A Somatic Mutation-Derived LncRNA Signature of Genomic Instability Predicts Prognosis for Patients With Liver Cancer

Cheng Guo; Jie Zhou; Boyu Ma; Rui Wang; Yanli Ge; Zhe Wang; Bing Ji; Wei Wang; Junjie Zhang; Zhirong Wang

doi:10.3389/fsurg.2021.724792

A Somatic Mutation-Derived LncRNA Signature of Genomic Instability Predicts Prognosis for Patients With Liver Cancer

Front Surg. 2021 Aug 24:8:724792. doi: 10.3389/fsurg.2021.724792. eCollection 2021.

Authors

Cheng Guo¹, Jie Zhou¹, Boyu Ma¹, Rui Wang¹, Yanli Ge¹, Zhe Wang¹, Bing Ji¹, Wei Wang¹, Junjie Zhang¹, Zhirong Wang¹

Affiliation

¹ Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.

Abstract

Background: Genomic instability is considered as one of the hallmarks of hepatocellular carcinoma (HCC) and poses a significant challenge to the clinical treatment. The emerging evidence has revealed the roles of long non-coding RNAs (lncRNAs) in the maintenance of genomic instability. This study is aimed to develop a genomic instability-related lncRNA signature for determining HCC prognosis and the suitability of patients for immunotherapy. Methods: In this study, data related to transcriptome profiling, clinical features, and the somatic mutations of patients with HCC were downloaded from The Cancer Genomic Atlas (TCGA). Bioinformatics analysis was performed to identify and construct a somatic mutation-derived genomic instability-associated lncRNA signature (GILncSig). Single-sample gene set enrichment analysis (ssGSEA) was applied to estimate the levels of immune cell infiltration. A nomogram was constructed, and calibration was performed to assess the effectiveness of the model. Results: In the study, seven genomic instability-related lncRNAs were identified and used to define a prognostic signature. Patients with HCC were stratified into high- and low-risk groups with significant differences in the survival (median survival time = 1.489, 1.748 year; p = 0.006) based on the optimal cutoff value (risk score = 1.010) of the risk score in the training group. In addition, GILncSig was demonstrated to be an independent risk factor for the patients with HCC when compared to the clinical parameters (p < 0.001). According to the receiver operating characteristic (ROC) curve, nomogram, and calibration plot, the signature could predict the survival rate for the patients with HCC in the 1st, 3rd, and 5th years. Furthermore, ssGSEA revealed the potential of the signature in guiding decisions for administering clinical treatment. Conclusions: In this study, we developed a novel prognostic model based on the somatic mutation-derived lncRNAs and validated it using an internal dataset. The independence of the GILncSig was estimated using univariate and follow-up multivariate analyses. Immunologic analysis was used to evaluate the complex factors involved in the HCC progression.

Keywords: genomic instability; hepatocellular carcinoma; immune infiltration; long non-coding RNA; prognosis.