Panel A shows a UMAP plot with points representing single cells colored according to cluster designation. Panel B displays bar graphs showing the frequencies of cell clusters in WT and CD1d-KO samples. Panel C presents a table with the number of cells per cluster in WT and CD1d-KO samples. Panel D features a heatmap showing the top differentially expressed genes per cluster. Panel E includes trajectory models showing pseudotime, cell types, and gene expression over pseudotime. Panel F shows violin plots comparing gene expression in WT and CD1d-KO c3_Inflam-Mono cells. Panel G contains a dot plot and a bar graph showing gene expression and pathway analysis in myeloid clusters from human breast cancer. Panel H presents forest plots from a multivariate Cox regression analysis. Panel I shows a table with the number of cells per cluster before and after PD-1 neoadjuvant therapy. Panel J features UMAP plots of myeloid cell clusters before and after PD-1 neoadjuvant therapy. Each graph and plot provides detailed insights into the transcriptional regulation of myeloid cell populations by CD1d in breast cancer.
Transcriptional regulation of myeloid cell populations by CD1d. (A) Workflow and UMAP plot of cell clusters from merged WT/CD1d-KO tumors. Each point represents a single cell colored according to cluster designation. (B and C) Frequencies of cell clusters (B) and number of cells per cluster (C) in WT and CD1d-KO samples. (D) Phenotype of the different clusters represented as a heatmap showing the top DEGs per cluster. (E) Differentiation trajectory model generated by RNA velocity analysis of c1–c8 clusters for WT and CD1d-KO samples, showing pseudotime (top), cell types (middle), and gene expression (Lyz2, Plac8) over pseudotime. (F) Violin plots showing the expression of the depicted genes in WT and CD1d-KO c3_Inflam-Mono cells. Wilcoxon rank-sum test. (G) Top: Dot plot showing expression for selected genes in each of the specified myeloid clusters from human breast cancer (Wu et al., 2021) as depicted in Fig. 5 A (right) and cell numbers per cluster (left). Bottom: GSEA Hallmark pathway analysis showing top positively enriched gene sets in c9_Macrophage_2_CXCL10 macrophages from human breast cancer (Wu et al., 2021). NES = normalized enrichment score. (H) Forest plots showing a multivariate Cox regression analysis for the indicated risk factors. (I and J) Number of cells per cluster (I) and UMAP plot (J) of myeloid cell clusters from breast cancer patients (Bassez et al., 2021) before (pretreatment) or after (on-treatment) αPD-1 neoadjuvant therapy.