Novel miRNA signature for predicting the stage of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer deaths worldwide. Recently, microRNAs (miRNAs) are reported to be altered and act as potential biomarkers in various cancers. However, miRNA biomarkers for predicting the stage of HCC are limitedly discovered. Hence, we sought to identify a novel miRNA signature associated with cancer stage in HCC. We proposed a support vector machine (SVM)-based cancer stage prediction method, SVM-HCC, which uses an inheritable bi-objective combinatorial genetic algorithm for selecting a minimal set of miRNA biomarkers while maximizing the accuracy of predicting the early and advanced stages of HCC. SVM-HCC identified a 23-miRNA signature that is associated with cancer stages in patients with HCC and achieved a 10-fold cross-validation accuracy, sensitivity, specificity, Matthews correlation coefficient, and area under the receiver operating characteristic curve (AUC) of 92.59%, 0.98, 0.74, 0.80, and 0.86, respectively; and test accuracy and test AUC of 74.28% and 0.73, respectively. We prioritized the miRNAs in the signature based on their contributions to predictive performance, and validated the prognostic power of the prioritized miRNAs using Kaplan–Meier survival curves. The results showed that seven miRNAs were significantly associated with prognosis in HCC patients. Correlation analysis of the miRNA signature and its co-expressed miRNAs revealed that hsa-let-7i and its 13 co-expressed miRNAs are significantly involved in the hepatitis B pathway. In clinical practice, a prediction model using the identified 23-miRNA signature could be valuable for early-stage detection, and could also help to develop miRNA-based therapeutic strategies for HCC.