Identiﬁcation of immune-related genes for Hepatocellular Carcinoma: a study based on TCGA data
1Department of General Surgery, People’s Hospital of Henan University of Chinese Medicine, 450003 Henan Province, P. R. China
2Department of General Surgery, The ﬁrst Clinical College of Zhengzhou University, Zhengzhou City, 450003 Henan Province, P. R. China
DOI: 10.31083/jomh.2021.028 Vol.17,Issue 2,April 2021 pp.101-113
Published: 08 April 2021
Background and objective: Hepatocellular Carcinoma (HCC) is frequently diagnosed at the advanced stage and current treatment methods are marginally effective. The immune system is critical for the development of HCC. However, the interplay between the immune system and HCC is not well illustrated. Hence, the aim of our work was to investigate the relationship between HCC and the abnormal immune gene expression to study the potential mechanism.
Material and methods: We downloaded RNA-seq data from TCGA database, identiﬁed differentially expressed genes (DEGs) using the edgeR package, and overlapped DEGs and immune-related genes from the InnateDB website to obtain immune-related DEGs. After survival analysis, the immune-related DEGs that were signiﬁcantly related to prognosis were analyzed by the STRING tool to construct PPI network. The genes in two signiﬁcant PPI network modules identiﬁed by MCODE plugin were investigated by functional enrichment analysis and tumor-inﬁltration analysis.
Results: 68 immune-related DEGs were found to be signiﬁcantly associated with prognosis in HCC, and then a PPI network was constructed. The genes in two signiﬁcant PPI network modules were enriched in 31 biological processes of GO (e.g. regulation of complement activation, extracellular matrix disassembly) and 12 KEGG pathways (e.g. complement and coagulation cascades, cell cycle, proteoglycans in cancer), which were highly involved in HCC. Furthermore, we obtained 7 genes whoes expressions were signiﬁcantly associated with immune inﬁltration levels, including E2F1, PLK1, MMP9, CDKN2A, BIRC5, CCNA2 and DCN, and 8 genes whoes copy number variations were signiﬁcantly related to immune cell inﬁltrations, including C8A, C8B, E2F1, C6, C7, BIRC5, CCNA2 and CFB.
Conclusions: These ﬁndings contribute to understand the mechanism of HCC and provide a direction for further research on the immunotherapy of HCC.
Hepatocellular Carcinoma; Immune cells; Immunotherapy; TCGA; GO; KEGG
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