Infection history imprints prolonged changes to the Kupffer cell epigenome, transcriptome and function of Kupffer cells

Background and aims: Macrophages are highly versatile innate phagocytes present in most organs of the body and perform various homeostatic and immunological functions. Macrophages are classically known for their important roles in compacting pathogens. Whereas, increasing evidence supports that exposure to infections invokes prolonged changes to tissue-resident macrophages, it remains unclear whether this occurs to liver macrophages. Methods: Here, we utilized a model of parasitic infection invoked by the protozoan parasite Trypanosoma brucei brucei to investigate whether infection history can durably reshape hepatic macrophage identity and function. Employing a combination of genetic lineage-tracing, single cell transcriptomics, epigenomic analysis, and functional assays, we studied the alterations to the liver macrophage compartment during and after the resolution of infection. Results: We show that the infection alters the composition of liver-resident macrophages, leading to the infiltration of monocytes that differentiate into various infection-associated macrophage populations with divergent transcriptomic profiles. Whereas infection-associated macrophages disappear post-resolution of infection, monocyte-derived macrophages assuming the Kupffer cell (KC)-like profile engraft in the liver and co-existed with embryonic KCs in the long-term. Remarkably, the prior exposure to infection imprinted a specific transcriptional program on post-resolution KCs that was independent of cell ontogeny. This reprogramming of KCs was driven by an epigenetic remodeling of KC chromatin landscapes and associated with altered KC function and was associated with increased resiliance to subsequent bacterial infection. Conclusion: Our study demonstrates that prior exposure to a parasitic infection can reshape the identity and function of the liver macrophage pool in the long-term. CITE-seq: Macrophages were FACS sorted ( 7AAD-negative/low CD45-positive CD11b-intermediate F4/80-high) from liver samples from non-infected, day 28-infected with Trypanosoma brucei brucei, 2 weeks and 8 weeks post-curing of the infection of Flt3-Cre Rosa26-Yfp mice. The cells were stained with antibody panel containing 158 oligo-conjugated antibodies and RNA and ADT libraries were prepared using the 10x Genomics platform. Multiome-seq: Single nuclei were extracted from non-infected mice and mice 8 weeks post-curing of Trypanosoma brucei brucei infection. Mice were from Flt3-Cre Rosa26-Yfp background. Joint snRNA- and scATAC libraries were prepared using the 10x Genomics platform. Bulk ATAC-seq: Macrophages were FACS sorted ( 7AAD-negative/low CD45-positive CD11b-intermediate F4/80-high TIM4-positive) from liver samples from non-infected (2 weeks post melarsoprol), 2 weeks and 8 weeks post-curing of the infection with Trypanosoma brucei brucei.