Aberrant expression of miR-199a-3p and its clinical significance in colorectal cancers

Altered Expressions of NF1 and NF1-Related microRNAs as Biomarkers in the Diagnosis of Undifferentiated Pleomorphic Sarcoma

Objective: Undifferentiated pleomorphic sarcoma (UPS) is a highly malignant, aggressive, and pleomorphic subtype of soft tissue sarcoma in adults. However, UPS is difficult to be diagnosed due to the lack of specific morphological and immunophenotypic features. Here, we aimed to identify new biomarkers for the diagnosis of UPS.

Methods: The mRNA and protein expression of neurofibromin 1 (NF1) in 68 pairs of UPS and adjacent normal tissues were detected by qRT-PCR and immunohistochemistry, and the correlation between the NF1 protein expression and clinicopathological characteristics was analyzed. Then, differentially expressed microRNAs (DE miRNAs) were identified between the UPS tumor tissue and matched adjacent normal tissue using Hisep sequencing, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG). The DE miRNAs of the regulating NF1 gene were also identified using the TargetScan and miRanda databases and validated by qRT-PCR.

Results: Compared with the adjacent normal tissue, both mRNA and protein expressions of NF1 in the UPS tumor tissue were significantly decreased, and the positive rate of NF1 protein was associated with the tumor size, metastasis, and recurrence. A total of 125 known DE miRNAs were identified from the screened miRNAs based on | log₂(Fold Change) ≥5 and p-value < 0.05 (A total of 82 upregulated and 43 downregulated DE miRNAs in the UPS tissue). Target genes regulated by the DE miRNAs were enriched in pathways of metabolisms, RNA degradation, PI3K-Akt, and Rap1 pathway. In total, 11 miRNAs which were predicted to regulate the NF1 gene were screened. After verification, the relative expressions of hsa-miR-199a-3p and hsa-miR-34a-5p were increased and decreased in the UPS tumor tissue compared with those in the adjacent normal tissue, respectively.

Conclusion: NF1 and NF1-related microRNAs including hsa-miR-199a-3p and hsa-miR-34a-5p may be novel biomarkers in the diagnosis of undifferentiated pleomorphic sarcoma (UPS).

Bipartite graph-based collaborative matrix factorization method for predicting miRNA-disease associations

BACKGROUND

With the rapid development of various advanced biotechnologies, researchers in related fields have realized that microRNAs (miRNAs) play critical roles in many serious human diseases. However, experimental identification of new miRNA-disease associations (MDAs) is expensive and time-consuming. Practitioners have shown growing interest in methods for predicting potential MDAs. In recent years, an increasing number of computational methods for predicting novel MDAs have been developed, making a huge contribution to the research of human diseases and saving considerable time. In this paper, we proposed an efficient computational method, named bipartite graph-based collaborative matrix factorization (BGCMF), which is highly advantageous for predicting novel MDAs.

RESULTS

By combining two improved recommendation methods, a new model for predicting MDAs is generated. Based on the idea that some new miRNAs and diseases do not have any associations, we adopt the bipartite graph based on the collaborative matrix factorization method to complete the prediction. The BGCMF achieves a desirable result, with AUC of up to 0.9514 ± (0.0007) in the five-fold cross-validation experiments.

CONCLUSIONS

Five-fold cross-validation is used to evaluate the capabilities of our method. Simulation experiments are implemented to predict new MDAs. More importantly, the AUC value of our method is higher than those of some state-of-the-art methods. Finally, many associations between new miRNAs and new diseases are successfully predicted by performing simulation experiments, indicating that BGCMF is a useful method to predict more potential miRNAs with roles in various diseases.

Tissue micro-RNAs associated with colorectal cancer prognosis: a systematic review

Colorectal cancer (CRC) is a multifactorial disease commonly diagnosed worldwide, with high mortality rates. Several studies demonstrate important associations between differential expression of micro-RNAs (miRs) and the prognosis of CRC. The present study aimed to identify differentially expressed tissue miRs associated with prognostic factors in CRC patients, through a systematic review of the Literature. Using the PubMed database, Cochrane Library and Web of Science, studies published in English evaluating miRs differentially expressed in tumor tissue and significantly associated with the prognostic aspects of CRC were selected. All the included studies used RT-PCR (Taqman or SYBR Green) for miR expression analysis and the period of publication was from 2009 to 2018. A total of 115 articles accomplished the inclusion criteria and were included in the review. The studies investigated the expression of 100 different miRs associated with prognostic aspects in colorectal cancer patients. The most frequent oncogenic miRs investigated were miR-21, miR-181a, miR-182, miR-183, miR-210 and miR-224 and the hyperexpression of these miRs was associated with distant metastasis, lymph node metastasis and worse survival in patients with CRC. The most frequent tumor suppressor miRs were miR-126, miR-199b and miR-22 and the hypoexpression of these miRs was associated with distant metastasis, worse prognosis and a higher risk of disease relapse (worse disease-free survival). Specific tissue miRs are shown to be promising prognostic biomarkers in patients with CRC, given their strong association with the prognostic aspects of these tumors, however, new studies are necessary to establish the sensibility and specificity of the individual miRs in order to use them in clinical practice.

microRNA-199a-3p inhibits hepatic apoptosis and hepatocarcinogenesis by targeting PDCD4

Hepatic apoptosis and the initiated liver inflammation play the initial roles in inflammation-induced hepatocarcinogenesis. Molecular mechanisms underlying the regulation of hepatocyte apoptosis and their roles in hepatocarcinogenesis have attracted much attention. A set of microRNAs (miRNAs) have been determined to be dysregulated in hepatocellular carcinoma (HCC) and participated in cancer progression, however, the roles of these dysregulated miRNAs in carcinogenesis are still poorly understood. We previously analyzed the dysregulated miRNAs in HCC using high-throughput sequencing, and found that miR-199a/b-3p was abundantly expressed in human normal liver while markedly decreased in HCC, which promotes HCC progression. Whether miR-199a/b-3p participates in HCC carcinogenesis is still unknown up to now. Hence, we focused on the role and mechanism of miR-199a/b-3p in hepatocarcinogenesis in this study. Hepatic miR-199a/b-3p was determined to be expressed by miR-199a-2 gene in mice, and we constructed miR-199a-2 knockout and hepatocyte-specific miR-199a-2 knockout mice. Diethylnitrosamine (DEN)-induced hepatocarcinogenesis were markedly increased by hepatocyte-specific miR-199a-3p knockout, which is mediated by the enhanced hepatocyte apoptosis and hepatic injury by DEN administration. In acetaminophen (APAP)-induced acute hepatic injury model, hepatocyte-specific miR-199a-3p knockout also aggravated hepatic apoptosis. By proteomic screening and reporter gene validation, we identified and verified that hepatic programed cell death 4 (PDCD4), which promotes apoptosis, was directly targeted by miR-199a-3p. Furthermore, we confirmed that miR-199a-3p-suppressed hepatocyte apoptosis and hepatic injury by targeting and suppressing PDCD4. Thus, hepatic miR-199a-3p inhibits hepatocyte apoptosis and hepatocarcinogenesis, and decreased miR-199a-3p in hepatocytes may aggravate hepatic injury and HCC development.

BHCMDA: A New Biased Heat Conduction Based Method for Potential MiRNA-Disease Association Prediction

Recent studies have indicated that microRNAs (miRNAs) are closely related to sundry human sophisticated diseases. According to the surmise that functionally similar miRNAs are more likely associated with phenotypically similar diseases, researchers have proposed a variety of valid computational models through integrating known miRNA-disease associations, disease semantic similarity, miRNA functional similarity, and Gaussian interaction profile kernel similarity to discover the potential miRNA-disease relationships in biomedical researches. Taking account of the limitations of previous computational models, a new computational model based on biased heat conduction for MiRNA-Disease Association prediction (BHCMDA) was proposed in this paper, which can achieve the AUC of 0.8890 in LOOCV (Leave-One-Out Cross Validation) and the mean AUC of 0.9060, 0.8931 under the framework of twofold cross validation, fivefold cross validation, respectively. In addition, BHCMDA was further implemented to the case studies of three vital human cancers, and simulation results illustrated that there were 88% (Esophageal Neoplasms), 92% (Colonic Neoplasms) and 92% (Lymphoma) out of top 50 predicted miRNAs having been confirmed by experimental literatures, separately, which demonstrated the good performance of BHCMDA as well. Thence, BHCMDA would be a useful calculative resource for potential miRNA-disease association prediction.

Improved Prediction of miRNA-Disease Associations Based on Matrix Completion with Network Regularization

The identification of potential microRNA (miRNA)-disease associations enables the elucidation of the pathogenesis of complex human diseases owing to the crucial role of miRNAs in various biologic processes and it yields insights into novel prognostic markers. In the consideration of the time and costs involved in wet experiments, computational models for finding novel miRNA-disease associations would be a great alternative. However, computational models, to date, are biased towards known miRNA-disease associations; this is not suitable for rare miRNAs (i.e., miRNAs with a few known disease associations) and uncommon diseases (i.e., diseases with a few known miRNA associations). This leads to poor prediction accuracies. The most straightforward way of improving the performance is by increasing the number of known miRNA-disease associations. However, due to lack of information, increasing attention has been paid to developing computational models that can handle insufficient data via a technical approach. In this paper, we present a general framework—improved prediction of miRNA-disease associations (IMDN)—based on matrix completion with network regularization to discover potential disease-related miRNAs. The success of adopting matrix factorization is demonstrated by its excellent performance in recommender systems. This approach considers a miRNA network as additional implicit feedback and makes predictions for disease associations relevant to a given miRNA based on its direct neighbors. Our experimental results demonstrate that IMDN achieved excellent performance with reliable area under the receiver operating characteristic (ROC) area under the curve (AUC) values of 0.9162 and 0.8965 in the frameworks of global and local leave-one-out cross-validations (LOOCV), respectively. Further, case studies demonstrated that our method can not only validate true miRNA-disease associations but also suggest novel disease-related miRNA candidates.

Expression and clinical significance of miR-4516 and miR-21-5p in serum of patients with colorectal cancer

Background

This study sought to detect the expression and clinical significance of miR-4516 and miR-21-5p in serum of patients with colorectal cancer.

Methods

Bioinformatics methods were used to analyze the expression patterns of miR-4516 and miR-21-5p in colorectal cancer. A total of 80 patients with colorectal cancer, 65 patients with benign colorectal tumors and 50 healthy persons were selected. qRT-PCR was performed to detect the expression levels of serum miR-4516 and miR-21-5p before and after operation or postoperative recurrence. The correlation of miR-4516 and miR-21-5p expression levels with the clinical characteristics and prognosis of colorectal cancer was analyzed, and that with the patient’s survival was further examined by Kaplan-Meier analysis.

Results

MiR-4516 was poorly expressed in colorectal cancer in the preoperative group, and miR-21-5p was highly expressed. While in the postoperative group, miR-4516 was up-regulated, and miR-21-5p was down-regulated. The low expression of miR-4516 was shown to be related to TNM staging, invasion degree, lymph node metastasis and distant metastasis of the patients. Whereas the high expression of miR-21-5p was proved to be correlated with TNM staging and lymph node metastasis. Kaplan-Meier survival analysis showed that high expression of miR-4516 or low expression of miR-21-5p could contribute to better overall survival.

Conclusion

Low miR-4516 or high miR-21-5p could be used as an independent risk factor for prognosis of colorectal cancer.

Overview of microRNA-199a Regulation in Cancer

microRNAs (miRNAs) are a class of endogenous short, non-coding RNAs that regulate a multitude of genes at the post-transcriptional level. miR-199, which is a highly conserved miRNA family, consists of miR-199a and miR-199b. Researchers mainly focused on miR-199a over the past few years. Functional studies have demonstrated that mature miR-199a is a key player in the maintenance of normal homeostasis and in the regulation of disease pathogenesis. Here, we summarize the biological functions of miR-199a and review recent research on its roles in the physiological processes of cancer cells, such as proliferation, migration, invasion, apoptosis, autophagy and glycometabolism.

miR-199a-3p targets ETNK1 to promote invasion and migration in gastric cancer cells and is associated with poor prognosis

PURPOSE

To investigate the prognostic significance of miR-199a-3p and its role in invasion and metastasis in gastric cancer.

METHODS

miR-199a-3p expression in 436 formalin-fixed and 39 frozen gastric cancer tissues was investigated by in situ hybridization and RT-PCR, respectively. The role of miR-199a-3p in the migration and invasion of gastric cancer cells was determined in overexpression and inhibitor studies using transwell assays and the SGC-7901, BGC-823 and MGC-803 gastric cancer cells lines. The effect of miR-199a-3p expression on ethanolamine kinase 1 (ETNK1) levels was determined by western botting.

RESULTS

miR-199a-3p was significantly up-regulated in AGS, SGC-7901, BGC-823 and MGC-803 gastric cancer cells, when compared with GES-1 non-malignant gastric epithelial cells. In situ hybridization studies revealed that human non-tumor gastric mucosa samples were negative for miR-199a-3p expression, while 162 of 436 (37.16%) cases of gastric cancer demonstrated positive expression. miR-199a-3p overexpression was associated with tumor size, Lauren classification, depth of invasion, lymph node and distant metastasis, TNM stage and prognosis. In patients with I, II and III stage tumors, high miR-199a-3p expression was associated with a significantly lower 5-year survival rate. miR-199a-3p overexpression was associated with increased cell migration and invasion. ETNK1 expression was inhibited following miR-199a-3p overexpression in BGC-823 and SGC-7901 cells, and elevated following miR-199a-3p suppression in MGC-803 cells.

CONCLUSION

miR-199a-3p is highly expressed in gastric cancer, and correlates with invasion, metastasis and prognosis. miR-199a-3p regulates the invasion and migration of gastric cancer cells by targeting ETNK1. Consequently, miR-199a-3p may serve as a prognostic indicator in gastric cancer.

MiR-199a-3p inhibition facilitates cardiomyocyte differentiation of embryonic stem cell through promotion of MEF2C

MicroRNAs (miRNAs) is a small molecule (19-25 nucleotide) noncoding RNA that inhibits the expression of target messenger RNA (mRNA) at the posttranscriptional level as an endogenous regulator. There is an increasing evidence that miR-199a-3p has a significant effect on the development of multiple tumors. However, the specific roles of miR-199a-3p in myocardial differentiation of embryonic stem cell still need to be investigated. Method of the hanging drop was used to build the model of cardiomyocyte differentiation of stem cell and beating rate of embryoid bodies (EBs) was calculated. The levels of intracellular MEF2C, a-MHC, GATA4, Nkx2.5, and cTnT mRNA were measured by real-time quantitative polymerase chain reaction, while the expressions of miR-199a-3p were detected simultaneously. Protein levels of MEF2C, a-MHC, GATA4, Nkx2.5, and cTnT were quantified by western blot analysis. Immunoreactivities of MEF2C and cTnT were analyzed by immunofluorescence. The interaction between miR-199a-3p and its predicted target (3'-untranslated region of MEF2C mRNA) was verified by luciferase assay. MiR-199a-3p levels increased during cardiogenesis. MiR-199a-3p inhibitor increased the beating rate of EBs and promoted expressions of cardiac-specific markers (GATA4, Nkx2.5, cTnT, and a-MHC). Notably, miR-199a-3p inhibition brought upregulation of MEF2C, which is the target of miR-199a-3p that we predicted and verified experimentally. In addition, MEF2C siRNA decreased miR-199a-3p inhibitor promoted EBs beating and attenuated miR-199a-3p inhibitor-induced cTnT and MEF2C expressions. The results above showed that MEF2C was involved in the process of promoting the differentiation of stem cells into cardiac myocytes by miR-199a-3p inhibitors.

Prognostic value of microRNAs in colorectal cancer: a meta-analysis

Background

Numerous studies have shown that miRNA levels are closely related to the survival time of patients with colon, rectal, or colorectal cancer (CRC). However, the outcomes of different investigations have been inconsistent. Accordingly, a meta-analysis was conducted to study associations among the three types of cancers.

Materials and methods

Studies published in English that estimated the expression levels of miRNAs with survival curves in CRC were identified until May 20, 2017 by online searches in PubMed, Embase, Web of Science, and the Cochrane Library by two independent authors. Pooled HRs with 95% CIs were used to estimate the correlation between miRNA expression and overall survival.

Results

A total of 63 relevant articles regarding 13 different miRNAs, with 10,254 patients were ultimately included. CRC patients with high expression of blood miR141 (HR 2.52, 95% CI 1.68-3.77), tissue miR21 (HR 1.31, 95% CI 1.12-1.53), miR181a (HR 1.52, 95% CI 1.26-1.83), or miR224 (HR 2.12, 95% CI 1.04-4.34), or low expression of tissue miR126 (HR 1.55, 95% CI 1.24-1.93) had significantly poor overall survival (P<0.05).

Conclusion

In general, blood miR141 and tissue miR21, miR181a, miR224, and miR126 had significant prognostic value. Among these, blood miR141 and tissue miR224 were strong biomarkers of prognosis for CRC.

MiR-199a-3p enhances cisplatin sensitivity of cholangiocarcinoma cells by inhibiting mTOR signaling pathway and expression of MDR1

Several studies have reported reduced miRNA-199a-3p (miR-199a-3p) in different human malignancies, however, little is known about miR-199a-3p in cholangiocarcinoma cells. In this study, we demonstrate the essential role and mechanism of miR-199a-3p in regulating cisplatin sensitivity in cholangiocarcinoma cell lines. Using a CCK-8 cell counting assay we found that expression of miR-199a-3p was positively correlated with cisplatin sensitivity in cholangiocarcinoma cell lines. MiR-199a-3p overexpression could decrease the proliferation rate and increase apoptosis of cholangiocarcinoma cells in the presence of cisplatin, while miR-199a-3p inhibition had the opposite effect. Further study demonstrated that mTOR was the target gene of miR-199a-3p, and that miR-199a-3p mimics could inhibit expression of mTOR, which consequently reduced the phosphorylation of its downstream proteins 4EBP1 and p70s6k. Rescue experiments proved that miR-199a-3p could increase the cisplatin sensitivity of cholangiocarcinoma cell lines by regulating mTOR expression. Moreover, we also found that miR-199a-3p overexpression could reduce cisplatin induced MDR1 expression by decreasing the synthesis and increasing the degradation of MDR1, thus enhancing the effectiveness of cisplatin in cholangiocarcinoma. In conclusion, miR-199a-3p could increase cisplatin sensitivity of cholangiocarcinoma cell lines by inhibiting the activity of the mTOR signaling pathway and decreasing the expression of MDR1.

EGBMMDA: Extreme Gradient Boosting Machine for MiRNA-Disease Association prediction

Associations between microRNAs (miRNAs) and human diseases have been identified by increasing studies and discovering new ones is an ongoing process in medical laboratories. To improve experiment productivity, researchers computationally infer potential associations from biological data, selecting the most promising candidates for experimental verification. Predicting potential miRNA–disease association has become a research area of growing importance. This paper presents a model of Extreme Gradient Boosting Machine for MiRNA-Disease Association (EGBMMDA) prediction by integrating the miRNA functional similarity, the disease semantic similarity, and known miRNA–disease associations. The statistical measures, graph theoretical measures, and matrix factorization results for each miRNA-disease pair were calculated and used to form an informative feature vector. The vector for known associated pairs obtained from the HMDD v2.0 database was used to train a regression tree under the gradient boosting framework. EGBMMDA was the first decision tree learning-based model used for predicting miRNA–disease associations. Respectively, AUCs of 0.9123 and 0.8221 in global and local leave-one-out cross-validation proved the model’s reliable performance. Moreover, the 0.9048 ± 0.0012 AUC in fivefold cross-validation confirmed its stability. We carried out three different types of case studies of predicting potential miRNAs related to Colon Neoplasms, Lymphoma, Prostate Neoplasms, Breast Neoplasms, and Esophageal Neoplasms. The results indicated that, respectively, 98%, 90%, 98%, 100%, and 98% of the top 50 predictions for the five diseases were confirmed by experiments. Therefore, EGBMMDA appears to be a useful computational resource for miRNA–disease association prediction.

miR-199a-5p inhibits proliferation and induces apoptosis in hemangioma cells through targeting HIF1A

MicroRNAs (miRNAs) exhibit a crucial role in the regulation of angiogenesis and tumor progression, of which miR-199a-5p (miR-199a) has been reported to function as a tumor suppressor in multiple malignancies. However, the precise mechanisms underlying miR-199a in hemangiomas (HAs) remain elusive. In this study, we found that miR-199a had low expression level, while proliferating cell nuclear antigen (PCNA) had high expression level in proliferating-phase HAs compared with the involuting-phase HAs and normal tissues. Spearman correlation analysis revealed the negative correlation of miR-199a with PCNA expression in proliferating-phase HAs. In vitro experiments showed that restoration of miR-199a suppressed cell proliferation capability and induced cell apoptosis in HA-derived endothelial cells (HDEC) and CRL-2586 EOMA cells, followed with decreased PCNA expression and increased cleaved caspase-3 expression, but miR-199a inhibitor reversed these effects. Furthermore, HIF1A was identified as a target of miR-199a and had negative correlation with miR-199a expression in proliferating-phase HAs. Overexpression of HIF1A attenuated the anti-proliferation effect of miR-199a mimic in HAs cells. Taken together, our findings demonstrate that miR-199a may inhibit proliferation and induce apoptosis in HAs cells via targeting HIF1A and provide a potential therapeutic target for HAs.

LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction

Predicting novel microRNA (miRNA)-disease associations is clinically significant due to miRNAs’ potential roles of diagnostic biomarkers and therapeutic targets for various human diseases. Previous studies have demonstrated the viability of utilizing different types of biological data to computationally infer new disease-related miRNAs. Yet researchers face the challenge of how to effectively integrate diverse datasets and make reliable predictions. In this study, we presented a computational model named Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction (LRSSLMDA), which projected miRNAs/diseases’ statistical feature profile and graph theoretical feature profile to a common subspace. It used Laplacian regularization to preserve the local structures of the training data and a L₁-norm constraint to select important miRNA/disease features for prediction. The strength of dimensionality reduction enabled the model to be easily extended to much higher dimensional datasets than those exploited in this study. Experimental results showed that LRSSLMDA outperformed ten previous models: the AUC of 0.9178 in global leave-one-out cross validation (LOOCV) and the AUC of 0.8418 in local LOOCV indicated the model’s superior prediction accuracy; and the average AUC of 0.9181+/-0.0004 in 5-fold cross validation justified its accuracy and stability. In addition, three types of case studies further demonstrated its predictive power. Potential miRNAs related to Colon Neoplasms, Lymphoma, Kidney Neoplasms, Esophageal Neoplasms and Breast Neoplasms were predicted by LRSSLMDA. Respectively, 98%, 88%, 96%, 98% and 98% out of the top 50 predictions were validated by experimental evidences. Therefore, we conclude that LRSSLMDA would be a valuable computational tool for miRNA-disease association prediction.

Discovering miRNA-disease associations promotes the understanding towards the molecular mechanisms of various human diseases at the miRNA level, and contributes to the development of diagnostic biomarkers and treatment tools for diseases. Computational models can make the discovery more efficient and experiments more productive. LRSSLMDA was proposed to computationally infer potential miRNA-disease associations via adopting sparse subspace learning with Laplacian regularization on the known miRNA-disease association network and the informative feature profiles extracted from the integrated miRNA/disease similarity networks. Experimental results in global and local leave-one-out cross validation and 5-fold cross validation showed a superior prediction performance of LRSSLMDA over previous models. Moreover, three types of case studies on five important human diseases were carried out to further demonstrate the model’s predictive power: respectively, 98%, 88%, 96%, 98% and 98% out of the top 50 predicted miRNAs were confirmed by experimental literatures. So, we believe that LRSSLMDA could make reliable predictions and might guide future experimental studies on miRNA-disease associations.

miR-199a-3p and miR-214-3p improve the overall survival prediction of muscle-invasive bladder cancer patients after radical cystectomy

To improve the clinical decision‐making regarding further treatment management and follow‐up scheduling for patients with muscle‐invasive bladder cancer (MIBC) after radical cystectomy (RC), a better prediction accuracy of prognosis for these patients is urgently needed. The objective of this study was to evaluate the validity of differentially expressed microRNAs (miRNAs) based on a previous study as prognostic markers for overall survival (OS) after RC in models combined with clinicopathological data. The expression of six miRNAs (miR‐100‐5p, miR‐130b‐3p, miR‐141‐3p, miR‐199a‐3p, miR‐205‐5p, and miR‐214‐3p) was measured by RT‐qPCR in formalin‐fixed, paraffin‐embedded tissue samples from 156 MIBC patients who received RC in three urological centers. Samples from 2000 to 2013 were used according to their tissue availability, with follow‐up until June 2016. The patient cohort was randomly divided into a training (n = 100) and test set (n = 56). Seventy‐three samples from adjacent normal tissue were used as controls. Kaplan–Meier, univariate and multivariate Cox regression, and decision curve analyses were carried out to assess the association of clinicopathological variables and miRNAs to OS. Both increased (miR‐130b‐3p and miR‐141‐3p) and reduced (miR‐100‐5p, miR‐199a‐3p, and miR‐214‐3p) miRNA expressions were found in MIBC samples in comparison to nonmalignant tissue samples (P < 0.0001). miR‐199a‐3p and miR‐214‐3p were independent markers of OS in Cox regression models with the significant clinicopathological variables age, tumor status, and lymph node status. The prediction model with the clinicopathological variables was improved by these two miRNAs in both sets. The predictive benefit was confirmed by decision curve analysis. In conclusion, the inclusion of both miRNAs into models based on clinical data for the outcome prediction of MIBC patients after RC could be a valuable approach to improve prognostic accuracy.

miR-199a-3p inhibits cell proliferation and induces apoptosis by targeting YAP1, suppressing Jagged1-Notch signaling in human hepatocellular carcinoma

BACKGROUND

miR-199a-3p was significantly downregulated in the majority of human hepatocellular carcinoma (HCC) tissues and HCC cell lines. Yes associated protein 1 (YAP1) was overexpressed in human HCC, which promoted HCC development and progression by upregulating Jagged1 and activating the Notch pathway. We searched potential targets of miR-199a-3p with DIANA, TargetScan and PicTar tools, and found that YAP1 is one of the potential targets. Based on these findings, we speculated that miR-199a-3p might suppress HCC growth by targeting YAP1, downregulating Jagged1 and suppressing the Notch pathway.

RESULTS

We determined the expression of miR-199a-3p and YAP1 by quantitative Real-Time PCR (qRT-PCR) and western blot assays, respectively, and found downregulation of miR-199a-3p and upregulation of YAP1 in HCC cell lines. Cell proliferation and apoptosis assays showed that miR-199a-3p suppresses HCC cell proliferation and promotes apoptosis, and knockdown of YAP1 has similar role. Furthermore, we verified that miR-199a-3p can directly target YAP1. We further investigated and confirmed that miR-199a-3p and YAP1 regulate HCC cell proliferation and apoptosis through Jagged1-Notch signaling.

CONCLUSION

miR-199a-3p targets YAP1, downregulates Jagged1 and suppresses the Notch signaling to inhibit HCC cell proliferation and promote apoptosis. These findings provide new insights into the mechanism by which miR-199a-3p suppresses HCC cell proliferation and induces apoptosis.

miR-199a-5p regulates HIF-1α and OSGIN2 and its expression is correlated to soft-tissue sarcoma patients' outcome

Soft tissue sarcomas are a heterogeneous group of malignant neoplasms of mesenchymal origin. Partly due to hypoxia, an aggressive and radioresistant phenotype frequently develops, resulting in poorer patient outcome. microRNAs (miRNAs) are tiny, non-coding regulators of gene expression and in situations of cellular stress situations may predict clinical progression and patient outcome. In the present study, hypoxia-associated miR-199a-5p expression in 96 soft tissue sarcoma samples was analysed by reverse transcription-quantitative polymerase chain reaction and associations between miR-199a-5p expression and patient clinicopathological characteristics and survival were measured. Additionally, luciferase reporter assays analyzed the post-transcriptional regulation of hypoxia-associated genes hypoxia-inducible factor 1α (HIF-1α), oxidative stress induced growth inhibitor 2 (OSGIN2) and vascular endothelial growth factor (VEGF) by miR-199a-5p. Survival analyses indicated that low expression of miR-199a-5p was significantly correlated with poorer tumor-specific survival (univariate Cox's-Regression analyses; relative risk=1.92, P=0.029). Furthermore, it was demonstrated that the 3'UTR of HIF-1α and OSGIN2 genes were regulated by miR-199a-5p in-vitro, although the 3'UTR of VEGF was not. To the best of our knowledge, this is the first report demonstrating the regulation of the 3'untranslated region of the OSGIN2 gene by miR-199a-5p and a significant correlation between low miR-199a-5p expression and a poor outcome of patients with soft tissue sarcoma.

microRNA-199a-3p functions as tumor suppressor by regulating glucose metabolism in testicular germ cell tumors

microRNA (miR)-199a-3p serves critical roles in cancer development and progression. In order to improve knowledge of the functional mechanism of miR‑199a‑3p in testicular tumors, the present study characterized the regulation of aerobic glycolysis by miR‑199a‑3p and its impact on metabolism. Using 3‑4,5‑dimethylthiazol‑2‑yl‑2,5 diphenyl tetrazolium bromide, wound healing and flow cytometry assays, it was determined that overexpression of miR‑199a‑3p in Ntera‑2 cells caused suppression of cell growth and migration. Further biochemical methods and high‑throughput quantitative polymerase chain reaction array of metabolic genes showed that inhibition of miR‑199a‑3p markedly elevated lactate production and 12 differentially expressed genes, including 2 upregulated and 10 downregulated genes, were identified following treatment with miR‑199a‑3p in Ntera‑2 cells. In clinical samples, four selected genes, lactate dehydrogenase A, monocarboxylate transporter 1, phosphoglycerate kinase 1 and TP53‑inducible glycolysis and apoptosis regulator, were significantly overexpressed in malignant testicular germ cell tumor, and their expression inversely correlated with the expression of miR‑199a‑3p, suggesting that these four genes may be affected by miR‑199a‑3p. Using bioinformatics analysis, the transcription factor Sp1 binding site was identified in the promoter region of the four selected genes. In addition, miR‑199a‑3p was predicted to bind to conservative target sequences in the 3'‑untranslated region of Sp1 mRNA, suggesting that miR-199a-3p may downregulate these four metabolic genes through Sp1. It was demonstrated the dysregulated expression and activation of miR‑199a‑3p may serve important roles in aerobic glycolysis and tumorigenesis in patients with testicular cancer. Therefore, miR-199a-3p may be a potential biomarker in the prognosis and treatment of testicular tumors.

Accuracy of novel diagnostic biomarkers for hepatocellular carcinoma: An update for clinicians (Review)

Hepatocellular carcinoma (HCC) is the most common liver malignancy and a leading cause of cancer-related mortality worldwide. Accurate detection and differential diagnosis of early HCC can significantly improve patient survival. Currently, detection of HCC in clinical practice is performed by diagnostic imaging techniques and determination of serum biomarkers, most notably α-fetoprotein (AFP), fucosylated AFP and des-γ-carboxyprothrombin. However, these methods display limitations in sensitivity and specificity, especially with respect to early stages of HCC. Recently, high-throughput technologies have elucidated many new pathways involved in hepatocarcinogenesis and have led to the discovery of a plethora of novel, non-invasive serum biomarkers. In particular, the combination of AFP with these new candidate molecules has yielded promising results. In this review, we aimed at recapitulating the most recent (2013–2015) developments in HCC biomarker research. We compared promising novel diagnostic serum protein biomarkers, such as annexin A2, the soluble form of the receptor tyrosine kinase Axl and thioredoxin, as well as their combinations with AFP. High diagnostic performance (area under the curve >0.75) as shown by threshold-independent receiver operating characteristic curve analysis was a prerequisite for inclusion in this review. In addition, we discuss the role and potential of microRNAs in HCC diagnosis and associated methodological challenges.

The conglomeration of diagnostic, prognostic and therapeutic potential of serum miR-199a and its association with clinicopathological features in epithelial ovarian cancer

Epithelial ovarian cancer (EOC) is the most lethal cause of morbidity and mortality worldwide. miRNA deregulation evinces a remarkable role in ovarian cancer tumorigenesis. miRNA-199a (miR-199a) is known to be involved in cancer development and progression. Although miR-199a has been studied in various cell types, its correlation with clinicopathological features in EOC has not been documented. In this study, we identified the clinicopathological hallmarks which might be perturbed due to the downregulation of serum miR-199a in EOC. Seventy serum samples from histopathologically confirmed EOC patients and 70 controls were collected. Total RNA from serum was isolated by Trizol method, polyadenylated and reverse transcribed into cDNA. Expression level of miR-199a was detected by using miRNA qRT-PCR. Relative expression was determined with matched controls using U6 snRNA as reference. Level of miR-199a expression was compared with distinct clinicopathological features. Expression of miR-199a was found to be significantly downregulated in comparison with matched normal controls. The expression level of miR-199a was found to be significantly associated with tumor stage, lymph node metastasis, and distal metastasis. Receiver operating characteristic (ROC) curve for diagnostic potential yielded significant area under the curve (AUC) with a considerable sensitivity and specificity. ROC curves for prognosis yielded significant AUCs for histological grade, distal metastasis, lymph node status, and survival. Our findings suggest that miR-199a downregulation might be a potential indicator for disease progression promoting the aggressive tumor progression and be identified as a diagnostic marker to predict the prognosis and survival in EOC patients.

The hypoxia-related microRNA miR-199a-3p displays tumor suppressor functions in ovarian carcinoma

During the dissemination of ovarian cancer cells, the cells float in the peritoneal cavity without access to a vascular supply and so are exposed to hypoxic conditions, which may cause the ovarian cancer cells to acquire a more aggressive and malignant phenotype. In this study, we screened microRNAs (miRNAs) to identify those that displayed altered expression patterns under hypoxic conditions and then analyzed their functional roles in ovarian cancer progression. miRNA PCR arrays performed on cells from 2 ovarian cancer cell lines (CaOV3 and RMUG-S) revealed miR-199a-3p as one of the miRNAs that are downregulated under hypoxia. In silico analyses indicated that MET is one of the target genes for miR-199a-3p; subsequently, miR-199a-3p expression was found to be inversely correlated with c-Met expression in ovarian cancer. Transfection of precursor miR-199a-3p into ovarian cancer cells reduced c-Met expression and inhibited the phosphorylation of c-Met, extracellular signal-regulated kinase, and AKT; in addition, proliferation, adhesion, and invasiveness were inhibited. Moreover, overexpression of miR-199a-3p in cancer cells significantly suppressed peritoneal dissemination in a xenograft model. In summary, the hypoxia-related microRNA miR-199a-3p drastically inhibits ovarian cancer progression through the downregulation of c-Met expression. Therefore, miR-199a-3p is a potential target for treating ovarian cancer dissemination.

Genome-Wide Expression of MicroRNAs Is Regulated by DNA Methylation in Hepatocarcinogenesis

Background. Previous studies, including ours, have examined the regulation of microRNAs (miRNAs) by DNA methylation, but whether this regulation occurs at a genome-wide level in hepatocellular carcinoma (HCC) is unclear. Subjects/Methods. Using a two-phase study design, we conducted genome-wide screening for DNA methylation and miRNA expression to explore the potential role of methylation alterations in miRNAs regulation. Results. We found that expressions of 25 miRNAs were statistically significantly different between tumor and nontumor tissues and perfectly differentiated HCC tumor from nontumor. Six miRNAs were overexpressed, and 19 were repressed in tumors. Among 133 miRNAs with inverse correlations between methylation and expression, 8 miRNAs (6%) showed statistically significant differences in expression between tumor and nontumor tissues. Six miRNAs were validated in 56 additional paired HCC tissues, and significant inverse correlations were observed for miR-125b and miR-199a, which is consistent with the inactive chromatin pattern found in HepG2 cells. Conclusion. These data suggest that the expressions of miR-125b and miR-199a are dramatically regulated by DNA hypermethylation that plays a key role in hepatocarcinogenesis.

Inhibition of EZH2 expression is associated with the proliferation, apoptosis and migration of SW620 colorectal cancer cells in vitro

Epigenetic changes have been recently recognized as important in many human cancers. Enhancer of zeste homologue 2 (EZH2) gene has shown overexpression in various human cancers, consistent with a straightforward role of EZH2 as an oncogene, but its function in carcinogenesis is partly contradictory. The role of EZH2 in development of human colorectal cancer (CRC) has not yet been clarified. In present study, we observed up-regulation of EZH2 expression in tumor tissues from CRC patients. The expression of EZH2 in CRC cell lines is consistent with the trend in cancer tissues using RT-PCR. We showed that TNM stage and lymph node metastasis in CRC patients are significantly correlated with EZH2 expression levels. EZH2 level of transcription and protein was inhibited by small interfering RNA (siRNA). More importantly, EZH2-siRNA inhibited the proliferation and migration of SW620 cells while promoting their apoptosis, and inducing G0/G1 cell cycle arrest of CRC cells. Collectively, our results suggest that up-regulated EZH2 expression may contribute to the progression of the patients with CRC. A comprehensive study of epigenetic mechanisms and the relevance of EZH2 in CRC is important for fully understanding this disease and as a basis for developing new treatment options in patients with CRC.

Circulating miR-375 and miR-199a-3p as potential biomarkers for the diagnosis of hepatocellular carcinoma

Aiming to find novel non-invasive biomarkers with high accuracy for the detention of early-stage hepatocellular carcinoma (HCC), we examined the predictive power of two microRNAs (miR; miR-375 and miR-199a-3p) as potential biomarkers in early-stage HCC. A total of 234 serum samples (78 samples from HCC patients, 156 samples from healthy controls) were collected. We measured the levels of the two mature microRNAs (miRNAs) (miR-375 and miR-199a-3p) with probe-based stem-loop quantitative reverse-transcriptase PCR (RT-qPCR) in all subjects. In addition, the correlation between the expression levels of two miRs and clinicopathological factors was explored. Receiver operating characteristic curve (ROC) analyses revealed that the two serum miRs could be promising biomarkers for HCC, with relatively high area under the curve (AUC) values as follows: miR-375, 0. 637 with 95 % confidence interval (CI) of 0.560-0.741; miR-199a-3p, 0. 883 with 95 % CI of 0.827-0.938. Stratified analyses indicated that circulating miR-199a-3p showed better predictive value in patients with long-term drinking. Our data suggested that circulating miR-375 and miR-199a-3p could be a novel serum biomarker for HCC. Nevertheless, further validating and improving study with larger sample should be conducted to confirm our results.

Effects of ephrinB2 gene siRNA on the biological behavior of human colorectal cancer cells

Colorectal cancer (CRC) is a common gastrointestinal malignancy worldwide and is a lethal and aggressive malignancy with a dismal prognosis. EphrinB2 is a membrane-bound ligand and has an intracellular domain that also possesses an intrinsic signaling capacity called 'reverse signaling'. In the present study, CRC cell lines were screened for high expression of ephrinB2. Small interfering RNA (siRNA) knockdown of ephrinB2 was performed in human SW480 CRC cells. The levels of expression of ephrinB2, VEGF, CD105 and matrix metalloproteinase 9 (MMP9) protein were measured by western blotting, and messenger RNA (mRNA) levels were measured using real-time PCR. Apoptosis and cell cycle distribution were determined using flow cytometry. Cell proliferation was measured by a methyl thiazole tetrazolium (MTT) test and a scratch healing experiment was used to measure the extent of cell migration. A Transwell assay was used to detect the extent of cell invasion. The results showed that RNA interference (RNAi) of ephrinB2 effectively silenced the ephrinB2 gene at both the mRNA and protein levels in SW480 cells and inhibited the proliferation, invasion, migration and angiogenesis and induced apoptosis in SW480 cells. These effects may be attributed to VEGF and MMP9 regulation.

An update on microRNAs as colorectal cancer biomarkers: where are we and what's next?

miRNAs are abundant classes of small, endogenous non-coding RNAs, which inhibit the expression of target gene via post-transcriptional regulation. In addition to an important functional role miRNAs play in carcinogenesis, emerging evidence has demonstrated their feasibility as robust cancer biomarkers. In particular, the recent discovery of miRNAs in the body fluids provides an attractive opportunity for the development of non-invasive biomarkers for the diagnosis, prognosis and predictive response to cancer therapy. Colorectal cancer (CRC) is one of the most common cancers worldwide, and accumulating data provides a compelling case for the potential exploitation of miRNAs as CRC-biomarkers. This review summarizes the current state of literature in the field, focusing on the clinical relevance of miRNAs as potential biomarkers for CRC treatment and discussing the forthcoming challenges to further advance this exciting field of 'academic research' into 'bedside clinical care' of patients suffering from CRC.

MSC-regulated microRNAs converge on the transcription factor FOXP2 and promote breast cancer metastasis

Mesenchymal stem/stromal cells (MSCs) are progenitor cells shown to participate in breast tumor stroma formation and to promote metastasis. Despite expanding knowledge of their contributions to breast malignancy, the underlying molecular responses of breast cancer cells (BCCs) to MSC influences remain incompletely understood. Here, we show that MSCs cause aberrant expression of microRNAs, which, led by microRNA-199a, provide BCCs with enhanced cancer stem cell (CSC) properties. We demonstrate that such MSC-deregulated microRNAs constitute a network that converges on and represses the expression of FOXP2, a forkhead transcription factor tightly associated with speech and language development. FOXP2 knockdown in BCCs was sufficient in promoting CSC propagation, tumor initiation, and metastasis. Importantly, elevated microRNA-199a and depressed FOXP2 expression levels are prominent features of malignant clinical breast cancer and are associated significantly with poor survival. Our results identify molecular determinants of cancer progression of potential utility in the prognosis and therapy of breast cancer.

Circulating miR-199a-3p as a novel serum biomarker for colorectal cancer

Serum microRNAs (miRNAs) have been shown to have potential for cancer diagnosis. The main objective of the present study was to identify a novel serum miRNA biomarker from patients with colorectal cancer (CRC). Microarray analysis of miRNA expression was performed using paired pre-operative and post-operative serum from 10 CRC patients. Expression of two miRNAs (let-7a and miR-199a-3p) was significantly decreased in the post-operative serum when compared to levels in the pre-operative serum (P=0.015 and 0.029, respectively). Quantitative real-time polymerase chain reaction (qRT-PCR) confirmed the decrease in the miRNAs in an extended number (n=30) of paired serum samples. Next, we examined the serum let-7a level in 32 non-cancer patients and 84 CRC patients but we found no significant difference (P=0.120). In contrast, miR199a-3p expression was significantly higher in the CRC patients than that in the non-cancer patients (P=0.016). Furthermore, clinical and pathological survey indicated that high expression of miR-199a-3p was significantly associated with deep wall invasion. Our data suggest that circulating miR-199a-3p could be a novel serum biomarker for CRC.

Inhibition of EZH2 expression is associated with the proliferation, apoptosis, and migration of SW620 colorectal cancer cells in vitro

Epigenetic changes have been recently recognized as important in many human cancers. Enhancer of zeste homologue 2 (EZH2)gene has shown overexpression in various human cancers, consistent with a straightforward role of EZH2 as an oncogene, but its function in carcinogenesis is partly contradictory. The role of EZH2 in development of human colorectal cancer (CRC) has not yet been clarified. In present study, we observed up-regulation of EZH2 expression in tumor tissues from CRC patients [corrected]. The expression of EZH2 in CRC cell lines is consistent with the trend in cancer tissues using RT-PCR. We showed that TNM stage and lymph node metastasis in CRC patients are significantly correlated with EZH2 expression levels [corrected]. EZH2 level of transcription and protein was inhibited by small interfering RNA (siRNA). More importantly, EZH2-siRNA inhibited the proliferation and migration of SW620 cells while promoting their apoptosis, and inducing G0/G1 cell cycle arrest of CRC cells. Collectively, our results suggest that upregulated EZH2 expression may contribute to the progression of the patients with CRC. A comprehensive study of epigenetic mechanisms and the relevance of EZH2 in CRC is important for fully understanding this disease and as a basis for developing new treatment options in patients with CRC [corrected].

NLK, a novel target of miR-199a-3p, functions as a tumor suppressor in colorectal cancer

We previously reported that miR-199a-3p is a newly biomarker for diagnosis and novel prognostic indicator in colorectal cancer. However, the miR-199a-3p regulatory mechanism and its target genes are still unclear. In our present study, we demonstrated miR-199a-3p could directly target 3'-UTR of NLK gene by luciferase reporter assay and western blot analysis. We detected NLK expressions in 92 colorectal cancer cases to evaluate its clinicopathologic characteristics in colorectal cancer. Our results showed that NLK expression was significantly downregulated in cancer tissues than NATs, and NLK low-expression was associated with lymph node metastasis, venous invasion, liver metastasis and the TNM stage (P<0.05). Moreover, Kaplan-Meier analysis showed that low expression of NLK correlated with a shorter overall survival rates of patients with CRC (P<0.05). In vitro, we also found that NLK suppressed the biological behaviors of colorectal cancer cells, including the abilities of cell proliferation, clone formation, wound healing, migration and invasion (P<0.05), while overexpression of NLK increased the apoptotic rate of colorectal cancer cells. All these results suggested that NLK was an identified miR-199a-3p target gene and functioned as a tumor suppressor gene in colorectal cancer. NLK could be a novel direction for developing diagnostic and therapeutic approaches in colorectal cancer.

Expression of Lgr5, a marker of intestinal stem cells, in colorectal cancer and its clinicopathological significance

Cancer stem cells (CSCs) have been the focus of intense investigations in cancer research although the cellular origin of CSCs has not been clearly determined. Lgr5 is a regulated target of Wnt/β-catenin signaling, which was first identified as a marker of intestinal stem cells. However, the expression of Lgr5 in human colorectal cancer (CRC) and its clinical clinicopathological significance in CRC patients as well as its correlation with Wnt/β-catenin pathway are not fully explored. Localization and expression of Lgr5 in CRC tissues was performed by immunohistochemical staining. The correlation between its expression levels and clinicopathological features as well as clinical outcomes of patients was analysed. The quantitative expression levels of Lgr5 in various CRC cell lines were determined using real-time RT-PCR. The relationship between Lgr5 expression and Wnt/β-catenin pathway in CRC was also investigated. Obviously elevated expression of Lgr5 was observed in CRC tissues, compared to the paired nontumor tissues. mRNA expression levels of Lgr5 was positively correlated with the expression of β-catenin in CRC tissues. The expression of Lgr5 was various in different CRC cell lines. Low and high expression levels of Lgr5 were significantly correlated with clinicopathological features such as TNM stage, lymph node metastasis and vascular invasion of CRC patients. More importantly, Lgr5 expression in CRC tissues was also associated with tumor angiogenesis as well as clinical outcomes. Taken together, these results suggest that elevated Lgr5 expression might contribute to the development and progression of CRC, and it could also be used a potential unfavorable prognostic biomarker for CRC. A better understanding of molecule mechanisms and the relevance of potential value for Lgr5 in the progression of CRC will help to identify a novel therapeutic strategy for CRC patients.

miR-199a-3p inhibits aurora kinase A and attenuates prostate cancer growth: new avenue for prostate cancer treatment

Prostate cancer (PCa) is the most common solid tumor malignancy in men that severely influences quality of life. Surgery is most often the recommended treatment for PCa, but radical prostatectomy can cause significant urinary adverse effects. Therefore, finding effective biochemical treatments for PCa remains a necessity. Aurora kinase A has been shown to be involved in PCa progression, thus making it a good target for PCa therapy. miRNAs are important regulators of gene expression, with some miRNAs specifically involved in carcinogenesis. Therefore, herein, we identified miRNAs targeted to aurora kinase A and examined their effects on the growth of PCa. We used primary samples from PCa patients and PCa cell lines as research subjects. We demonstrate that miR-199a-3p is down-regulated in PCa tissues compared with normal prostate tissues, with the expression pattern inversely correlated with the expression pattern of aurora kinase A. We find that miR-199a-3p agomir inhibits aurora kinase A and attenuates xenograft tumor growth of PCa. Moreover, we demonstrate that down-regulation of miR-199a-3p results from enhancement of the methylation of miR-199a gene in PCa. Furthermore, we find that the expression level of miR-199a-3p is inversely correlated to tumor stage and Gleason score of PCa. Revealing novel mechanisms for oncogene inhibition by miRNA-mediated pathways offers new avenues for PCa treatment.