Gene alterations by PPAR-gamma agonists in human colorectal adenocarcinoma HCT-116 cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE9183 | GEO | 2008/06/10
SECONDARY ACCESSION(S): PRJNA102749
REPOSITORIES: GEO
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Project description:Purpose: The goal of this study is to investigate the alteration of gene expression pattern induced by 15d-PGJ2 or 15d-PGJ2-PC in BMDMs. Method: BMDMs obtained from C57BL/6 mice were treated with 15d-PGJ2, 15d-PGJ2-PC or media control for 6h. Then RNA sequence was generated by using the Illumina system. Results: Using an optimized data analysis workflow, we mapped about 13 million sequence reads per sample to the mouse genome and identified about 14,500 transcripts in the macrophage mRNAs. Among them, 719 and 286 genes were differentially expressed in 15d-PGJ2 and 15d-PGJ2-PC group respectively. Conclusions: Deoxy-A2/J2-IsoP-PC are a novel series of oxidation products we identified in atherosclerotic plaques. 15d-PGJ2-PC is a representative compound of these oxidation products we chemically synthesised. Using RNA-seq technology, we provided 15d-PGJ2-PC induced gene expression profile and could contribute to study the roles of these novel oxidation products in the atherosclerosis.
2016-08-24 | GSE85931 | GEO
Project description:Purpose: The goal of this study is to investigate the alteration of gene expression pattern induced by 15d-PGJ2 or 15d-PGJ2-PC in BMDMs. Method: BMDMs obtained from C57BL/6 mice were treated with 15d-PGJ2, 15d-PGJ2-PC or media control for 6h. Then RNA sequence was generated by using the Illumina system. Results: Using an optimized data analysis workflow, we mapped about 13 million sequence reads per sample to the mouse genome and identified about 14,500 transcripts in the macrophage mRNAs. Among them, 719 and 286 genes were differentially expressed in 15d-PGJ2 and 15d-PGJ2-PC group respectively. Conclusions: Deoxy-A2/J2-IsoP-PC are a novel series of oxidation products we identified in atherosclerotic plaques. 15d-PGJ2-PC is a representative compound of these oxidation products we chemically synthesised. Using RNA-seq technology, we provided 15d-PGJ2-PC induced gene expression profile and could contribute to study the roles of these novel oxidation products in the atherosclerosis. mRNA profiles of BMDMs from C57B/L6 mice were generated by deep sequencing, in triplicate, using Illumina.
2016-08-24 | E-GEOD-85931 | biostudies-arrayexpress
Project description:15-deoxy-delta12,14-prostaglandin J2 (15d-PGJ2) is an endogenous anti-inflammatory lipid derived from PGD2. One potential mechanism for its activity is the covalent modification of cellular proteins, via a reactive alpha,beta-unsaturated carbonyl group in its cyclopentenone ring, which in turn alters protein function. In order to identify the target proteins covalently modified by 15d-PGJ2 in human aortic endothelial cell (EC), EC were treated with biotinylated-15d-PGJ2, the modified proteins extracted by Neutravidin affinity-purification and the proteins were identified by LTQ Orbitrap mass spectrometer.
2015-04-26 | PXD000006 | Pride
Project description:Cortisol, the central stress hormone in humans, activates the glucocorticoid receptor (GR). Anti-inflammatory effects are the most important pharmaceutical effects mediated by the GR. Inasmuch as electrophilic cyclopentenone prostaglandin 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2) has potent anti-inflammatory properties and activates the SUMOylation pathway, we have investigated the effect of 15d-PGJ2 on glucocorticoid signaling and receptor SUMOylation. To this end, we studied isogenic HEK293 cells expressing either wild-type GR or SUMOylation-defective GR. Interestingly, 15d-PGJ2 triggered SUMO-2/3 modification in the primary SUMOylation sites of the GR. Gene expression profiling and pathway analyses indicate that 15d-PGJ2 inhibits GR signaling in a genome-wide fashion that is significantly dependent on the GR SUMOylation sites. Chromatin immunoprecipitation assays showed that the repressive effect of 15d-PGJ2 on GR target gene expression occurs in parallel with the inhibition of receptor binding to the target gene chromatin. Furthermore, depletion of the sole SUMO E2 conjugase UBC9 from HEK293 cells confirmed the involvement of active SUMOylation in the regulatory process. Taken together, our data indicate that GR SUMOylation modulates the glucocorticoid signaling during acute cell stress. Our data also suggest that GR SUMOylation modulates crosstalk of the glucocorticoid signaling with other transcription factors that are responsive to cell stress.
2014-06-30 | GSE54087 | GEO
Project description:Cortisol, the central stress hormone in humans, activates the glucocorticoid receptor (GR). Anti-inflammatory effects are the most important pharmaceutical effects mediated by the GR. Inasmuch as electrophilic cyclopentenone prostaglandin 15-deoxy-M-NM-^T12,14-prostaglandin J2 (15d-PGJ2) has potent anti-inflammatory properties and activates the SUMOylation pathway, we have investigated the effect of 15d-PGJ2 on glucocorticoid signaling and receptor SUMOylation. To this end, we studied isogenic HEK293 cells expressing either wild-type GR or SUMOylation-defective GR. Interestingly, 15d-PGJ2 triggered SUMO-2/3 modification in the primary SUMOylation sites of the GR. Gene expression profiling and pathway analyses indicate that 15d-PGJ2 inhibits GR signaling in a genome-wide fashion that is significantly dependent on the GR SUMOylation sites. Chromatin immunoprecipitation assays showed that the repressive effect of 15d-PGJ2 on GR target gene expression occurs in parallel with the inhibition of receptor binding to the target gene chromatin. Furthermore, depletion of the sole SUMO E2 conjugase UBC9 from HEK293 cells confirmed the involvement of active SUMOylation in the regulatory process. Taken together, our data indicate that GR SUMOylation modulates the glucocorticoid signaling during acute cell stress. Our data also suggest that GR SUMOylation modulates crosstalk of the glucocorticoid signaling with other transcription factors that are responsive to cell stress. Total RNA isolated from isogenic HEK293 cell lines stably expressing either wild-type GR (wtGR) or SUMOylation-defective GR (GR3KR) treated with 100 nM of dexamethasone (dex) in the presence or absence of 5 M-BM-5M 15d-PGJ2 for 6h. All conditions are performed in triplicate
2014-06-30 | E-GEOD-54087 | biostudies-arrayexpress
Project description:A bioinformatic approach was applied to evaluate the effect of treatment with Bevacizumab on the gene expression profile of colorectal adenocarcinoma cells. The transcriptomic profile of Bevacizumab-adapted HCT-116 (Bev/A) colorectal adenocarcinoma cells was determined and compared with that of the corresponding control cell line by Agilent microarray analysis. Raw data were preprocessed, normalized, filtered, and subjected to a differential expression analysis using standard R/Bioconductor packages (i.e., limma, RankProd). As consequence of Bevacizumab adaptation, 166 differentially expressed genes (DEGs) emerged, most of them (123) resulted downregulated and 43 overexpressed. The list of statistically significant dysregulated genes was used as an input for functional overrepresentation analysis using ToppFun web tool. Such analysis pointed at cell adhesion, cell migration, extracellular matrix organization and angiogenesis as the main dysregulated biological process involved in Bevacizumab-adaptation of HCT116 cells. In addition, gene set enrichment analysis was performed using GSEA, searching for enriched terms within the Hallmarks (H), Canonical Pathways (CP), and Gene Ontology (GO) gene sets. GO terms that showed significant enrichment included: transportome, vascularization, cell adhesion and cytoskeleton, extra cellular matrix (ECM), differentiation and epithelial-mesenchymal transition (EMT), inflammation and immune response. Raw and normalized microarray data were deposited in the Gene Expression Omnibus (GEO) public repository with accession number GSE221948.
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Project description:Many neurodegenerative disorders are characterized by two pathological hallmarks: progressive loss of neurons and occurrence of inclusion bodies containing ubiquitinated proteins. The mechanisms responsible for these pathological features remain elusive. Inflammation may be critical to neurodegeneration associated with ubiquitin-protein aggregates. We previously showed that prostaglandin J2 (PGJ2), one of the endogenous products of inflammation, induces neuronal death and accumulation of ubiquitinated proteins into distinct aggregates. We now report that temporal microarray analysis of human neuroblastoma SK-N-SH cells treated with PGJ2 revealed changes relevant to neurodegeneration. PGJ2 triggered a “repair” response including increased expression of heat shock, protein folding, stress and cellular defense genes. PGJ2 also decreased expression of DNA repair genes and increased expression of apoptotic genes. Overtime pro-death responses prevailed over pro-survival responses, leading to cellular demise. Furthermore, PGJ2 increased the expression of proteasome and other ubiquitin-proteasome pathway genes. This increase failed to overcome PGJ2-inhibition of 26S proteasome activity. Ubiquitinated proteins are degraded by the 26S proteasome, shown here to be the most active proteasomal form in SK-N-SH cells. We demonstrate that PGJ2 impairs 26S proteasome assembly, which is an ATP-dependent process. Interestingly, PGJ2 is known to perturb mitochondrial function, which could be critical to the observed 26S proteasome disassembly and suggest a crosstalk between mitochondrial and proteasomal impairment. In conclusion neurotoxic products of inflammation, such as PGJ2, may play a role in neurodegenerative disorders associated with the aggregation of ubiquitinated proteins by impairing 26S proteasome activity and inducing a chain of events that culminates in neuronal cell death. Keywords: Drug response time course
2006-06-01 | GSE4329 | GEO
Project description:RationaleProteomic analysis of single multicellular spheroids has not been previously reported. As three-dimensional cell cultures are an increasingly popular model system for biological research, there is interest in obtaining proteomic profiles of these samples. We investigated the proteome of single HCT 116 multicellular spheroids using protocols optimized for small sample sizes.MethodsSix biological replicates were analyzed via microscopy for size. Total protein content was assessed via the bicinchoninic acid assay (BCA assay). Five separate biological replicate spheroids were analyzed via mass spectrometry in technical duplicate. An ultra-performance liquid chromatography (UPLC) system coupled with an LTQ Orbitrap Velos was used for peptide separation, analysis, and identification.ResultsThe average diameter of six replicate HCT 116 spheroids was 940 ± 30 µm and the average total protein amount was determined to be 39 ± 4 µg. At least 1300 protein groups were identified in each single LC/MS/MS run with 10% of the material from each single spheroid loaded. Database search results showed variation between spheroid protein group identifications. Pearson correlations show that the disparity in identifications is due to random variations in spectra and protocol.ConclusionsWe detected more than 1350 protein groups in each replicate HCT 116 spheroid. While some variation was detected between replicates, differences in the number of protein groups identified were determined to be the result of random variations in mass spectra acquisition.
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Project description:AIM:To investigate the inhibitory effect of kallistatin (KAL) on angiogenesis and HCT-116 xenograft tumor growth. METHODS:Heterotopic tumors were induced by subcutaneous injection of 2 multiply 10(6) HCT-11 cells in mice. Seven days later, 2 multiply 10(11) rAAV-GFP or rAAV-KAL was injected intratumorally (n = 5 for each group). The mice were sacrificed at d 28, by which time the tumors in the rAAV-GFP group had grown to beyond 5% of the total body weight. Tumor growth was measured by calipers in two dimensions. Tumor angiogenesis was determined with tumor microvessel density (MVD) by immunohistology. Tumor cell proliferation was assessed by Ki-67 staining. RESULTS:Intratumor injection of rAAV-KAL inhibited tumor growth in the treatment group by 78% (171 +/- 52 mm(3)) at d 21 after virus infection compared to the control group (776 +/- 241 mm(3)). Microvessel density was significantly inhibited in tumor tissues treated with rAAV-KAL. rAAV-KAL also decreased the proportion of proliferating cells (Ki-67 positive cells) in tumors compared with the control group. CONCLUSION:rAAV-mediated expression of KAL inhibits the growth of colon cancer by reducing angiogenesis and proliferation of tumor cells, and may provide a promising anti-angiogenesis-based approach to the treatment of metastatic colorectal cancer.
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Project description:Deregulated Wnt signaling initiates most cases of colorectal cancer (CRC). Butyrate, a product of dietary fiber, hyperactivates Wnt signaling, resulting in induction of CRC cell apoptosis, which may in part explain the protective action of fiber. Nonsense mediated decay (NMD) of mRNAs containing premature stop codons (PTCs) affects tumorigenesis and upregulates Wnt signaling in human embryonic stem cells. However, it is unknown how NMD affects Wnt activity in CRC cells that exhibit constitutively activated Wnt signaling. We hypothesize that expression of genes that contain PTCs modulates Wnt signaling and response to butyrate in CRC cells. Amlexanox is a clinically utilized anti-allergic and anti-inflammatory drug that inhibits NMD and promotes PTC read-through. Therefore, Amlexanox is a relevant agent for assessing the role of NMD and PTC read-through in the response of CRC cells to butyrate. To test our hypothesis, we treated HCT-116 CRC cells with Amlexanox and determined effects on Wnt signaling levels, apoptosis, and response to butyrate. Amlexanox enhanced basal Wnt signaling levels; however, it repressed butyrate-induced Wnt signaling hyperactivation and suppressed apoptosis. To evaluate the contribution of NMD and altered expression of PTC-containing genes to these effects, we upregulated NMD by overexpression of up-frameshift protein 1 (UPF1), and observed effects opposite to these of Amlexanox (i.e., Wnt signaling hyperactivation by butyrate was enhanced and levels of apoptosis were increased). Our results support the possibility that altered expression of PTC-containing genes affects butyrate sensitivity of CRC cells.
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