Integrated analysis of single-cell and bulk RNA sequencing predicts prognosis and therapeutic response using malignant epithelial cells marker genes in bladder cancer

Abstract Bladder cancer remains a prevalent malignancy of the urinary system, closely tied to aberrations in bladder epithelial tissue. To better understand its complexities, this study delved into single-cell data to identify key marker genes of malignant cells. Subsequent analyses uncovered significant pathways facilitating intercellular communication, including COLLAGEN, PTN, and MK pathways. Additionally, pivotal transcription factors like SMARCA4 and CEBPD were identified, shedding light on regulatory mechanisms within malignant cells. Furthermore, leveraging these marker genes, patients with bladder cancer were stratified into distinct groups, with implications for prognosis and immunotherapeutic response. Group C1 exhibited a favorable prognosis, contrasting with Group C2, characterized by heightened immune microenvironment infiltration and expression of immune checkpoints, particularly responsive to PD-1 inhibitors. Building upon these findings, a robust four-gene prognostic model was developed and validated across diverse datasets, offering insights into personalized treatment strategies. Moreover, the study spotlighted CD109 as a noteworthy player in bladder cancer pathogenesis, evidenced by its heightened expression in tumor tissues and its role in promoting proliferation, migration, and invasion of bladder cancer cells, as demonstrated through immunohistochemistry experiments following CD109 knockout. In summary, this research uncovers vital pathways and regulatory elements driving bladder cancer progression.