12 Survival-related differentially expressed genes based on the TARGET-osteosarcoma database. Issue 19 (October 2021)

• Record Type: Journal Article
• Authors: Rothzerg, Emel; Xu, Jiake; Wood, David; Kõks, Sulev
• Is Part Of: Experimental biology and medicine. Volume 246:Issue 19(2021)
• Page Start: 2072
• Page End: 2081
• Publication Date: 2021-10
• Subjects: Osteosarcoma -- sarcoma -- TARGET -- RNA sequencing -- survival analysis -- differential gene expression; Physiology -- Periodicals; Biology, Experimental -- Periodicals; Medicine, Experimental -- Periodicals; 610.72
• DOI: 10.1177/15353702211007410
• Languages: English
• ISSNs: 1535-3702

Abstract

The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) project aims to determine molecular changes that drive childhood cancers, including osteosarcoma. The main purpose of the program is to use the open-source database to develop novel, effective, and less toxic therapies. We downloaded TARGET-OS RNA-Sequencing data through R studio and merged the mRNA expression of genes with clinical information (vital status, survival time and gender). Further, we analyzed differential gene expressions between dead and alive patients based on TARGET-OS project. By this study, we found 5758 differentially expressed genes between deceased and alive patients with a false discovery rate below 0.05; 4469 genes were upregulated in deceased patients compared to alive, whereas 1289 genes were downregulated. The survival-related genes were obtained using Kaplan–Meier survival analysis and Cox univariate regression (KM < 0.05 and Cox P -value < 0.05). Out of 5758 differentially expressed genes, only 217 have been associated with overall survival. Eight survival-related downregulated genes ( ERCC4, CLUAP1, CTNNBIP1, GCA, RAB40C, SIRPA, USP11, and TCN2 ) and four survival-related upregulated genes ( MUC1, COL13A1, JAG2 and KAZALD1 ) were selected for further analysis as potential independent prognostic candidate genes. This study may help to discover novel prognostic markers and potential therapeutic targets for osteosarcoma.