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A genome-wide RNAi screen identifies genes and networks governing hematopoietic stem cell development [Illumina_Expression]

ABSTRACT: We report a genome-wide microarray analysis of gene expression in mouse embryonic stem cell (ESC) and in vitro ES-derived cells. iHoxB4 ESCs were transduced with a library of shRNAs targeting >15,000 genes, and were differentiated towards hematopoietic stem and progenitor cells by forcing HoxB4 expression in the cells. Five cell populations were isolated on differentiation days 6 and 20. Differentiated mesodermal/endothelium cell population D6F (Ssea1-Flkl+Cxcr4-), endodermal cell population D6C (Ssea1-Flkl-Cxcr4+), D20LS (Lin-Sca1+c-Kit–), D20LK (Lin–Sca1–c-Kit+), and D20LSK (Lin–Sca1+c-Kit+) cells were purified by FACS. Transduced iHoxB4 cells were analyzed as undifferentiated control cells. The experiment was performed three times independently.

ORGANISM(S): Mus musculus

PROVIDER: GSE86853 | GEO | 2016/12/31

SECONDARY ACCESSION(S): PRJNA342776

REPOSITORIES: GEO

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A genome-wide RNAi screen identifies genes and networks governing hematopoietic stem cell development

Project description:We report a functional genome-wide RNAi screen to identify genes required for embryonic stem cell (ESC) differentiation to hematopoietic stem/progenitor cells (HSPC) in vitro, and report the discovery of novel genes important for differentiation to the endothelial–hematopoietic transition and subsequently to HSPC specification. iHoxB4 ESCs were transduced with a library of shRNAs targeting >15,000 genes, and were differentiated towards hematopoietic stem and progenitor cells by forcing HoxB4 expression in the cells. Five cell populations were isolated on differentiation days 6 and 20. Differentiated mesodermal/endothelium cell population D6F (Ssea1–Flkl+Cxcr4–), endodermal cell population D6C (Ssea1–Flkl–Cxcr4+), D20LS (Lin–Sca1+c-Kit–), D20LK (Lin–Sca1–c-Kit+), and D20LSK (Lin–Sca1+c-Kit+) cells were purified by FACS. Transduced iHoxB4 cells were analyzed as undifferentiated control cells. The experiment was performed three times independently. High-throughput sequencing and bioinformatics analysis identified twelve groups of shRNA target genes implicated in ESC to HSPC development, including a group of 351 novel genes that appear to be required for HSPC specification. As proof of concept in vivo, four genes in this group, Ap2a1, Mettl22, Lrsam1, and Hal, were selected for validation and were confirmed to be essential for HSPC development in zebrafish and for maintenance of human HSCs. Taken together, our results not only identify a number of novel regulatory genes and pathways throughout HSPC development but also serve as a potentially valuable resource for directed differentiation of therapy-grade HSPCs from human pluripotent stem cells.

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Gene expression profiling of HOXB4-transduced murine hematopoietic stem cells

Project description:Overexpression of HOXB4 in hematopoietic stem cells (HSCs) leads to increased self-renewal without causing hematopoietic malignancies in transplanted mice. The molecular basis of HOXB4-mediated benign HSC expansion in vivo is not well understood. To gain further insight into the molecular events underlying HOXB4-mediated HSC expansion, we analyzed gene expression changes at multiple time points in Lin-Sca1+c-kit+ (LSK) cells from mice transplanted with bone marrow (BM) cells transduced with a MSCV-HOXB4-ires-YFP vector. A distinct HOXB4 transcriptional program was reproducibly induced and stabilized by 12 weeks after transplant. Dynamic expression changes were observed in genes critical for HSC self-renewal as well as genes involved in myeloid and B cell differentiation. Prdm16, a transcription factor associated with human acute myeloid leukemia (AML), was markedly repressed by HOXB4 but upregulated by HOXA9 and HOXA10, suggesting that Prdm16 downregulation was involved in preventing leukemia in HOXB4 transplanted mice. Functional evidence to support this mechanism was obtained by enforcing co-expression of sPrdm16 and HOXB4, which led to enhanced self-renewal, myeloid expansion, and leukemia. Altogether, these studies define the transcriptional pathways involved in HOXB4 HSC expansion in vivo and identify repression of Prdm16 transcription as a mechanism by which expanding HSCs avoid leukemic transformation.

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Gene expression profiling of HOXB4-transduced murine hematopoietic stem cells

2014-10-01 | E-GEOD-59804 | biostudies-arrayexpress

Downstream Targets of HOXB4 in the primitive hematopoietic progenitor EML Cell line

Project description:Enforced expression of the homeobox transcription factor HOXB4 has been shown to enhance hematopoietic stem cell (HSC) self-renewal and expansion ex vivo and in vivo. In order to investigate the largely unknown downstream targets of HOXB4 in hematopoietic progenitor cells, HOXB4 was constitutively overexpressed in the primitive hematopoietic progenitor cell line, EML. Gene expression differences were compared between KLS (c-Kit+, Lin-, Sca-1+)-EML cells that overexpressed HOXB4 (KLS-EML-HOXB4) to control KLS-EML cells that were transduced with vector alone. ChIP-chip was used to identify promoter regions bound by HOXB4. We overexpressed HOXB4 in EML cells. We isolated 3 separate single cell clones as assessed by Southern Blot Analysis (3 clones for EML-HOXB4 and 3 clones for control EML-GFP cells). RNA was isolated from the KLS (c-Kit+, Lin-, Sca-1+) fraction of each single cell clone population and processed for hybridization to array chips using established lab protocols. Chip-Chip analysis of the three HOXB4 overexpressing clones was performed to identify HOXB4 bound promoters.

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Project description:Runx/Cbfb heterodimers play important roles in the development of hematopoietic cells in mouse embryos and adults. In order to identify genes that are regulated by Runx/Cbfb, we purified Lin– c-kit+ Sca1+ (LSK) cells and Lin– c-kit+ Sca1– CD16/32+ (GMP) cells from Vav1-iCre x Cbfb(F/F) and Vav1-iCre x Cbfb(F/+) mice and profiled gene expression using microarray.

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IGR_NANBAKHSH_HOXB4

Project description:We have previously shown that human umbilical cord blood CD34+ progenitor cells undergo in vitro differentiation into functional NK cells and that their co-culture in the presence of HOXB4 transduced stromal MS5 cells resulted in an increase in differentiated NK number. The present study was conducted to compare the stromal effect on NK lytic potential in the presence and absence of HOXB4. Our results provide evidence that HOXB4 transduced MS5 cells as compared to transduced, GFP (+) MS5 cells induced highly differentiated cytotoxic NK cells. Importantly, this difference was not due to the expression of activating NK receptors but was associated with an increased induction of granzyme B degranulation in response to stimulation with NK cell-susceptible targets. DNA microarray-based global transcriptional profiling confirmed the up-regulation of granzyme B. These findings provide further evidence that HOXB4 is a crucial regulator of NK function and that its use in generating functional NK cells with increased lytic potential may be significant for cancer immunotherapy.

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