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Yan J, Ye G, Shao Y, Zhou H. Identification of novel prognostic biomarkers in the TF-enhancer-target regulatory network in hepatocellular carcinoma and immune infiltration analysis. Front Genet 2023; 14:1158341. [PMID: 37065474 PMCID: PMC10090374 DOI: 10.3389/fgene.2023.1158341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) remains notorious for its high malignancy, poor prognosis and high mortality. The exploration of novel therapeutic agents for HCC has remained challenging due to its complex aetiology. Therefore, it is necessary to elucidate the pathogenesis and mechanism of HCC for clinical intervention.Methods: We collected data from several public data portals and systematically analysed the association between transcription factors (TFs), eRNA-associated enhancers and downstream targets. We next filtered the prognostic genes and established a novel prognosis-related nomogram model. Moreover, we explored the potential mechanisms of the identified prognostic genes. The expression level was validated by several ways.Results: We first constructed a significant TF-enhancer-target regulatory network and identified DAPK1 as a coregulatory differentially expressed prognosis-related gene. We combined common clinicopathological factors and built a prognostic nomogram model for HCC. We found that our regulatory network was correlated with the processes of synthesizing various substances. Moreover, we explored the role of DAPK1 in HCC and found that it was associated with immune cell infiltration and DNA methylation. Several immunostimulators and targeting drugs could be promising immune therapy targets. The tumor immune microenvironment was analyzed. Finally, the lower DAPK1 expression in HCC was validated via the GEO database, UALCAN cohort, and qRT-PCR.Conclusion: In conclusion, we established a significant TF-enhancer-target regulatory network and identified downregulated DAPK1 as an important prognostic and diagnostic gene in HCC. Its potential biological functions and mechanisms were annotated using bioinformatics tools.
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Affiliation(s)
- Jianing Yan
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, China
- Department of Gastroenterology, Institute of Digestive Disease of Ningbo University, Ningbo, China
| | - Guoliang Ye
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, China
- Department of Gastroenterology, Institute of Digestive Disease of Ningbo University, Ningbo, China
| | - Yongfu Shao
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, China
- Department of Gastroenterology, Institute of Digestive Disease of Ningbo University, Ningbo, China
- *Correspondence: Yongfu Shao,
| | - Hanxuan Zhou
- Department of Pharmacy, Yinzhou Integrated TCM and Western Medicine Hospital, Ningbo, China
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