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28 April 2017 : Laboratory Research  

Identification of Key Genes Affecting Results of Hyperthermia in Osteosarcoma Based on Integrative ChIP-Seq/TargetScan Analysis

Yuxia Shi1ABCDEFG, Fan Yang1ABCDEFG, Shuqing Wei2ADF*, Gang Xu1BD

DOI: 10.12659/MSM.901191

Med Sci Monit 2017; 23:2042-2048

Abstract

BACKGROUND: The purpose of this study was to research the effects of hyperthermia on osteosarcoma (OS) by integrating the Chromatin Immunoprecipitation with the generation sequencing (ChIP-Seq) and TargetScan analysis of heat shock transcription factor 1 (HSF1).

MATERIAL AND METHODS: The HSF1 ChIP-seq dataset of GSE60984 was downloaded from the Gene Expressed Omnibus (GEO) database. The HSF1-binding sites were screened by MACS2 in OS cells after 10 and 20 min of hyperthermia, and they were annotated using the ChIPseeker package. The overlapped genes were selected out when HSF1-binding sites were located in the promoter region. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the overlaps. The miRNA-gene pairs of the overlaps were screened out via TargetScan, and the miRNA-gene-regulated network was constructed by Cytoscape software.

RESULTS: 1880 and 1283 genes of promoter regions were obtained in the osteosarcoma cells after 10 and 20 min of hyperthermia, respectively, and 889 of them were overlapped. The overlapped genes were enriched in 122 GO terms and 3 KEGG pathways. There were 13 657 pairs involved in the miRNA-gene regulated network of the overlaps.

CONCLUSIONS: Some biomarkers were identified for OS treated with hyperthermia. Moreover, some GO terms (regulation of programmed cell death and regulation of cell death) and pathways (p53 signaling pathway, methane metabolism, and viral myocarditis) might be involved.

Keywords: Gene Expression, Hyperthermia, Induced

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Medical Science Monitor eISSN: 1643-3750
Medical Science Monitor eISSN: 1643-3750