Gene expression profile of DLBCL cells emerged in Cg1-Cre Spi1 KO mice
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE117631 | GEO | 2018/07/26
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression profile of DLBCL cells emerged in Cg1-Cre Spi1 KO mice
| PRJNA482758 | ENA
Project description:The goal of the experiment was to understand the epigenetic effects of PU.1 haploinsufficiency on pro-B cells. The RS4:11 cell line was edited both mono and biallelicaly via electroporation of Cas9 and guides. Following editing, aliquots of unedited (SPI1 +/+), mono (SPI1 +/-) and biallellicaly edited (SPI1 -/-) cells were lysed before undergoing the transposition reaction. After transposition, the ATAC-seq libraries were purified and then amplified via PCR. Libraries were sequenced using the Illumina Novaseq platform.
2021-03-24 | E-MTAB-8676 | biostudies-arrayexpress
Project description:Background: Strict control of PU.1, encoded by SPI1, is importmant for myeloid development, and inhibition of PU.1 expression and activity, even moderate, can lead to acute myeloid leukemia (AML). Much effort has focused on regulatory elements at the SPI1 locus on controlling PU.1. Discovery of circular RNAs (circRNAs), a novel class of noncoding regulators, has raised additional questions regarding their impacts on PU.1 and the development of AML. Methods: We used the pan-cancer circRNA compendium MiOncoCirc to investigate the existence and expression pattern of circSPI1s. We designed short hairpin RNAs (shRNAs) targeting the back-spliced site to silence circSPI1 and then performed CCK8 proliferation assay, flow cytometry analysis and Wright-Giemsa stain to explore the function of circSPI1. We performed RNA-sequencing with and without circSPI1 knockdown, western bloting and luciferase assay to explore the potential mechanisms. We utilized machine learning techniques and integrated bioinformatic analysis to evaluate the prognostic value of circSPI1 for AML, based on TCGA and BeatAML cohorts. Results: We found that circSPI1, the circular RNA derived from the SPI1 gene (encoding PU.1), was highly expressed in AML than that in normal counterparts. Functional experiements showed circSPI1 acted as an oncogene, as evidenced by the observation that circSPI1 knockdown induced myeloid differentiation and apoptosis of AML cells. This was different from the parental gene SPI1 that is generally low expressed in AML and functions as a tumor suppressor. Mechanistic investigations revealed that circSPI1 exerted multiple regulatory roles in AML progression. On one hand, circSPI1 contributed to the orchestrated differentiation of AML cells by antagonizing SPI1 expression. On the other hand, circSPI1 was involved in proliferation and apoptosis by interacting with microRNAs miR-1307-3p, miR-382-5p and miR-767-5p, which was uncoupled with SPI1. Finally, circSPI1-regulated genes were associated with the clinical outcome of AML patients, implicating the clinical significance of circSPI1 in AML. Conclusions: We demonstrate that highly expressed circSPI1 acts as an oncogene in AML, through both antognizing PU.1 expression and binding to microRNAs that is independent to PU.1. Our data provide new insight into complex SPI1 gene regulation now involving cicrSPI1 as well as the independent role of cicrRNA in AML.
2021-03-24 | GSE159931 | GEO
Project description:The Spi1/ Pu.1 transcription factor plays a crucial role in myeloid cell development across many species. Several Spi1 target genes have been identified so far, yet the Spi1-dependent gene group remains largely unknown. To identify novel genes downstream of Spi1 we employed a microarray strategy using zebrafish embryos. We established the gene group down-regulated upon spi1 knockdown while simultaneously enriched in FACS-sorted embryonic myeloid cells of a spi1:GFP transgenic line, thus representing putative myeloid-specific Spi1 target genes. This gene group contained all previously identified Spi1-dependent zebrafish genes, confirming the validity of the approach, as well as novel immune-related genes. Colocalization studies with neutrophil and macrophage markers revealed that genes cxcr3.2, mpeg1, ptpn6 and mfap4 were expressed specifically in early embryonic macrophages. The analysis of adult zebrafish hematopoietic tissue showed that genes mfap4 and mpeg1 remained macrophage specific within the myeloid fraction throughout zebrafish life. We also demonstrated that gene cxcr3.2, coding for chemokine receptor 3.2, functions in macrophage migration to the site of bacterial infection. These results establish a myeloid-specific gene group dependent on Spi1 in zebrafish and identify novel early macrophage-specific marker genes, which will facilitate further studies of macrophage development and innate immune function.
2010-04-30 | GSE19206 | GEO
Project description:The Spi1/ Pu.1 transcription factor plays a crucial role in myeloid cell development across many species. Several Spi1 target genes have been identified so far, yet the Spi1-dependent gene group remains largely unknown. To identify novel genes downstream of Spi1 we employed a microarray strategy using zebrafish embryos. We established the gene group down-regulated upon spi1 knockdown while simultaneously enriched in FACS-sorted embryonic myeloid cells of a spi1:GFP transgenic line, thus representing putative myeloid-specific Spi1 target genes. This gene group contained all previously identified Spi1-dependent zebrafish genes, confirming the validity of the approach, as well as novel immune-related genes. Colocalization studies with neutrophil and macrophage markers revealed that genes cxcr3.2, mpeg1, ptpn6 and mfap4 were expressed specifically in early embryonic macrophages. The analysis of adult zebrafish hematopoietic tissue showed that genes mfap4 and mpeg1 remained macrophage specific within the myeloid fraction throughout zebrafish life. We also demonstrated that gene cxcr3.2, coding for chemokine receptor 3.2, functions in macrophage migration to the site of bacterial infection. These results establish a myeloid-specific gene group dependent on Spi1 in zebrafish and identify novel early macrophage-specific marker genes, which will facilitate further studies of macrophage development and innate immune function. Zebrafish strains Zebrafish (Danio rerio) were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). The spi1-gfp transgenic line used in this study (Pu1-lynEGFP, a gift from Franscesca Peri, EMBL, Heidelberg) contains 4 kb of spi1/pu.1 promoter sequence driving expression of membrane-targeted EGFP. Morpholino knock-down experiments Morpholino oligonucleotides (Gene Tools) were diluted to required concentration in 1x Danieu’s buffer (58 mM NaCl, 0.7 mM KCl, 0.4 mM MgSO4, 0.6 mM Ca(NO3)2, 5.0 mM HEPES; pH 7.6) containing 1% Phenol red (Sigma) and approximately 1 nl was injected into the 1-2 cell stage embryo using a Femtojet injector (Eppendorf). Embryo dissociation and FACS (Fluorescent activated cell sorting) Dissociation of embryos was performed according to Covassin et al. 30. In short, ~300 embryos of spi1:GFP line at 28 hpf were dechorionated by pronase treatment, rinsed in calcium free Ringer solution, followed by digestion with 0.25% trypsin. The obtained cell suspension was centrifuged, rinsed with PBS and resuspended in Leibovitz medium L15 without phenol red, 1% fetal calf serum, 0.8mM CaCl2, penicillin 50 U/ml and streptomycin 0.05 mg/ml. The single cell suspension was subject to FACS at room temperature using a FACSAria (Becton Dickinson) with the BD FACSDiva software version 5.0.3 and a Coherent Sapphire solid state laser 488 nm with 13 mW power. The GFP+ and GFP- cell fractions were collected separately into L15 medium supplemented with 0.8 mM CaCl2, 10% fetal calf serum and penicillin 50 U/ml and streptomycin 0.05 mg/ml. The standard yield from circa 300 embryos was approximately 2 x 105 GFP+ cells. Microarray experiment design and analysis Embryos injected either with 1 mM Pu1 morpholino19 or 1 mM Standard Control morpholino were harvested at 28 hours post fertilization (hpf). As a control, embryos injected with an equal volume of 1% Phenol red in Danieu’s buffer (1xPR/D) were used. Pools of 20-30 embryos were collected. RNA samples from spi1 morphants and standard control morphants were labelled with Cy5 and hybridized against a Cy3-labelled common reference (a mixture of all samples injected with 1xPR/D). This experiment was performed in triplicate. FACS sorted spi1-GFP zebrafish embryos at 28hpf were analyzed as follows: the RNA of GFP-positive fraction was labelled with Cy5 and hybridized against a Cy3-labelled RNA of corresponding GFP-negative fraction of cells from the same pool of embryos. This experiment was performed in duplicate. RNA isolation, synthesis of amino allyl labeled aRNA, coupling of Cy3 and Cy5 dyes, and hybridization conditions were as described31. Microarray analysis was performed using custom-designed 44k Agilent chips (platform accession number in GEO: GPL7735) described elsewhere 31. Microarray data were processed and analyzed as described 31. Significance cut-offs for differentially expressed probe sequences were set at 1.2 fold change at P <10-2.
2010-04-30 | E-GEOD-19206 | biostudies-arrayexpress
Project description:The goal of the experiment was to identify which genes are differentially expressed between the unedited and SPI1-edited populations. The RS4:11 cell line was edited both mono and biallelicaly via electroporation with guides and Cas9. Following editing, RNA from unedited (SPI1 +/+), mono (SPI1 +/-) and biallellicaly edited (SPI1 -/-) cells were extracted through the Direct-zol RNA Microprep kit. cDNA libraries for sequencing were then prepared using the TruSeq Stranded mRNA Library Prep Kit and the IDT for Illumina-TruSeq RNA UD Indexes (Illumina). Samples were then sequenced on the Illumina NovaSeq platform.
2021-03-24 | E-MTAB-8677 | biostudies-arrayexpress
Project description:SPI1 (PU.1) was recently reported as a genetic risk factor of Alzheimer’s disease (AD) in large-scale genome-wide association studies (GWAS). However, it is unknown whether PU.1 should be downregulated or increased to have therapeutic benefits. This is a critical question that must be answered before initiating any drug discovery project. To investigate the effect of modulating PU.1 level on AD pathology, we performed biochemical, histological, transcriptomic, and proteomic analyses using PU.1-knockdown and overexpression mouse models. PU.1-knockdown markedly increased amyloid-b (Ab) levels, amyloid plaque deposition, and gliosis. Conversely, PU.1-overexpression significantly decreased Ab levels, amyloid plaque deposition, gliosis, and dystrophic neurites. Furthermore, we identified several biological pathways, such as immune response pathways and complement system, regulated by the altered PU.1 expression through the analyses of proteomics as well as bulk and single-cell transcriptomics data. Our data provide crucial in vivo data to guide future therapeutic strategies for AD.
2024-03-18 | GSE222624 | GEO
Project description:SPI1 (PU.1) was recently reported as a genetic risk factor of Alzheimer’s disease (AD) in large-scale genome-wide association studies (GWAS). However, it is unknown whether PU.1 should be downregulated or increased to have therapeutic benefits. This is a critical question that must be answered before initiating any drug discovery project. To investigate the effect of modulating PU.1 level on AD pathology, we performed biochemical, histological, transcriptomic, and proteomic analyses using PU.1-knockdown and overexpression mouse models. PU.1-knockdown markedly increased amyloid-b (Ab) levels, amyloid plaque deposition, and gliosis. Conversely, PU.1-overexpression significantly decreased Ab levels, amyloid plaque deposition, gliosis, and dystrophic neurites. Furthermore, we identified several biological pathways, such as immune response pathways and complement system, regulated by the altered PU.1 expression through the analyses of proteomics as well as bulk and single-cell transcriptomics data. Our data provide crucial in vivo data to guide future therapeutic strategies for AD.
2024-03-18 | GSE225669 | GEO
Project description:SPI1/PU.1 controls fibroblast polarization and tissue fibrosis
| PRJNA504646 | ENA
Project description:Although originally described as transcriptional activator, SPI1/PU.1, a major player in haematopoiesis whose alterations are associated with haematological malignancies, has the ability to repress transcription. Here, we investigated the mechanisms underlying gene repression in the erythroid lineage, in which SPI1 exerts an oncogenic function by blocking differentiation. We show that SPI1 represses genes by binding active enhancers that are located in intergenic or gene body regions. HDAC1 acts as a cooperative mediator of SPI1-induced transcriptional repression by deacetylating SPI1-bound enhancers in a subset of genes, including those involved in erythroid differentiation. Enhancer deacetylation impacts on promoter acetylation, chromatin accessibility and RNA pol II occupancy. In addition to the activities of HDAC1, polycomb repressive complex 2 (PRC2) reinforces gene repression by depositing H3K27me3 at promoter sequences when SPI1 is located at enhancer sequences. Moreover, our study identified a synergistic relationship between PRC2 and HDAC1 complexes in mediating the transcriptional repression activity of SPI1, ultimately inducing synergistic adverse effects on leukaemic cell survival. Our results highlight the importance of the mechanism underlying transcriptional repression in leukemic cells, involving complex functional connections between SPI1 and the epigenetic regulators PRC2 and HDAC1.
2022-07-25 | GSE187909 | GEO