Conjoining cell reprogramming and mass spectrometry to identify the proteomic variations in the reprogrammed bladder cancer cells: finding cues of normalisation

Cancer cell reprogramming is a critical area of research that holds the power to transform malignancies into benign states while revealing key mechanisms of carcinogenesis. This study aimed to develop a more effective in vitro bladder cancer model using induced pluripotent stem cell technology and identify potential diagnostic and therapeutic biomarkers for bladder cancer. Sendai virus-based reprogramming was utilised to reprogram the bladder cancer cell line HTB-5. The reprogrammed cells were characterised by expressing pluripotency-associated markers, colony formation abilities, cell migration, and drug responses. LC-MS/MS reveals changes in protein composition among parental cancer cells, reprogrammed cancer cells, and normal uroepithelial cells. Reprogrammed bladder cancer cells display the expression of pluripotency-associated markers and demonstrate altered behaviours, including cell migration and responses to anticancer therapies. The genome-wide regulation by Sendai-virus delivery of Yamanaka factors resulted in distinctive protein expression patterns in reprogrammed bladder cancer cells, indicative of the pluripotency as well as spontaneous differentiation. A total of 297 dysregulated proteins in bladder cancer cells were normalised upon reprogramming. We proposed 25 potential biomarker candidates for diagnostic and therapeutic purposes, of which 12 candidates were demonstrated for the first time at the protein level. Differentially regulated proteins in parental bladder cancer cells and reprogrammed bladder cancer cells highlighted the critical protein-protein interactions that indicate the normalisation process of the parental bladder cancer cells. These cues could be used to pinpoint the candidate proteins to optimise the controlled partial/full reprogramming, to discover the therapeutic potential of reprogramming and to propose clinically relevant biomarker candidates. Cancer cell reprogramming highlights the early stages of bladder cancer, suggesting that the transient expression of pluripotency factors may serve as an initial step in the normalisation process of bladder cancer cells. Proteomic analysis of differentially expressed proteins in parental and reprogrammed cancer cells identifies potential biomarker candidates and paves the way for further exploration in future research. Created in BioRender. Iskender Izgi, B. (2025) https://BioRender.com/2aeyx7m