Spatially defined gene signatures uncover the association of extracellular matrix genes with immunotherapy resistance in head and neck squamous cell carcinoma. Spatially defined gene signatures uncover the association of extracellular matrix genes with immunotherapy resistance in head and neck squamous cell carcinoma

Background: Immune-checkpoint inhibition (ICI) only benefits a subgroup of patients with head and neck squamous cell carcinoma (HNSCC). Several molecular and cellular components of the tumor microenvironment (TME) have been hypothesized to drive either response or resistance. Here, spatially defined whole transcriptome data were analysed in search of associations of compartment-specific gene-signatures with HNSCC immunotherapy outcomes. Methods: Pre-treatment biopsy samples from 50 immunotherapy-treated recurrent or metastatic HNSCC patients as well as 12 matched post-treatment biopsies obtained after 4 weeks of treatment, constructed in tissue microarray format (YTMA496), were included in the study. The GeoMx Human Whole Transcriptome Atlas (NanoString Technologies) assay was performed on samples to allow RNA quantification of 18,677 protein encoding genes, using in situ hybridization, in three molecularly defined tissue compartments; tumor (CK), leukocyte (CD45), macrophage (CD68). Differentially expressed genes (DEGs) (P18,677 target genes) was used per manufacturer’s protocol. 240 ROIs corresponding to 240 AOIs were collected and analysed.