Comparative Analysis of Gene Regulation by theTranscription Factor PPARa between Mouse and HumanMaryam Rakhshandehroo1,2, Guido Hooiveld1,2, Michael Mu¨ller1,2, Sander Kersten1,2*1 Nutrigenomics Consortium, Top Institute (TI) Food and Nutrition, Wageningen, the Netherlands, 2 Nutrition, Metabolism and Genomics group, Division of HumanNutrition, Wageningen University, Wageningen, the NetherlandsAbstractBackground:Studies in mice have shown that PPARa is an important regulator of hepatic lipid metabolism and the acutephase response. However, little information is available on the role of PPARa in human liver. Here we set out to compare thefunction of PPARa in mouse and human hepatocytes via analysis of target gene regulation.Methodology/Principal Findings:Primary hepatocytes from 6 human and 6 mouse donors were treated with PPAR aagonist Wy14643 and gene expression profiling was performed using Affymetrix GeneChips followed by a systems biologyanalysis. Baseline PPARa expression was similar in human and mouse hepatocytes. Depending on species and time ofexposure, Wy14643 significantly induced the expression of 362–672 genes. Surprisingly minor overlap was observedbetween the Wy14643-regulated genes from mouse and human, although more substantial overlap was observed at thepathway level. Xenobiotics metabolism and apolipoprotein synthesis were specifically regulated by PPARa in humanhepatocytes, whereas glycolysis-gluconeogenesis was regulated specifically in mouse hepatocytes. Most of the genescommonly regulated in mouse and human were involved in lipid metabolism and many represented known PPARa targets,including CPT1A, HMGCS2, FABP1, ACSL1, and ADFP. Several genes were identified that were specifically induced by PPARain human (MBL2, ALAS1, CYP1A1, TSKU) or mouse (Fbp2, lgals4, Cd36, Ucp2, Pxmp4). Furthermore, several putative novelPPARa targets were identified that were commonly regulated in both species, including CREB3L3, KLF10, KLF11 andMAP3K8.Conclusions/Significance:Our results suggest that PPARa activation has a major impact on gene regulation in humanhepatocytes. Importantly, the role of PPARa as master regulator of hepatic lipid metabolism is generally well-conservedbetween mouse and human. Overall, however, PPARa regulates a mostly divergent set of genes in mouse and humanhepatocytes.Citation: Rakhshandehroo M, Hooiveld G, Mu¨ller M, Kersten S (2009) Comparative Analysis of Gene Regulation by the Transcription Factor PPARa betweenMouse and Human. PLoS ONE 4(8): e6796. doi:10.1371/journal.pone.0006796Editor: Vincent Laudet, Ecole Normale Supe´rieure de Lyon, FranceReceived April 14, 2009; Accepted July 15, 2009; Published August 27, 2009Copyright: ß 2009 Rakhshandehroo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permitsunrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Funding: The Project is funded by Top Institute Food and Nutrition (TIFN). The funders had no role in study design, data collection and analysis, decision topublish, or preparation of the manuscript.Competing Interests: The authors have declared that no competing interests exist.* E-mail: [email protected] liver plays a major role in the coordination of lipidmetabolism. It actively metabolizes fatty acids as fuel and isresponsible for triglyceride export via synthesis of very low densitylipoproteins. An imbalance between these pathways may lead totriglyceride accumulation and thus hepatic steatosis. Studies inmice have indicated that many aspects of hepatic lipid metabolismare under transcriptional control of the Peroxisome ProliferatorActivated Receptor a (PPARa), a transcription factor belonging tothe nuclear receptor superfamily. It is well established thatimpaired PPARa function is associated with hepatic lipidaccumulation [1–3]. Consequently, synthetic agonists for PPAR aare explored for the treatment of non-alcoholic fatty liver disease[4].Besides PPARa, two other PPARs isotypes are known to exist:PPARb/d and PPARc. The PPARs share a common mode ofaction that involves heterodimerization with the nuclear receptorRXR, followed by binding to PPAR response elements (PPREs) intarget genes [5]. Activation of transcription is induced by bindingof ligand, leading to recruitment of specific coactivator proteinsand dissociation of corepressors. Expression of PPARa andPPARb/d is relatively ubiquitous, whereas PPARc is mainlyexpressed in adipose tissue, macrophages and colon [6,7].PPARa can be ligand-activated by endogenous agonists, whichinclude fatty acids and fatty acid derivatives such as eicosanoidsand oxidized fatty acids, as well as by various synthetic compounds[5,8,9]. The latter group induces proliferation of peroxisomes inrodents and are thus referred to as peroxisome proliferators.Peroxisome proliferators encompass a diverse group of chemicalsranging from herbicides and insecticides to industrial plasticisers,halogenated hydrocarbons, and fibrate drugs [10,11].Most of the research concerning PPARa has focused on its rolein the liver. A wealth of studies performed almost exclusively inmice has revealed that PPARa serves as a key regulator of hepaticfatty acid catabolism (reviewed in [12]). Using PPARa null mice, ithas been shown that PPARa is especially important for theadaptive response to fasting by stimulating hepatic fatty acidPLoS ONE | www.plosone.org 1 August 2009 | Volume 4 | Issue 8 | e6796oxidation and ketogenesis [2,13,14]. In addition, PPARa has beenshown to govern liver inflammation, lipoprotein metabolism,glucose metabolism, and hepatocyte proliferation [12,15,16]. Thelatter response is known to be specific for rodents [17]. Thespecies-specific effects of PPARa agonists on hepatocyte prolifer-ation and associated hepatocarcinogenesis were ascribed to anumber of factors including properties intrinsic to the PPARaprotein, conservation and functionality of PPREs in the promoterof target genes, and presence or absence of co-regulatorsdepending on the cellular environment [18].However, apart from the differential effect on hepatocyte andperoxisome proliferation, it is not very clear whether PPARa has asimilar role in mice and humans and to what extent target genesare shared between the two species. Based on the lower expressionlevel of PPARa in human liver compared to mouse liver [19], thefunctionality of PPARa in human liver
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