Fig. 4: scFFPE-ATAC reveals spatially distinct epigenetic regulators in the tumor center and invasive edge of FFPE human lung cancer at single-cell resolution.

a Hematoxylin and eosin (H&E) staining of human lung cancer tissue, with the tumor center (TC) and invasive edge (IE) indicated by colored circles. Left: Whole H&E-stained section. The blue circle marks the tumor center, and the red circles indicate the invasive edge of the tumor. Right: Zoomed-in regions of the areas pointed to by the colored lines (blue = TC; red = IE) in the left panel, showing the tumor center and invasive edge. Three adjacent sections were cut and stained, showing consistent results. b Parameters for selecting high-quality cells from scFFPE-ATAC. TSS = transcription start site. c Cell type identification using a high-dimensional reduction technique. d Proportional distribution of different cell types in TC and IE. e Distribution of TC and IE across different clusters. f Proportional distribution of TC and IE within different cell types. g Predicted active genes from scFFPE-ATAC for each cell type. h Representative active genes from scFFPE-ATAC for each cell type. i Identification of differentially accessible chromatin peaks between TC and IE. Left: Volcano plot showing the cutoff (False Discovery Rate (FDR) ≤ 0.05, |Log₂(Fold change)| ≥ 1). Right: Heatmap displaying the identified peaks. A one-sided Fisher’s exact test was applied in the significance test. The FDR was corrected using the Benjamini–Hochberg (BH) method. j Enriched transcription factors on differentially accessible chromatin peaks between TC and IE. k Pseudotime trajectory analysis of epithelial cells from the tumor center to the invasive edge. Left: Two identified trajectory paths and four cell clusters along the trajectories. Middle: Distribution of epithelial cells from TC and IE across the two trajectories. Right: Distribution of epithelial cells from TC and IE across the four clusters. l Specific gene pathways identified from the two trajectories. m Specific transcription factors identified in the two trajectories. Source data are provided as a Source Data file for Fig. 4b-m.