Tumor-Initiating Stem Cells Fine-tune the Cell States of Neutrophils to Drive Cancer Relapse from Immunotherapy [SCC bulk RNA-Seq]

The highly heterogeneous and plastic nature of tumor-associated neutrophils (TANs) has been recognized, but how different cell states of TANs emerge, evolve, distribute, and impact cancer immunotherapy efficacy remains elusive. Using single-cell RNA sequencing, spatial transcriptomic analysis, and genetic manipulations, we show that, while anti-PDL1/CD40 agonist immunotherapy can reprogram TANs to gain strong anti-tumor activities in squamous cell carcinomas (SCCs), a subset of neutrophils residing at the tumor-stroma interface can preserve their immune-suppressive state. Importantly, we identified a group of Sox2Hi tumor-initiating stem cells (tSCs) at the tumor-stroma interface that can activate Fatty Acid Desaturase 1 (Fads1) and produce arachidonic acid (AA) to induce autocrine prostaglandin E2 signaling which can disrupt the interferon responses in neutrophils. Thus, through this interaction, tSCs fine-tunes the cell states of neutrophils, shapes neutrophil heterogeneity, and sculpts a protective micro-niche to drive cancer relapse following immunotherapy. Overall design: To investigate the mechanisms by which tSCs modulate neutrophils, we isolated Itga6hi CD80+ tumor stem-like cells and Itga6low CD80? differentiated cancer cells from DMBA/TPA-induced skin squamous cell carcinoma (SCC), and performed bulk RNA sequencing on these populations.