Fig. 6: Analysis of activated cell states in carcinosarcoma tissue.
From: Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states
a Schematic diagram of carcinosarcoma tissue analysis. Tissue RNA-seq data were used to design Seq-smFISH probes. Tissue was stained with 33 PECAbs followed by Seq-smFISH for 220 genes. All experiments were performed at least 2 times. b Profiling carcinosarcoma tissues. Sample 1, 2, and 3 were derived from different patients, respectively. The dashed-lined square shows the area analyzed by SeqIS and Seq-smFISH. Scale bar, 1000 μm. c Gene expression profiling to select carcinoma-associated genes. d Gene Set Enrichment Analysis using selected genes analyzed by seq-smFISH on MsigDB. e UMAP projection using the 220 Seq-smFISH genes. f Left panel, spatial mapping of clustered cells. Right panel, spatial positions of cells in individual clusters. g Spatial expressions of indicated genes. h PECAbs used in the carcinosarcoma analysis. Blue fill shows relevant features to the indicated antibody. i Average profiling of protein levels in each of the clusters. j Upper panel, the majority cell state groups in each 20 × 20 grid. Occupancy is the fraction of the dominant cell state in the grid. Lower panel, merged image of EMT markers. Scale bar, 400 μm. k Spatial expression profiles of indicated proteins. l Spatial expression of ZEB1 and DAP3 from Seq-smFISH analysis.
