Single-cell analysis reveals a LAMB3-dependent immunosuppressive environment in gallbladder neck/cystic duct carcinoma

Background & Aims Gallbladder cancer (GBC) originating from the fundus/body (GBC F/B ) and neck/cystic duct (GBC N/CD ) exhibits distinct clinical outcomes. Location-associated heterogeneity is intricately linked to oncogenic properties and multicellular interactions within the tumor microenvironment (TME). Methods Single-cell transcriptomic analysis was performed on 569,736 cells derived from 38 GBC F/B and 17 GBC N/CD samples. Whole-exome sequencing (WES) was employed to identify genomic alterations in malignant epithelial cells. Additionally, TCGA datasets, multiplex immunohistochemistry, scTCR-seq, spatial transcriptomics, and functional assays were integrated to investigate subtype-specific differences. Results The cellular atlas revealed distinct TME patterns. Hallmarked by TP53 mutations and robust antigen presentation, GBC F/B tumors were enriched with plasma cells ( P = 0.009), CXCL13 + T cells ( P = 0.046), CXCL9 + macrophages ( P = 0.042), and proliferative immune cells ( P = 0.015), constituting an immune-activated TME. Conversely, stem-like GBC N/CD tumor cells fostered an angiogenic, immunosuppressive milieu, enriched with endothelial cells ( P = 0.02), SPP1 + macrophages ( P = 0.006), MYH11 + vCAFs ( P = 0.029), and GZMK + NR4A2 + CD8 + T cells ( P = 0.028). Notably, elevated LAMB3 in GBC N/CD tumor cells emerged as a central immune regulator, driving macrophage infiltration and T-cell dysfunction to establish an immunosuppressive niche. Conclusion This study underscores the profoundly immunosuppressive microenvironment in gallbladder cancer originating from the neck/cystic duct (GBC N/CD ), highlights the role of LAMB3 + tumor cells in immune modulation, and identifies LAMB3 as a potential therapeutic target for GBC N/CD . Impact and implications By delineating distinct tumor microenvironment (TME) landscapes between gallbladder cancers (GBC) originating from the fundus/body (GBC F/B ) and those from the neck/cystic duct (GBC N/CD ), this study provides compelling evidence for site-specific precision therapeutic strategies. We demonstrate that GBC F/B tumors are highly enriched with established biomarkers predictive of immunotherapy responsiveness—including elevated tumor mutational burden (TMB), robust PD-L1 and interferon-γ signatures, and abundant CXCL13 + T cells, plasma cells, and CXCL9 + macrophages—indicating these patients are optimal candidates for immunotherapeutic interventions. Conversely, GBC N/CD tumors exhibit a profoundly immunosuppressive TME orchestrated by LAMB3 + tumor cells. Targeting LAMB3 therefore represents a promising approach to overcome immune resistance in patients with GBC N/CD .