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Three-Dimensional Bone Extracellular Matrix Model for Osteosarcoma

Three-Dimensional Bone Extracellular Matrix Model for Osteosarcoma

Published on: April 12, 2019

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

Bi-Yong Deng, Ying-Qi Hua¹, Zheng-Dong Cai

¹Department of Orthopedic Surgery, Shanghai Tenth people's Hospital, Tongji University School of Medicine, No,301 Middle Yan-Chang Road, Zha-Bei District, Shanghai 200072, China. huayingqihyq@gmail.com.

European Journal of Medical Research

|December 17, 2013

Abstract

Background:

The aim of this study was to establish an osteosarcoma (OS) associated protein-protein interaction network and explore the pathogenesis of osteosarcoma.

Methods:

The 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.

Results:

Compared 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.

Conclusions:

The hub genes from metastatic OS samples are not only bio-markers of OS, but also help to improve therapies for OS.

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