Review For reprint orders, please contact [email protected]

Integrating pharmacogenomics into oncology clinical practice Sharon Marsh† and Michael S Phillips

Germline genome

Oncology pharmacogenomics has seen a great deal of progress in the past 10 years. The release of the Human Genome Project data and the availability of fast, affordable genotyping platforms has allowed the field to expand and has provided invaluable data for pharmacogenomics research. The introduction of US FDA-approved targeted therapy (trastuzumab), package insert changes (irinotecan and tamoxifen) and the initiation of a genotype-guided clinical trial for cancer therapy (TYMS TSER in rectal cancer), along with panels of DNA and expression markers (Roche AmpliChip® and Oncotype Dx™ panel) are paving the way towards the integration of pharmacogenomics into clinical practice.

Tumor genome

Expert Rev. Clin. Pharmacol. 1(1), 73–80 (2008)

Expert commentary

Oncology offers an ideal opportunity for pharmacogenomics research. For many cancers, multiple treatment options are often available with no clear rationale for treatment selection [1–3]. Ideally, screening patients for pharmacogenomic markers prior to therapy selection would allow for personalized treatment, reducing the incidence and severity of adverse drug reactions, increasing the likelihood of response and allowing successful therapy to be performed before the ideal therapeutic window has passed [1]. However, although the ultimate goal of pharmacogenomics involves integration into clinical practice, there are still a limited number of examples in the field of oncology where this is either happening or likely to happen in the near future. Initial studies focusing on polymorphisms in the thiopurine methyltransferase (TPMT) gene identified a strong correlation between TPMT genotype and toxicity from drugs such as mercaptopurine [4], leading to the US FDA revising the mercaptopurine package insert to incorporate pharmacogenetic information [101]. The TPMT studies have been a building block for the use of pharmacogenomic markers in oncology. This review highlights recent work in oncology pharmacogenomics.


Five-year view Financial & competing interests disclosure Key issues References Affiliations

Author for correspondence Washington University in St Louis, Division of Oncology, 660 South Euclid Ave — Campus Box 8069, St Louis, MO 63110, USA Tel.: +1 314 747 5186 Fax: +1 314 362 3764 [email protected] KEYWORDS: chemotherapy, expression, genotype, oncology, pharmacogenetics, pharmacogenomics, polymorphism

Germline genome

Polymorphisms (mutations present in at least 1% of the population) are detectable in germline


DNA. This is ideal for pharmacogenomic studies as the DNA is readily accessible (e.g., blood or saliva), the collection procedure is minimally invasive and the DNA has a high yield and is good quality, making it amenable to a range of diagnostic techniques and allowing for a large number of analyses. Recently, the FDA have made efforts to include dosing information based on genotype into package inserts for medication where strong pharmacogenomic evidence is available. Irinotecan

Irinotecan is a chemotherapy drug often used in combination with 5-fluorouracil (5-FU) or oxaliplatin. Side effects for patients receiving irinotecan include severe life-threatening diarrhea and/or neutropenia [5]. The active form of irinotecan, SN-38, can be inactivated through glucuronidation by a member of the UDP-glucuronosyltransferase family, UGT1A1. The UGT1A1 enzyme is responsible for hepatic bilirubin glucuronidation and is the main UGT1A enzyme involved in SN-38 glucuronidation. A polymorphic dinucleotide repeat has been identified in the UGT1A1 promoter TATA element (standard nomenclature UGT1A1*28), consists of five, six, seven or eight copies of a TA repeat [(TA)nTAA], with the (TA)6TAA allele the most common and

© 2008 Future Drugs Ltd

ISSN 1751-2433


Marsh & Phillips

(TA)7TAA (*28) the most frequent variant allele [6]. The longer the repeat allele, the lower the corresponding UGT1A1 gene expression [6]. Consequently, patients with the seven and eight repeat alleles have significantly reduced UGT1A1 expression. The frequency of the UGT1A1*28 (TA)7TAA allele has been well characterized and is found in approximately 26–38% of Caucasian, Hispanic and African–American populations, with a lower frequency in Asians (∼15%) and higher in sub-Saharan Africans (∼45%) [7–9]. As UGT1A1 is responsible for the conversion of SN-38 to the inactive metabolite, SN-38G, via glucuronidation, variability in UGT1A1 expression leads to interindividual variation in SN-38G formation [10,11]. Consequently, the presence of seven or eight TA repeats in the UGT1A1 promoter region leads to reduced SN-38G formation and the potential for excess SN-38 to be retained in the cell, leading to severe toxicity. Several studies have confirmed the link between UGT1A1 genotype and severe toxicity from irinotecan therapy [9–13]. In 118 Japanese cancer patients treated with irinotecan-containing chemotherapy, UGT1A1*28 was an independent predictor of grade III/IV toxicity [9]. In addition, a study of 20 US patients treated with single-agent irinotecan identified associations in patients homozygous for UGT1A1*28 and with grade III/IV toxicity [12]. Subsequently, a prospective Phase I trial of 66 patients with solid tumors who were treated with irinotecan correlated the number of UGT1A1*28 alleles with the incidence of grade IV neutropenia (p < 0.001) [13]. Based on the available data for UGT1A1*28 and irinotecan toxicity, the FDA requested the inclusion of UGT1A1 genotype information in the drug package insert, with recommended dose reductions based on genotype [14]. The FDA have also approved a clinical test for the UGT1A1*28 allele, which is supplied by Third Wave Technologies (WI, USA) [102]. Concerns

The approval of the UGT1A1*28 clinical test and amendment of the irinotecan package insert by the FDA is excellent progress for pharmacogenomics research. However, there are concerns over the actual dosing required per genotype. Indeed, the relationship between UGT1A1*28 and irinotecan toxicity may well be dependant on the irinotecan regimen used. At lower doses (80–150 mg/m2), the relationship between genotype and toxicity does not appear to be clinically significant, whereas at a medium dose (150–250 mg/m2), the risk of severe (grade III/IV) hematological toxicity in patients homozygous for UGT1A1*28 is 3.2-times higher than for patients heterozygous or homozygous for UGT1A1*1 (p = 0.008) and, at high irinotecan doses (200–350 mg/m2), the risk is 27.8-times higher (p = 0.005) [15]. In addition, there is a potential risk of under-dosing patients with wild-type UGT1A1 activity when treating all patients with a standardized dose, and this possibility needs to be elucidated. This indicates that it might be necessary to further amend the irinotecan package insert to include specific dose/genotype guidelines.


In addition to possible dose specificity, UGT1A1*28 does not predict all irinotecan toxicity. Consequently, testing only for UGT1A1*28 may miss some of the patients at risk as it cannot be assumed that the absence of UGT1A1*28 means the patient is not at risk for toxicity, especially in the case of ethnic groups with low incidence of UGT1A1*28, such as Asian populations [16]. Other polymorphisms within UGT1A1 may also play a role in irinotecan toxicity [17–22]. For example, in 81 Korean patients with non-small-cell lung cancer treated with irinotecan and cisplatin, associations were identified between UGT1A1*6 (211G>A; G71R) genotype, irinotecan pharmacokinetics and toxicity [22]. Pharmacogenomic assessment of other genes encoding drugmetabolizing enzymes and transporters involved in the irinotecan pathway has been performed [19,23]. Variants in other members of the UGT gene family, specifically UGT1A7 and UGT1A9, are associated with irinotecan toxicities [24]. In addition, a haplotype in the multidrug transporter ABCC2 predicts toxicity in patients who do not carry UGT1A1*28 [21]. Pharmacodynamic irinotecan genes are less well characterized, but preliminary data suggest toxicity is associated with the topoisomerase (TOP)1 intronic variant IVS4+61, and a trend towards severe neutropenia is seen with a diplotype (combination of haplotypes) in PARP1 [20]. Although these studies require validation in further sample sets, it is clear that, ultimately, a panel of markers more clearly defining the risk profile for each patient will need to be identified to accurately and consistently predict irinotecan toxicity. 5-fluorouracil

5FU is a common chemotherapy agent used for the treatment of colorectal cancer and other solid tumors, often in combination with irinotecan or oxaliplatin. The main mechanism of action is to form a stable ternary complex with thymidylate synthase (TYMS) and 5,10-methylenetetrahydrofolate, blocking the conversion of dUMP to dTMP, leading to a depletion of thymidine in the cell and consequently inhibiting DNA synthesis. Overexpression of TYMS has been linked to resistance to 5FU [25,26]. The cause of the interindividual variability in TYMS expression is still unclear; however, a polymorphism in a promoter-enhancer region of the 5´untranslated region (5´UTR) of the TYMS gene has been described with predicted effect on TYMS expression [27,28]. This polymorphism (TYMS TSER) consists of a 28-bp tandem repeat resulting in between two and nine copies of the sequence [28–30]. Several studies have suggested that an increased number of repeats increases TYMS RNA and protein expression [28,31,32], frequency of the TYMS TSER alleles among different ethnic groups shows an interesting pattern. Caucasian and African populations have similar frequencies of the TSER*3 (three repeats) allele (49–54%) [29,33,34], whereas Asian populations have a significantly higher frequency of TSER*3 (62–95%) [30,33,35]. TSER*2 (two repeats) makes up the majority of the other alleles. The TSER*4 (four repeats) alleles are mainly found

Expert Rev. Clin. Pharmacol. 1(1), (2008)

Oncology pharmacogenomics

in African populations at low frequency (1–7%) [29,34], TSER*5 (five repeats) has been identified in a Chinese population (up to 4%) [30] and, to date, TSER*9 (nine repeats) alleles have only been identified in a population from Ghana (1%) [29]. The TSER repeat polymorphism has been linked to clinical outcome to 5FU in multiple studies [27,36–39]. A preliminary study of 24 metastatic colorectal cancer patients observed that patients had a stepwise decrease in median survival with increasing TSER repeat genotype (TSER*2/*2, TSER*2/*3 and TSER*3/*3) [34]. A subsequent report from 50 patients receiving 5FU for metastatic colorectal cancer found a 41% higher response rate in patients homozygous for TSER*2 compared with patients homozygous for TSER*3, with heterozygous patients falling in between [37]. In 117 patients receiving 5FU adjuvant therapy and 104 patients receiving surgery alone, no significant benefit of chemotherapy on survival was observed for TSER*3/TSER*3 patients. 5-FU provided improved survival compared with surgery alone for patients with at least one TSER*2 allele (relative risk of treatment failure 0.52 compared with surgery alone; p = 005) [39]. The TYMS TSER is also linked to tumor downstaging (a measurement of response) in 65 patients with rectal cancer who were treated preoperatively with 5FUbased chemoradiation [36]. Patients with at least one TSER*2 allele had a 38% increased frequency of tumor downstaging compared with patients homozygous for TSER*3 [36]. These studies have led to the introduction of a genotypeguided clinical cancer trial consisting of tandem Phase II studies [40]. Stage T2 and T4 rectal cancer patients with at least one TSER*2 allele have been treated in a Phase II study consisting of standard therapy (radiation and 5FU) using a sample size calculated to detect a downstaging rate of 60%, compared with the historical downstaging rate of 45%. Patients homozygous for TSER*3 were enrolled in a Phase II study where they received the standard therapy in combination with irinotecan, using a sample size calculated to detect an improvement from the previously reported TSER*3/*3 downstaging rate of 22–45% [36]. Preliminary data suggest an improved response rate in both Phase II studies [40]. Concerns

Despite the data suggesting genotyping for TYMS TSER in advance of therapy selection would be beneficial to patients where 5FU is a treatment option, there are still patients with the ‘good risk’ TSER*2 alleles who do not respond to 5FU therapy. Screening for other polymorphisms in TYMS, including a G>C polymorphism within the second repeat of the TSER*3 allele [41], might improve outcome prediction. This TSER*3G>C polymorphism disrupts a upstream stimulatory factor (USF)1 transcription factor binding site. In a study of 89 metastatic colorectal cancer patients receiving 5FU, patients with ‘low expression’ genotypes (i.e., patients without any TSER*3G alleles) had improved overall response (p = 0.035) [42]. It is possible that this single nucleotide polymorphism (SNP) will allow TSER*3 carriers to be further stratified into ‘good risk’ and ‘bad risk’ 5FU response categories.

In addition to other TYMS polymorphisms, TYMS status in the tumor genome needs to be taken into account. TYMS amplification has been shown in vitro and in vivo to influence resistance to 5FU [43,44]. Conversely, loss of the short arm of chromosome 18p is common in colorectal cancer, and loss of heterozygosity (LOH) of TYMS could also affect its expression in tumor [45], although the true extent of LOH at the TYMS region of chromosome 18 remains unclear. It is likely that a 3D pharmacogenomics approach, incorporating germline TYMS polymorphisms with tumor TYMS copy number, will provide a stronger indication of 5FU efficacy. Tamoxifen

Tamoxifen is commonly used in the treatment of breast cancer [46]. Side effects include hot flashes, irregular menses, thromboembolic events, endometrial cancer, endometrial polyps and ovarian cysts. Acquired resistance is also a problem with tamoxifen therapy [46]. Cytochrome P450 (CYP)2D6 catalyzes the conversion of tamoxifen into the active metabolite 4-hydroxytamoxifen (4-OH TAM) [47]. CYP2D6 is also responsible for the conversion of the metabolite N-desmethyltamoxifen to 4-hydroxy-Ndesmethyltamoxifen (endoxifen) [48], and the use of CYP2D6 inhibitors in conjunction with tamoxifen significantly alters the conversion to endoxifen [49]. There are multiple functional polymorphisms in CYP2D6, ranging from SNPs to variations in CYP2D6 gene copy number [50]. Several studies have assessed CYP2D6 polymorphisms in breast cancer patients treated with tamoxifen. In 80 patients, those homozygous for the CYP2D6*4 allele had significantly lower endoxifen levels than patients wild-type for CYP2D6 [51]. In addition, patients heterozygous for CYP2D6*3, *4, *5 or *6 alleles had intermediate endoxifen levels [51]. In 223 estrogen receptor-positive patients receiving tamoxifen, patients homozygous for CYP2D6*4 experienced significantly shorter relapse-free time (p = 0.023) and reduced disease-free survival (p = 0.012) than patients with at least one wild-type CYP2D6 allele [52]. CYP2D6 genotyping currently provides the most compelling evidence for the utility of a pharmacogenetic marker for tamoxifen treatment selection and, in October 2006, an FDA advisory committee recommended a change to the tamoxifen package insert to include CYP2D6 pharmacogenetic information [53]. The FDA has approved an AmpliChip® CYP test through Roche for screening CYP2D6 and CYP2C19 polymorphisms, although the primary use of this chip is currently for psychiatric medications [54]. Concerns

Clinical evidence for CYP2D6 screening prior to tamoxifen therapy selection is based on a small number of studies. In addition, significant ethnic variability in CYP2D6 variant allele frequencies exist [55], implying screening of multiple alleles may be essential to uncover the true extent of CYP26 variability. There is also evidence to suggest that combinations of genes/polymorphisms, for example UGT2B15


Marsh & Phillips

and SULT1A1 alleles, and SULT1A1 and CYP2D6 alleles, may be more clinically relevant than assessing each gene individually [56,57]. Tumor genome

Pharmacogenomic markers for toxicity experienced by patients receiving chemotherapy can be assessed using germline DNA. However, markers of response to chemotherapy may depend heavily on the tumor genome [58]. Changes in the tumor genome could have an effect on the presence and number of functional alleles. Consequently, for some therapies, it may be essential to screen the tumor genome instead of, or as well as, the germline genome for accurate therapy selection. Trastuzumab

ERBB2 (Her-2/neu) overexpression, usually caused by gene amplification, is associated with reduced survival in patients with breast cancer and occurs at a frequency of approximately 30% [59]. Trastuzumab (Herceptin®), a monoclonal antibody, was developed as a targeted therapy for patients overexpressing ERBB2 [60,61]. ERBB2 amplification can be identified clinically using fluorescence in situ hybridization and overexpression assessed by immunohistochemistry [59,62]. Only patients with ERBB2 amplification/overexpression are selected for trastuzumab therapy in conjunction with standard chemotherapy treatment (early-stage or metastatic breast cancer) or as monotherapy in patients with ERBB2-overexpressing metastatic breast cancer who have previously received chemotherapy. Multiple studies have shown significant increases in disease-free and overall survival in breast cancer patients with ERBB2 amplification/overexpression when treated with trastuzumab [59]. In a combined analysis of two US trials for early-stage breast cancer patients with amplified/overexpressed ERBB2 (combined total n = 3351) after 4 years, patients receiving paclitaxel with trastuzumab had significantly improved overall survival (p = 0.015) and disease-free survival (p < 0.0001) than patients only receiving paclitaxel [63]. In 469 metastatic breast cancer patients with amplified/overexpression of ERBB2, patients who were randomized to chemotherapy plus trastuzumab showed a significantly longer time to disease progression (p < 0.001) and longer overall survival (p = 0.01) than patients receiving chemotherapy only [64]. These and other studies highlight the effectiveness of trastuzumab therapy [59]. Trastuzumab was approved for use in 1998 and is one of the earliest FDA-approved treatments that involves screening markers for personalized therapy selection [60,61]. Concerns

A major cause for concern is in the inconsistency of ERBB2 testing. Patients who are negative for ERBB2 amplification by one or more clinical test may still benefit from trastuzumab [65]. Likewise, trastuzumab does not improve progression-free or overall survival in all patients overexpressing ERBB2 [66]. Consequently, other factors must be taken into


consideration, for example, if other polymorphisms are present within ERBB2 and if these may impact gene expression/activity [67]. Mechanisms of resistance to trastuzumab, either acquired or predetermined, for example mutations in tumor ERBB2, are also a problem, but further studies need to be performed to determine whether resistance can be predicted in advance of trastuzumab therapy. Additional therapeutic strategies may help to overcome trastuzumab resistance in these patients [68]. Gene-expression panels

For some oncology treatments, there are no clear DNA-based markers for pharmacogenomic therapy selection. For example, the taxanes paclitaxel and docetaxel are commonly used in the treatment of several solid tumors, including ovarian, breast and prostate cancer; however, despite multiple pharmacogenetic studies, there are limited data on putative pharmacogenomic markers and no putative association has yet been validated in subsequent studies [69,70]. In these instances, the development of expression profiles, providing a panel of genes whose tumor-expression patterns can help determine outcome, bridge an important gap. The commercially available Oncotype Dx™ panel is a 21-gene signature (five reference genes: ACTB, GAPDH, RPLPO, GUS and TFRC; and 16 cancer-related genes: ESR1, PGR, BCL2, SCUBE2, MKI67, MYBL2, BIRC5, CCNB1, AURKA, ERBB2, GRB7, MMP11, CTSL2, GSTM1, BAG1 and CD68) used for predicting recurrence in breast cancer [71]. However, studies have also shown that this panel can predict chemotherapy response in breast cancer [71–73]. This panel is particularly useful because it allows the use of paraffin-embedded tissue as a sample source, which is often easier to obtain, but harder to work with, than frozen tumor tissue. In a study of 89 breast cancer patients treated with paclitaxel and doxorubicin, the 21-gene signature was significantly associated with complete response (p = 0.005) [73]. In addition, in 97 patients treated with docetaxel, the 21-gene signature was also significantly associated with clinical complete response (p = 0.008) [72], indicating that the Oncotype Dx panel may be a useful screen for predicting taxane-therapy response where there are no current genotype-based markers available. Concerns

Although evidence suggests that the Onctotype Dx panel helps to predict chemotherapy response in breast cancer, it is clearly not the only answer. In conjunction with assessing the 21-gene signature of the Onctotype Dx panel, studies have also identified alternate gene panels that also predict response, showing very little overlap in the genes involved [72,73]. Consequently, more work is needed to identify a definitive panel of genes. In addition, although the panel is commercially available, its utility in guiding therapy is currently limited as there are no clear guidelines for interpreting the results for pharmacogenomic-based therapy selection.

Expert Rev. Clin. Pharmacol. 1(1), (2008)

Oncology pharmacogenomics

Expert commentary

In the last 2–3 years, the integration of pharmacogenomics into clinical practice has become a realistic possibility. The FDA approval of genetic tests to predict therapy selection and dosing (e.g., ERBB2 amplification and UGT1A1*28 genotype) and the introduction of genotype-guided trials (e.g., TYMS) are major milestones in pharmacogenomics research. However, genes do not act in isolation and chemotherapy is often used in combination. Identifying a risk for irinotecan toxicity in a patient does not rule out the risk of toxicities from alternate therapies where there may not be strong candidates for pharmacogenomic screening. In addition, there is considerable ethnic variability in the frequencies of the majority of clinically relevant polymorphisms and assumptions based on specific populations should not be applied worldwide without validation [74]. The development of gene signatures to identify expression patterns for chemotherapy drugs [71,75,76] is a useful step towards the generation of pharmacogenomic panels that can be screened in patients to predict the most appropriate therapy. In addition, screening for specific somatic mutations may also provide markers for therapy selection in the future. For example, mutations in the kinase domain of the EGFR gene in lung cancer cells are associated with response to gefitinib and erlotinib [77]. A Phase III trial is currently underway to determine the benefit of erlotinib versus chemotherapy in patients with somatic EGFR mutations in non-small-cell lung cancer cells [78]. Further identification of novel candidate genes for therapies where no clear candidates currently exist using genome-wide strategies is also ongoing [79,80]. One of the major limitations with the integration of pharmacogenomics into clinical practice is the lack of appropriate validation of statistically significant findings. Many preliminary studies are performed on small

sample sets and lack statistical power to conclusively identify genotype–phenotype associations. It is essential to replicate these findings in large, well-characterized sample sets. Five-year view

One of the major concerns for integrating pharmacogenomics into clinical practice is economics. The cost of the screening test versus the incidence and cost of treating adverse drug reactions must be weighed. However, the availability of affordable, highthroughput genotyping platforms makes pretherapy pharmacogenomic screening a realistic possibility [81–83]. The introduction of whole-genome technologies will alter the field in the next few years. However, there is a need to catch up with the increasing amount of data that can be readily collected, including the need for robust dosing algorithms to be developed based on a patient’s genetic information. It is highly likely that the field of pharmacogenomics will move from screening individual variants in individual genes to incorporating screens of panels of markers in the near future. Acknowledgements

The authors thank Janelle Hoskins for assistance with this manuscript. Financial & competing interests disclosure

S Marsh is funded by UO1 GM63340 and R21 CA113491. MS Phillips is funded by Genome Canada Competition III Project: ‘pharmacogenomics of drug efficacy and drug toxicity in the treatment of cardiovascular disease’. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.

Key issues • There are often multiple therapies available for many cancers, with no rational basis for their selection. • Pharmacogenomics will allow individualized therapy selection. • US FDA-approved clinical tests for genes/polymorphisms with well-defined associations to toxicity and outcomes are now available (UGT1A1*28 and Roche AmpliChip®). • Changes to package inserts for oncology therapeutics have been made (mercaptopurine, irinotecan and trastuzumab) or are in progress (tamoxifen), based on pharmacogenomic evidence. • Genotype-guided trials will help to identify appropriate markers and dosing regimens in the clinical setting. • Gene-expression panels can be useful for predicting chemotherapy response where no robust DNA markers are available. References Papers of special note have been highlighted as: • of interest •• of considerable interest 1

Evans WE, McLeod HL. Pharmacogenomics – drug disposition, drug targets, and side effects. N. Engl. J. Med. 348(6), 538–549 (2003).


Marsh S. Pharmacogenetics of colorectal cancer. Expert Opin. Pharmacother. 6(15), 2607–2616 (2005).


Marsh S, McLeod HL. Pharmacogenomics: from bedside to clinical practice. Hum. Mol. Genet. 15(Spec. No. 1), R89–R93 (2006).


McLeod HL, Siva C. The thiopurine S-methyltransferase gene locus – implications for clinical pharmacogenomics. Pharmacogenomics 3(1), 89–98 (2002).


Fuchs CS, Moore MR, Harker G et al. Phase III comparison of two irinotecan dosing regimens in second-line therapy


Marsh & Phillips

of metastatic colorectal cancer. J. Clin. Oncol. 21(5), 807–814 (2003). 6



Beutler E, Gelbart T, Demina A. Racial variability in the UDPglucuronosyltransferase 1 (UGT1A1) promoter: a balanced polymorphism for regulation of bilirubin metabolism? Proc. Natl Acad. Sci. USA 95(14), 8170–8174 (1998). Guillemette C, Millikan RC, Newman B, Housman DE. Genetic polymorphisms in uridine diphospho-glucuronosyltransferase 1A1 and association with breast cancer among African Americans. Cancer Res. 60(4), 950–956 (2000). Hall D, Ybazeta G, Destro-Bisol G, Petzl-Erler ML, Di Rienzo A. Variability at the uridine diphosphate glucuronosyltransferase 1A1 promoter in human populations and primates. Pharmacogenetics 9(5), 591–599 (1999).


Ando Y, Saka H, Ando M et al. Polymorphisms of UDPglucuronosyltransferase gene and irinotecan toxicity: a pharmacogenetic analysis. Cancer Res. 60(24), 6921–6926 (2000).


Innocenti F, Ratain MJ. Irinotecan treatment in cancer patients with UGT1A1 polymorphisms. Oncology (Williston Park, NY) 17(5 Suppl. 5), 52–55 (2003).









Iyer L, Hall D, Das S et al. Phenotypegenotype correlation of in vitro SN-38 (active metabolite of irinotecan) and bilirubin glucuronidation in human liver tissue with UGT1A1 promoter polymorphism. Clin. Pharmacol. Ther. 65(5), 576–582 (1999). Iyer L, Das S, Janisch L et al. UGT1A1*28 polymorphism as a determinant of irinotecan disposition and toxicity. Pharmacogenomics J. 2(1), 43–47 (2002). Innocenti F, Undevia SD, Iyer L et al. Genetic variants in the UDPglucuronosyltransferase 1A1 gene predict the risk of severe neutropenia of irinotecan. J. Clin. Oncol. 22(8), 1382–1388 (2004). Prospective study confirming the association of UGT1A1*28 and irinotecan toxicity. FDA clears Third Wave pharmacogenetic test. Pharmacogenomics 6(7), 671–672 (2005). Hoskins JM, Goldberg RM, Qu P, Ibrahim JG, McLeod HL. UGT1A1*28 genotype and irinotecan-induced neutropenia: dose matters. J. Natl Cancer Inst. 99, 1290–1295 (2007). Important study comparing irinotecan dose, genotype and toxicity from multiple studies.


Premawardhena A, Fisher CA, Liu YT et al. The global distribution of length polymorphisms of the promoters of the glucuronosyltransferase 1 gene (UGT1A1): hematologic and evolutionary implications. Blood Cells Mol. Dis. 31(1), 98–101 (2003).


Innocenti F, Undevia SD, Rosner GL et al. Irinotecan (CPT-11) pharmacokinetics (PK) and neutropenia: interaction among UGT1A1 and transporter genes. Proc. Am. Soc. Clin. Oncol. 23, 136S (2005).


Sai K, Saeki M, Saito Y et al. UGT1A1 haplotypes associated with reduced glucuronidation and increased serum bilirubin in irinotecan-administered Japanese patients with cancer. Clin. Pharmacol. Ther. 75(6), 501–515 (2004).


Marsh S, McLeod HL. Pharmacogenetics of irinotecan toxicity. Pharmacogenomics 5(7), 835–843 (2004).


Hoskins JM, Baiget M, Marcuello E, Altes A, Mcleod HL. Irinotecan pharmacogenetics: the influence of pharmacodynamic genes. Proceedings of the American Society of Clinical Oncology Annual Meeting. Atlanta, GA, USA, 2–6 June (2006) (Abstract 3075).



de Jong FA, Scott-Horton TJ, Kroetz DL et al. Irinotecan-induced diarrhea: functional significance of the polymorphic ABCC2 transporter protein. Clin. Pharmacol. Ther. 81(1), 42–49 (2007). Han JY, Lim HS, Shin ES et al. Comprehensive analysis of UGT1A polymorphisms predictive for pharmacokinetics and treatment outcome in patients with non-small-cell lung cancer treated with irinotecan and cisplatin. J. Clin. Oncol. 24(15), 2237–2244 (2006).


de Jong FA, de Jonge MJ, Verweij J, Mathijssen RH. Role of pharmacogenetics in irinotecan therapy. Cancer Lett. 234(1), 90–106 (2006).


Carlini LE, Meropol NJ, Bever J et al. UGT1A7 and UGT1A9 polymorphisms predict response and toxicity in colorectal cancer patients treated with capecitabine/irinotecan. Clin. Cancer Res. 11(3), 1226–1236 (2005).


Johnston PG, Lenz HJ, Leichman CG et al. Thymidylate synthase gene and protein expression correlate and are associated with response to 5-fluorouracil in human colorectal and gastric tumors. Cancer Res. 55(7), 1407–1412 (1995).


Leichman CG, Lenz HJ, Leichman L et al. Quantitation of intratumoral thymidylate synthase expression predicts for disseminated colorectal cancer response and

resistance to protracted-infusion fluorouracil and weekly leucovorin. J. Clin. Oncol. 15(10), 3223–3229 (1997). 27

Marsh S. Thymidylate synthase pharmacogenetics. Invest. New Drugs 23(6), 533–537 (2005).


Horie N, Aiba H, Oguro K, Hojo H, Takeishi K. Functional analysis and DNA polymorphism of the tandemly repeated sequences in the 5´-terminal regulatory region of the human gene for thymidylate synthase. Cell Struct. Funct. 20(3), 191–197 (1995).


Marsh S, Ameyaw MM, Githang’a J et al. Novel thymidylate synthase enhancer region alleles in African populations. Hum. Mutat. 16(6), 528 (2000).


Luo HR, Lu XM, Yao YG et al. Length polymorphism of thymidylate synthase regulatory region in Chinese populations and evolution of the novel alleles. Biochem. Genet. 40(1–2), 41–51 (2002).


Kawakami K, Omura K, Kanehira E, Watanabe Y. Polymorphic tandem repeats in the thymidylate synthase gene is associated with its protein expression in human gastrointestinal cancers. Anticancer Res. 19(4B), 3249–3252 (1999).


Morganti M, Ciantelli M, Giglioni B et al. Relationships between promoter polymorphisms in the thymidylate synthase gene and mRNA levels in colorectal cancers. Eur. J. Cancer 41(14), 2176–2183 (2005).


Marsh S, Collie-Duguid ES, Li T, Liu X, McLeod HL. Ethnic variation in the thymidylate synthase enhancer region polymorphism among Caucasian and Asian populations. Genomics 58(3), 310–312 (1999).


Marsh S, McLeod HL. Thymidylate synthase pharmacogenetics in colorectal cancer. Clin. Colorectal Cancer 1(3), 175–181 (2001).


Horie N, Takeishi K. Functional structure of the promoter region of the human thymidylate synthase gene and nuclear factors that regulate the expression of the gene. Nucleic Acids Symp. Ser. (34), 77–78 (1995).


Villafranca E, Okruzhnov Y, Dominguez MA et al. Polymorphisms of the repeated sequences in the enhancer region of the thymidylate synthase gene promoter may predict downstaging after preoperative chemoradiation in rectal cancer. J. Clin. Oncol. 19(6), 1779–1786 (2001). Rectal cancer study showing the association between the thymidylate synthase polymorphism (TYMS TSER) polymorphism and 5-fluorouracil treatment outcome.


Expert Rev. Clin. Pharmacol. 1(1), (2008)

Oncology pharmacogenomics


Pullarkat ST, Stoehlmacher J, Ghaderi V et al. Thymidylate synthase gene polymorphism determines response and toxicity of 5-FU chemotherapy. Pharmacogenomics J. 1(1), 65–70 (2001).


Lecomte T, Ferraz JM, Zinzindohoue F et al. Thymidylate synthase gene polymorphism predicts toxicity in colorectal cancer patients receiving 5-fluorouracil-based chemotherapy. Clin. Cancer Res. 10(17), 5880–5888 (2004).







Iacopetta B, Grieu F, Joseph D, Elsaleh H. A polymorphism in the enhancer region of the thymidylate synthase promoter influences the survival of colorectal cancer patients treated with 5-fluorouracil. Br. J. Cancer 85(6), 827–830 (2001). McLeod HL, Tan B, Malyapa R et al. Genotype-guided neoadjuvant therapy for rectal cancer. Proc. Am. Soc. Clin. Oncol. 23, 197 (2005). Mandola MV, Stoehlmacher J, Muller-Weeks S et al. A novel single nucleotide polymorphism within the 5´ tandem repeat polymorphism of the thymidylate synthase gene abolishes USF-1 binding and alters transcriptional activity. Cancer Res. 63(11), 2898–2904 (2003). Marcuello E, Altes A, del Rio E et al. Single nucleotide polymorphism in the 5´ tandem repeat sequences of thymidylate synthase gene predicts for response to fluorouracilbased chemotherapy in advanced colorectal cancer patients. Int. J. Cancer 112(5), 733–737 (2004). Wang TL, Diaz LA Jr, Romans K et al. Digital karyotyping identifies thymidylate synthase amplification as a mechanism of resistance to 5-fluorouracil in metastatic colorectal cancer patients. Proc. Natl Acad. Sci. USA 101(9), 3089–3094 (2004). Rooney PH, Stevenson DA, Marsh S et al. Comparative genomic hybridization analysis of chromosomal alterations induced by the development of resistance to thymidylate synthase inhibitors. Cancer Res. 58(22), 5042–5045 (1998).


Kawakami K. Thymidylate synthase gene in pharmacogenetics. Curr. Pharmacogenomics 2, 137–147 (2004).


Osborne CK. Tamoxifen in the treatment of breast cancer. N. Engl. J. Med. 339(22), 1609–1618 (1998).


Crewe HK, Ellis SW, Lennard MS, Tucker GT. Variable contribution of cytochromes P450 2D6, 2C9 and 3A4 to the 4-hydroxylation of tamoxifen by human liver microsomes. Biochem. Pharmacol. 53(2), 171–178 (1997).

Desta Z, Ward BA, Soukhova NV, Flockhart DA. Comprehensive evaluation of tamoxifen sequential biotransformation by the human cytochrome P450 system in vitro: prominent roles for CYP3A and CYP2D6. J. Pharmacol. Exp. Ther. 310(3), 1062–1075 (2004).


Bange J, Zwick E, Ullrich A. Molecular targets for breast cancer therapy and prevention. Nat. Med. 7(5), 548–552 (2001).


Engel RH, Kaklamani VG. HER2-positive breast cancer : current and future treatment strategies. Drugs 67(9), 1329–1341 (2007).


Borges S, Desta Z, Li L et al. Quantitative effect of CYP2D6 genotype and inhibitors on tamoxifen metabolism: implication for optimization of breast cancer treatment. Clin. Pharmacol. Ther. 80(1), 61–74 (2006).



Ingelman-Sundberg M. Genetic polymorphisms of cytochrome P450 2D6 (CYP2D6): clinical consequences, evolutionary aspects and functional diversity. Pharmacogenomics J. 5(1), 6–13 (2005).

Kim MA, Jung EJ, Lee HS et al. Evaluation of HER-2 gene status in gastric carcinoma using immunohistochemistry, fluorescence in situ hybridization, and real-time quantitative polymerase chain reaction. Hum. Pathol. 38(9), 1386–1393 (2007).


Romond EH, Perez EA, Bryant J et al. Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. N. Engl. J. Med. 353(16), 1673–1684 (2005).


Slamon DJ, Leyland-Jones B, Shak S et al. Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N. Engl. J. Med. 344(11), 783–792 (2001).


Tuma RS. Inconsistency of HER2 test raises questions. J. Natl Cancer Inst. 99(14), 1064–1065 (2007).


Nahta R, Esteva FJ. Trastuzumab: triumphs and tribulations. Oncogene 26(25), 3637–3643 (2007).


Ameyaw MM, Tayeb M, Thornton N et al. Ethnic variation in the HER-2 codon 655 genetic polymorphism previously associated with breast cancer. J. Hum. Genet. 47(4), 172–175 (2002).


Nahta R, Yuan LX, Du Y, Esteva FJ. Lapatinib induces apoptosis in trastuzumab-resistant breast cancer cells: effects on insulin-like growth factor I signaling. Mol. Cancer Ther. 6(2), 667–674 (2007).


Marsh S. Taxane pharmacogenetics. Personalized Med. 3(1), 33–43 (2006).


Marsh S, Paul J, King CR et al. Pharmacogenetic assessment of toxicity and outcome after platinum plus taxane chemotherapy in ovarian cancer: the Scottish Randomised Trial in Ovarian Cancer. J. Clin. Oncol. 25(29), 4528–4535 (2007).


Kaklamani V. A genetic signature can predict prognosis and response to therapy in breast cancer: oncotype DX. Expert Rev. Mol. Diagn. 6(6), 803–809 (2006).


Chang JC, Makris A, Gutierrez MC et al. Gene expression patterns in formalin-fixed, paraffin-embedded core biopsies predict docetaxel chemosensitivity in breast cancer patients. Breast Cancer Res. Treat. DOI: 10.1007/s10549-007-9590-z (2007) (Epub ahead of print).





Jin Y, Desta Z, Stearns V et al. CYP2D6 genotype, antidepressant use, and tamoxifen metabolism during adjuvant breast cancer treatment. J. Natl Cancer Inst. 97(1), 30–39 (2005). Study demonstrating the role of cytochrome P450 (CYP)2D6 polymorphisms on tamoxifen metabolism. Goetz MP, Rae JM, Suman VJ et al. Pharmacogenetics of tamoxifen biotransformation is associated with clinical outcomes of efficacy and hot flashes. J. Clin. Oncol. 23(36), 9312–9318 (2005).


Reynolds S. SPORE study provides new guidelines for tamoxifen use. NCI Cancer Bulletin 3(47), 1–2 (2006).


AmpliChip CYP450 test. Med. Lett. Drugs Ther. 47(1215–1216), 71–72 (2005).


Ozawa S, Soyama A, Saeki M et al. Ethnic differences in genetic polymorphisms of CYP2D6, CYP2C19, CYP3As and MDR1/ABCB1. Drug Metab. Pharmacokinet. 19(2), 83–95 (2004).


Nowell SA, Ahn J, Rae JM et al. Association of genetic variation in tamoxifen-metabolizing enzymes with overall survival and recurrence of disease in breast cancer patients. Breast Cancer Res. Treat. 91(3), 249–258 (2005).




Wegman P, Vainikka L, Stal O et al. Genotype of metabolic enzymes and the benefit of tamoxifen in postmenopausal breast cancer patients. Breast Cancer Res. 7(3), R284–R290 (2005). Hoskins JM, Mcleod HL. Cancer pharmacogenetics: the move from pharmacokinetics to pharmacodynamics. Curr. Pharmacogenomics 4, 39–46 (2006). Plosker GL, Keam SJ. Trastuzumab: a review of its use in the management of HER2-positive metastatic and early-stage breast cancer. Drugs 66(4), 449–475 (2006).


Marsh & Phillips


Gianni L, Zambetti M, Clark K et al. Gene expression profiles in paraffin-embedded core biopsy tissue predict response to chemotherapy in women with locally advanced breast cancer. J. Clin. Oncol. 23(29), 7265–7277 (2005).


Rosell R, Taron M, Sanchez JJ, Paz-Ares L. Setting the benchmark for tailoring treatment with EGFR tyrosine kinase inhibitors. Future Oncol. 3(3), 277–283 (2007).


Dolan ME, Newbold KG, Nagasubramanian R et al. Heritability and linkage analysis of sensitivity to cisplatininduced cytotoxicity. Cancer Res. 64(12), 4353–4356 (2004).


Engen RM, Marsh S, Van Booven DJ, McLeod HL. Ethnic differences in pharmacogenetically relevant genes. Curr. Drug Targets 7(12), 1641–1648 (2006).


Yu J, Shannon WD, Watson MA, McLeod HL. Gene expression profiling of the irinotecan pathway in colorectal cancer. Clin. Cancer Res. 11(5), 2053–2062 (2005).


Watters JW, Kraja A, Meucci MA, Province MA, McLeod HL. Genome-wide discovery of loci influencing chemotherapy cytotoxicity. Proc. Natl Acad. Sci. USA 101(32), 11809–11814 (2004).


Kidd EA, Yu J, Li X et al. Variance in the expression of 5-fluorouracil pathway genes in colorectal cancer. Clin. Cancer Res. 11(7), 2612–2619 (2005).


Freimuth RR, Ameyaw M-M, Pritchard SC, Kwok P-Y, McLeod HL. High-throughput genotyping methods for pharmacogenomic studies. Curr. Pharmacogenomics 2(1), 21–33 (2004).



Rosell R, Taron M, Reguart N, Isla D, Moran T. Epidermal growth factor receptor activation: how exon 19 and 21 mutations changed our understanding of the pathway. Clin. Cancer Res. 12(24), 7222–7231 (2006).


Syvanen AC. Toward genome-wide SNP genotyping. Nat. Genet. 37(Suppl.), S5–S10 (2005).


Kaller M, Lundeberg J, Ahmadian A. Arrayed identification of DNA signatures. Expert Rev. Mol. Diagn. 7(1), 65–76 (2007).

Websites 101

Package insert for mercaptopurine /jul_PI/Purinethol_PI.pdf


Third Wave Technologies – suppliers of the US FDA-approved clinical test for UGT1A1*28

Affiliations •

Sharon Marsh, PhD Washington University in St Louis, Division of Oncology, 660 South Euclid Ave – Campus Box 8069, St Louis, MO 63110, USA Tel.: +1 314 747 5186 Fax: +1 314 362 3764 [email protected]

Michael S Phillips, PhD Université de Montréal, Faculty of Medicine, Montréal, QC, Canada and Montréal Heart Institute, Pharmacogenomics Centre, Montréal, QC, Canada Tel.: +1 514 398 4400 ext. 00307 Fax: +1 514 398 1790 [email protected]

Expert Rev. Clin. Pharmacol. 1(1), (2008)

Integrating pharmacogenomics into oncology clinical practice.

Oncology pharmacogenomics has seen a great deal of progress in the past 10 years. The release of the Human Genome Project data and the availability of...
108KB Sizes 0 Downloads 0 Views