Fig 1.
Proportion of mutational signature 3 and overall mutation burden by BRCA status in WSI and TCGA breast cancers.
** P < 0.01.
Fig 2.
Volcano plots of immunostimulator (A-D) and immunoinhibitor (E-H) molecules in BRCA1- and BRCA2-deficient vs. BRCA-proficient breast cancers from WSI and TCGA. FC: fold change. KIR2DL3 with log2FC 14.5 in BRCA1-deficient vs. BRCA-proficient breast cancers from WSI shown at the boundary of the plot.
Fig 3.
Relative enrichment of immune infiltrates in BRCA1- (A-B) and BRCA2-deficient (C-D) breast cancers compared to BRCA-proficient breast cancers from WSI and TCGA. ACT_B_cell: Activated B cell, ACT_CD4: Activated CD4 T cell, ACT_CD8: Activated CD8 T cell, ADC: Activated dendritic cell, CD56_BRIGHT: CD56bright natural killer cell, CD56_DIM: CD56dim natural killer cell, EOS: Eosinophil, IMM_B_CELL: Immature B cell, IMM_DC: Immature dendritic cell, MAC: Macrophage, MAST: Mast cell, MDSC: Myeloid-derived suppressor cell, MEM_B_CELL: Memory B cell, MON: Monocyte, NEU: Neutrophil, NK: Natural killer cell; NES: Normalized enrichment score, NKT: Natural killer T cell, PDC: Plasmacytoid dendritic cell, TCM_CD4: Central memory CD4 T cell, TCM_CD8: Central memory CD8 T cell, TEM_CD4: Effector memory CD4 T cell, TEM_CD8: Effector memory CD8 T cell, TFH: T follicular helper cell, TGD: γδ T cell, TH1: Type 1 T helper cell, TH17: Type 17 helper cell, TH2: Type 2 T helper cell, TREG: Regulatory T cell.
Table 1.
Univariate linear regression analysis of BRCA1/2 status, clinicopathological features, and PAM50 subtypes with T cell-inflamed signature score.
Fig 4.
Association between BRCA status and T cell-inflamed signature in relation to PTEN mutation status.
(A) PTEN protein expression stratified by PTEN copy number alteration and point mutation. (B) Proportion of PTEN mutant samples stratified by BRCA status. (C-E) tSNE visualisation of BRCA1- and BRCA2-deficient breast cancers. Colour represents T cell-inflamed signature score divided at the median, PTEN mutation status, and BRCA status, respectively. (F-G) Distribution of T cell-inflamed signature scores in BRCA-proficient and BRCA1-deficient breast cancers with and without PTEN mutation. n.s.: Not statistically significant, ** P < 0.01.