Pharmacogenetics Research Network and Knowledge Base Second

antibody microarrays, in which thou Pharmacogenetics research network sands of monospecific antibodies are printed on a chip to permit clinical and knowledge base second monitoring of proteins in serum and other biological fluids for disease de scientific meeting tection, drug response, and toxicity.3

AF Davis1 and RM Long2 PHARMACOGENETIC STUDIES OF ENZYMES AND TRANSPORTERS Kathleen Giacomini (University of 1Office of Communications and Public Liaison, National Institute of General Medical California, San Francisco) reported Sciences, National Institutes of Health, Bethesda, MD, USA; 2Division of Pharmacology, her group’s progress on the analysis Physiology, and Biological Chemistry, National Institute of General Medical Sciences, of membrane transporters as candi National Institutes of Health, Bethesda, MD, USA dates for regulating drug responses. Giacomini’s group is pursuing 25 transporters of two general classes: The Pharmacogenomics Journal (2002) program director for the PGRN project, neurotransmitter transporters and 2, 293–296. doi:10.1038/sj.tpj.6500125 invited the scientific community to xenobiotic transporters. A set of 247 provide feedback on the PGRN and on ethnically diverse DNA samples PharmGKB on a continual basis. BACKGROUND derived from cell collections from the In April 2000, the National Institute of NIGMS Human Genetic Cell Reposi General Medical Sciences (NIGMS) of KEYNOTE: MICROARRAYS IN tory at the Coriell Institute for Medical the National Institutes of Health (NIH) PHARMACOGENOMIC STUDIES Research (http://locus.umdnj.edu/) established a nationwide research net Pat Brown (Stanford University) deliv has been analyzed to assess genetic work, the Pharmacogenetics Research ered the morning keynote address on variation in transporter sequences Network (PGRN), joining several the applicability and use of microarray across human populations. The nature teams of pharmacogenetics and phar technology in pharmacogenomic and extent of variation differed macogenomics investigators.1 In addi investigations. Brown began by noting widely; in general, neurotransmitter tion to NIGMS, other participating that Mendel’s seminal experiments transporters exhibited less variation NIH sponsors include the National revealed rich phenotypic variation than xenobiotic transporter genetic Cancer Institute, the National Heart, that can be seen in the expression of sequences. Two clinical studies have Lung and Blood Institute, the National plant genes, which culminate in the recently been launched to evaluate Human Genome Research Institute, formation of leaves, flowers, and how genetic variation in membrane the National Institute of Environmen stems. In a biomedical vein, the same transporter sequences may affect clin tal Health Sciences, and the National result is obvious if one considers that ical response. The first study, SOPHIE Library of Medicine. NIH created the every human cell contains an identical (principal investigator: Esteban Burch PGRN after discussions with the scien genome, yet markedly different prop ard, UCSF), will contain a cohort of tific community identified a need to erties. He described current efforts to 500 healthy volunteers in the San promote research in pharmacogenetics systematically survey gene expression Francisco Bay Area. Each volunteer’s and pharmacogenomics. The scientific in a wide variety of cell types, under ethnicity will be defined by the geo community also recognized the im many different conditions.2 Related to graphical origin of his or her four portance of full disclosure of data into pharmacogenomics, microarrays may grandparents, and subjects have con the public domain. The PGRN is linked be useful in correlating genes and sented to being called back in the to a research database called the variable drug responses. While micro- future for further pharmacogenetic Pharmacogenetics and Pharmacoge array applications to pharmaco studies. Individuals participating in nomics Knowledge Base (PharmGKB: genomic studies will undoubtedly be SOPHIE will be genotyped for genetic http://www.pharmgkb.org). challenging, the methodology may variation in the transporter gene OCT1 The second open scientific meeting also be useful in identifying tissue- (organic cation transporter 1). A second of the NIH PGRN was held on 12 specific drug toxicities, especially study, GRAD (principal investigator: March 2002 at Stanford University in those occurring in tissues not routi Cathy Schaefer, Kaiser Permanente), Stanford, CA. The program consisted nely accessible to biopsy. Other poten will investigate genetic components of two keynote talks and research tial microarray technologies that may of the response to anti-SSRI antide progress updates by PGRN team lea find welcome use in pharmaco pressants, a class of drugs that typi ders. Rochelle Long (NIGMS), NIH genomic research include the use of cally exhibits a wide range of drug Pharmacogenetics research network AF Davis and RM Long 294

response: 30% of patients have no being sought. Two clinical studies will Daniel T O’Connor (University of response, 70% have a variable re correlate SNP haplotypes with detailed California, San Diego) described on sponse, and approximately 10% ex phenotypes indicative of drug going studies to investigate pharmaco perience adverse effects. GRAD will response. Primary phenotypic corre dynamic determinants of human drug enroll 1500 people diagnosed with lates, such as LDL, cholesterol, and responses, especially autonomic cardio depression. These people will be eval blood pressure regulation, will be as vascular responses. O’Connor’s group uated before and after therapy with an sessed, along with secondary phenoty is investigating potential genetic anti-SSRI drug to determine the drug’s pic correlates, such as insulin levels and determinants that may affect responses efficacy and adverse effects. All study markers of inflammation. Candidate to autonomic control over systemic participants will be genotyped. genes that have already emerged and pulmonary circulatory processes, Richard Weinshilboum (Mayo Foun include those related to the angiotensin such as blood pressure, pulmonary dation) presented recent results on the and renin pathways. For the planned systems, dopaminergic responses, and pharmacogenetics of phase II drug- clinical studies of relatively small presynaptic adrenergic mechanisms. metabolizing enzymes. Weinshil numbers of patients, limited statistical The in vitro effects of identified SNPs boum’s group is continuing to rese power will necessitate follow-up con will be measured, followed by an quence phase II metabolism genes, firmatory testing. In addition, haplo analysis of in vivo effects in transgenic including approximately 10 sulfo types of potential importance may be animals. Cardiovascular drug targets transferases, approximately five examined in relation to clinical end such as alpha- and beta-adrenergic methyltransferases, and one phos points in larger clinical trials, such as receptors are being used to identify phoadenosine-50-phosphosulfate syn the Heart Protection Study (http:// potential genotype–phenotype rela thetase.4,5 Polymorphisms are common, www.ctsu.ox.ac.uk/Bhps/). tionships. To this end, variation has and significant variability has been Dan Roden (Vanderbilt University) been observed in the ability of humans found both within and between ethnic presented research plans and early to metabolize the alpha-2-adrenergic groups. In general, the common non- data pursuant to his group’s study of agonist yohimbine. Studies are in pro synonymous cSNPs identified lead to the pharmacogenomics of arrhythmia gress to investigate adrenergic receptor reduced quantities of enzyme produc therapy. Roden and his group are and CYP2D6 genomic diversity. tion. Ongoing efforts include structur testing the hypothesis that allelic Kelan Tantisira (Harvard University, al analysis of proteins to uncover variants in candidate genes identified representing PGRN member Scott potential explanations for variable by an emerging understanding of Weiss) presented recent results on the drug response among different alleles. molecular physiology and pharmacol pharmacogenetics of asthma treat A case study was presented on the ogy contribute to the variable drug ment.7 Ongoing studies seek to identi resequencing of the histamine N- responses typical of anti-arrhythmic fy the genes responsible for the methyl transferase (HNMT) gene.6 An treatments. Candidate genes for ion clinically apparent variable response increase in allelic frequency of HNMT channel proteins, drug-metabolizing to each of the three classes of medica has been observed in asthma. Protein enzymes, and components of intracell tions used to treat asthma: beta-ago degradation is being actively investi ular signaling systems are being ana nists, inhaled corticosteroids, and gated as a determinant for some of the lyzed for allelic variation. To date, leukotriene modifiers. Asthma pat phenotypic variability seen in phase II unique mutations have been found in ients are being genotyped at loci enzyme activity. several genes, including SCNSA associated with functional effects det (inward sodium flux), KCNQ1 (out ermined in vitro, then phenotyped ward potassium flux), as well as in according to individual response to CARDIOVASCULAR AND other potassium channel genes. In treatment with the class of asthma PULMONARY silico experiments are being conducted medication of interest. Polymorph PHARMACOGENETICS to reconstruct electrophysiological isms have been identified in the Ronald Krauss (Lawrence Berkeley parameters with variant channel promoter region of the ALOX5 gene, National Laboratory) presented his proteins, using Luo–Rudy action which encodes a key enzyme in gen group’s objectives and early data. potential modeling methods. Early erating leukotrienes that trigger an Krauss’ group is seeking to identify data from these experiments suggest asthmatic response.8 Progress was common genetic variants in candidate that observed sequence changes do reported on an ancillary genetics study genes that contribute to interindivi not affect the action potential, but component to the Childhood Asthma dual variation in responsiveness to do appear to exert an influence on Management Program (CAMP), in drugs used to reduce the risk of repolarization reserve. Other studies which 1041 children with mild to cardiovascular disease. Candidate in progress involve genotyping and moderate asthma are being evaluated genes involved in the response to monitoring the short- and long-term with respect to the effects of methacho treatment of the two most prevalent outcomes of 500–1000 patients line administration on lung function, cardiovascular risk factors, hyperlipi with long QT syndrome to track occurrence of respiratory symptoms, demia and hypertension (with simvas responses to anti-arrhythmic drugs and duration of disease. DNA infor tatin and ramipril, respectively), are and warfarin. mation has been obtained from most

The Pharmacogenomics Journal Pharmacogenetics research network AF Davis and RM Long 295

participants in this longitudinal study; by fostering the development and studying candidate systems known to genotypic analysis will be performed maturation of scientific results in the be altered in depression, such as the to assess the nature of genetic con pre-clinical realm. It may be that neuroendocrine axis and the leptin tributions to asthma drug treatment. putting SNPs in the public domain system. To offset possible negative The differential transmission of alleles prevents the fragmentation of social effects of studying one particular from parents to affected children is resources, avoiding lengthy and costly ethnic group, community consultations being investigated. Future studies will licensing procedures. Another conjec have been conducted. Numerous small continue haplotypic association stu ture stems from recent media meetings have been held at various dies in the CAMP population, in an reports9,10 suggesting that companies locations throughout Los Angeles. effort to define longitudinal response may use pharmacogenetics to patent phenotypes. Genotyping of 14 candi tests that may never be used, hence date genes in 481 subjects participat blocking the markets of competitors; PHARMACOGENETICS AND ing in an inhaled steroid trial is also in indeed, nothing in the US patent PHARMACOGENOMICS progress. system prevents the use of patents to KNOWLEDGE BASE suppress an invention. Regardless of Prakash Nadkarni (Yale University) the motivations for the application of described efforts to provide infor KEYNOTE PHARMACOGENETICS pharmacogenetics and pharmaco matics support to enable end users to AND INTELLECTUAL PROPERTY genomics to drug development, mar interface with the PharmGKB data Rebecca Eisenberg (University of Mi keting, and distribution, the tradi base. A primary goal of the Nadkarni chigan) delivered the afternoon key tional allocation of payoffs will group effort is to streamline the daily note address on pharmacogenetics and inevitably be altered. In contrast to a operations of the PGRN. While easy intellectual property. Eisenberg few ‘blockbuster’ drugs, there may be a submission of data is an important opened her talk stating that the ‘big larger number of products with smal aspect to optimizing the potential of story’ surrounding patent-related is ler markets, and products previously PharmGKB, other day-to-day issues sues may not be about how to use seen as ‘too risky’ may find their way include utilizing PharmGKB as well as patents, but rather about what is not to market in carefully targeted clinical efficiently organizing laboratory data getting patented. Eisenberg speculated populations. Another change may into smaller databases. Assistance is on how patent-related issues may relate to the types of firms that can tailored to the expertise of the labora unfold in the fields of pharmacoge develop drugs; an altered payoff struc tory seeking help, and in general the netics and pharmacogenomics, ack ture may change the traditional attrac strategy used is to ‘teach people to fish nowledging that outcomes are yet to tion of investors to companies. Still vs fishing for them’. Nadkarni outlined be determined. Pharmacogenetics as a other ramifications may include a shift the many advantages of storing experi whole may be value-enhancing for in the balance between therapeutics mental results in databases rather than consumers of drugs, potentially pro and diagnostics, the latter convention spreadsheets, making data analysis viding pre-selected drugs for indivi ally a less remunerative market. and later data transfer a much more duals, albeit likely at higher costs. To systematic process. the benefit of pharmaceutical compa PharmGKB team leader Russ Altman nies, so-called ‘orphan drugs’ may PHARMACOGENETIC STUDIES IN (Stanford University) debuted the have a better chance of making it to ETHNIC POPULATIONS newly launched version of PharmGKB. market if target populations can be Julio Licinio (University of California, The mission of PharmGKB is to be identified early on in the development Los Angeles) presented an update on come an imperative tool for the phar process. The cost of drug trials may studies of genetic determinants of the macogenetics and pharmacogenomics also be reduced if non-responders can response of Mexican-Americans to research community, akin to databases be ‘weeded out’ early on in the clinical antidepressant medications. Only 60– such as GenBanks and PubMed. The testing process. As a case in point, the 65% of patients respond to antidepre goal is to make PharmGKB an active, industrial firms participating in the ssant drugs. Licinio’s group is in the not archival, resource of pharmacoge SNP Consortium have all agreed to process of collecting DNA from 500– netic and pharmacogenomic data, and place SNPs they identify into the 600 Mexican-Americans, phenotyping to disseminate results gathered by the public domain. Eisenberg suggested individuals, treating them with fluox PGRN to network members and the that this implied an example of an etine or desipramine (following a one- broader scientific community. The unusual application of the patent week placebo trial), then assessing the new launch of PharmGKB presents an system, where companies intention drug responses on a weekly basis. DNA organizational structure to house gen ally put information into the public samples are being genotyped by collab otypic and phenotypic data according domain as a way of freeing potentially orators at Los Alamos National to four classifiers: functional assays, valuable information from third-party Laboratory for later analysis with pharmacokinetics/pharmacodynamics, encumbrances. Such a strategy may respect to drug response data. Other clinical drug response, and patient speed access to resources that can be experimental approaches include ap outcome. Discussions are under way further developed by academia, there plying genomic tools (in rat studies) to to optimize this structure for data

www.nature.com/tpj Pharmacogenetics research network AF Davis and RM Long 296

input from PGRN members and the utilizes long-range PCR and intramo luation). In contrast to the traditional wider scientific community. A critical lecular ligation to perform successive single gene-phenotype pharmacoge challenge is in determining how to get rounds of allele-specific amplification. netic paradigm, CREATE aims to in access to phenotype data. Ongoing David Flockhart (Indiana University) vestigate the genetic variation existing improvements to PharmGKB include presented progress to date on examin in entire pathways influencing drug the possibility of posting a commu ing the genetic influences of tamox activity, using colorectal cancer as a nity-based submission query tool, in ifen and other selective estrogen model system. Colorectal cancer is a which any scientist working in the receptor modulators (SERMs) on var malignancy for which three drugs are area of pharmacogenetics or pharma ious clinically important parameters. in clinical use. In 113 genes, 840 SNPs cogenomics could suggest a drug–gene Tamoxifen was chosen as a SERM that have been discovered to date. Rese relationship for further analysis. Also exhibits many different pharmacolo quencing efforts are under way, and being investigated is the possibility of gic effects of clinical importance, in genotyping and gene expression stu implementing a similar-minded data- cluding therapeutic effects on breast dies are being conducted using micro- mining tool that would automatically cancer, osteoporosis, and atherogen arrays and antibody arrays created harness information and vocabulary esis. However, the drug also causes using tissue from rigorously quality- terms from other existing databases adverse effects such as hot flashes and controlled tumor banks. SNP frequen such as PubMed and OMIM. blood clots. The Flockhart group’s cies are being analyzed in several PharmGKB is seeking feedback from goals are to characterize tamoxifen populations to validate gene variants end users; please visit http:// metabolism in vitro and in vivo,to within drug pathways. www.pharmgkb.org to sign up to re isolate, confirm, and synthesize active ceive the PharmGKB newsletter, search metabolites, and to test the association for information, find resources, submit of genetic polymorphisms in cyto ACKNOWLEDGEMENTS data, or provide feedback on the chrome P450, eNOS, and transporter AFD is under contract 263-MD-205019 general utility and limitations of the and estrogen receptors with clinically database. Periodic data submissions to important SERM effects. Previous re DUALITY OF INTEREST PharmGKB will be published in the sults of a pilot clinical study showed None declared. journal Pharmacological Reviews. that the efficacy of tamoxifen was compromised in poor metabolizers; Correspondence should be sent to RM Long, Pharmacological and Physiological CANCER PHARMACOGENETICS co-administration of paroxetine can Sciences Branch, Division of Pharmacology, Mark Ratain (University of Chicago) mimic this effect. This study has now Physiology, and Biological Chemistry, 45 Center presented an update on the Pharma been expanded into a larger, prospec Dr., Rm. 2AS-49G, National Institute of General tive effort for which the initial re Medical Sciences, National Institutes of Health, cogenetics of Anticancer Agents Re Bethesda, MD 20892-6200,USA. search (PAAR) Group’s investigation of sponse of bone, lipid and blood Tel: + 301 594 1826 the pharmacogenetics of anticancer clotting parameters were presented. Fax: +301 480 2802 agents. Ratain reported that a geno In order to identify useful genetic E-mail: [email protected] type (variant in the UGT1A1 promo predictors of clinical response, and to ter) correlates with the development of determine their value relative to rou neutropenia in patients treated with tinely used clinical predictors such as irinotecan. Resequencing of DNA from age and menopausal status, a two-step, 1LongR. The Pharmacologist 1999; 41:60–61. 2 Diehn M, Alizadeh AA, Brown PO. MS JAMA human liver samples has identified iterative statistical procedure (‘PRESS’) 2000; 283: 2298–2299. several new polymorphisms; ongoing was described. PRESS is being used to 3 Haab BB, Dunham MJ, Brown PO. Genome studies are investigating whether any identify and authenticate genotypic Biol 2001; 2: research0004.1–0004.13 of these displays a phenotype of inter associations with a variety of clinical 4 Xu ZH, Freimuth RR, Eckloff B, Wieben E, Weinshilboum RM. Pharmacogenetics 2002; est. As part of an ongoing clinical trial parameters (eg bone density, choles 12: 11–21. of morphine glucuronidation, DNA terol levels) in an effort to determine 5 Freimuth RR, Eckloff B, Wieben ED, Wein from an ethnically diverse group of the pharmacogenetic profiles of wo shilboum RM. Pharmacogenetics 2001; 11: patients self-administering morphine men administered tamoxifen. The 747–756. 6 Pang Y-P, Zheng X-E, Weinshilboum RM. is being screened for new polymorph PRESS method can iteratively correct Biochem Biophys Res Common 2001; 287: isms in the UGT2B7 gene. Morphine for multiple, independent variables 204–208. metabolites have been measured, and and appears to be an innovative way 7 Silverman ES, Liggett SB, Gelfand EW, one allele has been found to be more to identify the most likely genetic Rosenwasser LJ, Baron RM, Bolk S et al. Pharmacogenomics J 2001; 1: 27–37. prevalent in low glucuronidators. Link predictors of clinical responses. 8 Drazen JM, Yandava CN, Dube L, Szczerback age disequilibrium was found with a Howard McLeod (Washington Uni N, Hippensteel R, Pillari A et al. Nat Genet known missense SNP that is thought versity) presented the goals and emer 1999; 22: 168–170. to have minimal, if any, function. The ging data of his research group, 9 Anand G.Wall Street J 18 June 2001; Section B, p 1: column 5. PAAR Group is also using a novel CREATE (Comprehensive Research on 10 Sherrid P. US News & World Rep. August molecular haplotyping method that Expressed Alleles in Therapeutic Eva 13, 2001; p 30.

The Pharmacogenomics Journal