Immune context as a modulator of MSI-high and TMB-high as predictors of immune checkpoint inhibitor response in breast cancer.

Abstract

e17638 Background: Microsatellite instability–high (MSI-H) and tumor mutational burden–high (TMB-High) are tissue-agnostic biomarkers for immune checkpoint inhibitor (ICI) response. Their predictive value in breast cancer (BC) remains unclear due to low prevalence and heterogeneous immune contexts. We investigated the immune and transcriptomic features of MSI-H and TMB-High BC, with comparison to colorectal cancer (CRC) and uterine endometrial carcinoma (UCEC), where MSI-H/TMB-High are established predictors of ICI benefit. Methods: We analyzed TCGA BC (n = 402), CRC (n=355), and UCEC (n=173) cohorts, with an independent UAE BC cohort (n=85). Immune cell composition was inferred using xCell 2.0. Differential gene expression (DEG), gene set enrichment analysis (GSEA), and protein–protein interaction (PPI) network analyses were performed for TMB-High versus TMB-Low samples. Per-sample immune profiling was conducted for MSI-H BC cases treated with ICI. Results: MSI-H BC was rare (TCGA 0.5%; UAE 2.35%) and overlapped with TMB-High. In CRC and UCEC, MSI-H vs MSS comparisons revealed lymphoid-dominant immune-hot profiles, characterized by enrichment of CD8⁺ and CD4⁺ T cells, PD-1–expressing CD8⁺ T cells, NK cells, and B/plasma cells, consistent with established responsiveness to ICI. In TMB-High vs TMB-Low comparisons, CRC demonstrated coordinated immune activation supported by both immune cell enrichment and upregulation of immune-related differentially expressed genes, including pathways related to NK cell–mediated cytotoxicity and interferon signaling. In contrast, UCEC TMB-High tumors showed strong immune cell enrichment. In contrast, BC exhibited a distinct immune context. In TCGA BC, TMB-High samples showed significant immune differences relative to TMB-Low, but these reflected a mixed immune phenotype with concurrent activation of lymphoid, myeloid and regulatory populations. Comparison between TCGA MSI-H and MSS samples did not reveal significant difference in immune cell proportions. In the UAE BC cohort, TMB-High samples did not show enrichment of lymphoid immune populations, and MSI-H vs MSS comparisons revealed limited differences, with increased macrophage proportions observed in MSI-H cases. Per-sample analysis of MSI-H BC treated with ICI demonstrated that the responder exhibited coordinated adaptive immune infiltration resembling canonical MSI-H CRC/UCEC immune profiles, whereas the non-responder lacked such lymphoid engagement. Conclusions: MSI-H and TMB-High are tissue-agnostic biomarkers of ICI response. Canonical MSI-H tumor types such as CRC and UCEC exhibit lymphoid-dominant, immune-hot phenotypes that most reliably translate into clinical benefit. In contrast, MSI-H BC display a mixed immune context, often constrained by myeloid and stromal components, limiting the predictive utility of MSI-H and TMB-High status alone.