Enhanced formation of tertiary lymphoid structures shapes the anti-tumor microenvironment in gastrointestinal stromal tumors after imatinib targeted therapy

<b>Rationale:</b> Tertiary lymphoid structures (TLSs) play a key role in the adaptive immune response within the local tumor immune microenvironment (TIME) and can predict the clinical outcome of several solid tumors. However, the clinical relevance of TLSs and their formation mechanism in gastrointestinal stromal tumors (GISTs) remain unclear. <b>Methods:</b> Integration analysis was performed on a single-cell RNA sequencing (scRNA-seq) cohort (n = 8), a public transcriptome cohort (n = 65), a public scRNA-seq cohort (n = 7), a tissue cohort (n = 197) and a serum cohort (n = 169) to decode the characteristics of the immunological microenvironment of GIST. The multiplex immunohistochemistry (mIHC) staining, <i>in vitro</i> cell culture, chemotaxis assays and antibody-dependent cellular phagocytosis (ADCP) experiments were used to validate the results of the bioinformatics analysis. <b>Results:</b> Preoperative imatinib targeted therapy significantly enhanced TLS formation in GIST tissues, predicting improved therapeutic efficacy and favorable prognosis. Mechanistically, imatinib remodeled the local microenvironment via tumour-associated macrophages, recruiting B cells via the CXCR4-CXCL12 axis to drive TLS development. Functionally, TLS dominated germinal centre (GC) B-cell differentiation and the formation of IgG⁺ plasma cells (PCs), which preferentially enhanced the adaptive immune response through the ADCP effect. From a clinical perspective, we identified three distinct GIST immune classes (GICs A-C). GIC-A tumors featured abundant CD20⁺ B cells and TLS, as well as a favorable prognosis. They were accompanied by enhanced antigen presentation, accumulation of IgG⁺ PCs, increased immunosuppressive properties and a high frequency of <i>KIT</i> exon 11 mutations. These mutations potentially serve as a predictive biomarker for future targeted and immunotherapies. Furthermore, patients with high serum IgG levels experienced significant therapeutic benefits. <b>Conclusions:</b> Our data show that local adaptive immunity dominated by TLS is a key factor in the efficacy of targeted therapy, and suggest that inducing IgG could be a feasible strategy for improving the prognosis of patients with GIST.