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. 2024 Oct 9;635(8038):462–471. doi: 10.1038/s41586-024-07943-7

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

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Extended Data Fig. 7 — a. Multicolour immunofluorescence (mIF) analysis of surgically resected early-stage human nsNSCLC confirms a higher ratio of CD11b+/CD8+ cells (N = 13, STK11^MUT and/or KEAP1^MUT and N = 19, STK11^WT and KEAP1^WT) and lower abundance of CD8+ T cells (N = 14; STK11^MUT and/or KEAP1^MUT and N = 27; STK11^WT and KEAP1^WT) in STK11^MUT and/or KEAP1^MUT NSCLC. The Mann–Whitney U test was used for statistical comparisons. b. Inferred neutrophil: T lymphocyte and macrophage: T lymphocyte ratios in STK11 and/or KEAP1-mutant LUAD in the TCGA dataset. The Kruskal–Wallis test was used for the three-group statistical comparisons. c. Immune contexture of LKB1-deficient (N = 22) versus LKB1-proficient (N = 35) (top row) and NRF2^High (N = 8) versus NRF2^Low (N = 49) (bottom row) nsNSCLC in the ICON cohort, based on previously validated gene expression signatures. The Mann–Whitney U test was used for statistical comparisons and P ≤ 0.05 was considered statistically significant. d. xCell-based digital deconvolution of the tumour immune microenvironment in the ICON cohort of surgically resected nsNSCLC (N = 8, STK11^MUT;KEAP1^MUTorWT; N = 10, STK11^WT;KEAP1^MUT;N = 39, STK11^WT;KEAP1^WT). Each box indicates the interquartile range (IQR) with the median and whiskers indicate the upper and lower values within 1.5 times the IQR. The Kruskal–Wallis test was used for the three-group statistical comparison and P ≤ 0.05 was considered statistically significant. e. RNA-seq-based deconvolution of the STK11^MUT and or KEAP1^MUT TIME in the TCGA PanCancer Atlas lung adenocarcinoma cohort. Left to right: ImmuneScore (assessed by xCell); CD8+ T cells (evaluated by QuanTIseq); non-Treg CD4+ T cells (QuanTIseq); and T_H1 signature (xCell). Each box indicates the interquartile range (IQR) with the median and whiskers indicate the upper and lower values within 1.5 times the IQR. The Kruskal–Wallis H test was used for statistical comparisons.

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