Multi-Modal Profiling Reveals SERPINB3-Driven Immune Evasion and Stromal Immune Mimicry in Triple-Negative Breast Cancer

TL;DR

This study identifies SERPINB3-driven immune evasion and stromal immune mimicry in triple-negative breast cancer using multi-modal profiling.

Contribution

The study reveals novel TNBC-specific immune and stromal signatures linked to SERPINB3 and immune evasion mechanisms.

Findings

SERPINB3 is a TNBC-enriched epithelial gene associated with immune evasion and pathways like EMT and interferon signaling.

TNBC tumors show a humoral immune signature with B-cell enrichment and immunoglobulin gene expression in stromal cells.

Multiplex imaging shows coordinated immune suppression, stromal activation, and tumor proliferation in TNBC.

Abstract

Background/Objectives: Triple-negative breast cancer (TNBC) exhibits high immune infiltration yet remains clinically aggressive. Although immune checkpoint blockade benefits a subset of patients, the molecular programs enabling concurrent immune activation and immune evasion in TNBC are not fully defined. This study aimed to identify TNBC-specific tumor-intrinsic and tumor-extrinsic molecular features that may explain this paradox. Methods: Publicly available single-cell RNA-sequencing data from primary breast tumors were analyzed to characterize subtype-specific transcriptional programs across epithelial and stromal compartments. Tumor-intrinsic findings were independently validated using bulk transcriptomic and clinical data from the METABRIC cohort. Tumor microenvironment remodeling was evaluated using multiplexed tissue imaging of TNBC tumors. Functional analyses were done included Gene Ontology enrichment, Hallmark gene set enrichment analysis, and SERPINB3-centered protein–protein interaction network analysis using STRING. Results: Single-cell analysis identified SERPINB3 as a TNBC-enriched epithelial gene relative to ER+ and HER2+ tumors. This subtype-restricted pattern was validated in the METABRIC cohort and associated with pathways related to epithelial–mesenchymal transition, interferon signaling, and antigen presentation. TNBC tumors also displayed a humoral immune signature characterized by B-cell and plasmablast enrichment, as well as ectopic immunoglobulin gene expression in cancer-associated fibroblasts, endothelial cells, and myeloid populations. Multiplex imaging revealed coordinated associations between immune suppression, stromal activation, and tumor proliferation. Network analysis placed SERPINB3 within interconnected immune-regulatory and stromal signaling modules. Conclusions: Together, these data indicate that TNBC exhibits co-existing immune activation and immune-suppressive features. The identified epithelial and stromal signatures represent candidate biomarkers that may inform future studies of immune regulation and therapeutic stratification in TNBC.

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