Retracted: Influence of genetic variants of IDH1, IDH2, TET2 and DNMT3A on cytarabine cytotoxicity in different populations.

'Influence of genetic variants of IDH1, IDH2, TET2 and DNMT3A on cytarabine cytotoxicity in different populations' by Y. Wang & J. K. Lamba1 The above article from the Journal of Clinical Pharmacy and Therapeutics, published online on 21 November 2017 in Wiley Online Library (wileyonlinelibrary.com), has been retracted following discussions with the authors, the Journal Editors and John Wiley & Sons Ltd. The Retraction has been agreed as this paper was submitted under the joint names of Yan Wang, Jatinder K. Lamba and a third co-author. After acceptance of the paper, Dr Wang wrote to the EiC asking for the name of the third co-author to be dropped because of insufficient contribution. The EiC asked that the request be signed by all three authors. When this arrived, the paper was published online with only Dr Wang and Dr Lamba. However, Dr Lamba wrote to the EiC after publication indicating that she had not previously seen the manuscript and that there were co-authors missing. As it is clear that Dr Lamba's signature was forged, we cannot rely on the integrity of the report. The retraction is with the agreement of Dr Lamba but not of Dr Wang. REFERENCE 1. Wang Y, Lamba JK. Influence of genetic variants of IDH1, IDH2, TET2 and DNMT3A on cytarabine cytotoxicity in different populations. J Clin Pharm Ther. 2017;00:1-9. https://doi.org/10.1111/jcpt.12653.

SLC28A3 genotype and gemcitabine rate of infusion affect dFdCTP metabolite disposition in patients with solid tumours.

BACKGROUND: Gemcitabine is used for the treatment of several solid tumours and exhibits high inter-individual pharmacokinetic variability. In this study, we explore possible predictive covariates on drug and metabolite disposition. METHODS: Forty patients were enrolled. Gemcitabine and dFdU concentrations in the plasma and dFdCTP concentrations in peripheral blood mononuclear cell were measured to 72 h post infusion, and pharmacokinetic parameters were estimated by nonlinear mixed-effects modelling. Patient-specific covariates were tested in model development. RESULTS: The pharmacokinetics of gemcitabine was best described by a two-compartment model with body surface area, age and NT5C2 genotype as significant covariates. The pharmacokinetics of dFdU and dFdCTP were adequately described by three-compartment models. Creatinine clearance and cytidine deaminase genotype were significant covariates for dFdU pharmacokinetics. Rate of infusion of <25 mg m(-2) min(-1) and the presence of homozygous major allele for SLC28A3 (CC genotype) were each associated with an almost two-fold increase in the formation clearance of dFdCTP. CONCLUSION: Prolonged dFdCTP systemic exposures (≥72 h) were commonly observed. Infusion rate <25 mg m(-2) min(-1) and carriers for SLC28A3 variant were each associated with about two-fold higher dFdCTP formation clearance. The impacts of these covariates on treatment-related toxicity in more selected patient populations (that is, first-line treatment, single disease state and so on) are not yet clear.

Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies.

The main objective of this study was to investigate the feasibility of using PharmGKB, a pharmacogenomic database, as a source of training data in combination with text of MEDLINE abstracts for a text mining approach to identification of potential gene targets for pathway-driven pharmacogenomics research. We used the manually curated relations between drugs and genes in PharmGKB database to train a support vector machine predictive model and applied this model prospectively to MEDLINE abstracts. The gene targets suggested by this approach were subsequently manually reviewed. Our quantitative analysis showed that a support vector machine classifiers trained on MEDLINE abstracts with single words (unigrams) used as features and PharmGKB relations used for supervision, achieve an overall sensitivity of 85% and specificity of 69%. The subsequent qualitative analysis showed that gene targets "suggested" by the automatic classifier were not anticipated by expert reviewers but were subsequently found to be relevant to the three drugs that were investigated: carbamazepine, lamivudine and zidovudine. Our results show that this approach is not only feasible but may also find new gene targets not identifiable by other methods thus making it a valuable tool for pathway-driven pharmacogenomics research.

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.

Monitoring protein folding and unfolding pathways through surface hydrophobicity changes using fluorescence and circular dichroism spectroscopy.

In the present study we have investigated the characteristics of folding and unfolding pathways of two model proteins, ovalbumin and alpha-lactalbumin, monitored through the changes in surface hydrophobicity using fluorescence and circular dichroism spectroscopy. In the unfolding process, it was observed that ovalbumin and alpha-lactalbumin followed a three state transition pathway involving an intermediate state having high surface hydrophobicity. The intermediate state has also been characterized by circular dichroism spectroscopy, and it was found that the intermediate retained almost the same secondary structure as the native proteins, and therefore it can be referred to as molten globule state. The refolding process was monitored using fluorescence and circular dichroism spectroscopy, and it was observed that the refolding of alpha-lactalbumin was reversible and proceeded through the accumulation of similar type of intermediates as observed during its unfolding pathway. However, on refolding from the guanidine hydrochloride-denatured state, ovalbumin reached a different folded state.

A review of systematic reviews on pain interventions in hospitalized infants.

BACKGROUND: Hospitalized infants undergo multiple, repeated painful procedures. Despite continued efforts to prevent procedural pain and improve pain management, clinical guidelines and standards frequently do not reflect the highest quality evidence from systematic reviews. OBJECTIVE: To critically appraise all systematic reviews on the effectiveness of procedural pain interventions in hospitalized infants. METHODS: A structured review was conducted on published systematic reviews and meta-analyses of pharmacological and nonpharmacological interventions of acute procedural pain in hospitalized infants. Searches were completed in the Cochrane Database of Systematic Reviews, MEDLINE, EMBASE, CINAHL and PsycINFO. Two reviewers independently selected articles for review and rated the methodological quality of the included reviews using a validated seven-point quality assessment measure. Any discrepancies were resolved by a third reviewer. RESULTS: Of 1469 potential systematic reviews on interventions for painful procedures in hospitalized infants, 11 high-quality reviews were included in the analysis. Pharmacological interventions supported by research evidence included premedication for intubation, dorsal penile nerve block and EMLA (AstraZeneca Canada, Inc) for circumcision, and sucrose for single painful procedures. Non-nutritive sucking, swaddling, holding, touching, positioning, facilitative tucking, breast feeding and supplemental breast milk were nonpharmacological interventions supported for procedural pain. CONCLUSION: There is a growing number of high-quality reviews supporting procedural pain management in infants. Ongoing research of single, repeated and combined pharmacological and nonpharmacological interventions is required to provide the highest quality evidence to clinicians for decision-making on optimal pain management.

The impact of pharmacogenomic factors on acute persistent rejection in adult lung transplant patients.

Persistent rejection in the face of treatment and multiple episodes of rejection are associated with the development of chronic rejection and graft loss in solid organ transplantation. The factors that create an environment for rejection that persists in the face of treatment are as yet not understood. The objective of this study was to evaluate the risk factors, including human multidrug resistance gene (MDR1), cytochrome P4503A5 (CYP3A5) and cytokine gene polymorphisms, associated with acute persistent rejection (APR) in lung transplant patients. One hundred and twenty-five adult lung transplant patients were studied. MDR1 G2677T, C3435T and CYP3A5 polymorphisms were assessed by direct sequencing of the polymorphic region in patient DNA. Cytokine genotyping for five cytokines was performed using the polymerase chain reaction-sequence specific primers (PCR-SSP) technique. Multivariate regression analysis was used to identify the predictors of acute persistent rejection. The dependent variable was the presence or absence of acute persistent rejection based on lung biopsies during the first postoperative year. The independent variables were MDR1 G2677T and C3435T, CYP4503A5 and cytokine polymorphisms, survival status, age, gender, survival days and HLA mismatches. The MDR1 C3435T polymorphism and age were independently associated with acute persistent rejection (p = 0.025, odds ratio = 0.29, 95% CI 0.1-0.86 and p = 0.016, odds ratio = 0.94, 95% CI 0.89-0.98, respectively). For the MDR1 C3435T polymorphism, 72% of patients with the C allele had acute persistent rejection in comparison to 52% for TT patients (p = 0.04). For age, a significant difference was found between the nonrejection group and the rejection group (mean+/-S.D. 52.1+/-11.2 vs. 44.4+/-12.3, p = 0.01). This is the first report of the association of a drug disposition genotype with drug-resistant acute rejection in organ transplant patients. The major predictor of acute persistent rejection in the first postoperative year for lung transplant patients was the MDR1 C3435T genotype. This association could be due to drug resistance, altered drug disposition or other immunologic effects associated with P-glycoprotein (P-gp) function. Future prospective treatment algorithms should be developed that will incorporate the knowledge of gene polymorphisms into treatment regimens to improve the outcome following lung transplantation.

The impact of pharmacogenomic factors on steroid dependency in pediatric heart transplant patients using logistic regression analysis.

Many pharmacogenomic predictors of drug response are now available, and include both drug metabolism-disposition factors and drug targets. Information on statistical approaches to analyzing large clinical data sets in relation to genetic polymorphisms is limited. The objective of this study was to evaluate whether logistic regression could identify pharmacogenomic predictors of outcome in a large data set in a complex transplant patient population. Seventy pediatric heart transplant patients were studied. Patients were followed for at least 1 yr post-transplantation as outpatients, and weaned from corticosteroids if clinically appropriate. Logistic regression analysis was used to identify the predictors of steroid dependency. The dependent variable was the presence or absence of steroid therapy at 1 yr post-transplantation. The independent variables were the patients' transplant age, gender, MDR1 C3435T and G2677T, CYP3A53B and cytokine polymorphisms. By chi-square test for the MDR1 C3435T polymorphism, 12 of 18 (67%) patients in the CC group were still on prednisone, whereas only 18 of 47 (38%) of the CT/TT group were still receiving prednisone (p = 0.04). For the IL-10 groups, two of 15 patients with the high producer genotype (13.3%) remained on prednisone, in comparison with 16 of 28 patients with the intermediate producer genotype (57.1%) and 15 of 26 patients with the low producer genotype (57.7%, p = 0.01). Logistic regression analysis confirmed MDR1 C3435T (p = 0.021), and IL-10 polymorphisms (intermediate producer genotype p = 0.015; low producer genotype p = 0.013) as independent risk factors for steroid dependency at 1 yr after transplantation. This approach identifies pharmacogenomic factors, which can be studied more extensively in larger data sets, and used in prospective studies to individualize immunosuppressive therapy following solid organ transplantation.

Disrupted bile acid homeostasis reveals an unexpected interaction among nuclear hormone receptors, transporters, and cytochrome P450.

Sister of P-glycoprotein (SPGP) is the major hepatic bile salt export pump (BSEP). BSEP/SPGP expression varies dramatically among human livers. The potency and hierarchy of bile acids as ligands for the farnesyl/bile acid receptor (FXR/BAR) paralleled their ability to induce BSEP in human hepatocyte cultures. FXR:RXR heterodimers bound to IR1 elements and enhanced bile acid transcriptional activation of the mouse and human BSEP/SPGP promoters. In FXR/BAR nullizygous mice, which have dramatically reduced BSEP/SPGP levels, hepatic CYP3A11 and CYP2B10 were strongly but unexpectedly induced. Notably, the rank order of bile acids as CYP3A4 inducers and activators of pregnane X receptor/steroid and xenobiotic receptor (PXR/SXR) closely paralleled each other but was markedly different from their hierarchy and potency as inducers of BSEP in human hepatocytes. Moreover, the hepatoprotective bile acid ursodeoxycholic acid, which reverses hydrophobic bile acid hepatotoxicity, activates PXR and efficaciously induces CYP3A4 (a bile-metabolizing enzyme) in primary human hepatocytes thus providing one mechanism for its hepatoprotection. Because serum and urinary bile acids increased in FXR/BAR -/- mice, we evaluated hepatic transporters for compensatory changes that might circumvent the profound decrease in BSEP/SPGP. We found weak MRP3 up-regulation. In contrast, MRP4 was substantially increased in the FXR/BAR nullizygous mice and was further elevated by cholic acid. Thus, enhanced hepatocellular concentrations of bile acids, due to the down-regulation of BSEP/SPGP-mediated efflux in FXR nullizygous mice, result in an alternate but apparent compensatory up-regulation of CYP3A, CYP2B, and some ABC transporters that is consistent with activation of PXR/SXR by bile acids.

Control of the stereochemical impact of the lone pair in lead(II) tris(pyrazolyl)methane complexes. Improved preparation of Na[B[3,5-(CF3)2C6H3]4].

The reaction of Pb(acac)2 with 2 equiv of [H(Et2O)2][B[3,5-(CF3)2C6H3]4] (HBAr(f)) in CH2Cl2 followed by addition of 2 equiv of either HC(pz)3 or HC(3,5-Me2pz)3 (pz = pyrazolyl ring) leads to the formation of [Pb[HC(pz)3]2][B[3,5-(CF3)2C6H3]4]2 (1) and [Pb[HC(3,5-Me2pz)3]2][B[3,5-(CF3)2C6H3]4]2 (2), respectively. The cation in 1 has a distorted octahedral structure with a stereochemically active lone pair on lead(II). In contrast, the cation in 2 is trigonally distorted octahedral with the lone pair on the lead(II) clearly stereochemically inactive. The driving force for this cation to have a stereochemically inactive lone pair is that in this geometric arrangement the interligand distances between adjacent 3-position methyl groups are close to 4.0 A, the sum of the van der Waals radii of two methyl groups. To facilitate this chemistry, the synthesis of Na[B[3,5-(CF3)2C6H3]4], needed to prepare HBAr(f), has been dramatically improved. The main change is to add NaBF4 to the reaction mixture before forming the Grignard from the reaction of magnesium and 3,5-(CF3)2C6H3Br. The Grignard reacts with the NaBF4 as it forms, reducing the danger of explosion and leading to a higher isolated yield of the product. Crystallographic information: 1 is triclinic, P1, a = 13.0133(6) A, b = 17.2210(7) A, c = 24.7634(11) A, alpha = 71.7300(10) degrees, beta = 82.3630(10) degrees, gamma = 70.5120(10) degrees, Z = 2; 2 is triclinic, P1, a = 12.756(4) A, b = 13.469(4) A, c = 17.160(5) A, alpha = 82.454(7) degrees, beta = 89.904(8) degrees, gamma = 72.995(7) degrees, Z = 1.

Sequence diversity in CYP3A promoters and characterization of the genetic basis of polymorphic CYP3A5 expression.

Variation in the CYP3A enzymes, which act in drug metabolism, influences circulating steroid levels and responses to half of all oxidatively metabolized drugs. CYP3A activity is the sum activity of the family of CYP3A genes, including CYP3A5, which is polymorphically expressed at high levels in a minority of Americans of European descent and Europeans (hereafter collectively referred to as 'Caucasians'). Only people with at least one CYP3A5*1 allele express large amounts of CYP3A5. Our findings show that single-nucleotide polymorphisms (SNPs) in CYP3A5*3 and CYP3A5*6 that cause alternative splicing and protein truncation result in the absence of CYP3A5 from tissues of some people. CYP3A5 was more frequently expressed in livers of African Americans (60%) than in those of Caucasians (33%). Because CYP3A5 represents at least 50% of the total hepatic CYP3A content in people polymorphically expressing CYP3A5, CYP3A5 may be the most important genetic contributor to interindividual and interracial differences in CYP3A-dependent drug clearance and in responses to many medicines.

Correlation between omeprazole hydroxylase and CYP2C19 genotype in North Indians.

OBJECTIVE: To comprehend the correlation between the in vitro activity of hepatic omeprazole (OMZ) hydroxylase and genotype of North Indians with respect to CYP2C19. METHODS: Microsomes were prepared from the livers of 15 North Indians. Assay of OMZ hydroxylase was performed by incubating the microsomes with OMZ in the presence of reduced nicotinamide adenine dinucleotide phosphate (NADPH). The 5-OH-OMZ formed was assayed using high-performance liquid chromatography. Genomic DNA isolated from the blood of the same individuals was employed for genotyping of CYP2C19*2 and *3 using polymerase chain reaction-based diagnostic tests. RESULTS: Thirteen subjects demonstrated an average OMZ hydroxylase activity of 138 pmol 5-OH-OMZ formed/min/mg protein. They were designated as extensive metabolisers (EMs). Eight EMs were homozygous with CYP2C19*1/*1 genotype and demonstrated the highest average activity of OMZ hydroxylase (169 pmol 5-OH-OMZ formed/min/mg protein). Five heterozygous EMs (CYP2C19*1/*2) demonstrated 52% activity of OMZ hydroxylase compared with eight homozygous EMs (CYP2CI9*1/*1). Two subjects demonstrated 11% activity of OMZ hydroxylase (15 pmol 5-OH-OMZ formed/min/mg protein) compared with EMs. Hence, these individuals were designated as poor metabolisers (PMs). Both PMs had genotype CYP2C19*2/*2. None of the subjects had CYP2C19*3/*3 genotype. CONCLUSION: The results of the present study demonstrated concordance between the in vitro activity of OMZ hydroxylase and the CYP2C19 genotype in North Indians.

CYP2C19 genetic mutations in North Indians.

OBJECTIVES: To identify defective alleles of CYP2C19 (CYP2C19*2 and *3) in North Indians. METHODS: One hundred extensive metabolizers and 21 poor metabolizers of omeprazole were genotyped with respect to CYP2C19*2 and *3 alleles with polymerase chain reaction-based diagnostic tests. RESULTS: Fifty-two extensive metabolizers and six poor metabolizers were homozygous with the CYP2C19*1/*1 genotype, and 48 extensive metabolizers and six poor metabolizers were heterozygous with the CYP2C19*1/*2 genotype. Nine poor metabolizers were homozygous with the CYP2C19*2/*2 genotype. No extensive or poor metabolizers demonstrated the presence of the CYP2C19*3 allele. CYP2C19*2 could explain 43% (9/21) of the poor metabolizers and 57% (24/42) of the defective alleles in poor metabolizers. Allele frequency of CYP2C19*1 and *2 was 0.7 (95% confidence interval of 0.65 to 0.75) and 0.3 (95% confidence interval of 0.25 to 0.35), respectively. Homozygous extensive metabolizers excreted 7.85 +/- 7.6 micromol 5-hydroxyomeprazole in 8 hours, which was 28% more as compared with heterozygous extensive metabolizers who excreted 5.6 +/- 3.6 micromol 5-hydroxyomeprazole in 8 hours (P < .05). CONCLUSIONS: CYP2C19*2 demonstrated allele frequency of 0.3, whereas CYP2C19*3 was absent in North Indians. Because CYP2C19*2 is not able to explain 57% of poor metabolizers, other mutations (CYP2C19*4 to *8) might be present in North Indians. CYP2C19 demonstrated differential evolution in North Indians because the frequency of CYP2C19*2 was similar to that in Oriental subjects, but that of CYP2C19*3 was similar to that in white subjects.

Genetic polymorphism of the hepatic cytochrome P450 2C19 in north Indian subjects.

One hundred unrelated healthy North Indian subjects were phenotyped with respect to their ability to metabolize omeprazole to 5-hydroxyomeprazole. Each volunteer was requested to ingest 20 mg (57.9 mumol) omeprazole. Urine was collected for a period of 8 hours and the amount of 5-hydroxyomeprazole excreted was estimated by HPLC. Histogram, probit, and normal test variable plots showed the antimode value for the log hydroxylation index of omeprazole to be 1.7. Of 100 North Indian subjects, 11 demonstrated log hydroxylation index values more than 1.7. Thus it is inferred that the frequency of occurrence of poor metabolizers of omeprazole in North Indian subjects is 11% (95% confidence interval, 5% to 17%). From the Hardy-Weinberg Law it was computed that the frequency of occurrence of the mutant allele of hepatic CYP2C19 in the North Indian subjects was 0.33.

Genetic polymorphism of CYP2D6 in North Indian subjects.

OBJECTIVES: CYP2D6 polymorphism of clinical relevance occurs with variable frequency in different ethnic groups. Since this polymorphism has not been studied in a North Indian population, the present study was undertaken. METHODS: One hundred healthy unrelated North Indian subjects received 30 mg dextromethorphan (DM) orally at bed-time. The amounts of DM and its metabolite, dextrorphan (DR), excreted in 8 h urine were estimated by high performance liquid chromatography. Metabolic ratio (DM/DR excreted in 8 h) was used as an index of the metabolic status of an individual. RESULTS: The analysis of the data by frequency distribution histogram, probit and NTV plots demonstrated bimodal distribution of the North Indian subjects with respect to hepatic CYP2D6. Out of 100 subjects, 97 were extensive metabolizers (EMs), whereas three were poor metabolizers (PMs). EMs and PMs excreted 29.82 and 2.67 micromol DR (mean value) and 2.59 and 8.82 micromol DM (mean value) in 8 h, respectively. MR and log MR was 197- and 2.2-fold higher in PMs versus EMs. The antimode value of zero was determined by visual observation in frequency distribution histogram and inflection point in probit plot. CONCLUSION: From this study, it can be concluded that the PM phenotype of CYP2D6 occurs with a frequency of 3% (95% confidence interval of 0.33%-6.33%) in North Indians.