Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of rat liver pooled vs. individual samplesf rom a single-dose time-course rat study in response to the prototypical toxicants Clofibrate [CAS:637-07-0;CHEBI:3750], Diethylhexyl phthalate DEHP [CAS:117-81-7;CHEBI:17243], and valproic acid VPA [CAS:1069-66-5;CHEBI:9925],

ABSTRACT: Combining or pooling individual samples when carrying out transcript profiling using microarrays is a fairly common means to reduce both the cost and complexity of data analysis. However, pooling does not allow for statistical comparison of changes between samples and can result in a loss of information. Because a rigorous comparison of the identified expression changes from the two approaches has not been reported, we compared the results for hepatic transcript profiles from pooled vs. individual samples. Hepatic transcript profiles from a single-dose time-course rat study in response to the prototypical toxicants Clofibrate [CAS:637-07-0;CHEBI:3750], Diethylhexyl phthalate DEHP [CAS:117-81-7;CHEBI:17243], and valproic acid VPA [CAS:1069-66-5;CHEBI:9925],were evaluated. Approximately 50% more transcript expression changes were observed in the individual (statistical) analysis compared with the pooled analysis. While the majority of these changes were less than twofold in magnitude (~80%), a substantial number were greater than twofold (~20%). Transcript changes unique to the individual analysis were confirmed by quantitative RT-PCR, while all the changes unique to the pooled analysis did not confirm. The individual analysis identified more hits per biological pathway than the pooled approach. Many of the transcripts identified by the individual analysis were novel findings and may contribute to a better understanding of molecular mechanisms of these compounds. Furthermore, having individual animal data provided the opportunity to correlate changes in transcript expression to phenotypes (i.e., histology) observed in toxicology studies. The two approaches were similar when clustering methods were used despite the large difference in the absolute number of transcripts changed. In summary, pooling reduced resource requirements substantially, but the individual approach enabled statistical analysis that identified more gene expression changes to evaluate mechanisms of toxicity. An individual animal approach becomes more valuable when the overall expression response is subtle and/or when associating expression data to variable phenotypic responses.

INSTRUMENT(S): Scanning hardware

ORGANISM(S): Rattus norvegicus

SUBMITTER: Keith Goldstein

PROVIDER: E-TOXM-19 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Previously we demonstrated that the mouse liver tumor response to the non-genotoxic carcinogens oxazepam [CAS:604-75-1;CHEBI:7823] and Wyeth-14,643 [CAS:50892-23-4;CHEBI:32509] involved more differences than similarities in changes in early gene expression. In this study we used quantitative real-time PCR and oligonucleotide microarray analysis to identify genes that were up- or downregulated in mouse liver early after treatment with different known carcinogens, including oxazepam [CAS:604-75-1 CHEBI:7823] (125 and 2500 p.p.m.), o-nitrotoluene [CAS:88-72-2;CHEBI:33098] (1250 and 5000 p.p.m.) and methyleugenol [CAS:93-15-2;CHEBI:4918] (75 mg/kg/day), or the non-carcinogens p-nitrotoluene [CAS:99-99-0;CHEBI:33097] (5000 p.p.m.), eugenol [CAS:97-53-0;CHEBI:4917] (75 mg/kg/day) and acetaminophen [CAS:103-90-2;CHEBI:2386] (6000 p.p.m.). Starting at 6 weeks of age, mice were treated with the different compounds for 2 weeks in the diet, at which time the livers were collected. First, expression of 12 genes found previously to be altered in liver after 2 weeks treatment with oxazepam and/or Wyeth-14,643 was examined in livers from the various chemical treatment groups. These gene expression changes were confirmed for the livers from the oxazepam-treated mice in the present study, but were not good early markers for all the carcinogens in this study. In addition, expression of 20 842 genes was assessed by oligonucleotide microarray [n ¼ 4 livers/group, 2 hybridizations/liver (with fluor reversals)] and the results were analyzed using the Rosetta Resolver System and GeneSpring software. The analyses revealed that several cancer-related genes, including Fhit, Wwox, Tsc-22 and Gadd45b, were induced or repressed in unique patterns for specific carcinogens and not altered by the non-carcinogens. The data indicate that even if the tumor response, including molecular alterations, is similar, such as for oxazepam and methyleugenol, early gene expression changes appear to be carcinogen specific and seem to involve apoptosis and cell cyclerelated genes.

Project description:BACKGROUND: In a previous study, we determined the effects of 17-alpha-ethynyl estradiol (EE) [CAS:57-63-6;CHEBI:4903] on gene expression using microarrays that represented approximately 9,000 genes, which was the state of-the-art. Higher content arrays with almost double the number of genes have since become available. In order to better determine whether common sets of gene expression changes can be predictive of estrogenic activity, we have replicated the previous experiment using the more comprehensive microarray. METHODS: Immature 20-day-old Sprague-Dawley rats were exposed to 0.1, 1, and 10 microg EE/kg/day ( subcutaneously [s.c.]), for four days, dosing from postnatal day (PND) 20-23). Changes in a more comprehensive expression level of 15,923 rat annotated genes and expressed sequence tags were evaluated on PND 24. RESULTS: By comparing the response of the treatment groups versus controls using various statistical parameters, we determined that the expression of 1,394 genes showed a significant change with respect to control (p less than or =0.0001), to at least one of the EE dosages. The tissues from animals exposed to 0.1 microg EE/kg/day showed changes in the expression of only 33 genes, whereas when they were exposed to 1 or 10 microg EE/kg/day, the expression of 409 and 548 genes was modified, respectively. A dose-dependent analysis indicated that 592 genes showed a robust and significant response to EE exposure (increased or decreased). Our analysis confirmed the regulation of previously identified estrogen-sensitive genes, and clearly identified novel mediators of estrogen actions, both in the uterus as well as in the ovary. CONCLUSIONS: This compendium of genes represents the largest compilation of estrogen-responsive genes that has ever been identified for the immature uterus and ovary of any species, and can be used to generate testable hypothesis to improve the understanding of the molecular pathways associated with physiological and pathophysiological responses to exposure to chemicals with estrogenic properties.

Dataset Information

Transcription profiling of rat liver pooled vs. individual samplesf rom a single-dose time-course rat study in response to the prototypical toxicants Clofibrate [CAS:637-07-0;CHEBI:3750], Diethylhexyl phthalate DEHP [CAS:117-81-7;CHEBI:17243], and valproic acid VPA [CAS:1069-66-5;CHEBI:9925],

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets