Figure 5. The TME contains macrophages with a distinct phenotype.

(A) Bar plot of macrophage metacluster frequency from 18 lung adenocarcinoma patients across tissue (see Figure 4C).

(B) Comparison of average transcript expression between macrophage clusters enriched in tumor (cluster 7) or lung (weighted average of clusters 5 and 6; Figure 4A), showing highly expressed transcripts, genes with FC > 2 colored red (left), bar plots of indicated transcript expression (right).

(C) viSNE plots showing single-cell expression of CD68, CD163, PD-L1, and PPARγ across tissues in a representative patient.

(D) Heatmap showing relative normalized protein expression of tumor macrophages as ratio to those from nLung for 16 patients (left) and average expression across patients of indicated markers on mononuclear phagocyte metaclusters in tumor (right). Bar plots of normalized expression of indicated proteins by macrophages in tumor and nLung (n =18)

(E) Bar plot of normalized PD-L1 expression across metaclusters in tumor (n=18; top). MICSSS for CD3, CD68, and PD-L1 showing a macrophage-dense region at the tumor invasive margin (bottom).

(F) IL-6 expression in nLung and tumor macrophages. viSNE plots showing IL-6 expression of a representative patient (top). Bar plot showing expression of IL-6 transcripts (left) and normalized protein expression across macrophages in nLung and tumor (right; n=10).

Bar plots show mean ± SEM; *p<0.05, **p<0.01 and ***p<0.001 by paired t-test. Fold-change (FC).

See also Figure S5