Six immune-related promising biomarkers may promote hepatocellular carcinoma prognosis: a bioinformatics analysis and experimental validation

Xia-Hui Lin; Dong-Ping Li; Zhi-Yong Liu; Si Zhang; Wen-Qing Tang; Rong-Xin Chen; Shu-Qiang Weng; Yu-Jen Tseng; Ru-Yi Xue; Ling Dong

doi:10.1186/s12935-023-02888-9

Six immune-related promising biomarkers may promote hepatocellular carcinoma prognosis: a bioinformatics analysis and experimental validation

Cancer Cell Int. 2023 Mar 23;23(1):52. doi: 10.1186/s12935-023-02888-9.

Authors

Xia-Hui Lin^#^{1

2}, Dong-Ping Li^#^{1

2}, Zhi-Yong Liu^#^{1

2}, Si Zhang³, Wen-Qing Tang^{1

2}, Rong-Xin Chen⁴, Shu-Qiang Weng^{5

6}, Yu-Jen Tseng⁷, Ru-Yi Xue^{8

9}, Ling Dong^{10

11}

Affiliations

¹ Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
² Shanghai Institute of Liver Disease, Shanghai, 200032, China.
³ Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
⁴ Key Laboratory of Carcinogenesis and Cancer Invasion, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
⁵ Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. weng.shuqiang@zs-hospital.sh.cn.
⁶ Shanghai Institute of Liver Disease, Shanghai, 200032, China. weng.shuqiang@zs-hospital.sh.cn.
⁷ Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China. dianatseng14@163.com.
⁸ Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. xue.ruyi@zs-hospital.sh.cn.
⁹ Shanghai Institute of Liver Disease, Shanghai, 200032, China. xue.ruyi@zs-hospital.sh.cn.
¹⁰ Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. dong.ling@zs-hospital.sh.cn.
¹¹ Shanghai Institute of Liver Disease, Shanghai, 200032, China. dong.ling@zs-hospital.sh.cn.

^# Contributed equally.

Abstract

Background: Abnormal miRNA and mRNA expression and dysregulated immune microenvironment have been found to frequently induce the progression of hepatocellular carcinoma (HCC) in recent reports. In particular, the immune-related competing endogenous RNAs (ceRNA) mechanism plays a crucial role in HCC progression. However, the underlying mechanisms remain unclear.

Methods: Differentially expressed immune-related genes were obtained from the Immport, GEO, and TCGA databases. The mRNA and protein expression levels in HCC tissues and adjacent normal tissues were confirmed, and we further investigated the methylation levels of these biomarkers to explore their function. Then, the TIMER and TISCH databases were used to assess the relationship between immune infiltration and hub genes. Survival analysis and univariate and multivariate Cox models were used to evaluate the association between hub genes and HCC diagnosis. Hub gene expression was experimentally validated in six HCC cell lines and 15 HCC samples using qRT-PCR and immunohistochemistry. The hub genes were uploaded to DSigDB for drug prediction enrichment analysis.

Results: We identified that patients with abnormal miRNAs (hsa-miR-125b-5p and hsa-miR-21-5p) and their targeted genes (NTF3, PSMD14, CD320, and SORT1) had a worse prognosis. Methylation analysis of miRNA-targeted genes suggested that alteration of methylation levels is also a factor in the induction of tumorigenesis. We also found that the development of HCC progression caused by miRNA-mRNA interactions may be closely correlated with the infiltration of immunocytes. Moreover, the GSEA, GO, and KEGG analysis suggested that several common immune-related biological processes and pathways were related to miRNA-targeted genes. The results of qRT-PCR, immunohistochemistry, and western blotting were consistent with our bioinformatics results, suggesting that abnormal miRNAs and their targeted genes may affect HCC progression.

Conclusions: Briefly, our study systematically describes the mechanisms of miRNA-mRNA interactions in HCC and predicts promising biomarkers that are associated with immune filtration for HCC progression.

Keywords: Competing endogenous RNA; Hepatocellular carcinoma; Immune gene signature; Prognosis.

Abstract

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