Abstract 5541: Dissecting chemotherapy resistance development in triple negative breast cancer through single cell multiome and lineage tracing

Abstract Triple negative breast cancer (TNBC) is a breast cancer subtype that manifests fast disease progression and very poor overall survival. Despite initial response to standard of care, development of therapy resistance remains the major challenge in TNBC clinical management. Delineating the mechanisms underlying resistance development has been impeded by the still unknown cell population of origin and lack of longitudinal molecular profiling. To investigate this question, we applied a CRISPR based lineage tracing system into TNBC cell lines. Longitudinal samples from an Antibody Drug Conjugate (ADC), Sacituzumab Govitican sensitive to resistance were collected in vitro via stepwise drug dose escalation and in vivo via xnenograft serial transplantation. We leveraged cellular barcoding with single cell multiome from 10X genomics to simultaneously capture clonal identity, accessible chromatin and gene expression and hence, directly linked lineage with functional cell states. Preliminary results suggest that TNBC cells adopted distinct cell states shortly after drug exposure with characteristics including upregulation of epithelial-to-mesenchymal transition (EMT) genes, stemness markers and downregulation of immune related pathways. Clonal level analysis revealed only a subset of clones survived initial treatment and are enriched in specific “primed” cell states. Next, we will construct single cell lineage trees and quantify clonal dynamics and cell state transition rates. We will identify and validate regulators of cellular plasticity and explore if potential drug combinations will prevent emergence of resistance cell state. Overall, this study will build a comprehensive map of the phenotypic trajectory towards chemotherapy resistance and pinpoints biomarkers of therapy response in triple negative breast cancer. Citation Format: Chufan Zhang, Chu Pan, Dave Cescon, Mathieu Lupien. Dissecting chemotherapy resistance development in triple negative breast cancer through single cell multiome and lineage tracing [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 5541.