Data_Sheet_11_Comprehensive Analysis of N6-methyladenosine Modification Patterns Associated With Multiomic Characteristics of Bladder Cancer.ZIP

Purpose: To comprehensively analyze N6-methyladenosine modification patterns in bladder tumors and to further systematically explore the inherent relationships between these modification patterns and multiomic tumor characteristics.
Materials and Methods: A total of 901 bladder tumor samples, including 405 samples from TCGA database, 188 samples from GSE13507 and 308 samples from GSE32894, were included in this systematic analysis. The N6-methyladenosine modification patterns were identified utilizing unsupervised clustering analysis. To quantify N6-methyladenosine modification patterns, the m6Ascore of individual sample was developed using principal component analysis algorithms. Relationships among immune infiltration, tumor mutation burden, various clinical characteristics, molecular subtypes, and the m6Ascore were systematically analyzed. The guiding value of m6Ascore in immunotherapy was further validated in an external trial cohort. Genomics of Drug Sensitivity in Cancer expression references were also utilized to perform drug sensitivity analysis for patients with distinct m6A modification patterns.
Results: We determined three different N6-methyladenosine modification patterns for 901 bladder tumors. The quantitative m6Ascore of individual sample derived from N6-methyladenosine modification patterns could play a significant role in predicting overall survival, immune cell infiltration, and classic oncogene mutations. A low m6Ascore combined with high tumor mutation burden indicated better survival outcomes (p < 0.001). A higher m6Ascore also indicated a higher grade, higher T and N stage, elder ages, higher death rate, and higher PD1/PDL1/CTLA4 expressions (p < 0.01). The Basal type tended to exhibit significantly higher m6Ascores than the Luminal and Neuronal subtypes. External immunotherapy cohorts demonstrated that no difference in therapeutic effects was noted between the high and low m6Ascore groups when anti-PD1 immunotherapy was exclusively administered. When anti-PD1 and anti-CTLA4 immunotherapy were simultaneously administered, the high m6Ascore group had a significantly better prognosis than the low m6Ascore group (p < 0.001). High m6A groups were potentially sensitive to various medical treatments including Bleomycin, Bortezomib, Cisplatin, Cyclopamine, Dasatinib, Docetaxe, Rapamycin, and Vinblastine in this study.
Conclusions: This study systematically revealed the important roles of m6A methylation modification patterns in bladder tumors. Detailed quantification of m6A modification patterns could improve our understanding of the bladder tumor microenvironments and could provide guidance for future immunotherapy strategies.

研究目的：本研究旨在全面分析膀胱肿瘤中的N6-甲基腺嘌呤（N6-methyladenosine，简称m6A）修饰模式，并进一步系统探究此类修饰模式与肿瘤多组学特征之间的内在关联。
材料与方法：本系统分析共纳入901例膀胱肿瘤样本，其中405例来自癌症基因组图谱（TCGA）数据库，188例来自GSE13507数据集，308例来自GSE32894数据集。研究采用无监督聚类分析识别m6A修饰模式；通过主成分分析算法构建单样本m6A评分（m6Ascore）以量化个体的m6A修饰特征；系统分析肿瘤免疫浸润、肿瘤突变负荷、各类临床特征、分子亚型与m6A评分之间的关联；并在外部验证队列中进一步验证m6A评分在免疫治疗中的指导价值。此外，本研究还利用癌症药物敏感性基因组学（Genomics of Drug Sensitivity in Cancer, GDSC）表达参考数据集，对具有不同m6A修饰模式的患者开展药物敏感性分析。
结果：本研究在901例膀胱肿瘤中鉴定出3种不同的m6A修饰模式。基于m6A修饰模式构建的单样本量化m6A评分，可有效预测患者总生存期、肿瘤免疫浸润特征及经典癌基因突变状态。低m6A评分联合高肿瘤突变负荷提示更佳的生存结局（p < 0.001）。较高的m6A评分与更高的肿瘤分级、更晚的T分期与N分期、更高龄的患者、更高的死亡率以及更高的PD1/PDL1/CTLA4表达水平显著相关（p < 0.01）。基底型（Basal）分子亚型的m6A评分显著高于管腔型（Luminal）与神经元型（Neuronal）亚型。外部免疫治疗队列分析显示，仅接受抗PD1免疫治疗时，高、低m6A评分组的治疗效果无显著差异；而当联合接受抗PD1与抗CTLA4免疫治疗时，高m6A评分组患者的预后显著优于低m6A评分组（p < 0.001）。本研究发现，高m6A评分组患者对博来霉素、硼替佐米、顺铂、环巴胺、达沙替尼、多西他赛、雷帕霉素及长春花碱等多种治疗药物具有潜在敏感性。
结论：本研究系统揭示了m6A甲基化修饰模式在膀胱肿瘤中的重要作用。对m6A修饰模式的精细化量化，可加深我们对膀胱肿瘤微环境的理解，并为未来免疫治疗策略的制定提供指导。