miR-378a-3p modulates tamoxifen sensitivity in breast cancer MCF-7 cells through targeting GOLT1A

Turn On of a Ruthenium(II) Photocatalyst by DNA-Templated Ligation

Here, the synthesis of a Ru^II photocatalyst by light-directed oligonucleotide-templated ligation reaction is described. The photocatalyst was found to have tremendous potential for signal amplification with >15000 turnovers measured in 9 hours. A templated reaction was used to turn on the activity of this ruthenium(II) photocatalyst in response to a specific DNA sequence. The photocatalysis of the ruthenium(II) complex was harnessed to uncage a new precipitating dye that is highly fluorescent and photostable in the solid state. This reaction was used to discriminate between different DNA analytes based on localization of the precipitate as well as for in cellulo miRNA detection. Finally, a bipyridine ligand functionalized with two different peptide nucleic acid (PNA) sequences was shown to enable template-mediated ligation (turn on of the ruthenium(II) photocatalysis) and recruitment of substrate for templated photocatalysis.

microRNA Regulation in Estrogen Receptor-Positive Breast Cancer and Endocrine Therapy

As de novo and acquired resistance to standard first line endocrine therapies is a growing clinical challenge for estrogen receptor-positive (ER⁺) breast cancer patients, understanding the mechanisms of resistance is critical to develop novel therapeutic strategies to prevent therapeutic resistance and improve patient outcomes. The widespread post-transcriptional regulatory role that microRNAs (miRNAs) can have on various oncogenic pathways has been well-documented. In particular, several miRNAs are reported to suppress ERα expression via direct binding with the 3’ UTR of ESR1 mRNA, which can confer resistance to estrogen/ERα-targeted therapies. In turn, estrogen/ERα activation can modulate miRNA expression, which may contribute to ER⁺ breast carcinogenesis. Given the reported oncogenic and tumor suppressor functions of miRNAs in ER⁺ breast cancer, the targeted regulation of specific miRNAs is emerging as a promising strategy to treat ER⁺ breast cancer and significantly improve patient responsiveness to endocrine therapies. In this review, we highlight the major miRNA-ER regulatory mechanisms in context with ER⁺ breast carcinogenesis, as well as the critical miRNAs that contribute to endocrine therapy resistance or sensitivity. Collectively, this comprehensive review of the current literature sheds light on the clinical applications and challenges associated with miRNA regulatory mechanisms and novel miRNA targets that may have translational value as potential therapeutics for the treatment of ER⁺ breast cancer.

A Novel Computational Method for the Identification of Potential miRNA-Disease Association Based on Symmetric Non-negative Matrix Factorization and Kronecker Regularized Least Square

Increasing evidence has indicated that microRNAs (miRNAs) are associated with numerous human diseases. Studying the associations between miRNAs and diseases contributes to the exploration of effective diagnostic and treatment approaches for diseases. Unfortunately, the use of biological experiments to reveal the potential associations between miRNAs and diseases is time consuming and costly. Therefore, it is very necessary to use simple and efficient calculation models to predict potential disease-related miRNAs. Considering the limitations of other previous methods, we proposed a novel computational model of Symmetric Nonnegative Matrix Factorization for MiRNA-Disease Association prediction (SNMFMDA) to reveal the relation of miRNA-disease pairs. SNMFMDA could be applied to predict miRNAs associated with new diseases. Compared to the direct use of the integrated similarity in previous computational models, the integrated similarity need to be interpolated by symmetric non-negative matrix factorization (SymNMF) before application in SNMFMDA, and the relevant probability of disease-miRNA was obtained mainly through Kronecker regularized least square (KronRLS) method in our model. What's more, the AUC of global leave-one-out cross validation (LOOCV) reached 0.9007, and the AUC based on local LOOCV was 0.8426. Besides, the mean and the standard deviation of AUCs achieved 0.8830 and 0.0017 respectively in 5-fold cross validation. All of the above results demonstrated the superior prediction performance of SNMFMDA. We also conducted three different case studies on Esophageal Neoplasms, Breast Neoplasms and Lung Neoplasms, and 49, 49, and 48 of the top 50 of their predicted miRNAs respectively were confirmed by databases or related literatures. It could be expected that SNMFMDA would be a model with the ability to predict disease-related miRNAs efficiently and accurately.

MicroRNA‑663b mediates TAM resistance in breast cancer by modulating TP73 expression

Breast cancer is the second leading cause of cancer‑associated mortalities in women. Tamoxifen (TAM) is an endocrine therapy commonly used in the treatment of patients with breast cancer expressing estrogen receptor α. However, treatment often ends in failure due to the emergence of drug resistance. MicroRNAs (miRNAs), a family of small non‑coding RNAs, serve critical roles in the regulation of gene expression and cell events. To date, whether miRNA‑663b could mediate TAM resistance in breast cancer remains unknown. Therefore, the aim of the present study was to investigate the role of miRNA‑663b in TAM resistance in breast cancer. The results demonstrated that miRNA‑663b was upregulated in breast cancer with TAM resistance. Tumor protein 73 (TP73) was a direct target of miRNA‑663b, and was negatively regulated by miRNA‑663b in MCF‑7 cells. Furthermore, it was identified that downregulation of miRNA‑663b inhibited cell proliferation ability and promoted cell apoptosis, resulting in enhanced TAM sensitivity. In addition, these findings suggested that TP73 silencing may have eliminated the effects of miRNA‑663b inhibitor on breast cancer cells. In conclusion, the present study verified a novel molecular link between miRNA‑663b and TP73, and indicated that miRNA‑663b may be a critical therapeutic target in breast cancer.

miR‑378a‑3p exerts tumor suppressive function on the tumorigenesis of esophageal squamous cell carcinoma by targeting Rab10

Esophageal squamous cell carcinoma (ESCC) is a life-threatening cancer with increasing incidence worldwide. MicroRNAs (miRs) have been reported to be involved in the progression of various types of cancer. In previous studies, the expression of miR-378a-3p was shown to be reduced in ESCC tissues. However, the mechanism underlying the effect of miR-378a-3p in ESCC remains to be elucidated. By employing a reverse transcription-quantitative polymerase chain reaction, miR-378a-3p expression was tested in ESCC tissues and cell lines. In addition, the effects of miR-378a-3p on cell viability, proliferation, apoptosis, migration and invasion were studied using an MTT assay, an EdU assay, flow cytometry analysis, wound healing analysis and a Transwell assay. In the present study, the level of miR-378a-3p was significantly downregulated in ESCC clinical tissues and cell lines (EC109 and KYSE150). In addition, the overexpression of miR-378a-3p suppressed the viability, proliferation, migration and invasion of the ESCC cells. The upregulated expression of miR-378a-3p also increased the expression levels of B-cell lymphoma 2-associated X protein and caspase-3, and decreased the expression levels of matrix metalloproteinase (MMP)-2 and MMP-9, which attenuated ESCC tumorigenesis. Furthermore, Rab10 was confirmed to be a direct target gene of miR-378a-3p, and was negatively affected by miR-378a-3p. The silencing of Rab10 revealed antitumor effects in ESCC cell lines, and the expression of miR-378a-3p was negatively correlated with that of Rab10 in ESCC. Collectively, miR-378a-3p may act as a tumor-suppressor in ESCC cells through negatively regulating Rab10.

Functional miRNAs in breast cancer drug resistance

Owing to improved early surveillance and advanced therapy strategies, the current death rate due to breast cancer has decreased; nevertheless, drug resistance and relapse remain obstacles on the path to successful systematic treatment. Multiple mechanisms responsible for drug resistance have been elucidated, and miRNAs seem to play a major part in almost every aspect of cancer progression, including tumorigenesis, metastasis, and drug resistance. In recent years, exosomes have emerged as novel modes of intercellular signaling vehicles, initiating cell–cell communication through their fusion with target cell membranes, delivering functional molecules including miRNAs and proteins. This review particularly focuses on enumerating functional miRNAs involved in breast cancer drug resistance as well as their targets and related mechanisms. Subsequently, we discuss the prospects and challenges of miRNA function in drug resistance and highlight valuable approaches for the investigation of the role of exosomal miRNAs in breast cancer progression and drug resistance.

CTBP1 and metabolic syndrome induce an mRNA and miRNA expression profile critical for breast cancer progression and metastasis

Metastatic breast cancer (BrCa) is still one of the main causes of cancer death in women. Metabolic syndrome (MeS), a risk factor for BrCa, is associated to high grade tumors, increased metastasis and recurrence of this disease. C-terminal binding protein 1 (CTBP1) is a co-repressor of tumor suppressor genes that is activated by low NAD⁺/NADH ratio. Previously, we demonstrated that CTBP1 hyperactivation by MeS increased tumor growth in MDA-MB-231-derived xenografts regulating several genes and miRNAs. In this work, our aim was to elucidate the role of CTBP1 and MeS in BrCa metastasis. We found that CTBP1 protein diminished adhesion while increased migration of triple negative BrCa cells. CTBP1 and MeS modulated the expression of multiple genes (ITGB4, ITGB6, PRSS2, COL17A1 and FABP4) and miRNAs (miR-378a-3p, miR-146a-5p, let-7e-3p, miR-381-5p, miR-194-5p, miR-494-3p) involved in BrCa progression of MDA-MB-231-derived xenografts. Furthermore, we demonstrated that MeS increased lung micrometastasis and liver neoplastic disease in mice. CTBP1 hyperactivation seems to be critical for MeS effect on BrCa metastasis since CTBP1 depletion completely impaired the detection of circulating tumor cells. Our results highlight CTBP1 and MeS impact on BrCa progression positioning them as key properties to be considered for BrCa patient prognosis and management.

Bioinformatics-based identification of miR-542-5p as a predictive biomarker in breast cancer therapy

Background

Tamoxifen is the first-line hormone therapy for estrogen receptor alpha positive (ERα+) breast cancer. However, about 40% of patients with ERα + breast cancer who receive tamoxifen therapy eventually develop resistance resulting in a poor prognosis. The aim of this study was to mine available data sets in the Gene Expression Omnibus (GEO) database, including in vitro (cell lines) and in vivo (tissue samples), and to identify all miRNAs associated with tamoxifen resistance (TamR) in breast cancer. Secondly, this study aimed to predict the key gene regulatory networks of newly found TamR-related miRNAs and evaluate the potential role of the miRNAs and targets as potential prognosis biomarkers for breast cancer patients.

Result

Microarray data sets from two different studies were used from the GEO database: 1. GSE66607: miRNA of MCF-7 TamR cells; 2. GSE37405: TamR tissues. Differentially expressed microRNAs (miRNAs) were identified in both data sets and 5 differentially expressed miRNAs were found to overlap between the two data sets. Profiles of GSE37405 and data from the Kaplan-Meier Plotter Database (KMPD) along with Gene Expression Profiling Interactive Analysis (GEPIA) were used to reveal the relationship between these 5 miRNAs and overall survival. The results showed that has-miR-542-5p was the only miRNA associated with overall survival of ERα + breast cancer patients who received adjuvant tamoxifen. Targets of has-miR-542-5p were predicted by miRanda and TargetScan, and the mRNA expression of the three 3 target gene, Tyrosine 3-Monooxygenase/Tryptophan 5-Monooxygenase Activation Protein Beta (YWHAB), Lymphocyte Antigen 9 (LY9), and Secreted Frizzled Related Protein 1 (SFRP1) were associated with overall survival in 2 different databases. Copy-number alterations (CNAs) of SFRP1 confer survival disadvantage to breast cancer patients and alter the mRNA expression of SFRP1 in cBioPortal database.

Conclusion

This study indicates that miRNA has-miR-542-5p is associated with TamR and can predict prognosis of breast cancer patients. Furthermore, has-miR-542-5p may be acting through a mechanism involving the target genes YWHAB, LY9, and SFRP1. Overall, has-miR-542-5p is a predictive biomarker and potential target for therapy of breast cancer patients.

Electronic supplementary material

The online version of this article (10.1186/s41065-018-0055-7) contains supplementary material, which is available to authorized users.

miR‑378a enhances the sensitivity of liver cancer to sorafenib by targeting VEGFR, PDGFRβ and c‑Raf

Liver cancer is a globally prevalent cancer with poor prognosis. The present study investigated the link between microRNA-378a (miR‑378a) expression and the sensitivity of hepatocellular carcinoma (HCC) and hepatoblastoma (HB) cancers to sorafenib therapy. miR‑378a expression was determined in liver tissue samples from healthy candidates and patients with liver cancer using the reverse transcription‑quantitative polymerase chain reaction. The antitumor effects of miR‑378a alone and in combination with sorafenib were investigated in the HB cell line HepG2 and the HCC cell line SMMC‑7721 with methyl thiazoyl tetrazolium, colony formation, flow cytometry and Transwell migration assays. The underlying mechanisms were investigated using western blot analysis. miR‑378a expression was decreased in tissue samples from patients with liver cancer. HCC and HB cell line proliferation and invasion ability was inhibited by miR‑378a. The combination of miR‑378a and sorafenib provided the greatest inhibition. Western blot indicated that mitogen activated protein kinase signaling pathway proteins, vascular endothelial growth factor receptor, platelet derived growth factor receptor β, Raf‑1 proto‑oncogene, serine/threonine kinase and matrix metallopeptidase 2 were regulated by miR‑378a alone and to a greater extent when combined with sorafenib. Results suggest that miR‑378a can inhibit liver cancer cell growth and enhance the sensitivity of liver cancer cells to sorafenib‑based chemotherapies.

Collective Prediction of Disease-Associated miRNAs Based on Transduction Learning

The discovery of human disease-related miRNA is a challenging problem for complex disease biology research. For existing computational methods, it is difficult to achieve excellent performance with sparse known miRNA-disease association verified by biological experiment. Here, we develop CPTL, a Collective Prediction based on Transduction Learning, to systematically prioritize miRNAs related to disease. By combining disease similarity, miRNA similarity with known miRNA-disease association, we construct a miRNA-disease network for predicting miRNA-disease association. Then, CPTL calculates relevance score and updates the network structure iteratively, until a convergence criterion is reached. The relevance score of node including miRNA and disease is calculated by the use of transduction learning based on its neighbors. The network structure is updated using relevance score, which increases the weight of important links. To show the effectiveness of our method, we compared CPTL with existing methods based on HMDD datasets. Experimental results indicate that CPTL outperforms existing approaches in terms of AUC, precision, recall, and F1-score. Moreover, experiments performed with different number of iterations verify that CPTL has good convergence. Besides, it is analyzed that the varying of weighted parameters affect predicted results. Case study on breast cancer has further confirmed the identification ability of CPTL.

Metabolism-related microRNAs in maternal breast milk are influenced by premature delivery

BackgroundMaternal breast milk (MBM) is enriched in microRNAs, factors that regulate protein translation throughout the human body. MBM from mothers of term and preterm infants differs in nutrient, hormone, and bioactive-factor composition, but the microRNA differences between these groups have not been compared. We hypothesized that gestational age at delivery influences microRNA in MBM, particularly microRNAs involved in immunologic and metabolic regulation.MethodsMBM from mothers of premature infants (pMBM) obtained 3-4 weeks post delivery was compared with MBM from mothers of term infants obtained at birth (tColostrum) and 3-4 weeks post delivery (tMBM). The microRNA profile in lipid and skim fractions of each sample was evaluated with high-throughput sequencing.ResultsThe expression profiles of nine microRNAs in lipid and skim pMBM differed from those in tMBM. Gene targets of these microRNAs were functionally related to elemental metabolism and lipid biosynthesis. The microRNA profile of tColostrum was also distinct from that of pMBM, but it clustered closely with tMBM. Twenty-one microRNAs correlated with gestational age demonstrated limited relationships with method of delivery, but not other maternal-infant factors.ConclusionPremature delivery results in a unique MBM microRNA profile with metabolic targets. This suggests that preterm milk may have adaptive functions for growth in premature infants.

Lidocaine inhibits the proliferation of lung cancer by regulating the expression of GOLT1A

OBJECTIVES

Lidocaine is the most commonly used local anaesthetic in clinical and can inhibit proliferation, suppress invasion and migration and induce apoptosis in human lung adenocarcinoma (LAD) cells. However, its specific downstream molecular mechanism is unclear.

MATERIALS AND METHODS

LAD cell lines, A549 and H1299 cells, were treated with lidocaine. The proliferation was evaluated by the methylthiazolyldiphenyl-tetrazolium bromide (MTT) and bromodeoxyuridine (BrdU) assay. The expression level of related proteins was detected by real-time quantitative PCR (qPCR) and Western blot assay.

RESULTS

The results indicated that lidocaine dose-dependently suppressed the proliferation of A549 and H1299 cells. In the LAD patients' samples, GOLT1A was upregulated and involved in the poor prognosis and higher grade malignancy. Additionally, GOLT1A mediates the function of lidocaine on repressing proliferation by regulating the cell cycle in A549 cells.

CONCLUSIONS

Our findings suggest that lidocaine downregulates the GOLT1A expression to repress the proliferation of lung cancer cells.

Age and sex differences in microRNAs expression during the process of thymus aging

The gender-biased thymus involution and the importance of microRNAs (miRNAs, miRs) expression in modulating the thymus development have been reported in many studies. However, how males and females differ in so many ways in thymus involution remains unclear. To address this question, we investigated the miRNA expression profiles in both untreated 3- and 12-month-old female and male mice thymuses. The results showed that 7 and 18 miRNAs were defined as the sex- and age-specific miRNAs, respectively. The expression of miR-181c-5p, miR-20b-5p, miR-98b-5p, miR-329-3p, miR-341-5p, and miR-2137 showed significant age-difference in mice thymus by quantitative polymerase chain reaction. High expression levels of miR-2137 were detected in mice thymic epithelial cells and gradually increased during the process of thymus aging. MiR-27b-3p and miR-378a-3p of the female-biased miRNAs were confirmed as the sex- and estrogen-responsive miRNAs in mice thymus in vivo. Their potential target genes and the pathway were identified by the online software. Possible regulation roles of sex- and age-specific miRNA expression during the process of thymus aging were discussed. Our results suggested that these miRNAs may be potential biomarkers for the study of sex- and age-specific thymus aging and involution.

Integrated analysis profiles of long non-coding RNAs reveal potential biomarkers of drug resistance in lung cancer

Lung cancer is one of the leading causes of cancer-related death. Resistance to chemotherapy and molecularly targeted therapies is a major problem that can contribute substantially to high mortality. The roles of long non-coding RNAs (lncRNAs) in drug resistance of lung cancer are insufficiently understood. Here, we identified a distinct drug resistance-related transcriptional signature and constructed a functional lncRNA-mRNA co-expression network. We found that 34 lncRNAs and 103 mRNAs have differential expression in drug resistance of lung cancer, in which 10 lncRNAs were down regulated and 24 up regulated; 49 mRNAs were down regulated and 54 up regulated. LncRNAs-mRNAs expression network analysis revealed a role for lncRNAs in modulating cancer-related pathways. We also found that two pair lncRNAs and their subnetworks were highly related to drug resistance. NR_028502.1/NR_028505.1 were found differentially co-expressed with nine mRNAs, and highly correlated with better clinical outcome. NR_030725.1/NR_030726.1 co-expressed with eleven mRNAs, and were associated with poor survival in patients with lung cancer. Our work comprehensively identified expression signature of resistance-associated lncRNAs and their inter-regulated mRNAs in lung cancer.

Profile of the breast cancer susceptibility marker rs4245739 identifies a role for miRNAs

Objective:

To determine the influence of the single nucleotide polymorphism (SNP) rs4245739 on the binding and expression of microRNAs and subsequent MDM4 expression and the correlation of these factors with clinical determinants of ER-negative breast cancers.

Methods:

FindTar and miRanda were used to detect the manner in which potential microRNAs are affected by the SNP rs4245739-flanking sequence. RNA sequencing data for ER-negative breast cancer from The Cancer Genome Atlas (TCGA) were used to compare the expression of miR-184, miR-191, miR-193a, miR-378, and MDM4 in different rs4245739 genotypes.

Results:

Comparison of ER-negative cancer patients with and without the expression of miR-191 as well as profile microRNAs (miR-184, miR-191, miR-193a and miR-378 altogether) can differentiate the expression of MDM4 among different rs4245739 genotypes. Although simple genotyping alone did not reveal significant clinical relationships, the combination of genotyping and microRNA profiles was able to significantly differentiate individuals with larger tumor size and lower number of involved lymph nodes (P < 0.05) in the risk group (A allele).

Conclusions:

We present two novel methods to analyze SNPs within 3′UTRs that use: (i) a single miRNA marker expression and (ii) an expression profile of miRNAs predicted to bind to the SNP region. We demonstrate that the application of these two methods, in particular the miRNA profile approach, permits detection of new molecular and clinical features related to the rs4245739 variant in ER-negative breast cancer.

Downregulation of microRNA-27b-3p enhances tamoxifen resistance in breast cancer by increasing NR5A2 and CREB1 expression

Estrogen-dependent breast cancer is often treated with the aromatase inhibitors or estrogen receptor (ER) antagonists. Tamoxifen as a major ER antagonist is usually used to treat those patients with ERα-positive breast cancer. However, a majority of patients with ERα positive fail to respond to tamoxifen due to the presence of intrinsic or acquired resistance to the drug. Altered expression and functions of microRNAs (miRNAs) have been reportedly associated with tamoxifen resistance. In this study, we investigated the role of miR-27b-3p in resistance of breast cancer to tamoxifen. MiR-27b-3p levels were remarkably reduced in the tamoxifen-resistant breast cancer cells compared with their parental cells. In addition, miR-27b-3p was also significantly downregulated in breast tumor tissues relative to adjacent non-tumor tissues. Moreover, the expression levels of miR-27b-3p were lower in the breast cancer tissues from tamoxifen-resistant patients compared with that from untreated-tamoxifen patients. Notably, tamoxifen repressed miR-27b-3p expression, whereas estrogen induced miR-27b-3p expression in breast cancer cells. Besides, we provided experimental evidences that miR-27b-3p enhances the sensitivity of breast cancer cells to tamoxifen in vitro and in vivo models. More importantly, we validated that miR-27b-3p directly targeted and inhibited the expression of nuclear receptor subfamily 5 group A member 2 (NR5A2) and cAMP-response element binding protein 1 (CREB1) and therefore augmented tamoxifen-induced cytotoxicity in breast cancer. Lastly, miR-27b-3p levels were found to be significantly negatively correlated with both NR5A2 and CREB1 levels in breast cancer tissues. Our findings provided further evidence that miR-27b-3p might be considered as a novel and potential target for the diagnosis and treatment of tamoxifen-resistant breast cancer.