Characterization of the Breast Cancer Liver Metastasis Microenvironment via Machine Learning Analysis of the Primary Tumor Microenvironment

Abstract

Breast cancer liver metastases (BCLM) are hypovascular lesions that resist intravenously administered therapies and have grim prognosis. Immunotherapeutic strategies targeting BCLM critically depend on the tumor microenvironment (TME), including tumor-associated macrophages (TAM). However, a priori characterization of the BCLM TME to optimize therapy is challenging since BCLM tissue is rarely collected. In contrast to primary breast tumors for which tissue is usually obtained and histological analysis performed, biopsies or resections of BCLM are generally discouraged due to potential complications. This study tested the novel hypothesis that BCLM TME characteristics could be inferred from the primary tumor tissue. Matched primary and metastatic human breast cancer samples were analyzed by imaging mass cytometry (IMC), identifying 20 shared marker clusters denoting macrophages (CD68, CD163, CD206), monocytes (CD14), immune response (CD56, CD4, CD8a), Programmed Cell Death protein 1 (PD1), Programmed Death Ligand 1 (PD-L1), tumor tissue (Ki-67, pERK), cell adhesion (E-cad), hypoxia (HIF1α), vascularity (CD31), and ECM (αSMA, collagen, MMP9). A machine learning (ML) workflow was implemented and trained on primary tumor clusters to classify each metastatic cluster density as being either above or below median values. The proposed approach achieved robust classification of BCLM marker data from matched primary tumor samples (AUROC ≥0.75, 95% CI ≥0.7, on the validation subsets). Top clusters for prediction included CD68+, E-cad+, CD8a+PD1+, CD206+, and CD163+MMP9+. We conclude that the proposed workflow using primary breast tumor marker data offers the potential to predict BCLM TME characteristics, with the longer term goal to inform personalized immunotherapeutic strategies targeting BCLM.