Cell-type and donor-level epigenetic variation shape intestinal inflammatory responses to SARS-CoV-2 spike protein

Although coronavirus disease 2019 (COVID-19) is associated with gastrointestinal symptoms and systemic hyperinflammation, the epigenetic mechanisms linking SARS-CoV-2 to intestinal immune activation remain poorly understood. We investigated histone modifications in human ileum immune cells following ex vivo exposure to the recombinant SARS-CoV-2 spike protein using mass cytometry. Cytokine expression (TNF-α, IFN-γ, IL-17A, IL-6, and IL-10) and 14 histone marks were evaluated across eight major immune cell subsets, including B cells, T cells, resident T cells, natural killer (NK) cells, NKT cells, γδ T cells, mucosal-associated invariant T (MAIT) cells, and macrophages (MФ). Spike protein exposure induced coordinated inflammatory cytokine responses accompanied by extensive cell-type-specific epigenetic remodeling. MAIT cells, resident T cells, conventional T cells, and MФ exhibited the greatest chromatin remodeling. In contrast, NK cells, NKT cells, B cells, and γδ T cells showed no or few significant epigenetic changes. Linear mixed-effects modeling indicated that epigenetic associations with inflammatory responses were primarily attributable to differences between donors rather than variation among cell subsets within the same donor. Cell-subset identity remained independently associated with inflammatory response, with resident T cells showing significantly higher inflammatory scores, while the other cell subsets did not differ significantly. Together, these findings suggest that interindividual epigenetic variation and cell-subset identity are key determinants of intestinal inflammatory responses to SARS-CoV-2 spike protein.