Identification of dynamic alternative splicing during mammary epithelial-to-mesenchymal transition | LC26

Abstract
Breast cancer is the most common cancer among women worldwide and the second leading cause of cancer-related death among North American women. Metastatic breast cancer remains particularly challenging to treat due to its aggressiveness and resistance to standard therapies, resulting in a five-year survival rate of approximately 30%. Metastasis requires epithelial breast cells to undergo epithelial-to-mesenchymal transition (EMT), a reversible process involving extensive, context-dependent transcriptional reprogramming that confers mesenchymal traits. A deeper understanding of the molecular regulation of EMT is essential for identifying better therapeutic strategies. Although alternative splicing is known to contribute to EMT, its global dynamics during EMT remains incompletely defined. Here, we combined long-read nanopore cDNA-PCR sequencing with assay for transposase-accessible chromatin using sequencing (ATAC-Seq) to generate a time-resolved, transcriptome-wide map of alternative splicing events during breast EMT. Using a custom analysis pipeline, we quantified isoform diversity and RNA-level remodeling across time, revealing that EMT is accompanied by highly dynamic and widespread alternative splicing. These events constitute a major source of transcriptomic variation with potential functional consequences at the proteome level and allowed us to identify previously unannotated coding and noncoding isoforms. We prioritized key splicing events and validated their presence in metastatic patient tumors using short-read Illumina sequencing. To investigate their functional roles, we developed a quantitative EMT progression assay based on fluorescent markers and cellular phenotyping. We will employ CasRx to selectively target specific transcript isoforms and assess their contribution to EMT. This long-read sequencing-driven approach provides a framework for uncovering novel therapeutic targets in metastatic breast cancer.

Biography
Sophie Ehresmann completed a BSc in Biochemistry and molecular medicine, followed by a MSc in Molecular biology at the University of Montréal. Under the supervision of Dr Philippe Campeau, she wrote her MSc thesis titled "Epigenomic impact of mutations in chromatin regulators associated with neurodevelopmental disorders". Sophie then joined the laboratory of Dr Martin Sauvageau to pursue her PhD in molecular biology with an emphasis on RNA and cancer studies where she developed an expertise in both bioinformatics and biochemical assays.