Pharmacogenomics implementation across multiple clinic settings: a qualitative evaluation

Aim: To advance clinical adoption and implementation of pharmacogenomics (PGx) testing, barriers and facilitators to these efforts must be understood. This study identified and examined barriers and facilitators to active implementation of a PGx program across multiple clinic settings in an academic healthcare system. Materials & methods: 28 contributors to the PGx implementation (e.g., clinical providers, informatics specialists) completed an interview to elicit their perceptions of the implementation. Results: Qualitative analysis identified several barriers and facilitators that spanned different stages of the implementation process. Specifically, unclear test payment mechanisms, decision support tool development, rigid workflows and provider education were noted as barriers to the PGx implementation. A multidisciplinary implementation team and leadership support emerged as key facilitators. Furthermore, participants also suggested strategies to overcome or maintain these factors. Conclusion: Assessing real-world implementation perceptions and suggested strategies from a range of implementation contributors facilitates a more comprehensive framework and best-practice guidelines for PGx implementation.

Cytochrome P450 Oxidoreductase (POR) Associated with Severe Paclitaxel-Induced Peripheral Neuropathy in Patients of European Ancestry from ECOG-ACRIN E5103

PURPOSE

Paclitaxel is a widely used anticancer therapeutic. Peripheral neuropathy is the dose-limiting toxicity and negatively impacts quality of life. Rare germline gene markers were evaluated for predicting severe taxane-induced peripheral neuropathy (TIPN) in the patients of European ancestry. In addition, the impact of Cytochrome P450 (CYP) 2C8, CYP3A4, and CYP3A5 metabolizer status on likelihood of severe TIPN was also assessed.

EXPERIMENTAL DESIGN

Whole-exome sequencing analyses were performed in 340 patients of European ancestry who received a standard dose and schedule of paclitaxel in the adjuvant, randomized phase III breast cancer trial, E5103. Patients who experienced grade 3-4 (n = 168) TIPN were compared to controls (n = 172) who did not experience TIPN. For the analyses, rare variants with a minor allele frequency ≤ 3% and predicted to be deleterious by protein prediction programs were retained. A gene-based, case-control analysis using SKAT was performed to identify genes that harbored an imbalance of deleterious variants associated with increased risk of severe TIPN. CYP star alleles for CYP2C8, CYP3A4, and CYP3A5 were called. An additive logistic regression model was performed to test the association of CYP2C8, CYP3A4, and CYP3A5 metabolizer status with severe TIPN.

RESULTS

Cytochrome P450 oxidoreductase (POR) was significantly associated with severe TIPN (P value = 1.8 ×10-6). Six variants were predicted to be deleterious in POR. There were no associations between CYP2C8, CYP3A4, or CYP3A5 metabolizer status with severe TIPN.

CONCLUSIONS

Rare variants in POR predict an increased risk of severe TIPN in patients of European ancestry who receive paclitaxel.

Abstract 1151: Pharmacogenomics genotyping from clinical somatic whole exome sequencing: Aldy, a computational tool

Background Pharmacogenomics (PGx) testing can reduce toxicities and improve efficacy of several drugs used to treat cancer and associated symptoms. PGx results can be determined from germline whole-exome sequencing (WES), but somatic mutations may cause discordance between tumor and germline DNA. Since clinical diagnostic sequencing in oncology frequently only includes tumor DNA, there would be clinical value in calling germline PGx genotypes from tumor DNA. Thus, the purpose of this study was to assess the feasibility of using somatic WES data to call germline PGx genotypes.

Methods Germline and somatic WES data were obtained as part of the clinical workflow for 64 patients treated at the solid molecular tumor board clinic at Indiana University. Aldy v3.3 was implemented in LifeOmic’s Precision Health Cloud™ to call PGx genotypes from somatic WES. Somatic Aldy calls were compared with previously validated Aldy germline calls for 8 genes: CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, CYP4F2, DPYD, and TPMT. Somatic read depth was >100x, except for the intronic CYP3A4*22 variant, which was >30x.

Results Somatic and germline Aldy calls were compared for a total of 512 genotypes and 56 (11%) calls were discordant. Discordant calls were most common for CYP2B6 (23.4%), followed by CYP2D6 (14.1%), CYP2C19 (10.9%), CYP2C8 (6.3%), and DPYD (6.3%). In contrast, all Aldy calls were concordant for CYP3A5 and TPMT. 38 out of 64 subjects (59%) had discordant calls for at least one gene. The most common first cancer diagnoses in our cohort were colorectal (9.3%), breast (7.8%), and pancreatic (7.8%), and the rates of discordant Aldy calls did not differ by cancer type (p>0.05 for all cancer types). Based on our analyses of discordant calls, we anticipate that adjusting Aldy’s thresholds for variant calling may allow Aldy to determine genotypes from somatic WES data.

Conclusion In most cases, genotype calls of drug metabolism genes from tumor DNA reflected the germline genotypes; however, additional work needs to be done to determine if the remaining discordant calls can be corrected by modifying the informatics tools or if they are due to somatic mutations.

Citation Format: Wilberforce A. Osei, Tyler Shugg, Reynold C. Ly, Steven M. Bray, Benjamin A. Salisbury, Ryan R. Ratcliff, Victoria M. Pratt, Ibrahim Numanagić, Todd Skaar. Pharmacogenomics genotyping from clinical somatic whole exome sequencing: Aldy, a computational tool [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1151.

Abstract P1-08-02: Cytochrome P450 reductase gene, POR, associated with paclitaxel induced peripheral neuropathy in patients of European ancestry from the adjuvant breast cancer trial, ECOG-ACRIN E5103

Introduction: Paclitaxel induced peripheral neuropathy (TIPN) is one of the most important survivorship issues of cancer patients with the potential to substantially impact quality of life. TIPN can lead to dose reductions, early cessation, and has the potential to compromise treatment efficacy. We previously reported both rare (SBF2) and common germline (FCAMR) predictors for TIPN in patients of African descent through whole-exome sequencing (WES) and a genome-wide association study (GWAS), respectively, in the adjuvant, randomized phase III breast cancer trial, E5103. These predictors are now being evaluated in the prospective ECOG-ACRIN trial EAZ171 (NCT04001829). We have also previously reported our evaluation of common germline variants for patients of European descent through GWAS in E5103 with validation in another adjuvant breast cancer trial, E1199. Herein, we evaluated for rare variants that were associated with risk of TIPN in patients of European ancestry from WES in E5103. Methods: Gene-based rare variant analyses using SKAT were performed to compare select cases of severe TIPN (n=172) and controls without any evidence of TIPN (n=170) derived from E5103. Cases were defined as those with at least grade 3 TIPN and controls were optimally. matched by demographic and risk factors and had no reported evidence for TIPN of any grade. Germline WES was conducted using Ion Proton™ Sequencers from Life Technologies with an average >100X coverage of the exome. Rare variants with a minor allele frequency <3% predicted to be deleterious by protein prediction programs were retained for the analysis. 7,278 genes passed quality control and were included in the analysis, setting the threshold for significance at a p-value < 6.87 ×10-6 after Bonferroni correction. Results: Cytochrome P450 oxidoreductase (POR) was significantly associated with an increased risk of grade 3+ TIPN (p =1.82 ×10-6). Six variants predicted to be deleterious in POR were identified in the study population. Paclitaxel is predominately metabolized by cytochrome P450 (CYP) 2C8 and 3A4. A functional cytochrome P450 oxidoreductase is required for the catalytic activities of all 57 CYP family members to metabolize drugs, xenobiotics, and steroid hormones. Conclusion: Rare variants in cytochrome P450 oxidoreductase predicted an increased risk of severe TIPN in patients receiving paclitaxel. These rare variants in POR may modulate the catalytic activities of P450 enzymes that are responsible for paclitaxel metabolism and have a striking biological rationale as contributors to TIPN. Work is ongoing to validate these findings mechanistically and to identify strategies to nullify the impact of these deleterious variants.

Citation Format: Fei Shen, Guanglong Jiang, Laura Gardner, Gloria Xue, Santosh Philips, Reynold Ly, Osei Wilberforce, Xi Wu, Erica Cantor, Chau Dang, Donald Northfelt, Todd Skaar, Kathy D. Miller, George Sledge, Bryan P Schneider. Cytochrome P450 reductase gene, POR, associated with paclitaxel induced peripheral neuropathy in patients of European ancestry from the adjuvant breast cancer trial, ECOG-ACRIN E5103 [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-08-02.

Strategies to Integrate Genomic Medicine into Clinical Care: Evidence from the IGNITE Network

The complexity of genomic medicine can be streamlined by implementing some form of clinical decision support (CDS) to guide clinicians in how to use and interpret personalized data; however, it is not yet clear which strategies are best suited for this purpose. In this study, we used implementation science to identify common strategies for applying provider-based CDS interventions across six genomic medicine clinical research projects funded by an NIH consortium. Each project's strategies were elicited via a structured survey derived from a typology of implementation strategies, the Expert Recommendations for Implementing Change (ERIC), and follow-up interviews guided by both implementation strategy reporting criteria and a planning framework, RE-AIM, to obtain more detail about implementation strategies and desired outcomes. We found that, on average, the three pharmacogenomics implementation projects used more strategies than the disease-focused projects. Overall, projects had four implementation strategies in common; however, operationalization of each differed in accordance with each study's implementation outcomes. These four common strategies may be important for precision medicine program implementation, and pharmacogenomics may require more integration into clinical care. Understanding how and why these strategies were successfully employed could be useful for others implementing genomic or precision medicine programs in different contexts.

P741Next generation miRNA sequencing and changes in coagulation measured by thrombelastography (TEG) in patients with cardiovascular disease

Background

Thrombelastography (TEG), an ex-vivo clotting assay can identify subjects at high risk of subsequent coronary thrombotic events. Synthesis of clotting factors is subject to post-translational regulation, which is modulated at least in part by miRNA.

Hypothesis

We hypothesized that miRNA sequencing may identify specific miRNA linked with measures of hypercoaguability by TEG.

Methods

Kaolin activated thrombelastography was performed in platelet poor citrate plasma from 61 subjects referred for cardiac catheterization. Time to clot formation (R), clot stabilization time (K), and maximal fibrin clot strength (MA) was measured. Next generation miRNA sequencing was done from RNA isolated from whole blood samples, which includes miRNA derived from leukocytes and platelets. Prediction of miRNA gene targets was performed with targetscan.

Results

Sequencing resulted in quantification of 371 distinct miRNA from whole blood samples. We found 13 miRNA correlating with alteration in TEG-R, 33 miRNA correlating with TEG-K, and 21 miRNA correlating with TEG-MA. Coagulation factors or genes associated with coagulation were found to be among predicted targets in 49 out of these 67 miRNA. Most common predicted targets included factors II, V, VII, X, XIII, fibrinogen, plasminogen-activator inhibitor, and tissue factor. Factor XIIIA1 was highly conserved gene target by miR-96-5p (one of only 3miRNA predicted for this gene). MiR-96-5p correlated with clot stabilization time (ρ=-0.26, p=0.047) which has been shown to be dependent on FXIIIa activity. MiR-22-3p was significantly correlated with TEG-K (ρ=0.28, p=0.034) and was only miRNA with highly conserved target site for prothrombin (Factor II).

Conclusions

In patients with cardiovascular disease miRNA sequencing combined with coagulation phenotype in silico analysis may identify novel links to coagulation that are associated with increased thrombotic risk.

Acknowledgement/Funding

Charles Fisch Cardiovascular Research Award endowed by S. Knoebel

Medication Exposure Patterns in Primary Care Patients Prescribed Pharmacogenetically Actionable Opioids

Current approaches to assessing medication exposure fail to capture the complexity of the phenomenon and the context in which it occurs. This study's purpose was to develop a typology of subgroups of patients who share common patterns of medication exposure. To create the typology, we used an exemplar sample of 30 patients in a large public healthcare system who had been prescribed the pharmacogenetically actionable opioids codeine or tramadol. Data related to medication exposure were drawn from large data repositories. Using a person-oriented qualitative approach, eight subgroups of patients who shared common patterns of medication exposure were identified. The subgroups had one of five opioid prescription patterns (i.e., singular, episodic, switching, sustained, multiplex), and one of three types of primary foci of medical care (i.e., pain, comorbidities, both). The findings reveal medication exposure patterns that are dynamic, multidimensional, and complex, and the typology offers an innovative approach to assessing medication exposure.

CYP2D6 drug-gene and drug-drug-gene interactions among patients prescribed pharmacogenetically actionable opioids

PURPOSE

When codeine and tramadol are used for pain management, it is imperative that nurses are able to assess for potential drug-gene and drug-drug-gene interactions that could adversely impact drug metabolism and ultimately pain relief. Both drugs are metabolized through the CYP2D6 metabolic pathway which can be affected by medications as well the patient's own pharmacogenotype. The purpose of this brief report is to identify drug-gene and drug-drug-gene interactions in 30 adult patients prescribed codeine or tramadol for pain.

METHODS

We used three data sources: (1) six months of electronic health record data on the number and types of medications prescribed to each patient; (2) each patient's CYP2D6 pharmacogenotype, and (3) published data on known CYP2D6 gene-drug and drug-drug-gene interactions.

RESULTS

Ten patients (33%) had possible drug-gene or drug-drug-gene interactions. Five patients had CYP2D6 drug-gene interactions indicating they were not good candidates for codeine or tramadol. In addition, five patients had potential CYP2D6 drug-drug-gene interactions with either codeine or tramadol.

CONCLUSION

Our findings from this exploratory study underscores the importance of assessing and accounting for drug-gene and drug-drug-gene interactions in patients prescribed codeine or tramadol.

Abstract 2029: Precision therapeutic combinations are synergistic against triple negative breast cancer using compensatory pathways

Introduction: Triple negative breast cancer (TNBC) accounts for 15% of all breast cancer cases in the United States, and despite its lower incidence, contributes to a disproportionately higher rate of morbidity and mortality compared to other breast cancer subtypes. No FDA-approved targeted therapies are currently available. It has been hypothesized that drug combinations could potentially be chosen based on a tumor harboring two or more druggable genomic mutations. However, previously published data has noted that single agent treatment can change the genomic landscape and may be responsible for the lack of synergy of dual genomic drug targeting. Herein we show that targeting a compensatory pathway after treatment with a genomically-directed agent, results in synergistic combinations and can outperform choosing two drugs a priori based on genomic mutations.

Methods: Nine TNBC cell lines were chosen based on the presence of two or more clinically actionable genomics targets. Drug combinations based on targeting two genomic mutations were chosen using DNA-seq data from CCLE and a board consisting of oncologists and researchers. Compensatory therapies were found using RNA-seq data from untreated versus single-agent treated TNBC cell lines. The merged transcript RPKMs were transformed and analyzed for differential expression. Statistically significant genes were imported into Ingenuity Pathway Analysis (IPA) to identify therapeutics based on compensatory targets using the Causal Network Analysis and Upstream Regulator functions. Cell viability was assessed via Celltiter-Fluor. Synergy of the combinations was calculated using the Chou-Talalay method.

Results: Using two-drug combinations based on genomic mutations alone in all nine cell lines resulted only in additive or antagonistic responses. However, using RNA-seq data of each cell line treated with one genomically-directed agent, IPA analysis identified several compensatory targets that were upregulated or activated. Treating each cell line in combination with one genomically-directed agent plus one compensatory agent resulted in a striking increase in synergy. To understand why targeting compensatory pathways was superior to targeting two genomic mutations, we re-evaluated the RNA-seq data. This analysis revealed that treatment with the first genomically-directed agent, in many cases, resulted in down-regulation or inactivation of the second genomic-target. This may explain the lack of synergy when targeting cells with two drugs based only on genomic mutations.

Conclusion: Targeting TNBC cell lines based on drug combinations informed by compensatory pathways results in significant synergy and is superior to choosing drug combinations based on genomic alterations alone.

Citation Format: Jeffrey P. Solzak, Brad Hancock, Robin Paul, Patrick Kiel, Todd Skaar, Bryan Schneider, Milan Radovich. Precision therapeutic combinations are synergistic against triple negative breast cancer using compensatory pathways [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2029. doi:10.1158/1538-7445.AM2017-2029

Simultaneous inferences based on empirical Bayes methods and false discovery rates ineQTL data analysis

BACKGROUND

Genome-wide association studies (GWAS) have identified hundreds of genetic variants associated with complex human diseases, clinical conditions and traits. Genetic mapping of expression quantitative trait loci (eQTLs) is providing us with novel functional effects of thousands of single nucleotide polymorphisms (SNPs). In a classical quantitative trail loci (QTL) mapping problem multiple tests are done to assess whether one trait is associated with a number of loci. In contrast to QTL studies, thousands of traits are measured alongwith thousands of gene expressions in an eQTL study. For such a study, a huge number of tests have to be performed (~10(6)). This extreme multiplicity gives rise to many computational and statistical problems. In this paper we have tried to address these issues using two closely related inferential approaches: an empirical Bayes method that bears the Bayesian flavor without having much a priori knowledge and the frequentist method of false discovery rates. A three-component t-mixture model has been used for the parametric empirical Bayes (PEB) method. Inferences have been obtained using Expectation/Conditional Maximization Either (ECME) algorithm. A simulation study has also been performed and has been compared with a nonparametric empirical Bayes (NPEB) alternative.

RESULTS

The results show that PEB has an edge over NPEB. The proposed methodology has been applied to human liver cohort (LHC) data. Our method enables to discover more significant SNPs with FDR<10% compared to the previous study done by Yang et al. (Genome Research, 2010).

CONCLUSIONS

In contrast to previously available methods based on p-values, the empirical Bayes method uses local false discovery rate (lfdr) as the threshold. This method controls false positive rate.

Abstract P1-08-11: Association of variants in candidate genes on lipid profiles in women with early breast cancer on adjuvant aromatase inhibitor therapy

Background

Aromatase inhibitors (AI) can exert unfavorable effects on lipid profiles, but previous studies have reported inconsistent results. Given the intricate biological relationship between estrogen and lipid profiles, these mixed results may be explained in part by variation in genes encoding proteins involved in the drug's target and in estrogen metabolism and signaling. The purpose of this study was to investigate associations of single-nucleotide polymorphisms (SNP) in candidate genes with AI-mediated changes in lipid profiles.

Methods

We completed a prospective multicenter randomized observational open-label study to test the association of SNPs in candidate genes on biomarkers of estrogenic and anti-estrogenic activity in post-menopausal women with early breast cancer who were recommended adjuvant AI therapy. Eligible women were randomly assigned to exemestane or letrozole, and were followed for 2 years. We genotyped 137 SNPs from germ line DNA in the following candidate genes: ARVCF, COMT, CYP19A1, ESR1, ESR2, PGR, EP300, EZH2, NCOA1-3, NCOR1-2, NRIP, and PELP1. Lipid profiles including total cholesterol (TC), low-density lipoprotein (LDL), high-density lipoprotein (HDL), and triglycerides (TG) were measured at baseline and 3 months after initiating AI. We conducted genetic association data analysis and multivariate linear regressions to analyze the genetic effects using dominant, recessive, and additive models. Multivariate analysis included age, body mass index, prior hormone replacement therapy, and prior tamoxifen. To adjust for multiple comparisons, only SNPs with a p&lt;0.0003 were considered significant.

Results

We enrolled 502 women in to the study, but for this analysis we excluded women who did not have genetic data (n = 33), had incomplete data (n = 23), discontinued or crossed over AI therapy (n = 48), women not fasting at both time points (n = 89), or those on lipid-lowering medications (n = 162). A total of 200 women were evaluable (letrozole 107, exemestane 93). Lipid profiles in all patients (n = 200) at baseline and 3 months after initiating AI, respectively, were as follows: TC 204.9 and 203.3 (unchanged, p = 0.43); HDL 61.3 and 56.8 (decreased, p = 6.3E-10); LDL 122.2 and 124.6 (unchanged, p = 0.22); and TG 107.1 and 103.6 (unchanged, p = 0.26). Genetic association and multivariate analysis revealed that SNPs in ESR1 and NCOR1 are significantly associated with additional changes in lipid parameters as summarized in Table 1.

Table 1.Significant findings of multivariate linear regressions analyzing genetic associations between candidate gene SNPs and lipid profiles of AI-treated women.CohortNumberSNP (gene)Minor Allele FrequencyLipid ParameterModel UsedMean Absolute Change (mg/dL)P-valueAll patients184rs9340958 (ESR1)0.07TCRecessive-2.250.0003Letrozole96rs9340958 (ESR1)0.07TCRecessive5.280.00009 101rs3020368 (ESR1)0.09TCRecessive6.350.00007Exemestane93rs3798758 (ESR1)0.03HDLDominant, additive-7.970.00001 88rs926848 (ESR1)0.03HDLDominant, additive-7.970.00002 93rs61753150 (NCOR1)0.01TGDominant, additive-11.630.00003

Conclusions

Variants in genes involved in estrogen metabolism and signaling are associated with changes in lipid profiles in AI-treated women and should be validated in other studies.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-08-11.

Concordance between CYP2D6 genotypes obtained from tumor-derived and germline DNA

Formalin-fixed, paraffin-embedded tumors (FFPETs) are a valuable source of DNA for genotype association studies and are often the only germline DNA resource from cancer clinical trials. The anti-estrogen tamoxifen is metabolized into endoxifen by CYP2D6, leading to the hypothesis that patients with certain CYP2D6 genotypes may not receive benefit because of their inability to activate the drug. Studies testing this hypothesis using FFPETs have provided conflicting results. It has been postulated that CYP2D6 genotype determined using FFPET may not be accurate because of somatic tumor alterations. In this study, we determined the concordance between CYP2D6 genotypes generated using 3 tissue sources (FFPETs; formalin-fixed, paraffin-embedded unaffected lymph nodes [FFPELNs]; and whole blood cells [WBCs]) from 122 breast cancer patients. Compared with WBCs, FFPET and FFPELN genotypes were highly concordant (>94%), as were the predicted CYP2D6 metabolic phenotypes (>97%). We conclude that CYP2D6 genotypes obtained from FFPETs accurately represent the patient's CYP2D6 metabolic phenotype.

Efavirenz-mediated induction of omeprazole metabolism is CYP2C19 genotype dependent

Efavirenz increases CYP2C19- and CYP3A-mediated omeprazole metabolism. We hypothesized that CYP2C19 and CYP2B6 genetic polymorphisms influence the extent of induction of omeprazole metabolism by efavirenz. Healthy subjects (n=57) were administered a single 20mg oral dose of omeprazole with a single dose (600mg) or after multiple doses (600mg/day for 17 days) of efavirenz. DNA was genotyped for CYP2C19*2, *3 and *17 alleles and CYP2B6*6, *4 and *9 alleles using Taqman assays. Omeprazole, its enantiomers and metabolites were measured by LC/MS/MS. Our results showed that efavirenz increased omeprazole clearances in all CYP2C19 genotypes in non-stereoselective manner, but the magnitude of induction was genotype-dependent. Metabolic ratios of 5-hydroxylation of omeprazole were reduced in extensive and intermediate metabolizers of CYP2C19 (p<0.05). No significant associations were observed between CYP2B6 genotypes and induction by efavirenz on omeprazole metabolism. Our data indicate how interplays between drug interactions and CYP2C19 genetic variations may influence systemic exposure of CYP2C19 substrates.

CYP2D6 genotypes, endoxifen levels, and disease recurrence in 224 Filipino and Vietnamese women receiving adjuvant tamoxifen for operable breast cancer

Background

While tamoxifen activity is mainly due to endoxifen and the concentration of this active metabolite is, in part, controlled by CYP2D6 metabolic status, clinical correlative studies have produced mixed results.

Findings

In an exploratory study, we determined the CYP2D6 metabolic status and plasma concentrations of endoxifen among 224 Filipino and Vietnamese women participating in a clinical trial of adjuvant hormonal therapy for operable breast cancer. We further conducted a nested-case–control study among 48 women (half with recurrent disease, half without) investigating the relationship of endoxifen concentrations and recurrence of disease.

We found a significant association of reduced endoxifen plasma concentrations with functionally important CYP2D6 genotypes. High endoxifen concentrations were associated with higher risk of recurrence; with a quadratic trend fitted to a stratified Cox proportional hazards regression model, the likelihood ratio p-value was 0.002. The trend also showed that in 8 out of 9 pairs with low endoxifen concentrations, the recurrent case had lower endoxifen levels than the matched control.

Conclusions

This exploratory analysis suggests that there is an optimal range for endoxifen concentrations to achieve favorable effects as adjuvant therapy. In particular, at higher concentrations (>70 ng.ml), endoxifen may promote recurrence.

Electronic supplementary material

The online version of this article (doi:10.1186/2193-1801-2-52) contains supplementary material, which is available to authorized users.

The impact of drug metabolizing enzyme polymorphisms on outcomes after antenatal corticosteroid use

OBJECTIVE

To determine the impact of maternal and fetal single nucleotide polymorphisms in key betamethasone pathways on neonatal outcomes.

STUDY DESIGN

DNA was obtained from women given betamethasone and their infants. Samples were genotyped for 73 exploratory drug metabolism and glucocorticoid pathway single nucleotide polymorphisms. Clinical variables and neonatal outcomes were obtained. Logistic regression analysis using relevant clinical variables and genotypes to model for associations with neonatal respiratory distress syndrome was performed.

RESULTS

One hundred nine women delivering 117 infants were analyzed. Sixty-four infants (49%) developed respiratory distress syndrome. Multivariable analysis revealed that respiratory distress syndrome was associated with maternal single nucleotide polymorphisms in CYP3A5 (odds ratio [OR], 1.63; 95% confidence interval [CI], 1.16-2.30) and the glucocorticoid resistance (OR, 0.28; 95% CI, 0.08-0.95) and fetal single nucleotide polymorphisms in ADCY9 (OR, 0.17; 95% CI, 0.03-0.80) and CYP3A7*1E (rs28451617; OR, 23.68; 95% CI, 1.33-420.6).

CONCLUSION

Maternal and fetal genotypes are independently associated with neonatal respiratory distress syndrome after treatment with betamethasone for preterm labor.

Plasma letrozole concentrations in postmenopausal women with breast cancer are associated with CYP2A6 genetic variants, body mass index, and age

The associations between plasma letrozole concentrations and CYP2A6 and CYP3A5 genetic variants were tested in the Exemestane and Letrozole Pharmacogenomics (ELPH) trial. ELPH is a multicenter, open-label prospective clinical trial in women randomly assigned (n≈250 in each arm) to receive 2 years of treatment with either oral letrozole (2.5 mg/day) or oral exemestane (25 mg/day). CYP2A6 and CYP3A showed effects on letrozole metabolism in vitro. DNA samples were genotyped for variants in the CYP2A6 and CYP3A5 genes. Plasma letrozole concentrations showed high interpatient variability (>10-fold) and were associated significantly with CYP2A6 genotypes (P<0.0001), body mass index (BMI) (P<0.0001), and age (P=0.0035). However, CYP3A5 genotypes showed no association with plasma letrozole concentrations. These data suggest that CYP2A6 is the principal clearance mechanism for letrozole in vivo. CYP2A6 metabolic status, along with BMI and age, may serve as a biomarker of the efficacy of letrozole treatment or a predictor of adverse effects.

The emerging role of electronic medical records in pharmacogenomics

Health-care information technology and genotyping technology are both advancing rapidly, creating new opportunities for medical and scientific discovery. The convergence of these two technologies is now facilitating genetic association studies of unprecedented size within the context of routine clinical care. As a result, the medical community will soon be presented with a number of novel opportunities to bring functional genomics to the bedside in the area of pharmacotherapy. By linking biological material to comprehensive medical records, large multi-institutional biobanks are now poised to advance the field of pharmacogenomics through three distinct mechanisms: (i) retrospective assessment of previously known findings in a clinical practice-based setting, (ii) discovery of new associations in huge observational cohorts, and (iii) prospective application in a setting capable of providing real-time decision support. This review explores each of these translational mechanisms within a historical framework.

Evaluating the role of serotonin on neuropsychological function after breast cancer using acute tryptophan depletion

Although cognitive dysfunction is a prevalent and disruptive problem for many breast cancer survivors (BCSs), little research has examined its etiology. One potential mechanism that remains to be explored is serotonin. Serotonin has been implicated in normal and dysfunctional cognitive processes, and serotonin levels are significantly affected by estrogen withdrawal, a common side effect of breast cancer treatment. However, no study has evaluated serotonin's role on cognitive dysfunction in BCSs. The purpose of this study was to examine the role of serotonin in cognitive dysfunction in survivors by lowering central serotonin concentrations via acute tryptophan depletion (ATD). Based on previous research in noncancer populations, we hypothesized that alterations in central serotonin levels would induce cognitive dysfunction in these women controlling for confounding characteristics such as fluctuating mood and glucose levels. Secondarily, we explored whether genetic variations in serotonin genes would partly explain ATD. Participants included 20 female BCSs, posttreatment for nonmetastatic breast cancer, who received ATD or control in a double-blind, crossover design. Cognitive performance was measured at the 5-hr tryptophan/serotonin nadir on each test day using standardized neuropsychological tests. Specific impairment was noted in episodic memory (delayed recall) and motor speed during ATD versus control. ATD did not alter new learning (immediate recall), working memory, verbal fluency, or information processing speed. Findings suggest that serotonin may play a critical role in memory consolidation and motor functioning in BCSs.

Abstract P4-02-01: Correlations between Genetic Variants in CYP2D6 and UGT2B7 and Survival in Breast Cancer Patients Treated with or without Tamoxifen: Results from a Large Cohort Study

Background. A large number of studies testing the hypothesis that genetic variants in drug metabolizing enzymes can influence breast cancer patient response to the selective estrogen receptor modulator tamoxifen have provided equivocal and conflicting data. Possible confounding factors in all studies to date include the relatively small number of patients, lack of comprehensive genotyping analysis (in particular regarding the cytochrome P450 2D6 (CYP2D6) enzyme), use of selective serotonin reuptake inhibitors (SSRIs) (antidepressant medication), and lack of untreated (i.e. no tamoxifen treatment) control groups. Currently, it is not clear whether genotype determinations can predict which patients will likely benefit from tamoxifen therapy.

Methods: We conducted a large community-based cohort study to test for associations between clinical outcomes and variants in CYP2D6, one of the key enzymes responsible for the conversion of tamoxifen to its potent anti-estrogenic metabolite endoxifen, as well as variants in UDP-glucuronosyltransferase 2B7 (UGT2B7), an enzyme responsible for the elimination of endoxifen. The majority of patients in this cohort began their tamoxifen treatment more than twenty ago, at a time when SSRIs (a possible confounding factor in CYP2D6 studies) were not widely used. Five hundred patients with ER+ early breast cancer treated adjuvantly with tamoxifen monotherapy and 500 who did not receive any adjuvant therapy were genotyped and assigned a CYP2D6 “score” based on known specific allele activities from 0 (no activity) to 2 (high activity) and also grouped as either low, intermediate and high UGT2B7 activity based on the *2 allele.

Results: Univariately, Kaplan-Meier estimates in conjunction with the log-rank test did not reveal any significant associations between either CYP2D6 or UGT2B7 score and time to relapse (TTR). In tamoxifen treated cases, after adjustment for tumor size, nodal status and PgR, Cox regression found increased CYP2D6 score, reflecting increased conversion of tamoxifen to endoxifen, was significantly associated with worse time to relapse (HR=1.53, p=0.02). This was not seen in the patients without endocrine treatment (HR=0.73, p=0.10). Patients with high UGT2B7 activity, reflecting increased elimination of endoxifen had better survival rates (HR= 0.75, p = 0.04) in the tamoxifen treated group, while again no effect of UGT2B7 was seen in the untreated group (HR=1.0, p=0.78). Finally, CYP2D6 and UGT2B7 genotypes were not associated with any special tumor characteristics in either patient group. Conclusion: In our study, CYP2D6 and UGT2B7 genotypes associated with increased endoxifen levels were associated with worse outcome in tamoxifen treated (but not untreated) breast cancer patients. Thus, the data from this cohort study do not support the hypothesis that breast cancer patients with low CYP2D6 are resistant to tamoxifen.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-02-01.

A Single Nucleotide Polymorphism in Steroid Receptor Coactivator-1 Diminishes the Coactivation of ERα

Estrogen signaling is critical in the progression of a large fraction of breast cancers as well as in the maintenance of bone mineral density. Generally speaking, Tamoxifen, a selective estrogen receptor modulator (SERM), blocks estrogen signaling in the breast by acting as an antagonist at the same time as promoting estrogen signaling in the bone by acting as an agonist. This tissue specific action characteristic of SERMs is thought to be maintained by the balance of levels and/or activities of estrogen receptor (ER) coregulators. Because of this critical role, single nucleotide polymorphisms (SNPs) in ER coregulators could have a dramatic effect on tamoxifen action.Previous studies have implicated steroid receptor coactivator-1 (SRC-1) as a critical coregulator for the mixed antagonist-agonist specificity of tamoxifen. By using an ERE-Tk-Luciferase transient transfection assay, we have shown that a SNP causing the amino acid change P1272S in SRC-1 dramatically reduces its ability to coactivate ERα.To assess the impact of this SNP on tamoxifen action in breast cancer we decided to genotype the SRC-1 P1272S SNP in a breast tumor DNA bank. This bank was generated from archived tumors from individuals either exclusively receiving adjuvant tamoxifen or not receiving any adjuvant therapy following surgical resection. Currently, the bank is composed of 1000 samples divided equally among the two groups. Genotyping for the SRC-1 P1272S SNP is currently underway.Since SRC-1 has also been shown to be important in proper maintenance of bone mineral density (BMD) and in the agonist action of tamoxifen in certain tissues, we also assessed the impact of the P1272S SNP in bone following tamoxifen therapy. We genotyped breast cancer patients exclusively receiving tamoxifen therapy (i.e. no chemotherapy, no radiation) who had lumbar (n=113) and/or hip (n=108) BMD scans before and after 12 months of tamoxifen therapy. We observed a significant association between the SNP and bone loss; women harboring the P1272S SNP lost 6.4% of their lumbar BMD, while women with the WT version lost only 1.3% of their lumbar BMD.These findings illustrate the critical role of SRC-1 in tamoxifen action in bone, and potentially other hormone responsive tissues. Studies are ongoing to decipher the mechanism for decreased coactivation activity of the SNP, and also to extend the clinical association studies.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 66.

Resequencing of the Vascular Endothelial Growth Factor Promoter Reveals Haplotype Structure and Functional Diversity

Our group has previously reported that SNPs in the VEGF promoter are strongly associated with efficacy and toxicity to the anti-VEGF antibody bevacizumab in metastatic breast cancer. In order to better understand the biologic mechanism for our previously reported biomarkers, we embarked on a comprehensive evaluation of the genetic variation in the VEGF promoter coupled with a study of its intrinsic function. By resequencing 96 DNA samples (48 Caucasians, 48 African-Americans) for the VEGF promoter, we elucidated its complete haplotype structure and identified SNPs that were not previously reported in prior resequencing efforts. SNPs that were identified included twenty previously reported SNPs/insertions/deletions, one novel SNP, and one novel deletion. Among these variants, we identified five SNPs (VEGF-3818G/T, -2305G/T, -1210C/A, -1154G/A, & -7C/T) that tag six haplotypes capturing 74% of the genetic variation of the VEGF promoter. Subsequently, we cloned the six major haplotypes into reporter constructs in order to determine the effect of genetic variation on function. The reporter assays were performed in 5 breast cancer cell lines representing all ER and HER-2 statuses along with an inflammatory breast cancer cell line. We demonstrate that there is significant variation in promoter-induced expression among the haplotypes. More importantly, we show that the haplotypes containing the SNPs previously reported to be associated with increased survival with the use of bevacizumab are high-expressing haplotypes, thus lending putative functional evidence to the prior clinical finding. Further, we also report the presence of a low-expressing haplotype predominantly in African-Americans. Altogether, these results set the foundation for future studies elucidating the role of VEGF genetic variation with response to anti-angiogenic therapy and associations with angiogenesis-related diseases.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2122.

A phase II study of pemetrexed as second-line chemotherapy for the treatment of metastatic castrate-resistant prostate cancer (CRPC); Hoosier Oncology Group GU03-67

BACKGROUND

No standard therapy exists for post-docetaxel castrate-resistant prostate cancer (CRPC) patients. This trial aimed to determine the safety and efficacy of pemetrexed in post-docetaxel CRPC patients.

MATERIALS AND METHODS

CRPC patients with progression after docetaxel (Taxotere) therapy received pemetrexed (500 mg/m2) i.v. every 3 weeks. The primary end point was prostate-specific antigen (PSA) response. A pharmacogenetic analysis of the reduced folate carrier-1 gene (RFC1) G80A polymorphism was also carried out.

RESULTS

Forty-nine patients were enrolled: median age 68 years, median baseline PSA 72 ng/ml, and median Karnofsky performance status of 90. Grade 3 or 4 toxicity occurred in 20 (43%) and four patients (8%), respectively. Confirmed >50% PSA decline occurred in four patients (8%), stable PSA lasting at least 12 weeks in 10 patients (20%). A significant relationship was observed between time from prior docetaxel therapy and overall survival. Pharmacogenetic analyses of RFC1 G80A genotype frequencies showed no relationship between genotypes and clinical efficacy.

CONCLUSIONS

Pemetrexed treatment of CRPC patients after docetaxel therapy was associated with only modest clinical activity. Further investigation of pemetrexed as a single agent in a nonenriched CRPC population is unlikely to add significant clinical benefit over that seen with traditional second-line chemotherapy agents such as mitoxantrone.

Progression of pancreatic adenocarcinoma is significantly impeded with a combination of vaccine and COX-2 inhibition

With a 5-year survival rate of <5%, pancreatic cancer is one of the most rapidly fatal malignancies. Current protocols for the treatment of pancreas cancer are not as effective as we desire. In this study, we show that a novel Mucin-1 (MUC1)-based vaccine in combination with a cyclooxygenase-2 inhibitor (celecoxib), and low-dose chemotherapy (gemcitabine) was effective in preventing the progression of preneoplastic intraepithelial lesions to invasive pancreatic ductal adenocarcinomas. The study was conducted in an appropriate triple transgenic model of spontaneous pancreatic cancer induced by the KRAS(G12D) mutation and that expresses human MUC1 as a self molecule. The combination treatment elicited robust antitumor cellular and humoral immune responses and was associated with increased apoptosis in the tumor. The mechanism for the increased immune response was attributed to the down-regulation of circulating prostaglandin E(2) and indoleamine 2, 3,-dioxygenase enzymatic activity, as well as decreased levels of T regulatory and myeloid suppressor cells within the tumor microenvironment. The preclinical data provide the rationale to design clinical trials with a combination of MUC1-based vaccine, celecoxib, and gemcitabine for the treatment of pancreatic cancer.

A mixture model approach in gene-gene and gene-environmental interactions for binary phenotypes

In translational research, a genetic association study of a binary outcome has a twofold aim: test whether genetic/environmental variables or their combinations are associated with a clinical phenotype, and determine how those combinations are grouped to predict the phenotype (i.e., which combinations have a similarly distributed phenotype, and which ones have differently distributed phenotypes). The second part of this aim has high clinical appeal, because it can directly facilitate clinical decisions. Although traditional logistic regression can detect gene-gene or gene-environmental interaction effects on binary phenotypes, they cannot decisively determine how genotype combinations are grouped to predict the phenotype. Our proposed mixture model approach is valuable in this context. It concurrently detects main and interaction effects of genetic and environmental variables through a likelihood ratio test (LRT) and conducts phenotype cluster analysis based on genetic and environmental variable combinations. The theoretical distribution of the proposed mixture model's likelihood ratio test is robust not only to small sample size but also to unequal sample size in various genotype and environmental subgroups. Hypothesis testing through a likelihood ratio test results in a fast algorithm for p-value calculations. Extensive simulation studies demonstrate that mixture model, overall test in logistic regression, and Monte Carlo based logic regression constantly possess the best power to detect multi-way gene/environmental combinations. The mixture model approach has the highest recovery probability to recover the true partition in the simulation studies. Its applications are exemplified in interim data analyses for two cancer studies.

Associations between estrogen receptor (ER) Alpha expression levels and ER genotypes

Abstract #3049

Background: Estrogen receptors (ER) and associated factors, including progesterone receptors (PgR), modulate estrogenic effects both in normal tissue and in hormone receptor (HR)-positive breast cancers. ERα expression occurs in the majority of breast cancers, although the level of overexpression varies between tumors. Multiple single nucleotide polymorphisms (SNPs) in the genes that encode ER, termed ESR1 (ERα) and ESR2 (ERβ), have been shown to affect phenotypic outcomes, including breast cancer risk, bone mineral density, hot flashes, and lipid levels. We hypothesized that SNPs in genes that encode ER may affect level of ER overexpression.&#x2028; Methods: DNA was extracted from white blood cells from 100 subjects with HR-positive breast cancer enrolled in a tamoxifen observational study. SNPs in ESR1 (XbaI: rs#9340799, PvuII: rs#2234693) and ESR2 (01: rs#1256049; 02: rs#4986938) were determined from germline DNA using TaqMan. ER overexpression in paraffin-embedded formalin-fixed tumor specimens was quantified with immunohistochemistry (IHC) of tumor specimens on slides (Ventana Image Analysis System) and with RT-PCR using the Oncotype DX breast cancer assay (Genomic Health, Inc). Gene expression of other ER-associated genes (PgR, BCL2, and SCUBE2) was determined using RT-PCR (Oncotype DX). Expression of ER and associated genes across ER genotype was performed using the Kruskal-Wallis test. For all analyses, a p value of &lt;0.05 was considered statistically significant.&#x2028; Results: ER expression assessed using IHC and RT-PCR was statistically significantly correlated, with a Pearson correlation coefficient of 0.43 (p=0.0006). However, there was no association between the ESR1 or ESR2 genotypes and ER expression assessed by either method. A trend between ESR1 XbaI genotype and PgR expression by RT-PCR was noted (p=0.08 for gene-dose effect). No other associations between ER polymorphisms and expression of ER-related genes were identified.&#x2028; Conclusions: SNPs in genes encoding for ER do not appear to be associated with level of ER expression in breast cancer. Differences in ER expression between individual tumors are likely due to mechanisms other than these inherited mutations in the ER genes.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 3049.

MUC1 enhances tumor progression and contributes toward immunosuppression in a mouse model of spontaneous pancreatic adenocarcinoma

MUC1, a membrane tethered mucin glycoprotein, is overexpressed and aberrantly glycosylated in >80% of human ductal pancreatic adenocarcinoma. However, the role of MUC1 in pancreatic cancer has been elusive, partly due to the lack of an appropriate model. We report the characterization of a novel mouse model that expresses human MUC1 as a self molecule (PDA.MUC1 mice). Pancreatic tumors arise in an appropriate MUC1-tolerant background within an immune-competent host. Significant enhancement in the development of pancreatic intraepithelial preneoplastic lesions and progression to adenocarcinoma is observed in PDA.MUC1 mice, possibly due to increased proliferation. Tumors from PDA.MUC1 mice express higher levels of cyclooxygenase-2 and IDO compared with PDA mice lacking MUC1, especially during early stages of tumor development. The increased proinflammatory milieu correlates with an increased percentage of regulatory T cells and myeloid suppressor cells in the pancreatic tumor and tumor draining lymph nodes. Data shows that during pancreatic cancer progression, MUC1-mediated mechanisms enhance the onset and progression of the disease, which in turn regulate the immune responses. Thus, the mouse model is ideally suited for testing novel chemopreventive and therapeutic strategies against pancreatic cancer.

Relationship of cytochrome P450 pharmacogenetics to the effects of yohimbine on gastrointestinal transit and catecholamines in healthy subjects

Alpha-2 adrenergic receptors tonically inhibit colonic motility and the alpha(2)-adrenergic antagonist yohimbine, given intravenously, increased colonic tone in humans. However, the effect of yohimbine on colonic transit in humans is unknown. In this study, 30 healthy volunteers were randomized to yohimbine 16.2 mg p.o. t.i.d. or identical placebo for 7 days. We evaluated gastric emptying, small intestinal, and colonic transit by scinitigraphy, bowel habits, haemodynamics and plasma catecholamines. As cytochrome P450 enzymes metabolize yohimbine, P450 genotypes (CYP2D6 and CYP3A4) were determined in 25 of 30 subjects who consented to genetic studies. The relationship between drug metabolizer status predicted by CYP2D6 and CYP3A4 and effects of yohmibine were assessed. Compared to placebo, yohimbine increased (P < or = 0.02) diastolic blood pressure, plasma noradrenaline concentrations and maximum tolerated volume during the satiation test [yohimbine (1241 +/- 88, mean +/- SEM) vs placebo (1015 +/- 87), P = 0.054]. However, yohimbine did not affect gastrointestinal transit. Based on CYP2D6 and CYP3A4 alleles, seven and 18 subjects were, respectively, extensive (EM) and poor (PM) metabolizers of yohimbine. Compared to EM, PM of yohimbine had a greater increase in plasma noradrenaline (P = 0.1 for PM vs EM), lower maximum tolerated volumes (1120 +/- 95 vs 1484 + 131 mL, P = 0.02), and faster colonic transit (i.e. GC(24) was 3.0 +/- 0.4 vs 2.1 +/- 0.5, P = 0.1). These data suggest that CYP2D6 and CYP3A4 genotypes which determine the metabolism of yohimbine may influence its sympathetic and gastrointestinal effects.

Association of polymorphisms of angiogenesis genes with breast cancer

BACKGROUND

Few studies have systematically explored a pathway approach: to test the association of multiple polymorphisms from multiple genes important to angiogenesis simultaneously with risk of breast cancer. We report our preliminary data evaluating the association of polymorphisms from seven genes known to influence angiogenesis with the likelihood of having breast cancer.

METHODS

We recruited 715 controls and 520 subjects with breast cancer. Subjects provided a blood specimen and completed a questionnaire that included common breast cancer risk factors and breast cancer status. We evaluated candidate polymorphisms in the following genes: Hypoxia Inducible Factor-1 alpha (HIF1alpha), Vascular Endothelial Growth Factor (VEGF), VEGF Receptor 1 (VEGFR-1), VEGFR-2, endothelial Nitric Oxide Synthase (eNOS), Neuropilin-1 (NRP-1) and Neuropilin-2 (NRP-2). Testing for associations between each polymorphism and the presence or absence of breast cancer was performed.

RESULTS

VEGF-2578 AA and -1498 CC genotypes were more common in cancer cases than controls (P = 0.06 and P = 0.04, respectively). These two genotypes remained significant predictors of breast cancer status after adjusting for non-genetic risk factors estimated by the Gail model (P = 0.03 and P = 0.03, respectively). When comparing women with invasive versus pre-invasive breast cancer, the eNOS-786 TT and eNOS 894 GG genotypes were associated with a greater likelihood of invasive disease and the eNOS 894 GG genotype was associated with a greater likelihood of having metastatic disease.

CONCLUSION

There is an association of the VEGF-2578A and -1498C alleles with increased breast cancer risk. This association remains significant when adjusted for Gail score-related risk factors.

Estrogen receptor genotypes, menopausal status, and the lipid effects of tamoxifen

Tamoxifen induces important changes in serum lipid profiles in some women; however, little information is available to predict which women will experience improved lipid profiles during tamoxifen therapy. As part of a multicenter prospective observational trial in 176 breast cancer patients, we tested the hypothesis that tamoxifen-induced lipid changes were associated with genetic variants in candidate target genes (CYP2D6, ESR1, and ESR2). Tamoxifen lowered low-density lipoprotein cholesterol (P<0.0001) by 23.5 mg/dl (13.5-33.5 mg/dl) and increased triglycerides (P=0.006). In postmenopausal women, the ESR1-XbaI and ESR2-02 genotypes were associated with tamoxifen-induced changes in total cholesterol (P=0.03; GG vs GA/AA) and triglycerides (P=0.01; gene-dose effect), respectively. In premenopausal women, the ESR1-XbaI genotypes were associated with tamoxifen-induced changes in triglycerides (P=0.002; gene-dose effect) and high-density lipoprotein (P=0.004; gene-dose effect). Our results suggest that estrogen receptor genotyping may be useful in predicting which women would benefit more from tamoxifen.

Tamoxifen-induced hot flashes are associated with estrogen receptor polymorphisms

501

Background: Hot flashes are the most common side effect of tamoxifen. The pharmacogenetic predictors of hot flashes are not known. We hypothesized that estrogen receptor (ER) genotypes that have been associated with clinical phenotypes may predict the frequency and composite score of tamoxifen-associated hot flashes. Methods: We conducted a prospective observational study in 3 academic centers to evaluate the associations between ER and hot flash composite scores in women with breast cancer during the first year of adjuvant tamoxifen treatment. Menopausal status and prior chemotherapy history were collected at baseline. Medication records and validated hot flash diaries were prospectively collected before and following 1, 4, 8 and 12 months of starting tamoxifen. ERa (ESR1) PvuII (rs2234693) and XbaI (rs9340799) genotypes were determined using a Restriction Fragment Length Polymorphism (RFLP) assay; and ERβ (ESR2–02; rs4986938) genotype was determined using a Taqman™ assay. The haplotype of two ESR1 SNPs and their association with the baseline hot flash score were analyzed with haplo.stat function in R. Individual SNPs and their interactions in baseline hot flash score and month 4 hot flash score change were analyzed with SAS PROC GLM. Results: Of the 298 women recruited to the trial, 286 returned their baseline diaries and 251, 239, 214, and 213 women returned their diaries 1, 4, 8, and 12 months after tamoxifen treatment. At baseline, premenopausal women who were homozygous for the ESR1 CG haplotype reported higher hot flash scores (17.2±3.7) than carriers with one or less CG allele (5.2±3.9), p=0.01. After tamoxifen treatment, postmenopausal women with ESR1 PvuII CC and ESR2–02 GG genotype had the greatest increase (p=0.0004) in hot flash score (53.9±16.4) as compared with women with other genotypes (12.5±3.6). Women who were homozygous for the ESR2–02 AA allele were significantly less likely to experience tamoxifen-induced hot flashes than women with at least one G allele (OR=4.0, P=0.0006) regardless of menopausal status and chemotherapy history. CYP2D6 analysis in underway and results will be available for the meeting. Conclusions: Menopausal status, history of prior chemotherapy, and ER genotype may be used to predict who may suffer hot flashes during tamoxifen treatment.

[Table: see text]

The pharmacogenetics research network: from SNP discovery to clinical drug response

The NIH Pharmacogenetics Research Network (PGRN) is a collaborative group of investigators with a wide range of research interests, but all attempting to correlate drug response with genetic variation. Several research groups concentrate on drugs used to treat specific medical disorders (asthma, depression, cardiovascular disease, addiction of nicotine, and cancer), whereas others are focused on specific groups of proteins that interact with drugs (membrane transporters and phase II drug-metabolizing enzymes). The diverse scientific information is stored and annotated in a publicly accessible knowledge base, the Pharmacogenetics and Pharmacogenomics Knowledge base (PharmGKB). This report highlights selected achievements and scientific approaches as well as hypotheses about future directions of each of the groups within the PGRN. Seven major topics are included: informatics (PharmGKB), cardiovascular, pulmonary, addiction, cancer, transport, and metabolism.

Erlotinib-associated rash correlates with plasma levels at steady state

13008

Background: Erlotinib is a small molecule epidermal growth factor receptor tyrosine kinase inhibitor that is approved for non-small cell lung cancer as a single agent and for pancreatic cancer in combination with gemcitabine. Significant inter-individual variation in drug exposure may explain differential patient outcomes. Genetic polymorphisms of metabolizing enzymes of erlotinib may explain this variability in exposure. Biotransformation assays have implicated cytochrome 3A4/5 (CYP3A4/5) as the predominant metabolizing enzyme. Methods: Patients were enrolled onto a phase-1 dose-escalation study of weekly docetaxel with fixed oral daily dosing (150 mg) of erlotinib. Pharmacodynamic data regarding grade of rash per CTCAE v. 2 were recorded on all 23 patients. Samples for erlotinib pharmacokinetics were obtained after 28 days of continuous daily dosing. Pharmacokinetic (PK) data was attained in 21 patients using LC/MS/MS and analyzed using noncompartmental analysis. Genomic DNA was available for analysis in all 23 patients. Analysis for single nucleotide polymorphisms CYP3A5*3 and CYP2D6*4 were performed by real-time polymerase chain reaction and confirmed by restriction fragment length polymorphism analysis when needed. Results: Average age of patients was 56 (34–76). Nine patients had grade 0–1 rash and 12 had grade 2 rash. As summarized in the table below, the AUC for patients exhibiting grade 2 rash was approximately twice that of patients with grade 0–1 rash. No significant association was found between PK parameters and either CYP3A5 or CYP2D6 polymorphisms. Conclusions: In patients treated with erlotinib the pharmacodynamic endpoint of rash, which has been previously linked with improved patient outcomes, is significantly correlated to the degree of exposure to the drug at steady state. Preliminary data in this small study analyzing pharmacogenetics of erlotinib found no significant correlation between CYP3A5*3 and CYP2D6*4 polymorphic status in either PK or pharmacodynamic measures.

[Table: see text]

[Table: see text]

Inhibition of Human Intestinal Wall Metabolism by Macrolide Antibiotics: Effect of Clarithromycin on Cytochrome P450 3A4/5 Activity and Expression*

BACKGROUND

Clarithromycin increases both hepatic and intestinal availability of the selective cytochrome P450 (CYP) 3A probe midazolam. This study was designed to identify determinants of variability in the extent of intestinal wall CYP3A inhibition by clarithromycin, such as CYP3A5 genotype, and the mechanism of inhibition.

METHODS

Ten healthy volunteers received 500 mg oral clarithromycin twice a day for 7 days. Before and after administration of clarithromycin, small-bowel mucosal biopsy specimens were obtained endoscopically. Intestinal CYP3A activity was determined from the rate of 1'-hydroxymidazolam and 4-hydroxymidazolam formation by incubation of small-bowel homogenate with midazolam (25 micromol/L) and NADPH for 5 minutes. Intestinal CYP3A4 and CYP3A5 messenger ribonucleic acid was quantified by real-time reverse transcriptase-polymerase chain reaction. Intestinal CYP3A4 and CYP3A5 protein concentrations were determined by immunoblotting. Serum and homogenate concentrations of midazolam, clarithromycin, and metabolites were determined by liquid chromatography-mass spectrometry. CYP3A5 genotype was determined by real-time polymerase chain reaction.

RESULTS

The formation of 1'-hydroxymidazolam (1.36 +/- 0.46 pmol . min(-1) . mg(-1) at baseline versus 0.35 +/- 0.16 pmol . min(-1) . mg(-1) after administration) and 4-hydroxymidazolam (0.39 +/- 0.12 pmol . min(-1) . mg(-1) at baseline versus 0.12 +/- 0.05 pmol . min(-1) . mg(-1) after administration) was significantly (P < .001) reduced after clarithromycin administration. Clarithromycin administration did not result in a significant change in intestinal CYP3A4 and CYP3A5 messenger ribonucleic acid and protein expression. All subjects had detectable serum clarithromycin concentrations after 7 days of clarithromycin (3.71 +/- 2.43 micromol/L). The mean concentration of clarithromycin in the intestinal biopsy homogenate was 1.2 +/- 0.7 nmol/L (range, 0.42-2.39 nmol/L). Compared with CYP3A5 nonexpressers, subjects with at least 1 CYP3A5*1 allele (CYP3A5 expressers) had greater inhibition of intestinal CYP3A activity after treatment with clarithromycin. There was a strong linear relationship between the decrease in intestinal CYP3A activity and baseline catalytic activity (R(2) = 0.9).

CONCLUSION

Baseline intestinal activity of CYP3A4 was a key determinant of variability of the inhibitory effect of clarithromycin among individuals. CYP3A5*1 alleles were associated with greater baseline intestinal CYP3A activity and, therefore, greater extent of inhibition. The primary in vivo mechanism was not rapidly reversible competitive or irreversible inhibition but was likely formation of metabolic intermediate complexes.

CYP2D6 genotype, antidepressant use, and tamoxifen metabolism during adjuvant breast cancer treatment

BACKGROUND

The efficacy of tamoxifen therapy for the treatment of breast cancer varies widely among individuals. Plasma concentrations of the active tamoxifen metabolite endoxifen are associated with the cytochrome P450 (CYP) 2D6 genotype. We examined the effects of concomitant use of selective serotonin reuptake inhibitor antidepressants, which are CYP2D6 enzyme inhibitors commonly prescribed to treat hot flashes in women who take tamoxifen, and genotypes for genes that encode tamoxifen-metabolizing enzymes on plasma concentrations of tamoxifen and its metabolites.

METHODS

Eighty patients with newly diagnosed with breast cancer who were beginning tamoxifen therapy (20 mg/day orally), 24 of whom were taking CYP2D6 inhibitors, were genotyped for common alleles of the CYP2D6, CYP2C9, CYP3A5, and sulfotransferase (SULT) 1A1 genes. Plasma concentrations of tamoxifen and its metabolites were measured after 1 and 4 months of tamoxifen therapy. Differences in plasma concentrations of tamoxifen and its metabolites between genotype groups were analyzed by the Wilcoxon rank sum test. All statistical tests were two-sided.

RESULTS

Among all women, plasma endoxifen concentrations after 4 months of tamoxifen therapy were statistically significantly lower in subjects with a CYP2D6 homozygous variant genotype (20.0 nM, 95% confidence interval [CI] = 11.1 to 28.9 nM) or a heterozygous genotype (43.1 nM, 95% CI = 33.3 to 52.9 nM) than in those with a homozygous wild-type genotype (78.0 nM, 95%CI = 65.9 to 90.1 nM) (both P = .003). Among subjects who carried a homozygous wild-type genotype, the mean plasma endoxifen concentration for those who were using CYP2D6 inhibitors was 58% lower than that for those who were not (38.6 nM versus 91.4 nM, difference = -52.8 nM, 95% CI = -86.1 to -19.5 nM, P = .0025). The plasma endoxifen concentration was slightly reduced in women taking venlafaxine, a weak inhibitor of CYP2D6, whereas the plasma endoxifen concentration was reduced substantially in subjects who took paroxetine (a potent inhibitor of CYP2D6). Genetic variations of CYP2C9, CYP3A5, or SULT1A1 had no statistically significant associations with plasma concentrations of tamoxifen or its metabolites.

CONCLUSION

Interactions between CYP2D6 polymorphisms and coadministered antidepressants and other drugs that are CYP2D6 inhibitors may be associated with altered tamoxifen activity.

Prepubertal exposure to zearalenone or genistein reduces mammary tumorigenesis

Prepubertal exposure to a pharmacological dose (500 mg kg(-1)) of the phyto-oestrogen genistein can reduce the incidence and multiplicity of carcinogen-induced mammary tumours in rats. However, such an exposure also disrupts the function of the hypothalamic-pituitary-gonadal axis, making it unsuitable for breast cancer prevention. We studied whether prepubertal exposure to genistein at a total body dose broadly comparable to the level typical of Oriental countries, approximately 1 mg kg(-1) body weight, affects mammary tumorigenesis. We also studied whether prepubertal exposure to zearalenone, a major source for phyto-oestrogens in the USA, influences breast cancer risk. Prepubertal rats were treated between postnatal days 7 and 20, with 20 microg (approximately 1 mg kg(-1) body weight) of either genistein or zearalenone. Zearalenone exposure significantly reduced both the incidence and multiplicity of mammary tumours induced by 7,12-dimethylbenz(a)anthracene (DMBA). Genistein exposure significantly reduced tumour multiplicity, but not tumour incidence, when compared with vehicle-treated animals. Furthermore, 60% of the tumours in the genistein group were not malignant, while all the tumours analysed for histopathology in the vehicle and zearalenone groups were adenocarcinomas. A higher number of differentiated alveolar buds, and lower number of terminal ducts, were present in the DMBA-treated mammary glands of the phyto-oestrogen exposed rats. The concentration of oestrogen receptor (ER) binding sites after the DMBA treatment was low in the mammary glands of all groups but a significantly higher proportion of the glands in the zearalenone exposed rats were ER-positive (i.e. ER levels > or = 5 fmol mg(-1) protein) than the glands of the vehicle controls. Our data suggest that a prepubertal exposure to a low dose of either zearalenone or genistein may protect the mammary gland from carcinogen-induced malignant transformation, possibly by increasing differentiation of the mammary epithelial tree.

Use of ERE and reporter gene constructs to assess putative estrogenic activity

Estrogens primarily function through the activation of their receptors, which subsequently function as nuclear transcription factors. There are two estrogen receptor (ER) genes, now designated ERa (the classic ER gene) and ER/3. The key consequence of the activation of either gene product is the regulation of gene transcription. The extent and nature of transcription appear to be regulated by a series of coregulator proteins. One of the most sensitive assays for detection of potential estrogenic activity is measurement of the ability of a test compound to influence the transcription of reporter genes. In this regard, many investigators use promoter-reporter constructs. To assess putative estrogenic activity, an estrogen-responsive promoter is generally placed upstream of a reporter gene and transiently transfected into a target cell. When exposed to an estrogenic compound, expression of the reporter gene would normally be induced. We briefly discuss several issues pertinent to the use of these assays and the interpretation of resulting data, including estrogen-responsive, promoter-reporter constructs, reporter genes and measurements of activity, choice of target cell or cell line, transient introduction of promoter-reporter constructs into cells, basic statistical approaches to data analysis, and definitions of agonist, partial agonist, and antagonist.

Hormonal carcinogenesis in breast cancer: cellular and molecular studies of malignant progression

We have established and characterized a series of variant cell lines in which to identify the critical factors associated with E2-induced malignant progression, and the acquisition to tamoxifen resistance in human breast cancer. Sublines of the hormone-dependent MCF-7 cell line (MCF7/MIII and MCF7/LCC1) form stable, invasive, estrogen independent tumors in the mammary fat pads of ovariectomized athymic nude mice. These cells retain expression of both estrogen (ER) and progesterone receptors (PGR), but retain sensitivity to each of the major structural classes of antiestrogens. The tamoxifen-resistant MCF7/LCC2 cells retain sensitivity to the inhibitory effects of the steroidal antiestrogen ICI 182780. By comparing the parental hormone-dependent and variant hormone-independent cells, we have demonstrated an altered expression of some estrogen regulated genes (PGR, pS2, cathepsin D) in the hormone-independent variants. Other genes remain normally estrogen regulated (ER, laminin receptor, EGF-receptor). These data strongly implicate the altered regulation of a specific subset or network of estrogen regulated genes in the malignant progression of human breast cancer. Some of the primary response genes in this network may exhibit dose-response and induction kinetics similar to pS2, which is constitutively upregulated in the MCF7/MIII, MCF7/LCC1 and MCF7/LCC2 cells.