Figure 2.

Identification of transcriptional signatures for cancer cells from never-smoker and smoker LUADs

(A) UMAP view of all epithelial cells including epithelial cells from normal lung tissues, cancer cells, and non-malignant cells from tumor tissues identified by inferCNV analysis.

(B) UMAP view of subtypes of epithelial cells by tissue types.

(C) Boxplots showing the expression levels of AT2 signature across four tissue types. Two-sided Wilcoxon signed-rank test, ∗∗∗p < 0.001. Asterisks represent the significance of differences in the following comparisons: nNS vs. nS/tNS (black), nS vs. tS (red), and tNS vs. tS (green).

(D) mIHC staining of SFTPC in the four types of tissue samples (nNS/nS/tNS/tS). Nuclei with DAPI (blue) and SFTPC (green). Scale bars, 50 μm. The right side shows the SFTPC staining positivity in each tissue type. Each group contains three samples. Three random fields are derived from each sample. Two-sided Wilcoxon signed-rank test, ∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001. Asterisks represent the significance of differences in the following comparisons: nNS vs. nS/tNS (black), nS vs. tS (red), and tNS vs. tS (green).

(E) Heatmap of signatures for tNS and tS identified by Seurat FindMarkers function (fold change >2).

(F) IHC staining of specific genes from tNS/tS signatures in the four types of tissue samples (nNS/nS/tNS/tS). Scale bars, 100 μm. The immunoreactive scores (IRSs) of IHC in each tissue type are shown at the bottom. Each group contains three samples. Three random fields are derived from each sample. Data are represented as mean ± SD. Two-sided Wilcoxon signed-rank test, ∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001. Asterisks represent the significance of differences in the following comparisons: tNS vs. tS/nNS/nS (black), and tS vs. tNS/nNS/nS (red).

(G) Kaplan-Meier curves for the OS of TCGA-LUAD patients (n = 453), which were divided into two groups according to the mean expression of tS signature. Plus signs (+) indicate censored observations; p value was calculated using the two-sided log rank test.

(H–J) UMAP view of cancer cells, colored by clusters (H), patients (I), and smoking status (J).

(K) Boxplots showing the expression levels of the MHC-II signature across 16 clusters of cancer cells.