmonious manner. The development and application of machine learning have largely advanced our insights into biology and biomedicine and greatly promoted the development of therapeutic strategies, especially for precision medicine. Here, we propose a comprehensive survey and discussion on what happened, is happening and will happen when machine learning meets omics. Specifically, we describe how artificial intelligence can be applied to omics studies and review recent advancements at the interface between machine learning and the ever-widest range of omics including genomics, transcriptomics, proteomics, metabolomics, radiomics, as well as those at the single-cell resolution. We also discuss and provide a synthesis of ideas, new insights, current challenges and perspectives of machine learning in omics.

JAMIR-eQTL: Japanese genome-wide identification of microRNA expression quantitative trait loci across dementia types

MicroRNAs (miRNAs) are small non-coding RNAs shown to regulate gene expression by binding to complementary transcripts. Genetic variants, including single-nucleotide polymorphisms and short insertions/deletions, contribute to traits and diseases by influencing miRNA expression. However, the association between genetic variation and miRNA expression remains to be elucidated. Here, by using genotype data and miRNA expression data from 3448 Japanese serum samples, we developed a computational pipeline to systematically identify genome-wide miRNA expression quantitative trait loci (miR-eQTLs). Not only did we identify a total of 2487 cis-miR-eQTLs and 3 155 773 trans-miR-eQTLs at a false discovery rate of <0.05 in six dementia types (Alzheimer's disease, dementia with Lewy bodies, vascular dementia, frontotemporal lobar degeneration, normal-pressure hydrocephalus and mild cognitive impairment) and all samples, including those from patients with other types of dementia, but also we examined the commonality and specificity of miR-eQTLs among dementia types. To enable data searching and downloading of these cis- and trans-eQTLs, we developed a user-friendly database named JAMIR-eQTL, publicly available at https://www.jamir-eqtl.org/. This is the first miR-eQTL database designed for dementia types. Our integrative and comprehensive resource will contribute to understanding the genetic basis of miRNA expression as well as to the discovery of deleterious mutations, particularly in dementia studies. Database URL: https://www.jamir-eqtl.org/.

Near-Infrared Light Controllable DNA Walker Driven by Endogenous Adenosine Triphosphate for in Situ Spatiotemporal Imaging of Intracellular MicroRNA

As a powerful signal amplification tool, the DNA walker has been widely applied to detect rare microRNA (miRNA) in vivo. Despite the significant advances, a near-infrared (NIR) light controllable DNA walker for signal amplification powered by an endogenous initiator has not been realized, which is crucial for spatiotemporal imaging of miRNA in living cells with high sensitivity. Herein, we constructed a NIR-photoactivatable DNA walker system, which was powered by endogenous adenosine triphosphate (ATP) for in situ miRNA imaging with spatial and temporal resolution. The system was very stable with an extremely low fluorescent background for the bioimaging in living cells. We employed upconversion nanoparticles (UCNPs) as the carriers of the DNA probe and transducers of converting NIR to UV light. Coupled with the DNA walker fueled by intracellular ATP, a smart system based on the NIR light initiated DNA walker was successfully developed for precise spatiotemporal control in living cells. Triggered by NIR light, the DNA walker could autonomously and progressively travel along the track with the assistance of intracellular ATP. The system has been successfully applied for in situ miRNA imaging in different cell lines with highly spatial and temporal resolution. This strategy can expand NIR photocontrol the DNA walker for precise imaging in a biological system.

microRNA-146a-5p, Neurotropic Viral Infection and Prion Disease (PrD)

The human brain and central nervous system (CNS) harbor a select sub-group of potentially pathogenic microRNAs (miRNAs), including a well-characterized NF-kB-sensitive Homo sapiens microRNA hsa-miRNA-146a-5p (miRNA-146a). miRNA-146a is significantly over-expressed in progressive and often lethal viral- and prion-mediated and related neurological syndromes associated with progressive inflammatory neurodegeneration. These include ~18 different viral-induced encephalopathies for which data are available, at least ~10 known prion diseases (PrD) of animals and humans, Alzheimer’s disease (AD) and other sporadic and progressive age-related neurological disorders. Despite the apparent lack of nucleic acids in prions, both DNA- and RNA-containing viruses along with prions significantly induce miRNA-146a in the infected host, but whether this represents part of the host’s adaptive immunity, innate-immune response or a mechanism to enable the invading prion or virus a successful infection is not well understood. Current findings suggest an early and highly interactive role for miRNA-146a: (i) as a major small noncoding RNA (sncRNA) regulator of innate-immune responses and inflammatory signaling in cells of the human brain and CNS; (ii) as a critical component of the complement system and immune-related neurological dysfunction; (iii) as an inducible sncRNA of the brain and CNS that lies at a critical intersection of several important neurobiological adaptive immune response processes with highly interactive associations involving complement factor H (CFH), Toll-like receptor pathways, the innate-immunity, cytokine production, apoptosis and neural cell decline; and (iv) as a potential biomarker for viral infection, TSE and AD and other neurological diseases in both animals and humans. In this report, we review the recent data supporting the idea that miRNA-146a may represent a novel and unique sncRNA-based biomarker for inflammatory neurodegeneration in multiple species. This paper further reviews the current state of knowledge regarding the nature and mechanism of miRNA-146a in viral and prion infection of the human brain and CNS with reference to AD wherever possible.

MicroRNA and Hemophilia-A Disease: Bioinformatics Prediction and Experimental Analysis

Objective

Hemophilia-A is a common genetic abnormality resulted from decreased or lack of factor VIII (FVIII) pro-coagulant protein function caused by mutations in the F8 gene. Majority of molecular studies consider screening of mutations and their relevant impacts on the quality and expression levels of FVIII. Interestingly, some of the functions in FVIII suggest a probable involvement of small non-coding RNAs embedded within the sequence of F8 gene. Therefore, microRNAs which are encoded within the F8 gene might have a role in hemophilia development. In this study, miRNAs production in the F8 gene was investigated by bioinformatics prediction and experimental validation.

Materials and Methods

In this experimental study, bioinformatics tools have been utilized to seek the novel microRNAs inserted within human F8 gene. The ability to express new microRNAs in F8 locus was studied through reliable bioinformatics databases such as SSCProfiler, RNA fold, miREval, miR-FIND, UCSC genome browser and miRBase. Then, expression and processing of the predicted microRNAs were examined based on bioinformatics methods, in the HEK293 cell lines.

Results

We are unable to confirm existence of the considered mature microRNAs in the transfected cells.

Conclusion

We hope that through changing experimental conditions, designing new primers or altering cell lines as well as the expression of vectors, exogenous and endogenous expressions of the predicted miRNA will be confirmed.

A Comprehensive Analysis of Northern versus Liquid Hybridization Assays for mRNAs, Small RNAs, and miRNAs Using a Non-Radiolabeled Approach

Northern blotting (NB), a gold standard for RNA detection, has lost its charm due to its hands-on nature, need for good quality RNA, and radioactivity. With the emergence of the field of microRNAs (miRNAs), the necessity for sensitive and quantitative NBs has again emerged. Here, we developed highly sensitive yet non-radiolabeled, fast, economical NB, and liquid hybridization (LH) assays without radioactivity or specialized reagents like locked nucleic acid (LNA)- or digoxigenin-labeled probes for mRNAs/small RNAs, especially miRNAs using biotinylated probes. An improvised means of hybridizing oligo probes along with efficient transfer, cross-linking, and signal enhancement techniques was employed. Important caveats of each assay were elaborated upon, especially issues related to probe biotinylation, use of exonuclease, and bioimagers not reported earlier. We demonstrate that, while the NBs were sensitive for mRNAs and small RNAs, our LH protocol could efficiently detect these and miRNAs using less than 10-100 times the total amount of RNA, a sensitivity comparable to radiolabeled probes. Compared to NBs, LH was a faster, more sensitive, and specific approach for mRNA/small RNA/miRNA detection. A comparison of present work with six seminal studies is presented along with detailed protocols for easy reproducibility. Overall, our study provides effective platforms to study large and small RNAs in a sensitive, efficient, and cost-effective manner.

Critical roles of microRNA-196 in normal physiology and non-malignant diseases: Diagnostic and therapeutic implications

MicroRNAs (miRNAs) have emerged as a critical component of regulatory networks that modulate and fine-tune gene expression in a post-transcriptional manner. The microRNA-196 family is encoded by three loci in the human genome, namely hsa-mir-196a-1, hsa-mir-196a-2, and hsa-mir-196b. Increasing evidence supports the roles of different components of this miRNA family in regulating key cellular processes during differentiation and development, ranging from inflammation and differentiation of stem cells to limb development and remodeling and structure of adipose tissue. This review first discusses about the genomic context and regulation of this miRNA family and then take a bird's eye view on the updated list of its target genes and their biological processes to obtain insights about various functions played by members of the microRNA-196 family. We then describe evidence supporting the involvement of the human microRNA-196 family in regulating critical cellular processes both in physiological and non-malignant inflammatory conditions, highlighting recent seminal findings that carry implications for developing novel therapeutic or diagnostic strategies.

A History of Preterm Delivery Is Associated with Aberrant Postpartal MicroRNA Expression Profiles in Mothers with an Absence of Other Pregnancy-Related Complications

This prospective cross-sectional case-control study investigated the postpartal gene expression of microRNAs associated with diabetes/cardiovascular/cerebrovascular diseases in the peripheral white blood cells of women with anamnesis of preterm prelabor rupture of membranes (n = 58), spontaneous preterm birth (n = 55), and term delivery (n = 89) by a quantitative reverse transcription polymerase chain reaction. After pregnancies complicated by preterm prelabor rupture of membranes or spontaneous preterm birth, mothers showed diverse expression profiles for 25 out of 29 tested microRNAs (miR-1-3p, miR-16-5p, miR-17-5p, miR-20a-5p, miR-20b-5p, miR-21-5p, miR-23a-3p, miR-24-3p, miR-26a-5p, miR-29a-3p, miR-100-5p, miR-103a-3p, miR-125b-5p, miR-126-3p, miR-130b-3p, miR-133a-3p, miR-143-3p, miR-145-5p, miR-146a-5p, miR-181a-5p, miR-195-5p, miR-199a-5p, miR-221-3p, miR-499a-5p, and miR-574-3p). The earliest gestational ages at delivery and the lowest birth weights of newborns were associated with the highest postpartal levels of the previously mentioned microRNAs in maternal peripheral white blood cells. Administration of tocolytic drugs in order to prolong pregnancy, used in order to administer and complete a full course of antenatal corticosteroids, was associated with alterations in postpartal microRNA expression profiles to a lesser extent than in women with imminent delivery, where there was insufficient time for administration of tocolytics and antenatal corticosteroids. Overall, mothers who did not receive tocolytic therapy (miR-24-3p and miR-146a-5p) and mothers who did not receive corticosteroid therapy (miR-1-3p, miR-100-5p, and miR-143-3p) had increased or showed a trend toward increased postpartal microRNA expression when compared with mothers given tocolytic and corticosteroid therapy. In addition, mothers with serum C-reactive protein levels above 20 mg/L, who experienced preterm labour, showed a trend toward increased postpartal expression profiles of miR-143-3p and miR-199a-5p when compared with mothers with normal serum C-reactive protein levels. On the other hand, the occurrence of maternal leukocytosis, the presence of intra-amniotic inflammation (higher levels of interleukin 6 in the amniotic fluid), and the administration of antibiotics at the time of preterm delivery had no impact on postpartal microRNA expression profiles in mothers with a history of preterm delivery. Likewise, the condition of the newborns at the moment of birth, determined by Apgar scores at 5 and 10 min and the pH of cord arterial blood, had no influence on the postpartal expression profiles of mothers with a history of preterm delivery. These findings may contribute to explaining the increased cardiovascular risk in mothers with anamnesis of preterm delivery, and the greater increase of maternal cardiovascular risk with the decrease of gestational age at delivery. Women with preterm delivery in their anamnesis represent a high-risk group with special needs on a long-term basis, with a need to apply preventive and therapeutic interventions as early as possible.

MicroRNAs regulate distal region of mandibular development through Hh signaling

Mandibular anomalies are often seen in various congenital diseases, indicating that mandibular development is under strict molecular control. Therefore, it is crucial to understand the molecular mechanisms involved in mandibular development. MicroRNAs (miRNAs) are noncoding small single-stranded RNAs that play a critical role in regulating the level of gene expression. We found that the mesenchymal conditional deletion of miRNAs arising from a lack of Dicer (an essential molecule for miRNA processing, Dicer^fl/fl ;Wnt1Cre), led to an abnormal groove formation at the distal end of developing mandibles. At E10.5, when the region forms, inhibitors of Hh signaling, Ptch1 and Hhip1 showed increased expression at the region in Dicer mutant mandibles, while Gli1 (a major mediator of Hh signaling) was significantly downregulated in mutant mandibles. These suggest that Hh signaling was downregulated at the distal end of Dicer mutant mandibles by increased inhibitors. To understand whether the abnormal groove formation inDicer mutant mandibles was caused by the downregulation of Hh signaling, mice with a mesenchymal deletion of Hh signaling activity arising from a lack of Smo (an essential molecule for Hh signaling activation, Smo^fl/fl ;Wnt1Cre) were examined. Smo^fl/fl ;Wnt1Cre mice showed a similar phenotype in the distal region of their mandibles to those in Dicer^fl/fl ;Wnt1Cre mice. We also found that approximately 400 miRNAs were expressed in wild-type mandibular mesenchymes at E10.5, and six microRNAs were identified as miRNAs with binding potential against both Ptch1 and Hhip1. Their expressions at the distal end of the mandible were confirmed by in situ hybridization. This indicates that microRNAs regulate the distal part of mandibular formation at an early stage of development by involving Hh signaling activity through controlling its inhibitor expression level.

Identification and molecular characterization of miRNAs and their target genes associated with seed development through small RNA sequencing in chickpea

Multiple studies have attempted to dissect the molecular mechanism underlying seed development in chickpea (Cicer arietinum L.). These studies highlight the need to focus on the role of miRNAs in regulating storage protein accumulation in seeds. Therefore, a total of 8,856,691 short-read sequences were generated from a small RNA library of developing chickpea seeds and were analyzed using miRDeep-P to identify 74 known and 26 novel miRNA sequences. Known miRNAs were classified into 22 miRNA families with miRNA156 family being most abundant. Of the 26 putative novel miRNAs identified, only 22 could be experimentally validated using stem loop end point PCR. Differential expression analyses led to the identification of known as well as novel miRNAs that could regulate various stages of chickpea seed development. In silico target prediction revealed several important target genes and transcription factors like SPL, mediator of RNA Polymerase II transcription subunit 12, aspartic proteinase and NACs, which were further validated by real-time PCR analysis. A comparative expression analysis in chickpea genotypes with contrasting seed protein content revealed one known (Car-miR156h) and two novel miRNA (Car-novmiR7 and Car-novmiR23) candidates to be highly expressed in the LPC (low protein content) chickpea genotypes, targets of which are known to regulate seed storage protein accumulation. Therefore, this study provides a useful resource in the form of miRNA and their targets which can be further utilized to understand and manipulate various regulatory mechanisms involved in seed development with the overall aim of improving yield and nutrition attributes in chickpea.

Target-Cell-Specific Bioorthogonal and Endogenous ATP Control of Signal Amplification for Intracellular MicroRNA Imaging

A stringent signal amplification method to profile microRNA (miRNA) expression within a specific cell remains a key challenge in biology. To address this issue, we report a target-cell-specific DNA nanosystem for endogenous adenosine-5'-triphosphate (ATP) bioorthogonal activation of the hybridization chain reaction (HCR) to spatiotemporally controlled signal amplification detection of miRNA in vitro and in vivo. The system consists of ATP aptamer-sealed engineered HCR functional units combined with a cancer cell membrane-encapsulated glutathione (GSH)-responsive metal-organic framework (MOF). Once the nanosystem is specifically and efficiently internalized into a cancer cell through membrane-mediated homing targeting, the MOF structure degrades and releases HCR functional units. The endogenous high expressional ATP recognizes the aptamer, allowing the HCR functional units to adopt its active modality. The activated HCR functional units are then able to spatiotemporally and bioorthogonally image miRNA with high sensitivity in vitro and in vivo.

Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq

Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.

Comprehensive MicroRNA Expression Profile of the Mammary Gland in Lactating Dairy Cows With Extremely Different Milk Protein and Fat Percentages

A total of 31 differentially expressed genes in the mammary glands were identified in our previous study using RNA sequencing (RNA-Seq), for lactating cows with extremely high and low milk protein and fat percentages. To determine the regulation of milk composition traits, we herein investigated the expression profiles of microRNA (miRNA) using small RNA sequencing based on the same samples as in the previous RNA-Seq experiment. A total of 497 known miRNAs (miRBase, release 22.1) and 49 novel miRNAs among the reads were identified. Among these miRNAs, 71 were found differentially expressed between the high and low groups (p < 0.05, q < 0.05). Furthermore, 21 of the differentially expressed genes reported in our previous RNA-Seq study were predicted as target genes for some of the 71 miRNAs. Gene ontology and KEGG pathway analyses showed that these targets were enriched for functions such as metabolism of protein and fat, and development of mammary gland, which indicating the critical role of these miRNAs in regulating the formation of milk protein and fat. With dual luciferase report assay, we further validated the regulatory role of 7 differentially expressed miRNAs through interaction with the specific sequences in 3'UTR of the targets. In conclusion, the current study investigated the complexity of the mammary gland transcriptome in dairy cattle using small RNA-seq. Comprehensive analysis of differential miRNAs expression and the data from previous study RNA-seq provided the opportunity to identify the key candidate genes for milk composition traits.

LMI-DForest: A deep forest model towards the prediction of lncRNA-miRNA interactions

The interactions between miRNAs and long non-coding RNAs (lncRNAs) are subject to intensive recent studies due to its critical role in gene regulations. Computational prediction of lncRNA-miRNA interactions has become a popular alternative strategy to the experimental methods for identification of underlying interactions. It is desirable to develop the machine learning-based models for prediction of lncRNA-miRNA based on the experimentally validated interactions between lncRNAs and miRNAs. The accuracy and robustness of existing models based on machine learning techniques are subject to further improvement. Considering that the attributes of lncRNA and miRNA contribute key importance in the interaction between these two RNAs, a deep learning model, named LMI-DForest, is proposed here by combining the deep forest and autoencoder strategies. Systematic comparison on the experiment validated datasets for lncRNA-miRNA interaction datasets demonstrates that the proposed method consistently shows superior performance over the other machine learning models in the lncRNA-miRNA interaction prediction.

Identification of miRNAs encoded by Autographa californica nucleopolyhedrovirus

Two Autographa californica nucleopolyhedrovirus (AcMNPV) encoded miRNAs, AcMNPV-miR-1 and AcMNPV-miR-3, have been reported by us in 2013 and 2019, respectively. Here, we present an integrated investigation of AcMNPV-encoded miRNAs, which include the above two miRNAs and three additional newly identified miRNAs. Six candidate miRNAs were predicted through small RNA deep sequencing and bioinformatics, of which, five were validated. Three miRNAs are located opposite the coding sequences, the other two are located in the coding sequences of viral genes. Targets in both virus and host were predicted and subsequently tested using dual-luciferase reporter assays. The validated targets were found mainly in AcMNPV, except for the targets of AcMNPV-miR-4, which are all host genes. Based on reporter assays, the five miRNAs predominantly function by down-regulating their targets. The transcription start sites of these miRNAs were bioinformatic screened based on known baculovirus promoter motifs. Our study reveals that AcMNPV-encoded miRNAs function as fine modulators of the interactions between host and virus by regulating viral and/or host genes.

Targeting miRNAs by natural products: A new way for cancer therapy

MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression through mRNA degradation or translation inhibition. MiRNAs play important roles in a variety of biological processes, and dysregulation of miRNA expression is highly associated with cancer development. Individual miRNA regulates multiple gene expressions, enabling them to regulate multiple cellular signaling pathways simultaneously. Hence, miRNAs could be served as cancer biomarkers for diagnosis and prognosis, and also therapeutic targets. Recently, more and more evidences showed that natural products such as paclitaxel, curcumin, resveratrol, genistein or epigallocatechin-3-gallate exert their anti-proliferative and/or pro-apoptotic effects through regulating one or more miRNAs, leading to the inhibition of cancer cell growth, induction of apoptosis or enhancement of conventional cancer therapeutic efficacy. Herein, we outlined the recent advances in the regulation of miRNAs expression by the natural products and highlight the importance of these natural drugs as a potential strategy in cancer treatment. This review will help us better understand how natural products modulate miRNAs and contribute to the development of effective and safe natural drugs for therapeutic purposes.

Dysregulation of HULC promotes contrast-induced nephropathy (CIN) via regulating signaling pathway of miRNA-512 and prostaglandin E1 (PGE1)

It has been shown that contrast-induced nephropathy (CIN) can be attenuated by the administration of PGE1. As an enzyme responsible for the production of PGE1, PTGS1 was confirmed in this study as a miR-512 target. Meanwhile, HULC has been identified as a competing endogenous RNA of miR-512. Therefore, in this study, we tested the diagnostic value of HULC and miR-512 in subjects with or without CIN. In addition, we evaluated the regulatory relationship among HULC, miR-512, PTGS1 and PGE1 in vitro. We enrolled 320 patients with coronary heart disease and divided them into a CIN group and a non-CIN group. Subsequently, we detected the differential expression of miR-512, HULC and PGE1 in the two groups. We also used a dual luciferase reporter assay to evaluate the regulatory relationship among HULC, miR-512, PTGS1 and PGE1 in THP-1 cells. In patients with CIN, the expression levels of HULC and PGE1 were lower, but the expression level of miR-512 was higher. MiR-512 could directly bind to and negatively regulate the expression of PTGS1 and HULC. The expression of HULC was positively correlated with the expression of PTGS1 and PGE1, while negatively correlated with the expression of miR-512. The findings of this study demonstrated that deregulation of lncRNA-HULC/miR-512/PTGS1/PGE1 might be involved in the pathogenesis of CIN.

Role of microRNA dysregulation in childhood acute leukemias: Diagnostics, monitoring and therapeutics: A comprehensive review

MicroRNAs (miRNAs) are short noncoding RNAs that regulate the expression of genes by sequence-specific binding to mRNA to either promote or block its translation; they can also act as tumor suppressors (e.g., let-7b, miR-29a, miR-99, mir-100, miR-155, and miR-181) and/or oncogenes (e.g., miR-29a, miR-125b, miR-143-p3, mir-155, miR-181, miR-183, miR-196b, and miR-223) in childhood acute leukemia (AL). Differentially expressed miRNAs are important factors associated with the initiation and progression of AL. As shown in many studies, they can be used as noninvasive diagnostic and prognostic biomarkers, which are useful in monitoring early stages of AL development or during therapy (e.g., miR-125b, miR-146b, miR-181c, and miR-4786), accurate classification of different cellular or molecular AL subgroups (e.g., let-7b, miR-98, miR-100, miR-128b, and miR-223), and identification and development of new therapeutic agents (e.g., mir-10, miR-125b, miR-203, miR-210, miR-335). Specific miRNA patterns have also been described for commonly used AL therapy drugs (e.g., miR-125b and miR-223 for doxorubicin, miR-335 and miR-1208 for prednisolone, and miR-203 for imatinib), uncovering miRNAs that are associated with treatment response. In the current review, the role of miRNAs in the development, progression, and therapy monitoring of pediatric ALs will be presented and discussed.

PlantMirP-Rice: An Efficient Program for Rice Pre-miRNA Prediction

Rice microRNAs (miRNAs) are important post-transcriptional regulation factors and play vital roles in many biological processes, such as growth, development, and stress resistance. Identification of these molecules is the basis of dissecting their regulatory functions. Various machine learning techniques have been developed to identify precursor miRNAs (pre-miRNAs). However, no tool is implemented specifically for rice pre-miRNAs. This study aims at improving prediction performance of rice pre-miRNAs by constructing novel features with high discriminatory power and developing a training model with species-specific data. PlantMirP-rice, a stand-alone random forest-based miRNA prediction tool, achieves a promising accuracy of 93.48% based on independent (unseen) rice data. Comparisons with other competitive pre-miRNA prediction methods demonstrate that plantMirP-rice performs better than existing tools for rice and other plant pre-miRNA classification.

Identification of Known and Novel MicroRNAs in Raspberry Organs Through High-Throughput Sequencing

MicroRNAs (miRNAs) are a class of small endogenous RNAs that play important regulatory roles in plants by negatively affecting gene expression. Studies on the identification of miRNAs and their functions in various plant species and organs have significantly contributed to plant development research. In the current study, we utilized high-throughput sequencing to detect the miRNAs in the root, stem, and leaf tissues of raspberry (Rubus idaeus). A total of more than 35 million small RNA reads ranging in size from 18 to 35 nucleotides were obtained, with 147 known miRNAs and 542 novel miRNAs identified among the three organs. Sequence verification and the relative expression profiles of the six known miRNAs were investigated by stem-loop quantitative real-time PCR. Furthermore, the potential target genes of the known and novel miRNAs were predicted and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway annotation. Enrichment analysis of the GO-associated biological processes and molecular functions revealed that these target genes were potentially involved in a wide range of metabolic pathways and developmental processes. Moreover, the miRNA target prediction revealed that most of the targets predicted as transcription factor-coding genes are involved in cellular and metabolic processes. This report is the first to identify miRNAs in raspberry. The detected miRNAs were analyzed by cluster analysis according to their expression, which revealed that these conservative miRNAs are necessary for plant functioning. The results add novel miRNAs to the raspberry transcriptome, providing a useful resource for the further elucidation of the functional roles of miRNAs in raspberry growth and development.

miR-155 indicates the fate of CD4+ T cells

MicroRNAs (miRNAs) are a class of short noncoding RNAs that regulate the translation of target messenger RNA (mRNA) and consequently participate in a variety of biological processes at the posttranscriptional level. miR-155, encoded within a region known as the B cell integration cluster (BIC), plays multifunctional roles in shaping lymphocytes ranging from biological development to adaptive immunity. It has been revealed that miR-155 plays a key role in fine-tuning the regulation of lymphocyte subsets, including dendritic cells (DCs), macrophages, B cells, and CD8⁺ and CD4⁺ T cells. Antigen-specific CD4⁺ T lymphocytes are critical for host defense against pathogens and prevention of damage resulting from excessive inflammation. Over the past years, various studies have shown that miR-155 plays a critical role in CD4⁺ T cells function. Therefore, we summarize multiple target genes of miR-155 that regulate aspects of CD4⁺ T cells immunity, particularly CD4⁺ T cells differentiation, in this review. In addition, we also focus on the role of miR-155 in the regulation of immunological diseases, suggesting it as a potential disease biomarker and therapeutic target.

A Systemic Review on the Regulatory Roles of miR-34a in Gastrointestinal Cancer

MicroRNAs (miRNAs) are a class of endogenous non-coding single-stranded small-molecule RNAs that regulate gene expression by repressing target messenger RNA (mRNA) translation or degrading mRNA. miR-34a is one of the most important miRNAs participating in various physiological and pathological processes. miR-34a is abnormally expressed in a variety of tumors. The roles of miR-34a in gastrointestinal cancer (GIC) draw lots of attention. Numerous studies have demonstrated that dysregulated miR-34a is closely related to the proliferation, differentiation, migration, and invasion of tumor cells, as well as the diagnosis, prognosis, treatment, and chemo-resistance of tumors. Thus, we systematically reviewed the abnormal expression and regulatory roles of miR-34a in GICs including esophageal cancer (EC), gastric cancer (GC), colorectal cancer (CRC), hepatocellular carcinoma (HCC), pancreatic cancer (PC), and gallbladder cancer (GBC). It may provide a profile of versatile roles of miR-34a in GICs.

A self-powered 3D DNA walker with programmability and signal-amplification for illuminating microRNA in living cells

We construct a target-triggered, self-powered 3D DNA walker for achieving intracellular signal amplification and sensitive imaging analysis of microRNAs.