Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from myelo-dendritic progenitors as well as from mature myeloid and dendritic cells

ABSTRACT: Dendritic cells (DCs) are essential regulators of immune responses; however, transcriptional mechanisms establishing DC lineage commitment are poorly defined. Here we report that the PU.1 transcription factor induces specific remodeling of the higher-order chromatin structure at the Interferon Regulatory Factor-8 (Irf8) gene to initiate DC fate choice. Generation of an Irf8 reporter mouse enabled us to pinpoint an initial progenitor stage at which DCs separate from other myeloid lineages in the bone marrow. In the absence of Irf8, this progenitor undergoes DC-to-neutrophil reprogramming, indicating that DC commitment requires an active, Irf8-dependent escape from alternative myeloid lineage potential. Mechanistically, myeloid Irf8 expression depends on high PU.1 levels, resulting in local chromosomal looping and activation of a lineage- and developmental stage-specific cis-enhancer. These data delineate PU.1 as a concentration-dependent rheostat of myeloid lineage selection by controlling long-distance contacts between regulatory elements, and suggest that specific higher-order chromatin remodeling at the Irf8 gene determines DC differentiation. Mature macrophages, Granulocytes and DCs were isolated from wildtype mouse spleens for successive RNA extraction and hybridization on Affymetrix microarrays. 3 different pools, each consisting of splenic cells from 5 mice were prepared. Cell populations were isolated by flow cytometry. MDPs were isolated from Wildtype and IRF8 deficient bonemarrow by flowcytometry, again creating 3 biological replicates, each consisting of pooled cells from 5 mice. Differential gene expression between wildtype and IRF8 deficient MDPs was subgrouped into macrophage, granuloctic and DC signatures, derived from expression data of these cell populations.

ORGANISM(S): Mus musculus

SUBMITTER: Marie Gebhardt

PROVIDER: E-GEOD-45467 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:In the traditional model of hematopoiesis, blood lineages diversify from HSCs through a sequential process of hierarchical bifurcation. Each of these bifurcation nodes comprises multipotent progenitors that are assumed to be homogeneous and equipotent in terms of their potency. The isolation of dendritic cell (DC) progenitors with either myeloid or lymphoid potency has led to the notion of “convergent development”, and an ongoing debate on the origin of DCs and their relationship with myeloid and lymphoid lineages. We have used a clonal assay combining with statistical modeling to quantify the yield of granulocytes (G), monocytes (M), lymphocytes (L) and three subsets of DCs from single human CD34+ progenitor cells of nine different phenotypes, and traced the potency of their individual progeny. We show that multipotent progenitors are not in fact equipotent, but instead exhibit a bias toward one specific lineage; this lineage bias is established at the HSC stage and transmitted to most progeny, with bifurcation to other lineages only occurring infrequently. Critically, these lineage biases can be correlated to lineage-specific transcriptional programs that are reinforced during division. We performed computational analysis to correlate transcriptomes and lineage composition of individual phenotype-defined progenitor cells. This enabled us to identify 32 common transcription factor (TF) candidates that interact physically and form genetic regulatory networks, with lineage-specific developmental programs initiated and reinforced based on the distinct dosage combination of these common TFs. Our analysis reveals that early expression of high levels of IRF8 and intermediate levels of PU.1 protein correlates with a bias towards CD141+ DC and plasmacytoid DC lineages in vivo, and that this pattern is inheritable from progenitors to mature cells. We have therefore arrived at a coherent model of DC development driven by parallel and inheritable programs defined by distinct dosages of TFs including PU.1 and IRF8, a developmental model that may apply to other lineages as well.

Dataset Information

Expression data from myelo-dendritic progenitors as well as from mature myeloid and dendritic cells

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