Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines

OPEN The Pharmacogenomics Journal (2017) 17, 137–145 www.nature.com/tpj ORIGINAL ARTICLE Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines A Chhibber1,16, CE French2,16, SW Yee1,16, ER Gamazon3,4,16, E Theusch5, X Qin6, A Webb7, AC Papp8, A Wang5, CQ Simmons3, A Konkashbaev3, AS Chaudhry9, K Mitchel5, D Stryke10, TE Ferrin10, ST Weiss11, DL Kroetz1, W Sadee8,12, DA Nickerson13, RM Krauss5, AL George14, EG Schuetz9, MW Medina5, NJ Cox3, SE Scherer6, KM Giacomini1 and SE Brenner2,15 Variation in the expression level and activity of genes involved in drug disposition and action (‘pharmacogenes’) can affect drug response and toxicity, especially when in tissues of pharmacological importance. Previous studies have relied primarily on microarrays to understand gene expression differences, or have focused on a single tissue or small number of samples. The goal of this study was to use RNA-sequencing (RNA-seq) to determine the expression levels and alternative splicing of 389 Pharmacogenomics Research Network pharmacogenes across four tissues (liver, kidney, heart and adipose) and lymphoblastoid cell lines, which are used widely in pharmacogenomics studies. Analysis of RNA-seq data from 139 different individuals across the 5 tissues (20–45 individuals per tissue type) revealed substantial variation in both expression levels and splicing across samples and tissue types. Comparison with GTEx data yielded a consistent picture. This in-depth exploration also revealed 183 splicing events in pharmacogenes that were previously not annotated. Overall, this study serves as a rich resource for the research community to inform biomarker and drug discovery and use. The Pharmacogenomics Journal (2017) 17, 137–145; doi:10.1038/tpj.2015.93; published online 9 February 2016 INTRODUCTION Variation in the expression levels and splicing of drug metabolizing enzymes, transporters and targets, such as receptors and ion channels, has been associated with inter-individual differences in optimal drug dose, drug efficacy and adverse drug events.1,2 Thus, a comprehensive study of variation in the transcriptome profiles of pharmacologically relevant tissues promises to yield important insights into the molecular basis of variation in drug response. Technological advances in quantifying the transcriptome and the rapid development of high-throughput screening methodologies have led to the identification and characterization of many biomarkers of drug response.3,4 These innovations have transformed the way we design and analyze pharmacogenomics studies and are increasingly informing development of approaches to clinical practice. Transcriptome sequencing, or RNA-sequencing (RNA-seq), is facilitating analyses at the transcript level with an unprecedented resolution. As the technology has developed, longer reads and higher throughput have allowed for detailed evaluation of whole transcriptomes across many samples.5 Analytical approaches have emerged, including Cufflinks6 and DESeq7 for gene expression analysis and DEXSeq,8 MISO9 and JuncBASE10 for splicing analysis. However, the use of next-generation sequencing technology for pharmacogenomics research has been limited.4,11 Although community-wide efforts such as the Genotype Tissue Expression Project12 are facilitating studies of expression quantitative trait loci, there has not been an application of RNA-seq to large sample sets across diverse human tissues with a focus on genes involved in drug disposition and tissues of greater pharmacological relevance and action. In pharmacogenomics, polymorphisms that affect expression levels or result in alternative splicing of drug metabolizing enzymes are known to have large effects on drug disposition and response. For example, UGT1A1*28 (rs8175347), with seven thymine–adenine13 repeats in the promoter region, leads to reduced transcription rates of this enzyme and profound toxicity in patients receiving the topoisomerase inhibitor, irinotecan.14,15 Likewise, alternative splicing of CYP2D6 occurs frequently in human populations and is responsible for reduced activity of the enzyme.16 Given these large and clinically important effects in 1 Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; 2Departments of Molecular and Cell Biology, University of California, Berkeley, CA, USA; 3Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA; 4Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; 5Children's Hospital Oakland Research Institute, Oakland, CA, USA; 6Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; 7Department of Biomedical Informatics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA; 8Center for Pharmacogenomics; College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA; 9Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA; 10Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA; 11Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; 12Departments of Pharmacology, Psychiatry, and Human Genetics/Internal Medicine, College of Medicine; Colleges of Pharmacy and Environmental Health Sciences, The Ohio State University, Columbus, OH, USA; 13Department of Genome Sciences, University of Washington, Seattle, WA, USA; 14Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA and 15Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. Correspondence: Dr S Scherer, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA or Dr K Giacomini, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA or Dr SE Brenner, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA. E-mail: or or 16 Co-first authors. Received 8 May 2015; revised 6 November 2015; accepted 13 November 2015; published online 9 February 2016 Transcriptome profiles of 389 pharmacogenes A Chhibber et al 138 drug-metabolizing enzymes, a systematic study of the transcriptome with a focus on pharmacogenes is clearly needed. Although several research groups have performed transcriptome profiling and alternative splicing event analyses in human cell lines and tissues,17–19 these studies are limited to single tissue types or use pooled samples. Thus, information about inter-individual variation in gene expression and splicing from a given tissue type or inter-tissue variation is limited, despite the value of such studies in identifying biomarkers for differential drug response or toxicity. Given these limitations, the National Institutes of Healthsupport (...truncated)