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Screening of candidate key genes associated with human osteosarcoma using bioinformatics analysis
Kefeng Zhang1, Jianwen Gao1, Yong Ni1
1Department of Spinal Surgery, Shandong Jining No. 1 People's Hospital, Jining, Shandong 272011, P.R. China.
Oncology Letters
|September 21, 2017
Summary
This study identifies key genes linked to osteosarcoma (OS) development. Hyper-methylation of FCER1G, LEP, and FGR, and copy number alterations in ATAD2, CDK4, ARHGAP9, and HLA-DOA are crucial for OS progression and may offer diagnostic and therapeutic targets.
Area of Science:
- Oncology
- Genetics
- Bioinformatics
Background:
- Osteosarcoma (OS) is a primary bone cancer with complex genetic underpinnings.
- Identifying key genes involved in OS pathogenesis is crucial for developing effective diagnostic and therapeutic strategies.
Purpose of the Study:
- To identify key genes associated with osteosarcoma (OS) using a comprehensive bioinformatics approach.
- To investigate the roles of differential gene expression, methylation, and copy number alterations in OS development.
Main Methods:
- Utilized microarray data (GSE36004) from OS cell lines and normal controls.
- Employed bioinformatics tools including Limma, methyAnalysis, DNAcopy, cghMCR, DAVID, and STRING for DEG analysis, methylation screening, copy number analysis, functional enrichment, and protein-protein interactions.
Main Results:
- Identified 47 downregulated genes in hyper-methylated regions, including FCER1G, LEP, and FGR.
- Found 17 upregulated genes with copy number gains (e.g., ATAD2, CDK4) and 5 downregulated genes with copy number losses (e.g., ARHGAP9, HLA-DOA).
Conclusions:
- Hyper-methylation of FCER1G, LEP, and FGR is implicated in osteosarcoma development.
- Copy number alterations of ATAD2, CDK4, ARHGAP9, and HLA-DOA may contribute to OS progression.
- These differentially expressed genes represent potential candidate targets for osteosarcoma diagnosis and treatment.
