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. 2024 Dec 10;13:RP92672. doi: 10.7554/eLife.92672

Figure 6. CellChat communication indicates tissue-resident natural killer (trNK) communicate directly to cDCs.

(A) Uniform manifold approximation and projection (UMAP) of the dendritic cell sub-clusters from the Steele dataset. (B) Violin plot showing the expression of XCL1, XCL2, and XCR1 across all cell types. (C) Circle plots showing interactions across all cell types (top left), signals coming from the tissue-resident natural killer (trNK) cells (top right), the XCL1-XCR1 interaction (bottom left), and the XCL2-XCR1 interaction (bottom right). The width of edges represents the communication strength. (D) Heatmap showing the summary of secreted signaling communications of outgoing (left) and incoming (right) signals. The color bar represents the communication strength, and the size of the bars represents the sum of signaling strength for each pathway or cell type. (E) Schematic overview of the trNK to type 1 conventional dendritic cell (cDC1) and cDC1 to CD8 T-cell communication axis (top). Circle plots of all outgoing signals from cDC1 (bottom left) and the CXCL16-CXCR6 signaling (bottom right). (F) Correlation of HALO data on total NKNKG2D-ve NK cells (CD3-NK1.1+NKG2D-) with CD8 T-cells (CD3+CD8+) from stained sections of treated KPC_F orthotopic tumors, R2 and p-values indicate positive correlation across all tumors (gray, n=15) or limited to mock, CCR5i+IR and IR/CCR5i/αPD1 combination (red, n=9). (G) Correlation of trNK signature with CD8A (left) or CD8B (right) in bulk RNA-seq from TCGA_PAAD and binned into quartiles based on extent of cDC1 involvement as assumed by cDC1 signature (Figure 6—source data 1).

Figure 6—source data 1. Gene signatures for trNK and cDC1.

Figure 6.

Figure 6—figure supplement 1. Profiling of dendritic cells indicates specific communication.

Figure 6—figure supplement 1.

(A) Uniform manifold approximation and projection (UMAP) of the myeloid cell types from the Steele dataset (top) and the dot plot showing the canonical cell markers (bottom). (B) Heatmap of the top 15 markers for each DC sub-cluster. (C) Dot plot showing the estimated outgoing secreted signals from the natural killer (NK) C1 cell population. (D) Dot plot showing the estimated secreted and cell-cell contact signals from the type 1 conventional dendritic cell (cDC1) cell population. Color of the dots represents the communication probability, and the size of the dot represents the significance level.