Immunological Value of Prognostic Signature Based on Cancer Stem Cell Characteristics in Hepatocellular Carcinoma

Background: Liver cancer stem cells, characterized by self-renewal and initiating cancer cells, were decisive drivers of progression and therapeutic resistance in hepatocellular carcinoma (HCC). However, a comprehensive understanding of HCC stemness has not been identified. Methods: RNA sequencing information, corresponding clinical annotation, and mutation data of HCC were downloaded from The Cancer Genome Atlas-LIHC project. Two stemness indices, mRNA expression-based stemness index (mRNAsi) and epigenetically regulated-mRNAsi, were used to comprehensively analyze HCC stemness. Estimation of Stromal and Immune Cells in Malignant Tumors using Expression Data and single-sample gene-set enrichment analysis algorithm were performed to characterize the context of tumor immune microenvironment (TIME). Next, differentially expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) were employed to identify significant mRNAsi-related modules with hub genes. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment pathways were analyzed to functionally annotate these key genes. The least absolute shrinkage and selection operator (LASSO) Cox regression analysis was performed to establish a prognostic signature. Kaplan–Meier survival curves and receiver operating characteristic (ROC) analysis were applied for prognostic value validation. Seven algorithms (XCELL, TIMER, QUANTISEQ, MCPcounter, EPIC, CIBERSORT, and CIBERSORT-ABS) were utilized to draw the landscape of TIME. Finally, the mutation data were analyzed by employing “maftools” package. Results: mRNAsi was significantly elevated in HCC samples. mRNAsi escalated as tumor grade increased, with poor prognosis presenting the higher stemness index. The stemness-related (greenyellow) modules with 175 hub genes were screened based on DEGs and WGCNA. A prognostic signature was established using LASSO analysis of prognostic hub genes to classify samples into two risk subgroups, which exhibited good prognostic performance. Additionally, prognostic risk-clinical nomogram was drawn to estimate risk quantitatively. Moreover, risk score was significantly associated with contexture of TIME and immunotherapeutic targets. Finally, potential interaction between risk score with tumor mutation burden (TMB) was elucidated. Conclusion: This work comprehensively elucidated that stemness characteristics served as a crucial player in clinical outcome, complexity of TIME, and immunotherapeutic prediction from both mRNAsi and mRNA level. Quantitative identification of stemness characteristics in individual tumor will contribute into predicting clinical outcome, mapping landscape of TIME further optimizing precision immunotherapy.