Potential biomarkers for the prognosis and treatment of HCC immunotherapy

H. Li, Q. He, G.-M. Zhou, W.-J. Wang, P.-P. Shi, Z.-H. Wang

State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China. wangzihao1113@21cn.com

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• Immunology
• Oncology

OBJECTIVE: The liver is a unique organ containing large populations of immune cells. Immunotherapy for liver cancer is a promising yet particularly challenging method. Therefore, it harbors great significance for the identification of immune-related subtypes and the potential therapeutic targets for hepatocellular carcinoma (HCC).

MATERIALS AND METHODS: Firstly, we classified the HCC samples downloaded from the dataset of Cancer Genome Atlas (TCGA) into two clusters based on the immune cell infiltration. Thereafter, we identified the significant module and regulatory factors using the weighted gene co-expression network analysis (WGCNA). The immune competence of the regulatory factors was delineated through the ESTIMATE algorithm, the analysis of the tumor microenvironment, and pan-cancer analysis. In the single-cell RNA sequencing analysis, we further explored the immune competence of regulatory factors. We also collected the potential drugs targeting the regulatory factors. In addition, we constructed lncRNA-miRNA-mRNA interaction regulatory networks. Finally, western blot and quantitative real-time polymerase chain reaction (qRT-PCR) were conducted to verify the protein expression of regulatory genes in HCC cell lines and tissues.

RESULTS: According to the immune cell infiltration, two immune-related subtypes-cluster 1 and cluster 2-were found. Patients in cluster 2 had a more significant immune infiltration than in cluster 1. Afterward, six significant regulatory genes were identified through WGCNA, and the expression in cluster 2 was high in cluster 1. We performed a comprehensive analysis to clarify the immune signature. The results showed that the six genes had significant immunological competence. Moreover, the expression of the six genes was similar to the subtypes’ classification. In the analysis of the prognosis value, patients in cluster 2 had a better prognosis. In addition, the lncRNA in the lncRNA-miRNA-mRNA interaction regulatory networks was located in the nucleus and cytoplasm. In the single-cell RNA sequencing analysis, the six genes were related to the immune cell. We also identified potential drugs for CD6 and CLEC12A, which may provide potential therapeutic drugs. Finally, the regulatory genes were verified in the western blot and quantitative real-time polymerase chain reaction.

CONCLUSIONS: The classification into two clusters based on the immune cell infiltration may provide a promising prospect for HCC through immunotherapy. The six regulatory genes may be potential therapeutic targets in the treatment of HCC.

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