Whole transcriptome profiling of macrophage-DC progenitors (MDPs) and common monocyte progenitors (cMoPs) from Dnmt1+/+ and Dnmt1c/chip mice

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. MDPs (Lin-cKithiCD115+CD11b-Ly-6C-) and cMoPs (Lin-cKithiCD115+CD11b-Ly-6C+) were sorted from 8-12 weeks old Dnmt1+/+ and Dnmt1c/chip mice, total RNA was extracted using the RNeasy Micro kit (Qiagen) and gDNA was digested with the RNase-free DNAse provided in the Kit. Sample processing and hybridization on Affymetrix GeneChIPs (Mus musculus) MG 430 PM was carried out according to standard procedures at the Center of Excellence for Fluorescent Bioanalytics (KFB, University of Regensburg).