Tumor DNA‐methylome derived epigenetic fingerprint identifies HPV‐negative head and neck patients at risk for locoregional recurrence after postoperative radiochemotherapy

Abstract

Biomarkers with relevance for loco-regional therapy are needed in human papillomavirus negative aka HPV(À) head and neck squamous cell carcinoma (HNSCC). Based on the premise that DNA methylation pattern is highly conserved, we sought to develop a reliable and robust methylome-based classifier identifying HPV(À) HNSCC patients at risk for loco-regional recurrence (LR) and all-event progression after postoperative radiochemotherapy (PORT-C). The training cohort consisted of HPV-DNA negative HNSCC patients (n = 128) homogeneously treated with PORT-C in frame of the German Cancer Consortium-Radiation Oncology Group (DKTK-ROG) multicenter biomarker trial. DNA Methylation analysis was performed using Illumina 450 K and 850 K-EPIC microarray technology. The performance of the classifier was integrated with a series of biomarkers studied in the training set namely hypoxia-, 5-microRNA (5-miR), stem-cell gene-expression signatures and immunohistochemistry (IHC)-based immunological characterization of tumors (CD3/CD8/PD-L1/PD1). Validation occurred in an independent cohort of HPV(À) HNSCC patients, pooled from two German centers (n = 125). We identified a 38-methylation probe-based HPV(À)

Role of DNA Methylation Profiles as Potential Biomarkers and Novel Therapeutic Targets in Head and Neck Cancer

“…Multivariate analysis of the same study by Tawk et al [17] also showed that HICR high-risk tumors were enriched for younger patients with hypoxic tumors (15-gene hypoxia signature) and elevated 5-miRNA scores. The 5-miRNA signature (hsa-let-7g-3p, hsa-miR-6508-5p, hsa-miR-210-5p, hsa-miR-4306, and hsa-miR-7161-3p) was previously shown as a strong and independent prognostic factor for disease recurrence and survival of patients with HPV-negative HNSCC [23].…”

“…Regarding the role of DNA methylation profiles in HPV-negative HNSCC, hypermethylation of MGMT and COL1A2 is another example that can be considered a clinically valuable prognostic factor since there is a lack of biomarkers for HPV-negative HNSCC in general. Additionally, the future application of 38 differentially methylated probes as biomarkers to classify disease recurrence, distant metastasis, and overall survival [17] is also clinically valuable, as it may help stratify HPV-negative HNSCC patients. This could provide more personalized treatment based on methylation profiles with hopefully better clinical outcomes.…”

“…For this reason, a recent study by Tawk et al [17] developed a reliable and robust methylome-based classifier to identify HPV-negative HNSCC patients at risk for locoregional recurrence and all event progression after post-operative radiochemotherapy (PORT-C). The study identified a 38-methylation probe-based HPV-negative Independent Classifier of Disease Recurrence (HICR) with a high prognostic value for loco-regional recurrence, distant metastasis, and overall survival.…”

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

“…Patients with HPV DNA positivity were excluded, leaving 88 samples for validation. DNA methylation profiling was performed using Illumina 450 K microarrays (Illumina) as previously described ( 8 ). Functional normalization of DNA methylation was conducted using the minfi package in R ( 26, 27 ) and used as a validation cohort.…”

“…In particular, the presence of hypoxia in human papillomavirus (HPV)–negative patients with HNSCC confers poor prognosis. Patients with hypoxic tumors may benefit from stratified therapy intensification ( 8, 9 ). However, the robust, feasible, and reliable detection of tumor hypoxia remains a major challenge.…”