Data_Sheet_2_Comprehensive Analysis of RUNX and TGF-β Mediated Regulation of Immune Cell Infiltration in Breast Cancer.PDF

Runt-related transcription factors (RUNXs) can serve as both transcription activators and repressors during biological development, including immune cell maturation. RUNX factors have both tumor-promoting and tumor-suppressive roles in carcinogenesis. Immune cell infiltration and the tumor immune microenvironment have been found to be key regulators in breast cancer progression, treatment response, and patient outcome. However, the relationship between the RUNX family and immune cell infiltration in breast cancer remains unclear. We performed a comprehensive analysis to reveal the role of RUNX factors in breast cancer. Analysis of patient data in the Oncomine database showed that the transcriptional levels of RUNX proteins in breast cancer were elevated. Kaplan–Meier plotter (KM plotter) analysis showed that breast cancer patients with higher expression of RUNX proteins had better survival outcomes. Through analysis of the UALCAN database, we found that the transcriptional levels of RUNX factors were significantly correlated with some breast cancer patient characteristics. cBio Cancer Genomics Portal (cBioPortal) analysis showed the proportions of different RUNX genomic alterations in various subclasses of breast cancer. We also performed gene ontology (GO) and pathway analyses for the significantly differentially expressed genes that were correlated with RUNX factors in breast cancer. TIMER database analysis showed that immune cell infiltration in breast cancer could be affected by the transcriptional level, mutation, and gene copy number of RUNX proteins. Using the Gene Set Cancer Analysis (GSCA) database, we analyzed the effects of RUNX gene methylation on the level of immune cell infiltration in breast cancer. We found that the methylation level changes of RUNX2 and RUNX3 had opposite effects on immune cell infiltration in breast cancer. We also analyzed the relationship between the methylation level of RUNX genes and the TGF-β signaling pathway using the TISIDB database. The results showed that the methylation levels of RUNX1 and RUNX3 were correlated with the expression of TGF-β1. In summary, our analysis found that the RUNX family members can influence the infiltration of various immune cells in breast cancer depending on their expression level, mutation, gene copy number, and methylation. The RUNX family is an important regulator of immune cell infiltration in breast cancer and may serve as a potential prognostic biomarker.

Runt相关转录因子（Runt-related transcription factors，RUNXs）可在包括免疫细胞成熟在内的生物发育进程中，同时充当转录激活因子与转录抑制因子。RUNX家族因子在癌变过程中兼具促瘤与抑瘤双重功能。免疫细胞浸润与肿瘤免疫微环境是影响乳腺癌进展、治疗应答及患者预后的关键调控因素，但目前RUNX家族与乳腺癌免疫细胞浸润之间的关联仍未明确。本研究通过全面分析，旨在阐明RUNX家族因子在乳腺癌中的作用。通过分析Oncomine数据库中的患者数据，本研究发现乳腺癌组织中RUNX蛋白的转录水平显著升高。Kaplan-Meier绘图仪（Kaplan–Meier plotter，KM plotter）分析结果显示，RUNX蛋白高表达的乳腺癌患者拥有更优的生存结局。通过对UALCAN数据库的分析，本研究发现RUNX家族因子的转录水平与部分乳腺癌患者的临床特征显著相关。cBio癌症基因组学门户（cBio Cancer Genomics Portal，cBioPortal）分析结果揭示了乳腺癌不同亚型中各类RUNX基因组变异的占比情况。本研究还对乳腺癌中与RUNX家族因子显著相关的差异表达基因进行了基因本体（Gene Ontology，GO）富集分析及通路富集分析。TIMER数据库分析结果表明，乳腺癌中的免疫细胞浸润水平可受RUNX蛋白的转录水平、突变状态及基因拷贝数影响。本研究借助基因集癌症分析（Gene Set Cancer Analysis，GSCA）数据库，分析了RUNX基因甲基化对乳腺癌免疫细胞浸润水平的影响，发现RUNX2与RUNX3的甲基化水平变化对乳腺癌免疫细胞浸润产生了截然相反的调控作用。本研究还通过TISIDB数据库，分析了RUNX基因甲基化水平与转化生长因子-β（TGF-β）信号通路之间的关联，结果显示RUNX1与RUNX3的甲基化水平与TGF-β1的表达显著相关。综上，本研究分析表明，RUNX家族成员可通过其表达水平、突变状态、基因拷贝数及甲基化水平，调控乳腺癌内多种免疫细胞的浸润过程。RUNX家族是乳腺癌免疫细胞浸润的重要调控因子，有望成为潜在的预后生物标志物。