Establishing an osteosarcoma associated protein-protein interaction network to explore the pathogenesis of osteosarcoma

Abstract

BackgroundThe aim of this study was to establish an osteosarcoma (OS) associated protein-protein interaction network and explore the pathogenesis of osteosarcoma.MethodsThe gene expression profile GSE9508 was downloaded from the Gene Expression Omnibus database, including five samples of non-malignant bone (the control), seven samples for non-metastatic patients (six of which were analyzed in duplicate), and 11 samples for metastatic patients (10 of which were analyzed in duplicate). Differentially expressed genes (DEGs) between osteosarcoma and control samples were identified by packages in R with the threshold of |logFC (fold change)| > 1 and false discovery rate < 0.05. Osprey software was used to construct the interaction network of DEGs, and genes at protein-protein interaction (PPI) nodes with high degrees were identified. The Database for Annotation, Visualization and Integrated Discovery and WebGestalt software were then used to perform functional annotation and pathway enrichment analyses for PPI networks, in which P < 0.05 was considered statistically significant.ResultsCompared to the control samples, the expressions of 42 and 341 genes were altered in non-metastatic OS and metastatic OS samples, respectively. A total of 15 significantly enriched functions were obtained with Gene Ontology analysis (P < 0.05). The DEGs were classified and significantly enriched in three pathways, including the tricarboxylic acid cycle, lysosome and axon guidance. Genes such as HRAS, IDH3A, ATP6ap1, ATP6V0D2, SEMA3F and SEMA3A were involved in the enriched pathways.ConclusionsThe hub genes from metastatic OS samples are not only bio-markers of OS, but also help to improve therapies for OS.

Retraction Note: Establishing an osteosarcoma associated protein-protein interaction network to explore the pathogenesis of osteosarcoma

“…The Publisher and Editor regretfully retract this article [ 1 ] because the peer-review process was inappropriately influenced and compromised. As a result, the scientific integrity of the article cannot be guaranteed.…”

Curcumin may serve an anticancer role in human osteosarcoma cell line U-2 OS by targeting ITPR1

“…Although numerous modern therapies, including surgery, chemotherapy and radiotherapy have been used for treating osteosarcoma, the 5-year survival rate of patients with osteosarcoma is 60–70% ( 3 ). With the improvements in treatment techniques, the mortality rate of osteosarcoma is decreasing at ~1.3% per year ( 4 ). However, the etiology of osteosarcoma is unclear.…”