A Genome-Wide Investigation of Effects of Aberrant DNA Methylation on the Usage of Alternative Promoters in Hepatocellular Carcinoma

Yuting Dong; Xiaozhao Liu; Bijun Jiang; Siting Wei; Bangde Xiang; Ruichu Liao; Qiuyan Wang; Ximiao He

doi:10.3389/fonc.2021.780266

A Genome-Wide Investigation of Effects of Aberrant DNA Methylation on the Usage of Alternative Promoters in Hepatocellular Carcinoma

Front Oncol. 2022 Jan 17:11:780266. doi: 10.3389/fonc.2021.780266. eCollection 2021.

Authors

Yuting Dong^{1

2

3}, Xiaozhao Liu^{1

2

3}, Bijun Jiang^{1

2

3}, Siting Wei^{1

2

3}, Bangde Xiang⁴, Ruichu Liao^{1

2

3}, Qiuyan Wang^{5

6}, Ximiao He^{1

2

3}

Affiliations

¹ Department of Physiology, School of Basic Medical Science, Huazhong University of Science and Technology, Wuhan, China.
² Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
³ Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, China.
⁴ Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China.
⁵ Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.
⁶ Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi, Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China.

Abstract

Background: 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. 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.

Methods: Promoter 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.

Results: We 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.

Conclusion: The 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.

Keywords: DNA methylation; alternative promoters; diagnostic model; hepatocellular carcinoma; survival prediction.