Zhang Ruijie, Chen Zhengxin, Li Tianyi, Feng Dehua, Liu Xinying, Wang Xuefeng, Han Huirui, Yu Lei, Li Xia, Li Bing, Wang Limei, Li Jin
College of Biomedical Informatics and Engineering, Kidney Disease Research Institute at the second affiliated hospital, Hainan Engineering Research Center for Health Big Data, Hainan Medical University, 3 Xueyuan Rd, Longhua District, Haikou, Hainan 571199, China.
Brief Funct Genomics. 2025 Jan 15;24. doi: 10.1093/bfgp/elaf007.
Enhancer RNA (eRNA), a type of non-coding RNA transcribed from enhancer regions, serves as a class of critical regulatory elements in gene expression. In cancer biology, eRNAs exhibit profound roles in tumorigenesis, metastasis, and therapeutic response modulation. In this review, we outline eRNA identification methods utilizing enhancer region prediction, histone H3 lysine 4 monomethyl chromatin signatures, and nucleosome positioning analysis. We quantitate eRNA expression through RNA-seq, single-cell transcriptomics, and epigenomic integration approaches. Functionally, eRNAs regulate gene expression, protein function modulation, and chromatin modification. Key databases detailing eRNA annotations and interactions are highlighted. Furthermore, we analyze the connection of eRNA with immune cells and its potential in immunotherapy. Emerging evidence demonstrates eRNA's critical involvement in immune cell crosstalk and tumor microenvironment reprogramming. Notably, eRNA signatures show promise as predictive biomarkers for immunotherapy response and chemoresistance monitoring in multiple malignancies. This review underscores eRNA's transformative potential in precision oncology, advocating for integrated multiomics approaches to fully realize their clinical applicability.
增强子RNA（eRNA）是一类从增强子区域转录而来的非编码RNA，是基因表达中的一类关键调控元件。在癌症生物学中，eRNA在肿瘤发生、转移和治疗反应调节中发挥着重要作用。在本综述中，我们概述了利用增强子区域预测、组蛋白H3赖氨酸4单甲基化染色质特征和核小体定位分析的eRNA鉴定方法。我们通过RNA测序、单细胞转录组学和表观基因组整合方法对eRNA表达进行定量。在功能上，eRNA调节基因表达、蛋白质功能调节和染色质修饰。重点介绍了详细的eRNA注释和相互作用的关键数据库。此外，我们分析了eRNA与免疫细胞的联系及其在免疫治疗中的潜力。新出现的证据表明，eRNA在免疫细胞串扰和肿瘤微环境重编程中起着关键作用。值得注意的是，eRNA特征有望作为多种恶性肿瘤免疫治疗反应和化疗耐药监测的预测生物标志物。本综述强调了eRNA在精准肿瘤学中的变革潜力，提倡采用综合多组学方法来充分实现其临床应用价值。
