Fig. 3: Pro-inflammatory pathway transcriptionally upregulated in R- vs NR-mesotheliomas. | Nature Communications

Fig. 3: Pro-inflammatory pathway transcriptionally upregulated in R- vs NR-mesotheliomas.

From: Constitutive inflammation and epithelial-mesenchymal transition dictate sensitivity to nivolumab in CONFIRM: a placebo-controlled, randomised phase III trial

Fig. 3

A Box plots showing relative chemokine expression corresponding to CCL5, CCL16, CCL17, CCL19, CCL21 and CCL23 transcripts in R- vs NR-mesotheliomas (* indicates a Wilcoxon signed rank test, two-sided p-value equal to or less than 0.05, ** equal to or less than 0.01). Y-axis units correspond to fragments per kilobase of feature per million mapped reads (TPM) normalised counts. The boxplots show the median line and interquartile range (IQR, 25th−75th percentiles), with the whiskers extending to the maximum and minimum values. B Boxplots showing Interleukins IL17C, IL23A and IL24 transcripts in R- vs NR-mesotheliomas. The boxplots show the median line and interquartile range (IQR, 25th−75th percentiles), with the whiskers extending to the maximum and minimum values. C Scatter plot showing CCL19 versus B lymphocyte lineage as determined by transcriptome deconvolution. Blue dots correspond to R-mesotheliomas and purple to NR (spearman’s rank correlation coefficient= 0.85, p = 1.1 × 10−7). D Scatter plot showing IL24 versus B lymphocyte lineage as determined by transcriptome deconvolution. Blue dots correspond to R-mesotheliomas and purple to NR (spearman’s rank correlation coefficient= 0.66, two-sided p = 0.0006). E Box plot comparing IL24/EMT ratio in R- vs NR- mesotheliomas (*** indicates a significance p < 0.0001). F Receiver operating characteristics plot for the ratio of IL24 transcript levels to EMT enrichment score in R- vs NR-mesotheliomas. AUROC was 0.9. G Left. Box plot showing the relative enrichment of CD8 immune cells in R (blue) vs NR (purple) mesotheliomas deconvoluted using MCP-Counter, Wilcoxon two-sided p = 0.024). This boxplot shows the median line and interquartile range (IQR, 25th−75th percentiles), with the whiskers extending to the maximum and minimum values. Right. Scatter plots showing CD8 + T cell enumeration by deconvolution versus multiplex immunofluorescence (mIF) respectively. Spearman’s r = 0.6018, p = 0.002. H Correlation matrix showing a positive (blue) correlation between immune deconvolution algorithms (CIBERSORT, MCP Counter) and multiplex immunofluorescence for CD8 T cell enumeration. I Kaplan Meier curves showing progression free survival of CD8 T cells, EMT, or IL24/CCL19 ratio (dichotomised by the medians) in an independent (MEDUSA) cohort.

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