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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression-analysis of human peripheral blood mononuclear cells (PBMC) cocultivated with RT-4 cells transduced with a trivalent adenoviral vector (Im02) for expression of 4-1BBL, IL-12 and IL-2

ABSTRACT: The trivalent adenoviral vector Im02 encodes the cDNAs for human 4-1BBL, IL-12 and IL-2. This vector was designed to change the immune tumor microenvironment. At the outset, we investigated the immune stimulating effect of Im02 transduced urothelial cancer cells (RT-4). Human PBMCs of a healthy donor were cocultured with these cells in a time series experiment. An adenoviral vector without expression cassette and cultivation without a vector were applied as control.

ORGANISM(S): Homo sapiens

SUBMITTER: Carolin Biermann-Fleischhauer

PROVIDER: E-MTAB-7615 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression analysis of human ex vivo cultivated urothelial carcinoma samples transduced with a trivalent adenoviral vector (Im02) for activation of the immune tumor microenvironment.

Project description:The trivalent adenoviral vector Im02 encodes the cDNAs for human 4-1BBL, IL-12 and IL-2. This vector was designed to change the immune tumor microenvironment. In this study we investigated the immune stimulating effect of Im02 on human primary urothelial cancer specimens or normal urothelium by microarray RNA expression analysis. The tissues were transduced with Im02 or an adenoviral vector without expression cassette and were further cultivated for six days. Samples without transduction and cultivation were analysed to determine the status of the microenvironment.

2021-01-01 | E-MTAB-7623 | biostudies-arrayexpress

Regulation of gene expression by YAP1

Project description:In order to define YAP1-specific gene expression patterns in gastric cancer, the constitutively active mutant YAP1 (YAP1-S127A) was over-expressed in MKN45 gastric cancer cells. Defined gene expression signature was later used to stratify gastric cancer patients according to the presence of the YAP1-activated signature. Three groups of samples are included: 1. Mock control; 2. Vector control; 3. YAP-S127A expression. Gene expression profiles of YAP-S127A mutant-expressing cells were compared to that of mock and vector control. Experiments were done in MKN45 gastric cancer cells.

2013-10-01 | E-GEOD-41387 | biostudies-arrayexpress

Addition of IL-6 inhibition to standard GVHD prophylaxis to prevent GVHD after allogeneic stem cell transplantation

Project description:BACKGROUND - IL-6 mediates graft-versus-host disease (GVHD) in experimental allogeneic stem cell transplantation (alloSCT) and is an attractive therapeutic target. METHODS - A registered phase I/II study (ACTRN12612000726853) of IL-6 receptor (IL-6R) neutralizing antibody administration on day -1 to patients receiving full or reduced-intensity conditioning (RIC) and alloSCT from HLA-matched sibling or unrelated donors with standard cyclosporin and methotrexate GVHD prophylaxis. The primary endpoint was incidence of grade II-IV acute GVHD. Outcomes were compared to a non-randomized but contemporaneous group of study patients receiving the same alloSCT in the absence of IL-6R mAb. FINDINGS - Cytokine and pharmacokinetic analysis confirmed transient IL-6 dysregulation in the first month after alloSCT with complete inhibition following IL-6R mAb administration. With median follow up of 497 days, the incidence of grade II-IV GVHD was 12.5% in recipients of IL-6R inhibition (n = 48) versus 41.5% in the (n = 53) control cohort (P = 0.001). Low rates of acute GVHD were noted in patients receiving IL-6R inhibition relative to control patients following both myeloablative (12.5% vs. 46.4%, P = 0.03) and RIC (12.5% vs. 36.0%, P = 0.04). The incidence of severe (grade III/IV) acute GVHD was 4.2% in recipients of IL-6R inhibition versus 20.8% in the control cohort (P = 0.012). Relapse and chronic GVHD were unchanged. Immune reconstitution was preserved in recipients of IL-6R inhibition, but qualitatively modified with suppression of known pathogenic STAT3-dependent pathways. INTERPRETATION - IL-6 is the principal detectable and dysregulated cytokine secreted after alloSCT and its inhibition is a potential new and simple strategy to protect from acute GVHD despite robust immune reconstitution and a sustained graft-versus-leukemia effect. Single colour, Illumina Human HT12v4 Beadarrays.

2014-09-09 | E-GEOD-61201 | biostudies-arrayexpress

Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-06-30 | E-GEOD-55857 | biostudies-arrayexpress

Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer [Illumina]

Project description:Targeted cancer therapy for squamous cell carcinoma (SCC) has made little progress largely due to a lack of knowledge of the driving genomic alterations. Small non-coding RNAs (sncRNAs) as a potential biomarker and therapeutic target to SCC remain a challenge. We analyzed sncRNAs microarray in 108 fresh frozen specimens of esophageal squamous cell carcinoma (ESCC) as discovery set and assessed associations between sncRNAs and recurrence-free survival. SncRNA signature identified was externally validated in two independent cohorts. We investigated the functional consequences of sncRNA identified and its integrative analysis of complex cancer genomics. We identified 3 recurrence-associated sncRNAs (miR-223, miR-1269a and nc886) from discovery set and proved risk prediction model externally in high and low volume centers. We uncovered through in vitro experiment that nc886 was down-regulated by hypermethylation of its promoter region and influences splicing of pre-mRNAs with minor introns by regulating expression of minor spliceosomal small nuclear RNAs (snRNAs) such as RNU4atac. Integrative analysis from lung SCC data in The Cancer Genome Atlas revealed that patients with lower expression of nc886 had more genetic alterations of TP53, DNA damage response and cell cycle genes. nc886 inhibits minor splicing to suppress expression of certain oncogenes such as PARP1 and E2F family containing minor introns. We present risk prediction model with sncRNAs for ESCC. Among them, nc886 may contribute to complete minor splicing via regulation of minor spliceosomal snRNAs supporting the notion that aberrant alteration in minor splicing might be a key driver of ESCC. Pre-clinical study Analysis of Esophageal Squamous Cell Carcinoma cell lines knocked-down for nc886 and vault RNA VTRNA1-1 via antisense oligonucleotide (ASO)-targeting.

2016-06-30 | E-GEOD-55854 | biostudies-arrayexpress

Expression analysis of human ex vivo cultivated urothelial carcinoma samples transduced with a trivalent adenoviral vector (Im02) for activation of the immune tumor microenvironment.

Project description:The trivalent adenoviral vector Im02 encodes the cDNAs for human 4-1BBL, IL-12 and IL-2. This vector was designed to change the immune tumor microenvironment. In this study we investigated the immune stimulating effect of Im02 on human primary urothelial cancer specimens or normal urothelium by RNASeq expression analysis. The tissues were transduced with Im02 or an adenoviral vector without expression cassette and were further cultivated for six days. Samples without transduction and cultivation were analysed to determine the status of the microenvironment.

2020-06-18 | E-MTAB-7659 | biostudies-arrayexpress

Microarray of Human astrocytes transduced with lentivirus expressing FGFR3-TACC3 treated with vehicle, FGFR3-TACC3 treated with the FGFR inhibitor PD173074 for 12h, FGFR3-TACC3-K508M treated with vehicle or empty vector treated with vehicle

Project description:In order to interrogate the transcriptional changes elicited by FGFR3-TACC3, we expressed the FGFR3-TACC3 fusion protein in human astrocytes and compared the global gene expression profiles of cells treated with a specific inhibitor of FGFR3-TK (PD173074) or vehicle. FGFR3-TACC3 expressing HA were also compared with HA that expressed the kinase-inactive FGFR3-TACC3 (FGFR3-TACC3-K508M) and HA transduced with the empty vector. Gene Ontology-guided enrichment map demonstrated that, besides the expected enrichment for mitotic activity, oxidative phosphorylation and mitochondrial biogenesis were the most significant biological functions enriched in HA expressing active FGFR3-TACC3.

2017-10-17 | E-MTAB-6037 | biostudies-arrayexpress

Hepatic regeneration gene expression signature predicts late recurrence of hepatocellular carcinoma

Project description:While we and others have uncovered and validated several genomic predictors for metastatic recurrences, a molecular or genomic predictor that can reliably identify high-risk patients for late de novo recurrence has not been firmly established. We analyzed previously reported gene expression data from human livers that underwent partial hepatectomy or transplantation, which were representative physiological conditions that trigger liver regeneration signals. We generated gene expression data from tumor and matched non-tumor surrounding tissues of 72 hepatocellular carcinoma (HCC) patients who underwent surgical resection as the primary treatment. We used these gene expression data to develop a new prognostification model for recurrence of HCC after surgery. We generated gene expression data from tumor and matched non-tumor surrounding tissues of 72 HCC patients who underwent surgical resection as the primary treatment.

2014-11-03 | E-GEOD-39791 | biostudies-arrayexpress

Unexpected roles of ATP11B in platinum resistance

Project description:Platinum compounds display clinical activity against a wide variety of solid tumors. However, resistance to these agents is a major limitation in cancer therapy. Reduced platinum uptake and increased platinum export are examples of resistance mechanisms that limit the extent of DNA damage. Here, we report the discovery and characterization of the role of ATP11B, a P-type ATPase membrane protein, in cisplatin resistance. ATP11B gene silencing restored the sensitivity of ovarian cancer cell lines to cisplatin in vitro. Combined therapy of cisplatin and ATP11B-siRNA significantly decreased cancer growth in mice bearing ovarian tumors derived from cisplatin-sensitive and -resistant cells. In vitro mechanistic studies on cellular platinum content and cisplatin efflux-kinetics indicated that ATP11B enhances the export of cisplatin from cells. The co-localization of ATP11B with fluorescent cisplatin and with vesicular trafficking proteins such as syntaxin-6 (STX6) and vesicular associated membrane protein 4 (VAMP4) strongly suggests that ATP11B contributes to secretory vesicular transport of cisplatin from Golgi to plasma membrane. In conclusion, silencing ATP11B expression might be a therapeutic strategy to overcome cisplatin resistance. We performed the transfection of control-siRNA and ATP11B-siRNA to both cisplatin-sensitive A2780-PAR and cisplatin-resistant A2780-CP20 cells respectively.

2013-01-23 | E-GEOD-43694 | biostudies-arrayexpress

The orphan nuclear receptor NR4A1 (Nur77, TR3) regulates oxidative and endoplasmic reticulum stress in pancreatic cancer cells

Project description:NR4A1 (Nur77, TR3) is an orphan nuclear receptor that is overexpressed in pancreatic cancer cells and tumors and exhibits pro-oncogenic activity. Knockdown of NR4A1 by RNA interference (siNR4A1) in Panc1 cells and analysis of the proteome resulted in induction of several markers of endoplasmic reticulum (ER) stress including glucose-related protein 78 (GRP78), CCAAT/enhancer-binding protein-homologous protein (CHOP), activating transcription factor-3 (ATF-3) and AFT-6. These effects were accompanied by induction of apoptosis and similar results were observed after treatment of pancreatic cancer cells with the known inactivator of NR4A1, 1,1-bis(3’-indolyl)-1-(p-hydroxyphenyl)methane (DIM-C-pPhOH). Both siNR4A1 (transfected) and DIM-C-pPhOH also induced reactive oxygen species (ROS) and induction of ROS and ER stress by these agents was attenuated after cotreatment with antioxidants. Transfection of Panc1 cells with siNR4A1 follow by analysis of gene expression by arrays identified ROS metabolism genes regulated by NR4A1. Knockdown of one of these genes, thioredoxin domain containing 5 (TXNDC5) also resulted in induction of ROS and ER stress demonstrating that NR4A1 regulates levels of ER stress and ROS in pancreatic cancer cells to facilitate cell proliferation and survival. Inactivation of this receptor by siNR4A1 or DIM-C-pPhOH decreases TXNDC5 resulting in activation of ROS/ER stress and pro-apoptotic pathways and represents a novel pathway for inducing cell death in pancreatic cancer cells. Two groups of samples are included: 1. siControl; 2. siNR4A1 treatment in PAC1 cell. Transfection of Panc1 cells with siNR4A1 follow by analysis of gene expression by arrays identified ROS metabolism genes regulated by NR4A1.

2014-04-30 | E-GEOD-46994 | biostudies-arrayexpress

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