Associations of blood DNA methylation with immune checkpoint inhibitor related outcomes in patients with head and neck squamous cell carcinoma

In this exploratory epigenome-wide association study (EWAS), we sought to investigate associations of pre-treatment blood-derived DNA methylation with survival and response outcomes among patients with recurrent/metastatic (R/M) head and neck squamous cell carcinomas (HNSCCs) who received immune checkpoint inhibitor (ICI) therapy. Patients with R/M HNSCC were recruited from the Dana-Farber Cancer Institute, Dartmouth Cancer Center, and Rhode Island Hospital. Peripheral blood was collected prior to the start of ICI, and DNA methylation was measured using the Illumina EPIC V1 and V2 BeadArrays. After strict quality control, the top 10% most variable CpG sites ( n = 67,712) were included in an EWAS of methylation with overall survival (OS) and progression-free survival (PFS). Models were adjusted for key covariates, including the DNA methylation-derived immune cell-type proportions. Among the 116 patients enrolled, 64 (55.2%) died during follow-up, and 22 (19.0%) experienced cancer progression. Of the 30 patients (25.9%) who remained progression-free, 13 showed a complete response to the ICI therapy. We identified two CpG sites ( cg04079758 and cg10654272 ) that were associated with improved PFS (false discovery rate [FDR] < 0.05). The CpG sites cg04079758 and cg10654272 are located in the South Shelf region on chromosome 19 and in an OpenSea region on chromosome 6, respectively. Additionally, one of the CpG sites, cg04079758 , was located in Kallikrein 9 ( KLK9 ), a gene involved in tissue remodeling and inflammation within the tumor microenvironment. No CpG site was statistically significantly associated with OS. Distinct blood DNA methylation signatures may be associated with ICI therapy-related outcomes in patients with R/M HNSCC.