Zeng Yan-Li, Gao Fei, Zhang Can, Ren Pei-Pei, Ma Li, Wang Xin, Wang Ruzhen, Kang Yi, Li Ke
Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China.
Department of Infectious Diseases, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, P.R. China.
Oncol Lett. 2023 Oct 30;26(6):532. doi: 10.3892/ol.2023.14119. eCollection 2023 Dec.
Liver cancer, including hepatocellular carcinoma (HCC), is a malignant tumor that has high rates of metastasis and mortality worldwide. Upstream transcription factor 1 (USF1) is a canonical transcription factor (TF) and is associated with the pathogenesis of several cancers, but its biological functions and molecular targets in HCC remain unclear. Huh7 cells that overexpress USF1 were used with whole transcriptome profiling through RNA sequencing and chromatin immunoprecipitation (ChIP) sequencing methods to investigate the downstream targets of USF1. Reverse transcription-quantitative PCR was then used to validate the downstream targets. The results showed that USF1 significantly regulates 350 differentially expressed genes (DEGs). The upregulated DEGs were primarily protein-coding genes enriched in immune and inflammation response pathways, while the downregulated DEGs were mainly coding long non-coding (lnc)RNAs, indicating the regulatory function of USF1. It was also demonstrated that USF1 directly binds to the promoter region of 2,492 genes, which may be involved in the viral progression and cell proliferation pathways. By integrating these two datasets, 16 overlapped genes were detected, including downregulated lncRNA-NEAT1 and upregulated TF-ETV5. The downregulated lncRNA-NEAT1 showed reverse expression pattern and prognosis result compared with that of USF1 in patients with liver cancer, while upregulated TF-ETV5 showed consistent results with USF1. Promoter region motif analysis indicated that ETV5 has more binding motifs and genes than USF1 itself for USF1-regulated DEGs, indicating that USF1 may indirectly modulate gene expression by regulating ETV5 expression in Huh7 cells. The study also validated the direct interaction between USF1 and the promoter of ETV5 using ChIP-qPCR. In summary, the results demonstrated that USF1 binds to the promoter region of thousands of genes and affects a large part of DEGs indirectly. Downstream genes, including lncRNA-NEAT1 and TF-ETV5, may also have potential functions in the regulated network by USF1 and have potential functions in the progression of HCC. The present findings suggested that USF1 and its downstream targets could be potential targets for HCC therapy in the future.
肝癌，包括肝细胞癌（HCC），是一种在全球范围内具有高转移率和高死亡率的恶性肿瘤。上游转录因子1（USF1）是一种典型的转录因子（TF），与多种癌症的发病机制相关，但其在HCC中的生物学功能和分子靶点仍不清楚。通过RNA测序和染色质免疫沉淀（ChIP）测序方法，对过表达USF1的Huh7细胞进行全转录组分析，以研究USF1的下游靶点。然后使用逆转录定量PCR验证下游靶点。结果表明，USF1显著调控350个差异表达基因（DEG）。上调的DEG主要是富含免疫和炎症反应途径的蛋白质编码基因，而下调的DEG主要是编码长链非编码（lnc）RNA，表明USF1的调控功能。研究还表明，USF1直接结合2492个基因的启动子区域，这些基因可能参与病毒进展和细胞增殖途径。通过整合这两个数据集，检测到16个重叠基因，包括下调的lncRNA-NEAT1和上调的TF-ETV5。在肝癌患者中，下调的lncRNA-NEAT1与USF1相比呈现相反的表达模式和预后结果，而上调的TF-ETV5与USF1呈现一致的结果。启动子区域基序分析表明，对于USF1调控的DEG，ETV5比USF1本身具有更多的结合基序和基因，这表明USF1可能通过调节Huh7细胞中ETV5的表达间接调节基因表达。该研究还使用ChIP-qPCR验证了USF1与ETV5启动子之间的直接相互作用。总之，结果表明，USF1与数千个基因的启动子区域结合，并间接影响大部分DEG。包括lncRNA-NEAT1和TF-ETV5在内的下游基因，在USF1调控网络中可能也具有潜在功能，并在HCC进展中具有潜在作用。目前的研究结果表明，USF1及其下游靶点可能是未来HCC治疗的潜在靶点。
