Abstract 175: Characterising head and neck tumour microenvironment using high plex spatial omics technologies and analyses

Abstract Head and neck squamous cell carcinoma (HNSCC) is the cancer of different parts of the head and neck region originating from epithelial cells of the mucosal layer. Globally, it is the 7th most common cancer with over 89 thousand new cases each year. Its prognosis has not changed significantly in recent years despite improvements in treatments options like immunotherapy, radiotherapy (RT), chemotherapy (CT) and surgery. Using the latest spatial omics technologies and approaches, this work aims to develop a better insight of the tumour microenvironment (TME), particularly the association with typical clinical endpoints including Disease-Free Survival (DFS) and Overall Survival (OS). In this study, we utilised the latest ultra-high plex (580-proteins) spatial protein technology (GeoMx Immuno-Oncology Proteome Atlas, IPA) and full transcriptome profiling (18, 000 transcripts, Whole Transcriptome Atlas, WTA) from Bruker Spatial Biology (Nanostring Technologies) to analysed 84 mucosal HNSCC patient specimens collected during resection. Each patient tissue sample was subdivided into tumour and stromal regions prior to digital spatial profiling. Patients had either underwent CT and/or RT and samples were stratified as either tumour or stromal regions before processing. Till this end, results suggest that patient DFS and OS were associates with anatomical locality and stages of the tumour. We uncovered unique protein and transcript features that’s associated with either DFS and/or OS. We validated these findings (specifically CD34 and CD44) using an independent approach (i.e. single-cell proteomics using PhenoCycler-Fusion from Akoya Biosciences) and uncovered cell types associated with patient survival by applying cell type deconvolution on transcript data. This study demonstrated an integrated analysis workflow using high plex proteomics and transcriptomics profiling data for uncovering markers of clinical significance in mucosal HNSCC. Citation Format: Chin Wee Tan, Naomi Berrell, Meg L. Donovan, James Monkman, Habib Sadeghirad, Vahid Yaghoubi Naei, Jinjin Chen, Alyssa Rossenbloom, Shilah Bonnett, Mark Conner, Brian Filanoski, Christine Kang, Joseph M. Beechem, John F. Fraser, Catherine Barnett, Rahul Ladwa, Brett G. Hughes, Arutha Kulasinghe. Characterising head and neck tumour microenvironment using high plex spatial omics technologies and analyses [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 175.