Intratumor heterogeneity (ITH) of bladder cancer (BLCA) contributes to therapy resistance and immune evasion affecting clinical prognosis. The molecular and cellular mechanisms contributing to BLCA ITH generation remain elusive. It is found that a TM4SF1-positive cancer subpopulation (TPCS) can generate ITH in BLCA,evidenced by integrative single cell atlas analysis. Extensive profiling of the epigenome and transcriptome of all stages of BLCA revealed their evolutionary trajectories. Distinct ancestor cells gave rise to low-grade noninvasive and high-grade invasive BLCA. Epigenome reprograming led to transcriptional heterogeneity in BLCA. During early oncogenesis,epithelial-to-mesenchymal transition generated TPCS. TPCS has stem-cell-like properties and exhibited transcriptional plasticity,priming the development of transcriptionally heterogeneous descendent cell lineages. Moreover,TPCS prevalence in tumor is associated with advanced stage cancer and poor prognosis. The results of this study suggested that bladder cancer interacts with its environment by acquiring a stem cell-like epigenomic landscape,which might generate ITH without additional genetic diversification.

A subpopulation of bladder cancer cells,characterized by TM4SF1 expression,is identified as a source of intratumor heterogeneity (ITH). This group shows stem-cell traits and promotes diverse cell lineages within the tumor. Their presence correlates with advanced cancer stages and worse outcomes,suggesting they drive ITH through epigenomic reprogramming rather than genetic changes. image