title: Genome-wide discovery of drug-dependent human liver regulatory elements.
abstract: Inter-individual variation in gene regulatory elements is hypothesized to play a causative role in adverse drug reactions and reduced drug activity. However, relatively little is known about the location and function of drug-dependent elements. To uncover drug-associated elements in a genome-wide manner, we performed RNA-seq and ChIP-seq using antibodies against the pregnane X receptor (PXR) and three active regulatory marks (p300, H3K4me1, H3K27ac) on primary human hepatocytes treated with rifampin or vehicle control. Rifampin and PXR were chosen since they are part of the CYP3A4 pathway, which is known to account for the metabolism of more than 50% of all prescribed drugs. We selected 227 proximal promoters for genes with rifampin-dependent expression or nearby PXR/p300 occupancy sites and assayed their ability to induce luciferase in rifampin-treated HepG2 cells, finding only 10 (4.4%) that exhibited drug-dependent activity. As this result suggested a role for distal enhancer modules, we searched more broadly to identify 1,297 genomic regions bearing a conditional PXR occupancy as well as all three active regulatory marks. These regions are enriched near genes that function in the metabolism of xenobiotics, specifically members of the cytochrome P450 family. We performed enhancer assays in rifampin-treated HepG2 cells for 42 of these sequences as well as 7 sequences that overlap linkage-disequilibrium blocks defined by lead SNPs from pharmacogenomic GWAS studies, revealing 15/42 and 4/7 to be functional enhancers, respectively. A common African haplotype in one of these enhancers in the GSTA locus was found to exhibit potential rifampin hypersensitivity. Combined, our results further suggest that enhancers are the predominant targets of rifampin-induced PXR activation, provide a genome-wide catalog of PXR targets and serve as a model for the identification of drug-responsive regulatory elements.
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America.
authors.forename: Robin P
authors.initials: RP
authors.lastname: Smith
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America.
authors.forename: Walter L
authors.initials: WL
authors.lastname: Eckalbar
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America.
authors.forename: Kari M
authors.initials: KM
authors.lastname: Morrissey
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America.
authors.forename: Marcelo R
authors.initials: MR
authors.lastname: Luizon
authors.affiliation: Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Hoffmann
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America.
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Sun
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America.
authors.forename: Stacy L
authors.initials: SL
authors.lastname: Jones
authors.affiliation: SwitchGear Genomics, Menlo Park, California, United States of America.
authors.forename: Shelley
authors.initials: S
authors.lastname: Force Aldred
authors.affiliation: Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America.
authors.forename: Anuradha
authors.initials: A
authors.lastname: Ramamoorthy
authors.affiliation: Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America.
authors.forename: Zeruesenay
authors.initials: Z
authors.lastname: Desta
authors.affiliation: Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America.
authors.forename: Yunlong
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America.
authors.forename: Todd C
authors.initials: TC
authors.lastname: Skaar
authors.affiliation: SwitchGear Genomics, Menlo Park, California, United States of America.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Trinklein
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America.
authors.forename: Kathleen M
authors.initials: KM
authors.lastname: Giacomini
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America.
authors.forename: Nadav
authors.initials: N
authors.lastname: Ahituv
mesh_terms: D002478:Cells, Cultured; D051544:Cytochrome P-450 CYP3A / Q000235:genetics; D005786:Gene Expression Regulation / Q000187:drug effects*; D015894:Genome, Human; D056945:Hep G2 Cells / Q000187:drug effects; D022781:Hepatocytes / Q000187:drug effects / Q000502:physiology; D006657:Histones / Q000378:metabolism; D006801:Humans; D008099:Liver / Q000187:drug effects* / Q000502:physiology*; D020641:Polymorphism, Single Nucleotide; D000077297:Pregnane X Receptor; D011401:Promoter Regions, Genetic; D011987:Receptors, Steroid / Q000235:genetics* / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D015203:Reproducibility of Results; D012293:Rifampin / Q000494:pharmacology; D050880:p300-CBP Transcription Factors / Q000378:metabolism; D000099224:p300-CBP-Associated Factor
chemical_list: D051544:Cytochrome P-450 CYP3A; D006657:Histones; D000077297:Pregnane X Receptor; D011987:Receptors, Steroid; D012293:Rifampin; D050880:p300-CBP Transcription Factors; D000099224:p300-CBP-Associated Factor; C510163:CYP3A4 protein, human