The use of single-nucleotide polymorphism maps in pharmacogenomics

Single-nucleotide polymorphisms (SNPs), common variations among the DNA of individuals, are being uncovered and assembled into large SNP databases that promise to enable the dissection of the genetic basis of disease and drug response (i.e., pharmacogenomics). Although great strides have been made in understanding the diversity of the human genome, such as the frequency, distribution, and type of genetic variation that exists, the feasibility of applying this information to uncover useful pharmacogenomic markers is uncertain. The health care industry is clamoring for access to SNP databases for use in research in the hope of revolutionizing the drug development process. As the reality of using SNPs to uncover drug response markers is rarely addressed, this review discusses practical issues, such as patient sample size, SNP density and genome coverage, and data interpretation, that will be important for determining the applicability of pharmacogenomic information to medical practice.     

Pharmacogenomics: catechol O-methyltransferase to thiopurine S-methyltransferase

1. Pharmacogenomics is the study of the role of inheritance in variation in the drug response phenotype-a phenotype that can vary from adverse drug reactions at one end of the spectrum to lack of therapeutic efficacy at the other. 2. The thiopurine S-methyltransferase (TPMT) genetic polymorphism represents one of the best characterized and most clinically relevant examples of pharmacogenomics. This polymorphism has also served as a valuable "model system" for studies of the ways in which variation in DNA sequence might influence function. 3. The discovery and characterization of the TPMT polymorphism grew directly out of pharmacogenomic studies of catechol O-methyltransferase (COMT), an enzyme discovered by Julius (Julie) Axelrod and his coworkers. 4. This review will outline the process by which common, functionally significant genetic polymorphisms for both COMT and TPMT were discovered and will use these two methyltransferase enzymes to illustrate general principles of pharmacogenomic research-both basic mechanistic and clinical translational research-principles that have been applied to a series of genes encoding methyltransferase enzymes.     

Ethical and legal implications of pharmacogenomics

Pharmacogenomics is the application of genomics technology to the discovery and development of drugs. A greater understanding of the way in which individuals with a particular genotype respond to a drug allows manufacturers to identify population subgroups that will benefit most from a particular drug. The increasing emphasis on pharmacogenomics is likely to raise ethical and legal questions regarding, among other things, the design of research studies, the construction of clinical trials and the pricing of drugs.     

药物基因组学——个性化药物的开发

药物基因组学是研究药物反应的遗传机制及药物反应的个体差异性。本文详细讨论了药物基因组学的发展历史,种族,个体的遗传差异性对药物反应的影响;介绍了当前从事药物基因组学开发研究的公司情况及医药管理机构关于药物基因组学的指导性文件;本文也论述了遗传多态性及疾病诊断和疾病相关基因鉴定的最新研究进展 。     

Pharmacogenomics of Drug Metabolizing Enzymes and Transporters:Relevance to Precision Medicine

The interindividual genetic variations in drug metabolizing enzymes and transporters influence the efficacy and toxicity of numerous drugs. As a fundamental element in precision med-icine, pharmacogenomics, the study of responses of individuals to medication based on their genomic information, enables the evaluation of some specific genetic variants responsible for an individual’s particular drug response. In this article, we review the contributions of genetic polymorphisms to major individual variations in drug pharmacotherapy, focusing specifically on the pharmacoge-nomics of phase-I drug metabolizing enzymes and transporters. Substantial frequency differences in key variants of drug metabolizing enzymes and transporters, as well as their possible functional consequences, have also been discussed across geographic regions. The current effort illustrates the common presence of variability in drug responses among individuals and across all geographic regions. This information will aid health-care professionals in prescribing the most appropriate treatment aimed at achieving the best possible beneficial outcomes while avoiding unwanted effects for a particular patient.     

Pharmacogenetics and pharmacogenomics in oncology therapeutic antibody development

Pharmacogenetics and pharmacogenomics are keys to the success of personalized medicine, prescribing drugs based on a patient's individual genetic and biological profile. In this review, we will focus on the application of pharmacogenetics and pharmacogenomics in developing monoclonal antibody (MAb) therapeutics in oncology. The significance of pharmacogenomics in MAb therapeutics is highlighted by the association between polymorphisms in Fc receptors and clinical response to anti-CD20 MAb rituximab (Rituxan) or anti-ganglioside GD2 MAb 3F8, as well as the potential link between polymorphisms in HER2 and cardiac toxicity in patients treated with the anti-HER2 MAb trastuzumab (Herceptin). The dependence on gene copy number or expression levels of HER2 and epidermal growth factor receptor (EGFR) for therapeutic efficacy of trastuzumab and cetuximab (Erbitux), respectively, supports the importance of selecting suitable patient populations based on their pharmacogenetic profile. In addition, a better understanding of target mutation status and biological consequences will benefit MAAb development and may guide clinical development and use of these innovative therapeutics. The application of pharmacogenetics and pharmacogenomics in developing MAb therapeutics will be largely dependent on the discovery of novel surrogate biomarkers and identification of disease- and therapeutics-relevant polymorphisms. Challenges and opportunities in biomarker discovery and validation, and in implementing clinical pharmacogenetics and pharmacogenomics in oncology MAb development and clinical practice will also be discussed.     

Advances in pharmacogenomic research and development

Technological achievements in the last 5 to 10 yr and their application to sequencing and polymorphism discovery in the human genome have fostered a renewed interest in the genetic basis of drug response. Consequently, the field of pharmacogenetics/pharmacogenomics has been gaining momentum, fueled not only on technology but also on results of empirical studies of the human genome and on genetic epidemiology studies of real drugs in patient populations. This review discusses some of the recent advances in pharmacogenomic research and development over the last few years that include understanding the architecture of the human genome, the creation of population deoxyribonucleic acid (DNA)/data banks, assessment of the clinical validity of genetic markers, and experience with regulatory aspects of pharmacogenomics.     

Pharmacogenomics: Catechol O-Methyltransferase to Thiopurine S-Methyltransferase

1. Pharmacogenomics is the study of the role of inheritance in variation in the drug response phenotype—a phenotype that can vary from adverse drug reactions at one end of the spectrum to lack of therapeutic efficacy at the other.2. The thiopurine S-methyltransferase (TPMT) genetic polymorphism represents one of the best characterized and most clinically relevant examples of pharmacogenomics. This polymorphism has also served as a valuable “model system” for studies of the ways in which variation in DNA sequence might influence function.3. The discovery and characterization of the TPMT polymorphism grew directly out of pharmacogenomic studies of catechol O-methyltransferase (COMT), an enzyme discovered by Julius (Julie) Axelrod and his coworkers.4. This review will outline the process by which common, functionally significant genetic polymorphisms for both COMT and TPMT were discovered and will use these two methyltransferase enzymes to illustrate general principles of pharmacogenomic research—both basic mechanistic and clinical translational research—principles that have been applied to a series of genes encoding methyltransferase enzymes.     

Cancer pharmacogenomics: current and future applications

Heterogeneity in patient response to chemotherapy is consistently observed across patient populations. Pharmacogenomics is the study of inherited differences in interindividual drug disposition and effects, with the goal of selecting the optimal drug therapy and dosage for each patient. Pharmacogenomics is especially important for oncology, as severe systemic toxicity and unpredictable efficacy are hallmarks of cancer therapies. In addition, genetic polymorphisms in drug metabolizing enzymes and other molecules are responsible for much of the interindividual differences in the efficacy and toxicity of many chemotherapy agents. This review will discuss clinically relevant examples of gene polymorphisms that influence the outcome of cancer therapy, and whole-genome expression studies using microarray technology that have shown tremendous potential for benefiting cancer pharmacogenomics. The power and utility of the mouse as an experimental system for pharmacogenomic discovery will also be discussed in the context of cancer therapy.     

Pharmacogenomics of breast cancer targeted therapy: focus on recent patents

Adjuvant endocrine therapy as well as other forms of targeted therapy such as HER2 inhibitors and antiangiogenic agents reduce the risk of recurrence and improve survival among women with hormone receptor positive breast cancer. However, a significant percentage of women who receive targeted therapy as adjuvant or metastatic treatment do not benefit from this therapy, while a number of women who initially respond will eventually develop disease progression and relapse while on therapy. The observed variability in treatment response to targeted breast cancer treatment could be partly explained by pharmacogenomics. This paper reviews evidence on the role of pharmacogenomics of breast targeted therapy focusing on the clinical relevance of genetic variation. In particular, this article reviews the role of pharmacogenomics of tamoxifen, aromatase inhibitors, HER-2 inhibitors and anti-angiogenic agents. In addition, recent patents in the field are presented that provide promising steps in the field of personalized treatment of breast cancer, although future studies are needed for determining the clinical benefit of the proposed inventions. Finally, we present a testable hypothesis to aide the search for biologically meaningful genetic variation Specifically, we suggest the publication of negative results in the field of pharmacogenomics and pharmacoproteomics, will benefit future research in the field.     

Chapter 7: Pharmacogenomics

There is great variation in drug-response phenotypes, and a “one size fits all” paradigm for drug delivery is flawed. Pharmacogenomics is the study of how human genetic information impacts drug response, and it aims to improve efficacy and reduced side effects. In this article, we provide an overview of pharmacogenetics, including pharmacokinetics (PK), pharmacodynamics (PD), gene and pathway interactions, and off-target effects. We describe methods for discovering genetic factors in drug response, including genome-wide association studies (GWAS), expression analysis, and other methods such as chemoinformatics and natural language processing (NLP). We cover the practical applications of pharmacogenomics both in the pharmaceutical industry and in a clinical setting. In drug discovery, pharmacogenomics can be used to aid lead identification, anticipate adverse events, and assist in drug repurposing efforts. Moreover, pharmacogenomic discoveries show promise as important elements of physician decision support. Finally, we consider the ethical, regulatory, and reimbursement challenges that remain for the clinical implementation of pharmacogenomics.

What to Learn in This Chapter

• Interactions between drugs (small molecules) and genes (proteins)
• Methods for pharmacogenomic discovery
  • Association- and expression-based methods
  • Cheminformatics and pathway-based methods
• Database resources for pharmacogenomic discovery and application (PharmGKB)
• Applications of pharmacogenomics into a clinical setting

This article is part of the “Translational Bioinformatics” collection for PLOS Computational Biology.

     

Cholesterol-Secreting and Statin-Responsive Hepatocytes from Human ES and iPS Cells to Model Hepatic Involvement in Cardiovascular Health

Hepatocytes play a central and crucial role in cholesterol and lipid homeostasis, and their proper function is of key importance for cardiovascular health. In particular, hepatocytes (especially periportal hepatocytes) endogenously synthesize large amounts of cholesterol and secrete it into circulating blood via apolipoprotein particles. Cholesterol-secreting hepatocytes are also the clinically-relevant cells targeted by statin treatment in vivo. The study of cholesterol homeostasis is largely restricted to the use of animal models and immortalized cell lines that do not recapitulate those key aspects of normal human hepatocyte function that result from genetic variation of individuals within a population. Hepatocyte-like cells (HLCs) derived from human embryonic and induced pluripotent stem cells can provide a cell culture model for the study of cholesterol homeostasis, dyslipidemias, the action of statins and other pharmaceuticals important for cardiovascular health. We have analyzed expression of core components for cholesterol homeostasis in untreated human iPS cells and in response to pravastatin. Here we show the production of differentiated cells resembling periportal hepatocytes from human pluripotent stem cells. These cells express a broad range of apolipoproteins required for secretion and elimination of serum cholesterol, actively secrete cholesterol into the medium, and respond functionally to statin treatment by reduced cholesterol secretion. Our research shows that HLCs derived from human pluripotent cells provide a robust cell culture system for the investigation of the hepatic contribution to human cholesterol homeostasis at both cellular and molecular levels. Importantly, it permits for the first time to also functionally assess the impact of genetic polymorphisms on cholesterol homeostasis. Finally, the system will also be useful for mechanistic studies of heritable dyslipidemias, drug discovery, and investigation of modes of action of cholesterol-modulatory drugs.     

MicroRNA pharmacogenomics: post-transcriptional regulation of drug response

The field of pharmacogenomics aims to predict which drugs will be most effective and safe for a particular individual based on their genome sequence or expression profile, thereby allowing personalized treatment. The bulk of pharmacogenomic research has focused on the role of single nucleotide polymorphisms, copy number variations or differences in gene expression levels of drug metabolizing or transporting genes and drug targets. In this review paper, we focus instead on microRNAs (miRNAs): small noncoding RNAs, prevalent in metazoans, that negatively regulate gene expression in many cellular processes. We discuss how miRNAs, by regulating the expression of pharmacogenomic-related genes, can play a pivotal role in drug efficacy and toxicity and have potential clinical implications for personalized medicine.     

Genotyping in the MHC locus: potential for defining predictive markers in sarcoidosis

The availability of a draft sequence for the human genome will revolutionise research into airway disease. This review deals with two of the most important areas impinging on the treatment of patients: pharmacogenetics and pharmacogenomics. Considerable inter-individual variation exists at the DNA level in targets for medication, and variability in response to treatment may, in part, be determined by this genetic variation. Increased knowledge about the human genome might also permit the identification of novel therapeutic targets by expression profiling at the RNA (genomics) or protein (proteomics) level. This review describes recent advances in pharmacogenetics and pharmacogenomics with regard to airway disease.     

Pharmacogenetics, pharmacogenomics and airway disease

The availability of a draft sequence for the human genome will revolutionise research into airway disease. This review deals with two of the most important areas impinging on the treatment of patients: pharmacogenetics and pharmacogenomics. Considerable inter-individual variation exists at the DNA level in targets for medication, and variability in response to treatment may, in part, be determined by this genetic variation. Increased knowledge about the human genome might also permit the identification of novel therapeutic targets by expression profiling at the RNA (genomics) or protein (proteomics) level. This review describes recent advances in pharmacogenetics and pharmacogenomics with regard to airway disease.     

Cancer pharmacogenomics: role of DNA repair genetic polymorphisms in individualizing cancer therapy

The evolving field of cancer pharmacogenomics uses genetic profiling to predict the response of tumor and normal tissue to therapy. The narrow therapeutic index and heterogeneity of patient responses to chemotherapy and radiotherapy implies that the efficacy of these treatments could, potentially, be significantly enhanced by improving our understanding of the genetic bases for interindividual differences in their effects. The cytotoxicity of both chemotherapy and radiotherapy is to a large extent directly related to their ability to induce DNA damage. The ability of cancer cells to recognize and repair this damage contributes to therapeutic resistance. On the other hand, suboptimal DNA repair in normal tissue may negatively impact on normal tissue tolerance.More than 130 genes have been identified that are associated with human DNA repair, and single nucleotide polymorphisms of several of the DNA repair genes have been described recently. In this article, we present the current evidence implicating variations within DNA repair genes as important predictive and prognostic markers in cancer. We review evidence suggesting DNA repair genetic polymorphisms may significantly influence the clinical response to chemotherapy and radiotherapy, and may influence normal tissue tolerance to cancer treatments.     

The legacy of pharmacogenetics and potential applications

Some 40 years of pharmacogenetic research indicates that knowledge of human genetic diversity is essential to a broader understanding of variation in human drug response, and suggests that drug therapy tailored to the genetic characteristics of the individual may be a realistic goal. Aided by new technologies, molecular studies of genetic polymorphisms of many human enzymes, receptors, and other proteins indicate that only a limited number of important protein variants account for the diversity in drug response, raising the prospect that these variants may be cataloged relatively soon for many human populations. The next great challenge of pharmacogenetics is to pin down the cellular location and effect of these variant proteins on the pathways and networks that govern individual variation in responses to drugs and other exogenous chemicals. In this paper, we will discuss some the current challenges to progress in pharmacogenetics and newer strategies that might be used to improve prospects of drug design and personalized therapy.