IGHG1+ malignant epithelial Cell-myCAF crosstalk via MIF-CD74/APP-CD74 drives early brain metastasis in NSCLC: Delineated via primary tumor-brain metastasis single-cell and spatial transcriptomics.

To investigate the mechanisms of early brain metastasis in non-small cell lung cancer (NSCLC) using spatial multi-omics technology, develop predictive models, and identify potential therapeutic targets. A retrospective analysis was conducted on paraffin samples from 53 NSCLC patients (stages I-IV), including normal lung tissue (NL), primary tumors with/without brain metastasis (PTNBrM/PTBrM), brain metastases (BrM), and normal brain tissue. Integrated single-nucleus RNA sequencing, GeoMx DSP, and CosMx SMI. Augur, pseudo-time, and space communication analysis identified key cells and molecules. ROC and survival analysis evaluated predictive performance. Potential preventive targets screened from the Therapeutic Target Database. snRNA-seq revealed that IGHG1+ malignant epithelial cell (MEC) represent the terminal differentiation state of PTBrM epithelium, showing significant enrichment in EMT pathways. These cells uniquely responded to biological perturbations (NL→PTBrM vs NL→PTNBrM, 0.596 vs 0.000, P = 0.002). Spatial transcriptomics further indicated that IGHG1+ MEC predominantly localized at the invasive front of PTBrM, co-localizing with myofibroblastic cancer-associated fibroblast (myCAF; r = 0.900). Multi-omics demonstrated bidirectional interactions between IGHG1+ MEC and myCAF at PTBrM margins via MIF-CD74/APP-CD74 axes, which were also validated both clinically and in vitro. High CD74 at margins was an independent predictor of brain metastasis (AUC = 0.776; HR = 5.495), linked to shorter brain metastasis-free survival (37 vs 60 months, P < 0.0001). In vivo studies confirmed that the candidate drugs targeting CD74, doxorubicin and milatuzumab, have a tendency to inhibit EMT. IGHG1+ MEC collaborate with myCAF to shape a pro-metastatic microenvironment, with the MIF-CD74/APP-CD74 interaction network serving as a driver of NSCLC brain metastasis. CD74-targeting therapies show promising clinical potential.