Spatial transcriptomics identifies NGFR and EDIL3 as tumor budding-associated genes in triple-negative breast cancer

Tumor budding (TB) is associated with aggressiveness and poor outcomes in triple-negative breast cancer (TNBC), yet its molecular mechanisms remain incompletely defined. This study aimed to identify TB-associated genes and delineate their functional and prognostic relevance in TNBC. Spatial bulk transcriptomic profiling was performed on 13 TNBC tissues stratified by TB levels. Differential expression, mutual information analysis, and network diffusion identified 7 candidate high TB-associated genes, including PRICKLE2 , NGFR , LRIT3 , ATP7A , FAM110C , and EDIL3 , but downregulation of LRRCC1 . Only NGFR and EDIL3 confirmed significant upregulation in 4 independent TNBC tissues by real-time RT-PCR. Prognostic evaluation demonstrated that high NGFR , but not EDIL3, was correlated with shorter overall survival (OS) with statistical significance ( P  = 0.034). High NGFR/EDIL3 patients exhibited significantly worse OS compared to those with low expression of both ( P  = 0.039). Mechanistically, p75NTR pathways, phosphatidylinositol 3-kinase-Akt, neurotrophin signaling, nervous system development, and extracellular matrix proteoglycan pathways were implicated in high TB. These integrative spatial transcriptomic and computational analyses identify NGFR and EDIL3 as key mediators of TB-driven TNBC aggressiveness with value for prognosis and therapeutic development.