Methods for Studying MicroRNA Expression and Their Targets in Formalin-Fixed, Paraffin-Embedded (FFPE) Breast Cancer Tissues

Upregulation of miR-421 predicts poor prognosis and promotes proliferation, migration, and invasion of papillary thyroid cancer cells

BACKGROUND

Papillary thyroid carcinoma (PTC) represents the most frequent subtype of thyroid cancer (TC) with poor prognosis mainly due to the severe invasion and metastasis. As an oncogene, microRNA-421 (miR-421) is involved in the development of various cancers. This study was to investigate the clinical significance of miR-421 in PTC and its effects on the biological function of PTC cells.

METHODS

The expression level of miR-421 in all tissues and PTC cell lines was measured by quantitative real-time polymerase chain reaction (qRT-PCR). Subsequently, the relationship between miR-421 expression and the clinicopathological feature was detected by chi-square analysis in 106 patients with PTC. In addition, Kaplan-Meier and multivariate Cox regression analysis were used to detect the survival time and the prognostic value of miR-421. Finally, the regulatory effect of miR-421 on the proliferation, migration, and invasion ability of PTC cells was detected by Cell Counting Kit (CCK-8) and Transwell assay.

RESULTS

Compared with all control groups, the expression of miR-421 was significantly increased in 106 patients tissues and PTC cell lines (p < 0.001). In addition, patients with miR-421 upregulated in PTC showed more positive lymph node metastasis (p = 0.011), positive tumor infiltration (p = 0.031), and TNM stage III/IV (p = 0.019), and when miR-421 expression level was elevated, the survival rate of PTC patients was poor (log-rank test, p = 0.023). Furthermore, miR-421 might be an independent prognostic biomarker for PTC (hazard ratio [HR] = 3.172, 95% CI = 1.071-9.393, p = 0.037). Finally, increased levels of miR-421 can significantly promote cell proliferation, migration, and invasion (p < 0.01).

CONCLUSION

miR-421 is a novel oncogene of PTC and is a valuable prognostic biomarker. Moreover, the upregulation of miR-421 enhances the proliferation, migration, and invasion of PTC cells.

Quantifying the prognostic significance of microRNA-17/17-5P in cancers: a meta-analysis based on published studies

Objective

The aim of this study was to investigate the prognostic value of mircoRNA-17 and mircoRNA-17-5P (miR-17/17-5P) in patients with cancer.

Materials and methods

We conducted a comprehensive search on published literature following the guidelines of the meta-analysis of observational studies in epidemiology group for design, implementation, and reporting. The methodological qualities for included studies were assessed using the quality in prognosis studies. The pooled hazard ratios (HRs) with 95% CIs for overall survival (OS) and progression-free survival/recurrence-free survival/disease-free survival (PFS/RFS/DFS) were calculated to appraise the associations between miR-17/17-5P expression and cancer prognosis.

Results

A total of 21 studies involving 2099 subjects were analyzed in evidence synthesis. The results showed that high expression of miR-17 was associated with poor OS (HR=2.14; 95% CI: 1.69-2.71, P<0.001) in patients with cancer, especially in Caucasian (HR=2.23; 95% CI: 1.58-3.14, P<0.001) and digestive tract cancer (HR=1.29, 95% CI: 1.03-1.63, P=0.03), and miR-17 expression was significantly correlated with PFS/RFS in cancer patients (HR=1.69, 95% CI: 1.29-2.22, P<0.001). miR-17-5P overexpression was significantly linked with poor OS in cancer patients (HR=1.66; 95% CI: 1.31-2.09, P=0.00), especially in Asian (HR=1.81; 95% CI: 1.37-2.40, P<0.001), digestive tract cancer (HR=1.80; 95% CI: 1.29-2.50, P<0.001), and serum sample (HR=1.76; 95% CI: 1.29-2.41, P<0.001). miR-17-5P expression was significantly associated with DFS in cancer patients (HR=1.58, 95% CI: 1.07-2.35, P=0.02).

Conclusion

High expression of miR-17 and miR-17-5P are significantly associated with poor survival in patients with cancer. This indicated that miR-17/17-5P may be a novel prognostic indicator in cancer.

Comprehensive Assessment of the Relationship Between MicroRNA-124 and the Prognostic Significance of Cancer

BACKGROUND

Numerous studies have demonstrated the presence of microRNA-124 abnormalities involving gene expression, methylation, and single nucleotide polymorphism (SNP) in multiple and diverse cancers, but the prognostic value of these abnormalities in cancer remains inconclusive.

OBJECTIVE

The aim of this study is to determine the prognostic value of miR-124 in cancer.

METHODS

We scrutinized the electronic databases and estimate the association between miR-124 expression, methylation and single nucleotide polymorphisms (SNPs), and prognosis in cancers. The pooled hazard ratios with 95% confidence intervals (CIs) for overall survival (OS), and disease-free survival/recurrence-free survival (RFS)/progression-free survival (PFS) were calculated to estimate the effects of miR-124 expression, methylation, and SNPs on cancer prognosis. The Quality in Prognosis Studies and Newcastle-Ottawa Scale were utilized to assess the quality of included studies.

RESULTS

A total of 20 studies involving 3,574 participants were analyzed in evidence synthesis. Our findings showed that the low expression of miR-124 was significantly associated with poor OS (HR = 2.37, 95% CI: 1.91-2.94, P = 0.00; HR = 3.10, 95% CI: 2.04-4.70, P = 0.00) and PFS/RFS (HR = 2.21, 95% CI: 1.50-3.26, P = 0.00; HR = 2.12, 95% CI: 1.20-3.74, P = 0.00). The hyper-methylation of miR-124 was associated with poor OS (HR = 2.09, 95% CI: 1.48-2.95, P = 0.00) and PFS (HR = 3.70, 95% CI: 1.72-7.97, P = 0.00) (Table 3). The patients carrying with Allele C of miR-124 rs5315649 had a worse OS (HR = 1.50, 95% CI: 1.09-2.07, P = 0.00) and PFS (HR = 1.67, 95% CI: 1.20-2.33, P = 0.00) than the carriers with Allele G.

CONCLUSION

The low expression and hyper-methylation of miR-124 was strongly associated with poor prognosis, and genetic variations of miR-124 rs531564 affected prognosis in cancer patients.

MicroRNA signatures in cardiac biopsies and detection of allograft rejection

BACKGROUND

Identification of heart transplant (HTx) rejection currently relies on immunohistology and immunohistochemistry. We aimed to identify specific sets of microRNAs (miRNAs) to characterize acute cellular rejection (ACR), antibody-mediated rejection (pAMR), and mixed rejection (MR) in monitoring formalin-fixed paraffin-embedded (FFPE) endomyocardial biopsies (EMBs) in HTx patients.

METHODS

In this study we selected 33 adult HTx patients. For each, we chose the first positive EMB for study of each type of rejection. The next-generation sequencing (NGS) IonProton technique and reverse transcript quantitative polymerase chain reaction (RT-qPCR) analysis were performed on FFPE EMBs. Using logistic regression analysis we created unique miRNA signatures as predictive models of each rejection. In situ PCR was carried out on the same EMBs.

RESULTS

We obtained >2,257 mature miRNAs from all the EMBs. The 3 types of rejection showed a different miRNA profile for each group. The logistic regression model formed by miRNAs 208a, 126-5p, and 135a-5p identified MR; that formed by miRNAs 27b-3p, 29b-3p, and 199a-3p identified ACR; and that formed by miRNAs 208a, 29b-3p, 135a-5p, and 144-3p identified pAMR. The expression of miRNAs on tissue, through in situ PCR, showed different expressions of the same miRNA in different rejections. miRNA 126-5p was expressed in endothelial cells in ACR but in cardiomyocytes in pAMR. In ACR, miRNA 29b-3p was significantly overexpressed and detected in fibroblasts, whereas in pAMR it was underexpressed and detected only in cardiomyocytes.

CONCLUSIONS

miRNA profiling on FFPE EMBs differentiates the 3 types of rejection. Localization of expression of miRNAs on tissue showed different expression of the same miRNA for different cells, suggesting different roles of the same miRNA in different rejections.

miR-17 as a diagnostic biomarker regulates cell proliferation in breast cancer

Background

MicroRNAs (miRNAs) have been shown to be involved in the initiation and progression of cancers in the literature. In this study, we aimed to evaluate the clinicopathological role of miR-17 in breast cancer.

Materials and methods

The expression of miR-17 was measured in 132 breast cancer tissues and paired adjacent normal tissues by using real-time quantitative polymerase chain reaction. The association between miR-17 expression levels and clinicopathological parameters was also analyzed. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and flow cytometry assays were used to investigate the role of miR-17 in the regulation of breast cancer cells.

Results

The expression of miR-17 was remarkably increased in breast cancer tissues and cell lines. Clinical association analysis revealed that a high expression of miR-17 was prominently associated with poor survival time in breast cancer. Overexpression of miR-17 promoted cell proliferation and induced tumor growth.

Conclusion

Our findings clarified that the upregulation of miR-17 played a vital role in breast cancer progression and suggested that miR-17 could be used as a prognostic biomarker for breast cancer.

MicroRNA-186 suppresses cell proliferation and metastasis through targeting MAP3K2 in non-small cell lung cancer

MicroRNAs are a class of small endogenous non-coding RNAs that play crucial roles in the initiation and progression of human cancers. miR-186 was found decreased in various human malignancies and function as a tumor suppressor. However, the regulating mechanism of miR-186 in growth and metastasis of human non-small cell lung cancer (NSCLC) is still poorly understood. We investigated the role of miR-186 in the growth and metastasis of human NSCLC. In the present study, we found that miR-186 was significantly decreased in lung cancer tissues and cells. Furthermore, overexpression of miR-186 suppressed lung cancer cell proliferation, migration and invasion, and induced cell apoptosis. Moreover, we found that confirmed mitogen-activated protein kinase kinase kinase 2 (MAP3K2) protein was increased in lung cancer tissues and confirmed that MAP3K2 is a target gene of miR-186. In addition, knockdown of MAP3K2 by RNA interference inhibited lung cancer cell proliferation, migration and invasion, and promoted cell apoptosis in vitro. Furthermore, we observed tthat the overexpression of MAP3K2 partially reversed the inhibitory effect of miR-186 on the proliferation and metastasis of A549 and HCC827 cell lines. Taken together, our data indicated that miR-186 regulates lung cancer growth and metastasis through suppressing MAP3K2 expression, at least partly. Therefore, miR-186-MAP3K2 may represent a new and useful potential clinical treatment and diagnosis target for NSCLC.

Ewing's Sarcoma: An Analysis of miRNA Expression Profiles and Target Genes in Paraffin-Embedded Primary Tumor Tissue

The molecular mechanism responsible for Ewing’s Sarcoma (ES) remains largely unknown. MicroRNAs (miRNAs), a class of small non-coding RNAs able to regulate gene expression, are deregulated in tumors and may serve as a tool for diagnosis and prediction. However, the status of miRNAs in ES has not yet been thoroughly investigated. This study compared global miRNAs expression in paraffin-embedded tumor tissue samples from 20 ES patients, affected by primary untreated tumors, with miRNAs expressed in normal human mesenchymal stromal cells (MSCs) by microarray analysis. A miRTarBase database was used to identify the predicted target genes for differentially expressed miRNAs. The miRNAs microarray analysis revealed distinct patterns of miRNAs expression between ES samples and normal MSCs. 58 of the 954 analyzed miRNAs were significantly differentially expressed in ES samples compared to MSCs. Moreover, the qRT-PCR analysis carried out on three selected miRNAs showed that miR-181b, miR-1915 and miR-1275 were significantly aberrantly regulated, confirming the microarray results. Bio-database analysis identified BCL-2 as a bona fide target gene of the miR-21, miR-181a, miR-181b, miR-29a, miR-29b, miR-497, miR-195, miR-let-7a, miR-34a and miR-1915. Using paraffin-embedded tissues from ES patients, this study has identified several potential target miRNAs and one gene that might be considered a novel critical biomarker for ES pathogenesis.