Feasibility of methylated ctDNA detection in plasma samples of oropharyngeal squamous cell carcinoma patients

Abstract

Background: Oropharyngeal squamous cell carcinomas (OpSCCs) are commonly associated with high rates of treatment failure. Objectives: To evaluate methylation-based markers in plasma from OpSCC patients as emerging tools for accurate/noninvasive follow-up. Methods: Pretreatment formalin-fixed paraffin-embedded (FFPE) biopsies (n = 52) and paired plasma (n = 15) were tested for the methylation of CCNA1, DAPK, CDH8, and TIMP3 by droplet digital PCR (ddPCR). Results: Seventy-one percent (37/52) of the biopsies showed methylation of at least one of the evaluated genes and tumor CCNA1 methylation was associated with recurrence-free survival. Methylated circulating tumor DNA (meth-ctDNA) was detected in 11/15 (73.3%) plasma samples; conversely, plasma samples from healthy controls were all negative for DNA methylation (area under the curve = 0.867; 95% confidence interval = 0.720-1.000). Additionally, preliminary results on the detection of meth-ctDNA in plasma collected during follow-up closely matched patient outcome.

Tracking the Molecular Fingerprint of Head and Neck Cancer for Recurrence Detection in Liquid Biopsies

“…EBV ctDNA is another promising biomarker with low cost and high sensitivity for predicting disease recurrence [ 46 ]. For non-viral-driven subtypes of HNSCC, specific mutations, methylation markers, or RNA expression have been explored as biomarkers [ 24 , 26 , 50 , 51 , 52 , 53 , 56 , 57 , 64 , 67 , 68 , 69 , 79 , 80 , 81 , 82 ].…”

“…Importantly, in only one case did methylation scoring in ctDNA increase earlier than the detection of progressive disease. Similarly, Machado de Jesus and colleagues [ 69 ] used ddPCR to quantify CCNA1, CDH8, DAPK, and TIMP3 promoter methylation in pretreatment formalin-fixed paraffin-embedded (FFPE) biopsies (n = 52) and paired plasma (n = 20) samples. Concordant results were found between both sample types in 16 out of 20 patients, with 11 out of 15 FFPE methylation-positive patients also positive in pretreatment plasma and full concordance in negative cases (n = 5).…”

G Protein-Coupled Receptor Genes, PTGDR1, PTGDR2, and PTGIR, Are Candidate Epigenetic Biomarkers and Predictors for Treated Patients with HPV-Associated Oropharyngeal Cancer

“…Implementation of liquid biopsy should be further evaluated on the basis of methodological aspects and cost effectiveness [ 37 ]. At present, only a few studies have investigated the relationship between ctDNA methylation events and prognosis in HNSCC [ 38 , 39 , 40 ]. Recently, de Jesus et al reported that methylated ctDNA was detected in 11/15 (73.3%) of these samples: 7/11 with methylation in CCNA1 , 2/11 with methylation in TIMP3 , 1 case with methylation in CDH8 , and 1 in DAPK [ 38 ].…”

“…At present, only a few studies have investigated the relationship between ctDNA methylation events and prognosis in HNSCC [ 38 , 39 , 40 ]. Recently, de Jesus et al reported that methylated ctDNA was detected in 11/15 (73.3%) of these samples: 7/11 with methylation in CCNA1 , 2/11 with methylation in TIMP3 , 1 case with methylation in CDH8 , and 1 in DAPK [ 38 ]. Currently, there is a lack of an effective OPC screening program because there are no identified OPC precursor lesions.…”

Clinical applications of liquid biopsy in HPV‐negative and HPV‐positive head and neck squamous cell carcinoma: advances and challenges

“…Using ddPCR analysis, de Jesus et al [ 38 ] evaluated plasma DNA methylation quantitation from OPSCC patients. From 20 OPSCC patients with paired tumor and plasma samples, no methylation was detected in 5 paired samples.…”