Fig. 5: Spotiphy reveals tumor–TME changes across spatial domains in human breast tissue.
From: Spotiphy enables single-cell spatial whole transcriptomics across an entire section
a,b, UMAP of 23,200 cells from iscRNA data produced by applying Spotiphy to human breast tissue Visium data. Cells are color coded according to their cell type (a) or sample of origin (b). LumSec and LumHR cells are encircled by dashed black lines in a. c, Results of applying inferCNV to the iscRNA data in a. Tumor cells originating from BC1160920F (LumSec) and BCCID4535 (LumHR) are encircled by dashed black lines. d,e, Transcriptomic spots from the Visium data are color coded according to their constituent LumSec cell sample of origin: BCCID44971 (d) and BC1160920F (e). The opacity of the spots is representative of cell density; scale bars, 500 μm. f, Violin plots of the N-Sec and T-Sec scores for the LumSec cells identified in the iscRNA data from normal sample BCCID44971 and tumor sample BC1160920F. All P values are <\({2.2\times 10}^{-16}\). g, Violin plots of the N-Sec and T-Sec scores for the LumSec cells identified in the Resolve smFISH data of normal sample P69-S3 and tumor sample P35-S1; top, P = \({3.3\times 10}^{-2}\); bottom, P = \({2.3\times 10}^{-5}\). h, Visualization of signature genes in selected regions of the Resolve smFISH data. Blue and red represent the signature genes used to calculate the N-Sec and T-Sec scores, respectively. Cell boundaries are depicted with gray lines; LumSec cells are outlined in white. Resolve smFISH data include three biological replicates each for P69 and P35 samples; scale bar, 100 μm. i, Transcriptomic spots from the Visium data. Spots are color coded according to their constituent LumSec cell spatial domains; scale bar, 500 μm. j, Cell-type proportions of the three spatial domains based on the iscRNA data. k,l, Results of applying CellChat to the iscRNA data of the cells in the three LumSec spatial domains. k, Number of interactions among cell types across three spatial domains. l, Interaction strength among cell types across three spatial domains. Data were analyzed by two-sided t-tests (f and g); ***P < 0.01 and **P < 0.05.
