Definition of a novel vascular invasion-associated multi-gene signature for predicting survival in patients with hepatocellular carcinoma.

ABSTRACT: The aim of the present study was to identify a vascular invasion-associated gene signature for predicting prognosis in patients with hepatocellular carcinoma (HCC). Using RNA-sequencing data of 292 HCC samples from The Cancer Genome Atlas (TCGA), the present study screened differentially expressed genes (DEGs) between patients with and without vascular invasion. Feature genes were selected from the DEGs by support vector machine (SVM)-based recursive feature elimination (RFE-SVM) algorithm to build a classifier. A multi-gene signature was selected by L1 penalized (LASSO) Cox proportional hazards (PH) regression model from the feature genes selected by the RFE-SVM to develop a prognostic scoring model. TCGA set was defined as the training set and was divided by the gene signature into a high-risk group and a low-risk group. Involvement of the DEGs between the two risk groups in pathways was also investigated. The presence and absence of vascular invasion between patients of training set was 175 DEGs. A classification model of 42 genes performed well in differentiating patients with and without vascular invasion on the training set and the validation set. A 14-gene prognostic model was built that could divide the training set or the validation set into two risk groups with significantly different survival outcomes. A total of 762 DEGs in the two risk groups of the training set were revealed to be significantly associated with a number of signaling pathways. The present study provided a 42-gene classifier for predicting vascular invasion, and identified a vascular invasion-associated 14-gene signature for predicting prognosis in patients with HCC. Several genes and pathways in HCC development are characterized and may be potential therapeutic targets for this type of cancer.

SUBMITTER: Yi B 

PROVIDER: S-EPMC6923904 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature