Abstract 2755: The m6A epitranscriptomic landscape of bladder cancer is characterized by sequential 3'UTR hypermethylation and global methylation dilution

Abstract N6-Methyladenosine (m6A) is the most prevalent internal modification of eukaryotic mRNAs and affects the regulation of its target transcripts in all aspects of the mRNA life cycle. Cancer-associated changes in the m6A epitranscriptomic landscape as well as the deregulation of m6A regulators have been linked to cancer development. However, most studies have focused on in vitro or in vivo models and antibody-dependent mapping techniques, which have limited resolution and lack quantitative methylation information. Here, we provide the first transcriptome-wide, base-resolution map of m6A in cancer and determine methylation levels with absolute stoichiometric information by comparative sequencing of nine urothelial carcinoma of the bladder (UCB) and nine non-malignant uroepithelial control samples. Our results define key signatures of the cancer-associated m6A epitranscriptomic landscape of UCB, which was characterized by differential methylation of cancer-related mRNAs. m6A hypermethylation primarily occurred near stop codons and was associated with upregulation of the VIRMA subunit of the m6A methyltransferase complex, and alternative polyadenylation. Furthermore, the integration of methylation data and expression data revealed a global dilution of methylation marks in UCB, which was caused by the decreased expression of highly methylated transcripts, combined with the increased expression of unmethylated transcripts. Notably, both changes appeared sequentially during the progression to muscle-invasive bladder cancer. Our study thus characterizes the systematic differences in the m6A methylome of UCB and establishes the potential of m6A profiling for cancer biomarker development. Citation Format: Jonas Koch, Felix Bormann, Vitor Coutinho Carneiro, Manuel Neuberger, Katja Nitschke, Malin Nientiedt, Philipp Erben, Maurice S. Michel, Frank Lyko. The m6A epitranscriptomic landscape of bladder cancer is characterized by sequential 3'UTR hypermethylation and global methylation dilution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2755.