Fig. 5: Trem2⁺Vcam1⁺ skin cancer associated myeloid cells (SCAMs) are distinct from other non-cancer associated Trem2⁺ myeloid cells.

a UMAP of merged scRNA-Seq from our myeloid cells from mBCC (n = 2 primary tumors), normal skin (n = 4 independent samples), and during wound healing (n = 3 independent samples). Clusters: normal (green), wounded macrophages (blue), wounded dendritic cells (purple), and BCCs (red). b Feature plots for Itgax, Itgam, Adgre1, and Trem2. c Marker genes and GO analysis associated with a. d Stacked violin plots showing marker genes associated with clusters in a. e Feature plot of Vcam1 expression for the scRNA-Seq data in a. f Flow cytometry analysis and quantification of VCAM1/Vcam1 in human and mouse BCCs (n = 3 independent tumors). Error bars represent mean +/− SD. g RNAScope confirmation of Trem2 (green) and Vcam1 (magenta) in mBCCs. Magenta arrows indicate dual Trem2⁺Vcam1⁺ cells. Scale bar = 50 μm. Image is representative of n = 2 independent tumors. h Feature plot of VCAM1 expression for the scRNA-Seq data in Fig. 3b. i Updated macrophage polarization summary diagram. j Feature plot of Mki67 expression in the scRNA-Seq data in a. k Macrophage proliferation scoring of clusters in a. l Diagram of the sorting strategies for Trem2⁺ cells from normal skin, wounded skin, and BCCs. m PCA plot of the differential bulk ATAC-Seq analysis for Trem2⁺ cells form the different tissues (n = 2 samples from each tissue) in l. n DESeq comparisons between the Trem2⁺ cells form the different tissues in l. o GO terms are associated with the list of genes associated with the differential peaks from DESEq comparisons. p values were calculated from the hypergeometric distribution. p Example tracks for Trem2 and Vcam1 showing open peaks (highlighted in red) that are specific to Trem2⁺ cells from the mBCC. q Motifs enriched and de-enriched between SCAMs and Trem2⁺ cells from the normal tissue. Motifs and subsequent p values were derived from the HOMER pipeline, which uses cumulative binomial distribution. r Venn diagram of the AP-1 motif enrichment/de-enrichment at unique and shared sites that correspond to specific genes. Source data are provided as a Source data file.