Fig. 2
Different subclusters and signatures of tumor cells between HER2low TNBC and HER2neg TNBC. (A) Graphic view of the study design. (B) Representative IHC and FISH images showing different HER2 status (IHC 0, 1 + , 2 +) in tumor tissues from three primary TNBC patients (P7, P4 and P5). Scale bars: IHC, 50 μm; FISH, 20 μm. (C) UMAP plot of all the single cells in seven TNBC samples, containing eight identified cell types. SMCs, smooth muscle cells; ECs, endothelial cells. (D) Comparisons of the mean proportions of the eight cell types between the two TNBC groups. P value, Student’s t test (*P < 0.05; **P < 0.01). EC, endothelial cell; SMC, smooth muscle cell. See Additional file 13: Table S6 for details. (E) UMAP plot of tumor cells of HER2low TNBC and HER2neg TNBC. Orange, HER2low TNBC; blue, HER2neg TNBC; green, the common tumor clusters shared in two groups. (F) Heatmap of pathway activation scores by GSVA in two TNBC groups of the unique tumor cell clusters. Shown are GSVA scores from a lineal model. Tumor cell clusters are indicated on the top. The scores were estimated using SCENIC analysis with a Wilcoxon rank-sum test