Identification of potential key genes associated with osteosarcoma based on integrated bioinformatics analyses

Abstract

Due to high rates of metastasis and poor clinical outcomes for patients, it is important to study the pathomechanisms of osteosarcoma. However, due to the fact that osteosarcoma shows significant interindividual variation and high heterogeneity, the identification of differentially expressed genes (DEGs) at the population level cannot answer many important questions related to osteosarcoma tumorigenesis. Therefore, a new strategy to identify dysregulated genes in osteosarcoma samples is required. The aim of this study was to improve our understanding of osteosarcoma pathogenesis by identifying genes with universal aberrant expression in osteosarcoma samples. Because the relative expression ordering of genes is stable in normal bone tissues but is disrupted in osteosarcoma tissues, we used the RankComp algorithm to identify DEGs in normal and osteosarcoma tissue samples. We then calculated the dysregulation frequency for each gene. Genes with deregulation frequencies above 80% were deemed to be universal DEGs. Next, coexpression, pathway enrichment, and protein-protein interaction network analyses were performed to characterize the functions of these genes. From 188 samples of osteosarcoma obtained from four datasets measured on different platforms, 51 universal DEGs were identified, including 4 universally upregulated genes and 47 universally downregulated genes. Genes that were differentially coexpressed with these universal DEGs were found to be enriched in 46 cancer-related pathways. In addition, functional and network analyses showed that genes with high dysregulation frequencies were involved in cancer-related functions. Thus, the commonly aberrant genes identified in osteosarcoma tissues may be important targets for osteosarcoma diagnosis and therapy. K E Y W O R D S differentially expressed gene (DEGs), individualized analysis, osteosarcoma, relative expression ordering J Cell Biochem. 2019;120:13554-13561. wileyonlinelibrary.com/journal/jcb 13554 |Abbreviations: DEGs, differentially expressed genes; GEO, the Gene Expression Omnibus; GO, gene ontology; KEGG, kyoto encyclopedia of genes and genomes; PPI, protein-protein interaction; REO, relative expression ordering; STRING, search tool for the retrieval of interacting genes.Hu and Cheng have contributed equally to this study.

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