Pharmacogenomics of Human Drug Transporters

Clinical Impacts

Toshihisa Ishikawa, Richard B. Kim, Jörg König

• Publisher: Wiley
• Year: 2013
• Print ISBN: 9780470927946
• eBook ISBN: 9781118353257
• Edition: 1
• Topic: Medicine
• Subtopic: Pharmacology

Sets the foundation for safer, more effective drug therapies

With this book as their guide, readers will discover how to apply our current understanding of the pharmacogenomics of drug transporters to advance their own drug discovery and development efforts. In particular, the book explains how new findings in the field now enable researchers to more accurately predict drug interactions and adverse drug reactions. Moreover, it sets the foundation for the development of drug therapies that are tailored to an individual patient's genetics.

Pharmacogenomics of Human Drug Transporters serves as a comprehensive guide to how transporters regulate the absorption, distribution, and elimination of drugs in the body as well as how an individual's genome affects those processes. The book's eighteen chapters have been authored by a team of leading pioneers in the field. Based on their own laboratory and clinical experience as well as a thorough review of the literature, these authors explore all facets of drug transporter pharmacogenomics, including:

• Individual drug transporters and transporter families and their clinical significance
• Principles of altered drug transport in drug–drug interactions, pharmacotherapy, and personalized medicine
• Emerging new technologies for rapid detection of genetic polymorphisms
• Clinical aspects of genetic polymorphisms in major drug transporter genes
• Future research directions of drug transporter pharmacogenomics and the prospect of individualized medicine

Pharmacogenomics of Human Drug Transporters opens the door to new drug discovery and development breakthroughs leading to safer and more effective customized drug therapies.The book is recommended for pharmaceutical scientists, biochemists, pharmacologists, clinicians, and genetics and genomics researchers.

CHAPTER 1

INTRODUCTION TO PHARMACOGENOMICS OF DRUG TRANSPORTERS

Marianne K. DeGorter

Richard B. Kim

1.1 INTRODUCTION

Understanding the molecular mechanisms and clinical relevance of interindividual variability in drug response remains an important challenge. Pharmacogenomics, the study of genetic variation in the genes that influence drug effect, can provide insight into interindividual variability and a more accurate prediction of drug response than may be obtained by relying solely on a patient's clinical information. The goal of drug transporter pharmacogenomics is to understand the impact of genetic variation on the function of transporters that interact with medications. For many drugs in clinical use, transporters are important determinants of absorption, tissue accumulation, and elimination from the body, and thereby transporters significantly influence drug efficacy and toxicity. Adverse drug reactions can result from toxicity associated with high drug concentrations and lack of efficacy can result from subtherapeutic drug exposure. By understanding the genetic basis for drug transporter activity, it will be possible to enhance a predictive approach to individualization of drug therapy.

The purpose of this book is to highlight the advances in transporter pharmacogenomics that have been made since polymorphisms in drug transporter genes were first described in the late 1990s (Mickley et al., 1998; Hoffmeyer et al., 2000; Kim et al., 2001). As we enter the genomic era of medicine, pharmacogenomics will inform prescribing practices to maximize drug efficacy while minimizing risk for toxicity. Given the importance of transporters to the absorption, distribution, and elimination of many drugs, there is no doubt that transporter pharmacogenomics will make significant contributions to this aim.

1.2 OVERVIEW OF DRUG TRANSPORTERS

Membrane transporters have diverse and important roles in maintaining cellular homeostasis by the uptake and efflux of endogenous compounds to regulate solute and fluid balance, facilitate hormone signaling, and extrude potential toxins. Drug transport proteins are a functional subset of membrane transporters that also interact with drugs and their metabolites. Compounds that are most likely to rely on carrier mechanisms are polar and bulky, and less likely to pass through cell membranes by simple diffusion. Transporter substrates include numerous drugs, their hydroxylated metabolites, and the glutathione-, sulfate-, or glucuronide-conjugated products of Phase II metabolism. Transporters that are expressed in the epithelia of intestine, liver, and kidney are of particular importance for vectorial or directional movement of drugs, resulting in efficient and rapid drug absorption, distribution, metabolism, and elimination. Moreover, expression of drug transporters on the basolateral versus apical domain of polarized epithelial cells in organs such as the intestine and liver may also be critical for a drug to enter the tissue and interact with its target (Ho and Kim, 2005; Giacomini et al., 2010).

Membrane transporters are comprised of multiple transmembrane domains (TMDs) that form a pore in the membrane through which the substrates pass. These domains are joined by alternating intracellular and extracellular loops which, together with TMDs, facilitate substrate recognition, binding, and translocation. The functional mechanism and conformational changes required for transport are not completely understood, and remain an active area of investigation (Kerr et al., 2010). Of particular interest to transporter pharmacogenomics is the ability to predict the functional effect of novel mutations that are discovered in individual genomes.

Drug transporters belong to two major classes, the solute carrier (SLC) superfamily and ATP-binding cassette (ABC) superfamily. In the human genome, there are 350 transporters in the SLC superfamily and 48 ABC transporters; these transporters are divided into subfamilies based on sequence homology (Giacomini et al., 2010). ABC transporters are distinguished by the presence of an intracellular nucleotide-binding domain that catalyzes the hydrolysis of ATP to generate the energy required to transport substrates against their concentration gradient (Schinkel and Jonker, 2003). In contrast, SLC transporters utilize facilitated diffusion, ion coupling, or ion exchange to translocate their substrates. In some cases, transport relies on an ion gradient that is actively maintained by ABC transporters (Hediger et al., 2004).

Transporter function may be influenced by multiple factors, and interindividual variability in transporter function is now recognized as a major source of variability in drug disposition and response. We know that drug transporters can be inhibited by numerous compounds, typically by competition for recognition and binding, resulting in unexpected pharmacokinetics of substrate drugs, and drug–drug interactions. Genetic variants may also affect transporter function, and, in recent years, the discovery of genetic variation in drug transporters has opened up an area of research in transporter pharmacogenomics (Giacomini et al., 2010; Sissung et al., 2010a).

1.3 OVERVIEW OF PHARMACOGENOMICS

The study of inherited differences in drug response dates back to observations made in the 1950s; in the late 1980s, molecular advances provided a mechanistic explanation for these findings (Evans and Relling, 1999; Weinshilboum and Wang, 2006). Many early achievements in pharmacogenetics were in cytochrome P450 (CYP) drug-metabolizing enzyme research and the effect of genetic variation in these enzymes on metabolite concentrations. Pharmacogenomics studies have benefited from having well-defined phenotypes: a pharmacokinetic measure such as the plasma or urine concentration of a drug or its metabolite, or a measure of drug response, such as a change in blood pressure or heart rate. For monogenic traits, this approach has led to new insights into our understanding of the factors underlying drug disposition and response, and provided a solid foundation to study traits that are influenced by multiple genes and other clinical factors. Today, pharmacogenomics encompasses a broad spectrum of genes involved in metabolism as well as transport, and in drug targets and related pathways (Sim and Ingelman-Sundberg, 2011).

Genetic variants include single-nucleotide polymorphisms (SNPs), which are typically present in less than 1% of the population, while more rare variants are considered to be genetic mutations. SNPs in the coding regions of proteins may be classified as synonymous or nonsynonymous, depending on whether the amino acid sequence is altered in the variant allele. SNPs may also come in the form of small insertions or deletions, which result in frameshift of amino acid sequence or premature truncation of the protein, and likely a nonfunctional product (Urban et al., 2006). Duplication or deletion of larger regions of genomic sequence (>50 bp) are classified as copy number or structural variants (Alkan et al., 2011). A classic example of copy-number variation comes from the field of pharmacogenomics: CYP2D6 is commonly duplicated or deleted, resulting in profound differences in the rate of metabolism of its substrate drugs in individuals with these alleles (Zanger et al., 2004). There is a growing appreciation for the importance of structural differences as a source of variation in the human genome, and further study of this variation, as it relates to transporter genes, is expected (Alkan et al., 2011).

Pharmacogenomic information may be used to predict treatment outcomes and choose the best drug and its optimal dose. Pharmacogenomics may also be used to predict a patient's risk for an adverse drug reaction, including drug–drug interactions that may be more severe due to the genetics of the proteins involved. At the time of writing, the US Food and Drug Administration (FDA) listed nearly 80 drugs for which pharmacogenomic biomarkers in over 30 genes were included in some part of the label recommendations. To date, the FDA has focused on drug-metabolizing enzymes and target proteins; however, transporter genes are expected to be added in the future, following the work of the International Transporter Consortium, sponsored by the FDA's Critical Path Initiative (Giacomini et al., 2010).

1.4 PHARMACOGENOMICS OF DRUG TRANSPORTERS

Transporter polymorphisms may increase or reduce an individual's overall exposure to a substrate, depending on the tissue expression and localization of the transporter. For example, reduced function of an uptake transporter on the luminal membrane of the intestine would result in reduced systemic exposure of its substrate, whereas reduced function of an uptake transporter on the basolateral membrane of the liver or kidney may result in increased systemic exposure if the drug in question relies on these organs for its elimination. On the other hand, reduced function of an ABC efflux transporter present on the luminal membrane of the intestine will result in increased plasma concentration of the substrate drug, as less drug is returned to the intestinal lumen by the transporter. In some cases, the precise in vivo contribution of a transporter may be difficult to define, particularly if the transporter is present in multiple tissues, or has overlapping function with transporters of similar expression patterns. The extent of phenotypic variation observed will depend on how much the substrate relies on the single transporter in question, and the extent of genetic variation present in the other transporters, metabolizing enzymes and targets that interact with the drug.

To date, the best studied transporter polymorphisms have been those in the coding regions of transporter genes. Some variants cause reduced trafficking of the transporter to the cell membrane, resulting from incorrect folding or an inability to interact with molecular chaperones, and other variants may affect substrate recognition or binding. Certain amino acid changes, particularly in substrate binding regions, have been shown to alter transport in a substrate-specific fashion, making it difficult to fully predict the effect of a polymorphism on transport of a particular compound without testing that compound directly. Although numerous polymorphisms in transporter genes have been identified, not all polymorphisms appear to affect transporter function. One method to test the function of a SNP is to express its protein product and measure its transport function in vitro. Of the 88 protein-altering variants studied in 11 SLC transporters, 14% had decreased or total loss of functional activity in in vitro assays (Urban et al., 2006). This is likely an underestimation, due to the possibility of substrate-specific differences in effect.

Analysis of large numbers of SNPs in the coding regions of transporters demonstrated that genetic diversity is significantly higher in loop domains compared to TMDs, suggesting that there is selective pressure against amino acid changes in these regions (Leabman et al., 2003). Polymorphisms may also occur in intronic regions, affecting splicing, or in promoter and enhancer regions, affecting RNA expression. Analysis of proximal promoter region variation showed that SLC transporter promoters are more likely to contain variants than ABC transporter promoters, and highly active promoters are more likely to contain variants than less active ones (Hesselson et al., 2009). Genetic diversity in transporter genes also appears to be related to ethnicity. In a study of 680 SNPs identified from samples representing five ethnic populations, only 83 SNPs were present in all the five populations (Leabman et al., 2003). Thus, differences in transporter polymorphism frequency may account for some variability in drug response observed across ethnicities.

The pharmacogenomics of SLC transporters of particular importance to drug transport are described in the following chapters: organic anion transporting polypeptides (OATPs/SLCO; Chapters 6 and 7), organic anion transporters (OATs/SLC22A; Chapter 6), organic cation transporters (OCTs/SLC22A; Chapter 8), organic cation and carnitine transporters (OCTN/SLC22A; Chapter 8), multidrug and toxin extrusion transporters (MATEs/SLC47; Chapter 9), peptide transporters (PEPTs/SLC15A; Chapter 10), and nucleoside transporters (NTs/SLC28 and SLC29; Chapter 11). The pharmacogenomics of ABC transporters important to drug transport are covered in subsequent chapters: P-glycoprotein (ABCB1; Chapter 12), bile salt export pump (BSEP/ABCB11; Chapter 13), breast cancer resistance protein (BCRP/ABCG2; Chapter 14), multidrug resistance-associated proteins MRP2 (ABCC2; Chapter 15), MRP3 (ABCC3; Chapter 15), MRP4 (ABCC4; Chapter 16), and MRP8 (ABCC11; Chapter 17). Significant advances in transporter biology and pharmacogenomics of transporters have been made through the contributions of individual labs as well as large multi-investigator projects such as the Pharmacogenomics of Membrane Transporters project, funded by the National Institutes of Health as part of the Pharmacogenomics Research Network, and described in Chapter 4 (Kroetz et al., 2010).

1.5 TECHNIQUES TO STUDY DRUG TRANSPORTER FUNCTION

The application of advances in molecular biology techniques to the study of transporters over the last 20 years has made a significant contribution to our understanding of transporter biology. In vitro, transporter activity is often characterized in primary cells and in expression...

Table of contents

• COVER
• TITLE PAGE
• COPYRIGHT
• PREFACE
• CONTRIBUTORS
• CHAPTER 1: INTRODUCTION TO PHARMACOGENOMICS OF DRUG TRANSPORTERS
• CHAPTER 2: ADME PHARMACOGENOMICS IN DRUG DEVELOPMENT
• CHAPTER 3: REGULATORY PERSPECTIVE ON PHARMACOGENOMICS OF DRUG-METABOLIZING ENZYMES AND TRANSPORTERS
• CHAPTER 4: THE PHARMACOGENOMICS OF MEMBRANE TRANSPORTERS PROJECT
• CHAPTER 5: EMERGING NEW TECHNOLOGY OF SNP TYPING
• CHAPTER 6: OATP1A2, OAT1, AND OAT3
• CHAPTER 7: OATP1B1, OATP1B3, AND OATP2B1
• CHAPTER 8: OCT (SLC22A) AND OCTN FAMILY
• CHAPTER 9: MATE (SLC47) FAMILY
• CHAPTER 10: PEPT (SLC15A) FAMILY
• CHAPTER 11: NUCLEOSIDE TRANSPORTERS (SLC28 AND SLC29) FAMILY
• CHAPTER 12: P-GLYCOPROTEIN (MDR1/ABCB1)
• CHAPTER 13: BSEP (ABCB11)
• CHAPTER 14: BCRP (ABCG2)
• CHAPTER 15: MRP2 (ABCC2) AND MRP3 (ABCC3)
• CHAPTER 16: MRP4 (ABCC4)
• CHAPTER 17: MRP8 (ABCC11)
• CHAPTER 18: FUTURE PERSPECTIVES
• INDEX