Decoding clone evolution in HER2 amplified breast cancer through single-cell and spatial transcriptomics analysis of copy number variations

HER2-positive breast cancer exhibits marked genomic instability and heterogeneity, yet the clonal architecture and copy number variation (CNV) dynamics between ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC), remain poorly understood. We analyzed single-cell RNA sequencing data from 14 HER2-positive breast cancer patients and spatial transcriptomics from 8 patients. CNVs were inferred to evaluate genomic alterations and reconstruct tumor subclone evolutionary trajectories. Survival analyses were performed on CNV-correlated transcripts. We identified 68,064 cells and 4,764 spatial transcriptomic spots, and observed early and pervasive CNV events in DCIS. IDC exhibiting a higher CNV burden supported the hypothesis of progressive genomic instability during tumor evolution. Shared CNV regions across DCIS and IDC suggested the common clonal origin, favoring a multi-threaded evolutionary model. Amplifications in chromosome 17q12-21 were associated with poor prognosis. CNV-driven clonal evolution probably originates at early stages of HER2-positive breast cancer and persists through disease progression. Early CNV events may serve as predictive biomarkers and potential intervention targets to prevent disease advancement.