ETS2 and microRNA-155 regulate the pathogenesis of heart failure through targeting and regulating GPR18 expression.
ABSTRACT: Heart failure (HF) is a global pandemic cardiovascular disease with increasing prevalence, but the pathogenesis remains to be elucidated. The present study aimed to investigate the underlying mechanism in heart failure (HF) using bioinformatics and experimental validation. A HF-associated dataset GSE84796 was downloaded from the Gene Expression Omnibus database and differentially expressed genes (DEGs) were screened for using Bayes method in the Limma package. Kyoto Encyclopedia of Genes and Genomes pathway analysis was used to perform pathway enrichment analysis of these DEGs using The Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction (PPI) network of DEG-encoded proteins was subsequently constructed using the Search tool for the Retrieval of Interacting Genes/Proteins, and a transcription factor (TF)/miRNA-target network was constructed according to the WEB-based Gene SeT AnaLysis Tookit. The expression levels of microRNA (miRNA/miR)-155, G-protein coupled receptor 18 (GRP18) and E26 transformation-specific transcription factor 2 (ETS2) were analyzed in clinical HF samples, and functional validations were performed in H9c2 (2-1) cells. A total of 419 DEGs were identified, including 366 upregulated genes and 53 downregulated genes. The upregulated DEGs were significantly enriched in the pathways of 'cytokine-cytokine receptor interaction', 'natural killer cell mediated cytotoxicity' and 'primary immunodeficiency'. A total of two functional modules were identified in the PPI network: Module A was enriched in 3 KEGG pathways and module B was enriched in 15 KEGG pathways. Furthermore, a total of three miRNAs and eight TFs were identified in the TF/miRNA-target network. Specifically, GPR18 was discovered to be targeted by both ETS2 and miR-155. Clinical validation revealed that the expression levels of miR-155 were significantly decreased in the HF samples, whereas the expression levels of ETS2 and GPR18 were significantly increased in HF samples. In conclusion, the present study suggested that GPR18 may be a target of ETS2 and miR-155, and miR-155 may regulate cell viability and apoptosis in H9c2 (2-1) cells through targeting and regulating GPR18.
Project description:Nuclear factor??B (NF??B) is widely involved in various lymphoid malignancies. However, its exact functional role and potential regulatory mechanisms in Hodgkin's lymphoma (HL) remains unclear. The present study aimed to investigate the regulatory mechanism of NF??B in HL by analysis of a gene expression profile that was obtained from HL cells with or without NF??B subunit 2 (NFKB2) knockdown. The GSE64234 dataset containing 6 HL cell line specimens transfected with small interfering (si)RNA against NFKB2 and 6 control specimens transfected with non?targeting siRNA sequences was downloaded from the Gene Expression Omnibus database. Based on these data, differentially expressed genes (DEGs) were screened for following data preprocessing. Functional enrichment analysis was subsequently conducted among the identified upregulated and downregulated DEGs. Additionally, a protein?protein interaction (PPI) network was constructed and module analyses were performed. Finally, microRNAs (miRNAs/miRs) targeting the identified DEGs were predicted for the construction of a miRNA?target regulatory network. A total of 253 DEGs were identified, consisting of 109 upregulated and 144 downregulated DEGs. Pathway enrichment analysis revealed that B?cell lymphoma 2?like 1 (BCL2L1) was significantly enriched in the NF??B signaling pathway, and colony?stimulating factor 2 (CSF2) and BCL2L1 were enriched in the Jak?signal transducer and activator of transcription (STAT) signaling pathway. BCL2L1 and CSF2 were determined to be hub genes in the PPI network. A total of 6 miRNAs, including let?7a?5p, miR?9?5p, miR?155?5p, miR?135a?5p, miR?17?5p and miR?375, were identified in the miRNA?target regulatory network. The results of the present study indicated that NFKB2 may be involved in HL development through regulation of BCL2L1, CSF2, miR?135a?5p, miR?155?5p and miR?9?5p expression, as well as the modulation of Jak?STAT and NF??B signaling pathways.
Project description:BACKGROUND:We aimed to discover the potential microRNA (miRNA) targets and to explore the underlying molecular mechanisms of clear cell renal cell carcinoma (ccRCC). METHODS:Microarray data of GSE16441 was downloaded from Gene Expression Omnibus database. Differentially expressed genes (DEGs) and differentially expressed miRNAs between ccRCC tumors and matched non-tumor samples were analyzed. Target genes of differentially expressed miRNAs were screened. Besides, functional enrichment analysis of DEGs was performed, followed by protein-protein interaction (PPI) network construction and sub-module analysis. Finally, the integrated miRNA-DEGs network was constructed. RESULTS:A total of 1758 up- and 2465 down-regulated DEGs were identified. Moreover, 15 up- and 12 down-regulated differentially expressed miRNAs were screened. The up-regulated DEGs were significantly enriched in pathways such as cell adhesion molecules and focal adhesion. Besides, the down-regulated DEGs were enriched in oxidative phosphorylation, and citrate cycle (TCA cycle). Moreover, eight sub-modules of PPI network were obtained. Totally, eight down-regulated miRNAs were identified to significantly regulate the DEGs and miRNA-200c that could regulate collagen, type V, alpha 2 (COL5A2) as well as COL5A3 was found to be the most significant. Additionally, 10 up-regulated miRNAs were identified to be significantly associated with the DEGs. Thereinto, miRNA-15a that could regulate ATPase, H(+) transporting, lysosomal 21 kDa, V0 subunit b (ATP6V0B) and miRNA-155 were found to be the most significant. CONCLUSIONS:miRNA-200c that could regulate COL5A2 and COL5A3, miRNA-15a that could regulate ATP6V0B and miRNA-155 may play key roles in ccRCC progression. These miRNAs may be potential targets for ccRCC treatment.
Project description:Accumulating evidence has indicated that noncoding RNAs are involved in intervertebral disc degeneration (IDD); however, the competing endogenous RNA (ceRNA)?mediated regulatory mechanisms in IDD remain rarely reported. The present study aimed to comprehensively investigate the alterations in expression levels of circular RNA (circRNA), long noncoding RNA (lncRNA), microRNA (miRNA/miR) and mRNA in the nucleus pulposus (NP) of patients with IDD. In addition, crucial lncRNA/circRNA?miRNA?mRNA ceRNA interaction axes were screened using the GSE67567 microarray dataset obtained from the Gene Expression Omnibus database. After data preprocessing, differentially expressed circRNAs (DECs), lncRNAs (DELs), miRNAs (DEMs) or genes (DEGs) between IDD and normal controls were identified using the Linear Models for Microarray data method. A protein?protein interaction (PPI) network was constructed for DEGs based on protein databases, followed by module analysis. The ceRNA network was constructed based on the interaction between miRNAs and mRNAs, and lncRNAs/circRNAs and miRNAs. The underlying functions of mRNAs were predicted using the Database for Annotation, Visualization and Integrated Discovery database. The present study identified 636 DECs, 115 DELs, 84 DEMs and 1,040 DEGs between patients with IDD and control individuals. PPI network analysis demonstrated that Fos proto?oncogene, AP?1 transcription factor subunit (FOS), mitogen?activated protein kinase 1 (MAPK1), hypoxia inducible factor 1 subunit ? (HIF1A) and transforming growth factor ?1 (TGFB1) were hub genes and enriched in modules. Metastasis?associated lung adenocarcinoma transcript 1 (MALAT1)/hsa_circRNA_102348?hsa??miR?185?5p?TGFB1/FOS, MALAT1?hsa?miR?155?5p?HIF1A, hsa_circRNA_102399?hsa?miR?302a?3p?HIF1A, MALAT1?hsa??miR?519d?3p?MAPK1 and hsa_circRNA_100086?hsa?miR?509?3p?MAPK1 ceRNA axes were obtained by constructing the ceRNA networks. In conclusion, these identified ceRNA interaction axes may be crucial targets for the treatment of IDD.
Project description:Obesity paradox (OP) describes a widely observed clinical finding of improved cardiovascular fitness and survival in some overweight or obese patients. The molecular mechanisms underlying OP remain enigmatic partly due to a lack of animal models mirroring OP in patients. Using apolipoprotein E knock-out (apoE-/-) mice on a high fat (HF) diet as an atherosclerotic obesity model, we demonstrated 1) microRNA-155 (miRNA-155, miR-155) is significantly up-regulated in the aortas of apoE-/- mice, and miR-155 deficiency in apoE-/- mice inhibits atherosclerosis; 2) apoE-/-/miR-155-/- (double knock-out (DKO)) mice show HF diet-induced obesity, adipocyte hypertrophy, and present with non-alcoholic fatty liver disease; 3) DKO mice demonstrate HF diet-induced elevations of plasma leptin, resistin, fed-state and fasting insulin and increased expression of adipogenic transcription factors but lack glucose intolerance and insulin resistance. Our results are the first to present an OP model using DKO mice with features of decreased atherosclerosis, increased obesity, and non-alcoholic fatty liver disease. Our findings suggest the mechanistic role of reduced miR-155 expression in OP and present a new OP working model based on a single miRNA deficiency in diet-induced obese atherogenic mice. Furthermore, our results serve as a breakthrough in understanding the potential mechanism underlying OP and provide a new biomarker and novel therapeutic target for OP-related metabolic diseases.
Project description:BACKGROUND:The study aimed to identify the targeting genes and miRNAs using the microarray expression profile dataset for Osteoarthritis (OA) patients. Differentially expressed genes (DEGs) between OA and control samples were identified using Bayes method of limma package. Subsequently, a protein-protein interaction (PPI) network was constructed. miRNAs and transcription factor (TFs) based on DEGs in PPI network were identified using Webgestalt and ENCODE, respectively. Finally, MCODE, Gene Ontology (GO) function, and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed. The expressions of several DEGs and predicted miRNAs in OA rats were detected by RT-PCR. RESULTS:A total of 594 DEGs were identified. In PPI network, there were 313 upregulated DEGs and 22 downregulated DEGs. Besides, the regulatory relationships included 467 upregulated interactions and 85 downregulated interactions (miR-124A???QKI and MAP 1B) between miRNA and DEGs in PPI network. The module from downregulated DEGs-TFs-miRNA networks was mainly enriched to low-density lipoprotein particle clearance, response to linoleic acid, and small molecule metabolic process BP terms. Moreover, QKI, MAP 1B mRNA and miR-9 expressions were significantly reduced in OA rats. CONCLUSION:miR-9 might be a protective factor for OA patients via inhibiting proliferation and differentiation of cartilage progenitor cells. miR-124A might play an important role in progression of OA through targeting QKI and MAP 1B.
Project description:BACKGROUND:Gastric cancer (GC) is a prevalent malignant cancer of digestive system. To identify key genes in GC, mRNA microarray GSE27342, GSE29272, and GSE33335 were downloaded from GEO database. METHODS:Differentially expressed genes (DEGs) were obtained using GEO2R. DAVID database was used to analyze function and pathways enrichment of DEGs. Protein-protein interaction (PPI) network was established by STRING and visualized by Cytoscape software. Then, the influence of hub genes on overall survival (OS) was performed by the Kaplan-Meier plotter online tool. Module analysis of the PPI network was performed using MCODE. Additionally, potential stem loop miRNAs of hub genes were predicted by miRecords and screened by TCGA dataset. Transcription factors (TFs) of hub genes were detected by NetworkAnalyst. RESULTS:In total, 67 DEGs were identified; upregulated DEGs were mainly enriched in biological process (BP) related to angiogenesis and extracellular matrix organization and the downregulated DEGs were mainly enriched in BP related to ion transport and response to bacterium. KEGG pathways analysis showed that the upregulated DEGs were enriched in ECM-receptor interaction and the downregulated DEGs were enriched in gastric acid secretion. A PPI network of DEGs was constructed, consisting of 43 nodes and 87 edges. Twelve genes were considered as hub genes owing to high degrees in the network. Hsa-miR-29c, hsa-miR-30c, hsa-miR-335, hsa-miR-33b, and hsa-miR-101 might play a crucial role in hub genes regulation. In addition, the transcription factors-hub genes pairs were displayed with 182 edges and 102 nodes. The high expression of 7 out of 12 hub genes was associated with worse OS, including COL4A1, VCAN, THBS2, TIMP1, COL1A2, SERPINH1, and COL6A3. CONCLUSIONS:The miRNA and TFs regulation network of hub genes in GC may promote understanding of the molecular mechanisms underlying the development of gastric cancer and provide potential targets for GC diagnosis and treatment.
Project description:Off-pump coronary artery bypass (OPCAB) surgery is the most effective treatment for coronary heart disease. The aim of this study was to explore the effects of OPCAB on the basis of the associated molecular mechanisms. GSE12486 expression profiles downloaded from the Gene Expression Omnibus database (GEO) were analyzed to identify the differentially expressed genes (DEGs). Principal component analysis (PCA) was conducted based on the expression profiles of DEGs. Function and pathway enrichment of upregulated DEGs was performed, followed by protein-protein interaction (PPI) network construction. Gene Set Enrichment Analysis (GSEA) was used for miRNA enrichment analysis based on expression profiles and prediction of their association with the disease. Cytoscape was applied to construct miRNA regulatory networks of DEGs. In total 64 DEGs were identified, including 63 upregulated and 1 downregulated gene. The first principal component in the PCA analysis was able to distinguish between pre- and post-OPCAB samples. Upregulated DEGs mainly enriched 20 Gene Ontology terms, such as chemokine activity, and 5 pathways including the chemokine signaling pathway. The constructed PPI network contained 234 edges and 55 nodes, and 10 upregulated hub nodes, including FBJ murine osteosarcoma viral oncogene homolog (FOS), were screened. A total of 36 miRNAs, including MIR-224 and MIR-7, were screened by GSEA enrichment analysis. A miRNA regulatory network including 176 edges and 97 nodes was constructed, showing the regulatory relationships between miRNAs and DEGs. For example, early growth response 2 (EGR2) was regulated by 8 miRNAs including MIR-150, MIR-142-3P, MIR-367 and MIR-224. The identified DEGs might play important roles in patients pre- and post-OPCAB surgery via the regulation of associated genes.
Project description:To identify candidate key genes and miRNAs associated with esophageal squamous cell carcinoma (ESCC) development and prognosis, the gene expression profiles and miRNA microarray data including GSE20347, GSE38129, GSE23400, and GSE55856 were downloaded from the Gene Expression Omnibus (GEO) database. Clinical and survival data were retrieved from The Cancer Genome Atlas (TCGA). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes (DEGs) was analyzed via DAVID, while the DEG-associated protein-protein interaction network (PPI) was constructed using the STRING database. Additionally, the miRNA target gene regulatory network and miRNA coregulatory network were constructed, using the Cytoscape software. Survival analysis and prognostic model construction were performed via the survival (version 2.42-6) and rbsurv R packages, respectively. The results showed a total of 2575, 2111, and 1205 DEGs, and 226 differentially expressed miRNAs (DEMs) were identified. Pathway enrichment analyses revealed that DEGs were mainly enriched in 36 pathways, such as the proteasome, p53, and beta-alanine metabolism pathways. Furthermore, 448 nodes and 1144 interactions were identified in the PPI network, with MYC having the highest random walk score. In addition, 7 DEMs in the microarray data, including miR-196a, miR-21, miR-205, miR-194, miR-103, miR-223, and miR-375, were found in the regulatory network. Moreover, several reported disease-related miRNAs, including miR-198a, miR-103, miR-223, miR-21, miR-194, and miR-375, were found to have common target genes with other DEMs. Survival analysis revealed that 85 DEMs were related to prognosis, among which hsa-miR-1248, hsa-miR-1291, hsa-miR-421, and hsa-miR-7-5p were used for a prognostic survival model. Taken together, this study revealed the important roles of DEGs and DEMs in ESCC development, as well as DEMs in the prognosis of ESCC. This will provide potential therapeutic targets and prognostic predictors for ESCC.
Project description:BACKGROUND:This study was aimed to explore the molecular mechanisms of hypertensive nephropathy (HTN). METHODS:Gene expression profile of GSE37460, which based on 27 healthy living donor samples (HTN group) and 15 hypertensive nephropathy samples (control group), were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between two groups were identified. STRING database was used to reveal protein-protein interaction (PPI) network of DEGs, followed by the functional enrichment analysis of the PPI network. Additionally, miRNA-DEG regulatory network was constructed to reveal the validated miRNAs targeting the DEGs. RESULTS:In total, 51 up-regulated genes and 140 down-regulated genes were obtained. In the PPI network, cytochrome P450 3A4 (CYP3A4) and angiotensin II receptor type 1 (AGTR1) had a higher degree, and CYP3A4 interacted with CYP4A11. The DEGs in the network were significantly enriched in drug metabolism, focal adhesion and arachidonic acid metabolism. Furthermore, in the miRNA-DEG regulatory network, hsa-miR-335-5p and hsa-miR-26b-5p were the two most outstanding miRNAs. AGTR1, CYP3A4 and CYP4A11 were predicted to be regulated by hsa-miR-26b-5p. CONCLUSION:The DEGs, such as AGTR1, CYP3A4 and CYP4A11 may play critical roles in the development of HTN likely via the regulation by hsa-miR-26b-5p and taking part in some pathways.
Project description:Introduction:Idiopathic pulmonary arterial hypertension (IPAH) is a severe cardiopulmonary disease with a relatively low survival rate. Moreover, the pathogenesis of IPAH has not been fully recognized. Thus, comprehensive analyses of miRNA-mRNA network and potential drugs in IPAH are urgent requirements. Methods:Microarray datasets of mRNA and microRNA (miRNA) in IPAH were searched and downloaded from Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMIs) were identified. Then, the DEMI-DEG network was conducted with associated comprehensive analyses including Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) network analysis, while potential drugs targeting hub genes were investigated using L1000 platform. Results:30 DEGs and 6 DEMIs were identified in the lung tissue of IPAH. GO and KEGG pathway analyses revealed that these DEGs were mostly enriched in antimicrobial humoral response and African trypanosomiasis, respectively. The DEMI-DEG network was conducted subsequently with 4 DEMIs (hsa-miR-34b-5p, hsa-miR-26b-5p, hsa-miR-205-5p, and hsa-miR-199a-3p) and 16 DEGs, among which 5 DEGs (AQP9, SPP1, END1, VCAM1, and SAA1) were included in the top 10 hub genes of the PPI network. Nimodipine was identified with the highest CMap connectivity score in L1000 platform. Conclusion:Our study conducted a miRNA-mRNA network and identified 4 miRNAs as well as 5 mRNAs which may play important roles in the pathogenesis of IPAH. Moreover, we provided a new insight for future therapies by predicting potential drugs targeting hub genes.