Fig. 1

TAM as a Major Contributor to BC Clinical Outcomes. A UMAP visualization depicts three primary immune cell clusters from BC (n = 5) tissues, including T cells & NK cells, B cells & plasma cells, and myeloid cells. B Expression of classical marker genes used to identify the main clusters (myeloid cells: CSF1R, AIF1; T & NK cells: CD3D, PTPRC, NKG7; B & plasma cells: CD79A). C MetaTiME cell state annotations based on top-enriched MeC in BC cell clusters. D Differential enrichment of cell states in BC pre- and post-treatment, evaluated using MeC feature testing. X-axis: difference in average feature scores between pre- and post-chemotherapy conditions. Y-axis: -log(p-value) from two-sided t-tests. Significant cluster difference signatures are labeled as “EnrichedMeC@ClusterName”; when the enriched MeC coincides with the cluster name, the signature is marked as “ClusterName”. Red dots represent signatures with increased difference; dot size is proportional to the average feature score of cells in the cluster under post-immunotherapy conditions. Blue dots indicate suppressed features; dot size is proportional to the average feature score of cells in the cluster under pre-chemotherapy conditions. E Differential enrichment of cell states between BC treatment responders and non-responders, assessed using MeC feature testing