Spatiotemporal organisation of residual disease in mouse and human BRCA1-deficient mammary tumors and breast cancer

Breast cancer remains one of the prominent causes of death worldwide. Although chemotherapeutic agents often result in substantial reduction of primary or metastatic tumors, remaining drug-tolerant tumor cell populations, known as minimal residual disease (MRD), pose a significant risk of recurrence and therapy resistance. In this study, we describe the spatiotemporal organisation of therapy response and MRD in BRCA1;p53-deficient mouse mammary tumors and human clinical samples using a multimodal approach. By integrating single-cell RNA sequencing, spatial transcriptomics, and imaging mass cytometry across multiple treatment timepoints, we characterise dynamic interactions between tumor cell subpopulations and their surrounding microenvironment. Our analysis identifies a distinct, drug-tolerant epithelial-mesenchymal transition (EMT) cancer cell population, which exhibits a conserved expression program in human BRCA1-deficient tumors and significantly correlates with adverse clinical outcomes. We further reveal the spatial distribution of residual EMT-like tumor cells within specific anatomical niches, providing a framework for understanding the persistence of MRD and potential therapeutic vulnerabilities. These findings yield a comprehensive molecular roadmap of MRD, opening new avenues for therapeutic strategies targeting EMT-driven drug tolerance and tumor relapse. Overall design: Spatial transcriptomics: Mammary tumors derived from the K14cre;Brca1F/F;Trp53F/F (KB1P) mouse model were transplanted into the fourth mammary fat pad of syngeneic FVB/NJ mice. To minimise genetic variability, all tumors originated from two parental tumors that were subdivided before transplantation. Tumor-bearing mice were sacrificed at baseline or treated with a single dose of cisplatin or TAC therapy (doxorubicin, docetaxel, and cyclophosphamide). Spatial transcriptomics (ST) was applied to primary (n = 10), residual (n = 16), recurrent (n = 4) tumor sections, and healthy mammary glands (n = 2), (total n = 32). Residual tumors were collected at 7 (TAC: n = 2, Cisplatin: n = 2) or 12 days (TAC: n = 4, Cisplatin: n = 3) post-treatment. Recurrent tumors were harvested upon regrowth (TAC: n = 2, Cisplatin: n = 2). All animal experiments were approved by the Animal Ethics Committee of the canton of Bern (Switzerland) and are in accordance with the current Swiss Acts on Animal Experimentation. Additionally, tumor samples from five women carrying germline BRCA1 mutations were collected at surgery. ST was performed on primary (n = 2) and residual (n = 3) tumors (after neoadjuvant chemotherapy). Patients were treated at Geneva University Hospitals in Switzerland. The study was approved by the local ethical committee under protocol CCER 2019-00004, and all donors were coded. scRNA-seq: Mammary tumors derived from the K14cre;Brca1F/F;Trp53F/F (KB1P) mouse model were transplanted into the fourth mammary fat pad of syngeneic FVB/NJ mice. To minimise genetic variability, all tumors originated from two parental tumors that were subdivided before transplantation. Tumor-bearing mice were sacrificed at baseline or treated with a single dose of TAC therapy (doxorubicin, docetaxel, and cyclophosphamide). Single-cell RNA sequencing was performed on primary (n = 3) and residual (n = 3) tumors and collected 12 days post-treatment. All animal experiments were approved by the Animal Ethics Committee of the canton of Bern (Switzerland) and are in accordance with the current Swiss Acts on Animal Experimentation.