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. 2023 Jan 26;29(2):440–449. doi: 10.1038/s41591-022-02163-w

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 9 — Gene set enrichment analyses of on-treatment pTMB-high (n = 9) vs. pTMB-low (n = 22) melanomas revealed a marked enrichment of interferon-γ and inflammatory responses in the tumor microenvironment of pTMB-high vs pTMB-low tumors after ICB. In contrast, this profile was not observed in the tumor microenvironment of TMB-high (n = 8) compared to TMB-low (n = 23) melanomas. Pathways with a minimum adjusted p-value of 1e-05 in pTMB high vs low comparison are shown. The T Cell Inflamed GEP gene set was derived from Cristescu et al., Science, 2018 and the Inflammatory Response gene set was derived by Ayers et al., J Clin Invest, 2017, while the remainder of gene sets were included in the Molecular Signatures Database (Methods). Nominal two-sided p-values are calculated using permutation testing and FDR adjusted p-values shown for gene set differential expression are provided for comparison of pTMB/TMB-high vs low groups. Abbreviations; BC: Biocarta, HM: Hallmark, KG: KEGG, RT: Reactome, EMT: Epithelial–mesenchymal transition, Cyt: Cytokine, Rec: Receptor, Med: Mediated.