Table_7_Exploitation of tumor antigens and construction of immune subtype classifier for mRNA vaccine development in bladder cancer.xlsx

BackgroundBladder cancer (BLCA) is one of the most prevalent urinary system malignancies, with high mortality and recurrence. The present study aimed to identify potential tumor antigens for mRNA vaccines in BLCA and patient subtypes suitable for different immunotherapy.
MethodsGene expression profiles, mutation data, methylation data, and corresponding clinical information were obtained from the Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and ArrayExpress databases. Immunohistochemical staining of microarrays was performed to assess protein expression levels of IGF2BP2 and MMP9. Differential gene analysis, survival analysis, correlation analysis, consensus clustering analysis, and immune cell infiltration analysis were conducted using R software. Finally, the R package “immcluster” was used based on Combat and eXtreme Gradient Boosting algorithms to predict immune clusters of BLCA samples.
ResultsTwo mutated, amplified, and over-expressed tumor antigens, IGF2BP2 and MMP9, were found to be associated with clinical outcomes and the abundance of antigen-presenting cells (APCs). Subsequently, three immune subtypes (BIS1, BIS2, and BIS3) were defined in the BLCA cohort. BIS3 subtype exhibited an “active” immune phenotype, while BIS1 and BIS2 subtypes have a “suppressive” immune phenotype. Patients in BIS1 and BIS2 had a poor prognosis compared to BIS3. BIS3 had a higher score in checkpoints or immunomodulators (CP) and immunophenoscore (IPS), while BIS1 and BIS2 scored higher in major histocompatibility complex-related molecules (MHC molecules). Meanwhile, BIS2 and BIS3 had a significantly higher tumor mutational burden (TMB) compared to patients with BIS1. Finally, the “immcluster” package was applied to the dataset, which has been shown to accurately predict the immune subtypes of BLCA samples in many cohorts.
ConclusionsIGF2BP2 and MMP9 were potential antigens for developing mRNA vaccines against BLCA. The results in the present study suggested that immunotherapy targeting these two antigens would be suitable for patients falling under the BIS2 subtype. R package “immcluster” could assist in screening suitable BLCA patients for antitumor therapy.

【背景】膀胱癌（Bladder cancer, BLCA）是最常见的泌尿系统恶性肿瘤之一，具有较高的死亡率与复发率。本研究旨在识别膀胱癌mRNA疫苗的潜在肿瘤抗原，以及适配不同免疫治疗的患者亚型。
【方法】从癌症基因组图谱（The Cancer Genome Atlas, TCGA）、基因表达综合数据库（Gene Expression Omnibus, GEO）及ArrayExpress数据库获取基因表达谱、突变数据、甲基化数据及对应的临床信息。采用免疫组化芯片染色评估IGF2BP2与MMP9的蛋白表达水平。使用R软件开展差异基因分析、生存分析、相关性分析、一致性聚类分析以及免疫细胞浸润分析。最终基于Combat和极限梯度提升（eXtreme Gradient Boosting）算法，借助R包"immcluster"预测膀胱癌样本的免疫亚型。
【结果】本研究发现两个发生突变、扩增且过表达的肿瘤抗原IGF2BP2与MMP9，其与临床结局及抗原呈递细胞（antigen-presenting cells, APCs）的丰度密切相关。随后在膀胱癌队列中定义了三种免疫亚型（BIS1、BIS2与BIS3）：BIS3亚型呈现“活化型”免疫表型，而BIS1与BIS2亚型则表现为“抑制型”免疫表型。BIS1与BIS2亚型患者的预后较BIS3亚型更差。BIS3亚型在检查点或免疫调节因子（checkpoints or immunomodulators, CP）及免疫评分（immunophenoscore, IPS）中得分更高，而BIS1与BIS2亚型在主要组织相容性复合体相关分子（MHC分子）中得分更高。同时，BIS2与BIS3亚型的肿瘤突变负荷（tumor mutational burden, TMB）显著高于BIS1亚型患者。最后，将R包"immcluster"应用于本数据集，该工具已在多队列研究中被证实可精准预测膀胱癌样本的免疫亚型。
【结论】IGF2BP2与MMP9是开发膀胱癌mRNA疫苗的潜在靶点抗原。本研究结果提示，针对这两种抗原的免疫治疗方案适配BIS2亚型患者。R包"immcluster"可辅助筛选适合接受抗肿瘤治疗的膀胱癌患者。