Construction of survival-related co-expression modules and identification of potential prognostic biomarkers of osteosarcoma using WGCNA

Yiying Bian; Jintao Huang; Ziliang Zeng; Hao Yao; Jian Tu; Bo Wang; Yutong Zou; Xianbiao Xie; Jingnan Shen

doi:10.21037/atm-22-399

Construction of survival-related co-expression modules and identification of potential prognostic biomarkers of osteosarcoma using WGCNA

Ann Transl Med. 2022 Mar;10(6):296. doi: 10.21037/atm-22-399.

Authors

Yiying Bian¹, Jintao Huang², Ziliang Zeng³, Hao Yao¹, Jian Tu¹, Bo Wang¹, Yutong Zou¹, Xianbiao Xie¹, Jingnan Shen¹

Affiliations

¹ Department of Musculoskeletal Oncology Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
² Department of Medical Affairs, OrigiMed Co., Ltd, Shanghai, China.
³ Department of Orthopaedics, Sun Yat-sen Memorial Hospital, Guangzhou, China.

Abstract

Background: Osteosarcoma (OS) is a primary malignant bone tumor. Patients with different immune characteristics respond differently to chemotherapy and have a lower chance of survival. The potential pathogenesis and therapeutic targets of OS must be investigated further.

Methods: OS expression profile data and clinical information were downloaded from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and the Gene Expression Omnibus (GEO) databases. The immune-related gene set was obtained from the ImmPort database, and the immune-related gene expression profiles were used for non-negative matrix factorization (NMF) cluster analysis of patients in the 2 databases to find the best clustering number. In the TARGET database, OS patients were classified into low-risk and high-risk groups based on the differences in their survival rates. Weighted correlation network analysis (WGCNA) was applied to the low-risk and high-risk groups to determine the module with the lowest conservatism in order to differentiate the prognosis of the 2 groups.

Results: A total of 500 key genes associated with poor prognosis were identified. Gene Ontology (GO) enrichment analysis revealed that the biological processes of these genes were primarily focused on the regulation of small guanosine triphosphatase (GTPase) mediated signal transduction, collagen-containing extracellular matrix, and Rho GTPase binding. A random survival forest identified EPHB3, TEAD1, and KRR1P1 as key genes. Their expression level was linked to overall survival. We discovered that the core genes were associated to immune cell infiltration. Simultaneously, paired survival analysis of two genes revealed differences in survival. We also reverse-predicted the main genes and developed their competitive endogenous RNA (ceRNA) network. Finally, utilizing the CellMiner database, we observed that the genes TEAD1 and EPHB3 were connected to drug sensitivity.

Conclusions: In this study, we identified the modules and key genes related to the poor prognosis of OS patients by using WGCNA, and verified their impact on the prognosis of OS patients and their role in the immune microenvironment of OS. In addition, targeted gene related antitumor drugs were screened out. The discoveries may lead to novel molecular targets and treatment methods for OS patients.

Keywords: Osteosarcoma (OS); weighted gene co-expression network analysis (WGCNA); gene.