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Archive > Volume 27 Issue 7 > 2020,27(7):781-786. DOI:10.3872/j.issn.1007-385X.2020.07.010 Prev Next
Clinical Research
Identification and characteristic analysis of enhancer-miRNA regulatory pairs in hepatic carcinoma
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Abstract:
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.
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Project Supported:
Project supported by the China Mega-Project on Infectious Disease Prevention (No. 2018ZX10101-003-001-008)
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