Showing papers by "Richard M. Weinshilboum published in 2006"

Pharmacogenomics: Challenges and Opportunities

Abstract: The outcome of drug therapy is often unpredictable, ranging from beneficial effects to lack of efficacy to serious adverse effects. Variations in single genes are 1 well-recognized cause of such unpredictability, defining the field of pharmacogenetics (see Glossary). Such variations may involve genes controlling drug metabolism, drug transport, disease susceptibility, or drug targets. The sequencing of the human genome and the cataloguing of variants across human genomes are the enabling resources for the nascent field of pharmacogenomics (see Glossary), which tests the idea that genomic variability underlies variability in drug responses. However, there are many challenges that must be overcome to apply rapidly accumulating genomic information to understand variable drug responses, including defining candidate genes and pathways; relating disease genes to drug response genes; precisely defining drug response phenotypes; and addressing analytic, ethical, and technological issues involved in generation and management of large drug response data sets. Overcoming these challenges holds the promise of improving new drug development and ultimately individualizing the selection of appropriate drugs and dosages for individual patients.

Thiopurine S-methyltransferase pharmacogenetics: insights, challenges and future directions.

Abstract: The thiopurine S-methyltransferase (TPMT) genetic polymorphism is one of the most 'mature' examples in pharmacogenetics. That is true because of its importance clinically for the individualization of thiopurine drug therapy and also because TPMT has provided novel insights into molecular mechanisms responsible for the functional effects of common genetic polymorphisms. This review will summarize the development of our understanding of the role of inheritance in the regulation of TPMT as well as the clinical implications of that genetic regulation. It will also summarize recent studies in which TPMT pharmacogenetics has enhanced our understanding of molecular mechanisms by which common polymorphisms influence or alter function. TPMT pharmacogenetics highlights the potential clinical importance of the translation of pharmacogenetics from bench to bedside, the potential for basic pharmacogenetic research to provide insight into mechanisms by which genetic polymorphisms can alter function, and the challenges associated with the achievement of both of those goals.

Pharmacogenetics and pharmacogenomics: development, science, and translation.

Abstract: Pharmacogenetics and pharmacogenomics involve the study of the role of inheritance in individual variation in drug response, a phenotype that varies from potentially life-threatening adverse drug reactions to equally serious lack of therapeutic efficacy. This discipline evolved from the convergence of rapid advances in molecular pharmacology and genomics. Originally, pharmacogenetic studies focused on monogenic traits, often involving genetic variation in drug metabolism. However, contemporary studies increasingly involve entire "pathways" encoding proteins that influence both pharmacokinetics--factors that influence the concentration of a drug reaching its target(s)--and pharmacodynamics, the drug target itself, as well as genome-wide approaches. Pharmacogenomics is also increasingly moving across the "translational interface" into the clinic and is being incorporated into the drug development process and the governmental regulation of that process. However, significant challenges remain to be overcome if pharmacogenetics-pharmacogenomics is to achieve its full potential as a major medical application of genomic science.

Gemcitabine Pharmacogenomics: Cytidine Deaminase and Deoxycytidylate Deaminase Gene Resequencing and Functional Genomics

Abstract: Purpose: Gemcitabine is a nucleoside analogue with activity against solid tumors. Gemcitabine metabolic inactivation is catalyzed by cytidine deaminase (CDA) or, after phosphorylation, by deoxycytidylate deaminase (DCTD). We set out to study the pharmacogenomics of CDA and DCTD. Experimental Design: The genes encoding CDA and DCTD were resequenced using DNA from 60 African American and 60 Caucasian American subjects. Expression constructs were created for nonsynonymous coding single nucleotide polymorphisms (cSNP) and reporter gene constructs were created for 5′-flanking region polymorphisms. Functional genomic studies were then conducted after the transfection of mammalian cells. Results: CDA resequencing revealed 17 polymorphisms, including one common nonsynonymous cSNP, 79 A>C (Lys27Gln). Recombinant Gln27 CDA had 66 ± 5.1% (mean ± SE) of the wild-type (WT) activity for gemcitabine but without a significant decrease in level of immunoreactive protein. The apparent K m (397 ± 40 μmol/L) for the Gln27 allozyme was significantly higher than that for the WT (289 ± 20 μmol/L; P CDA 5′-flanking region reporter gene studies showed significant differences among 5′-flanking region haplotypes in their ability to drive transcription. There were 29 SNPs in DCTD , including one nonsynonymous cSNP, 172 A>G (Asn58Asp), in Caucasian American DNA. Recombinant Asp58 DCTD had 11 ± 1.4% of WT activity for gemcitabine monophosphate with a significantly elevated level of immunoreactive protein. No DCTD polymorphisms were observed in the initial 500 bp of the 5′-flanking region. Conclusions: These results suggest that pharmacogenomic variation in the deamination of gemcitabine and its monophosphate might contribute to variation in therapeutic response to this antineoplastic agent.

Role of the Glutathione Metabolic Pathway in Lung Cancer Treatment and Prognosis: A Review

Abstract: Inherent and acquired drug resistance is a cause of chemotherapy failure, and pharmacogenomic studies have begun to define gene variations responsible for varied drug metabolism, which influences drug efficacy. Platinum-based compounds are the most commonly used chemotherapeutic agents in the treatment of advanced stage lung cancer patients, and the glutathione metabolic pathway is directly involved in the detoxification or inactivation of platinum drugs. Consequently, genotypes corresponding to higher drug inactivation enzyme activity may predict poor treatment outcome. Available evidence is consistent with this hypothesis, although a definitive role for glutathione system genes in lung cancer prognosis needs to be elucidated. We present evidence supporting a role of the glutathione system in acquired and inherited drug resistance and/or adverse effects through the impact of either drug detoxification or drug inactivation, thus adversely effecting lung cancer treatment outcome. The potential application of glutathione system polymorphic genetic markers in identifying patients who may respond favorably, selecting effective antitumor drugs, and balancing drug efficacy and toxicity are discussed.

Glutathione S-transferase omega 1 and omega 2 pharmacogenomics

Abstract: Glutathione S-transferase omega 1 and omega 2 (GSTO1 and GSTO2) catalyze monomethyl arsenate reduction, the rate-limiting reaction in arsenic biotransformation. As a step toward pharmacogenomic studies of these phase II enzymes, we resequenced human GSTO1 and GSTO2 using DNA samples from four ethnic groups. We identified 31 and 66 polymorphisms in GSTO1 and GSTO2, respectively, with four nonsynonymous-coding single nucleotide polymorphisms (cSNPs) in each gene. There were striking variations among ethnic groups in polymorphism frequencies and types. Expression constructs were created for all eight nonsynonymous cSNPs, as well as a deletion of codon 155 in GSTO1, and those constructs were used to transfect COS-1 cells. Quantitative Western blot analysis, after correction for transfection efficiency, showed a reduction in protein level of greater than 50% for the GSTO1 Tyr32 variant allozyme compared with wild type (WT), whereas levels for the Asp140, Lys208, Val236, and codon 155 deletion variant constructs were similar to that of the WT. For GSTO2, the Tyr130 and Ile158 variant allozymes showed 50 and 84% reductions in levels of expression, respectively, compared with WT, whereas the Ile41 and Asp142 allozymes displayed levels similar to that of WT GSTO2. Rabbit reticulocyte lysate degradation studies showed that the GSTO1 Tyr32 and the GSTO2 Tyr130, Ile158, and Asp142/Ile158 variant allozymes were degraded more rapidly than were their respective WT allozymes. These observations raise the possibility of functionally significant pharmacogenomic variation in the expression and function of GSTO1 and GSTO2.

Human methylenetetrahydrofolate reductase pharmacogenomics: gene resequencing and functional genomics.

Abstract: 5,10-Methylenetetrahydrofolate reductase (MTHFR) is an important enzyme in the folate metabolic pathway. Common genetic polymorphisms in the human MTHFR gene are associated with individual variation in the efficacy and toxicity of chemotherapeutic agents, such as methotrexate and 5-fluorouracil. However, the full range of polymorphisms and intragene haplotypes in the human MTHFR gene remains unclear. Furthermore, cellular mechanisms by which common, naturally occurring nonsynonymous coding single nucleotide polymorphisms (cSNPs) might alter the function of this enzyme have not been defined. The present study focused on the systematic identification and investigation of common polymorphisms and haplotypes in the MTHFR gene using a genotype-to-phenotype strategy, followed by functional genomic studies. Specifically, we resequenced exons, splice junctions and portions of the 5'-flanking region (5'-FR) of the human MTHFR gene using 240 DNA samples from four ethnic groups. A total of 65 polymorphisms were observed, 11 of which were nonsynonymous cSNPs. We then performed functional genomic studies with constructs for wild-type and 15 variant allozymes (some with multiple alterations in amino acid sequence) using a mammalian expression system. Activity for the variant allozymes ranged from 13% to 149% of wild-type activity. Levels of immunoreactive protein for the allozymes ranged from 31% to 120% of wild-type and were significantly correlated with enzyme activity (Rp=0.85, P<0.0001), suggesting that a major mechanism by which nonsynonymous cSNPs influence the function of this gene is by alteration in the quantity of protein. These observations represent steps towards an understanding of molecular genetic mechanisms responsible for variation in MTHFR function that may contribute to individual differences in drug efficacy and toxicity, as well as disease risk.

Glutathione s-transferase sequence variants

Abstract: Isolated GSTO2 nucleic acid molecules that include a nucleotide sequence variant and nucleotides flanking the sequence variant are described, as well as GSTO2 allozymes. Methods for determining if a subject contains a GSTO2 sequence variant also are described.

Pharmacogenomics: Bench to Bedside

Abstract: Pharmacogenetics is the study of the role of inheritance in inter-individual variation in drug response. Since its origins in the mid-twentieth century, a major driving force in pharmacogenetics research has been the promise of individualized drug therapy to maximize drug efficacy and minimize drug toxicity. In recent years, the convergence of advances in pharmacogenetics with rapid developments in human genomics has resulted in the evolution of pharmacogenetics into pharmacogenomics, and led to increasing enthusiasm for the “translation” of this evolving discipline into clinical practice. Here, we briefly summarize the development of pharmacogenetics and pharmacogenomics, and then discuss the key factors that have had an influence on—and will continue to affect—the translation of pharmacogenomics from the research bench to the bedside, highlighting the challenges that need to be addressed to achieve this goal.

Pharmacogenomics: Catechol O-Methyltransferase to Thiopurine S-Methyltransferase

Abstract: 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.

Sulfotransferase sequence variants

Abstract: Isolated sulfotransferase nucleic acid molecules that include a nucleotide sequence variant and nucleotides flanking the sequence variant are described, as well as sulfotransferase allozymes. Methods for determining if a mammal is predisposed to thyroid disease or cancer also are described.

Methylenetetrahydrofolate reductase haplotype tag single-nucleotide polymorphisms and risk of breast cancer.

Abstract: The folate metabolism pathway contributes to important metabolic processes, such as RNA and DNA synthesis, DNA repair, and DNA methylation ([1][1]). Previous observations have suggested a potential relationship between altered folate levels and tumorigenesis ([2][2]). Therefore, inherited genetic

Method for rapid determination of thiopurine methyltransferase activity

Abstract: This document provides methods and materials related to rapid, quantitative determination of TPMT activity in biological samples. Also featured are compositions and kits useful for determination of TPMT activity in biological samples.

Assessing outcomes for breast cancer patients treated with tamoxifen

Abstract: This document provides methods and materials related to assessing the likely outcome for mammals (e.g., humans) with cancer (e.g., breast cancer). For example, methods and materials that involve assessing a breast cancer patient's cytochrome P450, family 2, subfamily D, polypeptide 6 (CYP2D6) genotype to determine the likelihood of the beast cancer patient to experience breast cancer relapse or death are provided. Methods and materials that involve assessing the likelihood that a breast cancer patient being treated with tamoxifen will experience side effects such as hot flashes also are provided.

HSD3B1 sequence variants

Abstract: Isolated HSD3B1 nucleic acid molecules that include a nucleotide sequence variant and nucleotides flanking the sequence variant are described, as are HSD3B1 allozymes. Methods for determining whether a subject contains an HSD3B1 sequence variant also are provided.

3′-phosphoadenosine-5′-phosphosulfate synthetase 1 (PAPSS1) sequence variants

Abstract: Isolated PAPSS1 nucleic acid molecules that include a nucleotide sequence variant and nucleotides flanking the sequence variant are described, as well as PAPSS1 allozymes. Methods for determining if a mammal is predisposed to joint disease or cancer also are described.