Abstract
BackgroundThe alternative usage of promoters provides a way to regulate gene expression, has a significant influence on the transcriptome, and contributes to the cellular transformation of cancer. However, the function of alternative promoters (APs) in hepatocellular carcinoma (HCC) has not been systematically studied yet. In addition, the potential mechanism of regulation to the usage of APs remains unclear. DNA methylation, one of the most aberrant epigenetic modifications in cancers, is known to regulate transcriptional activity. Whether DNA methylation regulates the usage of APs needs to be explored. Here, we aim to investigate the effects of DNA methylation on usage of APs in HCC.MethodsPromoter activities were calculated based on RNA-seq data. Functional enrichment analysis was implemented to conduct GO terms. Correlation tests were used to detect the correlation between promoter activity and methylation status. The LASSO regression model was used to generate a diagnostic model. Kaplan–Meier analysis was used to compare the overall survival between high and low methylation groups. RNA-seq and whole-genome bisulfite sequencing (WGBS) in HCC samples were performed to validate the correlation of promoter activity and methylation.ResultsWe identified 855 APs in total, which could be well used to distinguish cancer from normal samples. The correlation of promoter activity and DNA methylation in APs was observed, and the APs with negative correlation were defined as methylation-regulated APs (mrAPs). Six mrAPs were identified to generate a diagnostic model with good performance (AUC = 0.97). Notably, the majority of mrAPs had CpG sites that could be used to predict clinical outcomes by methylation status. Finally, we verified 85.6% of promoter activity variation and 92.3% of methylation changes in our paired RNA-seq and WGBS samples, respectively. The negative correlation between promoter activity and methylation status was further confirmed in our HCC samples.ConclusionThe aberrant methylation status plays a critical role in the precision usage of APs in HCC, which sheds light on the mechanism of cancer development and provides a new insight into cancer screening and treatment.
Highlights
Liver cancer is the sixth most prevalent cancer and fourth most lethal malignancy globally [1]
Using t-distributed stochastic neighbor embedding (t-SNE), it was hard to distinguish the tumor from normal samples by expression of either all genes or differentially expressed genes (DEGs) (Figure 1D), whereas distinguishment was successfully achieved by the activities of either all promoters or differentially regulated promoters (DRPs) (Figure 1E)
We found that PDZK1 promoter activity was significantly increased in the Hepatocellular carcinoma (HCC), and was significantly correlated with methylation status, which showed that the lower methylation group of patients would have a worse prognosis
Summary
Liver cancer is the sixth most prevalent cancer and fourth most lethal malignancy globally [1]. Hepatocellular carcinoma (HCC) is the dominant tissue subtype of aggressive primary liver cancer, accounting for a great majority of the diagnoses and deaths [2]. Most patients have reached the advanced stage of HCC when they are first diagnosed, and only about 20%–30% of patients are eligible for effective treatment [4]. Further study on the pathogenesis of HCC is of great significance to the diagnosis and prognosis of tumors. The alternative usage of promoters provides a way to regulate gene expression, has a significant influence on the transcriptome, and contributes to the cellular transformation of cancer. The function of alternative promoters (APs) in hepatocellular carcinoma (HCC) has not been systematically studied yet. Whether DNA methylation regulates the usage of APs needs to be explored. We aim to investigate the effects of DNA methylation on usage of APs in HCC
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