DNA-Methylome-Based Tumor Hypoxia Classifier Identifies HPV-Negative Head and Neck Cancer Patients at Risk for Locoregional Recurrence after Primary Radiochemotherapy

◥ Purpose: Tumor hypoxia is a paradigmatic negative prognosti-cator of treatment resistance in head and neck squamous cell carcinoma (HNSCC). The lack of robust and reliable hypoxia classifiers limits the adaptation of stratified therapies. We hypoth-esized that the tumor DNA methylation landscape might indicate epigenetic reprogramming induced by chronic intratumoral hypoxia. Experimental Design: A DNA-methylome-based tumor hyp-oxia classifier (Hypoxia-M) was trained in the TCGA (The Cancer Genome Atlas)-HNSCC cohort based on matched assignments using gene expression-based signatures of hypoxia (Hypoxia-GES). Hypoxia-M was validated in a multicenter DKTK-ROG trial con-sisting of human papillomavirus (HPV)-negative patients with HNSCC treated with primary radiochemotherapy (RCHT). Results: Although hypoxia-GES failed to stratify patients in the DKTK-ROG, Hypoxia-M was independently prognostic for local recurrence (HR, 4.3; P 1/4 0.001) and overall survival (HR, 2.34; P 1/4 0.03) but not distant metastasis after RCHT in both cohorts. Hyp-oxia-M status was inversely associated with CD8 T-cell infiltration in both cohorts. Hypoxia-M was further prognostic in the TCGA-PanCancer cohort (HR, 1.83; P 1/4 0.04), underscoring the breadth of this classifier for predicting tumor hypoxia status. Conclusions: Our findings highlight an unexplored avenue for DNA methylation-based classifiers as biomarkers of tumoral hyp-oxia for identifying high-risk features in patients with HNSCC tumors. See related commentary by Heft Neal and Brenner, p. 2954

Automated summary

This study suggests that the DNA methylation landscape of tumor cells may indicate epigenetic changes caused by chronic tumor hypoxia. The researchers developed a tumor hypoxia classifier (Hypoxia-M) based on DNA methylation profiles, which showed independent prognostic effects in patients with head and neck squamous cell carcinoma (HNSCC). These findings underscore the importance of DNA methylation-based classifiers as biomarkers of tumor hypoxia.