Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptional profiling of Hoxa9-expanded hematopoietic cells expressing distinct TALE genes

ABSTRACT: Primary murine hematopoietic cells were retrovirally transduced with Hoxa9 cDNA, expanded in vitro before undergoing secondary infection with the cDNA of Meis1, Prep1 and the Prep1-MC mutant. RNA was extracted and transcriptomes were analyzed. Background corrections and normalisations were performed using RMA in NimbleScan 2.5

ORGANISM(S): Mus musculus

SUBMITTER: Richard Bisaillon

PROVIDER: E-MTAB-671 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

C-terminal domain of MEIS1 converts PKNOX1 (PREP1) into a HOXA9-collaborating oncoprotein.

Bisaillon Richard R Wilhelm Brian T BT Krosl Jana J Sauvageau Guy G

Blood 20110907 17

The three-amino-acid loop extension (TALE) class homeodomain proteins MEIS1 and PKNOX1 (PREP1) share the ability to interact with PBX and HOX family members and bind similar DNA sequences but appear to play opposing roles in tumor development. Elevated levels of MEIS1 accelerate development of HOX- and MLL-induced leukemias, and this pro-tumorigenic property has been associated with transcriptional activity of MEIS1. In contrast, reduction of PKNOX1 levels has been linked with cancer development ...[more]

PMID: 21900201

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Project description:Macrophages rapidly engulf apoptotic cells to limit the release of noxious cellular contents and to restrict autoimmune responses against self antigens. Although factors participating in recognition and engulfment of apoptotic cells have been identified, the transcriptional basis for the sensing and silently disposing of apoptotic cells is unknown. Here we show that peroxisome proliferator activated receptor delta (PPARdelta) is induced when macrophages engulf apoptotic cells and functions as a transcriptional sensor of dying cells. Genetic deletion of PPARdelta decreases expression of opsonins, such as C1qb, resulting in impairment of apoptotic cell clearance and reduction in anti-inflammatory cytokine production. This increases autoantibody production and predisposes global and macrophage-specific PPARdelta deficient mice to autoimmune kidney disease, a phenotype resembling the human disease systemic lupus erythematosus. Thus, PPARdelta plays a pivotal role in orchestrating the timely disposal of apoptotic cells by macrophages, ensuring that tolerance to self is maintained. HoxA9 immortalized ES cell derived myeloid precursors were created and differentiated as in Odegaard et al, 2007. After expansion, macrophages were differentiated for 8 days in the presence of MCSF in 20% L929 conditioned media with 2.5% bovine serum albumin in low glucose media. Macrophages were harvested for RNA using Qiagen's RNeasy Kit. A common reference was generated using e17.5 C57Bl/6 embryos. 30ug of either reference or macrophage RNA was labeled with Cy3 and Cy5 (Amersham) and hybridized to Stanford Functional Genomics Facility mouse cDNA microarrays for 16 hours. The arrays were washed and scanned on an Agilent G2505A ChipScan v. A.6.3.1. Florescence values were extracted using GenePix Pro v. 5.0.0.51. The data were normalized using regression correlation. Subsequently, missing values were imputed and significantly differentially expressed genes were found with Significance Analysis of Microarrays. For the Nature Medicine manuscript, significantly differentially expressed genes including genes involved in the process of uptake of apoptotic cells were extracted and clustered by complete linkage using Cluster and visualized using TreeView. Key to genotypes: "J1 untreated" are WT differentiated macrophages; "18 Untreated" are PPARd-/- differentiated macrophages Genotype: Wild type (WT) or PPAR delta minus (PPARd -/-) macrophages genetic_modification_design

Dataset Information

Transcriptional profiling of Hoxa9-expanded hematopoietic cells expressing distinct TALE genes

Publications

C-terminal domain of MEIS1 converts PKNOX1 (PREP1) into a HOXA9-collaborating oncoprotein.

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