Differentiated vs. undifferentiated promyelocytic cell lines (HL-60 and KG-1) and Neutrophiles
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE43211 | GEO | 2013/08/05
SECONDARY ACCESSION(S): PRJNA184933
REPOSITORIES: GEO
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Project description:We identify the tetraspanin CD82 as the recognition site for xenogeneic endothelial cells independently of Gala1,3-gal structures. We demonstrate that in contrast to undifferentiated cells, differentiated promyelocytic cell lines (HL-60, THP-1 and KG-1) are capable of recognizing xenogeneic porcine endothelial cells in a calcium-dependent manner. We used serial analysis of gene expression (SAGE) to identify the differentially expressed transcripts in these cell lines. Interrogation of these transcripts revealed a number of differentially expressed genes that include the Gala1,3-gal-independent recognition moiety(s). Comparing these SAGE transcripts with those expressed in resting human naive neutrophils identified the tetraspanin CD82 as the most likely candidate responsible for xenogeneic recognition. Blocking antibodies to CD82 in human naive neutrophils inhibited the calcium response and abolished the subsequent Reactive Oxygen Metabolite (ROM) production evoked by the xenogeneic encounter of either Gala1,3-gal knockout or wild-type porcine aortic endothelial cells. Our data identify CD82 on innate immune cells as the major recognition moiety of the xenogeneic endothelium, independently of Gala1,3-gal-structures and open new avenues of intervention to making xenotransplantation a clinical reality. We used serial analysis of gene expression (SAGE) to identify the differentially expressed transcripts in promyelocytic cell lines (HL-60, THP-1 and KG-1) upon differentiation. We looked for genes common to the differentiation pathway in these cell lines but absent from the control naiive neutrophiles.
2013-08-05 | E-GEOD-43211 | biostudies-arrayexpress
Project description:We recently found that the tetraspanin family member, CD82, which is aberrantly expressed in chemotherapy-resistant CD34+/CD38− acute myelogenous leukemia (AML) cells, negatively regulates matrix metalloproteinase 9, and plays an important role in enabling CD34+/CD38− AML cells to adhere to the bone marrow microenvironment. This study explored novel functions of CD82 that contribute to AML progression. We employed microarray analysis comparing the gene expression profiles between CD34+/CD38− AML cells transduced with CD82 shRNA and CD34+/CD38− AML cells transduced with control shRNA. Real-time RT-PCR and western blot analysis were performed to examine the effect of CD82 knockdown on the expression of the polycomb group member, enhancer of zeste homolog 2 (EZH2), in leukemia cells. A chromatin immunoprecipitation assay was performed to examine the effect of CD82 expression on the amount of EZH2 bound to the promoter regions of tumor suppressor genes in leukemia cells. We also utilized methylation-specific PCR to examine whether CD82 expression influences the methylation status of the tumor suppressor gene promoter regions in leukemia cells. Microarray analysis revealed that levels of EZH2 decreased after shRNA-mediated depletion of CD82 in CD34+/CD38− AML cells. Moreover, the antibody-mediated blockade of CD82 in leukemia cells lowered EZH2 expression via activation of p38 MAPK signaling, decreased the amount of EZH2 bound to the promoter regions of the tumor suppressor genes, and inhibited histone H3 lysine 27 trimethylation in these promoter regions, resulting in upregulation of the tumor suppressors at both the mRNA and protein levels. The aim of this study was to explore the biological functions of a tetraspanin family protein––CD82–– expressed aberrantly in chemotherapy-resistant CD34+/CD38- acute myelogenous leukemia (AML) cells. Microarray analysis of patient-isolated CD34+/CD38- AML cells revealed that the levels of anti-apoptotic protein BCL2L12 were downregulated after CD82 depletion by specific shRNA. Western blot analysis indicated that BCL2L12 was aberrantly expressed in patient-isolated AML cells and AML cell lines. Furthermore, CD82 blockade by a specific antibody downregulated BCL2L12 in parallel with de-phosphorylation of STAT5 and AKT, while pharmacological inhibition of STAT5 and AKT activation decreased BCL2L12 expression in leukemia cells. In addition, shRNA-mediated downregulation of BCL2L12 increased the levels of cleaved caspase 3and suppressed proliferation of leukemia cells, impairing their engraftment in immunodeficient mice. Taken together, our results indicate that CD82 regulated BCL2L12 expression via STAT5A and AKT signaling and stimulated proliferation and engrafting of leukemia cells, suggesting that CD82 and BCL2L12 may be promising therapeutic targets in AML.
2014-12-30 | GSE64527 | GEO
Project description:Production of embryos in vitro has enormous potential for research and commercial applications. Unfortunately, in vitro production of porcine embryos is extremely inefficient. Despite the characterization of distinct phenotypes, little is known about the molecular mechanisms and altered physiological processes that account for poor IVP development. The objective of the current study was to compare global gene expression patterns from IVO and IVP embryos using small amplified RNA (SAR)-SAGE. Whole-cell RNA from pools of Day 6 in vivo-(IVO) and in vitro-produced (IVP) blastocysts was used to construct SAR-SAGE libraries. Sequence analysis of the IVO and IVP libraries yielded a total of 98,771 and 98,408 tags, respectively. A total of 20,029 and 23,453 unique putative transcripts were detected in the IVO and IVP libraries, respectively. Statistical analyses of SAGE tag frequencies between the IVO and IVP libraries indicated that 938 and 193 tags were differentially expressed at a P < 0.05 and P < 0.001 level of significance, respectively. Tentative annotation of the differentially expressed SAGE tags was determined using BLAST sequence alignment with the TIGR porcine specific gene index (SSGI) and cross-species alignment using RepeatMasker to determine homologous human orthologs. Annotated tags were categorized into functional groupings according to gene ontology annotations. Real-time PCR was used to confirm differential expression for several transcripts from IVO and IVP blastocysts. These results demonstrate compromised gene expression from IVP blastocysts compared with IVO blastocysts for a number of biological processes including cellular metabolism, organization and response to stress; thereby providing potential target pathways for improvement of IVP methods. Keywords: Comparative (in vivo- vs. in vitro-produced porcine embryos)
2006-08-23 | GSE5571 | GEO
Project description:Production of embryos in vitro has enormous potential for research and commercial applications. Unfortunately, in vitro production of porcine embryos is extremely inefficient. Despite the characterization of distinct phenotypes, little is known about the molecular mechanisms and altered physiological processes that account for poor IVP development. The objective of the current study was to compare global gene expression patterns from IVO and IVP embryos using small amplified RNA (SAR)-SAGE. Whole-cell RNA from pools of Day 6 in vivo-(IVO) and in vitro-produced (IVP) blastocysts was used to construct SAR-SAGE libraries. Sequence analysis of the IVO and IVP libraries yielded a total of 98,771 and 98,408 tags, respectively. A total of 20,029 and 23,453 unique putative transcripts were detected in the IVO and IVP libraries, respectively. Statistical analyses of SAGE tag frequencies between the IVO and IVP libraries indicated that 938 and 193 tags were differentially expressed at a P < 0.05 and P < 0.001 level of significance, respectively. Tentative annotation of the differentially expressed SAGE tags was determined using BLAST sequence alignment with the TIGR porcine specific gene index (SSGI) and cross-species alignment using RepeatMasker to determine homologous human orthologs. Annotated tags were categorized into functional groupings according to gene ontology annotations. Real-time PCR was used to confirm differential expression for several transcripts from IVO and IVP blastocysts. These results demonstrate compromised gene expression from IVP blastocysts compared with IVO blastocysts for a number of biological processes including cellular metabolism, organization and response to stress; thereby providing potential target pathways for improvement of IVP methods. Keywords: Comparative (in vivo- vs. in vitro-produced porcine embryos) Whole-cell RNA from pools of Day 6 in vivo- and in vitro-produced blastocysts was used to construct small amplified RNA (SAR)-SAGE libraries.
2006-08-23 | E-GEOD-5571 | biostudies-arrayexpress
Project description:Abundant donor cytotoxic T cells that attack normal host organs remain a major problem for patients receiving allogeneic hematopoietic cell transplantation (Allo-HCT). Despite an increase in our knowledge of the pathobiology of acute graft versus host disease (aGvHD), the mechanisms regulating the proliferation and function of donor T cells remain unclear. Here, we show that activated donor T cells express galectin-3 (Gal-3) after allo-HCT. In both major and minor histocompatibility–mismatched models of murine aGvHD, expression of Gal-3 is associated with decreased T cell activation and suppression of the secretion of effector cytokines including IFN-γ and GM-CSF. Mechanistically, Gal-3 results in activation of NFAT signaling which can induce T cell exhaustion. Gal-3 overexpression in human T cells prevents severe disease by suppressing cytotoxic T cells in xenogeneic aGvHD models. Together these data identify the Gal-3-dependent regulatory pathway in donor T cells as a critical component of inflammation in aGvHD.
2023-03-13 | GSE225756 | GEO
Project description:Using a single carbohydrate recognition domain of gal-8 on the C-terminus or full-length gal-8, we performed affinity chromatography followed by a proteomic approach with HL-60 cell membrane preparations to isolate and identify putative ligands.
2018-02-09 | PXD000664 | Pride
Project description:Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies. Keywords: other
2005-06-03 | GSE2347 | GEO
Project description:Aortic endothelia from mice exposed to dietary model of type II diabetes at 4, 6 and 8 weeks of exposure to Bio-Serv #S3282 diet. Objective: Type II diabetes is associated with endothelial dysfunction, which can contribute to accelerated atherosclerosis and subsequent cardiovascular events. We seek to identify transcripts dysregulated in vivo in response to chronic exposure to high dietary fat that leads to diabetes. Methods: Beginning at 8 weeks of age, male Tie2-GFP mice (transgenically expressing green fluorescent protein exclusively within the endothelia) were fed a 60% fat calorie diet (Bio-Serv #S3282); age-matched mice were fed normal chow. After 4, 6, and 8 weeks on the diet, aortae and skeletal muscles (gastrocnemius, biceps femoris, and plantaris) were excised, minced, and collagenolytically digested. Each tissue digest was then subjected to FACS in order to obtain 10,000 endothelial cells. Transcriptomic analyses were performed with microarrays containing the Operon Murine V4 oligo set, and highly dysregulated genes were confirmed by real-time PCR. Results: By 4 weeks, Tie2-GFP mice receiving a high fat diet exhibited a fasting glucose of 215+17 mg/dL vs. 134+23 mg/dL in controls; by 6 weeks, a high fat diet resulted in lower glucose tolerance vs. control diet. Following 4, 6, and 8 weeks of high-fat regimen, aortic endothelial transcripts up-regulated by greater than 2-fold in biologically replicate experiments included macrophage inflammatory protein 2 (Mip2), chemokine (C-C motif) ligand 9 (CCL9), galectin-3 (Gal-3), and 5-lipoxygenase-activating protein (FLAP). Endothelial transcripts up-regulated in skeletal muscle included Mip2, CCL8 and 9, FLAP, gal-1 and 3, and ferritin light chain 1 (FTL1); transcripts down-regulated in muscle included endothelin-1 (ET-1) and insulin-like growth factor II (IGF II). Discussion: Gal-3 and FTL-1 are known to increase in response to advanced glycation end-products and oxidized LDL, respectively. However, the down-regulation of ET-1 and IGFII was surprising, as the transcription of these genes has previously been thought to exacerbate atherosclerosis. In conclusion, a comprehensive analysis of the endothelial transcript-level response to a dietary model of Type II diabetes has revealed novel regulation of transcripts with roles in inflammation, insulin sensitivity, oxidative stress, and atherosclerosis. Understanding the mechanism of diabetes-associated endothelial dysfunction may lead to improved therapies that lower the risk of cardiovascular complications in diabetic patients. Each experiment is performed with a technical replicate i.e. dye reversal. there is a biological replicate of the 4 week time point
2009-03-27 | E-GEOD-14898 | biostudies-arrayexpress
Project description:Gene expression analysis of the differentiation process of iPS cells to pancreatic islet cells has revealed that expression of CD82 defines a subset of iPS cell-derived pancreatic endocrine progenitors (EP). While some cell surface proteins such as CD142, CD200 and SUSD2 have been reported as markers of pancreatic progenitor (PP) and EP, CD82+ EP cells are distinct from those PP and EP characterized by the previously identified markers. CD82+ cells isolated from EP cells efficiently differentiated into pancreatic endocrine cells, particularly β cells. Also, CD82+ cells isolated from human cadaver pancreases secreted insulin in response to a high glucose concentration. Furthermore, blocking of CD82 expression by siRNA or inhibition of CD82 in EP by monoclonal antibodies suppressed maturation of β cells, indicating that CD82 plays a role for maturation of EP to β cells. In conclusion, this study identified CD82 not only as a useful marker to isolate β cell precursors but also as an important molecule for functional maturation of β cells.
2022-03-01 | GSE142367 | GEO
Project description:Although pig-to-nonhuman primate (NHP) corneal xenotransplantation has shown long-term graft survival, xenogeneic antigenrelated immune responses are still stronger than allogenic antigen-associated responses. Therefore, there is an unmet need to investigate major rejection pathways in corneal xenotransplantation, even with immunosuppression. This study aimed to identify biomarkers in aqueous humor for predicting rejection and to investigate rejection-related pathways in grafts from NHPs transplanted with porcine corneas following administration of steroids combined with tacrolimus/rituximab. NHPs who had received corneas from wild‐type (WT) or α‐1,3‐galactosyltransferase gene‐knockout (GTKO) pigs were divided into groups with or without rejection according to clinical examinations. Liquid chromatography-mass spectrometry (LC-MS) was used to analyze the proteomes of corneal tissues or aqueous humor. The biological functions of differentially expressed proteins (DEPs) were assessed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for pathways and protein–protein interaction network analysis. Among the 66 DEPs in aqueous humor, complement proteins (C3, C5, and C9) and cholesterol metabolic proteins (APOA1 and APOA2) were related to xenogeneic rejection as biomarkers, and alternative pathways of the complement system seemed to be important in xenogeneic graft rejection. Among 416 DEPs of the cornea, NF‐κB1 and proteosomes (PSMD7, PSMA5, and PSMD3) seemed to be related with xenogeneic graft rejection. Additionally, oxidative phosphorylation and leukocyte activation‐related pathways are involved in rejection. Overall, our proteomic approach highlights the important role of NF‐κB1, proteosomes, oxidative phosphorylation, and leukocyte activation-related inflammation in the cornea, and the relevance of complement pathways of the aqueous humor as a predictive biomarker of xenogeneic rejection.
2022-05-20 | PXD031320 | Pride