trans-3′-Hydroxycotinine (3HC) and its glucuronide (3HC-Gluc) are major nicotine metabolites excreted in the urine of smokers and other tobacco users. While several members of the UDP-glucuronosyltransferase (UGT) family of enzymes were previously shown to be active in catalyzing the formation of 3HC-Gluc, a comprehensive screening of all known human UGT1A and 2B enzymes for glucuronidation activity against 3HC was not previously performed. In the present study, 8 UGT1A and 6 UGT2B enzymes were screened for activity against 3HC. UGT2B17 exhibited the highest O-glucuronidation activity, exhibiting a 4-fold lower (p<0.005) KM (8.3 mM) than that observed for UGTs 1A9 (35 mM) or 2B7 (31 mM) and a KM smaller than that observed for human liver microsomes (HLM; 26 mM). The KM for 3HC-O-Gluc formation was 3.1-fold lower (p<0.0005) in HLM from male subjects exhibiting the wild-type genotype UGT2B17 (*1/*1) than that in HLM from subjects homozygous for the UGT2B17 deletion genotype [UGT2B17 (*2/*2)]. Both UGTs 2B10 and 1A4 exhibited 3HC-N-Gluc formation activity, with UGT2B10 exhibiting a 4-fold lower (p<0.05) KM (13 mM) than that observed for UGT1A4 (57 mM) and which was similar to the KM observed in HLM (14 mM). There was a 91% (p<0.0001) and 39% (p<0.001) decrease in 3HC-N-Gluc formation activities in HLM from subjects with the UGT2B10 (*2/*2) and UGT2B10 (*1/*2) genotypes, respectively, compared to that of HLM from subjects with the wild-type UGT2B10 (*1/*1) genotype. These results suggest that UGT2B17 and UGT2B10 play key roles in the glucuronidation of 3HC in the human liver and that functional polymorphisms in UGT2B17 and UGT2B10 are associated with significantly reduced glucuronidation activities against 3HC.
Despite evidence in support of anti-inflammatory and triglyceride-lowering effects of fenofibrate, little is known about genetic determinants of the observed heterogeneity in treatment response. This study provides the first genome-wide examination of fenofibrate effects on systemic inflammation.
Biomarkers of inflammation were measured in participants of the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN, n=1092) before and after a 3-week daily treatment with 160 mg of fenofibrate. Two inflammatory patterns (hsCRP-IL6 and MCP1-TNF-α) were derived using principal component analysis. Associations between single nucleotide polymorphisms on the Affymetrix 6.0 chip and phenotypes were assessed using mixed linear models, adjusted for age, sex, study center, and ancestry as fixed effects and pedigree as a random effect.
Before fenofibrate treatment, the strongest evidence for association was observed for polymorphisms near or within the IL2RA gene with the hsCRP-IL6 pattern (rs7911500, P=5×10−9 and rs12722605, P=5×10−8). Associations of the MCP1-TNF-α pattern with loci in several biologically plausible genes (CYP4F8 (rs3764563), APBB1IP (rs1775246), COL13A1 (rs2683572), and COMMD10 (rs1396485)) approached genome-wide significance (P=3×10−7, 5×10−7, 6×10−7, and 7×10−7 respectively) before fenofibrate treatment. After fenofibrate treatment, the rs12722605 locus in IL2RA was also associated with the MCP1-TNF-α pattern (P=3×10−7). The analyses of individual biomarker response to fenofibrate did not yield genome-wide significant results, but the rs6517147 locus near the immunologically relevant IFNAR2 gene was suggestively associated with IL6 (P=7×10−7).
We have identified several novel biologically relevant loci associated with systemic inflammation before and after fenofibrate treatment.
fenofibrate; inflammation; genome-wide association study
drug-induced oxidative stress; glucose-6-phosphate dehydrogenase deficiency; hemolytic anemia; pharmacodynamics; pharmacokinetics; polymorphic variants
Human carboxylesterase 1(hCES1), encoded by the CES1 gene, is the predominant hepatic hydrolase responsible for the metabolism of many therapeutic agents, toxins, and endogenous substances. Genetic variants of CES1 can affect hCES1 function and expression and ultimately influence clinical outcomes of hCES1 substrate drugs. CES1 gene consists of three isoforms including the functional CES1A1 and CES1A2 genes and nonfunctional pseudogene CES1A3. Natural variants of these isoforms exert differing impacts on hCES1 function. However, the existing CES1 genotyping methods are incapable of discriminating between these variants due to the high similarity among these three genes. We report the development of a novel long-range PCR-based, discriminative genotyping assay with the capacity of specifically detecting the variants among CES1A1, CES1A2, and CES1A3 genes. The comparison of the genotyping results between this novel assay and those previously reported methods highlighted the necessity of applying the discriminative genotyping assay in pharmacogentic studies involving CES1 gene.
CES1A1; CES1A2; CES1A3; genotyping; long-range PCR
Background and objective
Gemcitabine is widely used to treat non-small cell lung cancer (NSCLC). To assess the pharmacogenomic effects of the entire gemcitabine metabolic pathway, we genotyped SNPs within the 17 pathway genes using DNA samples from NSCLC patients treated with gemcitabine to determine the effect of genetic variants within gemcitabine pathway genes on overall survival (OS) of NSCLC patients after treatment of gemcitabine.
Eight of the 17 pathway genes were resequenced with DNA samples from Coriell lymphoblastoid cell lines (LCLs) using Sanger sequencing for all exons, exon-intron junctions and 5′-, 3′-UTRs. A total of 107 tag SNPs were selected based on the resequencing data for the 8 genes and on HapMap data for the remaining 9 genes, followed by successful genotyping of 394 NSCLC patient DNA samples. Association of SNPs/haplotypes with OS was performed using the Cox regression model, followed by functional studies performed with LCLs and NSCLC cell lines.
5 SNPs in 4 genes (CDA, NT5C2, RRM1, and SLC29A1) showed associations with OS of those NSCLC patients, as well as 9 haplotypes in 4 genes (RRM1, RRM2, SLC28A3, and SLC29A1) with P < 0.05. Genotype imputation using the LCLs was performed for a region of 200kb surrounding those SNPs, followed by association studies with gemcitabine cytotoxicity. Functional studies demonstrated that downregulation of SLC29A1, NT5C2, and RRM1 in NSCLC cell lines altered cell susceptibility to gemcitabine.
These studies help identify biomarkers to predict gemcitabine response in NSCLC, a step toward the individualized chemotherapy of lung cancer.
gemcitabine; pharmacogenomics; metabolic pathway; lymphoblastoid cell lines; non-small cell lung cancer (NSCLC)
Little is known about genetic contributors to higher than usual warfarin dose requirements, particularly for African Americans. This study tested the hypothesis that the γ-glutamyl carboxylase (GGCX) genotype contributes to warfarin dose requirements >7.5 mg/day in an African American population.
A total of 338 African Americans on a stable dose of warfarin were enrolled. The GGCX rs10654848 (CAA)n, rs12714145 (G>A), and rs699664 (p.R325Q); VKORC1 c.-1639G>A and rs61162043; and CYP2C9*2, *3, *5, *8, *11, and rs7089580 genotypes tested for their association with dose requirements >7.5 mg/day alone and in the context of other variables known to influence dose variability.
The GGCX rs10654848 (CAA) 16 or 17 repeat occurred at a frequency of 2.6% in African Americans and was overrepresented among patients requiring >7.5mg/day versus those who required lower doses (12% vs 3%, p=0.003; odds ratio 4.0, 95% CI, 1.5–10.5). The GGCX rs10654848 genotype remained associated with high dose requirements on regression analysis including age, body size, and VKORC1 genotype. On linear regression, the GGCX rs10654848 genotype explained 2% of the overall variability in warfarin dose in African Americans. An examination of the GGCX rs10654848 genotype in warfarin-treated Caucasians revealed a (CAA)16 repeat allele frequency of only 0.27% (p=0.008 compared to African Americans).
These data support the GGCX rs10654848 genotype as a predictor of higher than usual warfarin doses in African Americans, who have a 10-fold higher frequency of the (CAA)16/17 repeat compared to Caucasians.
African American; GGCX; warfarin
The role of cholesteryl ester transfer protein (CETP) in the metabolism of HDL cholesterol (HDL-C) is well studied but still controversial. More recently, GWAS and metaanalyses reported the association of a promoter variant (rs3764261) with HDL-C in Caucasians and other ethnic groups. In this study, we have examined the role of genetic variation in the promoter region of CETP with HDL-C, CETP activity, coronary artery disease (CAD), CAD risk factors, and the interaction of genetic factors with environment in a unique diabetic cohort of Asian Indian Sikhs.
Methods and Results
We genotyped four variants; three tagSNPs from promoter (rs3764261, rs12447924, rs4783961) and one intronic variant (rs708272 Taq1B) on 2,431 individuals from the Sikh Diabetes Study. Two variants (rs3764261 and rs708272) exhibited a strong associations with HDL-C in both normo-glycemic (NG) controls (β= 0.12; p= 9.35 ×10−7 for rs3764261; β= 0.10, p= 0.002 for rs708272) and diabetic cases (β= 0.07, p= 0.016 for rs3764261; β= 0.08, p= 0.005 for rs708272) with increased levels among minor homozygous ‘AA’ carriers. In addition, the same ‘A’ allele carriers in rs376426 showed a significant decrease in systolic blood pressure (β= −0.08, p= 0.002) in NG controls. Haplotype analysis of rs3764261, rs12447924, rs4783961, and rs708272 further revealed a significant association of ‘ATAA’ haplotype with increased HDL-C (β= 2.71, p= 6.38 ×10−5) and ‘CTAG’ haplotype with decreased HDL–C levels (β= −1.78, p= 2.5×10−2). Although there was no direct association of CETP activity and CETP polymorphisms, low CETP activity was associated with increased risk to CAD (age, BMI and gender adjusted odds ratio 2.2 95% CI (1.4–3.4, p= 0.001) in this study. Our data revealed a strong interaction of rs3764261 and rs708272 for affecting the association between CETP activity and HDL–C levels; p= 2.2 × 10−6, and p= 4.4 × 10−4, respectively.
Our results, in conjunction with earlier reports confirm low CETP activity to be associated with higher CAD risk. Although there was no direct association of CETP activity with CETP polymorphisms, our findings revealed a significant interaction between CETP SNPs and CETP activity for affecting HDL-C levels. These results urge a deeper evaluation of the individual genetic variation in the CETP before implementing pharmaceutical intervention of blocking CETP for preventing CAD events.
This PharmGKB summary briefly discusses the CYP2C19 gene and current understanding of its function, regulation, and pharmacogenomic relevance.
antidepressants; clopidogrel; CYP2C19*17; CYP2C19*2; CYP2C19; proton pump inhibitors; rs4244285
Tacrolimus, an immunosuppressive drug widely prescribed in kidney transplantation, requires therapeutic drug monitoring due to its marked interindividual pharmacokinetic variability and narrow therapeutic index. Previous studies have established that CYP3A5 rs776746 is associated with tacrolimus clearance, blood concentration, and dose requirement. The importance of other drug absorption, distribution, metabolism, and elimination (ADME) gene variants has not been well characterized.
We used novel DNA biobank and electronic medical record resources to identify ADME variants associated with tacrolimus dose requirement. Broad ADME genotyping was performed on 446 kidney transplant recipients who had been dosed to steady state with tacrolimus. The cohort was obtained from Vanderbilt's DNA biobank, BioVU, which contains linked, de-identified electronic medical record data. Genotyping included Affymetrix DMET Plus (1936 polymorphisms), custom Sequenom MassARRAY iPLEX Gold assay (95 polymorphisms), and ancestry-informative markers. The primary outcome was tacrolimus dose requirement defined as blood concentration-to-dose ratio.
In analyses that adjusted for race and other clinical factors, we replicated the association of tacrolimus blood concentration-to-dose ratio with CYP3A5 rs776746 (p = 7.15 × 10−29), and identified associations with nine variants in linkage disequilibrium with rs776746, including eight CYP3A4 variants. No NR1/2 variants were significantly associated. Age, weight, and hemoglobin were also significantly associated with the outcome. In final models, rs776746 explained 39% of variability in dose requirement, and 46% was explained by the model containing clinical covariates.
This study highlights the utility of DNA biobanks and electronic medical records for tacrolimus pharmacogenomic research.
pharmacogenomics; pharmacokinetics; calcineurin inhibitor; tacrolimus; electronic medical records; kidney transplant; cytochrome P4503A5; genetic polymorphism; dosing
Vitamin A and D, and their receptors, are important regulators of the immune system, including vaccine immune response. We assessed the association between polymorphisms in the vitamin A (RARA, RARB and RARG) and vitamin D receptor (VDR)/RXRA genes and inter-individual variations in immune responses after two doses of measles vaccine in 745 subjects.
Using a tagSNP approach, we genotyped 745 healthy children for the 391 polymorphisms in vitamin A and D receptor genes.
The RARB haplotype (rs6800566/rs6550976/rs9834818) was significantly associated with variations in both measles antibody (global p=0.013) and cytokine secretion levels, such as IL-10 (global p=0.006), IFN-α (global p=0.008), and TNF-α (global p=0.039) in the Caucasian subgroup. Specifically, the RARB haplotype AAC was associated with higher (t-statistic 3.27, p=0.001) measles antibody levels. At the other end of the spectrum, haplotype GG for rs6550978/rs6777544 was associated with lower antibody levels (t-statistic −2.32, p=0.020) in the Caucasian subgroup. In a sensitivity analysis, the RARB haplotype CTGGGCAA remained marginally significant (p<0.02) when the single SNP rs12630816 was included in the model for IL-10 secretion levels. A significant association was found between lower measles-specific IFN-γ Elispot responses and haplotypes rs11102986/rs11103473/rs11103482/rs10776909/rs12004589/rs35780541/rs2266677/rs875444 (global p=0.004) and rs6537944/rs3118571 (global p<0.001) in the RXRA gene for Caucasians. We also found associations between multiple RARB, VDR and RXRA SNPs/haplotypes and measles-specific IL-2, IL-6, IL-10, IFN-α, IFN-γ, IFNλ-1, and TNF-α cytokine secretion.
Our results suggest that specific allelic variations and haplotypes in the vitamin A and D receptor genes may influence adaptive immune responses to measles vaccine.
Single Nucleotide Polymorphisms; Measles Vaccine Immunity; Vitamin A Receptor; Vitamin D Receptor; Genes; Immunogenetics
Xeroderma pigmentosum group G (XPG) protein is essential for the nucleotide excision repair (NER) system, and genetic variations in XPG/ERCC5 that affect DNA repair capacity may contribute to the risk of tobacco-induced cancers, including squamous cell carcinoma of the head and neck (SCCHN). We investigated the association between XPG/ERCC5 polymorphisms and risk of squamous cell carcinoma of the head and neck (SCCHN).
We genotyped 12 tagging and potentially functional single nucleotide polymorphisms (SNPs) of XPG/ERCC5 in a case-control study of 1,059 non-Hispanic white patients with SCCHN and 1,066 cancer-free age-and sex matched controls and evaluated their associations with SCCHN risk.
Multivariate logistic regression showed that only an intronic tagging SNP (rs4150351A/C) of XPG/ERCC5 was associated with a decreased risk of SCCHN (adjusted OR=0.76, 95% CI=0.62–0.92 for AC vs. AA; adjusted OR=0.81, 95% CI=0.67–0.98 for AC/CC vs. AA), but this association was nonsignificnant after corrections by the permutation test (empirical P=0.105). In the genotype-phenotype correlation analysis using peripheral lymphocytes from 44 SCCHN patients, we found that rs4150351 AC/CC was associated with a statistically significant increase in XPG/ERCC5 mRNA expression.
These findings suggest that genetic variation in XPG/ERCC5 may not affect the SCCHN risk, although rs4150351 C variant genotypes were associated with the increased expression of XPG/ERCC5 mRNA and nonsignificantly decreased risk of SCCHN. Larger population-based and additional functional studies are warranted to validate our findings.
ERCC5; polymorphism; SCCHN; risk
CYP1A2; caffeine; pharmacogene; pharmGKB
Genetic studies may help explain abnormalities of fat distribution in HIV-infected patients treated with antiretroviral therapy (ARV).
Subcutaneous adipose tissue (SAT) volume measured by magnetic resonance imaging (MRI) in leg, lower trunk, upper trunk, and arm was examined in 192 HIV-infected Caucasian men, ARV-treated from the Fat Redistribution and Metabolic Change in HIV infection (FRAM) study. Single nucleotide polymorphisms (SNPs) were assayed using the Illumina HumanCNV370-quad beadchip. Multivariate and univariate genome wide association analyses of the four SAT depots were implemented in PLINK software adjusted for age and ARV duration. Functional annotation analysis (FAA) using Ingenuity Systems Pathway Analysis tool (IPA) was carried out for markers with P<10-3 near known genes identified by multivariate analysis.
Loci (rs10504906, rs13267998, rs921231) in or near the anion exchanger solute carrier family 26, member 7 isoform a (SLC26A7) were strongly associated with upper trunk and arm SAT (9.8*10-7≤P<7.8*10-6). Loci (rs193139, rs7523050, rs1761621) in and near a gene rich region including G-protein-signaling modulator 2 (GPSM2) and syntaxin binding protein 3 (STXBP3) were significantly associated with lower body SAT depots (9.9*10-7≤P<9.5*10-6). GPSM2 is associated with cell division and cancer while STXBP3 is associated with glucose metabolism in adipoctyes. IPA identified atherosclerosis, mitochondrial function and T-Cell mediated apoptosis as processes related to SAT volume in HIV-infected individuals (P<5*10-3).
Our results are limited by the small sample size and replication is needed, however this genomic scan uncovered new genes associated with metabolism and inflammatory pathways that may affect SAT volume in ARV-treated HIV-infected patients.
HIV; HAART; GWAS; Subcutaneous Fat; SAT
Genetic factors may play a role in fibrosis progression in patients with chronic hepatitis C (CHC). A cirrhosis risk score (CRS7) with 7 SNPs was previously shown to correlate with cirrhosis in patients with CHC. This study aimed to assess the validity of CRS7 as a marker of fibrosis progression and cirrhosis and as a predictor of clinical outcomes in patients with CHC.
A total of 938 patients (677 Caucasians, 165 African Americans, and 96 Hispanic/Other) in the HALT-C Trial were studied. CRS7 was categorized a priori as high risk (n=440), medium risk (n=310) or low risk (n=188). Patients were assessed for four possible outcomes: fibrosis progression, cirrhosis, clinical outcomes (decompensation or hepatocellular carcinoma [HCC]), or HCC alone.
29% (142/493) developed an increase in fibrosis score by ≥ 2 points on follow-up biopsies, 58% had cirrhosis on one or more biopsies, 35% developed at least one clinical outcome, and 13% developed HCC. CRS7 (trend test) was associated with risk for fibrosis progression (p=0.04) with adjusted hazard ratio (HR) of 1.27 (95%CI: 1.01–1.58) and with cirrhosis (p=0.05) with adjusted odds ratio (OR) of 1.19 (1.00–1.41). Rates of HCC and clinical outcomes were increased in patients with higher CRS7 scores, but were not statistically significant (p=0.12 clinical outcomes, and p=0.07 HCC). A SNP in AZIN1 was significantly associated with fibrosis progression.
CRS7 was validated as a predictor of fibrosis progression and cirrhosis among HALT-C patients, who all had advanced fibrosis. CRS7 was not predictive of clinical outcome.
cirrhosis risk score; CRS7; Hepatitis C Antiviral Long-term Treatment against Cirrhosis (HALT-C); hepatitis C; hepatic decompensation; hepatocellular carcinoma (HCC); liver fibrosis
carbamazepine; cytochrome P450 metabolizing enzymes; HLA-B; pharmacogenomics; pharmacokinetics
Responses to therapies, either with regards to toxicities or efficacy, are expected to involve complex relationships of gene products within the same molecular pathway or functional gene set. Therefore, pathways or gene sets, as opposed to single genes, may better reflect the true underlying biology and may be more appropriate units for analysis of pharmacogenomic studies. Application of such methods to pharmacogenomic studies may enable the detection of more subtle effects of multiple genes in the same pathway that may be missed by assessing each gene individually.
A gene set analysis of 3,821 gene sets is presented assessing the association between basal mRNA expression and drug cytotoxicity using ethnically defined human lymphoblastoid cell lines for two classes of drugs: pyrimidines (dFdC and AraC) and purines (6-TG and 6-MP).
The gene set nucleoside-diphosphatase activity was found to be significantly associated with both dFdC and AraC, while gene set gamma-aminobutyric acid catabolic process was associated with dFdC and 6-TG. These gene sets were significantly associated with the phenotype even after adjusting for multiple testing. In addition, five associated gene sets were found in common between the pyrimidines and two gene sets for the purines (3′,5′-cyclic-AMP phosphodiesterase activity and gamma-aminobutyric acid catabolic process) with p < 0.0001. Functional validation was attempted with 4 genes each in gene sets for thiopurine and pyrimidine anti-metabolites. All four genes selected from the pyrimidine gene sets (PSME3, CANT1, ENTPD6, ADRM1) were validated, but only one (PDE4D) was validated for the thiopurine gene sets.
In summary, results from the gene set analysis of pyrimidine and purine therapies, used often in the treatment of various cancers, provide novel insight into the relationship between genomic variation and drug response.
gene set enrichment analysis; mRNA expression; cytotoxicity; pharmacogenomics; bioinformatics
citalopram; escitalopram; pharmacogenomics; pharmacokinetics; pharmGKB; selective serotonin reuptake inhibitor
methotrexate; 5,10-methylenetetrahydrofolate reductase; pathway; pharmacogenomic; SLC19A1; thymidylate synthetase
N-acetyltransferase 1 (NAT1) metabolizes drugs and environmental carcinogens. NAT1 alleles *10 and *11 have been proposed to alter protein level or enzyme activity compared to wild-type NAT1 *4 and to confer cancer risk, via uncertain pathways. This study characterizes regulatory polymorphisms and underlying mechanisms of NAT1 expression.
We measured allelic NAT1 mRNA expression and translation, as a function of multiple transcription start sites, alternative splicing, and three 3′-polyadenylation sites in human livers (one of which discovered in this study), B lymphocytes, and transfected cells. In a clinical study of 469 HIV/AIDS patients treated with the NAT1/NAT2 substrate sulfamethoxazole (SMX), associations were tested between SMX induced hypersensitivity and NAT1 *10 and *11 genotypes, together with known NAT2 polymorphisms.
NAT1*10 and *11 were determined to act as common regulatory alleles accounting for most NAT1 expression variability, both leading to increased translation into active protein. NAT1*11 (2.4% minor allele frequency) affected 3′polyadenylation site usage, thereby increasing formation of NAT1 mRNA with intermediate length 3′UTR (major isoform) at the expense of the short isoform, resulting in more efficient protein translation. NAT1 *10 (19% minor allele frequency) increased translation efficiency without affecting 3′-UTR polyadenylation site usage. Livers and B-lymphocytes with *11/*4 and *10/*10 genotypes displayed higher NAT1 immunoreactivity and NAT1 enzyme activity than the reference genotype *4/*4. Patients who carry *10/*10 and *11/*4 (‘fast NAT1 acetylators’) were less likely to develop hypersensitivity to SMX, but this was observed only in subjects also carrying a slow NAT2 acetylator genotype.
NAT1 *10 and *11 significantly increase NAT1 protein level/enzyme activity, enabling the classification of carriers into reference and rapid acetylators. Rapid NAT1 acetylator status appears to protect against SMX toxicity by compensating for slow NAT2 acetylator status.
N-acetyltransferase; NAT1; polyadenylation; allelic expression imbalance; sulfamethoxazole; cotrimoxazole; protein translation; acetylator phenotype; idiosyncratic drug reactions
To explore associations with prostate cancer and farming, it is important to investigate the relationship between pesticide use and single nucleotide polymorphisms (SNPs) in xenobiotic metabolic enzyme (XME) genes.
We evaluated pesticide-SNP interactions between 45 pesticides and 1,913 XME SNPs with respect to prostate cancer among 776 cases and 1,444 controls in the Agricultural Health Study.
We used unconditional logistic regression to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Multiplicative SNP-pesticide interactions were calculated using a likelihood ratio test.
A positive monotonic interaction was observed between petroleum oil/petroleum distillate use and rs1883633 in the oxidative stress gene glutamate-cysteine ligase (GCLC) (p-interaction=1.0×10−4); men carrying at least one variant allele (minor allele) experienced an increased prostate cancer risk (OR=3.7, 95% CI: 1.9–7.3). Among men carrying the variant allele for thioredoxin reductase 2 (TXNRD2) rs4485648, microsomal epoxide hyrdolase 1 (EPHX1) rs17309872, or myeloperoxidase (MPO) rs11079344, increased prostate cancer risk was observed with high compared to no petroleum oil/petroleum distillate (OR=1.9, 95% CI: 1.1–3.2, p-interaction=0.01), (OR=2.1, 95% CI: 1.1–4.0, p-interaction=0.01), or terbufos (OR=3.0, 95% CI: 1.5–6.0 p-interaction=2.0×10−3) use, respectively. No interactions were deemed noteworthy at the false discovery rate = 0.20 level; the number of observed interactions in XMEs was comparable to the number expected by chance alone.
We observed several pesticide-SNP interactions in oxidative stress and phase I/phase II enzyme genes and risk of prostate cancer. Additional work is needed to explain the joint contribution of genetic variation in XMEs, pesticide use, and prostate cancer risk.
Prostate cancer; pesticides; xenobiotic metabolizing enzymes; single nucleotide polymorphism; interaction
cyclooxygenase-2; coxibs; non-steroidal anti-inflammatory drugs; pharmacogenomics; PTGS2; rs20417; rs5275; rs689466
Lymphoblastoid cell lines have been used as a model system to identify genetic determinants of chemotherapeutic-induced cytotoxicity, a phenotype thought to represent cellular sensitivity to drug. However, cytotoxicity is a broad measurement encompassing cell cycle inhibition as well as cell death (apoptotic and non-apoptotic). We evaluated caspase 3/7 mediated cellular apoptosis with six chemotherapeutic agents: 5′-deoxy-fluorouridine, pemetrexed, cytarabine, paclitaxel, carboplatin and cisplatin. Using monozygotic twin pair and sibling pair lymphoblastoid cell lines, we identified conditions for measurement of caspase activity. Although treatment with 5′-deoxy-fluorouridine and pemetrexed for up to 24 h did not result in significant apoptosis or inter-individual variation in caspase dependent cell death; paclitaxel, cisplatin, carboplain and cytarabine treatment for 24 h resulted in 9.4, 9.1, 7.0 and 6.0 fold increases in apoptosis relative to control, respectively. There was a weak correlation between caspase activity and cytotoxicity (r2=0.03 to 0.29) demonstrating that cytotoxicity and apoptosis are two distinct phenotypes that may produce independent genetic associations. Estimated heritability (h2) for apoptosis was 0.57 and 0.29 for cytarabine (5 μM and 40 μM respectively), 0.22 for paclitaxel (12.5 nM), and 0.34 for cisplatin (5 μM). The HapMap CEU panel of lymphoblastoid cell lines (n = 77) were evaluated for sensitivity to cisplatin followed by genome wide association studies with over 2 million SNPs at p < 0.001. We identified a significant enrichment of cisplatin-induced apoptosis SNPs within the significant cisplatin induced cytotoxicity SNPs and an enrichment of expression quantitative trait loci.
apoptosis; caspase 3/7; lymphoblastoid cell lines; genome wide association study; toxicity
aspirin; clopidogrel; glycoprotein IIb– IIIa inhibitors; pharmacogenomics; PharmGKB; platelet activation; platelet aggregation; polymorphism
This PharmGKB summary briefly discusses the very important pharmacogene GSTT1 and its variants that can influence drug responses. A fully interactive version of this short review, with links to individual paper annotations and population descriptions can be found at http://www.pharmgkb.org/vip/PA183.
Cytochrome P450 2A6 (CYP2A6) is the primary catalyst of nicotine metabolism. To develop a predictive genetic model of nicotine metabolism, the conversion of deuterated (D2)-nicotine to D2-cotinine was quantified in 189 European Americans and the contribution of CYP2A6 genotype to variability in first-pass nicotine metabolism was assessed. Specifically, 1) single time-point measures of D2-cotinine/(D2-cotinine + D2-nicotine) following oral administration were used as a metric of CYP2A6 activity; 2) the impact of CYP2A6 haplotype was treated as acting multiplicatively; 3) parameter estimates were calculated for all haplotypes in the subject pool, defined by a set of polymorphisms previously reported to affect function, including gene copy number; and 4) a minimum number of predictive polymorphisms are justified to be included in the model based on statistical evidence of differences between haplotypes. The final model includes seven polymorphisms and fits the phenotype, 30 minutes following D2-nicotine oral administration, with R2=0.719. The predictive power of the model is robust: parameter estimates calculated in men (n=89) predict the phenotype in women (n=100) with R2=0.758 and vice versa with R2=0.617; estimates calculated in current smokers (n=102) predict phenotype in former smokers (n=86) with R2=0.690 and vice versa with R2=0.703. Comparisons of haplotypes also demonstrate that CYP2A6*12 is a loss of function allele indistinguishable from CYP2A6*4 and CYP2A6*2 and that the CYP2A6*1B 5′ UTR conversion has negligible impact on metabolism. After controlling for CYP2A6 genotype modest associations were found between increased metabolism and both female gender (p= 4.8×10−4) and current smoking (p=0.02).
CYP2A6; nicotine metabolism; cotinine