Bioinformatics Seminar
Time: 11AM
Venue: Davis Auditorium and Online
21 October 2025
Characterising HNSCC and Skin tumour microenvironment using ultra-high plex spatial omics analyses
Chin Wee TanWEHI Bioinformatics
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. Using the latest spatial omics technologies and innovative computational 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). We utilised the latest 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 to analysed 84 mucosal HNSCC patient specimens collected during resection. Results from our integrated analysis workflow suggest patient DFS and OS were associates with anatomical locality and tumour stages, uncovering unique protein and transcript features associated with either DFS and/or OS. We validated these findings using an independent single-cell proteomics approach (PhenoCycler-Fusion from Akoya Biosciences) and uncovered cell types associated with patient survival in the transcript data. We have now expanded our study to profile specimens from 4 cutaneous squamous cell carcinoma (cSCC) patients (190 ROIs) using the next generation ultra-high-plex spatial proteomics 1200-plex Discovery Protein Atlas (DPA) in tandem with the WTA. We have now mapped whole tissue sections at the tumour, boundary and stromal regions to uncover proteome and transcriptomics differences across the TME interface regions, enabling the elucidation of clinical significance markers in mucosal HNSCC and other cancers.