Poster Presentation 37th Lorne Cancer Conference 2025

The development of a high-plex spatial proteomic methodology for the characterisation of the head and neck tumour microenvironment (#134)

Chin Wee Tan 1 2 3 , Naomi Berrell 3 4 , Meg L Donovan 3 4 , James Monkman 3 , Habib Sadeghirad 3 , Vahid Yaghoubi Naei 3 , Jinjin Chen 1 5 , Alyssa Rossenbloom 6 , Catherine Barnett 5 , Rahul Ladwa 5 , Brett GM Hughes 7 8 , Arutha Kulasinghe 3 4
  1. Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia
  2. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
  3. Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
  4. Queensland Spatial Biology Centre, Wesley Research Institute, Level 8 East Wing, The Wesley Hospital, Auchenflower, QLD, Australia
  5. Department of Head & Neck Oncology, Princess Alexandra Hospital, Brisbane, QLD, Australia
  6. Bruker Spatial Biology Inc., Seattle, WA, USA
  7. The Royal Brisbane and Women’s Hospital, Herston, Brisbane, QLD, Australia
  8. School of Medicine, University of Queensland, Brisbane, QLD, Australia

Head and neck squamous cell carcinoma (HNSCC) is a debilitating disease that accounts for an estimated 890,000 new cases per year, making it the seventh most common cancer globally. It is a debilitating group of cancers that affect various regions of the head and neck which stem from the epithelial cells in the mucosal lining. Despite advancements in chemotherapy, radiotherapy, surgery and immunotherapy, the prognosis of HNSCC has remained relatively unchanged for more than a decade. There is a need to better understand of the tumour microenvironment (TME) using spatially resolved approaches, to gain insights into the TME associated with clinical endpoints such as Disease-Free Survival (DFS) and Overall Survival (OS). Here, we profiled 84 HNSCC tissue samples using next-generation ultra-high plex spatial protein profiling (580-proteins, Immuno-Oncology Proteome Atlas) and spatial transcriptome mapping (18,000 mRNA, Whole Transcriptome Atlas) from Nanostring Technologies (Bruker). Patient specimens were collected during tumour resection, where patients then went on to receive either chemotherapy and/or radiotherapy. Each patient tissue sample was subdivided into tumour and stromal regions prior to digital spatial profiling. We found that patient survival outcomes (both DFS and OS) were associated with anatomical locations and tumour stage. Notably, there were specific proteomic and transcriptomic features in both the tumour and stromal regions that associated with DFS and OS. Independent validation of key proteomic findings (including CD34 and CD44) was performed using single-cell protein profiling (PhenoCycler-Fusion, Akoya Biosciences). Finally, cell type deconvolution based on transcriptomic signatures revealed cell types associated with patient survival. Taken together, this study provides a systematic workflow for discovery and validation of high-plex protein and transcriptomic profiling in HNSCC.