Fig. 4: Diversity within the myeloid cell lineage and functionality according to tissue origins.
a tSNE plot of myeloid cells, color-coded by clusters and cell subsets as indicated. b Complex heatmap of selected myeloid cell marker genes in each cell cluster. Left: Tissue preference of each cluster. Right: Relative expression map of known marker genes associated with each cell subset. Mean expression values are scaled by mean-centering, and transformed to a scale from -2 to 2. Pro-: Pro-inflammatory; Anti-: Anti-inflammatory. c Average cell number and relative proportion of myeloid cell subsets from each tissue origin (excluding undetermined cells). nLung, n = 11 samples; tLung, n = 11; tL/B, n = 4; nLN, n = 10; mLN, n = 7; PE, n = 5, mBrain, n = 10. d, e tSNE plot of DCs, color-coded by clusters, cell subsets, and canonical marker gene expression (gray to red). f Partitioning of dendritic cell (DC) subsets on tSNE plot of myeloid cells in (a). g Cell number and relative proportion of DC subsets in each sample. h Tissue preference of DC subsets. RO/E is the relative score of observed cell numbers over expected cell numbers calculated by chi-square test. The RO/E values of all tissue origins are shown in different colors. Black dots represent different patients. *p < 0.05; **p < 0.01, two-sided Student’s t test. i Median expression of selected marker genes for DC subsets associated with their functionality in each DC subset. **, one-way ANOVA test p-value < 0.01. pDCs, n = 172 cells; Activated DCs, n = 456; CD1c+ DCs, n = 1,782; CD141+ DCs, n = 303; CD207+CD1a+ LCs, n = 177; CD163+CD14+ DCs, n = 1,197. j Representative flow cytometry plots showing pDC (CD11c-CD123+ DCs) populations in primary tumor (T09) and normal lung (N09) tissues. k Paired dot plot of the percentage of pDC (CD11c-CD123+ DCs) population in myeloid cells (CD45+Lin-HLA-DR+) derived from nLung-tLung paired samples (four pairs; P0009, P0014, P0019, P0041). The increase of pDC populations was detected in the selected primary tumor tissues (T09, T14, and T41). P-value = 0.26, two-sided Student’s t test. In the box plot in (h) and (i), each box represents the interquartile range (IQR, the range between the 25th and 75th percentile) with the mid-point of the data, whiskers indicate the upper and lower value within 1.5 times the IQR.
