Fig. 4: Single-cell expression analysis of resected tumors and uninvolved normal lung tissues from patients treated with neoadjuvant Nivo+CT and Ipi+Nivo+CT.

scRNA-seq analysis was performed on matched NSCLCs and uninvolved normal lung tissues from patients treated with Nivo+CT (n = 2) and Ipi+Nivo+CT (n = 5). scRNA-seq was also performed on an LN sample from a patient treated with Nivo+CT. a, Left: UMAP visualization of 95,417 high-quality and non-cycling cells after clustering. Clusters are color-coded by major cell lineage: lymphoid, myeloid, epithelial and stromal (fibroblasts and endothelial cells). Right: bubble plot showing mean expression and abundance of marker genes that are differentially expressed among the four major lineage groups. b, Fractions of the indicated cell subsets from their respective lineages were computed in tumors (red bars) and normal tissues (blue bars) as such: CD8⁺ TERM eff/TEM from CD8⁺ T cells; naive CD4⁺ T cells, T_reg cells and Tfh cells from all CD4⁺ T cells; B cells from lymphoid cells; classical monocytes and TAMs from myeloid cells; and NCAM1⁺/FCGR3A⁺CD56⁺/CD16⁺ NK cells from all innate lymphoid cells. Fractions of the indicated cell subsets were then statistically compared between matched tumor and normal tissues from all seven patients. P values are from two-sided proportion test. c, Fractions of the indicated cell subsets from their respective lineages were computed in tumors from Nivo+CT (green bars) and tumors from Ipi+Nivo+CT (red bars), as in b, and were then statistically compared between tumors from both treatment groups. P values are from two-sided proportion test. d, Correlation plots between fractions of the indicated cell subpopulations and the percentage of remaining viable tumor at the time of surgical resection. Fractions were computed in the manner described above: CD8⁺ memory T cells (CD8⁺ Mem) from all CD8⁺ T cells, B cells from all lymphoid cells and M2-like macrophages from all myeloid cells. Correlation coefficients were computed using Spearman’s correlation. P values were computed by two-sided Spearman’s correlation test. Source data for d are provided in Supplementary Table 8.