Identification of tumor repopulating–like epithelial cells and a repair-dominant niche in pathological responders after neoadjuvant chemo-immunotherapy for HNSCC.

Abstract

6070 Background: Neoadjuvant PD-1 blockade plus chemotherapy can induce deep pathologic responses in HNSCC. However, pCR is an imperfect surrogate for OS, and the prior study showed that >50% of patients achieving CR after neoadjuvant chemo-immunotherapy relapse rapidly without local therapy, suggesting post-treatment ecosystems may retain programs supporting residual cell persistence and relapse. Methods: We profiled tumors from treatment-naïve patients and from patients receiving neoadjuvant taxane/platinum (TP) plus PD-1 blockade with partial response or pCR using scRNA-seq and Xenium spatial transcriptomics. Integrated computational analyses mapped residual epithelial/microenvironmental programs and spatial organization, with validation by immunoblotting, flow cytometry, and mIHC. Translational strategies were evaluated in a 4NQO-induced murine model and a PD-1–resistant murine tongue cancer line. Results: We identified a KRT15+IL1R2+ stem-like epithelial population enriched after therapy, most prominent in pCR (61/78 patients), localized to post-treatment regression beds but not discernible on H&E. They were viable and quiescent, lacking DNA damage and cell-death activation; CytoTRACE indicated high differentiation potential, suggesting tumor-repopulating cells. Concerning the microenvironment, across the response continuum from treatment-naïve to partial pathologic response to pCR, scRNA-seq revealed stepwise enrichment of infiltrating non-exhausted cytotoxic CD8 effector T cells, consistent with progressively strengthened tumoricidal immunity. In contrast, deep responders displayed a shift toward a repair-dominant niche: macrophages progressively transitioned from CXCL9+ inflammatory monocytes to SPP1+ macrophages with reduced antigen-presentation programs and enhanced tissue-remodeling features, accompanied by enrichment of multiple repair-associated fibroblast states. Xenium further supported spatial proximity and putative interactions among IL1R2+ epithelium, macrophages, and fibroblasts, which may limited T cell–tumor contact. IL1R2 upregulation was also observed in a PD-1–resistant murine tongue cancer line. In vivo, IL-1β co-administration with PD-1 blockade attenuated treatment efficacy, whereas anti–IL-1β antibody combined with PD-1 blockade enhanced efficacy. Conclusions: Deep responses to neoadjuvant chemo-immunotherapy are coupled with a paradoxical repair program and enrichment of IL1R2+ stem-like epithelium that may permit residual persistence and recurrence. The IL-1β–IL1R2 axis is a translationally actionable lever to improve durability and mitigate relapse. Given residual risk even after pCR, de-escalation of local therapy (such as reducing surgical extent or altering definitive treatment strategies) warrants caution.