Single-Cell RNA and ATAC Sequencing Reveal Cellular Heterogeneity and Chromatin Accessibility Dynamics in Young Chinese Breast Cancer Patients across Pre- and Post-Neoadjuvant Therapy

Young breast cancer (YBC) patients (age ≤ 40) exhibit aggressive features and poor prognosis, while facing complex needs including breast-conserving surgery and fertility preservation. Neoadjuvant therapy (NAT) is important for tumor downstaging and breast-conserving surgery in YBC treatment, but the NAT response mechanisms in YBC patients remain unelucidated. Here, we analyzed pre- and post-NAT samples from Chinese YBC patients using scRNA-seq and scATAC-seq. We found that NAT reshaped cellular heterogeneity in the tumor microenvironment (TME), reducing epithelial and T cells while increasing endothelial cells and fibroblasts. Residual cancer cells showed enriched epithelial-mesenchymal transition (EMT) and stromal remodeling programs. NAT responders had fewer luminal-like cells and retained basal-like cells in an early hybrid EMT state, whereas non-responders maintained both populations with late hybrid EMT. We identified therapy-resistant genes and motifs (e.g., VTCN1, PROM1, MZB1, Fox family) and linked CXCL13 upregulation to poor NAT response and tumor-specific T-cell expansion. Cell–cell communication analysis revealed NAT reprograms the TME by suppressing VEGF and TNF signaling in basal cells, while residual luminal cells transmit EGFR and CD47–SIRPA signals.