Isoform switching as a key mechanism in chemotherapy resistance in triple-negative breast cancer

Background Triple-negative breast cancer (TNBC) is characterized by limited treatment options and high variability in response to neoadjuvant chemotherapy (NAC). While DNA-level alterations have been widely studied, post-transcriptional regulation through alternative splicing remains unexplored in this context. Methods We performed a transcriptome -wide analysis of differential isoform usage in pre-treatment TNBC biopsies from patients stratified by NAC response. Using IsoformSwitchAnalyzer and STRING, we assessed the functional consequences of isoform switching alterations in coding potential, protein domains, and pathway involvement. Structural models of XRCC3 isoforms were generated using AlphaFold and ChimeraX. Results Non-responder exhibited significantly higher rates of isoform switching, particularly involving transcription start/termination site changes and intron retention. Enrichment analyses revealed immune-related pathway signatures in complete responders and DNA repair in both complete and partial responders. Among key genes, the XRCC3 emerged as a notable candidate, with non-responder showing shift toward truncated isoform lacking domains required for interactions with RAD51 and RAD51C. This structural loss likely impairs homologs recombination repair and may contribute to the observed resistance phenotype. Conclusion Isoform switching is a significant regulatory mechanism associated with chemotherapy response in TNBC. Splicing alterations affecting DNA repair and immune may serve as predictive biomarkers. These findings support the integration of isoform-level analysis into clinical transcriptomics for precision oncology.