Abstract B040: Cell-free DNA captures inter- and intra-patient heterogeneity in advanced bladder cancer

Abstract Metastatic bladder cancer (BLCA) is an aggressive disease complicated by the emergence of variant histological subtypes. The UW/Fred Hutch metastatic BLCA rapid autopsy program is a first-of-its-kind program collecting cell-free DNA (cfDNA) and matched normal tissue, primary tumor, and metastatic tumor samples from advanced BLCA patients, with a focus on these variant subtype tumors. This dataset, consisting of 20 patients with up to five metastases per patient, is a unique opportunity to assess how cfDNA is able to capture heterogeneity across BLCA. We assessed both inter-patient heterogeneity between BLCA subtypes and inter-tumoral heterogeneity within each patient using epigenetic and genomic profiling. Using nucleosome profiling, we identified the activity of lineage markers and transcription factors that distinguish healthy individuals from BLCA patients, and between BLCA subtypes. Furthermore, we conducted a detailed analysis of whole genome (30X) and targeted (4,000X) cfDNA sequencing in their ability to capture the evolutionary history of tumor mutations. Detection of tumor mutations by cfDNA is highly dependent on clonality, with >90% of founder tumor mutations captured by either sequencing method, while capture is decreased for either subclonal mutations or those private to a single metastasis. Importantly, deleterious mutations in BLCA driver genes had close to 100% detection using targeted panel sequencing, even for subclonal mutations. These findings lay the groundwork for the use of cfDNA in clinical BLCA decision-making, including tracking the emergence of pathogenic, targetable mutations and variant subtypes. Citation Format: Samantha L Schuster, Pushpa Itagi, Sonali Arora, Patricia C Galipeau, Thomas W Persse, Michael Yang, Allie Kreitman, Alan Min, Funda Vakar-Lopez, John K Lee, Petros Grivas, Robert B Montgomery, Jonathan L Wright, Andrew C Hsieh, Hung- Ming Lam, Gavin Ha. Cell-free DNA captures inter- and intra-patient heterogeneity in advanced bladder cancer [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B040.