Abstract 5863: Mapping tumor metastasis and EMT-associated immune changes in HNSCC through spatial transcriptomic analysis

Abstract Head and neck squamous cell carcinoma (HNSCC) is a globally prevalent malignancy. Standard treatments typically include surgical resection, radiation therapy, and chemotherapy. However, for patients with recurrent or distantly metastatic tumors where surgery or radiation is no longer feasible, the primary treatment strategy shifts to combining targeted therapies with chemotherapy or immune checkpoint blockade (ICI) therapy. Despite these approaches, the overall prognosis remains poor. Therefore, identifying key changes in immune cell composition within the tumor microenvironment of malignant or metastatic tumors is crucial for improving the management and outcomes in HNSCC therapy. The aim of this study is to analyze changes in the immune microenvironment composition across different HNSCC specimens. We utilized tools including the GeoMx Digital Spatial Profiler (DSP) for imaging-based digitized gene expression analysis. We identified region of interesting (ROI) from distinct tumor regions, such as the tumor invasive front, tumor core, and paired lymph node metastases. Through the Cancer Transcriptome Atlas (CTA) analysis, we identified two distinct epithelial-mesenchymal transition (EMT) gene signatures, which were highly expressed in particularly aggressive tumor tissues. Additionally, within the myeloid activation signature, we observed that immune cell composition in primary tumor site was predominantly neutrophil-activated, whereas in lymph node metastases, macrophages were the dominant immune cells. To further validate these observations, we applied other spatial transcriptomics tools, including 10x Visium and 10x Xenium, to analyze specimens from six HNSCC patients. Transcriptomic trajectory analysis and ligand-receptor pair analysis revealed significant changes in the immune microenvironment of malignant HNSCC tissues. These results provide crucial insights into head and neck cancer treatment strategies tailored to different tumor microenvironment (TME) characteristics. Citation Format: Chih-Hung Chung, Muh-Hwa Yang. Mapping tumor metastasis and EMT-associated immune changes in HNSCC through spatial transcriptomic analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5863.