A TLS-associated immune-activation transcriptomic score is associated with prognosis and the immune landscape in breast cancer

Objective Tertiary lymphoid structures (TLS) are ectopic lymphoid aggregates that arise in non-lymphoid tissues during chronic inflammation and in tumors. We aimed to develop a TLS-associated immune-activation transcriptomic score and evaluate its prognostic and immune correlates in breast cancer. Methods TCGA-BRCA was used as the discovery cohort and METABRIC as an independent validation cohort. A published 39-gene cross-tumor TLS-related candidate panel was screened using Cox regression and Kaplan–Meier analysis. Benjamini–Hochberg correction was applied to the 39 Cox tests. A seven-gene score was calculated by single-sample gene set enrichment analysis (ssGSEA), and cohort-specific cutoffs were used for group-based analyses. The score was also evaluated continuously using Cox regression to assess whether the prognostic association depended on dichotomization. Differential expression, immune infiltration, genomic alterations, and tumor mutational burden (TMB) were evaluated. Histology from one patient was used only as a qualitative illustration. Results The seven selected genes remained significant after Benjamini–Hochberg correction (false-discovery rate < 0.05). TLS-high patients had longer overall survival than TLS-low patients in TCGA-BRCA and METABRIC, and a supplementary continuous-score Cox analysis gave concordant results. TLS-high tumors showed an immune-active profile, including higher B-cell, CD8+ T-cell, and T follicular helper-cell estimates. The association with TMB was statistically significant but weak (Spearman R = 0.11). A single illustrative specimen showed a lymphoid aggregate with CD20+ B-cell and CD8+ T-cell areas but did not validate score specificity. Conclusion The seven-gene TLS-associated immune-activation score was reproducibly associated with survival and immune infiltration in two retrospective breast cancer cohorts. It should be interpreted as a bulk-transcriptomic marker of an immune-active state rather than a histologically validated measure of TLS abundance. Prospective and spatial validation is required before clinical use.