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. 2024 Mar 8;5(3):101448. doi: 10.1016/j.xcrm.2024.101448

Figure 2.

Figure 2

Composition of immune cells during LUAD progression

(A) 2D density plots showing immune cell population enrichment over the metacell model in groups of patients with LUAD. (Left) Reference map of nLung and tumor immune populations as in Figure 1B. (Right) Immune cells of nLung and patients with AIS, MIA, and IAC are shown with contour lines indicating the density of projected cells (STAR Methods).

(B) Bar plots showing the immune cell-type composition within the nLung and patients with AIS, MIA, and IAC in each group. Cell types are colored the same as in (A).

(C) Dot plots showing percentages of partial immune cell subpopulation within nLung and patients with AIS, MIA, and IAC. ∗p < 0.05, ∗∗p < 0.01, and ∗∗∗p < 0.001, two-sided Mann-Whitney U test. Error bars indicate mean ± SEM.

(D) Bar plots showing proportion of CD45+ cells in all live cells and CD19+, CD4+, and CD8+ cells in all CD45+ cells; data from fluorescence-activated cell sorting (FACS) analysis. Data are presented as mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, and ∗∗∗p < 0.001, two-sided Mann-Whitney U test. Bars and error bars represent mean +/- standard error.

(E) Line plots showing changes for the activity score of inhibitory receptor genes and cytotoxic genes across four stages (STAR Methods).

(F) 2D projection of subclustered T and NK cells with subpopulations marked by a color code.

(G) Bar plots showing the T and NK cell-type composition within the nLung and patients with AIS, MIA, and IAC in each group. Cell types are colored the same as in (F).

(H) Dot plots showing percentages of partial T and NK cell subpopulation within nLung and patients with AIS, MIA, and IAC. ∗p < 0.05, ∗∗p < 0.01, and ∗∗∗p < 0.001, two-sided Mann-Whitney U test. Error bars indicate mean ± SEM.

(I) Projection of T cell subclusters and TCR clonotype size from 5′ 10× Genomics data.

(J) Fraction of proliferating cells per metacell calculated by defining a cell as proliferative by its fraction of cell-cycle gene expression out of total expression (STAR Methods). Circle size reflects the percentages of proliferating cells in the metacell using the 2D projection as in (F).