Fig. 5: Subclonal microenvironment and ligand and receptor analyses.

Using squidpy we surveyed the cell types neighbouring each cell type at 3 different distances (Supplementary Data 9). a Neighbouring cells at the shortest radius of 110 pixels (median of 3 neighbouring cells). Rows indicate query cell type. Columns are neighbouring cell types. Numbers in cells are the percentage across each row. Green indicates maximum value per row. Residual proportions after removing homotypic tumour cell-tumour cell neighbours are also shown. Enriched and depleted cell populations are indicated with e and d, respectively. b Cell neighbourhood analyses showing seven cell populations that each contribute at least 3% of the neighbouring non-tumour cells at three distances yielding medians of 3, 30 and 100 neighbouring cells, respectively. Populations significantly more abundant near the PIGR+ and PTGS1+ clones are indicated in blue and with *, and in pink with #, respectively. Ligand-receptors signalling between tumour subclones and cells in their microenvironment involving: c Ligands up-regulated in the PIGR+ subclone, d Ligands up-regulated in the PTGS1+ subclone, e Receptors up-regulated in the PIGR+ subclone, f Receptors up-regulated in the PTGS1+ subclone. Secreted ligands and plasma membrane ligands are indicated by red and blue bars, respectively. Magma palette used; dark pixels indicate strongest signalling and white indicates no signalling. Autocrine loops are indicated with a. Receptors and ligands needed to be detected in ≥ 10% of cells from a cell type to be shown. Note: only 281 of 828 ligands and 229 of 691 receptors in connectomeDB2020⁴⁶ are covered on the CosMx platform, thus many subclone-specific signalling events are likely missed in this analysis.