Drug pathways: moving beyond single gene pharmacogenetics

The increasing complexity of mercaptopurine pharmacogenomics

Thiopurine methyltransferase (TPMT) activity shows significant interindividual variation, with approximately 90% of individuals having high (wild-type) activity, 10% with intermediate activity, and 0.3% with low activity. Low and intermediate TPMT activity leads to toxicity from mercaptopurine and the need for dose reduction. Common variants in the TPMT gene have a strong association with mercaptopurine toxicity. However, recent research has shown that genetic contribution to mercaptopurine toxicity is more complex, possibly involving other genes, in particular ITPA, which encodes inosine triphosphate pyrophosphatase.

Cancer pharmacogenetics

Cancer pharmacogenetics is a burgeoning field. There are now many published associations between genotype and outcome or toxicity from chemotherapy treatment. Performing pharmacogenetics studies in cancer requires careful consideration of the sample type to be used (germline vs tumor); the genotyping platform to be used (medium, low, or high throughput); and the analysis and reporting of associations and observations.

Pharmacogenetics and oncology treatment for breast cancer

Breast cancer is the second most common cause of cancer-related death in women in the US and the UK, accounting for 15-17% of all female cancer deaths. Current treatment strategies include hormone therapy, such as anti-estrogens (tamoxifen) and aromatase inhibitors (exemastane, anastrozole, letrozole), as well as cytotoxics, such as the taxanes (paclitaxel, docetaxel). With multiple therapy choices, a method to prospectively screen patients prior to therapy selection is now needed. Pharmacogenetics seeks to develop screening mechanisms to optimise drug therapy. DNA variations in metabolism, transport and drug target genes may contribute to chemotherapy efficacy and toxicities. The status of the identification of genetic markers for breast cancer therapy selection is highlighted in this review.

Pharmacogenetic analysis of paclitaxel transport and metabolism genes in breast cancer

Paclitaxel is commonly used in the treatment of breast cancer. Variability in paclitaxel clearance may contribute to the unpredictability of clinical outcomes. We assessed genomic DNA from the plasma of 93 patients with high-risk primary or stage IV breast cancer, who received dose-intense paclitaxel, doxorubicin and cyclophosphamide. Eight polymorphisms in six genes associated with metabolism and transport of paclitaxel were analyzed using Pyrosequencing. We found no association between ABCB1, ABCG2, CYP1B1, CYP3A4, CYP3A5 and CYP2C8 genotypes and paclitaxel clearance. However, patients homozygous for the CYP1B1*3 allele had a significantly longer progression-free survival than patients with at least one Valine allele (P=0.037). This finding could reflect altered paclitaxel metabolism, however, the finding was independent of paclitaxel clearance. Alternatively, the role of CYP1B1 in estrogen metabolism may influence the risk of invasive or paclitaxel resistant breast cancer in patients carrying the CYP1B1*3 allele.

Pharmacogenetics of colorectal cancer

Colorectal cancer is one of the most common types of cancer in both men and women. Multiple chemotherapy combinations exist; however, there is currently no strategy for individualised therapy selection prior to treatment. Genetic polymorphisms in genes involved in the metabolism, transport or targets for the commonly used chemotherapy drugs (5-fluorouracil, irinotecan and oxaliplatin) have been described. Many require validation in large prospective trials before they can be used as markers for outcome and/or toxicity. This review describes the data available on polymorphisms in key genes that are associated with chemotherapy toxicity and response in colorectal cancer.

PolyMAPr: programs for polymorphism database mining, annotation, and functional analysis

Pharmacogenomic and disease-association studies rely on identifying a comprehensive set of polymorphisms within candidate genes. Public SNP databases are a rich source of polymorphism data, but mining them effectively requires overcoming at least four challenges: ensuring accurate annotations for genes and polymorphisms, eliminating both inter- and intra-database redundancy, integrating data from multiple public sources with data generated locally, and prioritizing the variants for further study. PolyMAPr (Polymorphism Mining and Annotation Programs)' was developed to overcome these challenges and to improve the efficiency of database mining and polymorphism annotation. PolyMAPr takes as input a file containing a list of genes to be processed and files containing each annotated gene sequence. Polymorphic sequences obtained from public databases (dbSNP, CGAP, and JSNP) or through local SNP discovery efforts, as well as oligonucleotide sequences (e.g., PCR primers), are mapped to the annotated gene sequences and named according to suggested nomenclature guidelines. The functional effects of nonsynonymous coding-region SNPs (cSNPs) and any variants that might alter exon splicing enhancer (ESE) sites, putative transcription factor binding sites, or intron-exon splice sites are predicted. The output files are accessible though a browser interface. In addition, the results are also provided in Extensible Markup Language (XML) format to facilitate uploading them into a local relational database. PolyMAPr increases the efficiency of mining public databases for genetic variants within candidate genes and provides a mechanism by which data from multiple sources (both public and private) can be uniformly integrated, thereby significantly reducing the effort required to obtain a comprehensive set of polymorphisms for pharmacogenomic and disease-association studies. PolyMAPr can be obtained from http://pharmacogenomics.wustl.edu.

Irinotecan in the treatment of small cell lung cancer: a review of patient safety considerations

A water soluble derivative of camptothecin, irinotecan (CPT-11) is effective against small-cell lung cancer (SCLC), as well as non-SCLC and gastrointestinal cancers. This extended review of recently concluded and ongoing studies focuses on irinotecan in the treatment of limited (LD) and extensive (ED) SCLC specifically considering the safety of patients. Irinotecan-induced diarrhoea is pervasive, and can be severe and life-threatening especially in combination with neutropenia. It can have a significant impact on patient quality of life, negatively influencing compliance with therapy and dose-intensity. For LD SCLC, irinotecan can be administered with radiotherapy concurrently or sequentially. In a Phase III study for ED SCLC comparing etoposide and cisplatin (EP) and irinotecan and cisplatin (IP) regimens, severe myelosuppression was more frequent in the EP arm than in the IP arm, and conversely severe or life-threatening diarrhoea was more frequent in the IP arm than in the EP arm. IP resulted in significantly higher response rates and overall survival in Japan, and confirmatory Phase III studies are ongoing. Irinotecan should not be administered to patients with any degree of ongoing diarrhoea above their baseline. Irinotecan can be administered with relative safety for patients with SCLC only through careful patient monitoring, especially regarding diarrhoea and myelosuppression.

Taxane pharmacogenetics

The taxanes paclitaxel and docetaxel exert their anticancer activity by stabilizing microtubules during cell division. There is significant interindividual variability in response and toxicity between paclitaxel and docetaxel. Interpatient variability also exists for response and toxicity from each drug. Variability within genes involved in paclitaxel and/or docetaxel metabolism and transport exists. However, to date there is little evidence to suggest useful markers for the selection of individualized therapy. Epigenetic regulation of taxane pathway genes may play a large role in explaining the variability in toxicity and response.

Polymorphism discovery in 51 chemotherapy pathway genes

Candidate gene pharmacogenetic studies offer a strategy for the rapid assessment of putative predictive markers. As a first step toward studying the pharmacogenetics of cancer chemotherapy, 51 candidate genes from the pathways of antineoplastic agents were resequenced to identify common genetic polymorphisms that might alter therapeutic response or toxicity. Forty DNA samples were screened from each of three population groups: African-Americans, Asian-Americans and European-Americans. Nearly 378 kb of genomic sequence was obtained from each sample. Nine hundred and four variants were identified, including 139 coding single nucleotide polymorphisms (cSNPs). Three hundred and fifty-six (40%) polymorphisms were common to all three populations and 366 (41%) were population specific. Three hundred and forty-six (38%) variants were novel polymorphisms that were not present in the three public databases that were examined. One hundred and eleven (35%) of the 319 non-synonymous cSNPs that were identified by either resequencing or database mining were predicted by PolyPhen to be either possibly or probably damaging. For the non-synonymous cSNPs identified by resequencing, both the number of cSNPs found and the maximum estimated allele frequency decreased with increasing predicted severity. These results provide experimental validation and estimated allele frequencies for polymorphisms in three common ethnic groups and facilitate applied pharmacogenetic studies of anticancer drugs.

Pharmacogenetics of irinotecan toxicity

Irinotecan is an anticancer drug approved in combination therapy for advanced colorectal cancer. Severe, life-threatening toxicities can occur from irinotecan treatment. Although multiple genes may play a role in irinotecan activity, the UDP glycuronosyltransferase 1 family, polypeptide A1 (UGT1A1) enzyme has been strongly associated with toxicity. A common dinucleotide repeat polymorphism in the UGT1A1 promoter region (UGT1A1*28) has been correlated with severe toxicity in cancer patients receiving irinotecan-containing therapy. Prospective screening of patients prior to chemotherapy selection may reduce the frequency of severe toxicities by allowing alternate therapy selections for patients carrying the UGT1A1*28 polymorphism.