Longitudinal Analysis of Influenza Vaccines on DNA methylation Identifies the RIG-I Signaling Pathway

Influenza virus infection was previously found to alter the promoter DNA methylation of key immune response-related genes, including type-1 interferons and proinflammatory cytokines. However, less is known about the effect of the influenza vaccine on the epigenome. Therefore, we utilized a targeted DNA methylation to study the longitudinal effects (day 0 pre-vaccination and day 28 post-vaccination) of influenza vaccination responses in peripheral blood mononuclear cells. We found that baseline methylation profiles are associated with protective immunity and immune conversion prior to influenza vaccination. Moreover, we identified 481 differentially methylated sites 28 days post-vaccination. These sites were enriched for genes involved in the regulation of the RIG-I signaling pathway, an important regulator of viral response. Our results suggest that DNA methylation changes to components of the RIG-1 pathway may impact vaccine effectiveness. The samples in our study were from the University of Georgia (UGA) cohorts. The influenza vaccines administered by the University of Georgia had four different cohorts, with partially overlapping participants. In this study, we focused on the third and the fourth cohorts. Peripheral blood mononuclear cells were collected, and targeted bisulfite sequencing was then performed on 63 individuals for day 0 (before influenza vaccine injection) and 96 individuals for day 28 (28 days after vaccine injection with FluZone). 55 samples were paired between pre-vaccination and post-vaccination. We sequenced approximately 5000 targeted regions within the genome that were selected based on previous evidence that they were associated with viral infections. In total, we quantified levels of DNA methylation at approximately 70,000 CpG sites.