Panel A shows a tumor experiment schematic and a uniform manifold approximation and projection (UMAP) plot of enriched myeloid cell clusters. Panel B shows a dot plot of marker gene expression across annotated myeloid cell clusters. Panel C shows uniform manifold approximation and projection (UMAP) feature plots of Lyz2, Sell, inflammatory monocytes, Spp1 tumor-associated macrophages, C1q tumor-associated macrophages, and immature tumor-associated macrophages. Panel D shows uniform manifold approximation and projection (UMAP) signature plots comparing classically activated M1 and alternatively activated M2 macrophages. Panel E shows violin plots of pseudotime distributions for WT and CD1d-knockout myeloid cell populations. Panel F shows gene set enrichment analysis plots comparing Spp1 and C1q tumor-associated macrophage signatures in CD1d-knockout and WT macrophages. Panel G shows a heat map of Hallmark pathway enrichment across myeloid cell subsets using normalized enrichment scores.
CD1d controls the myeloid transcriptional program in the TME. (A–G) scRNA-seq was performed for myeloid cells enriched from EO771 tumors from WT and CD1d-KO mice at day 15 (n = 3 mice per condition). (A) Experimental setup and UMAP plot of myeloid cell clusters (subsetted for monocytes, TAMs, DCs, and pDCs) from merged WT/CD1d-KO tumors. Each point represents a single cell colored according to cluster designation. (B) Dot plot showing expression for selected genes in each of the specified myeloid populations. (C and D) Expression levels of selected genes/gene signatures displayed on UMAP plots of myeloid clusters (as in Fig. 3 A). (E) Differentiation trajectory model generated by RNA velocity analysis of c1–c8 clusters. Graphs show c1–c8 over pseudotime (ordered by median) estimated from velocity analysis for WT and CD1d-KO samples. (F) GSEA enrichment plot for transcriptional signature of CD1d-KO (versus WT) Trans-Mac (c4 [top] and c5 [bottom]) compared with signatures from Spp1 and C1q TAMs. (G) GSEA Hallmark pathway analysis showing top enriched signatures. NES values indicate enrichment (red, positive NES) in CD1d-KO or WT cells (blue, negative NES). NES, normalized enrichment score.