American Association for Cancer Research
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Supplementary Materials and Methods, Supplementary Figures 1 through 6, and Supplementary Tables 1 through 8 from Broad and Conserved Immune Regulation by Genetically Heterogeneous Melanoma Cells

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journal contribution
posted on 2023-03-31, 01:10 authored by Natalie J. Neubert, Laure Tillé, David Barras, Charlotte Soneson, Petra Baumgaertner, Donata Rimoldi, David Gfeller, Mauro Delorenzi, Silvia A. Fuertes Marraco, Daniel E. Speiser

Supplementary Materials and Methods. Supplementary Figures: Fig. S1. Sorting strategy and purity. Fig. S2. Comparison of the two batches of NanoString experiments shown in Fig. 1 and Fig. 4. Fig. S3. Melanoma cells respond to CTL attack with gene expression changes. Fig. S4. CTL-induced gene expression changes are driven by IFNgamma and TNFalpha. Fig. S5. Representative histograms of protein expression regulated by cytokines. Fig. S6. Characterization of untreated and CTL-exposed melanocytes. Supplementary Tables: Table S1. Source of the 17 melanoma cell lines used in this study. Table S2. Antibodies (including isotype-matched controls) used to assess protein expression by flow cytometry. Table S3. Differential expression of genes that are part of the enriched gene sets in Supplementary Figs. S3C and S3E. Table S4. Selection of genes for 181-gene panel. Table S5. Differential expression of genes in melanoma cell lines after 24h treatment. Table S6. Protein expression of melanoma cells after 48h culture in presence or absence of IFNgamma and TNFalpha. Table S7. Differential expression of genes in melanocyte cell lines after 24h treatment. Table S8. Genes that have statistically different fold-changes (MelanA-specific CTLs/untreated) between melanoma cell lines and melanocyte lines. Supplementary References.


ISREC Foundation

Emma Muschamp Foundation

Swiss Cancer Research Foundation

Swiss National Science Foundation


Medic Foundation

Alfred and Annemarie von Sick

Wilhelm Sander Foundation

Cancer Research Institute

Campbell Family Institute



Although mutations drive cancer, it is less clear to what extent genetic defects control immune mechanisms and confer resistance to T-cell-based immunotherapy. Here, we studied the reactions of malignant and benign melanocyte lines to cytotoxic CD8+ T cells (CTL) using flow cytometry and gene expression analyses. We found rapid and broad upregulation of immune-regulatory genes, essentially triggered by CTL-derived IFNγ and augmented by TNFα. These reactions were predominantly homogenous, independent of oncogenic driver mutations, and similar in benign and malignant cells. The reactions exhibited both pro- and antitumorigenic potential and primarily corresponded to mechanisms that were conserved, rather than acquired, by mutations. Similar results were obtained from direct ex vivo analysis of the tumor microenvironment. Thus, immune regulation in the tumor landscape may often be driven by conserved mechanisms, which may explain why T-cell–based immunotherapy can provide durable benefits with relatively infrequent escape. Cancer Res; 77(7); 1623–36. ©2017 AACR.