Comprehensive Analysis of Hub Genes Associated With Competing Endogenous RNA Networks in Stroke Using Bioinformatics Analysis

Background: Acute ischemic stroke (AIS) is the second leading cause of death and the third leading cause of disability worldwide. Long noncoding RNAs (lncRNAs) are promising biomarkers for the early diagnosis of AIS and closely participate in the mechanism of stroke onset. However, studies focusing on lncRNAs functioning as microRNA (miRNA) sponges to regulate the mRNA expression are rare and superficial.Methods: In this study, we systematically analyzed the expression profiles of lncRNA, mRNA (GSE58294), and miRNA (GSE110993) from the GEO database. Gene ontology (GO) analysis was performed to reveal the functions of differentially expressed genes (DEGs), and we used weighted gene co-expression network analysis (WGCNA) to investigate the relationships between clinical features and expression profiles and the co-expression of miRNA and lncRNA. Finally, we constructed a lncRNA–miRNA–mRNA competing endogenous RNA (ceRNA) network with selected DEGs using bioinformatics methods and obtained ROC curves to assess the diagnostic efficacy of differentially expressed lncRNAs (DElncRNAs) and differentially expressed mRNAs (DEmRNAs) in our network. The GSE22255 dataset was used to confirm the diagnostic value of candidate genes.Results: In total, 199 DElncRNAs, 2068 DEmRNAs, and 96 differentially expressed miRNAs were detected. The GO analysis revealed that DEmRNAs primarily participate in neutrophil activation, neutrophil degranulation, vacuolar transport, and lysosomal transport. WGCNA screened out 16 lncRNAs and 195 mRNAs from DEGs, and only eight DElncRNAs maintained an area under the curve higher than 0.9. By investigating the relationships between lncRNAs and mRNAs, a ceRNA network containing three lncRNAs, three miRNAs, and seven mRNAs was constructed. GSE22255 confirmed that RP1-193H18.2 is more advantageous for diagnosing stroke, whereas no mRNA showed realistic diagnostic efficacy.Conclusion: The ceRNA network may broaden our understanding of AIS pathology, and the candidate lncRNA from the ceRNA network is assumed to be a promising therapeutic target and diagnostic biomarker for AIS.

Integrative Analysis of MALT1 as a Potential Therapeutic Target for Prostate Cancer and its Immunological Role in Pan-Cancer

Background: Mucosa-associated lymphoma antigen 1 (MALT1) is an oncogene in subsets of diffuse large B cell lymphoma (DLBCL) and mucosa-associated lymphoid tissue type (MALT) lymphoma. However, the role of MALT1 across cancers, especially in prostate cancer is still poorly understood.Methods: Here, we used several public datasets to evaluate MALT1 expression. Then, PCa cell lines and nude mice were used to investigate the cellular functions in vitro and in vivo. Microarray data were downloaded from The Cancer Genome Atlas and MALT1 was subjected to gene set enrichment analysis (GSEA) and Gene Ontology (GO) analysis to identify the biological functions and relevant pathways. Additionally, the correlations between MALT1 expression and mismatch repair (MMR) gene mutation, immune checkpoint gene expression, tumor mutational burden (TMB), and microsatellite instability (MSI) were investigated by Pearson correlation analysis. Moreover, the correlation between MALT1 expression and tumor immune infiltration was analyzed by the Tumor Immune Evaluation Resource (TIMER) database.Results: MALT1 overexpression was significantly correlated with MMR gene mutation levels and crucially promoted proliferation and colony genesis while reducing PCa cell apoptosis levels in vivo and in vitro. MALT1 expression showed strong correlations with immune checkpoint genes, TMB, and MSI in most cancers. The GO analysis indicated that MALT1-coexpressed genes were involved in heterotypic cell-cell adhesion, actin filament-based movement regulation, and action potential regulation. GSEA revealed that MALT1 expression was associated with several signaling pathways, including the NF-κB signaling, Wnt/β-catenin and TGF-β signaling pathways, in PCa. Additionally, MALT1 expression was significantly correlated with the infiltration of immune cells, including B cells, CD8+ T cells, dendritic cells and macrophages, and negatively correlated with CD4+ cell infiltration in PCa.Conclusion: MALT1 expression is higher in pancancer samples than in normal tissues. MALT1 promoted proliferation and colony genesis while reducing PCa cell apoptosis levels, and MALT1 suppression could inhibit xenograft tumor establishment in nude mice. Furthermore, MALT1 expression is closely related to the occurrence and development of multiple tumors in multiple ways. Therefore, MALT1 may be an emerging therapeutic target for a variety of cancers especially PCa.

In silico investigation of the mechanism of action of kojic acid effects via protein-protein interaction network

Purpose: To evaluate the molecular mechanism of kojic acid by network pharmacology.Methods: This study was conducted by designing a protein-protein interaction network through the STITCH database and analyzing biological processes via Cytoscape plugin ClueGO.Results: A total of 19 protein targets of kojic acid including TYR, NOS3, NOS2, and NOS1 were found. The PPI network helped to understand the mode of action of kojic acid at a molecular level. Gene Ontology (GO) analysis resulted in the retrieval of 104 GO terms which were related to variousphysiological processes. GO analysis revealed that kojic acid might be involved in the regulation of several biological processes such as circadian gene expression and transcription initiation of RNA polymerase 2.Conclusion: The findings from this study reveal that the retrieved GO pathways are known to be involved in several diseases such as inflammation, cancer, aging, pigmentation, and melisma. Furthermore, these pathways are directly or indirectly related to kojic acid. Thus, this study has contributed to a better understanding of the mode of action of kojic acid.

miRNA target prediction of avian Z-linked DMRT1 gene during sex determination in chicken (G. Gallus)

Sex determination in dimorphic animal, such as chicken (G. Gallus), is controlled by the expression of doublesex and mab-3 related transcription factor 1 (DMRT1) gene. This gene act as sex determination switch by critically needed for testis differentiation and as antagonist of ovarian development. miRNA, is belongs to short noncoding RNA which modulate gene expression in specific or board targeted genes. This study was aimed to predict miRNA(s) candidate targeted to DMRT1 expression in chicken. In silico method was employed to mining miRNA targeted to DMRT1 using three online databases namely miRDB, TargetScan, and microT-CDS. Following prediction, clustering was performed to select common miRNA(s) in minimal two databases for gene ontology (GO) analysis. Totally 78 miRNAs were targeted to DMRT1 3’UTR, and eight miRNA(s) were found in minimal two databases. The GO analysis found seven distinct biological functions in membrane, cytoplasm, protein binding, nucleus, integral component of membrane and molecular function, and all are related to the cell growth namely cell proliferation. According to the result, it shows the possibility to use selected candidate of miRNA(s) targeted to DMRT1 to reveal the sex determination mechanism at early stage of chicken development.

Comprehensive Gene Expression Signature Using RNA-Seq in Airways of Mouse Model of Severe Asthma with Fungal Sensitization

<b><i>Introduction:</i></b> Inhalation of fungal allergens induces airway epithelial damage following airway inflammation and excessive mucus secretion, which can lead to severe asthma with fungal sensitization (SAFS). Comprehensive gene expression analysis in <i>Alternaria</i>-exposed mouse airways, a model of SAFS, has not been conducted. <b><i>Methods:</i></b> BALB/c mice received intranasal administration of <i>Alternaria</i> extract or phosphate-buffered saline twice a week for 6 weeks. Lung sections and bronchoalveolar lavage fluid were obtained to assess airway inflammation. RNA-Seq in the central airway was performed, and gene ontology (GO) analysis and gene set enrichment analysis (GSEA) were conducted for pathway analyses. An in vitro experiment using human airway epithelial cell 16HBE14o- was performed to validate the RNA-Seq findings. <b><i>Results:</i></b> Eosinophilic airway inflammation with mucus overproduction and airway remodeling was observed in mice exposed to <i>Alternaria</i>. RNA-Seq analysis revealed 403 upregulated and 108 downregulated genes in airways of <i>Alternaria-</i>exposed mice. In GO analysis, the functions of immunoglobulin (Ig) receptor binding, Ig production, inflammatory response, and T-cell activation were upregulated, while those of keratinization and defense response to other organisms were downregulated. GSEA revealed positive enrichment in T-cell receptor complex, immunological synapse, antigen binding, mast cell activation, and Ig receptor binding, and negative enrichment in keratinization and cornification in <i>Alternaria</i>-exposed mice relative to control. <i>Alternaria</i> exposure to 16HBE14o- cells validated the downregulation of epithelial keratinization-related genes, including <i>SPRR1A</i>, <i>SPRR1B</i>, and <i>KRT6B</i>. <b><i>Conclusion:</i></b> RNA-Seq analysis showed that <i>Alternaria</i> exposure induced inflammatory response and impaired defense mechanisms in mice airway epithelium, which might be therapeutic targets for SAFS.

Cadherin and Wnt signaling pathways as key regulators in diabetic nephropathy

Aim A recent meta-analysis of genome-wide linkage studies (GWLS) has identified multiple genetic regions suggestive of linkage with DN harboring hundreds of genes. Moving this number of genetic loci forward into biological insight is truly the next step. Here, we approach this challenge with a gene ontology (GO) analysis in order to yield biological and functional role to the genes, an over-representation test to find which GO terms are enriched in the gene list, pathway analysis, as well as protein network analysis. Method GO analysis was performed using protein analysis through evolutionary relationships (PANTHER) version 14.0 software and P-values less than 0.05 were considered statistically significant. GO analysis was followed by over-representation test for the identification of enriched terms. Statistical significance was calculated by Fisher’s exact test and adjusted using the false discovery rate (FDR) for correction of multiple tests. Cytoscape with the relevant plugins was used for the construction of the protein network and clustering analysis. Results The GO analysis assign multiple GO terms to the genes regarding the molecular function, the biological process and the cellular component, protein class and pathway analysis. The findings of the over-representation test highlight the contribution of cell adhesion regarding the biological process, integral components of plasma membrane regarding the cellular component, chemokines and cytokines with regard to protein class, while the pathway analysis emphasizes the contribution of Wnt and cadherin signaling pathways. Conclusions Our results suggest that a core feature of the pathogenesis of DN may be a disturbance in Wnt and cadherin signaling pathways, whereas the contribution of chemokines and cytokines need to be studied in additional studies.

BRIX1 Promotes Ribosome Synthesis and Enhances Glycolysis by Selected Translation of GLUT1 in Colorectal Cancer

Background: Ribosome biogenesis protein BRX1 homolog (BRIX1) is a vital member for synthesizing 60S subunit of ribosome. However, the role and mechanism of BRIX1 in colorectal cancer (CRC) are still unclear. Methods: KEGG pathway analysis and Gene Ontology (GO) analysis were used for bioinformatics analysis. Ribosome RNAs (rRNAs) levels were detected in CRC tissues and cells. Nascent RNA synthesis were detected by cellular immunofluorescence. Correlation was analysis between PET-CT value and BRIX1 expression. Extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) were conducted by seahorse analyses. Polysome fractions were collected for BRIX1 mRNA used in translation. Orthotopic model and CCK-8 assay were used for BRIX1 function in CRC.Results: We found that BRIX1 is a core gene of ribosome-related pathway changes in CRC. GO analysis showed BRIX1 primarily enriched RIBOSOME ASSEMBLY and RIBOSOME BIOGENESIS pathways. In fresh CRC tissue, rRNAs levels (5S, 5.8S, 18S and 28S) were obvious higher in BRIX1-high group than BRIX1-Low group. Similarly, BRIX1 knockdown and overexpression significantly dereased and increased rRNAs levels (5S, 5.8S, 18S and 28S) in CRC cells, respectively. In addition, BRIX1 knockdown inhibited nascent RNA synthesis of CRC cells. In clinical data analysis, we found that BRIX1 expression is related to the glucose uptake of PET-CT. Consistently, BRIX1 knockdown and overexpression significantly dereased and increased ECAR valve, glucose uptake and lactic acid production in CRC cells. Subsequently, we found BRIX1 knockdown and overexpression significantly dereased and increased the protein expression of GLUT1, but not affect its mRNA expression. Interestingly, we found BRIX1 knockdown and overexpression obviously decreased and increased mRNA level of GLUT1 in polysome fractions. Blocking glycolysis by si-GLUT1 or galactose reversed the promoting role of BRIX1 in glycolysis and cell proliferation of CRC cells. Conclusion: In this study, BRIX1 plays a tumor-promoting role in CRC via regulating glycolysis by selecting GLUT1 translation, indicating a correlation between ribosome activation and metabolic reprogramming in CRC.

Investigating the Mechanism of Scutellariae barbata Herba in the Treatment of Colorectal Cancer by Network Pharmacology and Molecular Docking

Background. Colorectal cancer (CRC) is one of the most common gastrointestinal tumors, which accounts for approximately 10% of all diagnosed cancers and cancer deaths worldwide per year. Scutellariae barbatae Herba (SBH) is one of the most frequently used traditional Chinese medicine (TCM) in the treatment of CRC. Although many experiments have been carried out to explain the mechanisms of SBH, the mechanisms of SBH have not been illuminated fully. Thus, we constructed a network pharmacology and molecular docking to investigate the mechanisms of SBH. Methods. We adopted active constituent prescreening, target predicting, protein-protein interaction (PPI) analysis, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, differentially expressed gene analysis, and molecular docking to establish a system pharmacology database of SBH against CRC. Results. A total of 64 active constituents of SBH were obtained and 377 targets were predicted, and the result indicated that quercetin, luteolin, wogonin, and apigenin were the main active constituents of SBH. Glucocorticoid receptor (NR3C1), pPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (PIK3CA), cellular tumor antigen p53 (TP53), transcription factor AP-1 (JUN), mitogen-activated protein kinase 1 (MAPK1), Myc protooncogene protein (MYC), cyclin-dependent kinase 1 (CDK1), and broad substrate specificity ATP-binding cassette transporter ABCG2 (ABCG2) were the major targets of SBH in the treatment of CRC. GO analysis illustrated that the core biological process regulated by SBH was the regulation of the cell cycle. Thirty pathways were presented and 8 pathways related to CRC were involved. Molecular docking presented the binding details of 3 key targets with 6 active constituents. Conclusions. The mechanisms of SBH against CRC depend on the synergistic effect of multiple active constituents, multiple targets, and multiple pathways.

Molecular Characterization of AEBP1 at Transcriptional Level in Glioma

Background. Glioma is the most common malignant tumor of the brain in adult patients. The standardized treatment protocol is based on surgical therapy, supplemented with radiotherapy and chemotherapy. However, the prognosis is still unsatisfied. Chemoresistance is one of the most important reason for the poor prognosis of glioma patients. It has confirmed that glioma stem cell (GSC) is one of the reasons for chemoresistance. Methods. In this study, three datasets (GSE23806, COSMIC, and TCGA) were used to perform the analysis to search for the key genes related to GSC, temozolomide (TMZ) resistance, and prognosis. The key gene for further research was selected by reviewing the previous studies. The selected gene investigated the relation between expression levels and clinical characteristics in both TCGA and CGGA dataset. The bioinformatics analysis was performed by Gene Ontology (GO) analysis. The survival analysis was performed by Kaplan–Meier survival analysis. Results. AE binding protein 1 (AEBP1) was selected for further analysis. AEBP1 was overexpressed in GSCs and TMZ resistance cells. In both TCGA and CGGA dataset, the results showed that the expression level of AEBP1 was increased in glioblastoma (GBM) samples, IDH wild-type samples, and MGMT promoter unmethylated samples. Meanwhile, AEBP1 expression was positively related to several GSC markers. GO analysis showed that AEBP1 was related to immune response, cell adhesion, apoptotic process, inflammatory response, positive regulation of cell proliferation, angiogenesis, response to drug, and response to hypoxia. The survival analysis showed that the overexpressed level of AEBP1 was correlated with short survival time in both glioma and GBM patients. Conclusion. In summary, AEBP1 was related with GSC-induced TMZ resistance. Our study showed that AEBP1 might be an oncogene and a new effective therapeutic target for the treatment of glioma.

Integrating Transcriptome-Wide Association Study and mRNA Expression Profiling Identifies Novel Genes Associated With Osteonecrosis of the Femoral Head

ObjectiveThis study aims to identify novel candidate genes associated with osteonecrosis of the femoral head (ONFH).MethodsA transcriptome-wide association study (TWAS) was performed by integrating the genome-wide association study dataset of osteonecrosis (ON) in the UK Biobank with pre-computed mRNA expression reference weights of muscle skeleton (MS) and blood. The ON-associated genes identified by TWAS were further subjected to gene ontology (GO) analysis by the DAVID tool. Finally, a trans-omics comparative analysis of TWAS and genome-wide mRNA expression profiling was conducted to identify the common genes and the GO terms shared by both DNA-level TWAS and mRNA-level expression profile for ONFH.ResultsTWAS totally identified 564 genes that were with PTWAS value &lt;0.05 for MS and blood, such as CBX1 (PTWAS = 0.0001 for MS), SRPK2 (PTWAS = 0.0002 for blood), and MYO5A (PTWAS = 0.0005 for blood). After comparing the genes detected by TWAS with the differentially expressed genes identified by mRNA expression profiling, we detected 59 overlapped genes, such as STEAP4 [PTWAS = 0.0270, FC (fold change)mRNA = 7.03], RABEP1 (PTWAS = 0.010, FCmRNA = 2.22), and MORC3 (PTWAS = 0.0053, FCmRNA = 2.92). The GO analysis of TWAS-identified genes discovered 53 GO terms for ON. Further comparing the GO results of TWAS and mRNA expression profiling identified four overlapped GO terms, including cysteine-type endopeptidase activity (PTWAS = 0.0006, PmRNA = 0.0227), extracellular space (PTWAS = 0.0342, PmRNA = 0.0012), protein binding (PTWAS = 0.0112, PmRNA = 0.0106), and ATP binding (PTWAS = 0.0464, PmRNA = 0.0033).ConclusionSeveral ONFH-associated genes and GO terms were identified by integrating TWAS and mRNA expression profiling. It provides novel clues to reveal the pathogenesis of ONFH.