最近，增强子RNA（eRNA）作为癌症发生和进展的关键生物标志物引起了广泛关注。然而，eRNA的全景图及其在II/III期结直肠癌（CRC）中的分子亚型意义尚未被充分研究。我们对一组公开的II/III期CRC患者RNA-seq数据进行了eRNA的全面分析。我们使用无监督聚类方法对预后相关eRNA进行分类，建立了基于eRNA的亚型系统。进一步的评估包括分子特征、免疫浸润、临床结果和药物反应。最后，我们在TCGA CRC数据集中验证了基于eRNA的亚型系统。我们共鉴定出6453个表达的eRNA，在其中237个是与预后相关的。在微卫星稳定型（MSS）CRC中，我们观察到eRNA的全局上调，相比之下微卫星不稳定高（MSI-H）CRC表达较低。通过一致性聚类，我们进一步确定了两个新的分子亚型，命名为Cluster 1（C1）和Cluster 2（C2）。C1与上皮-间质转化（EMT）、缺氧和KRAS信号通路的活化相关，并显示出较差的预后。C2与经典CRC亚型相关，表现出更好的生存结果。此外，C1在免疫浸润方面富集，并对免疫检查点抑制剂显示出更高的敏感性。我们的研究揭示了II/III期CRC在eRNA水平上的分子异质性，并强调了新型基于eRNA的亚型系统在预测预后和指导免疫治疗方面的潜在应用。 © 2023. 作者，在FESEO的专属许可下。

Recently, enhancer RNAs (eRNAs) have garnered attention as pivotal biomarkers for the onset and progression of cancer. However, the landscape of eRNAs and the implications of eRNA-based molecular subtypes in stage II/III colorectal cancer (CRC) remain largely unexplored.Comprehensive profiling of eRNAs was conducted on a public stage II/III CRC cohort with total RNA-seq data. We used unsupervised clustering of prognostic eRNAs to establish an eRNA-based subtyping system. Further evaluations included molecular characteristics, immune infiltration, clinical outcomes, and drug responses. Finally, we validated the eRNA-based subtyping system in The Cancer Genome Atlas (TCGA) CRC cohort.We identified a total of 6453 expressed eRNAs, among which 237 were prognostic. A global upregulation of eRNAs was observed in microsatellite-stable (MSS) CRCs when compared to microsatellite instability-high (MSI-H) CRCs. Through consensus clustering, two novel molecular subtypes, termed Cluster 1(C1) and Cluster 2(C2), were further identified. C1, associated with the activation of epithelial-mesenchymal transition (EMT), hypoxia, and KRAS signaling pathways, showed poorer prognosis. C2, correlated with the canonical CRC subtype, exhibited superior survival outcomes. In addition, C1 showed enrichment with immune infiltration and more sensitivity to immune checkpoint inhibitors.Our study unravels the molecular heterogeneity of stage II/III CRC at the eRNA level and highlights the potential applications of the novel eRNA-based subtyping system in predicting prognosis and guiding immunotherapy.© 2023. The Author(s), under exclusive licence to Federación de Sociedades Españolas de Oncología (FESEO).