Dataset Information

Screening of candidate key genes associated with human osteosarcoma using bioinformatics analysis.

ABSTRACT: The aim of the present study was to identify the key genes associated with osteosarcoma (OS) using a bioinformatics approach. Microarray data (GSE36004) was downloaded from the Gene Expression Omnibus database, including 19 OS cell lines and 6 normal controls. Differentially expressed genes (DEGs) in the OS cell lines were identified using the Limma package, and differentially methylated regions were screened with methyAnalysis in R. Copy number analysis was performed and genes with copy number gains/losses were further screened using DNAcopy and cghMCR packages. Functional enrichment analyses were performed using the Database for Annotation, Visualization and Integrated Discovery online tool, and protein-protein interactions were identified based on information obtained from the Search Tool for the Retrieval of Interacting Genes database. A total of 47 downregulated genes were screened in hyper-methylated regions, including the fragment crystallizable (Fc) region of immunoglobulin E, high affinity I, receptor for; ? polypeptide (FCER1G), leptin (LEP) and feline Gardner-Rasheed sarcoma viral oncogene homolog (FGR). In addition, a total of 17 upregulated genes, including the TPase family, AAA domain containing 2 (ATAD2) and cyclin-dependent kinase 4 (CDK4), exhibited copy number gains, while 5 downregulated genes, including Rho GTPase activating protein 9 (ARHGAP9) and major histocompatibility complex, class II, DO ? (HLA-DOA), exhibited copy number losses. These results indicate that hyper-methylation of FCER1G, LEP, and FGR may serve a crucial function in the development of OS. In addition, copy number alterations of these DEGs, including ATAD2, CDK4, ARHGAP9 and HLA-DOA, may also contribute to OS progression. These DEGs may be candidate targets for the diagnosis and treatment of this disease.

SUBMITTER: Zhang K

PROVIDER: S-EPMC5588164 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Screening of candidate key genes associated with human osteosarcoma using bioinformatics analysis.

Zhang Kefeng K Gao Jianwen J Ni Yong Y

Oncology letters 20170704 3

The aim of the present study was to identify the key genes associated with osteosarcoma (OS) using a bioinformatics approach. Microarray data (GSE36004) was downloaded from the Gene Expression Omnibus database, including 19 OS cell lines and 6 normal controls. Differentially expressed genes (DEGs) in the OS cell lines were identified using the Limma package, and differentially methylated regions were screened with methyAnalysis in R. Copy number analysis was performed and genes with copy number ...[more]

PMID: 28928828

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Project description:Osteosarcoma (OS) is an invasive malignant neoplasm of the bones. The present study identified and analyzed key genes associated with OS. Expression profiling of the dataset GSE49003, which included 6 metastatic and 6 non-metastatic OS cell lines and was obtained from the Gene Expression Omnibus, was performed. Following data preprocessing, the differentially expressed genes (DEGs) were selected using the limma package in R. Subsequently, bidirectional hierarchical clustering using the pheatmap package in R and an unpaired Students' t-test was performed for the DEGs. Based on the Search Tool for the Retrieval of Interacting Genes database and Cytoscape software, a protein-protein interaction (PPI) network for the DEGs was constructed. Using Database for Annotation, Visualization and Integrated Discovery software and the Kyoto Encyclopedia of Genes and Genomes Orthology Based Annotation System server, functional and pathway enrichment analyses were performed for the DEGs corresponding to the proteins of the network. In addition, the transcription factors (TFs) and CpG islands of the gene promoter were searched for using the TRANSFAC database and CpG Island Searcher software, respectively. A total of 323 DEGs were identified between the metastatic and non-metastatic samples. In the PPI network, upregulated epidermal growth factor receptor (EGFR) exhibits a high degree and was therefore highly interconnected with other proteins. Enrichment analysis revealed that EGFR was enriched in cytoskeleton organization, organic substance response and the signaling pathway of focal adhesion. The TFs early growth response 1, nuclear factor-?B complex subunits, peroxisome proliferator activated receptor ?, signal transducer and activator of transcription 3 and MYC proto-oncogene were identified in the EGFR promoter region. Furthermore, multiple CpG islands, starting from the 400 bp of the EGFR promoter sequence, were predicted. Methylated modification of the CpG islands in the EGFR promoter may help to regulate EGFR expression. The TFs identified in the EGFR promoter may function in the progression of OS.

Project description:BackgroundOsteosarcoma (OS) metastasis is the most common cause of cancer-related mortality, however, no sufficient clinical biomarkers have been identified. In this study, we identified five genes to help predict metastasis at diagnosis.MethodsWe performed weighted gene co-expression network analysis (WGCNA) to identify the most relevant gene modules associated with OS metastasis. An important machine learning algorithm, the support vector machine (SVM), was employed to predict key genes for classifying the OS metastasis phenotype. Finally, we investigated the clinical significance of key genes and their enriched pathways.ResultsEighteen modules were identified in WGCNA, among which the pink, red, brown, blue, and turquoise modules demonstrated good preservation. In the five modules, the brown and red modules were highly correlated with OS metastasis. Genes in the two modules closely interacted in protein-protein interaction networks and were therefore chosen for further analysis. Genes in the two modules were primarily enriched in the biological processes associated with tumorigenesis and development. Furthermore, 65 differentially expressed genes were identified as common hub genes in both WGCNA and protein-protein interaction networks. SVM classifiers with the maximum area under the curve were based on 30 and 15 genes in the brown and red modules, respectively. The clinical significance of the 45 hub genes was analyzed. Of the 45 genes, 17 were found to be significantly correlated with survival time. Finally, 5/17 genes, including ADAP2 (P = 0.0094), LCP2 (P = 0.013), ARHGAP25 (P = 0.0049), CD53 (P = 0.016), and TLR7 (P = 0.04) were significantly correlated with the metastatic phenotype. In vitro verification, western blotting, wound healing analyses, transwell invasion assays, proliferation assays, and colony formation assays indicated that ARHGAP25 promoted OS cell migration, invasion, proliferation, and epithelial-mesenchymal transition.ConclusionWe identified five genes, namely ADAP2, LCP2, ARHGAP25, CD53, and TLR7, as candidate biomarkers for the prediction of OS metastasis; ARHGAP25 inhibits MG63 OS cell growth, migration, and invasion in vitro, indicating that ARHGAP25 can serve as a promising specific and prognostic biomarker for OS metastasis.

Project description:Osteosarcoma, which arises from bone tissue, is considered to be one of the most common types of cancer in children and teenagers. As the etiology of osteosarcoma has not been fully elucidated, the overall prognosis for patients is generally poor. In recent years, the development of bioinformatical technology has allowed researchers to identify numerous molecular biological characteristics associated with the prognosis of osteosarcoma using online databases. In the present study, Gene Expression Omnibus (GEO) database was used and three microarray datasets were obtained. The GEO2R web tool was utilized and differentially expressed genes (DEGs) in osteosarcoma tissue were identified. Venn analysis was performed to determine the intersection of the DEG profiles. DEGs were analyzed by Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Protein-protein interactions (PPIs) between these DEGs were analyzed using the Search Tool for the Retrieval of Interacting Genes database, and the PPI network was then visualized using Cytoscape software. The top ten genes were identified based on measurement of degree, density of maximum neighborhood component, maximal clique centrality and mononuclear cell counts in the PPI network, and five overlapping genes [origin recognition complex subunit 6 (ORC6), IGF-binding protein 5 (IGFBP5), minichromosome maintenance 10 replication initiation factor (MCM10), MET proto-oncogene, receptor tyrosine kinase (MET) and centromere protein F (CENPF)] were identified. Additionally, three module networks were analyzed by Molecular Complex Detection (MCODE), and six key genes [ORC6, MCM10, DEP domain containing 1 (DEPDC1), CENPF, TIMELESS interacting protein (TIPIN) and shugoshin 1 (SGOL1)] were screened. Combined with the results from Cytoscape and MCODE, eight hub genes (ORC6, MCM10, DEPDC1, CENPF, TIPIN, SGOL1, MET and IGFBP5) were obtained. Furthermore, Kaplan-Meier plotter survival analysis was used to evaluate the prognostic value of these eight hub genes in patients with osteosarcoma. Oncomine and GEPIA databases were applied to further confirm the expression levels of hub genes in tissue. Finally, the functional roles of the core gene CENPF were investigated using Cell Counting Kit-8, wound healing and Transwell assays, which indicated that CENPF knockdown inhibited the proliferation, migration and invasion of osteosarcoma cells. These results provided potential prognostic markers, as well as a basis for further investigation of the mechanism underlying osteosarcoma.

Dataset Information

Screening of candidate key genes associated with human osteosarcoma using bioinformatics analysis.

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Screening of candidate key genes associated with human osteosarcoma using bioinformatics analysis.

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