Gene expression data of Peyer's patch LysoDC differentiation states and macrophages at steady state and under TLR7 ligand stimulation

The specialized monocyte-derived phagocytes termed LysoDC are hallmarks of Peyer’s patches where their main function is to sample pathogens. However, their differentiation pathway and migratory properties remain uncharacterized. From single-cell RNA sequencing, we built LysoDC differentiation trajectories and fate diversity in correlation with their location and functions. All LysoDC differentiation states display similar phagocytic activity. One of them is located in follicles in a CXCR5-independent manner whereas the others reside in subepithelial domes (SED) and mature as they get closer to the epithelium. Immature LysoDC proliferate. Mature LysoDC acquire a gene signature shared with SIRP alpha-expressing conventional DC and prime naïve T cells in vitro but, at steady state, do not migrate in naïve T cells-enriched interfollicular regions (IFR). However, upon stimulation, they express the chemokine receptor CCR7 and migrate from the SED to the IFR periphery where they strongly interact with proliferative T cells. Finally, we show that LysoDC populates human Peyer’s patches. Three to five independent replicates of the 4 LysoDC differentiation states (TN, SP, DP, TP) were sorted from Peyer's patch of C57BL/6 mice at steady state. In addition, three to four independant replicates of 2 LysoDC differentiation states (DP and TP) and of TIM-4- and TIM-4+ macrophages (LysoMac) were sorted from Peyer's patch of C57BL/6 mice 9 hours after R848 gavage. Total RNA of Peyer's patch sorted cells was extracted with a Qiagen RNeasy Plus Micro Kit. Quantity, quality and absence of genomic DNA contamination were assessed with a Bioanalyser (Agilent). Microarray experiments were performed by the Plateforme Biopuces of Strasbourg (France) using the Affymetrix GeneChip® Mouse Gene 1.0 ST Array.