Construction and validation of somatic mutation-derived long non-coding RNAs signatures of genomic instability to predict prognosis of hepatocellular carcinoma

Bo-Tao Duan; Xue-Kai Zhao; Yang-Yang Cui; De-Zheng Liu; Lin Wang; Lei Zhou; Xing-Yuan Zhang

doi:10.4240/wjgs.v16.i3.842

Construction and validation of somatic mutation-derived long non-coding RNAs signatures of genomic instability to predict prognosis of hepatocellular carcinoma

World J Gastrointest Surg. 2024 Mar 27;16(3):842-859. doi: 10.4240/wjgs.v16.i3.842.

Authors

Bo-Tao Duan¹, Xue-Kai Zhao¹, Yang-Yang Cui¹, De-Zheng Liu¹, Lin Wang², Lei Zhou³, Xing-Yuan Zhang¹

Affiliations

¹ Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China.
² Department of Ophthalmology, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China.
³ Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China. [email protected].

Abstract

Background: Long non-coding RNAs (LncRNAs) have been found to be a potential prognostic factor for cancers, including hepatocellular carcinoma (HCC). Some LncRNAs have been confirmed as potential indicators to quantify genomic instability (GI). Nevertheless, GI-LncRNAs remain largely unexplored. This study established a GI-derived LncRNA signature (GILncSig) that can predict the prognosis of HCC patients.

Aim: To establish a GILncSig that can predict the prognosis of HCC patients.

Methods: Identification of GI-LncRNAs was conducted by combining LncRNA expression and somatic mutation profiles. The GI-LncRNAs were then analyzed for functional enrichment. The GILncSig was established in the training set by Cox regression analysis, and its predictive ability was verified in the testing set and TCGA set. In addition, we explored the effects of the GILncSig and TP53 on prognosis.

Results: A total of 88 GI-LncRNAs were found, and functional enrichment analysis showed that their functions were mainly involved in small molecule metabolism and GI. The GILncSig was constructed by 5 LncRNAs (miR210HG, AC016735.1, AC116351.1, AC010643.1, LUCAT1). In the training set, the prognosis of high-risk patients was significantly worse than that of low-risk patients, and similar results were verified in the testing set and TCGA set. Multivariate Cox regression analysis and stratified analysis confirmed that the GILncSig could be used as an independent prognostic factor. Receiver operating characteristic curve analysis of the GILncSig showed that the area under the curve (0.773) was higher than the two LncRNA signatures published recently. Furthermore, the GILncSig may have a better predictive performance than TP53 mutation status alone.

Conclusion: We established a GILncSig that can predict the prognosis of HCC patients, which will help to guide prognostic evaluation and treatment decisions.

Keywords: Diagnosis; Genomic instability; Hepatocellular carcinoma; Long noncoding RNA; Prognosis.