Fig. 3: Tumour sections from TNBC patients reveal the spatial transcriptomic landscape of immunofluorescence (IF)-stained tissue sections.

a Number of genes detected in the isolated target regions according to the four staining groups (n = 106 biologically independent samples (ROI)). Interquartile range (IQR) of boxplot is between Q1 and Q3 and centre line indicates median value. Whiskers of boxplot is extended to the maxima and minima. Maxima is Q3 + 1.5*IQR and minima is Q1 − 1.5*IQR. b Haematoxylin and eosin (H&E) stained serial tissue section (left). ERBB2 gene expression data from Select-seq (middle). RNA-fluorescence in situ hybridization (FISH) of serial tissue sections (right) (scale bar, 500 μm). We obtained the above results from three different tissue sections. c Lehmann TNBC subtyping. Red and green boxes indicate upregulated and downregulated gene pathways. BL1 basal-like type 1, BL2 basal-like type 2, IM immunomodulatory, ML mesenchymal-like, MSL mesenchymal stem cell-like, LAR luminal androgen receptor. Source data are provided as a Source Data file. d Gene expression heatmap of the target regions. e Principal component analysis (PCA) of the target regions. f RNA velocity analysis of the target regions. Arrow indicates the A-to-I-edited sample in GPX4. g Mean and standard deviation (SD) of immunosuppressive gene signature and GPX4 gene expression in different spatial groups. h Spatial mapping of signature genes related to immunosuppression. Yellow, green, red, and blue marks indicate (i) CD44⁺/ALDH1⁺, (ii) CD44^low/−/ALDH1^high, (iii) CD44^high/ALDH1^low/−, and (iv) CD44⁻/ALDH1⁻ regions, respectively, as determined by IF.