Background

Pre-vaccination immune states predict vaccine responsiveness, particularly those enriched in innate and interferon-related programs. While hematopoietic stem and progenitor cells (HSPCs) exhibit epigenetically encoded, clone-specific behaviors, whether these interferon-enriched states are established at the stem cell level and maintained across differentiation remains poorly defined.

Methods

Integrated multi-omic profiling using single-cell RNA sequencing (scRNA-seq) and plasma proteomics (Olink) was performed in a longitudinal healthy cohort vaccinated with Fluarix Quadrivalent. Adults aged 25–65 years were recruited through the Sound Life Project, with longitudinal collection of PBMCs and matched plasma.

Results

Antibody titers peaked at day 7 following influenza vaccination across both Year 1 and Year 2, enabling stratification of individuals into high, intermediate, and low responders. Low responders showed elevated TGF-β1 levels inversely correlated with antibody titers and antiviral programs, whereas high responders displayed a transcriptomic profile consistent with interferon pathway activation, including genes such as GBP4 alongside inflammatory and metabolic markers (e.g., MMP9, PKLR). At the single-cell level, high responders showed upregulation of interferon-responsive genes in HSPCs, including common myeloid progenitors, with key interferon-stimulated genes (IFITM3, DDX60, ISG15), consistent with a pre-programmed interferon state sustained from day 0 to 90 across both study years. Trajectory analysis revealed that this state was maintained from progenitor compartments toward more differentiated hematopoietic lineages. Notably, the same signature was recapitulated in myeloid populations, including monocytes and cDC2 subsets, indicating propagation of a stem cell–encoded interferon program across innate immune lineages.

Conclusion

This study defines a human in vivo framework in which pre-programmed hematopoietic stem cell states govern vaccine responsiveness through innate antiviral immunity, providing a mechanistic basis to enhance vaccine efficacy and antiviral responses.