Screening for Metastatic Osteosarcoma Biomarkers with a DNA Microarray

Abstract

Objective: The aim of this study was to screen for possible biomarkers of metastatic osteosarcoma (OS) using a DNA microarray. Methods: We downloaded the gene expression profile GSE49003 from Gene Expression Omnibus database, which included 6 gene chips from metastatic and 6 from non-metastatic OS patients. The R package was used to screen and identify differentially expressed genes (DEGs) between metastatic and non-metastatic OS patients. Then we compared the expression of DEGs in the two groups and sub-grouped into up-regulated and down-regulated, followed by functional enrichment analysis using the DAVID system. Subsequently, we constructed an miRNA-DEG regulatory network with the help of WebGestalt software. Results: A total of 323 DEGs, including 134 up-regulated and 189 down-regulated, were screened out. The up-regulated DEGs were enriched in 14 subcategories and most significantly in cytoskeleton organization, while the down-regulated DEGs were prevalent in 13 subcategories, especially wound healing. In addition, we identified two important miRNAs (miR-202 and miR-9) pivotal for OS metastasis, and their relevant genes, CALD1 and STX1A. Conclusions: MiR-202 and miR-9 are potential key factors affecting the metastasis of OS and CALD1 and STX1A may be possible targets beneficial for the treatment of metastatic OS. However, further experimental studies are needed to confirm our results.

Demethylation of microRNA-142 induced by demethylation agents plays a suppressive role in osteosarcoma cells

“…OS develops from a common mesenchymal stem cell progenitor exhibiting a disruption of normal osteoblast differentiation (2). Although the 5-year survival rate has increased to 60-70%, a significant proportion of patients respond poorly to chemotherapy and are at high risk of relapse or metastasis, even following curative resection (3). The majority of OSs exhibit numerous and highly variable genomic aberrations.…”

Clinicopathologic Features and Prognosis of Osteosarcoma in Turkish Adults

“…Previously 80 to 90 percent of osteosarcoma patients developed metastases despite achieving local tumor control, and died of their disease. As a result of the use of effective chemotherapy the long term survival rates had improved from 10-20% to 60-70% (Eilber et al, 1987;Bielack et al, 2009;Diao et al, 2014). In our patients the 5 year survival rate for non-metastatic patients was 83%.…”

Identification and Functional Analysis of Differentially Expressed Genes Related to Metastatic Osteosarcoma

“…Microarray analysis has been widely used in screening the possible targets for the treatment of metastatic OS (Diao et al, 2013). With the utilization of cDNA microarrays, the transcriptome profile of two OS cell lines has been detected, and 1098 DEGs were identified including 796 functionally characterized genes (Trougakos et al, 2010).…”