Molecular landscapes and mechanisms of squamous bladder cancer

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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.