Background: Bacillus Calmette-Guérin (BCG) immunotherapy, the standard adjuvant intravesical therapy for some intermediate and most high-risk non-muscle invasive bladder cancers (NMIBCs), suffers from a heterogenous response rate. Molecular markers to help guide responses are scarce and currently not used in the clinical setting. Methods: To identify novel biomarkers and pathways involved in response to BCG immunotherapy, we performed a genome-wide DNA methylation analysis of NMIBCs before BCG therapy. Genome-wide DNA methylation profiles of DNA isolated from tumors of 26 BCG responders and 27 failures were obtained using the Infinium MethylationEPIC BeadChip. Results: Distinct DNA methylation patterns were found by genome-wide analysis in the two groups. Differentially methylated CpG sites were predominantly located in gene promoters and gene bodies associated with bacterial invasion of epithelial cells, chemokine signaling, endocytosis, and focal adhesion. In total, 40 genomic regions with a significant difference in methylation between responders and failures were detected. The differential methylation state of six of these regions, localized in the promoters of the genes GPR158, KLF8, C12orf42, WDR44, FLT1, and CHST11, were internally validated by bisulfite-sequencing. GPR158 promoter hypermethylation was the best predictor of BCG failure with an AUC of 0.809 (p-value < 0.001). Conclusions: Tumors from BCG responders and BCG failures harbor distinct DNA methylation profiles. Differentially methylated DNA regions were detected in genes related to pathways involved in bacterial invasion of cells or focal adhesion. We identified candidate DNA methylation biomarkers that may help to predict patient prognosis after external validation in larger, well-designed cohorts.

中文翻译：

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通过对膀胱癌的BCG响应模式的全基因组分析发现基于分子DNA甲基化的生物标记物。

背景：卡介苗芽孢杆菌（BCG）免疫疗法是一些中度和高危非肌肉浸润性膀胱癌（NMIBC）的标准辅助膀胱内治疗，其反应率异质性高。用于指导反应的分子标记物稀少，目前在临床中并未使用。方法：为了确定与BCG免疫治疗反应有关的新型生物标志物和途径，我们在BCG治疗之前对NMIBCs进行了全基因组DNA甲基化分析。使用Infinium MethylationEPIC BeadChip获得了从26个BCG应答者和27个失败者的肿瘤中分离的DNA的全基因组DNA甲基化谱。结果：两组通过全基因组分析发现了不同的DNA甲基化模式。差异甲基化的CpG位点主要位于基因启动子和与上皮细胞的细菌入侵，趋化因子信号传导，内吞作用和粘着斑有关的基因体中。总共检测到40个基因组区域，在响应者和失败者之间的甲基化差异显着。这些区域中六个区域的甲基化状态差异，位于基因的启动子中GPR158，KLF8，C12orf42，WDR44，FLT1和CHST11在内部通过亚硫酸氢盐测序进行了验证。GPR158启动子高甲基化是BCG失败的最佳预测指标，AUC为0.809（p值<0.001）。结论：来自BCG应答者的肿瘤和BCG失败的肿瘤具有独特的DNA甲基化特征。在与细菌侵袭细胞或粘着斑有关的途径相关的基因中检测到差异甲基化的DNA区域。我们确定了候选DNA甲基化生物标记物，这些标记物可在较大的设计良好的队列中进行外部验证后帮助预测患者的预后。