Fig. 3. Single-cell analyses reflect extensive intratumoral heterogeneity in protein expression and tumor immune microenvironment.

a HER2–IHC staining in clinical core biopsy specimens of HER2 + (HP) cases. Corresponding FISH (HER2/CEP17 ratio), HER2 average signal/cell (HER2 copy number), HER2 IHC scores, hormone receptor (HR) status, neoadjuvant (NACT) regimen, and pathologic response are reported on the bottom panels. ddAC–TH dose-dense doxorubicin cyclophosphamide followed by paclitaxel/trastuzumab, TCHP docetaxel carboplatin trastuzumab pertuzumab, THP paclitaxel trastuzumab pertuzumab, pCR pathologic complete response, RCB residual cancer burden²³. Images are at 20x magnification. b Intertumoral and intratumoral heterogeneity of HER2 expression in HER2 + research core biopsy specimens, assessed by flow cytometry. Corresponding research core specimens in a were stained for EpCAM and HER2. The distribution of HER2 expression level (x-axis) reflects the extent of HER2 heterogeneity in the EpCAM + cells. Histograms are color-coded according to cases in (a). The percentage indicates the proportion of HER2 + cells in the EpCAM + population. c Heat map showing eight transcriptionally distinct clusters of cells (columns), comprising epithelial and immune cells, identified through unsupervised analysis of single-cell transcriptome data from a triple-negative biopsy specimen. Rows show the expression of key genes that define each cluster.