Integrating single-cell and spatial transcriptomics to decipher the neuro-immune microenvironment of breast cancer brain metastasis: a key regulatory axis, prognostic model, and drug discovery

<h4>Background</h4>Breast cancer brain metastasis (BCBM) is a lethal complication of advanced disease, facilitated by a specialized neuro-immune microenvironment, whereas its molecular regulators and spatial dynamics remain poorly understood. This study aimed to resolve cellular heterogeneity and intercellular signaling networks crosstalk in BCBM microenvironment by using integrated single-cell RNA sequencing (scRNA-seq) single-cell and spatial transcriptomics to identify key regulators, build a prognostic model, and computationally screen for potential therapies.<h4>Methods</h4>We analyzed public scRNA-seq and 10× Visium spatial transcriptomics datasets. Cell landscapes were resolved with Seurat, communication networks were inferred with CellChat, and spatial mapping was performed with Tangram. A prognostic risk model was developed from bulk RNA sequencing (RNA-seq) data from The Cancer Genome Atlas-Breast Cancer (TCGA-BRCA), the Gene Expression Omnibus (GEO) datasets using Least Absolute Shrinkage and Selection Operator-Cox (LASSO-Cox) regression and validated in an independent cohort. Potential small-molecule inhibitors were screened by molecular docking (AutoDock Vina) against AlphaFold-predicted target structures.<h4>Results</h4>The BCBM microenvironment exhibited high heterogeneity, with macrophages serving as the central signaling hub. A novel regulatory axis, interleukin-18 and myosin light chain kinase (<i>IL-18/MYLK</i>), was found to be specifically upregulated and co-localized at the tumor-brain interface. A risk-score model based on the <i>IL-18/MYLK</i> axis demonstrated robust prognostic value in both training and validation cohorts. The model further revealed that the upregulation of <i>IL-18</i> and <i>MYLK</i> was associated with better overall survival. Virtual screening identified the MEK inhibitor, <i>PD98059</i>, as a high-affinity dual inhibitor of <i>IL-18</i> and <i>MYLK</i>.<h4>Conclusions</h4>This study delineates the neuro-immune landscape of BCBM progression and proposes the <i>IL-18/MYLK</i> axis as a critical driver of neuroinflammation and cytoskeletal remodeling. The prognostic model and the candidate compound <i>PD98059</i> provide avenues for novel targeted therapeutic strategies.