Gene expression profiling of FUT8 knockdown CL1-5 cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Chi-Huey Wong
PROVIDER: E-GEOD-42405 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Overexpression of fucosyltransferase 8 (FUT8) is found in many cancers including liver, ovarian, thyroid, colorectal and non-small cell lung cancers. Unlike other FUTs which are functionally redundant, FUT8 is the only enzyme responsible for the alpha1,6-linked fucosylation (core fucosylation) by adding fucose to the innermost GlcNAc residue of an N-linked glycan. A growing body of evidence indicates that core fucosylation is important for regulating protein functions, such as EGFR, TGF beta receptor and integrins. To understand the downstream molecular events in response to the global alteration of core fucosylation during cancer progression, microarray analysis was employed to profile the changes in gene expression following FUT8 silencing. The genes significantly (2-fold, P<0.01) changed in CL1-5/shFUT8 cells were selected for functional annotations using a Gene Ontology database. The result revealed that many genes involved in cell adhesion, motility, growth, angiogenesis, and inflammation were under the control of core fucosylation.
2012-12-07 | GSE42405 | GEO
Project description:Transcriptional profiling of SAS cells transfected with pLKO.1-LYRIC shRNA-B expression vector (desinaged as B) and control SAS cells (transfected with pLKO.1 vector, designated as CTL). Goal was to determine the effects of LYRIC knockdown on global SAS cells gene expression. Two-condition experiment, SAS cells transfected with pLKO.1-LYRIC shRNA-B expression vector (desinaged as B) v.s. control SAS cells (transfected with pLKO.1 vector, designated as CTL). Biological replicates: 4 control replicates, 4 transfected replicates.
2016-02-28 | E-GEOD-44766 | biostudies-arrayexpress
Project description:Background: The well-characterized function of the transcriptional repressor, Slug, is to promote EMT and tumor invasion/metastasis by down-regulating E-cadherin expression. In this study, we investigated the significance of Slug during the S phase. Method: Slug mRNA expression was isolated from thymidine-arrested CL1-5/AS2neo (control) and CL1-5/AS2neo-Slug-WT stable cells. The Agilent oligonucleotide microarray analysis was performed to identify Slug downstream genes. Results: Overexpression of Slug inhibited lung [3H]-thymidine incorporation and delayed S phase progression. By using Agilent microarray we have identified panel of genes altered by Slug overexpression. Slug can down-regulate target genes about cell cycle networks for DNA replication, DNA replication checkpoint and genomic stability, such as TOP1, ORC4, RFC3, and Rad17. Conclusions: the multifaceted role of Slug in cancer progression by controlling the epithelial-mesenchymal transition and genome stability. Two-condition experiment, Vector vs. Slug overexpression cells. The cDNAs encoding full-length human Slug were amplified and subcloned into lentiviral pLKO_AS2.neo which generated full-length Slug. Vector control or Slug lentivirus were transduced into CL1-5 cells and Gentamycin was used to select stable cells.
2012-02-09 | E-GEOD-35617 | biostudies-arrayexpress
Project description:Natural Killer (NK) cell development and effector function requires context-dependent signalling via numerous receptors including the IL-15 receptor. The modulation of receptor signalling can be regulated by the post-translational modifications affecting receptor turnover and trafficking. Core fucosylation is one such modification known to impact receptor expression and is uniquely mediated by fucosyltransferase 8 (FUT8). To investigate core fucosylation in NK cell biology, we generated mice lacking FUT8 in NK cells (Fut8fl/flNcr1cre/+). Loss of core fucose resulted in pronounced NK lymphopenia in Fut8fl/flNcr1cre/+ mice associated with a reduction in IL-15 receptor expression and loss of in vivo proliferation. Inhibition of intrinsic apoptosis pathways could not overcome compromised IL-15 receptor signalling to rescue FUT8-null NK cell development delineating the contribution of proliferation to NK cell homeostasis. Surprisingly, loss of core fucose enhanced NK cell expansion following viral infection and this was associated with upregulation of IL-2Rα following pro-inflammatory cytokine exposure and enhanced IL-2-mediated proliferation. Lastly, loss of FUT8 activity impaired TGFBR2 expression and immunosuppressive effects of TGF-β on NK cells. Taken together, we have identified fucosyltransferase 8 as a key modulator of NK cell development and function by regulating IL-15 receptor responsiveness.
2024-01-01 | GSE243190 | GEO
Project description:We examined the extent to which different Trypanosoma cruzi strains induce transcriptomic changes in cultured L6E9 myoblasts 72 hours or 48 hours after infection with four strains of the parasite [Brazil (TCI); Y, CL and Tulahuen (TC II) strains]. Expression of 6,289 distinct fully annotated unigenes was quantified with 27k rat oligonucleotide arrays in each of the four replicas of all control and infected RNA samples. Considering changes >1.5-fold and p-val<0.05, the Tulahuen strain was the most disruptive to host transcriptome, with (17% significantly altered genes), while in Y strain altered only 6% of the genes were altered. The significantly altered genes in the infected cells were largely different among the four strains, with only 21 genes changed in the same direction being similarly changed by all four strains. However, when expression ratios of all genes were compared, myoblasts infected with different strains showed proportional overall genbe expression alterations. These results indicate that infection with different parasite strains modulates similar but not identical pathways in the host cells. 20 µg total RNA extracted in Trizol from each of the 20 cell culture dishes containing control or infected with (Y, CL, Tulahuen or Brazil) Trypanosoma cruzi strains (4 dishes for each strain) was reverse transcribed in the presence of fluorescent Alexa Fluor®_647 or Alexa Fluor®_555-aha-dUTPs (Invitrogen, CA) to obtain labeled cDNAs. Red and green-labeled samples of biological replicas were then co-hybridized (“multiple yellow” strategy) overnight at 50°C with Operon v3.0 Rat 27k oligonucleotide arrays printed by Duke University (GPL9207). After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNA, each array was scanned with GenePix 4000B scanner (MDS, Toronto, Canada) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).
2009-09-22 | E-GEOD-18175 | biostudies-arrayexpress
Project description:One way by which astrocytes modulate oligodendrocytes’ activity is by delivering neurotransmitters and leukemia inhibitory factor (Lif) in the medium that bind oligodendrocyte receptors. Most of these receptors are involved in intercellular Ca2+-signaling (ICS). However, not much is known about the interactions between myelination (MYE) and ICS genes and how astrocyte nearness modulates the oligodendrocyte genomic myelination fabric. We profiled the transcriptomes of immortalized oligodendrocyte precursor cells (Oli-neu) when cultured alone or co-cultured with cortical astrocytes. The astrocytes were plated in cell culture insert systems that did not allow formation of gap junction channels with oligodendrocytes but permitted exchange of soluble factors via the culture medium. Remarkably, astrocyte proximity induced a larger increase of the overall expression level and interlinkage of MYE genes than the differentiating 10d treatment with 1 mM dibutyryl cAMP that turns Oli-neu cells into myelin-associated glycoprotein-positive oligodendrocyte-like cells. Moreover, more MYE and ICS genes were turned on and fewer turned off by astrocyte proximity than by differentiating treatment. Lif receptor was up-regulated by astrocyte proximity but not by the differentiating treatment. We have identified the responsible transcriptomic networks by which the intercellular ICS gene web controls MYE gene web, with genes encoding the gap junction proteins (connexins, Cx) Cx29, Cx32 and Cx47 playing central roles. The novel Prominent Gene Analysis (that refines iteratively the functional webs to optimize the interconnectivity and expression stability of the associated genes) was used to select and rank the most relevant MYE and ICS genes and build the corresponding gene webs. Determine the modifications of the myelination transcriptome induced in Oli- neu control cells by differentiating treatment and proximity of cortical astrocytes. Four culture dishes of each of control, differentiated and in the astrocyte proximity Oli-neu cells were profiled using Duke mouse 30K and 36k oligonucleotide arrays in the "multiple yellow" hybrization design.
2009-10-26 | E-GEOD-18726 | biostudies-arrayexpress
Project description:Chronic chagasic cardiomyopathy is one of the leading causes of heart failure in Latin American countries, being associated with intense inflammatory response and fibrosis. We have previously shown that bone marrow mononuclear cell (BMC) transplantation improves inflammation, fibrosis and ventricular diameter in hearts of mice with chronic Chagas’ disease. Here we investigated alterations of gene expression in the hearts of chronic chagasic mice submitted or not to BMC therapy. C57Bl/6 mice chronically infected with T. cruzi (6 months) were transplanted with BMC or saline i.v. and sacrificed 2 months later. RNA was extracted from the hearts of normal controls, chagasic and BMC transplanted mice and microarray analysis was performed using MO30k oligonucleotide arrays. Out of the 9390 unigenes quantified in all samples, 1702 had their expression altered in chronic chagasic hearts compared to those of normal mice. Major categories of significantly upregulated genes were related to inflammation, fibrosis and immune responses, while genes involved in mitochondrion function were downregulated. When BMC-treated chagasic hearts were compared to infected mice, 1631 (96%) of the alterations detected in infected hearts were not found, although an additional 109 genes were altered by treatment, indicating a remarkable 84% transcriptomic recovery. Immunofluorescence and morphometric analyses confirmed the effects of BMC therapy in the pattern of inflammatory-immune response and expression of adhesion molecules. Our results demonstrate important immunomodulatory effects of BMC therapy in chagasic cardiomyopathy and indicate potentially relevant factors involved in the pathogenesis of the disease that may provide new therapeutic targets. We compared RNA samples extracted from whole hearts of 4 control, 4 chagasic and 4 BMC-treated chagasic mice by analyzing hybridization to microarrays printed by Duke University (http://www.ncbi.nlm.nih.gove/geo/query/acc.cgi?acc=GPL8938) spotted with MO30k mouse Operon version 3.0 70-mer oligonucleotides. The hybridization protocol (see Soares et al, 2010), the slide type and the scanner settings were uniform throughout the entire experiment to minimize the technical noise. Briefly, 20 ug total RNA extracted in Trizol from each of the twelve samples (individual hearts) was reverse transcribed in the presence of fluorescent Alexa Fluor® 555- and Alexa Fluor®647-aha-dUTPs (Invitrogen, Carlsbad, CA) to obtain labeled cDNA. Red and green labeled samples of biological replicas were then co-hybridized (“multiple yellow” strategy, 22) overnight at 50° C. After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNA, each array was scanned at 630V (635 nm) and 580V (532 nm) with GenePix 4100B scanner (Axon Instruments, Union City, CA) and images were primarily analyzed with GenePixPro 6.0 (Molecular Devices, Sunnyvale, CA). Microarray data were processed as described previously (Soares et al, 2010). A gene was considered as significantly up- or down-regulated when comparing four hearts from one condition to those from another if the absolute fold change was >1.5x and the p-vlaue of the Sutdent”s heteroscedastic t-test of equality of the means of the distributions with a Bonferroni-type adjustment for each redundancy group (set of spots probing the same gene) was <0.05.
2010-09-17 | E-GEOD-24088 | biostudies-arrayexpress
Project description:Although bone marrow-derived mononuclear cells (BMNC) have been extensively used in cell therapy for cardiac diseases, little mechanistic information is available to support reports of their efficacy. To address this shortcoming, we compared structural and functional recovery and associated global gene expression profiles in post-ischaemic myocardium treated with BMNC transplantation. BMNC suspensions were injected into cardiac scar tissue 10 days after experimental myocardial infarction. Six weeks later, mice undergoing BMNC therapy were found to have normalized antibody repertoire and improved cardiac performance measured by ECG, treadmill exercise time and echocardiography. After functional testing, gene expression profiles in cardiac tissue were evaluated using high-density oligonucleotide arrays. Expression of more than 18% of the 11981 quantified unigenes was significantly altered in the infarcted hearts. BMNC therapy restored expression of 2099 (96.2%) of the genes that were altered by infarction but led to altered expression of 286 other genes, considered to be a side effect of the treatment. Transcriptional therapeutic efficacy, a metric calculated using a formula that incorporates both recovery and side effect of treatment, was 73%. In conclusion, our results confirm a beneficial role for bone marrow-derived cell therapy and provide new information on molecular mechanisms operating after BMNC transplantation on post ischemic heart failure in mice. We compared RNA samples extracted from whole hearts of infarcted mouse myocardium treated with bone marrow mononuclear cells control with untreated infarcted and control mice samples by analyzing hybridization to AECOM 32k mouse microarrays (http://microarray1k.aecom.yu.edu/) spotted with Operon version 3.0 70-mer oligonucleotides. The hybridization protocol and the slide type were uniform throughout the entire experiment to minimize the technical noise. Treated, control (sham) and infarcted red-labeled heart samples were hybridized against an in-house prepared green-labeled universal mouse reference.
2011-06-08 | E-GEOD-29769 | biostudies-arrayexpress
Project description:To identify new markers for colorectal cancer we scrutinized the methylation status by methyl-CpG immunoprecipitation followed by global methylation profiling on a CpG island microarray, as altered expression could drive genomic and chromosomal instability observed in these tumors. We show for the first time hypermethylation of MMP9, DNMT3A, and LIG4 in CRC which was confirmed in two independent ethnic CRC patients groups. Hypermethylation of the LIG4 promoter is a new mechanism to control ligase IV expression. It may represent a new epigenetic marker for colorectal cancer independent of known markers. Methylation profiling in 16 tumors of colorectal cancer patients compared to matched normal tissue of these patients
2013-12-31 | E-GEOD-47413 | biostudies-arrayexpress
Project description:BACKGROUND & AIMS: Pancreatic ductal adenocarcinoma (PDAC) is usually incurable. Contrary to genetic mechanisms involved in PDAC pathogenesis, epigenetic alterations are ill defined. Here we determine the contribution of epigenetically silenced genes to the development of PDAC. METHODS: We investigated methylated DNAs from PDACs, chronic pancreatitis and normal pancreatic tissues using Methyl-CpG immunoprecipitation followed by microarray hybridization. Promoter methylation of selected genes was confirmed with the Epityper assay. Expression levels were evaluated by quantitative RT-PCR. WNK2 was further investigated in tissue microarrays, methylation analysis of early pancreatic intraepithelial neoplasia (PanINs), mouse models for PDAC and pancreatitis, re-expression studies after demethylation, and cell growth assays using WNK2 overexpression. RESULTS: A total of 3.8% of 27.800 interrogated CpG islands were hypermethylated in PDAC versus normal and chronic pancreatitis tissues. Hypermethylation was confirmed in 12 out of 13 selected islands and was associated with gene silencing in 4 of them. The most prominently hypermethylated gene, WNK2, was further investigated. Demethylation assays confirmed the link between methylation and expression. WNK2 hypermethylation was higher in pancreatic tumor cells than in surrounding inflamed tissues and was observed in PanIN lesions as well as in a PDAC mouse model. WNK2 mRNA and protein expression were lower in PDAC and chronic pancreatitis compared to normal tissues both in patients and mouse models. Overexpression of WNK2 led to a reduced cell growth and WNK2 expression in tissues correlated negatively with the expression of pERK1/2, a downstream target of WNK2 responsible for cell proliferation. CONCLUSIONS: WNK2 is downregulated by promoter hypermethylation early in PDAC pathogenesis and may support tumor cell growth via the ERK-MAPK pathway. 3 types of pancreatic tissue samples: 5 normals, 2 chronic pancreatitis, 7 tumors (PDAC)
2012-11-01 | E-GEOD-37480 | biostudies-arrayexpress