Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases

Brain metastases (BrMets), common for advanced-stage breast cancer patients, are associated with poor median survival and accompanied by severe neurologic decline. Halting the progression of breast cancer brain metastases (BCBMs) may require modulation of the tumor microenvironment (TME), yet little is known about the impact of the primary breast TME on brain tropism, or how, once there, metastatic breast cancer cells coexist with brain-resident cells (e.g., neurons and glia). Traditionally, studies in this space have focused on differential expression analysis, overlooking potential insights gained from investigating genes with equivalent expression between groups. This is particularly crucial in distant metastasis, where tumor cells may co-opt the transcriptional programs of the host organ (e.g., brain) to facilitate successful seeding and outgrowth. Prior to our work, no computational framework existed to determine biologically-relevant equivalent gene expression. To resolve molecular mechanisms of BCBM enabled by metastatic cancer cells and/or resident brain cells, we leveraged Nanostring GeoMx to perform spatially-resolved transcriptomic profiling on 235 patient-derived tissue cores from BCBM (including adjacent normal brain), primary invasive breast cancers, and normal (non-cancer) brain; analyzing 18,677 RNAs in 450 areas of interest (AOIs). We introduce the “Equivalent Expression Index” a highly specific and accurate algorithm that identifies statistically significant “Equivalently-Expressed Genes”. This method facilitated the identification of molecular remodeling and mimicry genes within tissue-specific TMEs. By integrating differential expression analysis with the Equivalent Expression Index, we discovered multiple novel gene signatures associated with BCBM and primary tumor brain-metastatic potential. We demonstrate that the Equivalent Expression Index is a powerful tool to uncover shared gene expression programs representing the adaptation of metastatic cells and brain-resident cells to the BCBM microenvironment.