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食道鳞状细胞癌(esophagus squamous cell carcinoma, ESCC)是侵袭性恶性肿瘤，预后较差。Diffbind用于H3K27ac ChIP-seq差异分析以鉴定异常增强子(aberrant enhancer loci, AEL)在食管鳞癌发生中的作用。ROSE、HOMER软件分别用于鉴定超级增强子、计算转录因子。ClusterProfiler程序包用于GO和KEGG富集分析。根据异常增强子相关基因的表达，采用LASSO Cox回归构建风险评分模型。本研究在ESCC中鉴定了3 323个激活和955个沉默的AEL，多数位于超级增强子内，被转录因子AP-1占据。对GSE53625等数据集进行差异分析发现，相比于癌旁组织，活化AEL基因在食管鳞癌组织中表达上调，而沉默AEL基因被抑制。AEL基因与染色质结合等功能密切相关，参与细胞粘附、细胞骨架、Rap1等信号通路。DNA甲基化差异分析发现，相比于癌旁组织，活化AEL在食管鳞癌组织中被低甲基化，而沉默的AEL被高甲基化。EGFR基因上游存在AEL，为超级增强子，该AEL在肿瘤细胞中被特异性激活，细胞实验证实此AEL对EGFR启动子有显著的增强作用。与低风险组相比，高风险组的患者在训练集(P=3.331×10-16)和测试集(P=4.5×10-2)中的总生存率显着降低。训练集和测试集的多因素Cox回归分析证明AEL基因风险评分模型是影响患者总生存率的独立因素。ESCC恶化过程中存在高频率的增强子活性改变，这些异常增强子可能是ESCC肿瘤发生中基因表达失调的驱动因素。根据AEL基因表达构建的风险评估模型在训练集和测试集中表现优异，有望作为ESCC患者预后的预测工具。
Abstract：Esophagus squamous cell carcinoma(ESCC) is an aggressive malignancy with a poor prognosis. DiffBind was used to identify aberrant enhancer loci(AEL) in the occurrence of esophageal squamous cell carcinoma by Chip-Seq differential analysis of H3K27ac. ROSE and HOMER software were used to identify super-enhancers and calculate transcription factors respectively. ClusterProfiler package was used for GO and KEGG enrichment analysis. According to AEL gene expression, a LASSO Cox regression was used to construct a risk score model. We identified 3 323 activated and 955 silenced AELs in ESCCs. Most of the enhancers were constituents of super-enhancers, and occupied by AP-1. Differential analysis of data sets such as GSE53625 indicated that genes associated with gain＿AEL genes showed elevated expression and lost＿AEL genes were silenced relative to adjacent tissues. AEL genes were closely related to chromatin binding and other functions, and were involved in cell adhesion, regulation of cytoskeleton and Rap1 signaling pathways. Analysis of DNA methylation showed that gain＿AELs were hypomethylated and lost＿AELs were hypermethylated in ESCCs compared to adjacent tissues. A super-enhancer AEL, located upstream of EGFR gene, was specifically activated in ESCC cells. Cell experiments confirmed that this AEL could significantly enhance the EGFR promoter. Patients in the high-risk group had considerably worse overall survival than low-risk group in train(P = 3.331 × 10-16) and test(P = 4.5 × 10-2) cohorts.Multivariate Cox regression analysis of training and the test cohorts showed that AEL gene risk score model was an independent factor affecting overall survival. There exist the extensive alternations of enhancer landscape, and these abnormal enhancers may be the driving factors of gene expression disorders in ESCC tumorigenesis. The risk assessment model constructed based on AEL gene expression performed well in the training and test cohorts,and was expected to be a predictive tool for the prognosis of ESCC patients.
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基本信息:
DOI：10.13417/j.gab.040.003824
中图分类号:R735.1
引用信息:
[1]杨莹莹,刘贤贤,陈平,等.食管鳞癌中异常增强子促进肿瘤发生[J].基因组学与应用生物学,2021,40(Z4):3824-3838.DOI:10.13417/j.gab.040.003824.
基金信息:
河南省重点研发与推广专项(科技攻关)项目(192102310108); 河南省青年人才托举工程(2021HYTP040); 国家级大学生创新创业训练计划重点项目(202012949005); 郑州师范学院大学生科研创新基金项目(2019dc10)共同资助
2021-12-25
2021-12-25