Proliferative Tumor States and Immunogenic Ecosystems Predict Neoadjuvant Chemotherapy Response in Triple-Negative Breast Cancer

Background: Triple-negative breast cancer lacks established targeted therapies, and only a subset of patients achieves a pathologic complete response to neoadjuvant chemotherapy. We aimed to integrate bulk cohorts with an exploratory single-cell multi-omic dataset from only five patients to identify tumor and immune-related features associated with chemotherapy response. Methods: Bulk analyses were performed in two public breast cancer cohorts (GSE76275 and GSE25065) to compare triple-negative versus non-triple-negative tumors and to relate pretreatment transcriptional and inferred immune infiltration patterns to neoadjuvant chemotherapy response. Separately, in a hypothesis-generating single-cell cohort of five triple-negative breast cancers (n = 5; four responders, one non-responder), we performed single-cell RNA sequencing, T cell and B cell receptor sequencing, single-cell ATAC sequencing, and glycosylation tag profiling. Results: In bulk data, triple-negative tumors showed a loss of luminal estrogen receptor-associated programs, higher proliferation, and CIBERSORT-estimated enrichment of myeloid-associated immune fractions compared with non-triple-negative tumors. Chemotherapy response was associated with modest transcriptional shifts and inferred immune composition differences in triple-negative tumors and more pronounced epithelial, stromal, and inflamed immune changes in non-triple-negative disease. Single-cell data suggested that responder tumors were enriched for T and natural killer cells, antigen-presenting myeloid cells, expanded and diverse T and B cell clonotypes, and immune-associated glycosylation signals, whereas the non-responder sample was dominated by epithelial and fibroblast compartments with secretory, adhesion, and potential immune evasion programs. Checkpoint-related analyses reflected expression patterns and predicted ligand–receptor communication, nominating TIGIT–NECTIN2 as a candidate axis for further investigation. Conclusions: Integrating public bulk cohorts with exploratory single-cell multi-omics supports a model in which chemotherapy sensitivity in triple-negative breast cancer is linked to inflamed, antigen-presenting microenvironments and adaptable antitumor immunity, whereas resistance is associated with stromal and tumor dominance. These candidate biomarkers and pathways require validation in larger independent cohorts, and clinical translation is premature given the exploratory single-cell cohort.