Abstract A004: Blood DNA methylation in association with immune checkpoint inhibitor related outcomes among patients with head and neck squamous cell carcinoma
Authors: Gyeyoon Yim, Lucas Salas, Kartik Sehgal, Keisuke Shirai, Rondi Butler, Julianna Miller, Hannah Stolrow, Md Saiful Islam Saif, Devin Koestler, John Wiencke, Robert Haddad, Karl Kelsey, Brock Christensen
Journal: Cancer Research (2025)

Abstract Background: Head and neck squamous cell carcinomas (HNSCC) can occur in the oral cavity, pharynx, larynx, paranasal sinuses, and nasal cavity. Immune checkpoint inhibitors (ICI) have improved survival in multiple cancer types, including recurrent/metastatic (R/M) HNSCC. However, the majority of patients with R/M HNSCC did not achieve objective response with ICI in clinical trials. Although tumor tissue DNA methylation has been proposed as a potential biomarker for ICI response, less is known about blood DNA methylation as a potential biomarker for ICI treatment related outcomes in HNSCC. Objective: Investigate associations of pre-treatment blood-derived DNA methylation profiles with survival and response outcomes among patients with R/M HNSCC who receive ICI therapy. Methods: Patients with R/M HNSCC were recruited from the Dana-Farber Cancer Institute, Dartmouth Cancer Center, and Rhode Island Hospital in an ongoing prospective study in the U.S. (data cutoff: September 2024). Peripheral blood was collected from each patient prior to start of ICI based therapy. DNA methylation was measured using the Illumina EPIC array V1 and V2. After strict quality control, the top 10% most variable CpG sites (n=67,713) were included in the analysis. Epigenome-wide association study analysis was conducted for overall survival (OS), progression-free survival (PFS), and treatment response (durable benefit, non-durable benefit, and non-benefit) in association with normalized CpG beta-values. Models were adjusted for age, sex, smoking status, and DNA methylation-dervied estimated blood cell type proportions. Results: Among the 113 subjects enrolled so far, 59 (52.2%) died during follow-up and 18 (15.9%) experienced cancer progression. Of 36 patients (31.9%) who have remained progression-free survivors, 11 patients showed a complete response to the ICI therapy. The median OS and PFS were 428 and 279 days, respectively. Approximately half of the patients were categorized in the durable benefit group (n=57, 50.4 %), followed by the non-benefit group (n=30, 26.5 %) and the non-durable benefit group (n=26, 23.0 %). We identified two CpG sites (cg04997743 and cg25104727) that were associated with improved OS; and three (cg03090869, cg19041076, and cg22088248) that were associated with worse OS (false discovery rate [FDR] &amp;lt; 0.05). Similarly, six CpG sites (cg04079758, cg10654272, cg14132225, cg14812628, cg20071413, and cg25104727) were associated with improved PFS while a single CpG (cg24138433) was correlated with worse PFS (FDR &amp;lt; 0.05). The CpG sites associated with OS or PFS were annotated to CpG islands chr11:69924338-69925197, chr18:72916107-72917233, and chr19:51505914-51506363. Additionally, these CpG sites were located in genes that are broadly characterized by metabolism-related (ZADH2 and PPT1) or inflammation-related (KLK9 and ANO1) pathways. No CpG site was associated with the treatment response categories (FDR &amp;gt; 0.85). Conclusions: Distinct blood DNA methylation signatures may be associated with ICI therapy-related outcomes in patients with R/M HNSCC. Citation Format: Gyeyoon Yim, Lucas Salas, Kartik Sehgal, Keisuke Shirai, Rondi Butler, Julianna Miller, Hannah Stolrow, Md Saiful Islam Saif, Devin Koestler, John Wiencke, Robert Haddad, Karl Kelsey, Brock Christensen. Blood DNA methylation in association with immune checkpoint inhibitor related outcomes among patients with head and neck squamous cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr A004.