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. 2019 Oct 29;112(7):708–719. doi: 10.1093/jnci/djz208

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© The Author(s) 2019. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 3. — Chromosomal instability association with immune escape. A) Associations between tumor microenvironment (TME) and tumor-specific features with local cytotoxic immune activity (CYT) in cohorts A and B. Spearman correlation was used to evaluate associations between each TME and tumor-specific gene expression signature with the CYT gene signature. The x- and y-axis represent Spearman ρ and the −log10(FDR), respectively. The horizontal bold dotted line represents the FDR threshold at 0.05 for statistically significant association. Chromosomal instability (CIN) distribution within each triple-negative breast cancer (TNBC) molecular (B) and tumor immune microenvironment (TIME) (C) subtype in cohorts A and B. Differences between each subtype and the rest of the cohort were assessed using a two-sided Mann-Whitney U test. A black star was displayed when statistically significant CIN score enrichment was observed within a specific TNBC and TIME subtype. D) Gene ontology analyses of genes with mRNA expression statistically significant (FDR ≤ .05) negatively (left, in red) and positively (right, in blue) correlated with CIN scores (Spearman correlation) in cohorts A and B. BL = Basal-like; CAF = Cancer-associated fibroblast; CIN = Chromosomal instability; FI = Fully-inflammed; HRD = Homologous recombination deficiency; IM = Immunomodulatory; ITH = Intra-tumoral heterogeneity; LAR = Luminal androgen receptor; M = Mesenchymal; MR = Margin restricted; MSL = Mesenchymal stem-like; SR = Stroma restricted; TMB = Tumor mutational burden.