Machine learning-based spatial characterization of tumor-immune microenvironment in the EORTC 10994/BIG 1-00 early breast cancer trial

Breast cancer (BC) represents a heterogeneous ecosystem and elucidation of tumor microenvironment components remains essential. Our study aimed to depict the composition and prognostic correlates of immune infiltrate in early BC, at a multiplex and spatial resolution. Pretreatment tumor biopsies from patients enrolled in the EORTC 10994/BIG 1-00 randomized phase III neoadjuvant trial (NCT00017095) were used; the CNN11 classifier for H&E-based digital TILs (dTILs) quantification and multiplex immunofluorescence were applied, coupled with machine learning (ML)-based spatial features. dTILs were higher in the triple-negative (TN) subtype, and associated with pathological complete response (pCR) in the whole cohort. Total CD4+ and intra-tumoral CD8+ T-cells expression was associated with pCR. Higher immune-tumor cell colocalization was observed in TN tumors of patients achieving pCR. Immune cell subsets were enriched in TP53-mutated tumors. Our results indicate the feasibility of ML-based algorithms for immune infiltrate characterization and the prognostic implications of its abundance and tumor-host interactions.