Figure 6: SCLC tumors are associated with a pro-fibrotic, immunosuppressive Mono/Mφ subset.

(A) UMAP of SCLC myeloid cells (N=2,951 cells) annotated by myeloid cell type (left) and clusters within the SCLC compartment only (right).

(B) Heatmap showing normalized mean expression of select markers from the IPF-associated profibrotic macrophage gene signature(Adams et al., 2020) (N=143 genes with log fold change > 0.3) per Mono/Mφ subsets. Expression is imputed using MAGIC (k=30, t=3) and scaled from 0 to 1 across clusters. Left barplot shows average z-scored gene expression across the entire gene signature per cluster. Clusters (rows) ordered by signature score.

(C) UMAP of SCLC myeloid cells showing gene signature scores for IPF-associated pro-fibrotic macrophages (left) and monocytes (right). Scores are calculated by taking the average Z-score of imputed expression of a given gene set, taken from(Adams et al., 2020).

(D) Heatmaps showing normalized mean imputed expression of IPF-associated pro-fibrotic macrophage (left) and monocytic (right) gene signatures(Adams et al., 2020) per SCLC Mono/Mφ cluster, as described in (B).

(E) Boxplot showing the proportion of pro-fibrotic Mono/Mφ in each sample of the combined LUAD and SCLC myeloid compartment (combined myeloid cluster 6, which includes SCLC clusters 1 and 7) in different histologies for all samples (N=48) and treatment-naive samples (N=23). We also denote in the overlying swarmplot which samples are matched to the same patient (Mann-Whitney test; error bars: 95% confidence interval). p-values: *<0.05, **<0.01, ***<0.001.

See also Figures S6–S7 and Tables S18–S19.