Single-cell and spatial multi-omics reveal a recurrent multicellular niche at the tumor-stroma interface in multidrug resistance.

Abstract

Multi-drug resistance (MDR) is an almost inevitable endpoint of cancer therapy, driving rapid tumor progression, yet its evolutionary logic remains unclear because MDR tumors are rarely resected. Using paired therapy-naive and MDR melanoma specimens from a clinical trial, integrated with single-cell and spatial multi-omics and evaluated together with datasets from 10 additional cancer types, we identify a recurrent MDR-associated spatial nexus along the tumor-stroma interface. This niche juxtaposes CXCL14⁺ inflammatory cancer-associated fibroblasts (iCAFs), TREM2⁺ tumor-associated macrophages (TAMs), and AXL⁺ dedifferentiated tumor cells, and is accompanied by loss of tumor-reactive CXCL13⁺CD8⁺ T cells. In vitro, CXCL14 promotes macrophage migration and TREM2 induction, while TREM2⁺ TAMs suppress CXCL13⁺CD8⁺ T cells via CD86-CTLA4 signaling. TREM2⁺ TAMs also promote tumor dedifferentiation through oleic acid-driven GAS6-AXL activation. We develop an FAP/TREM2-targeting bispecific antibody to disrupt this spatial nexus and restore therapeutic sensitivity in MDR patient-derived xenograft models with favorable safety.