1. Tumor CompartmentStromal Compartment mask C D EF A B Supplemental Fig 1. Epithelial and stromal PD-L1 expression. AQUA scores for PD-L1 in the epithelium (A) and stroma (B) represented in heat maps for a single whole tissue section. Examples of PD-L1 staining in epithelium (C) and stroma (D) with insets of the tumor (green) and stromal (blue) compartments. Higher magnification in (E,F). (blue=DAPI, green=pan-cytokeratin, red=PD- L1)

2. CST-E1L3N Average Standard Deviation P-Value mel624729.73101.31 0.0087 mel624+B7H11179.1741.01 CST-E1L3N AQUA1050 102ms Supplemental Fig 2. Validation of specificity of PD-L1 antibody used in this study. (A) Western blot of positive and negative cell line controls (provided by Cell Signaling Technology). (B) average quantitative scores of PD-L1 expression in mel624 and mel624- transfected with PD-L1 as positive controls. (C) regression of quantitative scores of antibody used in this study with previously published specific anti-PD-L1 antibody clone 5H1 (Ref Vamsi’s paper). (D,E) Image of tissue microarray histospot of placental tissue (D) and at higher magnification (E). A B C D E

3. Supplemental Fig 3. Correlation with PD-L1 expression and pCR in patient subsets. Continuous epithelial and stromal PD-L1 expression stratified by no pCR vs. pCR in A) lymphocyte-predominant breast cancers, B) hormone receptor positive breast cancers, C) HER2-amplified, D) triple-negative breast cancers. AB CD

4. 1 2 3 1 2 3 Supplemental Fig 4. Joinpoint analysis of PD-L1 quantitative scores in the tumor mask (A) and stromal compartment (B). Visual threshold of detection for both epithelial and stromal AQUA scores lay within the range of 500-800. Joinpoint #2 for both graphs lies within this range and was used as a cut off for PD-L1 low vs. high expression. A B 1 428(386-437) 2 584(555-598) 3 727(721-876) JoinpointAQUA(95%CI) 1 423(382-441) 2 722(678-758) 3 951(893-1015) JoinpointAQUA(95%CI)

5. Supplemental Fig 5. Contingency tables of PD-L1 in the epithelium (A) and stroma (B) binarized into low and high with pCR. A B