Mo Zhuomao, Cao Zhirui, Luo Shaoju, Chen Yan, Zhang Shijun
Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
Department of Traditional Chinese Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
Front Mol Biosci. 2020 Oct 23;7:562441. doi: 10.3389/fmolb.2020.562441. eCollection 2020.
5-methylcytosine (5mC) has been reported in the prognosis of a variety of cancers, however, its role in hepatocellular carcinoma (HCC) has not been investigated yet. This study aimed at identifying the molecular subtypes associated with 5mC and establishing a relevant score to predict its prognosis in HCC.
Somatic gene mutation data and gene expression data were retrieved from The Cancer Genome Atlas database. Molecular subtypes were identified by unsupervised clustering based on the expression of 5mC regulators, and the molecular features of each subtype were investigated by survival, mutation, gene set variation, and immune cell infiltration analyses. Next, we performed a differentially expressed analysis based on the new subtypes and selected the overlapping genes for further analysis. We undertook univariate Cox analysis to analyze these genes and constructed a prognostic model by lasso regression analysis. Meanwhile, survival and gene set enrichment analyses were used to explore the prognosis and the relevant pathways, respectively. The LIRI cohort from the International Cancer Genome Consortium database was used as a reference to validate the 5mC subtypes and 5mC score.
Twenty-one types of 5mC regulators were employed in this study, and three 5mC-associated molecular subtypes were identified. These three subtypes presented significant differences in prognosis, immune cell infiltration, immune checkpoint inhibitors, signaling pathways, and mutational features. Compared with cluster 3, cluster 2 exhibited significantly increased expression of , and , while , and were higher in cluster 2 than in cluster 1. Furthermore, a 5mC-related score, composed of seven genes (, and CAND2), was proven to be significantly associated with prognosis. The established subtypes and scores were thus successfully verified by the validated cohort.
To the best of our knowledge, this is the first study to identify a novel molecular subtype based on 5mC regulators. The identification of the 5mC-associated subtype may help reveal the potential relation between 5mC and immunity and provide novel insights for the development of individualized therapy for HCC.
5-甲基胞嘧啶（5mC）已被报道与多种癌症的预后相关，然而，其在肝细胞癌（HCC）中的作用尚未得到研究。本研究旨在识别与5mC相关的分子亚型，并建立一个相关评分以预测其在HCC中的预后。
从癌症基因组图谱数据库中检索体细胞基因突变数据和基因表达数据。基于5mC调节因子的表达通过无监督聚类识别分子亚型，并通过生存、突变、基因集变异和免疫细胞浸润分析研究每个亚型的分子特征。接下来，我们基于新的亚型进行差异表达分析，并选择重叠基因进行进一步分析。我们进行单变量Cox分析以分析这些基因，并通过套索回归分析构建预后模型。同时，分别使用生存分析和基因集富集分析来探索预后和相关途径。来自国际癌症基因组联盟数据库的LIRI队列用作验证5mC亚型和5mC评分的参考。
本研究使用了21种5mC调节因子，并识别出三种与5mC相关的分子亚型。这三种亚型在预后、免疫细胞浸润、免疫检查点抑制剂、信号通路和突变特征方面存在显著差异。与簇3相比，簇2中 、 和 的表达显著增加，而簇2中 、 和 高于簇1。此外，由七个基因（ 、 和CAND2）组成的5mC相关评分被证明与预后显著相关。因此，已建立的亚型和评分通过验证队列成功得到验证。
据我们所知，这是第一项基于5mC调节因子识别新型分子亚型的研究。5mC相关亚型的识别可能有助于揭示5mC与免疫之间的潜在关系，并为HCC个体化治疗的发展提供新的见解。
