Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53

Abstract

Lymphocytic infiltration is associated with better prognosis in several epithelial malignancies including breast cancer. The tumor suppressor TP53 is mutated in approximately 30% of breast adenocarcinomas, with varying frequency across molecular subtypes. In this study of 1,420 breast tumors, we tested for interaction between TP53 mutation status and tumor subtype determined by PAM50 and integrative cluster analysis. In integrative cluster 10 (IC10)/basal-like breast cancer, we identify an association between lymphocytic infiltration, determined by an expression score, and retention of wild-type TP53. The expression-derived score agreed with the degree of lymphocytic infiltration assessed by pathologic review, and application of the Nanodissect algorithm was suggestive of this infiltration being primarily of cytotoxic T lymphocytes (CTL). Elevated expression of this CTL signature was associated with longer survival in IC10/Basal-like tumors. These findings identify a new link between the TP53 pathway and the adaptive immune response in estrogen receptor (ER)-negative breast tumors, suggesting a connection between TP53 inactivation and failure of tumor immunosurveillance.

Implications: The association of lymphocytic invasion of ER-negative breast tumors with the retention of wild-type TP53 implies a novel protective connection between TP53 function and tumor immunosurveillance.

FIGURE 1. TP53 mutation status is associated with gene expression in Basal-like tumors

(a) Heat maps showing standardized expression levels (left) and relative fold-change (right) of 124 probes with significant interaction between TP53 status and PAM50 subtype in both METABRIC discovery and validation cohorts. TP53-WT tumors labeled “WT”, TP53-mutant tumors labeled “mut”. Darker red indicates higher expression and darker blue indicates lower expression. Probes were plotted in the same order, sorted by the magnitude of fold-change in Basal-like tumors (see Supplementary Table 1). (b) Effect plots of expression of CCR7, CD2, CD3E, LY9, and perforin (PRF1) grouped by PAM50 subtype and TP53 mutation status. TP53-WT plotted in black, TP53-mutant plotted in blue. Points indicate mean, error bars indicate 95% confidence intervals calculated from twice the standard error. (c) Using data from Miller et al., effect plots of expression of CCR7, CD2, CD3E, LY9, and perforin (PRF1) grouped by ER status and TP53 mutation status show significant interaction as in the METABRIC data set. Drawn as in Fig. 1B.

FIGURE 2. Severe immune infiltration was correlated with elevated expression of CTL surface markers

(a) Box plots showing expression of CCR7, CD2, CD3E, LY9, and PRF1 increases with increasing severity of pathologically determined lymphocytic infiltration, with a qualitatively higher jump between “mild” and “severe” than between “absent” and “mild”. (b) Box plots showing expression of the CTL pathway generated from Nanodissect analysis also increases with increasing severity of pathologically determined lymphocytic infiltration.

FIGURE 3. Immune infiltrate is enriched for CTL and T_H1 pathways

Plots of estimated fold-change distributions of standardized CTL scores derived from log₂-transformed gene expression measurements comparing TP53-WT to TP53-mutant tumors separated by (a) ER status, (b) intrinsic subtype, and (c) integrated cluster. Significant differential expression (FDR ≤ 0.05) plotted in thick solid lines, non-significant plotted with thin dotted lines. Distribution peaks on the right side of the zero line indicate higher expression in TP53-WT tumors. Plots represent a convolution of signal from individual probes in the pathway; for probe lists see supplementary Tables 2 and 3.

FIGURE 4. Either TP53-mutation or TP53-LOH is associated with lower expression of the CTL pathway

Plots of CTL pathway expression gene expression divided by TP53 mutation and LOH status in (a) ER-negative, (b) Basal-like, (c) IC10, and (d) IC4 tumors, where + indicates mutation or LOH is present. TP53-WT tumors plotted in black, TP53-mutant tumors plotted in blue. Tumors without TP53-LOH plotted as open circles, tumors with TP53-LOH plotted using triangles. Horizontal lines indicate mean expression.

FIGURE 5. elevated CTL expression is associated with better survival in ER-negative tumors

Kaplan-Meier plots comparing breast-cancer-specific survival dividing tumors by those with the highest quartile of CTL expression (blue) or lower CTL expression (black) in (a) ER-negative, (b) ER-positive, (c) Basal-like, (d) HER2-enriched, (e) IC10, and (f) IC4 tumors. Elevated expression of the CTL gene signature was associated with significantly better survival in ER-negative, Basal-like, and IC10 tumors.