Molecular Mechanisms of Bortezomib Resistant Adenocarcinoma cells [CGH data]
ABSTRACT: Copy number and Gene expression profiling of HT-29 wild-type and bortezomib resistant cell lines Identification of mechanisms of bortezomib resistance Copy number differences between HT-29 cell line variants and a HapMap control population of 9 female samples were identified using the Agilent 1M Human CGH microarray
Project description:Copy number and Gene expression profiling of HT-29 wild-type and bortezomib resistant cell lines Identification of mechanisms of bortezomib resistance Gene expression differences between HT-29 cell line variants
Project description:This SuperSeries is composed of the following subset Series: GSE29711: Molecular Mechanisms of Bortezomib Resistant Adenocarcinoma cells [CGH data] GSE29712: Molecular Mechanisms of Bortezomib Resistant Adenocarcinoma cells [GEP data] Refer to individual Series
Project description:Bortezomib is a proteasome inhibitor used in severel different hematological malignancies. Resistance to this drug is still poorly understood. In order get more insight in the resistance mechanism, we developed several bortezomib resistant subclones of the THP-1 monocytic/macrophage cell line. On these subclones expression arrays were performed. We performed expression array three different bortezomib resistant subclones of the THP-1 cell line. The resistant subclones were spotted against the parental THP-1 wildtype cell line.
Project description:Expression data from HT-29 human colon adenocarcinoma cells treated with IFN-γ for 24 hr Total RNA was isolated from HT-29 cells after 24h stimulation with 200 U ml-1 IFN-γ (Roche). The experiment was done on three biological replicates.
Project description:Microarray analysis of HT-29 cells co-cultured with tumor necrosis factor (TNF-a) in the presence or absence of polymeric formula as used for Exclusive Enteral Nutrition (EEN) therapy. Results provide insights into the molecular mechanisms underlying the anti-inflammatory effect of polymeric formula on intestinal epithelium. Total RNA obtained from 9 samples of HT-29 cells. Six samples were treated with TNF-a in the presence (3 samples) or absence (3 samples) of Polymeric Formula. Three samples were untreated and used as a control.
Project description:Cancer cells consume large amounts of glucose because of their specific metabolic pathway. However, cancer cells exist in tumor tissue where glucose is insufficient. To survive, cancer cells likely have the mechanism to elude their glucose addiction. Here we show that functional mitochondria are essential if cancer cells are to avoid glucose addiction. Cancer cells with dysfunctional mitochondria, such as mitochondrial DNA-deficient rho0 cells and electron transport chain blocker-treated cells, were highly sensitive to glucose deprivation. Our data demonstrated that this sensitization was caused by failure of the unfolded protein response (UPR), an adaptive response mediated by the endoplasmic reticulum (ER). This study suggests a link between mitochondria and the ER during the UPR under glucose deprivation conditions and that mitochondria govern cell fate, not only through ATP production and apoptosis regulation but also through modulating the UPR for cell survival. Human cancer cell lines (HT-1080, HT-29, and mtDNA-deficient cells derived from these cell lines) were selected for RNA extraction and hybridization on Affymetrix microarrays. We examined the unfolded protein response (UPR), an adaptive response mediated by the endoplasmic reticulum (ER), of cancer cells under stress conditions. Abbreviations List: AA, antimycin A; Bu, buformin; Met, metformin; Phen, phenformin; Rot, rotenone; VST, versipelostatin; TM, tunicamycin; 2DG, 2-deoxyglucose; GS, glucose starvation. Capital S (_S) indicates the supernatant of sample including floating cells.
Project description:Achaete scute-like 2 (Ascl2), a basic helix-loop-helix (bHLH) transcription factor, controls the fate of intestinal stem cells. However, the role of Ascl2 in colon cancer progenitor cells remains unknown. The cell lines HT-29 (47.5-95% of CD133+ population) and LS174T (0.45% of CD133+ population) were chosen for functional evaluation of Ascl2 in colon cancer progenitor cells after gene knockdown by RNA interference. The microRNA (miRNA) microarrays identified 26 two-fold up-regulated miRNAs and 58 two-fold down-regulated miRNAs in shRNA-Ascl2/HT-29 cells and 178 two-fold up-regulated miRNAs and 172 two-fold down-regulated miRNAs in shRNA-Ascl2/LS174T cells. Two-condition experiment: shRNA-Ascl2/HT-29 cells vs. shRNA-Ctr/HT-29 cells, and shRNA-Ascl2/LS174T cells vs. shRNA-Ctr/LS174T cells. Biological replicates: 1 HT-29 cells stably transfected with shRNA-Ascl2/EGFP, 1 LS174T cells stably transfected with shRNA-Ascl2/EGFP, 1 HT-29 cells stably transfected with shRNA-Control/EGFP, and 1 LS174T cells stably transfected with shRNA-Control/EGFP, independently grown and harvested. One replicate per array.
Project description:RNA-seq data from HT-29 cells treated with IFN-γ for 24 hr, MCF10A cells, and MDA-MB-436 cells. mRNA profiles of HT-29, MCF10A, and MDA-MB-436 were generated by deep sequencing using Illumina HiSeq 2000. All RNA sequencing data was generated by the Genomics Services Lab at the HudsonAlpha Institute for Biotechnology (Huntsville, AL).
Project description:Colorectal cancers have a rare population of cells that express specific cell surface markers, and are referred to as cancer stem cells (CSC). Targeting CSCs, implicated in tumor relapse, is a paradigm shifting approach for colorectal cancer. We used gene microarray to analyze gene expression in HT-29, a colon cancer cell line, grown as monolayer and spheroid and identify metabolic pathways that are upregulated. HT-29 monolayer cells were grown in DMEM/F12 media supplemented with 10% FBS, and 1X Antibiotic-Antimycotic liquid (AA); and spheroids were grown in stem cell media [DMEM:F12, 1X AA, 1X B27, epidermal growth factors, and fibroblast growth factor for five days. Total RNA was isolated using the mirVana™ miRNA Isolation Kit according to the manufacturer's protocol. RNA intergrity was confirmed on the Nanodrop ND-1000 and analyzed with Agilent 2100 bioanalyzer. The arrays were scanned with the Affymetrix 3000 7G plus scanner.
Project description:The RNA samples from HT-29 (ATCC) colon cancer cell line were reverse transcribed into cDNAs and categorized in 3 groups with different concentrations of 5-aza-deoxy-cytidine (5-Aza); in each group three replicative 150 mm cultures were treated with: 1) dimethyl sulfoxide (vehicle alone, 0 μM 5-Aza); 2) 5μM 5-Aza and 3) 10 μM 5-Aza; for five days We then used Affymetrix microarray platform to profile the gene expression of the 3 HT29 cell groups (3 replicates in each group) in order to search for differentially expressed genes The transcriptional response of HT-29 (ATCC) colon cancer cell line under 3 concentrations of 5-aza-deoxy-cytidine was investigated based on their RNA expression profiles