Objective: To explore the driving gene of hepatocellular carcinoma (HCC) occurrence and progression and its potential as new therapeutic target of HCC.
Methods: The transcriptome and genomic data of 858 HCC tissues and 493 adjacent tissues were obtained from TCGA, GEO, and ICGC databases. Gene Set Enrichment Analysis (GSEA) identified EHHADH (encoding enoyl-CoA hydratase/L-3-hydroxyacyl-CoA dehydrogenase) as the hub gene in the significantly enriched differential pathways in HCC. The downregulation of EHHADH expression at the transcriptome level was found to correlate with TP53 mutation based on analysis of the TCGA- HCC dataset, and the mechanism by which TP53 mutation caused EHHADH downregulation was explored through correlation analysis. Analysis of the data from the Metascape database suggested that EHHADH was strongly correlated with the ferroptosis signaling pathway in HCC progression, and to verify this result, immunohistochemical staining was used to examine EHHADH expression in 30 HCC tissues and paired adjacent tissues.
Results: All the 3 HCC datasets showed signficnatly lowered EHHADH expression in HCC tissues as compared with the adjacent tissues (P < 0.05) with a close correlation with the degree of hepatocyte de-differentiation (P < 0.01). The somatic landscape of HCC cohort in TCGA dataset showed that HCC patients had the highest genomic TP53 mutation rate. The transcriptomic level of PPARGC1A, the upstream gene of EHHADH, was significantly downregulated in HCC patients with TP53 mutation as compared with those without the mutation (P < 0.05), and was significantly correlated with EHHADH expression level. GO and KEGG enrichment analyses showed that EHHADH expression was significantly correlated with abnormal fatty acid metabolism in HCC. The immunohistochemical results showd that the expression level of EHHADH in HCC tissues was down-regulated, and its expression level was related to the degree of hepatocytes de-differentiation and the process of ferroptosis.
Conclusion: TP53 mutations may induce abnormal expression of PPARGC1A to cause downregulation of EHHADH expression in HCC. The low expression of EHHADH is closely associated with aggravation of de-differentiation and ferroptosis escape in HCC tissues, suggesting the potential of EHHADH as a therapeutic target for HCC.
目的: 基于多数据库数据探索肝细胞癌（HCC）发生发展的驱动基因并挖掘HCC治疗的新生物靶点。
方法: 采用从TCGA、GEO和ICGC数据库中获取的858例HCC组织数据与493例癌旁组织数据（共1351例转录组和基因组数据），运用GSEA筛选HCC与癌旁的差异通路，进而筛选差异通路中显著富集的基因，获得Hub基因3-hydroxyacyl CoA脱氢酶（EHHADH）。基于TCGA的HCC数据集分析与EHHADH转录组水平下调相关的基因突变，发现TP53突变最显著相关。利用相关性分析探究TP53突变导致EHHADH表达下调的机制。基于Metascape数据库预测EHHADH参与HCC发展的信号通路，发现与铁死亡信号通路显著相关。对30例HCC癌组织及配对的癌旁正常组织进行免疫组化染色，验证EHHADH的表达情况。
结果: 三个HCC数据集均显示EHHADH在癌组织中相对于癌旁组织显著低表达（P < 0.05），且和肝细胞去分化程度显著相关（P < 0.01）。TCGA的HCC数据集体细胞突变景观分析显示HCC患者基因组中TP53突变率比例最高。EHHADH上游基因PPARGC1A转录组水平在TP53突变的HCC患者组中较未突变组显著下调（P < 0.05），并与EHHADH表达水平相关。GO和KEGG富集分析结果显示EHHADH参与到肿瘤脂肪酸代谢通路中。免疫组化结果验证HCC组织中EHHADH表达水平下调，且其表达水平与肝细胞去分化程度及铁死亡进程相关。
结论: HCC组织中TP53突变可能诱导EHHADH上游基因PPARGC1A表达异常从而下调EHHADH表达。EHHADH在HCC癌组织中低表达与HCC癌组织的去分化程度加重及出现铁死亡逃逸现象密不可分，有可能成为HCC潜在治疗靶点。
Keywords: TP53 mutation; de-differentiation; enoyl-CoA hydratase/L-3-hydroxyacyl-CoA dehydrogenase; ferroptosis; hepatocellular carcinoma.