Pharmacogenomic approaches in clinical studies to identify biomarkers of safety and efficacy

Although toxicogenomics originated as a field of primarily preclinical investigation, a variety of genomic approaches can also be employed during or after clinical development to identify biomarkers linked to drug exposure and/or drug safety. Comparing and contrasting the different pharmacogenomic approaches according to their scale (targeted, focused or exploratory) illustrates the potential utility of each type of strategy in characterizing the genetic determinants that may play roles in various aspects of drug activity. Examples of targeted ADME genotyping, focused SNP panels, and exploratory whole genome association studies are briefly reviewed to provide an overview of the range of pharmacogenetic options available to the research community to support the ongoing efforts to identify biomarkers predictive of drug exposure and/or safety in human subjects.     

Gap between the US and Japan in coverage of pharmacogenomic biomarkers by health insurance programs: More coverage is needed in Japan

In this study, we aimed to understand the gap in coverage of pharmacogenomic (PGx) biomarkers between Japan and the US. PGx biomarkers (1) in the Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines; (2) that are CPIC level A or B; or (3) have US Food and Drug Administration (FDA)-approved drug labels, were determined. Subsequently, their coverage by US health insurance companies and the National Health Insurance (NHI) in Japan was investigated. We identified the top six health insurance companies with the largest market shares in the US and investigated the coverage for the PGx biomarkers by these health insurers, Medicare, Medicaid, and the NHI in Japan. We found that 19.9% of these biomarkers are covered by the six companies (10.0%, the CPIC guidelines; 25.1%, the FDA-approved drug labels). The coverage of somatic and germline biomarkers was respectively 86.8% and 8.5% in the US and 56.3% and 0.6% in Japan. A few germline PGx biomarkers are covered both in Japan and the US, but the coverage of both somatic and germline biomarkers was lower in Japan. Therefore, more coverage should be considered to improve patient outcomes after prescribing medications in Japan.     

Mechanism-based biomarker gene sets for glutathione depletion-related hepatotoxicity in rats

Chemical-induced glutathione depletion is thought to be caused by two types of toxicological mechanisms: PHO-type glutathione depletion [glutathione conjugated with chemicals such as phorone (PHO) or diethyl maleate (DEM)], and BSO-type glutathione depletion [i.e., glutathione synthesis inhibited by chemicals such as l-buthionine-sulfoximine (BSO)]. In order to identify mechanism-based biomarker gene sets for glutathione depletion in rat liver, male SD rats were treated with various chemicals including PHO (40, 120 and 400 mg/kg), DEM (80, 240 and 800 mg/kg), BSO (150, 450 and 1500 mg/kg), and bromobenzene (BBZ, 10, 100 and 300 mg/kg). Liver samples were taken 3, 6, 9 and 24 h after administration and examined for hepatic glutathione content, physiological and pathological changes, and gene expression changes using Affymetrix GeneChip Arrays. To identify differentially expressed probe sets in response to glutathione depletion, we focused on the following two courses of events for the two types of mechanisms of glutathione depletion: a) gene expression changes occurring simultaneously in response to glutathione depletion, and b) gene expression changes after glutathione was depleted. The gene expression profiles of the identified probe sets for the two types of glutathione depletion differed markedly at times during and after glutathione depletion, whereas Srxn1 was markedly increased for both types as glutathione was depleted, suggesting that Srxn1 is a key molecule in oxidative stress related to glutathione. The extracted probe sets were refined and verified using various compounds including 13 additional positive or negative compounds, and they established two useful marker sets. One contained three probe sets (Akr7a3, Trib3 and Gstp1) that could detect conjugation-type glutathione depletors any time within 24 h after dosing, and the other contained 14 probe sets that could detect glutathione depletors by any mechanism. These two sets, with appropriate scoring systems, could be promising biomarkers for preclinical examination of hepatotoxicity.     

Genomic biomarkers of toxicity

The difference between measuring changes in gene expression levels in a toxicogenomics study and actually achieving reduced drug development costs is in the knowledge of which gene expression changes are predictive of toxicity. Whether the cost savings are in high-throughput screening, in discovery or in preclinical, testing, the application of genomics, proteomics or metabonomics will require a clear understanding of what these methods actually measure. Results of studies published over the past year have set valuable benchmarks for genomic studies, transforming this technology into a source of candidates for validation as predictive biomarkers of toxicity. This review will summarize some of the publications that have achieved this transformation, and the steps that are still needed for the implementation of predictive tests derived from these genomic biomarkers of toxicity.     

Scoring multiple toxicological endpoints using a toxicogenomic database

As information regarding microarray data sets and toxicogenomic biomarkers grows rapidly, the process of analyzing data and interpreting the results is increasingly complicated. To facilitate data analysis, a simple expression ratio-based scoring method called the TGP1 score was previously proposed [Kiyosawa, N., Shiwaku, K., Hirode, M., Omura, K., Uehara, T., Shimizu, T., Mizukawa, Y., Miyagishima, T., Ono, A., Nagao, T., Urushidani, T., 2006. Utilization of a one-dimensional score for surveying chemical-induced changes in expression levels of multiple biomarker gene sets using a large-scale toxicogenomics database. J. Toxicol. Sci. 31, 433–448]. Although the TGP1 score has demonstrated its efficacy for rapid comprehension of large-scale toxicogenomic data sets, inclusion of low quality gene expression data in the biomarker gene set produced flaws in the calculated score. To overcome this shortcoming, we tested a new scoring method called the differentially expressed gene score (D-score), where Detection Call as well as signal log ratios generated by MAS5 algorithm on Affymetrix GeneChip data were considered for the calculation. Four prototypical toxicants, namely acetaminophen, phenobarbital, clofibrate and acetamidofluorene, were used for detailed analysis. A toxicogenomics database (TG-GATEs) was utilized as a reference data set. The D-score successfully alleviated the effects of low quality data on the score calculation, and captured the overall direction of expression changes as well as the magnitude of expression change level of a set of genes, highlighting the affected toxicological endpoints elicited by chemical treatment. The D-score will be useful for high-throughput toxicity screening using a toxicogenomic database and biomarkers.     

抗哮喘药物β2肾上腺素受体激动剂的药物基因组学研究进展

尽管目前临床上用于治疗哮喘的药物有许多种,但这些药物对部分患者的疗效却很差。有证据表明这种个体差异与个人的基因差异密切相关。本文主要针对临床上常用的治疗哮喘的药物β2-肾上腺素受体激动剂的药物基因组学进行综述,并提出了今后有关这一领域的研究方向,用以提高药物治疗效果,减少副作用,并降低患者的治疗费用。     

Differences in gene expression profiles in the liver between carcinogenic and non-carcinogenic isomers of compounds given to rats in a 28-day repeat-dose toxicity study

Some compounds have structural isomers of which one is apparently carcinogenic, and the other not. Because of the similarity of their chemical structures, comparisons of their effects can allow gene expression elicited in response to the basic skeletons of the isomers to be disregarded. We compared the gene expression profiles of male Fischer 344 rats administered by daily oral gavage up to 28 days using an in-house oligo microarray. 2-Acetylaminofluorene (2-AAF), 2,4-diaminotoluene (2,4-DAT), 2-nitropropane (2-NP), and 2-nitro-p-phenylenediamine (2-NpP) are hepatocarcinogenic. However, their isomers, 4-acetylaminofluorene (4-AAF), 2,6-diaminotoluene (2,6-DAT), 1-nitropropane (1-NP), and 4-nitro-o-phenylenediamine (4-NoP), are non-hepatocarcinogenic. Because of the limited carcinogenicity of 2-NpP, we attempted to perform two-parametric comparison analyses with (1) a set of 4 isomers: 2-AAF, 2,4-DAT, 2-NP, and 2-NpP as "carcinogenic", and 4-AAF, 2,6-DAT, 1-NP, and 4-NoP as "non-carcinogenic"; and (2) a set of 3 isomers: 2-AAF, 2,4-DAT, and 2-NP, as "carcinogenic", and 4-AAF, 2,6-DAT, and 1-NP as "non-carcinogenic". After ratio filtering and Welch's approximate t-test analysis, 54 and 28 genes were selected from comparisons between the sets of 3 and 4 isomers, respectively, for day 28 data. Using hierarchical clustering analysis with the 54 or 28 genes, 2-AAF, 2,4-DAT, and 2-NP clustered into a "carcinogenic" branch. 2-NpP was in the same cluster as 4-NoP and 4-AAF. This clustering corresponded to the previous finding that 2-NpP is not carcinogenic in male Fischer 344 rats, which indicates that comparing the differences in gene expression elicited by different isomers is an effective method of developing a prediction system for carcinogenicity.     

Identification of genomic biomarkers for concurrent diagnosis of drug-induced renal tubular injury using a large-scale toxicogenomics database

Drug-induced renal tubular injury is one of the major concerns in preclinical safety evaluations. Toxicogenomics is becoming a generally accepted approach for identifying chemicals with potential safety problems. In the present study, we analyzed 33 nephrotoxicants and 8 non-nephrotoxic hepatotoxicants to elucidate time- and dose-dependent global gene expression changes associated with proximal tubular toxicity. The compounds were administered orally or intravenously once daily to male Sprague-Dawley rats. The animals were exposed to four different doses of the compounds, and kidney tissues were collected on days 4, 8, 15, and 29. Gene expression profiles were generated from kidney RNA by using Affymetrix GeneChips and analyzed in conjunction with the histopathological changes. We used the filter-type gene selection algorithm based on t-statistics conjugated with the SVM classifier, and achieved a sensitivity of 90% with a selectivity of 90%. Then, 92 genes were extracted as the genomic biomarker candidates that were used to construct the classifier. The gene list contains well-known biomarkers, such as Kidney injury molecule 1, Ceruloplasmin, Clusterin, Tissue inhibitor of metallopeptidase 1, and also novel biomarker candidates. Most of the genes involved in tissue remodeling, the immune/inflammatory response, cell adhesion/proliferation/migration, and metabolism were predominantly up-regulated. Down-regulated genes participated in cell adhesion/proliferation/migration, membrane transport, and signal transduction. Our classifier has better prediction accuracy than any of the well-known biomarkers. Therefore, the toxicogenomics approach would be useful for concurrent diagnosis of renal tubular injury.     

Cancer Pharmacogenomics: DNA Genotyping and Gene Expression Profiling to Identify Molecular Determinants of Chemosensitivity

Cancer patients exhibit a wide heterogeneity in their responses to chemotherapy. Improvement in chemotherapeutic responses could be achieved by gaining more detailed information on the molecular determinants (i.e., DNA, RNA or protein) underlying this heterogeneity. Pharmacogenomics approaches can be used to integrate information on drug responsiveness with alterations in molecular entities, often on a genome-wide scale. By using information gleaned from pharmacogenomics studies, it is anticipated that cancer chemotherapy can be tailored to the individual patient or tumor phenotype. This review focuses on pharmacogenomics studies conducted to gain insight into the molecular determinants of chemosensitivity to cancer chemotherapeutics.     

Functional Genomics Approaches to Studies of the Cytochrome P450 Superfamily

Functional genomics approaches are widely implemented in current research and have found application in many areas of biology. This review will present research fields, novel findings and new tools developed in the cytochrome P450 field using the functional genomics techniques. The most widely used method is microarray technology, which has already greatly contributed to the understanding of the cytochromes P450 function and expression. Several focused CYP microarrays have been developed for genotyping, toxicogenomics and studies of CYP function of many different organisms. Our contribution to the CYP field by development of Steroltalk microarrays to study the cross-talk of cholesterol homeostasis and drug metabolism is also presented.     

Pharmacogenetics, the next challenge for pharmacy?

This commentary draws attention to and raises awareness of forthcoming pharmacogenetic technologies amongst the pharmacy profession. It aims to stimulate debate around the potential role that the pharmacy profession can play in the introduction of pharmacogenetic technologies into primary healthcare. This commentary discusses potential new roles for pharmacists involving pharmacogenetic technologies, giving attention to the way the profession may need to adapt to accommodate these.     

Searching for biomarkers of developmental toxicity with microarrays: normal eye morphogenesis in rodent embryos

Gene expression arrays reveal the potential linkage of altered gene expression with specific adverse effects leading to disease phenotypes. But how closely do microarray data reflect early physiological or pharmacological measures that predict toxic event(s)? To explore this issue, we have undertaken experiments in early mouse embryos exposed to various teratogens during neurulation stages with the aim of correlating large-scale changes in gene expression across the critical period during exposure. This study reports some of the large-scale changes in gene expression that can be detected in the optic rudiment of the developing mouse and rat embryo across the window of development during which the eye is exceedingly sensitive to teratogen-induced micro-/anophthalmia. Microarray analysis was performed on RNA from the headfold or ocular region at the optic vesicle and optic cup stages when the ocular primordium is enriched for Pax-6, a master control gene for eye morphogenesis. Statistical selection of differentially regulated genes and various clustering techniques identified groups of genes in upward or downward trajectories in the normal optic primordium during early eye development in mouse and rat species. We identified 165 genes with significant differential expression during eye development, and a smaller subset of 58 genes that showed a tight correlation between mouse-rat development. Significantly over-represented functional categories included fatty acid metabolism (up-regulated) and glycolysis (down-regulated). From studies such as these that benchmark large-scale gene expression during normal embryonic development, we may be able to identify the panel of biomarkers that best correlate with species differences and the risks for developmental toxicity.     

遗传药理学与高血压药物治疗进展

遗传药理学对于解释药物反应的个体差异并进行个体化用药具有重要意义。近年来其新技术在高血压治疗等方面的临床应用引起了广泛关注。本文结合本临床评价中心实践经验,从药代动力学和药效动力学方面对与高血压治疗相关的基因多态性研究进展,及其对高血压个体化治疗的影响进行综述。可以认为基因芯片技术等药物基因组学的新发展,必将对高血压等疾病的个体化治疗发挥更显著的促进作用。     

Gene expression profiles of murine fatty liver induced by the administration of methotrexate

Methotrexate (MTX) is used to treat a variety of chronic inflammatory and neoplastic diseases. However, it can induce hepatotoxicity such as microvesicular steatosis and necrosis. To explore the mechanisms of MTX-induced hepatic steatosis, we used microarray analysis to profile the gene expression patterns of mouse liver after MTX treatment. MTX was administered orally as a single dose of 10mg/kg (low dose) or 100 mg/kg (high dose) to ICR mice, and the livers were obtained 6 h, 24 h, and 72 h after treatment. Serum alanine aminotransferase, aspartate aminotransferase and triacylglycerol levels were not significantly altered in the experimental animals. Signs of steatosis were observed at 24 h after administration of high dose of MTX. From microarray data analysis, 908 genes were selected as MTX-responsive genes (P<0.05, two-way ANOVA; cutoff > or =1.5-fold). Database for Annotation, Visualization and Integrated Discovery (DAVID) analysis revealed that the predominant biological processes associated with these genes are response to unfolded proteins, phosphate metabolism, and cellular lipid metabolism. Functional categorization of these genes identified 28 genes involved in lipid metabolism that was interconnected with the biological pathways of biosynthesis, catabolism, and transport of lipids and fatty acids. Taken together, these data provide a better understanding of the molecular mechanisms of MTX-induced steatogenic hepatotoxicity, and useful information for predicting hepatotoxicity through pattern recognition.     

Use of toxicogenomics to understand mechanisms of drug-induced hepatotoxicity during drug discovery and development

Hepatotoxicity is a common cause of failure in drug discovery and development and is also frequently the source of adverse drug reactions. Therefore, a better prediction, characterization and understanding of drug-induced hepatotoxicity could result in safer drugs and a more efficient drug discovery and development process. Among the 'omics technologies, toxicogenomics (or the use of gene expression profiling in toxicology) represents an attractive approach to predict toxicity and to gain a mechanistic understanding of toxic changes. In this review, we illustrate, using selected examples, how toxicogenomics can be applied to investigate drug-induced hepatotoxicity in animal models and in vitro systems. In general, this technology can not only improve the discipline of toxicology and risk assessment but also represent an extremely effective, hypothesis-generating alternative to rapidly understand mechanisms of hepatotoxicity.     

CYP3A phenotypes and genotypes in North Indians

Objectives To phenotype 200 healthy North Indians for cytochrome P450 3A (CYP3A) activity by measuring urinary ratio of 6β-OH-cortisol/cortisol (6β-OH-CS/CS) and to genotype the subjects demonstrating low and high CYP3A activity for the presence of CYP3A4*1B, *2, *4, *5, *6 and *10 alleles.Methods Morning spot urine samples were collected from 200 healthy North Indians. CS and 6β-OH-CS were extracted and quantified by HPLC. Genotyping was performed by polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP).Results Urinary 6β-OH-CS/CS ratio demonstrated a mean of 52.0 ± 46 (1.1–290). North Indians demonstrated unimodal distribution with respect to urinary 6β-OH-CS/CS ratio. On the basis of phenotypes, the subjects were divided into three groups demonstrating low (n=50), intermediate (n=100) and high (n=50) CYP3A activity. These groups demonstrated 6β-OH-CS/CS ratio of 13.4 ± 5.2 (1.1–21.0), 40 ± 11.9 (21.2–63.2) and 114 ± 51.0 (66–290), respectively. One hundred subjects, 50 in the low and 50 in the high activity group, were genotyped for CYP3A4*1B, *2, *4, *5, *6 and *10. Only 2 heterozygotes with genotype CYP3A4*1/*1B were found in the high CYP3A activity group. CYP3A4*2, *4, *5, *6 and *10 were not found in the subjects studied.Conclusion This is the first investigation establishing CYP3A phenotypes and demonstrating the absence of common CYP3A4 genotypes in North Indians.