Identification of biomarkers and construction of a microRNA-mRNA regulatory network for ependymoma using integrated bioinformatics analysis

Identification of key genes unique to the luminal a and basal-like breast cancer subtypes via bioinformatic analysis

Background

Breast cancer subtypes are statistically associated with prognosis. The search for markers of breast tumor heterogeneity and the development of precision medicine for patients are the current focuses of the field.

Methods

We used a bioinformatic approach to identify key disease-causing genes unique to the luminal A and basal-like subtypes of breast cancer. First, we retrieved gene expression data for luminal A breast cancer, basal-like breast cancer, and normal breast tissue samples from The Cancer Genome Atlas database. The differentially expressed genes unique to the 2 breast cancer subtypes were identified and subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. We constructed protein–protein interaction networks of the differentially expressed genes. Finally, we analyzed the key modules of the networks, which we combined with survival data to identify the unique cancer genes associated with each breast cancer subtype.

Results

We identified 1114 differentially expressed genes in luminal A breast cancer and 1042 differentially expressed genes in basal-like breast cancer, of which the subtypes shared 500. We observed 614 and 542 differentially expressed genes unique to luminal A and basal-like breast cancer, respectively. Through enrichment analyses, protein–protein interaction network analysis, and module mining, we identified 8 key differentially expressed genes unique to each subtype. Analysis of the gene expression data in the context of the survival data revealed that high expression of NMUR1 and NCAM1 in luminal A breast cancer statistically correlated with poor prognosis, whereas the low expression levels of CDC7, KIF18A, STIL, and CKS2 in basal-like breast cancer statistically correlated with poor prognosis.

Conclusions

NMUR1 and NCAM1 are novel key disease-causing genes for luminal A breast cancer, and STIL is a novel key disease-causing gene for basal-like breast cancer. These genes are potential targets for clinical treatment.

Talk about micromanaging! Role of microRNAs in intestinal barrier function

Defective intestinal tight-junction (TJ) barrier has been implicated in the pathogenesis of inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), and other inflammatory conditions of the gut. The role of microRNAs (miRNA's or miR's) has also been demonstrated in the last two decades in the pathogenesis of IBD and in the regulation of intestinal TJ barrier function. MiRNAs are noncoding regulators of gene expression at the posttranscription level that have an essential role in targeting transcripts encoding proteins of intestinal TJs and their regulators. Many miRNAs have been reported to regulate or deregulate the TJ proteins responsible for the intestinal barrier integrity and intestinal permeability. Many of those miRNAs have been reported to have essential roles in the pathogenesis of IBD. In this mini-review, we summarize the results of studies in the last three years that implicate miRNAs in the defective TJ barrier in relation to IBD. The therapeutic potential of using specific miRNAs to target the intestinal TJ barrier might be of great insight for IBD therapy.

MicroRNA‑449a regulates the progression of brain aging by targeting SCN2B in SAMP8 mice

Our previous study demonstrated that the expression of sodium channel voltage-gated beta 2 (SCN2B) increased with aging in senescence-accelerated mouse prone 8 (SAMP8) mice, and was identified to be associated with a decline in learning and memory, while the underlying mechanism is unclear. In the present study, multiple differentially expressed miRNAs, which may be involved in the process of aging by regulating target genes, were identified in the prefrontal cortex and hippocampus of SAMP8 mice though miRNA microarray analysis. Using bioinformatics prediction, SCN2B was identified to be one of the potential target genes of miR-449a, which was downregulated in the hippocampus. Previous studies demonstrated that miR-449a is involved in the occurrence and progression of aging by regulating a variety of target genes. Therefore, it was hypothesized that miR-449a may be involved in the process of brain aging by targeting SCN2B. To verify this hypothesis, the following experiments were conducted: A reverse transcription-quantitative polymerase chain reaction assay revealed that the expression level of miR-449a was significantly decreased in the prefrontal cortex and hippocampus of 12-month old SAMP8 mice; a dual-luciferase reporter assay verified that miR-449a regulated SCN2B expression by binding to the 3′-UTR 'seed region'; an anti-Ago co-immunoprecipitation combined with Affymetrix micro-array analyses demonstrated that the target mRNA highly enriched with Ago-miRNPs was confirmed to be SCN2B. Finally, overexpression of miR-449a or inhibition of SCN2B promoted the extension of hippocampal neurons in vitro. The results of the present study suggested that miR-449a was downregulated in the prefrontal cortex and hippocampus of SAMP8 mice and may regulate the process of brain aging by targeting SCN2B.