A Potential circRNA-miRNA-mRNA Regulatory Network in Asthmatic Airway Epithelial Cells Identified by Integrated Analysis of Microarray Datasets

Background: Asthma is one of the most prevalent chronic respiratory diseases worldwide. Bronchial epithelial cells play a critical role in the pathogenesis of asthma. Circular RNAs (circRNAs) act as microRNA (miRNA) sponges to regulate downstream gene expression. However, the role of epithelial circRNAs in asthma remains to be investigated. This study aims to explore the potential circRNA-miRNA-messenger RNA (mRNA) regulatory network in asthma by integrated analysis of publicly available microarray datasets.Methods: Five mRNA microarray datasets derived from bronchial brushing samples from asthma patients and control subjects were downloaded from the Gene Expression Omnibus (GEO) database. The robust rank aggregation (RRA) method was used to identify robust differentially expressed genes (DEGs) in bronchial epithelial cells between asthma patients and controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to annotate the functions of the DEGs. Protein-protein interaction (PPI) analysis was performed to identify hub genes. Three miRNA databases (Targetscan, miRDB, and miRWalk) were used to predict the miRNAs which potentially target the hub genes. A miRNA microarray dataset derived from bronchial brushings was used to validate the miRNA-mRNA relationships. Finally, a circRNA-miRNA-mRNA network was constructed via the ENCORI database.Results: A total of 127 robust DEGs in bronchial epithelial cells between steroid-naïve asthma patients (n = 272) and healthy controls (n = 165) were identified from five mRNA microarray datasets. Enrichment analyses showed that DEGs were mainly enriched in several biological processes related to asthma, including humoral immune response, salivary secretion, and IL-17 signaling pathway. Nineteen hub genes were identified and were used to construct a potential epithelial circRNA-miRNA-mRNA network. The top 10 competing endogenous RNAs were hsa_circ_0001585, hsa_circ_0078031, hsa_circ_0000552, hsa-miR-30a-3p, hsa-miR-30d-3p, KIT, CD69, ADRA2A, BPIFA1, and GGH.Conclusion: Our study reveals a potential role for epithelial circRNA-miRNA-mRNA network in the pathogenesis of asthma.

LINC01278 Sponges miR‐500b‐5p to Regulate the Expression of ACTG2 to Control Phenotypic Switching in Human Vascular Smooth Muscle Cells During Aortic Dissection

Background Phenotypic switching in vascular smooth muscle cells (VSMCs) is involved in the pathogenesis of aortic dissection (AD). This study aims to explore the potential mechanisms of linc01278 during VSMC phenotypic switching. Methods and Results Twelve samples (6 AD and 6 control) were used for lncRNA, microRNA, and mRNA microarray analysis. We integrated the mRNA microarray data set with GSE52093 to determine the differentially expressed genes. Bioinformatic analysis, including Gene Expression Omnibus 2R, Venn diagram analysis, gene ontology, pathway enrichment, and protein–protein interaction networks were used to identify the target lncRNA, microRNA, and mRNA involved in AD. Subsequently, we validated the bioinformatics data using techniques in molecular biology in human tissues and VSMCs. Linc01278, microRNA‐500b‐5p, and ACTG2 played an important role in the vascular smooth muscle contraction pathway. Linc01278 and ACTG2 were downregulated and miR‐500b‐5p was upregulated in AD tissues. Molecular markers of VSMC phenotypic switching, including SM22α, SMA, calponin, and MYH11, were downregulated in AD tissues. Plasmid‐based overexpression and RNA interference‐mediated downregulation of linc01278 weakened and enhanced VSMC proliferation and phenotypic switching, respectively. Dual‐luciferase reporter assays confirmed that linc01278 regulated miR‐500b‐5p that directly targeted ACTG2 in HEK293T cells. Conclusions These data demonstrate that linc01278 regulates ACTG2 to control the phenotypic switch in VSMCs by sponging miR‐500b‐5p. This linc01278‐miR‐500b‐5p‐ACTG2 axis has a potential role in developing diagnostic markers and therapeutic targets for AD.

On predicting highy the y expressed genes for Escherichia coli based on mRNA microarray data

Highly expressed genes [HEG] are genees available in the organism, which carry the preferred codons for the expression system. Identifying HEG helps to find preferred codons and use them in the gene optimization to express target protein. Currently, HEG-DB are the only database to store HEG data of many strains of microorganisms, but the data are still not updated and maintained. Therefore, our research is carried out to predict HEG in the E. coli K-12 MG1655 strain based on reference sets that are the mostly used ribosomal protein coding genes and genes with high transcription levels from microarray data proposed by the research. Next, the results of HEG from the two above reference sets, HEG-RP and HEG-mRNA, were compared. Finally, we analyzed and compared the HEG that the project predicted with HEG from HEG-DB database. The results from RP and 100-mRNA reference sets were completely identical and were better than data from HEG-DB in the number of HEGs, CAI values and the number of genes contributing to important metabolic pathways. The results showed that it was possible to use reference sets from mRNA microarray data instead of ribosomal protein reference sets in HEG prediction

Behavioral sensitization induced by methamphetamine causes differential alterations in gene expression and histone acetylation of the prefrontal cortex in rats

Background Methamphetamine (METH) is one of the most widely abused illicit substances worldwide; unfortunately, its addiction mechanism remains unclear. Based on accumulating evidence, changes in gene expression and chromatin modifications might be related to the persistent effects of METH on the brain. In the present study, we took advantage of METH-induced behavioral sensitization as an animal model that reflects some aspects of drug addiction and examined the changes in gene expression and histone acetylation in the prefrontal cortex (PFC) of adult rats. Methods We conducted mRNA microarray and chromatin immunoprecipitation (ChIP) coupled to DNA microarray (ChIP-chip) analyses to screen and identify changes in transcript levels and histone acetylation patterns. Functional enrichment analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, were performed to analyze the differentially expressed genes. We then further identified alterations in ANP32A (acidic leucine-rich nuclear phosphoprotein-32A) and POU3F2 (POU domain, class 3, transcription factor 2) using qPCR and ChIP-PCR assays. Results In the rat model of METH-induced behavioral sensitization, METH challenge caused 275 differentially expressed genes and a number of hyperacetylated genes (821 genes with H3 acetylation and 10 genes with H4 acetylation). Based on mRNA microarray and GO and KEGG enrichment analyses, 24 genes may be involved in METH-induced behavioral sensitization, and 7 genes were confirmed using qPCR. We further examined the alterations in the levels of the ANP32A and POU3F2 transcripts and histone acetylation at different periods of METH-induced behavioral sensitization. H4 hyperacetylation contributed to the increased levels of ANP32A mRNA and H3/H4 hyperacetylation contributed to the increased levels of POU3F2 mRNA induced by METH challenge-induced behavioral sensitization, but not by acute METH exposure. Conclusions The present results revealed alterations in transcription and histone acetylation in the rat PFC by METH exposure and provided evidence that modifications of histone acetylation contributed to the alterations in gene expression caused by METH-induced behavioral sensitization.

Behavioral Sensitization Induced by Methamphetamine Causes Differential Alterations in Gene Expression and Histone Acetylation of the Prefrontal Cortex in Rats

Background: Methamphetamine (METH) is one of the most widely abused illicit substances worldwide; unfortunately, its addiction mechanism remains unclear. Based on accumulating evidence, changes in gene expression and chromatin modifications might be related to the persistent effects of METH on the brain. In the present study, we took advantage of METH-induced behavioral sensitization as an animal model that reflects some aspects of drug addiction and examined the changes in gene expression and histone acetylation in the prefrontal cortex (PFC) of adult rats.Methods: We conducted mRNA microarray and chromatin immunoprecipitation (ChIP) coupled to DNA microarray (ChIP-chip) analyses to screen and identify changes in transcript levels and histone acetylation patterns. Functional enrichment analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, were performed to analyze the differentially expressed genes. We then further identified alterations in ANP32A (acidic leucine-rich nuclear phosphoprotein-32A) and POU3F2 (POU domain, class 3, transcription factor 2) using qPCR and ChIP-PCR assays.Results: In the rat model of METH-induced behavioral sensitization, METH challenge caused 275 differentially expressed genes and a number of hyperacetylated genes (821 genes with H3 acetylation and 10 genes with H4 acetylation). Based on mRNA microarray and GO and KEGG enrichment analyses, 24 genes may be involved in METH-induced behavioral sensitization, and 7 were confirmed using qPCR. We further examined the alterations in the levels of the ANP32A and POU3F2 transcripts and histone acetylation at different periods of METH-induced behavioral sensitization. H4 hyperacetylation contributed to the increased levels of ANP32A mRNA and H3/H4 hyperacetylation contributed to the increased levels of POU3F2 mRNA induced by METH challenge-induced behavioral sensitization, but not by acute METH exposure.Conclusions: The present results revealed alterations in transcription and histone acetylation in the rat PFC by METH exposure and provided evidence that modifications of histone acetylation contributed to the alterations in gene expression caused by METH-induced behavioral sensitization.

Transcriptomic Profiling of Buffalo Spermatozoa Reveals Dysregulation of Functionally Relevant mRNAs in Low-Fertile Bulls

Although, it is known that spermatozoa harbor a variety of RNAs that may influence embryonic development, little is understood about sperm transcriptomic differences in relation to fertility, especially in buffaloes. In the present study, we compared the differences in sperm functional attributes and transcriptomic profile between high- and low-fertile buffalo bulls. Sperm membrane and acrosomal integrity were lower (P < 0.05), while protamine deficiency and lipid peroxidation were higher (P < 0.05) in low- compared to high-fertile bulls. Transcriptomic analysis using mRNA microarray technology detected a total of 51,282 transcripts in buffalo spermatozoa, of which 4,050 transcripts were differentially expressed, and 709 transcripts were found to be significantly dysregulated (P < 0.05 and fold change >1) between high- and low-fertile bulls. Majority of the dysregulated transcripts were related to binding activity, transcription, translation, and metabolic processes with primary localization in the cell nucleus, nucleoplasm, and in cytosol. Pathways related to MAPK signaling, ribosome pathway, and oxidative phosphorylation were dysregulated in low-fertile bull spermatozoa. Using bioinformatics analysis, we observed that several genes related to sperm functional attributes were significantly downregulated in low-fertile bull spermatozoa. Validation of the results of microarray analysis was carried out using real-time qPCR expression analysis of selected genes (YBX1, ORAI3, and TFAP2C). The relative expression of these genes followed the same trend in both the techniques. Collectively, this is the first study to report the transcriptomic profile of buffalo spermatozoa and to demonstrate the dysregulation of functionally relevant transcripts in low-fertile bull spermatozoa. The results of the present study open up new avenues for understanding the etiology for poor fertility in buffalo bulls and to identify fertility biomarkers.

Minichromosome maintenance deficient 6 as a core biomarker for the identification of gynecological pan-carcinoma

Cervical, endometrial, and breast cancers are common diseases studied in the field of gynecology. We conducted a series of bioinformatics analyses on these different gynecological cancers. After downloading mRNA microarray data on these gynecological cancers from the TCGA database, we applied a differential analysis. We combined the differential genes obtained from each disease sample and obtained 2,353 public differential genes (P <0.01). Through a weighted gene co-expression network analysis, we obtained five functional disorder modules, and found the essential genes to be LHFP, DNAJC27, GIMAP4, MCM6, and AIM1L. The analysis results showed that dysfunctional genes are associated with ameoidal-type cell migration and DNA replication. We predicted the regulator using cpRNA and a pivot analysis of the transcription factors. Studies have shown that miR-21-5p and miR-300 regulate three modules, MSC regulates m3 and m5, and YBX1 regulates m4 and m5. All are involved in the regulation of m5, and the co-regulated core gene of m5 is MCM6. We believe that MCM6 has a central regulatory role in a disease network and that MCM6 can be considered as a core biomarker for gynecological pan-cancer.

Silencing MASTL Inhibits Cell Proliferation and Migration of Gastric Cancer MGC-803 Cells Via Suprressing AKT, mTOR, p38 Signal Pathways

Background: Microtubule-associated serine/threonine kinase (MASTL) functions to regulate chromosome condensation and mitotic progression. Emerging reports showed that aberrant MASTL expression is commonly implicated in various human cancers and act as an oncogene. This study aimed to discover the potential significance of MASTL in gastric cancer, and to uncover relevant mechanisms. Methods: Lentivirus MASTL-shRNA was constructed and infected into MGC-803 cells to analysis its influences on cell proliferation by Green fluorescent protein (GFP)-based cellomics and colony formation assay, cell invasion and migration by transwell assay, apoptosis and cell cycle by flow cytometry detection, respectively. Nude mice and fluorescence imaging were used to characterize the regulation of tumor growth in vivo. Affymetrix mRNA microarray assay combined KEGG enrichment analysis were used to screen relevant molecules related to MASTL silencing. Finally，several aberrantly expressed genes were validated by quantitative reverse transcription PCR(RT-qPCR)and western blot detection. Results: Silencing MASTL significantly inhibited cell proliferation, migration and invasion, arrested cell cycle at G1 stage. Silencing MASTL reduced tumor growth in nude mice, and fluorescence imaging indicated that the total radiant efficiency of mice in the Lv-shMAST group was markedly reduced compared with in mice in the Lv-shCtrl group in vivo. Affymetrix mRNA microarray assay revealed that 124 genes upregulated, 167 genes downregulated. RT-qPCR and western blotting validation showed that cyclin dependent kinase 6(CDK6), bone morphogenetic protein 2(BMP2), snail family transcriptional repressor 2(SNAI2), phosphorylation-mechanistic target of rapamycin kinase (p-mTOR), phosphorylation-AKT serine/threonine kinase (p-AKT) and phosphorylation-p38 kinase (p-p38) are downregulated, and cyclin dependent kinase inhibitor 1A (CDKN1A) is upregulated. Conclusions: Silencing MASTL could significantly inhibit cell growth, migration ability, induce apoptosis, arrest cell cycle at G1 stage, and the mechanisms of which were mediated via inactivation of mTOR, AKT, p38 signal pathways.