Quiescent cancer cells resist T cell attack by forming an immunosuppressive niche

Immunotherapy is a promising treatment for triple-negative breast cancer (TNBC), but patients relapse, highlighting the need to understand the mechanisms of resistance. We discovered that in primary breast cancer, tumor cells that resist T cell attack are quiescent. Quiescent cancer cells (QCCs) form clusters with reduced immune infiltration. They also display superior tumorigenic capacity and higher expression of chemotherapy resistance and stemness genes. We adapted single-cell RNA-sequencing with precise spatial resolution to profile infiltrating cells inside and outside the QCC niche. This transcriptomic analysis revealed hypoxia-induced programs and identified more exhausted T cells, tumor-protective fibroblasts, and dysfunctional dendritic cells inside clusters of QCCs. This uncovered differential phenotypes in infiltrating cells based on their intra-tumor location. Thus, QCCs constitute immunotherapy-resistant reservoirs by orchestrating a local hypoxic immune-suppressive milieu that blocks T cell function. Eliminating QCCs holds the promise to counteract immunotherapy resistance and prevent disease recurrence in TNBC. [Display omitted] •Antigen-expressing tumor cells that escape from T cell attack are quiescent•Quiescent cancer cells (QCCs) form clusters that exclude immune infiltrates•PADME-seq reveals an increase in terminally exhausted T cells in the QCC niche•HIF1a activation in cancer cells augments T cell exhaustion and reduces T cell killing Spatially resolved transcriptome analysis of tumors identifies quiescent cell niches that instruct T cells to be hyporesponsive, thus suggesting a route for therapeutic targeting in triple-negative breast cancer.