Implications of Stemness Features in 1059 Hepatocellular Carcinoma Patients from Five Cohorts: Prognosis, Treatment Response, and Identification of Potential Compounds

SIMPLE SUMMARY: Cancer stemness has been reported to drive hepatocellular carcinoma (HCC) tumorigenesis and treatment resistance. However, comprehensive interpretations of transcriptomic stemness features in HCC patients have not been conducted in multiple cohorts. Our aim was to interpret clinical and therapeutic implications of transcriptional stemness features and explore potential compounds for HCC treatment. We found that transcriptional stemness indexes (mRNAsi) were independently associated with worse HCC prognosis. The HCC stemness risk model (HSRM) developed in this study significantly predicted prognosis and treatment response in various HCC cohorts. Analysis of two stemness subtypes suggested several liver-specific metabolic pathways, and mutations of TP53 and RB1 were associated with HCC transcriptional stemness. Moreover, we also identified potential compounds that target HCC transcriptional stemness. Our findings comprehensively characterized transcriptional stemness as a risk factor in HCC progression and treatment. ABSTRACT: Cancer stemness has been reported to drive hepatocellular carcinoma (HCC) tumorigenesis and treatment resistance. In this study, five HCC cohorts with 1059 patients were collected to calculate transcriptional stemness indexes (mRNAsi) by the one-class logistic regression machine learning algorithm. In the TCGA-LIHC cohort, we found mRNAsi was an independent prognostic factor, and 626 mRNAsi-related genes were identified by Spearman correlation analysis. The HCC stemness risk model (HSRM) was trained in the TCGA-LIHC cohort and significantly discriminated overall survival in four independent cohorts. HSRM was also significantly associated with transarterial chemoembolization treatment response and rapid tumor growth in HCC patients. Consensus clustering was conducted based on mRNAsi-related genes to divide 1059 patients into two stemness subtypes. On gene set variation analysis, samples of subtype I were found enriched with pathways such as DNA replication and cell cycle, while several liver-specific metabolic pathways were inhibited in these samples. Somatic mutation analysis revealed more frequent mutations of TP53 and RB1 in the subtype I samples. In silico analysis suggested topoisomerase, cyclin-dependent kinase, and histone deacetylase as potential targets to inhibit HCC stemness. In vitro assay showed two predicted compounds, Aminopurvalanol-a and NCH-51, effectively suppressed oncosphere formation and impaired viability of HCC cell lines, which may shed new light on HCC treatment.