Spatial Analysis of FAP Gene Expression in Breast Cancer.

Abstract

Introduction: Fibroblast Activation Protein (FAP) is a key marker of Cancer-Associated Fibroblasts (CAFs) and a promising target for cancer theranostics. However, its expression in both stromal and tumor cells complicates therapeutic strategies.

Methods: This study employed spatial transcriptomics to analyze FAP gene expression patterns in luminal breast cancer, revealing distinct molecular profiles in FAP+ stromal cells, FAP+ tumor cells, and tumor cells proximal to FAP+ stroma.

Results: FAP+ stromal cells exhibited upregulation of Extracellular Matrix (ECM) remodeling genes (COL1A1, MMP2, TIMP2), secreted factors (CXCL12, POSTN), and immune modulators (CD276), confirming their role in desmoplasia and immunosuppression. In contrast, FAP+ tumor cells showed limited transcriptional changes but elevated POSTN, CD24, and EPCAM, suggesting roles in immune evasion and epithelial plasticity.

Discussion: Spatial analysis revealed that tumor cells within 700 μm of FAP+ stroma displayed an aggressive phenotype, marked by ECM degradation (MMP14, COL6A1), mesenchymal markers (VIM), and immune suppression (HLA-DRA, CD276). Conversely, distal tumor cells exhibited metabolic adaptations (ACADSB, SCD) and survival mechanisms (SQSTM1, NUPR1), potentially conferring resistance to therapy.

Conclusion: This spatial transcriptomics study elucidates the complex and context-dependent roles of FAP in luminal breast cancer, revealing distinct molecular programs driven by its cellular source and spatial location. We demonstrate that FAP+ CAFs are the primary architects of a profoundly immunosuppressive and pro-fibrotic tumor microenvironment, characterized by extensive ECM remodeling and secretion of CXCL12 and CD276. Furthermore, we identify a novel, aggressive tumor cell subpopulation defined by its proximity to FAP+ stroma, exhibiting a hybrid phenotype with features of ECM degradation, mesenchymal transition, and immune suppression.