Epigenetic Reprogramming Mediates Monocyte and Heterologous T Cell-derived Cytokine Responses after BCG Vaccination

Epigenetic reprogramming plays an important role in shaping immune memory traits within both innate (trained immunity) and adaptive immune cells following Bacillus Calmette-Guérin (BCG) vaccination. However, the precise impact of dynamic DNA methylation alterations on immunological responses after BCG vaccination remains inadequately elucidated. To address this knowledge gap, we conducted a comprehensive study by integrating longitudinal analysis and systems biology approaches. We established a cohort of 284 healthy Dutch individuals, capturing data on genetics, cytokine responses to ex vivo stimulation and genome-wide DNA methylation at baseline, as well as at 14 days and 90 days after BCG vaccination. Our findings revealed distinct patterns of DNA methylation alternations in the short- and long-term following BCG vaccination. Moreover, we established that baseline DNA methylation profiles exert influence on the change in interferon-γ (IFN-γ) production upon heterologous ( Staphylococcus aureus) stimulation before and after BCG vaccination. Specifically, we identified the regulation of kisspeptin as a novel pathway implicated in the modulation of IFN-γ production, and this finding has been substantiated through experiment validation. We also observed associations between BCG-induced DNA methylation changes and increased IFN-γ and Interleukin-1 β (IL-1β) production upon S. aureus stimulation. Interestingly, by integrating with genetic, epigenetic, and cytokine response data from the same individuals, mediation analysis demonstrated that most of the identified DNA methylation changes played a mediating role between genetic variants and cytokine responses, for example, the changes of cg21375332 near SLC12A3 gene mediated the regulation of genetic variants on IFN-γ changes after BCG vaccination. Sex-specific effects consistently manifested in DNA methylation changes after BCG vaccination and in the association between baseline methylation and cytokine responses. Together, our findings provide deeper insights into immune response mechanisms, crucial for developing effective epigenetic-based medical interventions for personalized medicine.