The Steroltalk microarray: a systemic approach to studies of cholesterol
homeostasis and drug metabolism
T. Režen1, P. Juvan1, J. Acimovic1, A. Belic2, J.A. Contreras1, U.A Meyer3, K.
Monostory4, H. Delacroix5, J.M. Pascussi6, I. Bjorkhem7, D. Rozman1
1
Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of
Medicine, 2Faculty of Electrical Engineering, University of Ljubljana, Slovenia, 3Biozentrum,
University of Basel, Switzerland, 4Chemical Research Center, Hungarian Academy of
Sciences, Budapest, Hungary, 5CNRS, Gif-sur-Ivette, France, 6INSERM UMR-U632,
University of Montpellier, France; 6Karolinska University Hospital at Huddinge, Stockholm,
Sweden.
Cholesterol homeostasis and xenobiotic metabolism are complex biological processes
which are difficult to study with traditional methods. Deciphering complex regulation
and response of these two processes to different factors is crucial for understanding of
the disease development (Rezen T. et al., Drug Metab Rev. 39:389, 2007). We have
developed a series of low density Steroltalk cDNA microarrays as original tools for
systemic studies of the crosstalk between cholesterol homeostasis and xenobiotic
metabolism. The arrays include genes involved in cholesterol synthesis and
metabolism, drug metabolism, nuclear receptors, transporters, regulators and circadian
regulators. In the mouse liver, we observed down-regulation of cholesterol
biosynthesis by high-cholesterol diet. Drug metabolism was up-regulated by
phenobarbital treatment and high-cholesterol diet. The performance of the Sterolgene
v0 was compared to the two commercial high density microarray platforms: the
Agilent cDNA (G4104A) and the Affymetrix MOE430A GeneChip. We show that the
Sterolgene performance is comparable in terms of cholesterol homeostasis and drug
metabolism (Rezen T. et al., BMC Genomics 9:76, 2008). The human primary
hepatocytes have been treated by rifampicin, rosuvastatin and atorvastatin and
changes in expression have been monitored after 12, 24 and 48h. For rifampicin,
transcriptome analyses shows that the primary response to the drug happened before
12h while later the secondary effects have been observed. Some genes from
cholesterol biosynthesis were up-regulated at 12h, but not at 24 h. At 48h the
induction of drug metabolism genes was still increasing. The response time of the
hepatocytes was different for the two statins. Gene expression peaked at 24h for
rosuvastatin and at 48h for atorvastatin. Most genes regulated via SREBFs as and
genes involved in the degradation drugs (Cytochromes P450) were up-regulated by
the two statins To study the system, a mathematical model of cholesterol biosynthesis
has been constructed and its properties studied through simulation. Bayesian inference
has been employed to identify gene-to-gene interactions from both microarray
measurements and the simulated data. Simulations showed that a large number of
perturbations of the system are critical for identification of genetic interactions, and
that differences in gene expression between human individuals pose a serious
problem. Bayesian networks show that expression of cholesterogenic genes can be
predicted from expression of 4 key genes, one of them being SREBF2 (Juvan et al.,
ACSi, in press).
Acknowledgements: This abstract and work it concerns was generated in the context
of the STEROLTALK project, funded by the European Community as contract No.
LSHG-CT-2005-512096.