Current Pharmacogenomics

ISSN: 1570-1603

Current Pharmacogenomics
Volume 5, Number 2, June 2007

Contents


Cancer Pharmacogenomics: Germline DNA, Tumor DNA, or Both? Pp. 87-101
E. Cerri, A. Falcone and F. Innocenti
[Abstract]


Clinical Significance of Thiopurine S-Methyltransferase Gene Polymorphisms Pp. 103-115
S.-F. Zhou and B. Chowbay
[Abstract]


Pharmacogenomics in Colorectal Cancer Pp. 117-123
F. Meriggi, B. Di Biasi, C. Caliolo and A. Zaniboni
[Abstract]


Genetics and the Mechanisms of Action of Inhaled Anesthetics Pp. 125-147
L.M. Steele, P.G. Morgan and M.M. Sedensky
[Abstract]


Pharmacogenetics of Oxazaphosphorines and its Clinical Implications Pp. 143-156
S.-F. Zhou, B. Chowbay and C.C. Xue
[Abstract]


Structural and Functional Organization of miRNAs Pp. 157-166
E. Enerly, R. Sachidanandam, D.K. Pant, A.L. Børresen-Dale and V.N. Kristensen
[Abstract]




Abstracts


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Cancer Pharmacogenomics: Germline DNA, Tumor DNA, or Both?
E. Cerri, A. Falcone and F. Innocenti

There is clear evidence that genetic information could be used to optimize treatment of cancer patients. The therapeutic index of chemotherapy could be enlarged by reducing the risk of toxicity, increasing the likelihood of tumor response, or both. Although germline DNA information has been already used to identify patients at high risk of toxicity, it is a matter of debate whether it could be also used to predict tumor response. Due to the intrinsic chromosomal and genetic instability of the tumor genome, recent evidence supports the concept that tailoring of chemotherapy in cancer patients might be better achieved by mutational analysis of patient tumor DNA. However, a proportion of germline variation is still retained in the DNA of cancer cells. Hence, we cannot exclude that germline genetic variation might be informative of a particular tumor phenotype.

This review will provide a thorough analysis of the role of germline and tumor DNA variation in cancer pharmacogenomics. It will discuss the prediction of toxicity risk by means of germline genetic make up of patients, using irinotecan-UGT1A1 and 6-mercaptopurine-TPMT as two examples. This review will also provide evidence of the role of tumor mutational analysis to predict tumor response and the emergence of clinical resistance to therapy, using the examples of 1) EGFR somatic mutations in lung cancer patients treated with EGFR-inhibitors, and 2) BCR-ABL and KIT somatic mutations in chronic myeloid leukemia and gastrointestinal stromal tumor patients treated with imatinib. The clinical relevance of loss of heterozygosity in tumor samples will be elucidated by describing the findings on the thymidylate synthase gene in colorectal cancer patients treated with fluoropyrimidines. The karyotypic abnormalities in the TPMT in acute lymphoblastic leukemia patients provide evidence that the germline genotype of cancer cells might be different from the cellular phenotypes. In addition, the clinical impact of the germline TPMT and CYP2D6 genetic variation for patient response will be discussed. Finally, the role of gene amplification and its interplay with somatic mutations of the EGFR in lung cancer patients will be reviewed.


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Clinical Significance of Thiopurine S-Methyltransferase Gene Polymorphisms
S.-F. Zhou and B. Chowbay

Thiopurine methyltransferase (TPMT) is an important enzyme that catalyzes the S-methylation of a series of thiopurine drugs, including 6-mercaptopurine (6-MP), thioguanine and azathiopurine (AZA), to generate inactive methylated metabolites. Thiopurine drugs are widely used to treat malignancies such as acute lymphoblastic leukemia, autoimmune diseases (e.g. inflammatory bowel disease and rheumatoid arthritis), and organ transplant rejection. TPMT activity and TPMT gene exhibit marked polymorphic phenomenon among all ethnic populations studied, though ethnic differences are always observed. To date, a number of TPMT alleles have been identified. The three major alleles of TPMT, namely TPMT *2, *3A and *3C, lead to intermediate and low enzyme activity in 80–95% carriers. Almost all alleles of TPMT result from single nucleotide polymorphisms (SNPs). Patients with very low levels of TPMT activity due to genetic mutation suffer from greatly increased risk for thiopurine-induced toxicity such as myelosuppression when treated with standard doses of thiopurine drugs, while subjects with very high activity may be under-treated. Drug interactions, less frequently observed, may occur due to TMPT induction or inhibition when thiopurine drugs are combined with other agents. It is important to identify the TPMT mutant alleles with functional impact and the clinical relevance to thiopurine therapy. This allows us to avoid severe toxicity and improve therapeutic outcome by tailoring dosage and regimens in individual patients.


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Pharmacogenomics in Colorectal Cancer
F. Meriggi, B. Di Biasi, C. Caliolo and A. Zaniboni

Several developments in the past few years have incrementally progressed the field and provided additional insights into the management of advanced colorectal cancer. The equivalence of several front-line regimens based on fluorouracil, capecitabine, oxaliplatin, irinotecan, bevacizumab, and cetuximab has provided opportunities for increased tailoring of therapies for individual patients. Nevertheless, some patients may suffer from the adverse drug reactions which will probably be the main cause of chemotherapy failure. The goal of pharmacogenomics is to find correlations between clinical responses to drugs and the genetic profiles of patients. Genes which codify for the metabolism enzymes, receptor proteins, or protein targets of chemotherapy agents often present various genetic polymorphisms. An assay is already commercially available for genotypic testing of the enzyme UGT1A1 which is predictive of toxicity from irinotecan. The advent of high-throughput methodologies, such as microarrays, enables tumor samples to be profiled on a global scale. Genes which may represent molecular signatures of sensitivity to fluorouracil and oxaliplatin has been identified with DNA microarray analysis.


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Genetics and the Mechanisms of Action of Inhaled Anesthetics
L.M. Steele, P.G. Morgan and M.M. Sedensky

Inhaled anesthetics have been used for more than a century, and they are currently administered to millions of patients each year. Although well understood in an empirical sense, their basic molecular mechanisms of action are still unknown. During the past two decades, a large amount of evidence has been presented that is most consistent with the hypothesis that inhaled anesthetics act at multiple sites. For example, genetic mutations exist that distinguish between different inhaled anesthetics, i.e. the mutations alter sensitivity to some anesthetics differently than others. Since it is probable that multiple mechanisms contribute to inhaled anesthetic action, a genetic approach is a powerful method for sorting out which molecules are involved in specific anesthetic effects. This review describes recent pharmacogenetic studies performed using model organisms, including yeast, nematodes, fruit flies, and mice. At first glance, the results of these studies are notable for their lack of a common putative molecular target. In fact, the results suggest that anesthetics interact with a seemingly broad range of cellular components including ion channels, membrane receptors, lipid rafts, and the mitochondrial electron transport chain. However, a unifying theme is beginning to emerge, one that implicates the presynaptic neuron as a common functional target for inhaled anesthetics. Intriguing similarities among the results suggest that many of the findings obtained in model organisms can be generalized across disparate phyla, and that the findings will be applicable in humans. By continuing to exploit the power of genetics, such studies are likely to unravel the great mystery of how inhaled anesthetics produce their effects.


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Pharmacogenetics of Oxazaphosphorines and its Clinical Implications
S.-F. Zhou, B. Chowbay and C.C. Xue

The oxazaphosphorines including cyclophosphamide and ifosfamide represent an important group of drugs because of their wide use as antitumor and immuno-modulating agents. This review highlights the effects of polymorphisms of genes involved in the action, distribution, metabolism, and transport of oxazaphosphorines on their pharmacokinetic variability and therapeutic outcomes. Emerging data indicate that polymorphisms of genes encoding cytochrome P450 (CYP) enzymes (CYP3A4, CYP2B6, and CYP2C9), aldehyde dehydrogenases (ALDH1A1, ALDH3A1), glutathione S-transferases (GSTT1, GSTM1, GSTP1), multidrug resistance-associated proteins (ABCC1 and ABCC2), and methylguanine-DNA methyltransferase (MGMT) play an important role in the wide interindividual pharmacokinetic variability and altered clinical outcome of oxazaphosphorine chemotherapy. For example, CYP2B6*5 (C1459T giving rise to an Arg487Cys substitution) and CYP2C19*2 (C430T) are associated with altered response, toxicity, and survival in patients with proliferative lupus nephritis when treated with pulse cyclophosphamide regimens. In paediatric patients with corticosteroid-sensitive nephrotic syndrome, treatment with cyclophosphamide in patients with a GSTM1 null polymorphism gave a significantly higher rate of sustained remission than in patients with the heterozygous or homozygous GSTM1 wildtype. Preliminary preclinical and clinical studies indicate that a number of genetic polimorphisms can affect the disposition and action of oxazaphosphorines, causing large interpatient variability in their pharmacokinetics, response rate and toxicity. A full identification of the role of these genetic polymorphisms would allow the identification of useful and novel strategies to overcome the resistance and toxicity of oxazaphosphorines and to design optimal therapeutic regimens.


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Structural and Functional Organization of miRNAs
E. Enerly, R. Sachidanandam, D.K. Pant, A.L. Børresen-Dale and V.N. Kristensen

Understanding human gene regulation is of pivotal importance in the field of genetics and genomics, including pharmacogenomics. Increasingly many described effects of natural genetic variation are exerted on the level of gene regulation. A novel mechanism of regulation of gene expression involving the so called the non coding microRNAs (miRNAs) has attracted a lot of attentions during the last years. MicroRNAs are a class of endogenous small regulatory RNA molecules that target mRNAs and trigger either translation repression or mRNA degradation. They are known to regulate genes involved in the control of development, proliferation, apoptosis, stress response, and tumourigenesis. They are transcribed as individual units, polycistronic clusters or in concert with a protein coding host gene. The picture emerging reveals a widespread influence on many cellular processes. The analysis of miRNA regulation and its involvement in diseases is hampered by the great redundancy of miRNA genes and the unknown complexity in the modular regulatory mechanisms they may exert. An individual’s genetic background will in addition influence this regulation. This review provides insights into the complexity of human miRNA organization, and may facilitate future analysis of miRNA expression as well as studies of the modular regulatory effects of miRNAs.