Reconstruction of temporal activity of microRNAs from gene expression data in breast cancer cell line

Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions

BACKGROUND

Biological data suffers from noise that is inherent in the measurements. This is particularly true for time-series gene expression measurements. Nevertheless, in order to to explore cellular dynamics, scientists employ such noisy measurements in predictive and clustering tools. However, noisy data can not only obscure the genes temporal patterns, but applying predictive and clustering tools on noisy data may yield inconsistent, and potentially incorrect, results.

RESULTS

To reduce the noise of short-term (< 48 h) time-series expression data, we relied on the three basic temporal patterns of gene expression: waves, impulses and sustained responses. We constrained the estimation of the true signals to these patterns by estimating the parameters of first and second-order Fourier functions and using the nonlinear least-squares trust-region optimization technique. Our approach lowered the noise in at least 85% of synthetic time-series expression data, significantly more than the spline method ([Formula: see text]). When the data contained a higher signal-to-noise ratio, our method allowed downstream network component analyses to calculate consistent and accurate predictions, particularly when the noise variance was high. Conversely, these tools led to erroneous results from untreated noisy data. Our results suggest that at least 5-7 time points are required to efficiently de-noise logarithmic scaled time-series expression data. Investing in sampling additional time points provides little benefit to clustering and prediction accuracy.

CONCLUSIONS

Our constrained Fourier de-noising method helps to cluster noisy gene expression and interpret dynamic gene networks more accurately. The benefit of noise reduction is large and can constitute the difference between a successful application and a failing one.

MicroRNA-615-5p regulates the proliferation and apoptosis of breast cancer cells by targeting HSF1

Breast cancer, which commonly occurs in the epithelium of the mammary gland, is a malignant tumor. MicroRNAs are involved in various cancer-associated processes, and microRNA-615-5p has been identified to be decreased in the pathological tissues from patients with breast cancer. In the present study, the possible mechanism of microRNA-615-5p in the progression of breast cancer was investigated in order to identify potential novel targets for clinical treatment. Heat shock factor 1 (HSF1) was identified as a predictive target gene of microRNA-615-5p using TargetScan analysis. The expression levels of microRNA-615-5p and its target gene, HSF1, were measured in breast cancer tissues and normal adjacent tissues. Additionally, the effects of microRNA-615-5p on MCF-7 breast cancer cell growth and apoptosis were examined. Furthermore, the interaction between HSF1 and microRNA-615-5p was investigated by a dual luciferase gene reporter assay. The expression levels of HSF1 were measured following transfection with microRNA-615-5p or pcDNA3.1-HSF1. Finally, the expression levels of proliferation- and apoptosis-associated factors such as B-cell lymphoma 2 (Bcl-2), cyclin D1, proliferating cell nuclear antigen (PCNA) and bcl-2-like protein 4 (Bax) were determined. The results demonstrated that lower microRNA-615-5p expression and higher HSF1 mRNA expression were present in tumor tissues compared with adjacent tissues (P<0.01). HSF1 was verified as a direct target of microRNA-615-5p using the dual luciferase gene reporter assay. In comparison with untransfected control and mimic-transfected negative control (NC) cells, MCF-7 cells transfected with microRNA-615-5p mimics exhibited reduced cell proliferation and increased apoptosis (P<0.01). However, the overexpression of HSF1 using a vector reversed the suppression of HSF1 induced by microRNA-615-5p mimics (P<0.01). The mRNA and protein expression levels of Bax were significantly increased, whereas those of Bcl-2, cyclin D1 and PCNA were decreased in the cells transfected with microRNA-615-5p mimics compared with the control and NC cells (P<0.01). Collectively, the present study indicated that microRNA-615-5p may mediate the progression of breast cancer by targeting HSF1.

Identification of molecular targets for esophageal carcinoma diagnosis using miRNA-seq and RNA-seq data from The Cancer Genome Atlas: a study of 187 cases

Esophageal carcinoma (ESCA) is one of the most common malignancies worldwide, and its pathogenesis is complex. In this study, we identified differentially expressed miRNAs (DEMs) and genes (DEGs) of ESCA from The Cancer Genome Atlas (TCGA) database. The diagnostic values of DEMs were determined by receiver operating characteristic (ROC) analyses and validated based on data from Gene Expression Omnibus (GEO). The top five DEMs with the best diagnostic values were selected, and their potential targets were predicted by various in silico methods. These target genes were then identified among the DEGs from TCGA. Furthermore, the overlapping genes were subjected to protein-protein interaction (PPI) analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The miRNA-transcription factor (TF) regulatory relations were determined using CircuitsDB and TransmiR. Finally, the regulatory networks of miRNA-TF and miRNA-gene were constructed and analyzed. A total of 136 DEMs and 3541 DEGs were identified in ESCA. The top five DEMs with the highest area under the receiver operating characteristic curve (AUC) values were miRNA-93 (0.953), miRNA-21 (0.928), miRNA-4746 (0.915), miRNA-196a-1 (0.906) and miRNA-196a-2 (0.906). The combined AUC of these five DEMs was 0.985. The KEGG analysis with 349 overlapping genes showed that the calcium signaling pathway and the neuroactive ligand-receptor interaction were the most relevant pathways. The regulatory networks of miRNA-TF and miRNA-gene, including 38 miRNA-TF and 560 miRNA-gene pairs, were successfully established. Our findings may provide new insights into the molecular mechanisms of ESCA pathogenesis. Future research will aim to explore the role of novel miRNAs in the pathogenesis and improve the early diagnosis of ESCA.

Omega-3 Polyunsaturated Fatty Acids Time-Dependently Reduce Cell Viability and Oncogenic MicroRNA-21 Expression in Estrogen Receptor-Positive Breast Cancer Cells (MCF-7)

The omega-3 polyunsaturated fatty acid (n-3 PUFA), α-linolenic acid (ALA), and its metabolites, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), independently reduce the growth of breast cancer cells in vitro, but the mechanisms, which may involve microRNA (miRNA), are still unclear. The expression of the oncomiR, miR-21, is reduced by DHA treatment, but the effects of ALA on miR-21, alone or combined with EPA and DHA under physiologically relevant concentrations, have not been investigated. The effects of ALA alone and +/-EPA and DHA at the blood molar ratios seen in either humans (1.0:1.0:2.5, ALA:EPA:DHA) or mice (1.0:0.4:3.1, ALA:EPA:DHA) post flaxseed oil consumption (containing ALA) were assessed in vitro in MCF-7 breast cancer cells. Cell viability and the expression of miR-21 and its molecular target, phosphatase and tension homolog (PTEN, gene and protein), at different time points, were examined. At 1, 3, 48 and 96 h ALA alone and 24 h animal ratio treatments significantly reduced MCF-7 cell viability, while 1 and 3 h ALA alone and human and animal ratio treatments all significantly reduced miR-21 expression, and 24 h animal ratio treatment reduced miR-21 expression; these effects were not associated with changes in PTEN gene or protein expressions. We showed for the first time that ALA alone or combined with EPA and DHA at levels seen in human and animal blood post-ALA consumption can significantly reduce cell viability and modulate miR-21 expression in a time- and concentration-dependent manner, with the animal ratio containing higher DHA having a greater effect. The time dependency of miR-21 effects suggests the significance of considering time as a variable in miRNA studies, particularly of miR-21.