Fig. 1: Single-cell RNA profiling unveils tissue-specific immune landscape of tVAT.
a, Study design illustrating the data analysis (left), and representative images of surgical specimens from patients with CRC (Stage, T4a; right). b, Uniform Manifold Approximation and Projection (UMAP) visualization showing major cell clusters from tumour, normal, tVAT and dVAT samples derived from patients with CRC. The cell types shown NK cells, DC, Mono (monocytes), Mφ (macrophages), Neutro (neutrophils), Mast (mast cells), Endo (endothelial cells) and Epi (epithelial cells). c, Heatmap showing the tissue preferences of 13 cell types by the Ratio of observed to expected (Ro/e) index, illustrating preferential cell type enrichment across different tissue regions. d, UMAP visualization of neighbourhoods (Nhoods) identified by Milo, highlighting the differentially abundant neighbourhoods between tVAT and dVAT. Each Nhood is represented as a node, coloured according to log2 fold change (FC) between tVAT (n = 12) and dVAT (n = 12). Non-differentially abundant neighbourhoods (false discovery rate ≥ 0.1) are displayed in white. Node sizes are proportional to the number of cells in each Nhood, with graph edges representing shared cell quantities between adjacent neighbourhoods. e, Beeswarm plot illustrating the distribution of adjusted log2 FC in abundance of Nhoods between tVAT (n = 12) and dVAT (n = 12) across all cell types. The cell types shown include major immune cell and stromal cell lineages. f, Boxplot comparing the relative abundance of CD4+ T cells, CD8+ T cells, B cells and stromal cells between tVAT (n = 12) and dVAT (n = 12), analysed using a two-sided paired Wilcoxon test. The box hinges denote the first and third quartiles, the median is represented by the centre line and the whiskers encompass the full data range. Individual data points are shown as dots. g, Representative images of hematoxylin and eosin staining (23 samples) and mIHC staining (four samples) for TLSs in dVAT and tVAT sections from patients with CRC. Scale bar, 200 μm. Panel a created in BioRender: Huaiqiang, J. https://biorender.com/vnv4y0b (2026).
