Identifying genes associated with Sorafenib resistance in hepatocellular carcinoma to develop risk model

Hepatocellular carcinoma (HCC) poses a considerable global health challenge, notably due to the resistance to sorafenib therapy, which significantly impedes effective treatment strategies. This study aimed to identify potential resistance-associated genes and develop a robust prognostic model to predict patient outcomes.

We utilized transcriptomic data from the gene expression omnibus (GEO) database, focusing on sorafenib-resistant Huh7 and MHCC97H cell lines (GSE94550 and GSE176151), and integrated expression, mutation, and clinical data from the cancer genome atlas (TCGA) and international cancer genome consortium (ICGC) databases. Single-cell RNA sequencing data (GSE149614) were processed with the Seurat and Harmony R packages for quality control and integration. Differential gene expression analysis, consensus clustering, and principal component analysis were performed to identify significant genes and stratify patients based on prognostic outcomes.

The analysis revealed 305 potential resistance-associated genes, with a seven-gene (ANAPC13, NCAPD2, KIF2C, CDK5RAP2, MANBA, PPAT, and LPCAT1) risk model demonstrating significant prognostic capability, indicated by area under curve values of 0.824, 0.746, and 0.717 for 1, 3, and 5-year survival predictions, respectively. Notably, immune cell infiltration analyses highlighted significant correlations between risk scores and specific immune cell types, suggesting potential therapeutic targets. Drug sensitivity analysis further identified various compounds with lower IC50 values in high-risk groups. To facilitate clinical application, a nomogram plot was designed.

This study provides a comprehensive framework for understanding sorafenib resistance in HCC, alongside a validated prognostic model that holds potential for clinical application.