Huang Peng, Xu Mengxiang, Han Haijun, Zhao Xinyi, Li Ming D, Yang Zhongli
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China.
Front Oncol. 2021 Nov 10;11:769390. doi: 10.3389/fonc.2021.769390. eCollection 2021.
DNA methylation is a key transcription regulator, whose aberration was ubiquitous and important in most cancers including hepatocellular carcinoma (HCC). Whole-genome bisulfite sequencing (WGBS) was conducted for comparison of DNA methylation in tumor and adjacent tissues from 33 HCC patients, accompanying RNA-seq to determine differentially methylated region-associated, differentially expressed genes (DMR-DEGs), which were independently replicated in the TCGA-LIHC cohort and experimentally validated 5-aza-2-deoxycytidine (5-azadC) demethylation. A total of 9,867,700 CpG sites showed significantly differential methylation in HCC. Integrations of mRNA-seq, histone ChIP-seq, and WGBS data identified 611 high-confidence DMR-DEGs. Enrichment analysis demonstrated activation of multiple molecular pathways related to cell cycle and DNA repair, accompanying repression of several critical metabolism pathways such as tyrosine and monocarboxylic acid metabolism. In TCGA-LIHC, we replicated about 53% of identified DMR-DEGs and highlighted the prognostic significance of combinations of methylation and expression of nine DMR-DEGs, which were more efficient prognostic biomarkers than considering either type of data alone. Finally, we validated 22/23 (95.7%) DMR-DEGs in 5-azadC-treated LO2 and/or HepG2 cells. In conclusion, integration of epigenome and transcriptome data depicted activation of multiple pivotal cell cycle-related pathways and repression of several metabolic pathways triggered by aberrant DNA methylation of promoters and enhancers in HCC.
DNA甲基化是一种关键的转录调节因子，其异常在包括肝细胞癌（HCC）在内的大多数癌症中普遍存在且至关重要。对33例HCC患者的肿瘤组织和癌旁组织进行了全基因组亚硫酸氢盐测序（WGBS），同时进行RNA测序以确定差异甲基化区域相关的差异表达基因（DMR-DEGs），这些基因在TCGA-LIHC队列中进行了独立验证，并通过5-氮杂-2'-脱氧胞苷（5-azadC）去甲基化进行了实验验证。共有9,867,700个CpG位点在HCC中显示出显著的差异甲基化。mRNA测序、组蛋白ChIP测序和WGBS数据的整合鉴定出611个高可信度的DMR-DEGs。富集分析表明，与细胞周期和DNA修复相关的多个分子途径被激活，同时一些关键的代谢途径如酪氨酸和单羧酸代谢受到抑制。在TCGA-LIHC中，我们复制了约53%已鉴定的DMR-DEGs，并强调了9个DMR-DEGs甲基化和表达组合的预后意义，这些组合作为预后生物标志物比单独考虑任何一种数据类型更有效。最后，我们在5-azadC处理的LO2和/或HepG2细胞中验证了22/23（95.7%）个DMR-DEGs。总之，表观基因组和转录组数据的整合描绘了HCC中启动子和增强子异常DNA甲基化引发的多个关键细胞周期相关途径的激活以及几种代谢途径的抑制。
