Molecular landscapes and mechanisms of squamous bladder cancer

膀胱单纯鳞状细胞癌是一种罕见的诊断，但它与不良预后和辅助治疗的选择有限。SCC被认为是从称为鳞状化生和异型增生的显微镜可识别的前驱病变的动态相变演变而来。然而，促进尿路上皮内鳞状上皮细胞的异常分化和随后的癌变的分子机制知之甚少。尽管有高通量测序方法和对不同癌症类型分子景观的详细了解，但尚未收集到膀胱纯SCC的全基因组数据。特别是癌前病变的组学数据完全缺失。因此，我们建立了一个队列的新鲜冷冻组织从完全包埋的膀胱标本，包括患者匹配的正常尿路上皮，鳞状上皮化生，部分异型增生和伴随的SCC病变，以破译从尿路上皮鳞状上皮化生，异型增生和SCC的阶段性转变的分子机制。我们的目标是进行整合基因组（全外显子组测序），转录组（Affyssa阵列）和表观基因组（Infinium MethylationEPIC BeadChip）分析，涉及生物信息学和实验分析的不同步骤：1）通过个体和多方向分析，我们将确定DNA机制的相变特异性合作贡献（基因组学，表观基因组学），其可以解释参与良性到恶性鳞状分化的多步相变的差异基因表达。2)基于严格生物信息学的调控机制评估将减少已鉴定的（表观）遗传调控候选物，这些候选物还将通过公开可用的数据集（例如TCGA）和文献进一步交叉验证，以揭示候选基因和/或复杂特征以及具有临床和功能意义的信号传导途径。3)基于RT-PCR、焦磷酸测序或蛋白质印迹，在独立的FFPE群组和细胞系模型中进一步验证所选候选物将进一步加强或排除候选物。4)此外，将与计算生物医学研究所的Schuppert教授和干细胞生物学和细胞工程研究所的瓦格纳教授一起进行高风险综合生物信息学方法。通过这项研究，我们将提供全面的新见解，了解鳞状膀胱癌的多步骤致癌作用，我们的数据将为进一步的体外和体内模型提供基础。

Pure squamous cell carcinoma (SCC) of the urinary bladder is an infrequent diagnosis, but it is associated with unfavorable prognosis and limited options for adjuvant therapy. SCC are believed to evolve from a dynamic phase transition of microscopically recognizable precursor lesions referred to as squamous metaplasia and dysplasia. However, the molecular mechanisms facilitating the aberrant differentiation of squamous epithelial cells within the urothelium and subsequent cancerogenesis are poorly understood. Despite high-throughput sequencing approaches and detailed understanding of molecular landscapes across different cancer types, genome-wide data of pure SCC of the urinary bladder have not yet been collected. In particular, omics data of precancerous lesions are completely missing. Therefore, we have established a cohort of fresh frozen tissues from completely embedded cystectomy specimens comprising patient matched normal urothelium, squamous metaplasia, partly dysplasia and concomitant SCC lesions in order to decipher the molecular mechanisms of the phase transition from urothelium to squamous metaplasia, dysplasia and SCC. We aim to perform an integrative genomic (Whole Exome Sequencing), transcriptomic (Affymetrix arrays) and epigenomic (Infinium MethylationEPIC BeadChip) analysis involving different steps of bioinformatics and experimental analyses: 1) By individual and multidirectional analyses we will identify phase transition specific co-operative contributions of DNA mechanisms (genomic, epigenomic) which could explain differential gene expression involved in multistep phase transition of benign to malignant squamous differentiation. 2) A strict bioinformatics based evaluation of regulatory mechanisms will reduce identified (epi-)genetic regulatory candidates which will also be further cross-validated by publicly available datasets (e.g. TCGA) and literature to reveal candidate genes and/or complex signatures as well as signaling pathways of clinical and functional significance. 3) Further validation of selected candidates in independent FFPE cohorts and cell line models based on RT-PCR, pyrosequencing or western blots will further strengthen or dismiss candidates. 4) Additionally, a high risk integrative bioinformatics approach will be conducted with Prof. Schuppert at the Institute for Computational Biomedicine and Prof. Wagner at the Departenment of Stem Cell Biology and Cellular Engineering. With this study, we will provide comprehensive novel insights into the poorly understood multistep carcinogenesis of squamous bladder cancer and our data will provide the basis for further in vitro and in vivo models of putative key regulatory players.