Tumor Predisposing Post-Zygotic Chromosomal Alterations in Bladder Cancer-Insights from Histologically Normal Urothelium

Simple Summary We were motivated by the need to improve early detection of bladder cancer (BLCA). Our aim was to uncover genetic alterations within the bladder's lining, called urothelium, where BLCA starts. We examined normal tissue margins near and far away from tumors, studying the abnormalities that may predispose to BLCA. Recognizing the post-zygotic variability in bladder urothelium resulting from exposure to carcinogens in urine, our novel approach examined up to eight fragments of normal epithelium from each individual. Using a sensitive computational method, we successfully identified novel, but also well-known cancer-related regions across normal samples, confirming the efficacy of our methodology. Additionally, we provide further evidence for the already recognized connection between the loss of chromosome Y in men and BLCA. This positions our method for broader use in larger cohorts and different cancer types. Looking ahead, our methodology holds promise for identifying biomarkers that predict BLCA in analysis of urine.Abstract Bladder urothelial carcinoma (BLCA) is the 10th most common cancer with a low survival rate and strong male bias. We studied the field cancerization in BLCA using multi-sample- and multi-tissue-per-patient protocol for sensitive detection of autosomal post-zygotic chromosomal alterations and loss of chromosome Y (LOY). We analysed 277 samples of histologically normal urothelium, 145 tumors and 63 blood samples from 52 males and 15 females, using the in-house adapted Mosaic Chromosomal Alterations (MoChA) pipeline. This approach allows identification of the early aberrations in urothelium from BLCA patients. Overall, 45% of patients exhibited at least one alteration in at least one normal urothelium sample. Recurrence analysis resulted in 16 hotspots composed of either gains and copy number neutral loss of heterozygosity (CN-LOH) or deletions and CN-LOH, encompassing well-known and new BLCA cancer driver genes. Conservative assessment of LOY showed 29%, 27% and 18% of LOY-cells in tumors, blood and normal urothelium, respectively. We provide a proof of principle that our approach can characterize the earliest alterations preconditioning normal urothelium to BLCA development. Frequent LOY in blood and urothelium-derived tissues suggest its involvement in BLCA.