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. 2020 Feb 12;11:853. doi: 10.1038/s41467-020-14632-2

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© The Author(s) 2020

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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Fig. 3 — a Principal component analysis (PCA) plot of RNA-seq data from DR (green, n = 6 tumors) and NR (orange, n = 8 tumors). Dot, single tumor; PC, principal component. b Volcano plot of DEGs (differentially expressed genes, magenta) in DR and NR tumors with FDR (false discovery rate) < 0.05 and |log2FC| (absolute log2 fold change) >1. c Heatmap representing gene expression of previously reported lineage-specific markers²³ of cancer-associated fibroblasts (CAFs) in DR (green, n = 6 tumors) and NR (orange, n = 8 tumors). Significantly differentially expressed genes (pink, p < 0.05) are highlighted using DESeq2 algorithm. Column, single tumor; row, gene; ns, not significant (gray). d Gene expression of the top ten CAF markers significantly upregulated in DR (green, n = 6 tumors) versus NR (orange, n = 8 tumors). FPKM values for each gene are normalized to the mean expression obtained from all tumors. Triangle, single tumor; bar, mean of the response group; error bar, standard deviation. e Stroma score generated from the 10-gene CAF signature in d for DR (green, n = 6 tumors) and NR (orange, n = 8 tumors). Two-tailed Mann–Whitney U test was performed to determine statistical difference between the response groups. Dot, single tumor; hinges, 25th and 75th percentiles; middle line, median; whiskers, minimum to maximum value. f Stroma score of melanoma samples from ICI-naive patients on-treatment with nivolumab monotherapy or in combination with ipilimumab from MDACC (left; pCR = 7 and NR = 13) and Riaz ipilimumab-naive¹⁸ (right; DC = 9 and PD = 10) cohorts. Two-tailed Mann–Whitney U test was performed to determine statistical difference between the response groups. Dot, single tumor; hinges, 25th and 75th percentiles; middle line, median; whiskers, minimum to maximum value. g Stroma score for paired pre- and on-treatment tumor samples from MDACC (left; pCR = 7 and NR = 12 patients) and Riaz ipilimumab-naive¹⁸ (right; DC = 8 and PD = 9 patients) cohorts. Two-tailed Wilcoxon test was performed to determine statistical difference between matched pre- and on-treatment samples, two-tailed Mann–Whitney U test was performed to determine statistical difference between response groups in pre- or on-treatment samples. pCR pathologic complete response, NR non-responder, DC disease control, PD progressive disease. Dot, single tumor; line, paired samples; ns, not significant.