Abstract
The role of the tumor microenvironment (TME) in immuno‐oncology has driven demand for technologies that deliver in situ, or spatial, molecular information. Compartmentalized heterogeneity that traditional methods miss is becoming key to predicting both acquired drug resistance to targeted therapies and patient response to immunotherapy. Here, we describe a novel method for assay‐agnostic spatial profiling and demonstrate its ability to detect immune microenvironment signatures in breast cancer patients that are unresolved by the immunohistochemical (IHC) assessment of programmed cell death ligand‐1 (PD‐L1) on immune cells, which represents the only FDA microenvironment‐based companion diagnostic test that has been approved for triple‐negative breast cancer (TNBC). Two distinct physiological states were found that are uncorrelated to tumor mutational burden (TMB), microsatellite instability (MSI), PD‐L1 expression, and intrinsic cancer subtypes. The immune microenvironment in breast cancer is poorly understood, and consequently, the success rate of immunotherapy is low. This study demonstrates the clinical utility of a novel spatial profiling method and reveals distinct immune microenvironments in triple‐negative breast cancer (TNBC) patients that are unresolved by current clinical indicators such as tumor mutational burden (TMB), microsatellite instability (MSI), and tumor subtype.