肝癌增强子-miRNA调控作用对的识别与特征分析

Identification and characteristic analysis of enhancer-miRNA regulatory pairs in hepatic carcinoma

目的:探讨肝癌和正常肝组织中增强子与miRNA形成的调控关系及调控miRNA的增强子的特征,筛选出由增强子调控的差异表达miRNA并探讨其与肝癌治疗靶点的相关性。方法:基于TCGA与FANTOM5数据库,对肝癌和正常肝组织中共417个样本的增强子与miRNA进行共表达与3D基因组分析得到调控关系。通过ENCODE数据库中肝癌与正常肝组织的组蛋白修饰与转录因子的ChIP-seq数据分析调控miRNA的增强子上信号值的差异。筛选由增强子调控的差异表达的miRNA,并对患者的生存期与治疗靶点进行相关性分析。结果:在肝癌与正常肝组织中分别识别增强子-miRNA作用对93对和40对。ChIP-seq数据比对分析发现,肝癌中组蛋白修饰H3K27ac、H3K4me1和H3K4me3信号在调控miRNA增强子区域显著高于不调控miRNA的增强子区域(|rho|>0.3,P<0.05);多种转录因子在肝癌相关增强子中的富集显著低于正常肝组织(|rho|>0.3,P<0.05)。对增强子调控的miRNA进行差异表达分析,识别了6个与肝癌患者生存相关miRNA(hsa-miR-4664、hsa-miR-5003、hsa-miR-1915、hsa-miR-3619、hsa-miR-4745、hsa-miR-6728),发现这些miRNA与87个用于靶向治疗的基因以及8个免疫检查点基因显著相关(|rho|>0.1,FDR<0.05)。结论:成功在肝癌中识别出增强子-miRNA调控作用对与调控miRNA的增强子的特征,并筛选出由增强子调控的与肝癌患者生存和治疗靶点相关的miRNA,为后续深入开展肝癌的基础与临床研究提供了参考依据。

Objective:To explore the regulatory relationship between enhancer and miRNA and the characteristics of the enhancers that regulate miRNA in hepatic carcinoma and normal hepatic tissues,and to screen the differentially expressed miRNAs regulated by enhancers as well as their association with the treatment targets in liver cancer.Methods:Based on the TCGA and FANTOM5 databases,Co-expression and 3D genomic analysis were performed on 417 samples of enhancers and miRNAs in liver cancer and normal liver tissues.The difference in signal value of the enhancer that regulates miRNA was analyzed by ChIP-seq data of histone modification and transcription factor in liver cancer and normal liver tissues in ENCODE database.The differentially expressed miRNAs regulated by enhancers were screened out,and the correlation analysis was performed on the patient's survival and treatment targets.Results:93 and 40 pairs of enhancer-miRNA were identified in liver cancer and normal liver tissues,respectively.ChIP-seq data comparison analysis found that the signal of H3K27ac,H3K4me1 and sH3K4me3 histone modification in the region of enhancers regulating miRNA was significantly higher than that in the region of enhancers not regulating miRNA(|rho|>0.3,P<0.05).Moreover,the enrichment of multiple transcription factors in liver cancer-related enhancers was significantly lower than that in normal liver tissue-realted enhancers(|rho|>0.3,P<0.05).Differential expression analysis of enhancer-regulated miRNAs identified 6 miRNAs related to the survival of liver cancer patients(hsa-miR-4664,hsa-miR-5003,hsa-miR-1915,hsa-miR-3619,hsa-miR-4745,hsa-miR-6728),and found that these miRNAs were significantly associated with 87 genes for targeted therapy and 8 tumor immune checkpoint genes(|rho|>0.1,FDR<0.05).Conclusion:The enhancer-miRNA regulatory pairs and the characteristics of the enhancer that regulates miRNA were successfully identified in liver cancer.The miRNAs regulated by enhancers and related to the therapeutic targets and survival of patients with liver cancer were also screened out.It provides a valuable preliminary basis for future in-depth basic and clinical research in hepatic carcinoma.