Entangling Relation of Micro RNA-let7, miRNA-200 and miRNA-125 with Various Cancers

Identifying key factors in cell fate decisions by machine learning interpretable strategies

Cell fate decisions and transitions are common in almost all developmental processes. Therefore, it is important to identify the decision-making mechanisms and important individual molecules behind the fate decision processes. In this paper, we propose an interpretable strategy based on systematic perturbation, unsupervised hierarchical cluster analysis (HCA), machine learning (ML), and Shapley additive explanation (SHAP) analysis for inferring the contribution and importance of individual molecules in cell fate decision and transition processes. In order to verify feasibility of the approach, we apply it to the core epithelial to mesenchymal transition (EMT)-metastasis network. The key factors identified in EMT-metastasis are consistent with relevant experimental observations. The approach presented here can be applied to other biological networks to identify important factors related to cell fate decisions and transitions.

The Role of miRNAs in the Development, Proliferation, and Progression of Endometrial Cancer

Endometrial cancer is one of the most common cancers in developing and developed countries. Although the detection of this cancer is high at the early stages, there is still a lack of markers to monitor the disease, its recurrence, and metastasis. MiRNAs are in charge of the post-transcriptional regulation of genes responsible for the most important biological processes, which is why they are increasingly used as biomarkers in many types of cancer. Many studies have demonstrated the influence of miRNAs on the processes related to carcinogenesis. The characteristics of miRNA expression profiles in endometrial cancer will allow their use as diagnostic and prognostic biomarkers. This paper focuses on the discussion of selected miRNAs based on the literature and their role in the development of endometrial cancer.

miR 31-3p Has the Highest Expression in Cesarean Scar Endometriosis

Micro-RNAs expression can vary between different forms of endometriosis, but data on miRNA expression in cesarean scar endometriosis is lacking. The present study is comprised of 30 patients with endometriosis in the cesarean scar (scar endometriosis, SE), 14 patients with deep infiltrating endometriosis (DIE), 47 patients with endometrioma (ovarian endometrial cyst, OE), and 33 patients with healthy ovarian tissue as the control group (CG). In the initial experiment to identify possible dysregulated miRNAs, the levels of 754 miRNAs in formalin-fixed paraffin-embedded tissue (FFPE) samples from OE, high-grade ovarian cancer, endometrioid ovarian cancer, and CG were measured. We identified seven potentially dysregulated miRNAs: miR-1-3p, miR-31-3p, miR-125b-1-3p, miR-200b-3p, miR-548d, miR-502, and miR-503. We then examined the expression profiles of each of these miRNAs individually in the SE, DIE, OE, and CG FFPE samples using RT-qPCR. miR-31-3p had significantly higher levels of expression and miR-125b-1-3p had significantly lower levels of expression in SE compared to the controls. Overall, the higher expression levels of miR-31-3p and the lower expression levels of miR-125b-1-3p are consistent with the benign nature of SE. Importantly, the results of the present study demonstrate the possibility of using miRNA to monitor the risk of malignant transformation of endometriosis tissue.

MiR-196a promotes the proliferation and migration of esophageal cancer via the UHRF2/TET2 axis

The aim of this study was to investigate the functions and molecular mechanism of miR-196a in esophageal cancer (EC). miR-196a as well as UHRF2 and TET2 mRNA and protein levels in EC tissues and cells were detected using quantitative real-time PCR or western blot, respectively. Cell proliferation was evaluated via MTT assay. Transwell assays were used to detect cell migration. In addition, the targeted relationship between miR-196a and UHRF2 was assessed through a dual luciferase reporter assay. Enzyme-linked immunosorbent assay was performed to detect the levels of the cytosine intermediates 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). We found increased miR-196a expression in EC tissues and cells but decreased UHRF2 and TET2 expression. Next, functional experiments showed that knockdown of miR-196a or UHRF2 overexpression suppress EC cell proliferation and migration. miR-196a negatively regulates TET2 expression by directly targeting UHRF2. UHRF2 overexpression decreased 5mC levels but increased 5hmC levels. Furthermore, TET2 downregulation reversed the functions of miR-196a inhibition on EC cell proliferation and migration. Collectively, our study suggested that miR-196a was closely related to the progression of EC possibly by regulating the UHRF2/TET2 axis. Thus, miR-196a represents a potential new EC therapeutic target.

Roles of NPAS2 in circadian rhythm and disease

NPAS2, a circadian rhythm gene encoding the neuronal PAS domain protein 2 (NPAS2), has received widespread attention because of its complex functions in cells and diverse roles in disease progression, especially tumorigenesis. NPAS2 binds with DNA at E-box sequences and forms heterodimers with another circadian protein, brain and muscle ARNT-like protein 1 (BMAL1). Nucleotide variations of the NPAS2 gene have been shown to influence the overall survival and risk of death of cancer patients, and differential expression of NPAS2 has been linked to patient outcomes in breast cancer, lung cancer, non-Hodgkin's lymphoma, and other diseases. Here, we review the latest advances in our understanding of NPAS2 with the aim of drawing attention to its potential clinical applications and prospects.

Low miR-1231 expression predicts poor prognosis in non-small-cell lung cancer and accelerates cell proliferation, migration and invasion

Aim: miRNAs have been found to be involved in the tumor progression. This study aimed to assess the prognostic significance and biological function of miRNA-1231 (miR-1231) in non-small-cell lung cancer (NSCLC). Materials & methods: Expression of miR-1231 was measured by using quantitative real-time PCR. The prognosis value of miR-1231 was evaluated by Kaplan-Meier survival curves and Cox regression analysis. The biological function of miR-1231 was further studied. Results: Expression of miR-1231 in NSCLC patients and NSCLC cell lines were decreased. MiR-1231 was an independent prognostic biomarker. Overexpression of miR-1231 inhibited NSCLC cell proliferation, migration and invasion. Conclusion: Downregulated expression of miR-1231 serves as a prognostic biomarker of NSCLC and may be a potential therapeutic target.

Inhibitory effect of miR-140-5p on doxorubicin resistance of hepatocellular carcinoma

To investigate the role of microRNA (miR)-140-5p in doxorubicin (DOX) sensitivity in hepatocellular carcinoma, miR-140-5p and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1) expression was first evaluated in hepatocellular carcinoma tissues using starBase. Next, in vitro experiments were performed. Cell line expression of miR-140-5p and PIN1 expression was detected by reverse transcription polymerase chain reaction. Cell viability and proliferation were determined by the Cell Counting Kit-8 and EdU assays. The relationship between miR-140-5p and PIN1 was evaluated by TargetScan and a luciferase reporter system. Western blotting was used to detect the expression of PIN1. It was observed that miR-140-5p was downregulated in hepatocellular carcinoma tissues and cell lines compared with normal samples in HCC or normal liver cells. Gain-of-function experiments revealed that miR-140-5p mimics were able to enhance DOX sensitivity of hepatocellular carcinoma cells. Further studies revealed that PIN1 was a target gene of miR-140-5p. Suppression of PIN1 led to higher DOX sensitivity in hepatocellular carcinoma cells. Finally, when comparing a PIN1-siRNA alone group and a PIN1-siRNA plus miR-140-5p inhibitor group, there was no significant difference in cell viability. Furthermore, miR-140-5p mimics did not reduce the sensitivity of PIN1mut plasmid to DOX in HUH7 and SNU449 cells. The present study demonstrated that miR-140-5p could enhance DOX sensitivity in hepatocellular carcinoma cells by targeting PIN1.

The Role and Expression of Angiogenesis-Related miRNAs in Gastric Cancer

Gastric cancer (GC) is the fifth most frequently diagnosed malignant tumor and the third highest cause of cancer mortality worldwide. For advanced GC, many novel drugs and combinations have been tested, but results are still disappointing, and the disease is incurable in the majority of cases. In this regard, it is critical to investigate the molecular mechanisms underlying GC development. Angiogenesis is one of the hallmarks of cancer with a fundamental role in GC growth and progression. Ramucirumab, a monoclonal antibody that binds to vascular endothelial growth factor-2 (VEGFR-2), is approved in the treatment of advanced and pretreated GC. However, no predictive biomarkers for ramucirumab have been identified so far. Micro RNAs (miRNAs) are a class of evolutionarily-conserved single-stranded non-coding RNAs that play an important role (via post-transcriptional regulation) in essentially all biologic processes, such as cell proliferation, differentiation, apoptosis, survival, invasion, and migration. In our review, we aimed to analyze the available data on the role of angiogenesis-related miRNAs in GC.

Urinary Exosomal MicroRNAs as Potential Non-invasive Biomarkers in Breast Cancer Detection

INTRODUCTION

Breast cancer (BC) is the most frequent malignant disease in women worldwide and is therefore challenging for the healthcare system. Early BC detection remains a leading factor that improves overall outcome and disease management. Aside from established screening procedures, there is a constant demand for additional BC detection methods. Routine BC screening via non-invasive liquid biopsy biomarkers is one auspicious approach to either complete or even replace the current state-of-the-art diagnostics. The study explores the diagnostic potential of urinary exosomal microRNAs with specific BC biomarker characteristics to initiate the potential prospective application of non-invasive BC screening as routine practice.

METHODS

Based on a case-control study (69 BC vs. 40 healthy controls), expression level quantification and subsequent biostatistical computation of 13 urine-derived microRNAs were performed to evaluate their diagnostic relevance in BC.

RESULTS

Multilateral statistical assessment determined and repeatedly confirmed a specific panel of four urinary microRNA types (miR-424, miR-423, miR-660, and let7-i) as a highly specific combinatory biomarker tool discriminating BC patients from healthy controls, with 98.6% sensitivity and 100% specificity.

DISCUSSION

Urine-based BC diagnosis may be achieved through the analysis of distinct microRNA panels with proven biomarker abilities. Subject to further validation, the implementation of urinary BC detection in routine screening offers a promising non-invasive alternative in women's healthcare.

MicroRNAs in endometriosis: biological function and emerging biomarker candidates†

MicroRNAs (miRNAs), a class of small noncoding RNA molecules, have been recognized as key post-transcriptional regulators associated with a multitude of human diseases. Global expression profiling studies have uncovered hundreds of miRNAs that are dysregulated in several diseases, and yielded many candidate biomarkers. This review will focus on miRNAs in endometriosis, a common chronic disease affecting nearly 10% of reproductive-aged women, which can cause pelvic pain, infertility, and a myriad of other symptoms. Endometriosis has delayed time to diagnosis when compared to other chronic diseases, as there is no current accurate, easily accessible, and noninvasive tool for diagnosis. Specific miRNAs have been identified as potential biomarkers for this disease in multiple studies. These and other miRNAs have been linked to target genes and functional pathways in disease-specific pathophysiology. Highlighting investigations into the roles of tissue and circulating miRNAs in endometriosis, published through June 2018, this review summarizes new connections between miRNA expression and the pathophysiology of endometriosis, including impacts on fertility. Future applications of miRNA biomarkers for precision medicine in diagnosing and managing endometriosis treatment are also discussed.

CircAKT3 inhibits glycolysis balance in lung cancer cells by regulating miR-516b-5p/STAT3 to inhibit cisplatin sensitivity

OBJECTIVE

Lung cancer was one of the most deadly cancers around the world. Circular RNA AKT3 (CircAKT3) was highly expressed in lung cancer and could inhibit cell proliferation, but there were few studies on the mechanism of specific regulation of drug resistance. Therefore, we aimed to provide new ideas and perspectives for the role of circAKT3 in the mechanism of tumor resistance.

METHODS

The levels of circAKT3, miR-516b-5p and STAT3 in lung cancer tissues and cells were examined using quantitative real-time polymerase chain reaction (qRT-PCR) or western blot assays. 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) assay was used to examine the sensitivity of cells treated under different conditions to cisplatin (DDP). A glucose assay kit and lactate assay kit were used to assess glycolysis and lactate production of cells treated with different plasmids and 2-deoxy-glucose (2-DG). Western blot analysis was used to detect the expression level of the hypoxia-inducible factor (HIF-1α) in A549 and H1299 cells. Starbase 3.0 predicted a targeted relationship between circAKT3 and miR-516b-5p, STAT3 and miR-516b-5p, and the relationship was proved by a dual-luciferase reporter assay. Knockdown of circAKT3 was used to study the effects of circAKT3 on tumor development in vivo.

RESULTS

The levels of circAKT3 and STAT3 were upregulated, miR-516b-5p was downregulation in lung cancer tissues and cells. Functionally, circAKT3 knockdown improved cell sensitivity to DDP, and repressed glycolysis in lung cancer cells. Meanwhile, inhibition of HIF-1α-dependent glycolysis attenuated the circAKT3-induced increase of chemo-resistance in A549 cells. Mechanistically, miR-516b-5p was found to possess some binding sites with circAKT3. Noticeably, the inhibitory action of circAKT3 knockdown on DDP resistance and glycolysis was overturned through inhibitor of miR-516b-5p in lung cancer cells. Furthermore, besides, circAKT3 knockdown suppressed lung tumor cell growth by the miR-516b-5p/STAT3 axis in vivo.

CONCLUSIONS

CircAKT3 inhibit cisplatin sensitivity of lung cancer cells at least partly through regulating miR-516b-5p/STAT3 axis-mediated glycolysis balance, providing a possible long noncoding RNA -targeted therapy for lung cancer.

Terminal nucleotidyl transferases (TENTs) in mammalian RNA metabolism

In eukaryotes, almost all RNA species are processed at their 3′ ends and most mRNAs are polyadenylated in the nucleus by canonical poly(A) polymerases. In recent years, several terminal nucleotidyl transferases (TENTs) including non-canonical poly(A) polymerases (ncPAPs) and terminal uridyl transferases (TUTases) have been discovered. In contrast to canonical polymerases, TENTs' functions are more diverse; some, especially TUTases, induce RNA decay while others, such as cytoplasmic ncPAPs, activate translationally dormant deadenylated mRNAs. The mammalian genome encodes 11 different TENTs. This review summarizes the current knowledge about the functions and mechanisms of action of these enzymes.

This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.

Next Generation Sequencing of urine exfoliated cells: an approach of prostate cancer microRNAs research

There is emerging evidence that microRNAs (miRNAs) dysregulation is involved in the genesis and the progression of Prostate Cancer (PCa), thus potentially increasing their use in urological clinical practice. This is the first pilot study which utilizes Illumina Deep Sequencing to examine the entire miRNAs spectrum existent in urine exfoliated prostate cells (UEPCs) of PCa patients. A total of 11 male patients with histological diagnosis of PCa were enrolled in the present study. First-catch urine (30 mL) was collected following a prostate massage. Total RNA was extracted from urine and sequenced using an HiSeq2500 System (Illumina). QPCR assay was used to validate the highest NGS results in PCA patients and in age-matched, caucasian men. Remarkably, PCA let-7 family was down-regulated (P < 0.01), compared to the controls. The results of our study support the notion of a relatively high diagnostic value of miRNA family for PCa detection, especially in the let-7 family. The present research confirmed the potential use of miRNAs as non-invasive biomarkers in the diagnosis of PCa, potentially reducing the invasiveness of actual clinical strategy.

MiR-30b-5p modulates glioma cell proliferation by direct targeting MTDH

Malignant glioma is the most common and lethal type of primary tumor of the central nervous system. The incidence of glioma is increasing year by year. In recent years, a variety of new treatment methods have emerged, among which gene therapy has become a hotspot. MicroRNAs (miRNAs) are a class of small non-coding single-strand RNAs that negatively regulate gene expression at the post-transcriptional and/or translational level by binding loosely complimentary sequences in the 3′ untranslated regions (UTRs) of target mRNAs. Several miRNAs have been reported to modulate glioma progression. This study aimed to determine the function of miR-30b-5p in glioma and its underlying molecular mechanism. miR-30b-5p expression was significantly lower in gliomas than the normal brain tissues. Overexpression of miR-30b-5p was found to significantly inhibit glioma cell proliferation in vitro. Further, MTDH expression was significantly higher in the gliomas compared with the normal brain tissues. In addition, MTDH was validated as direct target of miR-30b-5p. Moreover, cellular proliferation was increased after MTDH overexpression in the glioma cells, which reversed the effects of miR-30b-5p. Taken together, these results reveal miR-30b-5p impacts glioma cell proliferation via direct targeting MTDH and could be a potential novel therapeutic target for the treatment of glioma.

Ailanthone Promotes Human Vestibular Schwannoma Cell Apoptosis and Autophagy by Downregulation of miR-21

Ailanthone (AIL) is a quassinoid isolated from the traditional Chinese medicinal herb Ailanthus altissima. The antitumor activities of AIL have been reported in several cancers. The purpose of the present study was to explore the effect of AIL on vestibular schwannomas (VSs). Various concentrations of AIL (0–1 μM) were used to treat human primary VS cells, and then cell viability, proliferation, apoptosis, and autophagy were assessed. Expression of miR-21 in VS cells was altered by miRNA transfection. The functional actions of AIL on miR-21 dysregulated cells were also assessed. AIL significantly reduced the viability of VS cells, and the IC₅₀ value was 0.48 ± 0.023 μM. In response to 0.6 μM AIL, BrdU⁺ cell rate and cyclin D1 expression were reduced, apoptotic cell rate was increased, caspase 3 and caspase 9 were cleaved, Beclin-1 and LC3-II were accumulated, and p62 was downregulated. miR-21 was lowly expressed in AIL-treated cells, and AIL-induced apoptosis and autophagy were attenuated by miR-21 overexpression. In addition, AIL downregulated Ras and Raf and deactivated MEK, ERK, mTOR, and p70S6K, while the downregulation and deactivation induced by AIL were reversed by miR-21 overexpression. To conclude, AIL inhibited VS cell proliferation and induced apoptosis and autophagy. The antitumor activities of AIL in VS cells were realized possibly via downregulation of miR-21 and blocking the Ras/Raf/MEK/ERK and mTOR pathways.