The liver is the largest solid organ in the body, yet it remains incompletely characterized. Here we present a spatial proteogenomic atlas of the healthy and obese human and murine liver combining single-cell CITE-seq, single-nuclei sequencing, spatial transcriptomics, and spatial proteomics. By integrating these multi-omic datasets, we provide validated strategies to reliably discriminate and localize all hepatic cells, including a population of lipid-associated macrophages (LAMs) at the bile ducts. We then align this atlas across seven species, revealing the conserved program of bona fide Kupffer cells and LAMs. We also uncover the respective spatially resolved cellular niches of these macrophages and the microenvironmental circuits driving their unique transcriptomic identities. We demonstrate that LAMs are induced by local lipid exposure, leading to their induction in steatotic regions of the murine and human liver, while Kupffer cell development crucially depends on their cross-talk with hepatic stellate cells via the evolutionarily conserved ALK1-BMP9/10 axis.

Peyer's patches (PPs) are secondary lymphoid organs in contact with the external environment via the intestinal lumen, thus combining antigen sampling and immune response initiation sites. Therefore, they provide a unique opportunity to study the entire process of phagocyte differentiation and activation in vivo. Here, we deciphered the transcriptional and spatial landscape of PP phagocyte populations from their emergence in the tissue to their final maturation state at homeostasis and under stimulation. Activation of monocyte-derived LysoDCs differs from that of macrophages by their upregulation of conventional dendritic cell (cDC) signature genes such as Ccr7 and downregulation of typical monocyte-derived cell genes such as Cx3cr1. We identified gene sets that distinguish PP cDCs from the villus ones and from LysoDCs. We also identified key immature, early, intermediate and late maturation markers of PP phagocytes. Finally, exploiting of the ability of the PP interfollicular region to host both villous and subepithelial dome emigrated cDCs, we showed that the type of stimulus, the subset, but also the initial location of cDCs shape their activation profile and thus direct the immune response. Our study highlights the importance of targeting the right phagocyte subset at the right place and time to manipulate the immune response.

Différenciation et activation des phagocytes de plaques de Peyer à l'âge adulte et au sevrage: La réponse immunitaire intestinale est initiée dans les plaques de Peyer (PP). Les PP contiennent des phagocytes appelés LysoDC excellant dans la phagocytose des antigènes in vivo et activant les lymphocytes T (LT) naïfs in vitro. Nous avons effectué une analyse des ARNm en cellule unique des LysoDC qui a révélé que les LysoDC immatures évoluent soit vers des LysoDC sous-épithéliales matures avec acquisition d’une signature transcriptionnelle typique des cellules dendritiques et la capacité à activer les LT naïfs ; soit vers des LysoDC folliculaires sans acquisition de cette signature ni de cette capacité. Après stimulation in vivo, les LysoDC matures migrent à la périphérie de la zone T où elles interagissent avec les LT prolifératifs.Le changement de diète au sevrage entraîne une diversification du microbiote qui active le système immunitaire intestinal. Au sevrage, les LysoDC, essentiellement matures, échantillonnent la lumière intestinale et interagissent avec des cellules prolifératives dans le dôme sous-épithélial, dont des lymphocytes B en cours d’activation qui migrent ensuite pour former les premiers centres germinatifs et qui persistent chez l’adulte. Cette activation nécessite le microbiote mais pas les espèces sensibles à la vancomycine. En conclusion, l’étude des LysoDC chez l’adulte et au sevrage m’a permis d’élucider leurs voies de différenciation, liées à leur localisation, leur capacité de migration et leur fonction de présentation aux LT, et de caractériser l’activation spatio-temporelle des cellules immunitaires des PP après le sevrage.