Table_3_Correlations Between the Characteristics of Alternative Splicing Events, Prognosis, and the Immune Microenvironment in Breast Cancer.XLSX

ObjectiveAlternative splicing (AS) is the mechanism by which a few genes encode numerous proteins, and it redefines the concept of gene expression regulation. Recent studies showed that dysregulation of AS was an important cause of tumorigenesis and microenvironment formation. Therefore, we performed a systematic analysis to examine the role of AS in breast cancer (Breast Cancer, BrCa) progression.MethodsThe present study included 993 BrCa patients from The Cancer Genome Atlas (TCGA) database in the genome-wide analysis of AS events. We used differential and prognostic analyses and found differentially expressed alternative splicing (DEAS) events and independent prognostic factors related to patients’ overall survival (OS) and disease-free survival (DFS). We divided the patients into two groups based on these AS events and analyzed their clinical features, molecular subtyping and immune characteristics. We also constructed a splicing factor (SF) regulation network for key AS events and verified the existence of AS events in tissue samples using real-time quantitative PCR.ResultsA total of 678 AS events were identified as differentially expressed, of which 13 and 10 AS events were independent prognostic factors of patients’ OS and DFS, respectively. Unsupervised clustering analysis based on these prognostic factors indicated that the Cluster 1 group had a better prognosis and more immune cell infiltration. SFs were significantly related to the expression of AS events, and AA-RPS21 was significantly upregulated in tumors.ConclusionAlternative splicing expands the mechanism of breast cancer progression from a new perspective. Notably, alternative splicing may affect the patient’s prognosis by affecting the infiltration of immune cells. Our research provides important guidance for subsequent studies of AS in breast cancer.

目的：可变剪接（AS）是一种通过少量基因编码众多蛋白质的机制，它重新界定了基因表达调控的概念。近期研究显示，可变剪接的失调是肿瘤发生和微环境形成的重要因素。因此，本研究对可变剪接在乳腺癌（乳腺癌，BrCa）进展中的作用进行了系统性分析。方法：本研究纳入了来自癌症基因组图谱（TCGA）数据库的993例乳腺癌患者，对其进行了全基因组可变剪接事件的分析。我们运用差异分析和预后分析，识别了与患者总生存期（OS）和无病生存期（DFS）相关的差异表达可变剪接（DEAS）事件和独立预后因素。基于这些可变剪接事件，我们将患者分为两组，分析了他们的临床特征、分子亚型和免疫特征。此外，我们构建了关键可变剪接事件的相关剪接因子（SF）调控网络，并使用实时定量PCR验证了组织样本中可变剪接事件的存在。结果：共确定了678个差异表达的可变剪接事件，其中13个和10个事件分别作为患者OS和DFS的独立预后因素。基于这些预后因素的无监督聚类分析表明，Cluster 1组预后较好，免疫细胞浸润程度更高。剪接因子（SFs）与可变剪接事件的表达显著相关，且肿瘤中AA-RPS21表达显著上调。结论：可变剪接从新的视角扩展了乳腺癌进展的机制。值得注意的是，可变剪接可能通过影响免疫细胞的浸润来影响患者的预后。本研究为后续乳腺癌中可变剪接的研究提供了重要指导。