Abstract 4081: A multimodal single-cell atlas reveals a pathogenic epithelial-myeloid circuit driving HNSCC progression

Abstract In this study, we performed single-cell RNA sequencing (scRNA-seq) on 167 samples from patients with head and neck squamous cell carcinoma (HNSCC), including distal normal tissues, premalignant lesions, peri-tumor regions, primary tumors, lymph node metastases, and distant metastatic or recurrent tumors. This comprehensive atlas allowed us to profile the full spectrum of immune and stromal populations across the continuum of HNSCC progression. By integrating transcriptional states, cellular compositions, and intercellular communication networks, we uncovered key features of the dynamically evolving tumor microenvironment and identified stage-specific mechanisms that shape tumor development, metastatic competence, and therapeutic resistance. A central finding was the discovery of a previously unrecognized intratumoral monocytic subset, which we termed Tumor-Reprogrammed Monocyte (TrMo). TrMo cells are markedly enriched in tumor tissues and strongly associated with adverse pathological features and poor patient survival. We also delineated major epithelial heterogeneity programs—including cell-cycle activation, hybrid epithelial-mesenchymal transition (hEMT), and epithelial senescence (EpiSen) —and validated these states in patient-derived organoid models. Notably, normal tissues were dominated by high EpiSen scores, whereas tumors exhibited diverse and spatially organized transcriptional programs. Using co-association analyses, we identified a robust multicellular module composed of hEMT cancer cells, TrMo cells, myofibroblastic CAFs, regulatory T cells, and EndoC3-RGCC endothelial cells. Spatial transcriptomic profiling confirmed the physical co-localization of this module in tumor tissues, highlighting a coordinated, tumor-promoting niche. To investigate its functional relevance, we focused on the bidirectional communication between hEMT tumor cells and TrMo cells. Spatial data demonstrated their intimate juxtaposition in situ, while in vitro co-culture experiments revealed a reciprocal signaling loop. TrMo cells enhanced EMT features in cancer cells by activating the EGFR pathway, whereas hEMT tumor cells induced TrMo activation through CD44-dependent cues. Using patient-derived tumor organoids, we further validated this reciprocal circuit and showed that disrupting either EGFR signaling in tumor cells or CD44 signaling in monocytes attenuated the tumor-promoting phenotypes. Together, these findings define a pathogenic epithelial-myeloid signaling axis that emerges early in HNSCC progression, becomes reinforced in advanced disease, and represents a promising therapeutic vulnerability. Our work provides a comprehensive multi-modal atlas of the HNSCC microenvironment and establishes a mechanistic framework for targeting multicellular tumor niches that drive aggressive behavior and treatment failure. Citation Format: Chehyun Nam, Hua Zhao, Elissa Salman, Daniel Arnaudov, Uttam K. Sinha, Young Min Park, De-Chen Lin. A multimodal single-cell atlas reveals a pathogenic epithelial-myeloid circuit driving HNSCC progression abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts) ; 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86 (7 Suppl): Abstract nr 4081.