Predicting Functional MicroRNA-mRNA Interactions

Integrated Analysis of miRNA and mRNA Regulation Network in Hypertension

Hypertension is the most common chronic disease. Early diagnosis is helpful for early medical intervention. The miRNAs and the messenger RNAs (mRNAs) network may be valuable disease diagnosis markers. We aimed to explore the diagnostic value of the miRNA-mRNA network for hypertension patients. Data of miRNAs and mRNAs expression were obtained from the Gene Expression Omnibus database. The weighted gene co-expression network analysis was performed to screen hypertension-related gene modules, and these genes undergone functional enrichment analysis using "clusterProfiler" package. Differential expression analysis was applied on miRNAs expression profiles using "limma" package. TargetScanHuman and miRDB databases were used to select target mRNAs. Cytoscape software was used to visualize the miRNA-mRNA regulation network. P value < 0.05 was considered statistically significant after t test. There were 123 screened mRNAs which were enriched in 161 Gene ontology (GO) terms and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Thirty-five differentially expressed miRNAs (DEMs) are found in the GSE75670. Totally 36 miRNA-mRNA pairs were obtained after the integrated analysis, and three mRNAs and the hsa-miRNA-5589-5p were identified as key joints. Hub genes, KIAA0513, ARID3A and LRPAP1, and key hsa-miRNA-5589-5p are potential diagnostic biomarkers for hypertension. Our findings are promising in the clinical application, conducive to early detection and prompt intervention of hypertension.

LncRNA HOTAIR enhances RCC2 to accelerate cervical cancer progression by sponging miR-331-3p

PURPOSE

Long noncoding RNAs (lncRNAs) have been gradually regarded as influential indicators of various cancers. The present study aimed to identify the effects of lncRNA HOTAIR on cervical cancer progression.

METHODS

RNA and protein expressions were quantified by RT-qPCR and western blot assays. Fluorescence in situ hybridization (FISH) assay was carried out to examine the intracellular location of HOTAIR. Cancer cell viability and mobility were detected by CCK-8, colony formation, transwell and wound healing assays. Binding relationships between miR-331-3p and HOTAIR/RCC2 were validated by luciferase reporter assay.

RESULTS

RT-qPCR assays showed that HOTAIR levels were notably upregulated in cervical cancer tissues and cell lines. Furthermore, a fluorescence in situ hybridization (FISH) assay suggested that HOTAIR was mostly located in the cytoplasm of cancer cells, indicating a sponging function. CCK-8, colony formation, Transwell and wound-healing assays indicated that knockdown of HOTAIR in HeLa and SiHa cells significantly reduced cell growth, migration and invasion. Subsequently, miR-331-3p was proven to be the target molecule of HOTAIR. In addition, results from Pearson's correlation analysis indicated negative correlation between HOTAIR and miR-331-3p in cervical cancer tissues. HOTAIR negatively modulated miR-331-3p expression. Ultimately, the target gene of miR-331-3p was verified to be RCC2, and miR-331-3p negatively modulated RCC2 expression. In addition, analysis on clinical cervical cancer tissues confirmed the negative correlation between miR-331-3p and RCC2. HOTAIR and RCC2 showed oncogenic functions in HeLa and SiHa cells, while miR-331-3p exerted the reverse effect.

CONCLUSIONS

HOTAIR plays a carcinogenic role in cervical cancer by targeting the miR-331-3p/RCC2 axis. Moreover, clinical cervical cancer tissues confirmed the negative correlation between miR-331-3p with lncRNA HOTAIR and RCC2. These data suggested an underlying therapeutic target for cervical cancer.

miR‑150‑5p inhibits osteogenic differentiation of fibroblasts in ankylosing spondylitis by targeting VDR

Dysregulated microRNAs (miRNAs or miRs) serve potential roles in inflammatory systemic disease, including ankylosing spondylitis (AS). The aim of the present study was to investigate the potential function of miR-150-5p in osteogenic differentiation of AS fibroblasts and its underlying mechanism. The expression of miR-150-5p and vitamin D receptor (VDR) in AS joint capsules and fibroblasts was detected by reverse transcription-quantitative (RT-q)PCR and western blotting. Following overexpression of miR-150-5p, the alteration in osteogenic gene expression was detected by RT-qPCR, western blotting and alkaline phosphatase activity assay, as well as alizarin red staining. The association between miR-150-5p and VDR was confirmed by luciferase assay and rescue experiments were performed. Patients with AS exhibited decreased expression of miR-150-5p in joint capsules. Treatment with bone morphogenic protein 2 (BMP-2) and transforming growth factor-β1 (TGF-β1) led to downregulation of miR-150-5p in AS fibroblasts. Enforced expression of miR-150-5p attenuated osteogenic differentiation of AS fibroblasts. These results demonstrated that miR-150-5p inhibited osteogenic differentiation of AS fibroblasts by targeting VDR. miR-150-5p overexpression decreased osteogenic transformation of fibroblasts by decreasing VDR expression in AS.

Circular RNA NEK6 contributes to the development of non-small-cell lung cancer by competitively binding with miR-382-5p to elevate BCAS2 expression at post-transcriptional level

Background

Non-small-cell lung cancer (NSCLC) is the commonest type of lung cancer, which is one of most deadly cancers that possess high morbidity and mortality all over the world. The function of circular RNA NIMA related kinase 6 (circ_NEK6) in NSCLC is still unknown. Therefore, circ_NEK6 is worth studying in detail.

Methods

RT-qPCR and western blot assays were employed to detect gene expression. Colony formation, EdU, JC-1, flow cytometry, and Transwell assays were implemented to explore the function of circ_NEK6 on biological activities of NSCLC cells. Mechanism experiments were conducted to unveil the relationship among molecules.

Results

Circ_NEK6 expression was highly expressed in NSCLC tissues and cells. Functionally, the silencing of circ_NEK6 could effectively suppress NSCLC cell proliferation, migration and invasion. Circ_NEK6 sequestered miR-382-5p to fortify the expression of breast carcinoma amplified sequence 2 (BCAS2) in NSCLC. Besides, BCAS2 had tumor-promoting function in NSCLC. Furthermore, the effects of down-regulated circ_NEK6 on the malignant behaviors of NSCLC cells were totally recovered by miR-382-5p inhibition or BCAS2 overexpression.

Conclusions

Circ_NEK6 served as a competing endogenous RNA (ceRNA) of BCAS2 by absorbing miR-382-5p, which may be treated as a novel promising target for the treatment of NSCLC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12890-021-01617-0.

miR-3146 induces neutrophil extracellular traps to aggravate gout flare

Background

Gout is an inflammatory arthritis and is characterized by the accumulation of deposited monosodium urate (MSU) crystals in the joints. miRNAs may act as key regulators of gout pathogenesis. The aim of our study was to explore the underlying role and molecular mechanism of miR‐3146 in the formation of neutrophil extracellular traps (NETs) during the pathogenesis of gout.

Methods

The expression of miR‐3146 and sirtuin 1 (SIRT1) was determined by real‐time reverse transcription‐polymerase chain reaction and Western blot, respectively. The luciferase reporter assay was performed to identify the targeting relationship between miR‐3146 and SIRT1. Reactive oxygen species (ROS) production was detected by fluorescent staining. NETs formation was demonstrated via immunofluorescence staining and ELISA method. Gout model was induced in rats to verify the effects of miR‐3146 inhibition on histopathological changes and NETs.

Results

Here, we found miR‐3146 expression was dramatically increased in neutrophils of patients with gout, which was accompanied with the higher levels of NETs. MSU crystals significantly increased miR‐3146 expression and ROS production in neutrophils. The NETs process was also triggered by MSU crystals. Furthermore, we verified the interaction between miR‐3146 and SIRT1. Additionally, antagomir‐3146‐based therapy effectively inhibited the formation of NETs in rats with gout.

Conclusion

Our findings indicated that miR‐3146‐mediated NETs formation may play a potential role in the pathogenesis of gout. These results suggested that miR‐3146 could be used as a potential therapeutic target for the treatment of gout.

miRNA-877-5p inhibits malignant progression of prostate cancer by directly targeting SSFA2

In this study, we aimed to investigate the role of miR-877-5p in the malignant phenotypes of prostate cancer (PCa) cells and its underlying mechanism. RT-qPCR analysis was performed to examine the expression of miR- 877-5p and sperm-specific antigen 2 (SSFA2) in PCa tissues and cells. Cell counting kit-8 (CCK-8) assay, 5- ethynyl-20-deoxyuridine (EdU) assay, flow cytometry, wound-healing assay, and Transwell invasion assay were performed to determine the functional roles of miR-877-5p in PCa cells. The association of miR-877-5p with SSFA2 was determined by luciferase reporter and RNA pull-down assays. In this study, we found that the expression level of miR-877-5p was decreased in PCa tissues and cells. Functionally, overexpression of miR- 877-5p exerted tumor suppressor properties in PCa cells. Mechanistically, SSFA2 was identified as a target gene of miR-877-5p, while overexpression of SSFA2 could abrogate the anti-tumor effects of miR-877-5p in PCa cells. These findings demonstrated that miR-877-5p/SSFA2 axis functioned as a potential target for PCa treatment.

Circular RNA hsa_circ_0026552 inhibits the proliferation, migration and invasion of trophoblast cells via the miR‑331‑3p/TGF‑βR1 axis in pre‑eclampsia

Globally, pre-eclampsia (PE) is a gestational disorder that causes increased morbidity of the fetus and mortality induced by pregnancy. Despite various studies, the understanding of the causes or mechanism of the development of PE remains elusive. Thus, the present study aimed to investigate the role of circular (circ)RNA hsa_circ_0026552 (hsa_circ_0026552) in the development of PE and its mechanism of regulation. hsa_circ_0026552 differential expression in PE tissue data and clinical samples were analyzed and it was observed that hsa_circ_0026552 is highly upregulated in PE samples. Furthermore, miR-331-3p was detected as an hsa_circ_0026552 target miRNA and TGF-βR1 gene as a target of miR-331-3p. These results were confirmed using various assays, including dual-luciferase reporter, reverse transcription-quantitative PCR and RNA pull-down assay. It was observed that miR-331-3p expression was negatively correlated to hsa_circ_0026552 relative expression, while TGF-βR1 expression was positively correlated to hsa_circ_0026552 expression evaluated by Pearson's correlation test. The functional experiments, including Cell Counting Kit-8, colony formation and Transwell assay, showed that silencing hsa_circ_0026552 could significantly strengthen the proliferation, migration and invasion of the trophoblastic HTR-8/SVneo cells, but the subsequent overexpression of hsa_circ_0026552 reversed this. Mechanistically, it was concluded that hsa_circ_0026552 acts as a miR-331-3p sponge to upregulate TGF-βR1 expression in trophoblasts and is involved significantly in PE development and progression in pregnant women. The circRNA hsa_circ_0026552 could be a novel therapeutic target and prognostic biomarker for PE.

miR-125 family regulates XIRP1 and FIH in response to myocardial infarction

MicroRNAs (miRNAs) are powerful regulators of protein expression. Many play important roles in cardiac development and disease. While several miRNAs and targets have been well characterized, the abundance of miRNAs and the numerous potential targets for each suggest that the vast majority of these interactions have yet to be described. The goal of this study was to characterize miRNA expression in the mouse heart after coronary artery ligation (LIG) and identify novel mRNA targets altered during the initial response to ischemic stress. We performed small RNA sequencing (RNA-Seq) of ischemic heart tissue 1 day and 3 days after ligation and identified 182 differentially expressed miRNAs. We then selected relevant mRNA targets from all potential targets by correlating miRNA and mRNA expression from a corresponding RNA-Seq data set. From this analysis we chose to focus, as proof of principle, on two miRNAs from the miR-125 family, miR-125a and miR-351, and two of their potential mRNA targets, Xin actin-binding repeat-containing protein 1 (XIRP1) and factor inhibiting hypoxia-inducible factor (FIH). We found miR-125a to be less abundant and XIRP1 more abundant after ligation. In contrast, the related murine miRNA miR-351 was substantially upregulated in response to ischemic injury, and FIH expression correspondingly decreased. Luciferase reporter assays confirmed direct interactions between these miRNAs and targets. In summary, we utilized a correlative analysis strategy combining miRNA and mRNA expression data to identify functional miRNA-mRNA relationships in the heart after ligation. These findings provide insight into the response to ischemic injury and suggest future therapeutic targets.

Role of exosomes and exosomal microRNAs in cancer

A growing body of evidence indicates that exosomes play a critical role in the cell-cell communication process. Exosomes are biological nanoparticles with an average diameter of 30-100 nm in size and are produced by almost all cell types in the human body; however, cancer cells contain higher concentrations of exosomes than healthy cells. They are released into all body fluids and contain double-stranded DNA (originated from nucleus and mitochondria), a variety of RNA species, and specific protein biomarkers that can be utilized as cancer biomarkers and therapeutic targets, and lipids. Therefore, the specific exosomes secreted by tumor cells could be used to predict the existence of the presence of a tumor in cancer patients. This review summarizes the role of exosomes in cancer development and their potential utility in the clinic.

Small Nucleolar RNA Host Gene 1 (SNHG1) and Chromosome 2 Open Reading Frame 48 (C2orf48) as Potential Prognostic Signatures for Liver Cancer by Constructing Regulatory Networks

Background

Liver cancer is a common malignant tumor with poor prognosis. The present study sought to identify potential signatures that can predict the prognosis of patients with liver cancer.

Material/Methods

The RNA sequencing (RNA-seq) and clinical information of liver cancer patients were obtained from the Cancer Genome Atlas (TCGA) database. Differentially expressed long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) were identified between liver cancer and adjacent normal tissues. After predicting lncRNA–miRNA and miRNA–mRNA pairs using online databases, the competing endogenous RNA (ceRNA) networks were constructed. Furthermore, the prognostic value of these differentially expressed genes was evaluated using univariate and multivariate Cox regression analyses.

Results

After constructing the ceRNA network, 2 lncRNAs small nucleolar RNA host gene 1 (SNHG1) and chromosome 2 open reading frame 48 (C2orf48) with the most nodes were identified. Correlation analysis revealed that SNHG1 was correlated with miR-195 and C2orf48 was correlated with miR-195 and miR-93. High expression of SNHG1, C2orf48, and miR-93 can contribute to poorer clinical outcomes compared to low expression. Furthermore, low miR-195 expression was correlated with shorter survival time than was high expression. SNHG1 and C2orf48 were closely associated with histology grade. Univariate and multivariate Cox regression analyses confirmed that SNHG1 and C2orf48 are risk factors for liver cancer.

Conclusions

Our findings revealed that SNHG1 and C2orf48 possess potential prognostic value and should be considered as possible biomarkers for predicting clinical outcomes for patients with liver cancer.

MiR-25 exerts cardioprotective effect in a rat model of myocardial ischemia-reperfusion injury by targeting high-mobility group box 1

BACKGROUND

We previously confirmed the targeting of high-mobility group box 1 (HMGB1) by miR-25. This project aims to further investigate whether miR-25 improves myocardial ischemia-reperfusion injury (IRI) in vivo by targeting HMGB1.

METHODS

A rat model of myocardial IRI was established by the ligation of the left anterior descending coronary artery for 45 minutes followed by 2, 4, or 6 hours reperfusion. The expression of miR-25, HMGB1, and apoptosis-related proteins in the myocardium was determined by quantitative real-time polymerase chain reaction (PCR) and western blotting. The activities of myocardial enzymes and the release of inflammatory cytokines were evaluated by enzyme-linked immunosorbent assay. Evans blue/triphenyltetrazolium chloride double staining was performed to assess infarct size. Myocardial apoptosis was detected by terminal deoxynucleotidyl transferase dUTP nick end labeling staining.

RESULTS

MiR-25 expression was significantly downregulated, while HMGB1 was highly expressed at the mRNA and protein levels in myocardial tissues after induction of the IRI model. MiR-25 agomir administration suppressed the expression of HMGB1 in myocardial tissues. Furthermore, administration of both miR-25 agomir and lentivirus-mediated short hairpin RNA (shRNA) interference targeting HMGB1 sh-HMGB1 resulted in reduced serum myocardial enzyme activities, cytokine secretion, and myocardial apoptosis during myocardial IRI.

CONCLUSION

MiR-25 mitigated myocardial IRI-induced damage by targeting HMGB1.