Use Of Pharmacogenomics Research Articles

Improving Training in Laboratory Medicine

In this issue of Clinical Chemistry , we publish a proposal for curriculum content of residency training in laboratory medicine and for evaluation of resident competency (1). The proposal was developed by the Academy of Clinical Laboratory Physicians and Scientists (ACLPS) and covers residency training in all areas of laboratory medicine. Why have we chosen to publish this curriculum? Why did we publish the entire document, rather than just the portion related to clinical chemistry? Why is the curriculum important to the readers of Clinical Chemistry —particularly PhD and MD laboratory directors? In a broad sense, the first reason for publishing the document is that it represents a comprehensive, well-written template for curriculum content for training of residents in laboratory medicine. Because Clinical Chemistry is a leading journal in laboratory medicine, we know that many of those individuals who are responsible for training pathology residents are among our readers and are members of AACC, which publishes the journal. Now is an important time to address the curriculum of residency programs. As the authors of the curriculum document clearly state in their introduction, the field of laboratory medicine and training in pathology have changed dramatically since the last consensus recommendations were published in 1995 (2). At that time, routine molecular diagnostics was just beginning, the clinical use of pharmacogenomics was only being hinted at, “proteomics” consisted of 2-dimensional gels and serum protein electrophoresis, point-of-care testing was primarily portable glucose meters, and electronic medical records existed only in the VA system. Simultaneous to this explosion of knowledge and technology, the length of residency training in pathology was decreased by 1 year for both combined anatomic pathology/clinical …

Pharmacogenomics: Its Role in Re-establishing Coumarin as Treatment for Lymphedema

Although there remains some significant controversy regarding the use and benefits of coumarin (5,6-benzo-alpha pyrone), it would seem that targeted appropriate and monitored use of the drug does have a significant role in the treatment of lymphedemas. The particular benefits are its cost and ease of administration. Given today's demands for high level investigative clinical trials, it would be virtually impossible to conduct a study large enough to make any significant conclusions about hepatotoxic effects. However, it seems without doubt that the majority of studies conducted thus far suggest that coumarin (and other benzopyrones, i.e., the ruto-sides, which do not have hepatotoxic effects and which are often discussed in aggregate with coumarin) is effective in treating lymphedema, particularly when used in conjunction with complex physical therapy. The use of pharmacogenomics could significantly lower the risk of coumarin-associated hepatotoxicity, by targeting the use of coumarin to those with functional CYP2A6. Further research in this area will be required to re-evaluate the cost- benefit ratio and to determine the potential for the reintroduction of coumarin as a potent treatment for lymphedema. The perceived negative image of coumarin should not be allowed to carry across to the other benzopyrones, as they still confer a significant benefit in the management of lymphedemas.

Ethics, genetics and familial cancer

Genomics is hailed as the solution to many of the healthcare challenges of our generation. In the UK, where morbidity from most infectious diseases has been dramatically reduced for decades, inherited conditions have taken on a new prominence. Analysis of the human genome by the oft-cited Human Genome Project is seen as the door to a technological world where drug therapy will be made more effective by the use of pharmacogenomics, and where treatment of disease with gene-based therapies will be a realistic option.

Pharmacology of oxaliplatin and the use of pharmacogenomics to individualize therapy

Oxaliplatin is a relatively new platinum analogue that is currently used in pharmacotherapy of metastatic colorectal cancer. Its dose-limiting toxicity is sensory neuropathy, which can be modulated by infusion of calcium and magnesium. Oxaliplatin exerts its anti-tumour effects by platinum-adduct formation, binding to cellular proteins and possibly interfering with RNA synthesis as well. If they are not removed from DNA, oxaliplatin adducts are lethal. Cellular defense mechanisms prevent adduct formation (e.g., glutathione-S-transferase) or remove DNA adducts (e.g., nucleotide excision repair). Depending on the activity of necessary enzymes in these cellular defense pathways, oxaliplatin induced damage varies from one individual to another. There is growing evidence that polymorphisms in genes coding for DNA repair enzymes and metabolic inactivation routes contribute to the interindividual differences in anti-tumour efficacy and toxicity of oxaliplatin. Single nucleotide polymorphisms (SNPs) may yield inactive enzymes, or increased gene transcription and hence increased enzyme production. This review covers findings of recent investigations on the associations of SNPs and clinical outcome after oxaliplatin chemotherapy in metastatic colorectal cancer.

A systematic review of cost-effectiveness analyses of pharmacogenomic interventions

Cost-effectiveness analysis is a widely used tool to assess the value of healthcare interventions. Our objective was to conduct a systematic review of the literature on the cost effectiveness of pharmacogenomic interventions. We found 11 studies that met our inclusion criteria. The most commonly examined disease was deep vein thrombosis (n=4), followed by cancer (n=3) and viral infections (n=3); the most frequently examined mutation was factor V Leiden (n=5); and the majority of the mutations examined were inherited mutations (n=7), although several studies looked at acquired (tumor or viral) mutations (n=4). The majority of the studies reported a favorable cost-effectiveness ratio for the pharmacogenomic-based strategy (n=7), while two studies reported that the pharmacogenomic-based strategy was not cost effective and two were equivocal. We conclude that there have been few evaluations of the economic costs and benefits of pharmacogenomic interventions and they have covered a limited number of conditions. Further analyses that can be used to guide the use of pharmacogenomics in clinical practice and in developing health policies are urgently needed.

Growth factor signaling and resistance to cancer chemotherapy.

Multiple mechanisms contribute to chemoresistance, eventually leading to failure of cancer chemotherapy. Deregulated growth factor signaling pathways promote cell proliferation and render cancer cells resistant to apoptosis, a common mechanism of chemoresistance. Therefore, inhibitors of growth factor signaling, including antibodies and small molecules, are promising drug candidates for chemotherapy, either given alone or as adjuvants to overcome general drug resistance. While dramatic responses have been attained in some cases, innate or acquired resistance to these novel anticancer drugs is common and limits broad applicability. Treatment failure may arise from complexity of growth factor signaling, with numerous parallel pathways and diverse downstream events. This review discusses the use of pharmacogenomics, assessing multiple growth factor signaling pathways and complex chemoresistance mechanisms. Monitoring expression profiles and activating mutations in growth factor receptors holds promise for the design of individualized therapy with a combination of drugs.

Use of pharmacogenomics in predicting bleomycin-induced pulmonary toxicity in testicular cancer patients

4531 Background:Use of bleomycin, important for treatment efficacy in testicular cancer, is limited by its pulmonary toxicity. Bleomycin is mainly excreted by the kidneys, but can also be inactivated by bleomycin hydrolase (BLH). An A1450G polymorphic site in the BLH gene results in an amino acid substitution in the C-terminal domain of the protein. Deletion of this domain reduces enzymatic activity. We investigated whether the homozygote polymorphic BLH genotype increases sensitivity to bleomycin and risk of bleomycin-induced pulmonary toxicity (BIP) in testicular cancer patients. METHODS: For all patients with testicular cancer treated with bleomycin combination chemotherapy at our institution between 1977 and 2003, data were collected on age, pretreatment creatinine clearance, and occurrence of BIP, which was defined as: death due to BIP, or clinical and/or radiographic signs of BIP either following treatment or during treatment leading to cessation of bleomycin administration. PCR and restriction fragment length polymorphism were used to determine A/A (wild-type), A/G, and G/G (two polymorphic alleles, possibly reduced enzymatic activity)genotypes. RESULTS: Both genotype and clinical data were available for 246 patients (60% of cohort; median age 29 yrs, range 16-64; median cumulative bleomycin dose 270 mg, range 60-360; median pretreatment creatinine clearance 122 ml/min, range 64-202), of whom 27 (11%) had BIP. A/A, A/G, and G/G genotype frequencies were 41.9%, 48.4% and 9.7%. G/G genotype distribution did not differ between patients with and without BIP (7.4% versus 10.0%; odds-ratio G/G versus A/A genotype: 0.53, 95% confidence interval 0.11-2.51). Patients with BIP had a lower creatinine clearance. CONCLUSIONS: Compared with patients without BIP, patients with BIP were not more likely to have a G/G than an A/A genotype. However, effects of BLH genotype may become visible in patients with markedly reduced creatinine clearance. Supported by grants from the Dutch Cancer Society and the University Hospital Groningen. No significant financial relationships to disclose.

Use of pharmacogenomics in predicting bleomycin-induced pulmonary toxicity in testicular cancer patients

4531 Background:Use of bleomycin, important for treatment efficacy in testicular cancer, is limited by its pulmonary toxicity. Bleomycin is mainly excreted by the kidneys, but can also be inactivated by bleomycin hydrolase (BLH). An A1450G polymorphic site in the BLH gene results in an amino acid substitution in the C-terminal domain of the protein. Deletion of this domain reduces enzymatic activity. We investigated whether the homozygote polymorphic BLH genotype increases sensitivity to bleomycin and risk of bleomycin-induced pulmonary toxicity (BIP) in testicular cancer patients. Methods:For all patients with testicular cancer treated with bleomycin combination chemotherapy at our institution between 1977 and 2003, data were collected on age, pretreatment creatinine clearance, and occurrence of BIP, which was defined as: death due to BIP, or clinical and/or radiographic signs of BIP either following treatment or during treatment leading to cessation of bleomycin administration. PCR and restriction fragment length polymorphism were used to determine A/A (wild-type), A/G, and G/G (two polymorphic alleles, possibly reduced enzymatic activity)genotypes. Results:Both genotype and clinical data were available for 246 patients (60% of cohort; median age 29 yrs, range 16–64; median cumulative bleomycin dose 270 mg, range 60–360; median pretreatment creatinine clearance 122 ml/min, range 64–202), of whom 27 (11%) had BIP. A/A, A/G, and G/G genotype frequencies were 41.9%, 48.4% and 9.7%. G/G genotype distribution did not differ between patients with and without BIP (7.4% versus 10.0%; odds-ratio G/G versus A/A genotype: 0.53, 95% confidence interval 0.11–2.51). Patients with BIP had a lower creatinine clearance. Conclusions:Compared with patients without BIP, patients with BIP were not more likely to have a G/G than an A/A genotype. However, effects of BLH genotype may become visible in patients with markedly reduced creatinine clearance. Supported by grants from the Dutch Cancer Society and the University Hospital Groningen. No significant financial relationships to disclose.

Adverse drug reactions: role of pharmacogenomics

Adverse drug reactions (ADRs) are a significant cause of morbidity and mortality. The majority of ADRs can be considered common disorders with considerable clinical variability (clinical phenotype) in which many different genes are involved together with environmental variables. Pharmacogenomics is the study of how genes affect the individual response to drugs. There is some evidence that in the future the use of pharmacogenomics could help to reduce ADRs, as it aims to predict which patients are likely to respond to a particular drug and which patients are likely to have significant ADRs. In this article some examples of genetic polymorphisms affecting drug kinetics, drug toxicity and hypersensitivity related to ADRs are illustrated.

Use of pharmacogenomics in clinical trials for multiple sclerosis

Multiple sclerosis (MS) is a T‐cell mediated autoimmune disease of the central nervous system. Its pathology is characterized by inflammation, demyelination, gliosis and axonal loss. Substantial heterogeneity exists at the levels of genetic susceptibility, clinical presentation and immunological factors as well. While we begin to realize the complexity of multiple sclerosis, it is currently not possible to assess the contributing factors appropriately since biomarkers other than magnetic resonance imaging are lacking. Standard treatment of MS includes interferon‐beta and glatiramer acetate for relapsing–remitting MS. Rapidly progressing and very active disease is treated by conventional immunosuppression with mitoxantrone, cyclophosphamide or other chemotherapeutics, and numerous experimental treatments are currently in testing. Given the complexity of the disease process and its variability between patients, it is no surprise that the response to each of the above treatments is overall modest. Recent developments of large scale gene expression arrays and proteomics approaches allow us to capture many markers and parts of entire biochemical pathways such as apoptosis or proinflammatory responses simultaneously in individual patients. We have begun to employ cDNA or oligonucleotide microarrays to assess the response to the above therapies first in vitro and later, after initiation of treatment, in vivo. These tools will be useful in defining new biomarkers for MS, to gain a better understanding of disease pathogenesis, but particularly also for developing new therapies for MS, identifying responders and nonresponders and rationale combination therapies.

Ethical perspectives on pharmacogenomic profiling in the drug development process.

Pharmacogenomics, which is a field that encompasses the study of genetic polymorphisms that underlie individual differences in drug response, is rapidly advancing. The potential for the widespread use of pharmacogenomics in the drug development process merits an examination of its fundamental impact on clinical-trial design and practice. This article provides a critical analysis of some of the issues that pertain to pharmacogenomics in the drug development process. In particular, four areas will be discussed: clinical-trial design; subject stratification; some new social risks; and economic concerns. Recommendations are offered for addressing the issues that are discussed and anticipating the regulatory needs for pharmacogenomics-based trials.

Cystic fibrosis and the use of pharmacogenomics to determine surrogate endpoints for drug discovery.

Cystic fibrosis (CF) is caused by a mutation in the CFTR gene, encoding a chloride channel. For the most common mutation, Delta F508, the basis of the deficit is the failure of the mutant CFTR channel protein to traffic properly to the apical plasma membrane of the affected epithelial cell. The trafficking failure results in loss of the cyclic adenosine monophosphate (cAMP)-activated chloride channel function of the CFTR protein in the plasma membrane. The lung is the principal site affecting patient morbidity and mortality in CF. The main reason is that the CF airway epithelial cells also secrete high levels of the proinflammatory cytokine interleukin (IL)-8, resulting in massive cellular inflammation, infection, tissue damage and lung destruction. The relationship between the trafficking defect, the loss of chloride channel activity, and inflammation is not known. However, gene therapy of CF lung epithelial cells with the wild-type CFTR gene can repair the chloride channel defect, as well as suppress the intrinsic hypersecretion of IL-8. Repair of both defective channels and high IL-8 secretion can also be effected by treatment with the candidate CF drug CPX, which is in clinical trials in CF patients. CPX acts by binding to the mutant CFTR protein, and helps the protein to mature and gain access to the plasma membrane. CPX also suppresses the synthesis and secretion of IL-8 from CF epithelial cells, presumably by virtue of its repair of the trafficking defect of mutant CFTR. To guide pharmacogenomic experiments we have therefore hypothesized that the genomic signature of CF epithelial cells treated with CPX should resemble the signature of the same cells repaired by gene therapy. We have developed two algorithms for identifying genes modified by repair of CFTR defects. The GRASP algorithm uses a statistical test to identify the most profoundly changing genes. The GENESAVER algorithm allows us to identify those genes whose pattern of expression changes in-phase or out-of-phase with IL-8 secretion by CF cells. For the latter algorithm we modified IL-8 secretion from CF cells by treatment with wild-type CFTR, with CPX, or by exposure to bacteria. The results have supported the hypothesis, and have provided a basis for considering the common pharmacogenomic expression signature as a surrogate endpoint for CF drug discovery. Significantly, the nature of the hypothesis, as well as the algorithm developed for this study, can be easily applied to pharmacogenomic studies with other goals.

Ethical considerations in clinical pharmacogenomics research

In recent years there have been unprecedented advances in our understanding of the involvement of genetic polymorphisms in the response to drug therapies. Polymorphisms have been identified that lead to variable patient responses to several medications including cardiovascular, psychiatric, anti-infective and analgesic therapies. The potential for the development of customized, genotype-based therapies is scientifically and clinically attractive. However, these developments, although bearing scientific promise, raise ethical concerns for the conduct of research with human subjects, particularly with respect to confidentiality, risk–benefit analysis, DNA-banking and pharmacoeconomic issues. This article discusses some of the ethical considerations that are related to the use of pharmacogenomics in clinical research protocols.

Role of pharmacogenomics in the drug development

Individuals respond differently to drugs and sometimes the effects are unpredictable. Differences in DNA that alter the expression or function of proteins targeted by drugs can contribute significantly to the variation in the individuals responses. The use of pharmacogenomics is to identify genetic polymorphisms that predispose patients to adverse drug effects that, although they may occur in only a small subset of the people treated with a new medication, are sufficiently toxic to jeopardise further development of the drug for all patients. Given the potential value of knowing all the possible factors that influence the effects of new agents, it is likely that pharmacogenomics will have an increasingly important role in drug discovery and development. This article briefly reviews concepts that underlie the emerging fields of pharmacogenetics and pharmacogenomics, with an emphasis on the pharmacogenetics of drug metabolism. Although only a few examples will be provided to illustrate concepts and to demonstrate the potential contribution of pharmacogenetics to medical practice, it is now clear that virtually every pathway of drug metabolism will eventually be found to have genetic variation.