publication_authors:Wrzodek C Results

Showing of 12 results

Sort by

Hide non-downloadable experiments

Filters

Technology

Microarray (749)

Platform

Affymetrix Mouse Genome 430 2.0 Array (mouse4302) (534)

Affymetrix Rat Expression 230A Array (rae230a) (518)

Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2) (146)

Affymetrix Human Genome U133A Array (hgu133a) (54)

Affymetrix Mouse Gene 2.0 ST Array (mogene20st) (15)

Includes Publication

GSE44783

Expression data from CD-1 mouse liver samples obtained from in-vivo treatment with genotoxic carcinogens, non-genotoxic carcinogens or non-hepatocarcinogens.

Mus musculus
449 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302), Affymetrix Rat Expression 230A Array (rae230a)

Description

Assessing the carcinogenic potential of drug candidates is a costly procedure which requires the life-long treatment of rodents at different dose levels. A promising approach, which may to a certain degree reduce the need for animal studies in the future is toxicogenomics. The idea is to employ microarray platforms for the genome-wide expression profiling of compounds, which may facilitate the discovery of biomarker genes and provide insights in molecular mechanisms.

Publication Title

A toxicogenomic approach for the prediction of murine hepatocarcinogenesis using ensemble feature selection.

Sample Metadata Fields

Sex, Specimen part, Treatment, Time

View Samples

GSE29868

Inferring drug-induced gene regulatory relationships in primary human hepatocytes

Homo sapiens
50 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Statins are widely used cholesterol-lowering drugs that inhibit HMG-CoA reductase, a key enzyme in cholesterol synthesis. In some cases, however, these drugs may cause a number of toxic side effects in hepatocytes and skeletal muscle tissue. Currently, the specific molecular mechanisms that cause these adverse effects are not sufficiently understood. In this work, genome-wide RNA expression changes in primary human hepatocytes of six individuals were measured at five time points upon atorvastatin treatment. A novel systems-level analysis workflow was applied to reconstruct regulatory mechanisms based on these drug-response data and available knowledge about transcription factor binding specificities, protein-protein interactions and protein-drug interactions. Several previously unknown transcription factors, regulatory cofactors and signaling molecules were found to be involved in atorvastatin-responsive gene expression. Some novel relationships, e.g., the regulatory influence of nuclear receptor NR2C2 on CYP3A4, were successfully validated in wet-lab experiments.

Publication Title

Inferring statin-induced gene regulatory relationships in primary human hepatocytes.

Sample Metadata Fields

Specimen part, Treatment, Subject

View Samples

GSE51358

Metabolic programs orchestrated by the activated Ha-ras and -catenin oncoproteins in mouse liver tumors

Mus musculus
16 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Ha-ras and β-catenin oncoproteins orchestrate metabolic programs in mouse liver tumors.

Sample Metadata Fields

Sex, Specimen part

View Samples

GSE51355

Metabolic programs orchestrated by the activated Ha-ras and -catenin oncoproteins in mouse liver tumors [mRNA]

Mus musculus
16 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The process of hepatocarcinogenesis in the diethylnitrosamine (DEN) initiation/phenobarbital (PB) promotion mouse model involves the selective clonal outgrowth of cells harboring oncogene mutations in Ha-ras, B-raf, or Ctnnb1. Here, we have characterized mouse liver tumors harboring either Ctnnb1 or Ha-ras mutations via integrated molecular profiling at the transcriptional and translational and post-translational levels. In addition, metabolites of the intermediary metabolism were quantified by high resultion 1H magic angle nuclear magnetic resonance (HR-MAS NMR). We have identified tumor characteristic genotype-specific differences in mRNA and miRNA expression, protein levels, and post-translational modifications and in metabolite levels that facilitate the molecular and biochemical stratification of tumor phenotypes. Bioinformatic integration of these data at the pathway level led to novel insights into tumor genotype-specific aberrant cell signaling and in particular to a better understanding of alterations in pathways of the cell intermediary metabolism, which are driven by the constitutive activation of the -Catenin and Ha-ras oncoproteins in tumors of the two genotypes.

Publication Title

Ha-ras and β-catenin oncoproteins orchestrate metabolic programs in mouse liver tumors.

Sample Metadata Fields

Sex, Specimen part

View Samples

GSE80018

Time series trancriptional profiling of mouse liver after up to 13 weeks administration of Phenobarbital [mRNA]

Mus musculus
69 Downloadable Samples
Affymetrix Rat Expression 230A Array (rae230a), Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The molecular events during nongenotoxic carcinogenesis and their temporal order are poorly understood but thought to include long-lasting perturbations of gene expression. Here, we have investigated the temporal sequence of molecular and pathological perturbations at early stages of phenobarbital (PB) mediated liver tumor promotion in vivo. Molecular profiling (mRNA, microRNA [miRNA], DNA methylation, and proteins) of mouse liver during 13 weeks of PB treatment revealed progressive increases in hepatic expression of long noncoding RNAs and miRNAs originating from the Dlk1-Dio3 imprinted gene cluster, a locus that has recently been associated with stem cell pluripotency in mice and various neoplasms in humans. PB induction of the Dlk1-Dio3 cluster noncoding RNA (ncRNA) Meg3 was localized to glutamine synthetase-positive hypertrophic perivenous hepatocytes, sug- gesting a role for -catenin signaling in the dysregulation of Dlk1-Dio3 ncRNAs. The carcinogenic relevance of Dlk1-Dio3 locus ncRNA induction was further supported by in vivo genetic dependence on constitutive androstane receptor and -catenin pathways. Our data identify Dlk1-Dio3 ncRNAs as novel candidate early biomarkers for mouse liver tumor promotion and provide new opportunities for assessing the carcinogenic potential of novel compounds.

Publication Title

Identification of Dlk1-Dio3 imprinted gene cluster noncoding RNAs as novel candidate biomarkers for liver tumor promotion.

Sample Metadata Fields

Specimen part

View Samples

GSE11943

Human Dendritic Cell Subtype Gene Arrays

Homo sapiens
8 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)

Description

Among the dendritic cell (DC) subsets, plasmacytoid DCs are thought to be important in both generating antiviral and antitumor responses. These cells may be useful in developing dendritic cell-based tumor vaccines, however, the rarity of these cells in the peripheral blood have hampered attempts to understand their biology. To provide better insight into the biology of plasmacytoid DCs, we isolated these cells from the peripheral blood of healthy donors in order to further characterize their gene expression. Using gene array technology we compared the genetic profiles of these cells to those of CD14+ monocytes isolated from the same donors and found several immune related genes upregulated in this cell population. Understanding the genetic profiles of this dendritic cell subtype as well as others such as the BDCA-1 expressing myeloid DCs may enable us to manipulate these cells ex-vivo to generate enhanced DC-based tumor vaccines inducing more robust antitumor responses.

Publication Title

Genetic profiles of plasmacytoid (BDCA-4 expressing) DC subtypes-clues to DC subtype function in vivo.

Sample Metadata Fields

No sample metadata fields

View Samples

GSE28015

Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer

Homo sapiens
46 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer.

Sample Metadata Fields

Sex, Disease, Disease stage, Treatment

View Samples

GSE27943

Gene Expression Array of Human Ovarian Cancer.

Homo sapiens
46 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)

Description

The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 44 primary ovarian cancer samples and 7 ovarian normal samples using our MOMA-ROMA technology and Affymetrix expression data as well as 379 tumor samples analyzed by The Cancer Genome Atlas. We have identified 346 genes with significant deletions or amplifications among the tumor samples. Utilizing associated gene expression data we predict 156 genes with significantly altered copy number and correlated changes in expression. We identify changes in DNA methylation and expression for all amplified and deleted genes. We predicted 615 potential oncogenes and tumor suppressors candidates by integrating these multiple genomic and epigenetic data types.