A four-methylated LncRNA signature predicts survival of osteosarcoma patients based on machine learning

• Published in: Genomics (San Diego, Calif.) Calif.), 2021-01, Vol.113 (1), p.785-794
• Main Authors: Deng, Yajun, Yuan, Wenhua, Ren, Enhui, Wu, Zuolong, Zhang, Guangzhi, Xie, Qiqi
• Format: Article
• Language: English
• Subjects: Biomarker; Biomarkers, Tumor - genetics; DNA Methylation; Humans; LncRNA; Machine Learning; Osteosarcoma; Osteosarcoma - genetics; Osteosarcoma - pathology; Prognosis; RNA, Long Noncoding - genetics
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2020.10.010

Risk stratification using prognostic markers facilitates clinical decision-making in treatment of osteosarcoma (OS). In this study, we performed a comprehensive analysis of DNA methylation and transcriptome data from OS patients to establish an optimal methylated lncRNA signature for determining OS patient prognosis. The original OS datasets were downloaded from the the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Univariate, Lasso, and machine learning algorithm-iterative Lasso Cox regression analyses were used to establish a methylated lncRNA signature that significantly correlated with OS patient survival. The validity of this signature was verified by the Kaplan-Meier curves, Receiver Operating Characteristic (ROC) curves. We established a four-methylated lncRNA signature that can predict OS patient survival (verified in independent cohort [GSE39055]). Kaplan-Meier analysis showed that the signature can distinguish between the survival of high- and low-risk patients. ROC analysis corroborated this finding and revealed that the signature had higher prediction accuracy than known biomarkers. Kaplan-Meier analysis of the clinical subgroup showed that the signature's prognostic ability was independent of clinicopathological factors. The four-methylated lncRNA signature is an independent prognostic biomarker of OS. •A four-methylated lncRNA signature prognostic model was established for osteosarcoma based on machine learning.•The signature can distinguish between the survival of high- and low-risk patients.•The signature had higher prediction accuracy than known biomarkers.•Our four-methylated lncRNA signature's prognostic ability was independent of clinicopathological factors.