Unraveling cetuximab response in head and neck cancer with APHRODYTHE, a multi-omics patient-derived xenograft platform

The anti-EGFR antibody cetuximab is an established therapy for head and neck squamous cell carcinoma (HNSCC), yet robust predictive biomarkers of response remain elusive. To address this gap, we established APHRODYTHE, a resource of 79 HPV-negative HNSCC patient-derived xenografts (PDXs), including 61 with genomic annotation, 52 with RNA-seq profiling, and 63 tested with cetuximab in a population-scale preclinical trial. APHRODYTHE faithfully recapitulated the mutational, copy number, and transcriptional landscapes of human HNSCC, enabling systematic discovery of response determinants. Integrated multi-omics analyses revealed that tumors with pronounced squamous differentiation and keratinization were more likely to respond, whereas high Sonic Hedgehog (SHH) pathway activity was associated with intrinsic resistance. Cetuximab-sensitive tumors were also enriched for EGFR amplification, elevated EGFR ligand expression, and mutations in NOTCH1, FAT1, and ATM. Immunohistochemistry validated keratinization markers as candidate predictors of benefit with potential clinical applicability. Functionally, SHH pathway activation conferred antibody resistance, while pharmacologic SHH inhibition restored cetuximab sensitivity in resistant models. Together, these findings position APHRODYTHE as a robust translational platform, identify squamous keratinization and SHH activity as complementary biomarkers for patient stratification, and motivate SHH inhibition as a rational combination strategy to enhance cetuximab efficacy in HNSCC.