Extended Data Fig. 1: BRCA1-associated TNBC are highly infiltrated with T-cells and macrophages.

CyCIF was performed on BRCA-WT (n = 6) and BRCA1-associated (n = 10) triple negative breast cancer tumors from consented patients. a, Antibody panel for CyCIF shows the staining strategy for each cycle of CyCIF. b, Representative images for each cycle are shown. c, Representative images of merged antibodies for each cycle. d-f, The overview of image processing and data analysis workflow. d, The multiplexed images were segmented, and single-cell data were collected via customized ImageJ scripts. Digital representation of Keratin staining is shown. e, An example of gating for positive cells for CD163 are shown. Note that the distribution is similar for Keratin and CD163, but number/level is different due to different background subtraction methods. The CD163 distribution is continuous whereas the Keratin distribution is more bi-modal. f, Individual antibodies corresponding to Fig. 1a. g, T-regulatory cells were identified using FoxP3 positivity of CD3⁺CD4⁺ cells. h, Cytotoxic T-cells were identified using Granzyme B positivity of CD3⁺CD8⁺ cells. i, Macrophages were identified by CD68 and CD163.