Transcription profiling of human pDC cell line
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Babacar Cisse
PROVIDER: E-GEOD-12507 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The interferon-producing plasmacytoid dendritic cells (PDC) share common progenitors with antigen-presenting classical dendritic cells (cDC), yet they possess distinct morphology and molecular features resembling those of lymphocytes. It is unclear whether the unique cell fate of PDC is actively maintained in the steady state. We report that the deletion of transcription factor E2-2 from mature peripheral PDC caused their spontaneous differentiation into cells with cDC properties. This included the loss of PDC markers, increase in MHC class II expression and T cell priming capacity, acquisition of dendritic morphology and induction of cDC signature genes. Genome-wide chromatin immunoprecipitation revealed direct binding of E2-2 to key PDC-specific and lymphoid genes, as well as to certain genes enriched in cDC. Thus, E2-2 actively maintains the cell fate of mature PDC and opposes the “default” cDC fate, in part through direct regulation of lineage-specific gene expression programs. Inducible deletion of E2-2 (Tcf4) has been performed by administering tamoxifen to conditional E2-2flox/flox Rosa26-CreER+ mice or to E2-2flox/flox Rosa26-CreER- control littermates. Four or six days later total splenocytes were isolated, pooled from 2-3 mice and PDC (CD11b- B220+ CD11clow Bst2+) were isolated by sorting. Global gene expression profiles of E2-2-deficient (null) and control (Ctrl) PDC were compared using Affymetrix microarrays (GPL1261).
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Project description:The abstract of the manuscript titled "Signalling pathways involved in adult heart formation revealed by gene expression profiling in Drosophila" is given below: "Drosophila provides a powerful system for defining the complex genetic programs that drive organogenesis. Under control of the steroid hormone ecdysone, the adult heart in Drosophila forms during metamorphosis by a remodelling of the larval cardiac organ. Here, we evaluated the extent to which transcriptional signatures revealed by genomic approaches can provide new insights into the molecular pathways that underlie heart organogenesis. Whole-genome expression profiling at 8 successive time-points covering adult heart formation revealed a highly dynamic temporal map of gene expression through 13 transcript clusters with distinct expression kinetics. A functional atlas of the transcriptome profile strikingly points to the genomic transcriptional response of the ecdysone cascade, and a sharp regulation of key components belonging to a few evolutionary conserved signalling pathways. A reverse genetic analysis provided evidence that these specific signalling pathways are involved in discrete steps of adult heart formation. In particular, the Wnt signalling pathway is shown to participate in inflow tract and cardiomyocyte differentiation, while activation of the PDGF-VEGF pathway is required for cardiac valve formation. Thus, a detailed temporal map of gene expression can reveal signalling pathways responsible for specific developmental programs and provides here substantial grasp into heart formation." Keywords: Time-course analysis Total RNAs were prepared from dissected cardiac tubes of Drosophila staged pupae at 8 successive time-points 21, 24, 27, 30, 33, 36, 42 and 48 hours after puparium formation covering adult heart organogenesis. For each time-point sample, 5 cardiac tubes were hand dissected from staged individuals. Four independent biological replicates were analyzed to confer a high reproducibility and statistical significance of the expression data. PolyA+ RNAs were linearly amplified (32 amplifications), labelled (32 with Cy3 and 32 with Cy5), and used for hybridization on Drosophila high-density oligonucleotide (INDAC) dual-channel microarrays (32 arrays) according to a loop-design dedicated to time-course experiments. Given the same number of arrays (8), a simple loop design is more efficient than a reference design: direct comparisons, smallest variance for log ratios, balancing varieties with dye-swapping (including technical replicates) and no reference sample needed (which has no intrinsic interest in our study). A graphical representation of the loop design used on this study is showed in the associated manuscript.
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