Methylomes of macrophage-DC progenitors (MDPs), monocytes, common monocyte progenitors (cMoPs), common dendritic cell progenitors (CDPs), plasmacytoid dendritic cells (pDCs), and cDC CD8a+ as well as cDC CD11b+ dendritic cells

Dendritic cells (DCs) are critical immune regulators involved in autoimmune diseases, but exploiting them clinically requires a detailed picture on the mechanisms orchestrating their development. DNA methylation is attractive in this regard because it is reversible and as such allows therapeutic manipulation. Combining single cell transplantation assays with whole-genome methylation assessment and with mice expressing reduced DNA methyltransferase 1 levels, we show that conventional and plasmacytoid DCs arise from myeloid-restricted hematopoietic stem cells (HSCs), suggesting that both subsets can develop independently of the lymphoid pathway. DC commitment by these HSCs requires an intrinsically high methylation threshold to establish expression of DC genes, particularly the Flt3 cytokine receptor. Reducing methylation depleted DCs and ameliorated systemic lupus erythematosus in mice. These studies shed novel light on the DC origin, show how lineage- and subset-specific methylation dynamics regulate DC fate and provide a potential rationale for targeting DCs in autoimmunity by hypomethylating agents. Overall design: Tagmentation-based whole-genome bisulfite sequencing (TWGBS) of MDPs (Lin- cKithi CD115+ Flt3+, 2 Replicates), Monocytes (CD11b+ Ly6Chi B220- CD5- CD8a- Ter119- SiglecF- Ly6G- FceRI-, 3 Replicates), cMoPs (Lin- cKithi CD115+ Flt3- CD11b- Ly6C+, 2 Replicates), CDPs (Lin- cKitlo CD115+ Flt3+, 4 replicates), pDCs (PDCA+ CD11cint, 3 replicates), cDC CD8a+ (MHC II+ CD11chi CD11b- CD8a+, 3 replicates) and cDC CD11b+ (MHC II+ CD11chi CD11b+ CD8a-, 3 replicates). Lineage markers (Lin): (B220, CD4, CD8a, CD3, CD19, CD11c, Ter119, NK1.1, expanded by antibodies to CD11b and Gr-1 for isolation of MDP and CDP or Ly-6G for cMoP isolation). For each replicate, four separate TWGBS libraries were prepared and pools of four libraries were sequenced on three separate HiSeq2000 lanes using the 125bp paired-end mode.