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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 01, 2014 |
| Title |
Toxicogenomics in the 3T3-L1 cell line, a new approach for screening of obesogenic compounds |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
The obesogen hypothesis states that exposure to environmental compounds early in life or throughout lifetime might have an influence on obesity development. In this paper a new approach for obesogen screening is proposed, namely the use of transcriptomics in the 3T3-L1 pre-adipocyte cell line. Based on the data from a previous study of our group using a lipid accumulation based adipocyte differentiation assay, several humanly relevant obesogenic compounds were selected: reference obesogens [Rosiglitazone (ROSI), Tributyltin (TBT)], test obesogens [Butylbenzyl phthalate (BBP), butylparaben (BP), propylparaben (PP), Bisphenol A (BPA)] and non-obesogens [Ethylene Brassylate (EB), Bis (2-ethylhexyl)phthalate (DEHP)].
In this paper, the high stability and reproducibility of the 3T3-L1 gene transcription patterns over different experiments and cell batches was shown. Obesogens and non-obesogen gene transcription profiles were clearly distinguished using hierarchical clustering. Furthermore, a gradual distinction corresponding to differences in induction of lipid accumulation could be made between test and reference obesogens based on transcription patterns, indicating the potential use of this strategy for classification of obesogens. Marker genes that are able to distinguish between non, test and reference obesogens were identified. Well known genes involved in adipocyte differentiation, as well as genes with unknown functions were selected, implying a potential adipocyte related function of the latter. Cell physiological lipid accumulation was well predicted based on transcription levels of the marker genes, indicating the biological relevance of omics data.
In conclusion, this study shows the high relevance and reproducibility of this 3T3-L1 based in vitro toxicogenomics tool for classification of obesogens and biomarker discovery.
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| Overall design |
The hybridization design was a reference design (reference sample was a mixture of equal aliquots from control and exposed samples), recommended for class discovery purposes (Knapen et al. 2009). The reference sample was labeled with Cy5, and the exposed samples with Cy3. Three biological replicates were measured for every condition.
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| Contributor(s) |
Pereira-Fernandes A, Vanparys C, Hectors TL, Vergauwen L, Knapen D, Jorens P, Blust R |
| Citation(s) |
24848799 |
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| Submission date |
Dec 04, 2013 |
| Last update date |
Nov 01, 2017 |
| Contact name |
Anna Pereira-Fernandes |
| E-mail(s) |
Anna.Pereira-Fernandes@ua.ac.be
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| Organization name |
University of Antwerp
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| Department |
Biology
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| Lab |
SPHERE
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| Street address |
Groenenborgerlaan 171
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| City |
Antwerp |
| ZIP/Postal code |
2020 |
| Country |
Belgium |
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| Platforms (1) |
| GPL11202 |
Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 (Probe Name version) |
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| Samples (30)
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| Relations |
| BioProject |
PRJNA230649 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE53004_RAW.tar |
185.1 Mb |
(http)(custom) |
TAR (of GPR) |
| GSE53004_genes.BBPvsDMSO.txt.gz |
297.1 Kb |
(ftp)(http) |
TXT |
| GSE53004_genes.BPAvsDMSO.txt.gz |
305.6 Kb |
(ftp)(http) |
TXT |
| GSE53004_genes.BPvsDMSO.txt.gz |
306.0 Kb |
(ftp)(http) |
TXT |
| GSE53004_genes.DEHPvsDMSO.txt.gz |
278.8 Kb |
(ftp)(http) |
TXT |
| GSE53004_genes.EBvsDMSO.txt.gz |
283.0 Kb |
(ftp)(http) |
TXT |
| GSE53004_genes.MDIvsDMSO.txt.gz |
309.5 Kb |
(ftp)(http) |
TXT |
| GSE53004_genes.PPvsDMSO.txt.gz |
303.6 Kb |
(ftp)(http) |
TXT |
| GSE53004_genes.ROSIvsDMSO.txt.gz |
308.2 Kb |
(ftp)(http) |
TXT |
| GSE53004_genes.TBTvsDMSO.txt.gz |
306.5 Kb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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