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Alzheimer's disease (AD), the most frequently diagnosed dementia, is a senile neurodegenerative disorder characterized by amnesia and cognitive dysfunction. Unfortunately, there are still no successful strategies to prevent AD progression. Thus, the vast majority of research focuses on recognizing risk factors for developing and progressing this disease. Human spirochetes, fungi, Borrelia burgdorferi, Chlamydophila pneumoniae, Helicobacter pylori, and human herpes simplex virus type 1 (HSV-1) have all been implicated in the development and progression of AD. Identifying microRNAs (miRs) encoded by DNA viruses has indicated that viruses can be evolved to exploit RNA silencing to regulate host and viral genes. Similar to host miR, v-miR can interact with the 3' untranslated region (UTR) of the target mRNA to regulate gene expression. Although HSV-1 can also encode various miRs, their significance in the development and progression of AD is still unclear. In the present study, utilizing the bioinformatics approach (R software and related packages), we analyzed the differentially expressed genes (DEGs) in AD samples (grey matter) of GSE37263 dataset obtained from the NCBI Gene Expression Omnibus (GEO). Then, the sequences of HSV-1-encoded-miRs were retrieved from miRbase, and their targets were predicted by miRDB. Afterward, the common genes between downregulated DEGs in AD and targets of HSV-1-encoded miRs were identified to shed new light on the relationship between HSV-1 infection and AD development. Our results have indicated that HSV-1-encoded-miRs can target the downregulated DEGs in AD, and these aberrant interactions can offer valuable diagnostic/prognostic biomarkers for affected patients.

Hepatocellular carcinoma is one of the major health problems throughout the world with a very poor prognosis. MicroRNAs are small regulatory non-protein-coding RNA molecules. We aimed at investigating microRNA-199 as a potential therapeutic tool for HCC both in vitro and in an experimental model. A therapeutic strategy based on the effect of microRNAs to target genes responsible for liver cancer was adopted in this work. The ability of these small RNAs to potently influence cellular behavior was also investigated. The role of miR-199a in the development of liver cancer has been identified using a systematic literature search using miRBase. HepG2 cell line was used to test the effect of miRNA199a in vitro. Hepatocellular carcinoma was induced in Male Balb/C mice by diethylnitrosamine (DEN). Mice were treated with miRNA-199a and sacrificed after 16 weeks and blood samples and liver specimens were collected for biochemical and histopathological assessment. Histopathological examination of liver specimens after miRNA 199a treatment showed regression of Hepatocellular carcinoma with restoration of normal architecture. AFP, VEGF and TNFα levels decreased after treatment with miRNA 199a. Caspase 3 and 9; showed decreased expression in animals treated with miRNA 199a than non-treated ones.

An oligonucleotide DNA probe has been developed for the application in the DNA electrochemical biosensor for the early diagnosis of coronavirus disease (COVID‐19). Here, the virus microRNA from the N‐gene of severe acute respiratory syndrome‐2 (SARS‐CoV‐2) was used for the first time as a specific target for detecting the virus and became a framework for developing the complementary DNA probe. The sequence analysis of the virus microRNA was carried out using bioinformatics tools including basic local alignment search tools, multiple sequence alignment from CLUSTLW, microRNA database (miRbase), microRNA target database, and gene analysis. Cross‐validation of distinct strains of coronavirus and human microRNA sequences was completed to validate the percentage of identical and consent regions. The percent identity parameter from the bioinformatics tools revealed the virus microRNAs’ sequence has a 100% match with the genome of SARS‐CoV‐2 compared with other coronavirus strains, hence improving the selectivity of the complementary DNA probe. The 30 mer with 53.0% GC content of complementary DNA probe 5′ GCC TGA GTT GAG TCA GCA CTG CTC ATG GAT 3′ was designed and could be used as a bioreceptor for the biosensor development in the clinical and environmental diagnosis of COVID‐19., An oligonucleotide DNA probe has been developed for the application in the DNA electrochemical biosensor for the early diagnosis of coronavirus disease (COVID‐19). Here, the virus microRNA from the N‐gene of severe acute respiratory syndrome‐2 (SARS‐CoV‐2) was used for the first time as a specific target for detecting the virus and became a framework for developing the complementary DNA probe.

MiRNA-size small RNAs, abbreviated as sRNAs, are increasingly being discovered as research progresses and omics technologies development in prokaryotes. However, there is a paucity of data concerning whether or not sRNAs exist in cyanobacteria and regulate the resistance to oxidative stress. In this investigation, small RNA libraries were constructed from the control, 50-nM and 100-nM H2O2 treatments of Spirulina platensis. By high-throughput sequencing, 23 candidate sRNAs showed significantly differential expression under oxidative stress, among which eight sRNAs were identified with the similar expression patterns as the sequencing results by real-time qPCR. By nucleic acid hybridisation, the corresponding expression changes also demonstrated that sequencing results of sRNAs were feasible and credible. By bioinformatics prediction and structure identification, 43 target genes were predicted for 8 sRNAs in plant miRNA database, among which 29 were annotated into the genome and related metabolic pathways of S. platensis. By COG functional classification and KEGG pathway analysis, 31 target genes were predicted to be directly or indirectly involved in the defence mechanism of H2O2 stress. Thirteen target genes displayed reversely changing patterns compared with those of their sRNAs under H2O2 treatment. These findings provide compelling evidence that these sRNAs in S. platensis play a crucial role in oxidative stress responses, and thus provide a theoretical reference for improving the stress-triggering physiological regulation.

MicroRNAs (miRNAs) are small single-stranded non-coding RNAs that act as the master regulator of animal growth and development. RNA-RNA interaction is an important mechanism of gene regulation during biotic and abiotic stress. Heat stress (HS) is one of the most important abiotic factors which affect the growth, milk yield and reproductive health of the dairy animals. In the present investigation, we identified 387 known and 77 novel miRNAs from Tharparkar (TH) and Karan Fries (KF) cattle under HS condition. Family distribution analysis showed the identified miRNAs belong to more than 15 different families in which miR-2284 was the most abundant. We identified 42,350 targets for the known miRNAs reported in cattle. Pathway analysis of the identified targets showed most of the target genes were involved in cancer, mitogen-activated protein kinase (MAPK) signaling, calcium signaling, Ras signaling, and cAMP signaling pathways. Differential gene expression showed more than 344 miRNAs changed their expression significantly between control and HS condition. Heat map was generated for the top 20 most up and downregulated miRNAs. Ten miRNAs were validated using qRT-PCR to be heat responsive, based on read count value and differential gene expression. These novel miRNAs are new addition to the miRNA database of cattle. This study provides an overview of miRNA profile and their interaction with the target genes which leads to further understanding in deciphering the thermotolerance mechanism in cattle.

Wen-Ying Yu,1,* Wei Cai,2,* Hua-Zhong Ying,1 Wen-You Zhang,1 Huan-Huan Zhang,1 Chen-Huan Yu1,3,4 1Zhejiang Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences (Hangzhou Medical College), Hangzhou, People’s Republic of China; 2Department of Traditional Chinese Medicine, Zhejiang Pharmaceutical College, Ningbo, People’s Republic of China; 3Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou, People’s Republic of China; 4Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, People’s Republic of China*These authors contributed equally to this workCorrespondence: Chen-Huan YuInstitute of Cancer and Basic Medicine, Chinese Academy of Sciences, Dongfang Street 150, Hangzhou, Zhejiang, 310018, People’s Republic of ChinaEmail yuchenhuan2002@163.comPurpose: Plant-derived exogenous microRNAs (miRNAs) regulate human physiological functions by blocking the translation of target mRNAs. Although several computational approaches have been developed to elucidate the interactions of cross-species miRNAs and their targets in mammals, the number of verified plant miRNAs is still limited, and the biological roles of most exogenous plant miRNAs remain unknown.Methods: A miRNA mimic library-based phenotypic screening, which contained 8394 plant mature miRNAs published in the official database miRbase, was performed to identify more novel bioactive plant miRNAs for the prevention of hepatic fibrosis. Inhibition of candidates for the activation of hepatic stellate cells (HSCs) and the underlying mechanisms were evaluated in TGF-β 1- and PDGF-exposed HSC models. The protective effects of the candidates against CCl4-induced liver fibrosis were evaluated in a mouse model.Results: Among the 8394 plant mature miRNAs reported in the official database miRBase, five candidates were found to effectively inhibit the differentiation of HSCs. gma-miR-159a (miR159a) exerted the strongest inhibitory activities on both TGF-β 1- and PDGF-induced HSC activation and proliferation by inhibiting the GSK-3β-mediated NF-κB and TGF-β 1 pathways. Moreover, miR159a was mainly accumulated in the liver after intravenous injection, and it reduced CCl4-induced hepatic fibrosis and inflammation in mice.Conclusion: Results indicated that miR159a has the therapeutic potential for preventing hepatic fibrosis. This study provides a novel strategy for achieving natural nucleic acid drugs.Keywords: cross-kingdom regulation, miRNA library, GSK-3β, apoptosis, hepatic fibrosis, inflammation

Exosomes are membrane vesicles containing proteins, lipids, DNA, mRNA, and micro RNA (miRNA). Exosomal miRNA from donor cells can regulate the gene expression of recipient cells. Here, Ri chickens were divided into resistant (Mx/A; BF2/B21) and susceptible (Mx/G; BF2/B13) trait by genotyping of Mx and BF2 genes. Then, Ri chickens were infected with H5N1, a highly pathogenic avian influenza virus (HPAIV). Exosomes were purified from blood serum of resistant chickens for small RNA sequencing. Sequencing data were analysed using FastQCv0.11.7, Cutadapt 1.16, miRBase v21, non-coding RNA database, RNAcentral 10.0, and miRDeep2. Differentially expressed miRNAs were determined using statistical methods, including fold-change, exactTest using edgeR, and hierarchical clustering. Target genes were predicted using miRDB. Gene ontology analysis was performed using gProfiler. Twenty miRNAs showed significantly different expression patterns between resistant control and infected chickens. Nine miRNAs were up-regulated and 11 miRNAs were down-regulated in the infected chickens compared with that in the control chickens. In target gene analysis, various immune-related genes, such as cytokines, chemokines, and signalling molecules, were detected. In particular, mitogen-activated protein kinase (MAPK) pathway molecules were highly controlled by differentially expressed miRNAs. The result of qRT-PCR for miRNAs was identical with sequencing data and miRNA expression level was higher in resistant than susceptible chickens. This study will help to better understand the host immune response, particularly exosomal miRNA expression against HPAIV H5N1 and could help to determine biomarkers for disease resistance.

Background Coronavirus disease 2019 (COVID-19) caused by a novel betacoronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has attracted top health concerns worldwide within a few months after its appearance. Since viruses are highly dependent on the host small RNAs (microRNAs) for their replication and propagation, in this study, top miRNAs targeting SARS-CoV-2 genome and top miRNAs targeting differentially expressed genes (DEGs) in lungs of patients infected with SARS-CoV-2, were predicted. Methods All human mature miRNA sequences were acquired from miRBase database. MiRanda tool was used to predict the potential human miRNA binding sites on the SARS-CoV-2 genome. EdgeR identified differentially expressed genes (DEGs) in response to SARS-CoV-2 infection from GEO147507 data. Gene Set Enrichment Analysis (GSEA) and DEGs annotation analysis were performed using ToppGene and Metascape tools. Results 160 miRNAs with a perfect matching in the seed region were identified. Among them, there was 15 miRNAs with more than three binding sites and 12 miRNAs with a free energy binding of −29 kCal/Mol. MiR-29 family had the most binding sites (11 sites) on the SARS-CoV-2 genome. MiR-21 occupied four binding sites and was among the top miRNAs that targeted up-regulated DEGs. In addition to miR-21, miR-16, let-7b, let-7e, and miR-146a were the top miRNAs targeting DEGs. Conclusion Collectively, more experimental studies especially miRNA-based studies are needed to explore detailed molecular mechanisms of SARS-CoV-2 infection. Moreover, the role of DEGs including STAT1, CCND1, CXCL-10, and MAPKAPK2 in SARS-CoV-2 should be investigated to identify the similarities and differences between SARS-CoV-2 and other respiratory viruses., Highlights • miR-29 family had 11 binding site on the SARS-COV-2 genome. • miR-29a/b, 21, 761, 3130, 3167 and miR-3175 bound to the spike coding sequence. • miR-16, 146a, 21, 615 and let-7b/e targeted SARS-CoV-2 induced DEGs. • miR-146a, 203a, 24, 615 and miR-16 targeted DEGs involved in viral prosesess

Purpose To investigate the microRNA (miRNA) profile in patients with different stages of pseudoexfoliation (PXF). Methods Peripheral blood of patients with PXF (naive to medical therapy and with no systemic disease/drugs) with ocular hypertension (OHT) and pseudoexfoliation glaucoma (PXG) was evaluated in triplicate for miRNA profiling using polymerase chain reaction (PCR) arrays. Those identified in the discovery stage were validated with evaluation of serum transforming growth factor-β1 (TGF-β1) levels by ELISA. The downstream targets of TGF-β1 and unfolded protein response (UPR) were analyzed using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Predicted targets of the identified miRNA and KEGG pathway analysis were done using miRbase and DIANA tools mirPathv3.1. Results We found hsa-miR-122-5p, hsa-miR-124-3p and hsa-miR-424-5p to be upregulated in PXG targeting 3 specific pathways namely TGF-β1, fibrosis/ECM and proteoglycan metabolism with common effectors like SMAD/3/2. The unfolded protein response (UPR) genes were significantly downregulated in all stages of PXF suggesting this as the key mechanism for protein aggregates in PXF syndrome. Serum TGF-β1 was significantly upregulated as disease progressed to later stages in PXG. This elevation in advanced stages was associated with significantly differential expression of downstream pathways and fibrotic genes in OHT compared to PXG predominantly through the SMAD3, a canonical pathway marker. Conclusion Circulatory miRNA differentially regulating TGF-β1 and downstream targets including UPR genes may be the key mechanisms for glaucoma onset in PXF.

With fast-evolving next-generation sequencing technology, a great amount of plant genome and transcriptome data are becoming available. Due to the availability of mature microRNA (miRNA) sequence information from the miRBase (release 21) database, it is possible to predict endogenous target mimics (eTMs) in plant by searching seed-matched target sites. We identified a total of 2669 non-redundant eTM records in 43 plant species to create a specialized web-based database platform. The platform is named PendoTMBase, which can provide details of the eTMs. Predicted pairing structure between eTMs and their target miRNA, expression levels of eTMs pairs and associated GO annotations are also stored in the database. With evaluations performed in silico, we have found that the eTMs are representative and fit for genetic studies and high value-added plants breeding. The platform also provides a function of predicting novel eTMs based on the miRNA sequences submitted by users.

Gene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, the same statistical principles are now available for all omics types. In 2016, we published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs. Here, we present miEAA 2.0, supporting miRNA input from ten frequently investigated organisms. To facilitate inclusion of miEAA in workflow systems, we implemented an Application Programming Interface (API). Users can perform miRNA set enrichment analysis using either the web-interface, a dedicated Python package, or custom remote clients. Moreover, the number of category sets was raised by an order of magnitude. We implemented novel categories like annotation confidence level or localisation in biological compartments. In combination with the miRBase miRNA-version and miRNA-to-precursor converters, miEAA supports research settings where older releases of miRBase are in use. The web server also offers novel comprehensive visualizations such as heatmaps and running sum curves with background distributions. We demonstrate the new features with case studies for human kidney cancer, a biomarker study on Parkinson’s disease from the PPMI cohort, and a mouse model for breast cancer. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2.

MicroRNAs (miRNAs) are small RNAs that regulate mRNA expression and have been targeted as biomarkers of organ damage and disease. To explore the utility of miRNAs to assess injury to specific tissues, a tissue atlas of miRNA abundance was constructed. The Rat Atlas of Tissue-specific and Enriched miRNAs (RATEmiRs) catalogues miRNA sequencing data from 21 and 23 tissues in male and female Sprague-Dawley rats, respectively. RATEmiRs identifies tissue-enriched (TE), tissue-specific (TS), or organ-specific (OS) miRNAs via comparisons of one or more tissue or organ vs others. We provide a brief overview of RATEmiRs and present how to use it to detect miRNA expression abundance of candidate biomarkers as well as to compare the expression of miRNAs between rat and human. The database is available at https://www.niehs.nih.gov/ratemirs/.

Marek's disease (MD) is a lymphoproliferative disease of domestic chickens caused by a cell-associated oncogenic alpha-herpesvirus, Marek's disease virus (MDV). Clinical signs of MD include bursal/thymic atrophy, neurologic disorders, and T cell lymphomas. MiRNAs play key roles in regulation of gene expression by targeting translational suppression or mRNA degradation. MDV encodes miRNAs that are associated with viral pathogenicity and oncogenesis. In this study, we performed miRNA sequencing in the bursal tissues, non-tumorous but viral-induced atrophied lymphoid organ, from control and infected MD-resistant and susceptible chickens at 21 days post infection. In addition to some known miRNAs, a minimum of 300 novel miRNAs were identified in each group that mapped to the chicken genome with no sequence homology to existing miRNAs in chicken miRbase. Comparative analysis identified 54 deferentially expressed miRNAs between the chicken lines that might shed light on underlying mechanism of bursal atrophy and resistance or susceptibility to MD.

Pseudorabies virus (PRV) belongs to the Alphaherpesvirinae subfamily of Herpesviridae. PRV-induced pseudorabies is a highly contagious disease that has caused huge economic losses to the global swine industry. The PRV gE/gI gene deletion vaccine strain (Fa ΔgE/gI strain) constructed from the PRV Fa wild-type strain was shown to have a protective effect against infection. However, the interaction between PRV gE/gI genes and host miRNA needs further exploration, and little is known about the regulatory mechanisms of non-coding RNAs during PRV infection. miRNAs play a key regulatory role in viral infection and immune responses, so we analyzed the differential expression of miRNAs induced by the PRV Fa ΔgE/gI strain and Fa wild-type strain in the PK15 cell line. High-throughput sequencing reads were aligned to known Sus scrofa pre-miRNAs in the miRBase database. Target genes of differentially expressed miRNAs were predicted using the miRGen 3.0 database, then filtered miRNA target genes were subjected to Gene Ontology (GO) analysis and Search Tool for the Retrieval of Interacting Genes/ Proteins (STRING) analysis. Stem-loop quantitative real-time PCR was performed to confirm the accuracy of high-throughput sequencing data. In total, 387, 472, and 490 annotated and novel mature miRNAs were identified from PRV Fa ΔgE/gI strain-infected, Fa wild-type strain-infected, and non-infected PK-15 cells, respectively. Five PRV-encoded miRNAs were also identified. GO analysis showed that target genes of differentially expressed miRNAs in PRV Fa ΔgE/gI strain-infected and Fa wild-type strain-infected PK-15 cells were mainly involved in biological regulation and metabolic processes. STRING analysis showed that immune-related target genes of differentially expressed miRNAs in the Toll-like receptor signaling pathway, B cell receptor signaling pathway, T cell receptor signaling pathway, nuclear factor-κB signaling pathway, and transforming growth factor-β signaling pathway were interrelated. This is the first report of the small RNA transcriptome in PRV mutant wild-type strain-infected and Fa ΔgE/gI strain-infected porcine cell lines. Our findings will contribute to the prevention and treatment of PRV mutant strains. Electronic supplementary material The online version of this article (10.1007/s11262-020-01760-6) contains supplementary material, which is available to authorized users.

Food-derived plant microRNAs are suggested to control human genes by “cross-kingdom” regulation. We examined microRNAs in sprouts from Brassica rapa sylvestris, known as broccoletti, which are widely used as sulforaphane supplements, and assessed their influence on pancreatic cancer. RNA was isolated from 4-day-old sprouts, followed by deep sequencing and bioinformatic analysis. We identified 2 new and 745 known plant microRNA sequences in the miRbase database and predicted 15,494 human target genes and 76,747 putative 3′-UTR binding sites in these target genes. The most promising candidates were the already known microRNA sequence bra-miR156g-5p and the new sequence Myseq-330, both with predicted human target genes related to apoptosis. The overexpression of the respective oligonucleotides by lipofection did not alter the viability, apoptosis, clonogenicity, migration or associated protein expression patterns in pancreatic cancer cells. These data demonstrate that broccoletti sprouts contain microRNA sequences with putative binding sites in human genes, but the sequences evaluated here did not affect cancer growth. Our database of broccoletti-derived microRNA sequences provides a valuable tool for future analysis.

BACKGROUND: Triple-negative breast cancers (TNBC) represent an important subtype characterized by an absence of ER, PR, and HER2, and therefore are not responsive to current targeted therapies. TNBC is considered a clinically aggressive subtype of breast cancer with lower survival rates and a higher risk of metastasis development. There is a higher prevalence of TNBC in women of African descent. Furthermore, there is evidence that African American (AA) women have worse clinical outcomes compared with Caucasian American (CA) women with TNBC. Several studies have begun to evaluate the major drivers of this health disparity including socio-economic status, cultural influences, and biological factors; however, to date, researchers have not been able to elucidate the mechanisms behind the aggressive biology seen in AA women with TNBC. Recently miRNAs were identified to play a role in breast cancer through the regulation of cellular processes associated with aggressive tumor phenotypes, such as TNBC. MiRNAs are a likely therapeutic target because they are involved in the regulation of several essential functions in cancer cells such as proliferation, migration, invasion, and apoptosis. For miRNAs to reliably be used as cancer therapeutic agents in clinical settings, miRNA signatures of specific cancer subtypes based on ethnicity must be identified. Here, we hypothesize that differential expression of miRNAs contributes to the more aggressive phenotype observed in AA patients compared to CA patients with TNBC. In this study, our primary goal is to characterize and compare the miRNA expression profiles of breast tumor tissue from AA and CA patients. METHODS: miRNA expression data of TNBC patients, contained in the TCGA database, were analyzed to identify a set of miRNAs with prognostics significance to be used as potential biomarkers. From the acquired miRNA-seq data we determined a total of 175 differentially expressed miRNAs between AAW and CA triple negative breast cancer tissue and decided to characterize 8 miRNAs that have been previously determined to have a role in breast cancer. RESULTS: In AA tumor tissue there was the marked loss of the following tumor suppressors: let-7b, miR-200b,-130b, and -375 and the overexpression of the following oncogenic miRNAs: miR-181c, 17, 21, 29c. In TNBC, miR-200 and 130b are known to sensitize cells to apoptosis, inhibit metastasis formation, and are associated with patient survival. Additionally, the expression of oncogenic miRNAs; miR-181c, 17, 21, 29c are associated with worse prognosis in TNBC. Target gene prediction using miRBase revealed that several of the dysregulated miRNAs were involved in the epithelial-mesenchymal transition, a key step in metastasis formation. Next, we evaluated how miRNA dysregulation could potentially affect patient survival. Using data from the TCGA we were able to extrapolate survival probability data (combined CAW and AAW n=203). We determined that 5-year survival was significantly decreased in patients that had high expression of miR-181c and miR-17 and let-7b and miR-200b had protective effects. CONCLUSIONS: These results support that there is a distinct miRNA expression signature in AAW and CAW with TNBC which may correlate to prognosis. Our results will contribute to the application of miRNAs as novel therapeutic tools against TNBC in AA patients and represents an innovative approach to address the health disparities seen in the AA population. Citation Format: Ches'que M. Phillips, Yaguang Xi. The effect of microRNA dysregulation on health disparities observed in African American women in triple negative breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P1-05-05.

In the present study, we used microRNA (miRNA) sequencing to discover and explore the expression profiles of known and novel miRNAs in 1000 ng/ml LPS stimulated for 8 h vis-à-vis non-stimulated (i.e. control) PBMCs isolated from the blood of healthy pigs. A total of 291 known miRNAs were bio-computationally identified in porcine PBMCs, and 228 novel miRNAs (not enlisted in the swine mirBase) were identified. Among these miRNAs, ssc-miR-148a-3p, ssc-let-7g, ssc-let-7f, 3_8760, ssc-miR-26a, ssc-miR-451, ssc-miR-21, ssc-miR-30d, ssc-miR-99a and ssc-miR-103 were the top 10 most abundant miRNAs in porcine PBMCs. Through miRNA differential analysis combined with quantitative PCR, we found the expressions of ssc-miR-122, ssc-miR-129b, ssc-miR-17-5p and ssc-miR-152 were significantly changed in porcine PBMCs after LPS stimulation. Furthermore, targets prediction and function analysis indicated a significant enrichment in gene ontology functional categories related to diseases, immunity and inflammation. In conclusion, this study on profiling of miRNAs expressed in LPS-stimulated PBMCs provides an important reference point for future studies on regulatory roles of miRNAs in porcine immune system.

Primary immune thrombocytopenia (ITP) is an autoimmune bleeding disorder which characterizes with platelet production impairment and platelet destruction increment. CD4+CD25+ Foxp3+ Treg cells (Tregs) are involved in the immune pathogenesis of ITP. MicroRNAs (miRNAs) are also involved in ITP and their loss of function is shown to facilitate immune disorders. Thus, the miRNA expression profile in Tregs from ITP was analyzed in this study. We assessed the genome-wide miRNA expression profile of three newly diagnosed adult patients with ITP and three healthy controls using microarray analysis of CD4+CD25+CD127dim/− Tregs that were sorted using an immune magnetic bead kit. The miRNA microarray chip was based on miRBase 18.0 and Volcano Plot filtering software used to analyze the miRNA profile in Tregs. Distinct miRNA expression was further validated by fluorescence-based real-time quantitative PCR (qPCR). We found that 502 human miRNAs were differentially expressed (244 upregulated and 258 downregulated) in patients with ITP compared with healthy donors. We identified 37 miRNAs expressed significantly, including 26 upregulated and 11 downregulated. Among the deregulated miRNAs, three downregulated miRNAs including miR-155–5p, miR-146b-5p, and miR-142–3p were selected for qPCR verification. We confirmed that miR-155–5p, miR-146b–5p, and miR-142–3p were significantly decreased in Tregs from patients with ITP compared with healthy controls. Compared with the healthy controls, miRNAs expressed differentially in the Tregs of patients with ITP. The levels of expression of miR-155–5p, miR-146b-5p, and miR-142–3p were significantly decreased. Therefore, the deregulation of miRNAs may affect the function of Tregs in the course of ITP.

Background MicroRNAs (miRNAs) are non-coding short, single-stranded RNA molecules that may serve as biomarkers for various inflammatory and molecular mechanisms underlying bone and tissue remodeling consequent to orthodontic force application. Methods A thorough literature search in major databases was conducted in March 2021 to generate evidence for miRNAs in orthodontics, with prior PROSPERO registration. The initial search revealed 920 articles, subjected to strict selection criteria according to PRISMA, and resulted in final inclusion of four studies. Quality assessment by QUADAS-2 classified three studies as unclear risk-of-bias while the applicability was high. Further, bioinformatic analysis was performed to identify the target genes from the miRNA database (miRDB) and TargetScan databases and their protein-protein interaction pathways with the STRING analysis. Results Multiple miRNAs in gingival crevicular fluid (GCF) of orthodontic patients were seen, including miRNA-21, 27(a/b), 29(a/b/c), 34,146(a/b), 101, and 214 along with matrix metalloproteinases (MMPs)-1, 2, 3, 8, 9, 14 in one study. A statistically significant increase in expression of miRNA-29a/b/c,101, 21 from pre-treatment (before initiation of retraction) was seen to reach a peak at 4–6 weeks (wk) of retraction. On the contrary, miRNA-34a showed downregulation from the 1 day to 4 wk of retraction and also, negatively correlated with MMPs-2,9,14 levels at the same observation times. The distance of canine movement showed mild correlation with miRNA-27a/b, 214 at 2 wk of retraction. Bioinformatics revealed 1213 mutual target genes which were analyzed for inter-relational pathways using Cytoscape plugin, MCODE. Further, 894 prominent protein interactions were identified from the STRING database and SMAD4, IGF1, ADAMTS6, COL4A1, COL1A1, COL3A1, FGFR1, COL19A1, FBN1, COL5A1, MGAT4A, LTBP1, MSR1, COL11A1, and COL5A3 were recognized as the hub genes. Their interactions were able to isolate multiple miRNAs: hsa-miR-34a-5p, hsa-miR-29b-2-5p, hsa-miR-29b-3p, hsa-miR-34a-3p, hsa-miR-27a-5p, hsa-miR-29a-5p, hsa-miR-29b-1-5p, hsa-miR-29c-3p, hsa-miR-214-5p, hsa-miR-27a-3p, hsa-miR-29a-3p, hsamiR-146-5p, which were found promising as biomarkers for tooth movement. Conclusions Our results support using miRNAs as biomarkers in varied orthodontic study designs and for inter-relationships with pathological settings like periodontal disease, pre-malignancies, or conditions like obesity or metabolic irregularities, etc. The identified target genes and their protein interaction pathways can be used to propose precision therapies, focusing on ideal tooth movement with minimal iatrogenic side-effects.

We have predicted miRNAs, their targets and lncRNAs from the genome of Brassica oleracea along with their functional annotation. Selected miRNAs and their targets are experimentally validated. Roles of these non-coding RNAs in post-transcriptional gene regulation are also deciphered. Cauliflower (Brassica oleracea var. Botrytis) is an important vegetable crop for its dietary and medicinal values with rich source of vitamins, dietary fibers, flavonoids and antioxidants. MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs), which regulate gene expression by inhibiting translation or by degrading messenger RNAs (mRNAs). On the other hand, long non-coding RNAs (lncRNAs) are responsible for the up regulation and the down regulation of transcription. Although the genome of cauliflower is reported, yet the roles of these ncRNAs in post-transcriptional gene regulation (PTGR) remain elusive. In this study, we have computationally predicted 355 miRNAs, of which 280 miRNAs are novel compared to miRBase 22.1. All the predicted miRNAs belong to 121 different families. We have also identified 934 targets of 125 miRNAs along with their functional annotation. These targets are further classified into biological processes, molecular functions and cellular components. Moreover, we have predicted 634 lncRNAs, of which 61 are targeted by 30 novel miRNAs. Randomly chosen 10 miRNAs and 10 lncRNAs are experimentally validated. Five miRNA targets including squamosa promoter-binding-like protein 9, homeobox-leucine zipper protein HDG12-like, NAC domain-containing protein 100, CUP-SHAPED COTYLEDON 1 and kinesin-like protein NACK2 of four miRNAs including bol-miR156a, bol-miR162a, bol-miR164d and bol-miR2673 are also experimentally validated. We have built network models of interactions between miRNAs and their target mRNAs, as well as between miRNAs and lncRNAs. Our findings enhance the knowledge of non-coding genome of cauliflower and their roles in PTGR, and might play important roles in improving agronomic traits of this economically important crop.

Gene regulation is of utmost importance to cell homeostasis; thus, any dysregulation in it often leads to disease. MicroRNAs (miRNAs) are involved in posttranscriptional gene regulation and consequently, their dysregulation has been associated with many diseases.MiRBase version 21 contains microRNAs from about 200 species organized into about 70 clades. It has been shown that not all miRNAs collected in the database are likely to be real and, therefore, novel routes to delineate between correct and false miRNAs should be explored. We introduce a novel approach based on k-mer frequencies and machine learning that assigns an unknown/unlabeled miRNA to its most likely clade/species of origin. A simple way to filter new data would be to ensure that the novel miRNA categorizes closely to the species it is said to originate from. For that, an ensemble classifier of multiple two-class random forest classifiers was designed, where each random forest was trained on one species-clade pair. The approach was tested with different sampling methods on a dataset that was taken from miRBase version 21 and it was evaluated using a hierarchical F-measure. The approach predicted 81% to 94% of the test data correctly, depending on the sampling method. This is the first classifier that can classify miRNAs to their species of origin. This method will aid in the evaluation of miRNA database integrity and analysis of noisy miRNA samples.

In this era of big data, sets of methodologies and strategies are designed to extract knowledge from huge volumes of data. However, the cost of where and how to get this information accurately and quickly is extremely important, given the diversity of genomes and the different ways of representing that information. Among the huge set of information and relationships that the genome carries, there are sequences called miRNAs (microRNAs). These sequences were described in the 1990s and are mainly involved in mechanisms of regulation and gene expression. Having this in mind, this chapter focuses on exploring the available literature and providing useful and practical guidance on the miRNA database and tools topic. For that, we organized and present this text in two ways: (a) the update reviews and articles, which best summarize and discuss the theme; and (b) our update investigation on miRNA literature and portals about databases and tools. Finally, we present the main challenge and a possible solution to improve resources and tools.

MicroRNA-like small RNAs (milRNAs) and their regulatory roles in the interaction between plant and fungus have recently aroused keen interest of plant pathologists. Trichoderma spp., one of the widespread biocontrol fungi, can promote plant growth and induce plant disease resistance. To investigate milRNAs potentially involved in the interaction between Trichoderma and tomato roots, a small RNA (sRNA) library expressed during the interaction of T. asperellum DQ-1 and tomato roots was constructed and sequenced using the Illumina HiSeqTM 2500 sequencing platform. From 13,464,142 sRNA reads, we identified 21 milRNA candidates that were similar to other known microRNAs in the miRBase database and 22 novel milRNA candidates that possessed a stable microRNA precursor hairpin structure. Among them, three milRNA candidates showed different expression level in the interaction according to the result of stem-loop RT-PCR indicating that these milRNAs may play a distinct regulatory role in the interaction between Trichoderma and tomato roots. The potential transboundary milRNAs from T. asperellum and their target genes in tomato were predicted by bioinformatics analysis. The results revealed that several interesting proteins involved in plant growth and development, disease resistance, seed maturation, and osmotic stress signal transduction might be regulated by the transboundary milRNAs. To our knowledge, this is the first report of milRNAs taking part in the process of interaction of T. asperellum and tomato roots and associated with plant promotion and disease resistance. The results might be useful to unravel the mechanism of interaction between Trichoderma and tomato.

Pancreatic cancer is one of the most malignant digestive tract tumors with the worst prognosis. Dauricine (Dau) can inhibit the proliferation of the pancreatic cancer cell line, and has the potential to be used as an adjuvant drug against pancreatic cancer; however, the working mechanism of Dau has not been elucidated. To unravel the effects and mechanisms of Dau on proteins and metabolic pathways, we evaluated the mRNA and microRNA expression in BxPC3 cells treated with Dau. The differences in the gene expression were compared using principal component analysis using mRNA and miRNA data to detect and analyze the sample discrimination. 187 miRNA and 907 mRNA that were significantly differentially expressed were identified using Python programming. On comparing genes and miRNAs in the DISEASES database, 79 known miRNA and 47 mRNA were found to be affected by Dau. The up-regulated and down-regulated genes were annotated with GO biological processes to determine the functional effect. Interactions between mRNA and mRNA were analyzed using the STRING database and the miRBase database was queried to obtain experimentally verified interactions between miRNA and mRNA as edges of miRNA and mRNA in the network. Finally, 413 sites and 2125 sides of the network were obtained, including 1 up-regulated and 18 down-regulated miRNAs. The expression of 19 miRNAs was identified by qPCR. The analysis of the protein-protein interaction network, using the Molecular Complex Detection (MCODE) plug-in of cytoscape, helped in identifying 12 important sub-networks. Most subnets are indirectly or directly related to specific miRNAs. This study provides evidence for the anticancer effect of Dau as a potential anticancer compound.

Background/Aims: This study aimed to compare the clinical value of the peak time point and area under the curve (AUC) of miRNAs and conventional biomarkers in acute myocardial infarction (AMI).Methods: A literature search was carried out in PubMed, Web of Science, Embase, and Cochrane systematically. Screening studies, extracting data, and assessing article quality were performed independently by two researchers. Also, the names of miRNAs in the included studies were standardized by the miRBase database.Results: A total of 40 studies, encompassing 6,960 participants, were included in this systematic review. The samples of circulating miRNAs were mainly from the plasma. The results of this systematic review displayed that miR-1-3p, miR-19b-3p, miR-22-5p, miR-122-5p, miR-124-3p, miR-133a/b, miR-134-5p, miR-150-5p, miR-186-5p, miR-208a, miR-223-3p, miR-483-5p, and miR-499a-5p reached peak time earlier and showed a shorter time window than the conventional biomarkers despite the different collection times of initial blood samples. miR-1-3p, miR-19b-3p, miR-133a/b, miR-208a/b, miR-223-3p, miR-483-5p, and miR-499a-5p were shown to be more valuable than classical biomarkers for the early diagnosis of AMI, and these miRNAs appeared to have the most potential biomarkers within 4 h of the onset of symptoms except miR-133a/b and miR-208b. Moreover, combined miRNAs or miRNAs combined with classical biomarkers could compensate for the deficiency of single miRNA and conventional biomarker in sensitivity or specificity for an optimal clinical value.Conclusions: miR-1-3p, miR-19b-3p, miR-208a, miR-223-3p, miR-483-5p, and miR-499a-5p are promising biomarkers for AMI due to their satisfactory diagnostic accuracy and short time window (within 4 h of the onset of symptoms).

BackgroundCoronavirus disease 2019 is characterized by the elevation of a wide spectrum of inflammatory mediators, which are associated with poor disease outcomes. We aimed at an in-silico analysis of regulatory microRNA and their transcription factors (TF) for these inflammatory genes that may help to devise potential therapeutic strategies in the future.MethodsThe cytokine regulating immune-expressed genes (CRIEG) was sorted from literature and the GEO microarray dataset. Their co-differentially expressed miRNA and transcription factors were predicted from publicly available databases. Enrichment analysis was done through mienturnet, MiEAA, Gene Ontology, and pathways predicted by KEGG and Reactome pathways. Finally, the functional and regulatory features were analyzed and visualized through Cytoscape.ResultsSixteen CRIEG were observed to have a significant protein-protein interaction network. The ontological analysis revealed significantly enriched pathways for biological processes, molecular functions, and cellular components. The search performed in the MiRNA database yielded 10 (ten) miRNAs that are significantly involved in regulating these genes and their transcription factors.ConclusionAn in-silico representation of a network involving miRNAs, CRIEGs, and TF which take part in the inflammatory response in COVID-19 has been elucidated. These regulatory factors may have potentially critical roles in the inflammatory response in COVID-19 and may be explored further to develop targeted therapeutic strategies and mechanistic validation.

Background Coronavirus disease 2019 is characterized by the elevation of a broad spectrum of inflammatory mediators associated with poor disease outcomes. We aimed at an in-silico analysis of regulatory microRNA and their transcription factors (TF) for these inflammatory genes that may help to devise potential therapeutic strategies in the future. Methods The cytokine regulating immune-expressed genes (CRIEG) were sorted from literature and the GEO microarray dataset. Their co-differentially expressed miRNA and transcription factors were predicted from publicly available databases. Enrichment analysis was done through mienturnet, MiEAA, Gene Ontology, and pathways predicted by KEGG and Reactome pathways. Finally, the functional and regulatory features were analyzed and visualized through Cytoscape. Results Sixteen CRIEG were observed to have a significant protein-protein interaction network. The ontological analysis revealed significantly enriched pathways for biological processes, molecular functions, and cellular components. The search performed in the miRNA database yielded ten miRNAs that are significantly involved in regulating these genes and their transcription factors. Conclusion An in-silico representation of a network involving miRNAs, CRIEGs, and TF, which take part in the inflammatory response in COVID-19, has been elucidated. Thus, these regulatory factors may have potentially critical roles in the inflammatory response in COVID-19 and may be explored further to develop targeted therapeutic strategies and mechanistic validation.