Inferring statin-induced gene regulatory relationships in primary human hepatocytes

MOTIVATION Statins are the most widely used cholesterol-lowering drugs. The primary target of statins is HMG-CoA reductase, a key enzyme in cholesterol synthesis. However, statins elicit pleitropic responses including beneficial as well as adverse effects in the liver or other organs. Today, the regulatory mechanisms that cause these pleiotropic effects are not sufficiently understood. RESULTS In this work, genome-wide RNA expression changes in primary human hepatocytes of six individuals were measured at up to six time points upon atorvastatin treatment. A computational analysis workflow was applied to reconstruct regulatory mechanisms based on these drug-response data and available knowledge about transcription factor (TF) binding specificities and protein-drug interactions. Several previously unknown TFs were predicted to be involved in atorvastatin-responsive gene expression. The novel relationships of nuclear receptors NR2C2 and PPARA on CYP3A4 were successfully validated in wet-lab experiments. AVAILABILITY Microarray data are available at the Gene Expression Omnibus (GEO) database at www.ncbi.nlm.nih.gov/geo/, under accession number GSE29868. CONTACT andreas.zell@uni-tuebingen.de; adrian.schroeder@uni-tuebingen.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

[1]  S. Falcon,et al.  Hypergeometric Testing Used for Gene Set Enrichment Analysis , 2008 .

[2]  Peter Van Loo,et al.  Computational methods for the detection of cis-regulatory modules , 2009, Briefings Bioinform..

[3]  P. Neuvonen,et al.  Drug interactions with lipid‐lowering drugs: Mechanisms and clinical relevance , 2006, Clinical pharmacology and therapeutics.

[4]  Andreas Zell,et al.  BowTieBuilder: modeling signal transduction pathways , 2009, BMC Systems Biology.

[5]  J Ludbrook,et al.  MULTIPLE COMPARISON PROCEDURES UPDATED , 1998, Clinical and experimental pharmacology & physiology.

[6]  J. Farmer Pleiotropic effects of statins , 2000, Current atherosclerosis reports.

[7]  J. Egido,et al.  3-Hydroxy-3-methylglutaryl coenzyme A reductase inhibitors increase the binding activity and nuclear level of Oct-1 in mononuclear cells. , 2002, European journal of pharmacology.

[8]  I. Young,et al.  Statin safety and chronic liver disease , 2008, International journal of clinical practice.

[9]  Oliver Burk,et al.  Nuclear Receptor Response Elements Mediate Induction of Intestinal MDR1 by Rifampin* , 2001, The Journal of Biological Chemistry.

[10]  Andreas Zell,et al.  EDISA: extracting biclusters from multiple time-series of gene expression profiles , 2007, BMC Bioinformatics.

[11]  M. Traber,et al.  Vitamin E, nuclear receptors and xenobiotic metabolism. , 2004, Archives of biochemistry and biophysics.

[12]  S. Strom,et al.  Regulation of CYP3A4 and CYP2B6 expression by liver X receptor agonists. , 2007, Biochemical pharmacology.

[13]  Andreas Zell,et al.  Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors , 2010, PloS one.

[14]  Andreas Zell,et al.  ModuleMaster: A new tool to decipher transcriptional regulatory networks , 2010, Biosyst..

[15]  Ute Hofmann,et al.  Profiling Induction of Cytochrome P450 Enzyme Activity by Statins Using a New Liquid Chromatography-Tandem Mass Spectrometry Cocktail Assay in Human Hepatocytes , 2010, Drug Metabolism and Disposition.

[16]  Michiaki Yamashita,et al.  The muscle-specific ubiquitin ligase atrogin-1/MAFbx mediates statin-induced muscle toxicity. , 2007, The Journal of clinical investigation.

[17]  K. Zou,et al.  Correlation and simple linear regression. , 2003, Radiology.

[18]  A. Medvedev,et al.  Regulation of Peroxisome Proliferator-activated Receptor α-Induced Transactivation by the Nuclear Orphan Receptor TAK1/TR4* , 1998, The Journal of Biological Chemistry.

[19]  Damian Szklarczyk,et al.  STITCH 2: an interaction network database for small molecules and proteins , 2009, Nucleic Acids Res..

[20]  Robert Gentleman,et al.  Bioconductor Case Studies , 2008 .

[21]  E. Wingender,et al.  MATCH: A tool for searching transcription factor binding sites in DNA sequences. , 2003, Nucleic acids research.

[22]  A. Sandelin,et al.  Applied bioinformatics for the identification of regulatory elements , 2004, Nature Reviews Genetics.

[23]  Bart De Moor,et al.  A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes , 2004, Bioinform..

[24]  P. Kollman,et al.  Lactonization is the critical first step in the disposition of the 3-hydroxy-3-methylglutaryl-CoA reductase inhibitor atorvastatin. , 2000, Drug metabolism and disposition: the biological fate of chemicals.

[25]  Seppo Ylä-Herttuala,et al.  Simvastatin has an anti-inflammatory effect on macrophages via upregulation of an atheroprotective transcription factor, Kruppel-like factor 2. , 2008, Cardiovascular research.

[26]  I. Filippi,et al.  Regulation of HMG‐CoA reductase expression by hypoxia , 2008, Journal of cellular biochemistry.

[27]  C. Brey,et al.  Krüppel-like family of transcription factors: an emerging new frontier in fat biology , 2009, International journal of biological sciences.

[28]  Rosario Dominguez Crespo Hirata,et al.  The expression of efflux and uptake transporters are regulated by statins in Caco-2 and HepG2 cells , 2009, Acta Pharmacologica Sinica.

[29]  C. Vock,et al.  Transcriptional Regulation of HMG-CoA Synthase and HMG-CoA Reductase Genes by Human ACBP , 2008, Cellular Physiology and Biochemistry.

[30]  Peter Oelkers,et al.  Bile acid transporters , 1995, Current opinion in lipidology.

[31]  J. Pascussi,et al.  The tangle of nuclear receptors that controls xenobiotic metabolism and transport: crosstalk and consequences. , 2008, Annual review of pharmacology and toxicology.

[32]  Jung-Hsin Lin,et al.  Statins increase p21 through inhibition of histone deacetylase activity and release of promoter-associated HDAC1/2. , 2008, Cancer research.

[33]  T. Heinemeyer,et al.  TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation , 1997, Nucleic Acids Res..

[34]  Gerd Schmitz,et al.  HIF-1beta determines ABCA1 expression under hypoxia in human macrophages. , 2010, The international journal of biochemistry & cell biology.

[35]  Christian von Mering,et al.  STRING 8—a global view on proteins and their functional interactions in 630 organisms , 2008, Nucleic Acids Res..