Tumor-Naïve Multimodal Profiling of Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma.

Abstract

PURPOSE:

Circulating tumor DNA (ctDNA) enables personalized treatment strategies in oncology by providing a noninvasive source of clinical biomarkers. In patients with low ctDNA abundance, tumor-naïve methods are needed to facilitate clinical implementation. Here, using locoregionally confined head and neck squamous cell carcinoma (HNSCC) as an example, we demonstrate tumor-naïve detection of ctDNA by simultaneous profiling of mutations and methylation.

EXPERIMENTAL DESIGN:

We conducted CAncer Personalized Profiling by deep Sequencing (CAPP-seq) and cell-free Methylated DNA ImmunoPrecipitation and high-throughput sequencing (cfMeDIP-seq) for detection of ctDNA-derived somatic mutations and aberrant methylation, respectively. We analyzed 77 plasma samples from 30 patients with stage I-IVA human papillomavirus-negative HNSCC as well as plasma samples from 20 risk-matched healthy controls. In addition, we analyzed leukocytes from patients and controls.

RESULTS:

CAPP-seq identified mutations in 20 of 30 patients at frequencies similar to that of The Tumor Genome Atlas (TCGA). Differential methylation analysis of cfMeDIP-seq profiles identified 941 ctDNA-derived hypermethylated regions enriched for CpG islands and HNSCC-specific methylation patterns. Both methods demonstrated an association between ctDNA abundance and shorter fragment lengths. In addition, mutation- and methylation-based ctDNA abundance was highly correlated (r > 0.85). Patients with detectable pretreatment ctDNA by both methods demonstrated significantly worse overall survival (HR = 7.5; P = 0.025) independent of clinical stage, with lack of ctDNA clearance post-treatment strongly correlating with recurrence. We further leveraged cfMeDIP-seq profiles to validate a prognostic signature identified from TCGA samples.

CONCLUSIONS:

Tumor-naïve detection of ctDNA by multimodal profiling may facilitate biomarker discovery and clinical use in low ctDNA abundance applications.

• Authors: Justin M Burgener, Jinfeng Zou, Zhen Zhao, Yangqiao Zheng, Shu Yi Shen, Shao Hui Huang, Sareh Keshavarzi, Wei Xu, Fei-Fei Liu, Geoffrey Liu, John N Waldron, Ilan Weinreb, Anna Spreafico, Lillian L Siu, John R de Almeida, David P Goldstein, Michael M Hoffman, Daniel D De Carvalho, Scott V Bratman
• Journal: Clinical cancer research : an official journal of the American Association for Cancer Research (Clin Cancer Res) Vol. 27 Issue 15 Pg. 4230-4244 (08 01 2021) ISSN: 1557-3265 [Electronic] United States
• PMID: 34158359 (Publication Type: Journal Article, Observational Study, Research Support, Non-U.S. Gov't)
• Copyright: ©2021 The Authors; Published by the American Association for Cancer Research.

Chemical References

• Circulating Tumor DNA

Topics

• Circulating Tumor DNA (blood, genetics)
• DNA Methylation
• Head and Neck Neoplasms (blood, genetics)
• Humans
• Mutation
• Prospective Studies
• Squamous Cell Carcinoma of Head and Neck (blood, genetics)