Implementing single nuclei RNA sequencing to study tumor-host interaction in bladder cancer resected by Transurethral Resection of Bladder Tumor (TURBT)

Bladder cancer's significant intratumoral heterogeneity poses challenges to accurate diagnosis and effective treatment. While genomic and transcriptomic analyses have advanced our understanding, bulk sequencing methods often mask this heterogeneity, potentially overlooking aggressive subclones contributing to treatment resistance. This study leveraged single-nucleus RNA sequencing (snRNA-seq), a technology newly implemented in Qatar, to characterize the cellular composition and transcriptional landscape of bladder tumors. We established a standardized protocol for isolating single nuclei from both fresh and snap-frozen tissue obtained from eight patients undergoing transurethral resection (TURBT). Robust bioinformatics pipelines facilitated the identification of distinct cellular populations within the tumor microenvironment, encompassing epithelial, stromal, and diverse immune cell types. Comparative analysis of muscle-invasive (MIBC) and non-muscle-invasive (NMIBC) samples revealed significant differences in immune cell profiles and enriched signaling pathways. Specifically, MIBC tumors displayed enrichment of pathways implicated in tumorigenesis, progression, and immune evasion, including WNT/β-catenin, KRAS, and hypoxia signaling, alongside increased macrophage and T regulatory (Treg) cell infiltration and a relative depletion of cytotoxic CD8+ T cells. These findings underscore the intricate interplay between tumor cells and the immune microenvironment in bladder cancer, suggesting potential targets for personalized therapeutic interventions. Future research directions will incorporate spatial transcriptomics, multi-omics integration, and longitudinal studies to further dissect these complex interactions and refine treatment strategies.