Three meta-analyses define a set of commonly overexpressed genes from microarray datasets on astrocytomas

Microarray meta-analysis reveals comprehensive effects of 3,4,5-tricaffeolyquinic acid in cell differentiation and signaling

Caffeoylquinic acids (CQA) are polyphenolic compounds found in fruits, vegetables, coffee, and spices that have exhibited several beneficial activities, including antioxidant, antibacterial, neuroprotective, anti-inflammatory, anticancer, antiviral, antidiabetic, and cardiovascular effects. A derivative, TCQA (3,4,5-Tri-O-caffeoylquinic acid), has also shown both neurogenic and pigment differentiation potential. A transcriptomic-based meta-analysis was conducted to explore potential biochemical processes and molecular targets of TCQA. This approach involved integrating data from various cell and tissue types, including human amniotic stem cells, human neural stem cells, human dermal papilla cells, and the brain cortex of aging model mice. It offered a comprehensive perspective on the significant gene regulations in response to TCQA treatment. The objective was to uncover the mechanism and novel targets of TCQA, facilitating a further understanding of its functions. New areas of interest found were TCQA's effect on adipogenesis, heart, and muscle tissue development. In addition, significantly enhanced biological activities found through meta-analysis included cell cycle, VEGFA-VEGFR2 pathway, and BMP signaling. Overall, a comprehensive functional and visual analysis using available biological databases uncovered the multi-target potential of this natural compound.

Integrated microarray analysis of key genes and a miRNA‑mRNA regulatory network of early‑onset preeclampsia

Early‑onset preeclampsia (EOPE) is a serious threat to maternal and foetal health. The present study aimed to identify potential biomarkers and targets for the treatment of EOPE. Expression profiles of placenta from patients with EOPE and healthy controls (GSE103542, GSE74341 and GSE44711) were downloaded from the Gene Expression Omnibus database. Integrated analysis revealed 246 genes and 28 microRNAs (miRNAs) that were differentially expressed between patients with EOPE and healthy controls. Differentially expressed genes (DEGs) were primarily enriched in 'biological processes', such as 'cell adhesion', 'female pregnancy', 'extracellular matrix organization' and 'response to hypoxia'. Significant pathways associated with DEGs primarily included 'focal adhesion', 'ECM‑receptor interaction', 'PI3K‑Akt signaling' and 'ovarian steroidogenesis'. A Protein‑Protein Interaction network of DEGs was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins online database, and epidermal growth factor receptor, collagen α‑1(I) chain, secreted phosphoprotein 1, leptin (LEP), collagen α‑2(I) chain (COL1A2), plasminogen activator inhibitor 1 (SERPINE1), Thy‑1 membrane glycoprotein, bone morphogenetic protein 4, vascular cell adhesion protein 1 and matrix metallopeptidase 1 were identified as hub genes. The alterations of hsa‑miR‑937, hsa‑miR‑148b*, hsa‑miR‑3907, hsa‑miR‑367*, COL1A2, LEP and SERPINE1 in placenta were validated using our local samples. Our research showed that the expression of hsa‑miR‑937, hsa‑miR‑1486*, hsa‑miR‑3907, hsa‑miR‑367* and hub genes in the placenta were closely associated with the pathophysiology of EOPE. hsa‑miR‑937, hsa‑miR‑1486*, hsa‑miR‑3907, hsa‑miR‑367* and hub genes could serve as biomarkers for diagnosis and as potential targets for the treatment of EOPE.

Expression Profile of MiR-128 in the Astrocytoma Patients and Cell Lines

Malignant astrocytomas are the most common primary brain tumors. The critical characterizes of astrocyomas are their aggressive and infiltrative in the brain, which leads to uncontrollable by conventional forms of therapy. MicroRNAs are small RNAs that had been found to regulate their targets by specific binding to the 3'-untranslated region (3'UTR) of mRNA. Recent advances in understanding the molecular biology of these tumors have revealed that microRNA (miRNA) disruption may play important roles in the pathogenesis of astrocytomas. And some of the miRNA alterations were found in the serum of astrocytoma patients. In this study, we studied the expression profile of miR-128, in the different stages of astrocytoma tissues and two human astrocytoma cell lines, A172 and T98G cells. We found that the levels of miR-128 are decreased in the A172 and T98G cells when compared to normal human astrocyte (NHA). Furthermore, the levels of miR-128 decreased gradually to the pathological stages of astrocytomas. We also identified that TROVE2 is a novel target of miR-128 by the luciferase reporter system. Furthermore, the expression levels of TROVE2 are dramatically increased with the pathological stages increasing. Finally, the levels of TROVE2 are negatively correlated with miR-128 in astrocytoma tissues. Our data provided novel evidence for the miR-128 and TROVE2 in the development of human astrocytomas.

Identification of differentially expressed genes regulated by transcription factors in glioblastomas by bioinformatics analysis

The present study aimed to identify differentially expressed genes (DEGs) regulated by transcription factors (TFs) in glioblastoma, by conducting a bioinformatics analysis. The results of the present study may provide potential therapeutic targets that are involved in the development of glioblastoma. The GSE4290 raw data set was downloaded from the Gene Expression Omnibus database, and consisted of 23 non‑tumor samples and 77 glioblastoma (grade 4) tumor samples. Robust Multichip Averaging was used to identify DEGs between the glioblastoma and non‑tumor samples. Functional enrichment analysis of the DEGs was also performed. Based on the TRANSFAC® database, TFs associated with the glioblastoma gene expression profile were used to construct a regulatory network. Furthermore, trimmed subnets were identified according to calculated Z‑scores. A total of 676 DEGs were identified, of which 190 were upregulated and 496 were downregulated. Gene Ontology analysis demonstrated that the majority of these DEGs were functionally enriched in synaptic transmission, regulation of vesicle‑mediated transport and ion‑gated channel activity. In addition, the enriched Kyoto Encyclopedia of Genes and Genomes pathway included neuroactive ligand‑receptor interaction, calcium signaling pathway, p53 signaling pathway and cell cycle. Based on the TRANSFAC® database, transcriptional regulatory networks with 2,246 nodes and 4,515 regulatory pairs were constructed. According to the Z‑scores, the following candidate TFs were identified: TP53, SP1, JUN, STAT3 and SPI1; alongside their downstream DEGs. TP53 was the only differentially expressed TF. These candidate TFs and their downstream DEGs may have important roles in the progression of glioblastoma, and could be potential biomarkers for clinical treatment.

Global gene expression analysis of canine cutaneous mast cell tumor: could molecular profiling be useful for subtype classification and prognostication?

Prognosis and therapeutic management of dogs with cutaneous mast cell tumors (MCTs) depend on clinical stage and histological grade. However, the prognostic value of this latter is still questionable. In the present study, MCT transcriptome was analyzed to identify a set of candidate genes potentially useful for predicting the biological behavior of MCTs. Fifty-one canine MCT biopsies were analyzed. Isolated and purified total RNAs were individually hybridized to the Agilent Canine V2 4x44k DNA microarray. The comparison of reference differentiated and undifferentiated MCT transcriptome revealed a total of 597 differentially expressed genes (147 down-regulated and 450 up-regulated). The functional analysis of this set of genes provided evidence that they were mainly involved in cell cycle, DNA replication, p53 signaling pathway, nucleotide excision repair and pyrimidine metabolism. Class prediction analysis identified 13 transcripts providing the greatest accuracy of class prediction and divided samples into two categories (differentiated and undifferentiated), harboring a different prognosis. The Principal Component Analysis of all samples, made by using the selected 13 markers, confirmed MCT classification. The first three components accounted for 99.924% of the total variance. This molecular classification significantly correlated with survival time (p = 0.0026). Furthermore, among all marker genes, a significant association was found between mRNA expression and MCT-related mortality for FOXM1, GSN, FEN1 and KPNA2 (p<0.05). Finally, marker genes mRNA expression was evaluated in a cohort of 22 independent samples. Data obtained enabled to identify MCT cases with different prognosis. Overall, the molecular characterization of canine MCT transcriptome allowed the identification of a set of 13 transcripts that clearly separated differentiated from undifferentiated MCTs, thus predicting outcome regardless of the histological grade. These results may have clinical relevance and warrant future validation in a prospective study.