622 research outputs found
Interindividual Variability in the Cytochrome P450 3A4 Drug Metabolizing Enzyme: Effect of the CYP3A4*1G Genetic Variant
Researchers and clinicians are interested in how a patient’s individual genetic makeup could predict the appropriate medication and dose for that patient. One way to predict drug response, or efficacy, is by looking at enzymes within the liver that metabolize drugs. Many of these enzymes belong to a class called the Cytochrome P450s (CYPs). Specifically, two closely related enzymes, CYP3A4 and CYP3A5, are involved in metabolizing 50% of drugs currently on the market (eg: statins, antiepileptics, anticancer agents, and antidepressants). There can be differences in the genetic code of these enzymes that can causes changes in drug metabolism. We completed a study with participants from the Confederated Salish and Kootenai Tribes (CSKT), located on the Flathead Reservation in northwest Montana. Select CYP enzymes were genotyped, including CYP3A4 and CYP3A5. Most SNPs identified in the CSKT participants were found at frequencies similar to those reported in European-descended populations. Interestingly, one specific SNP, called CYP3A4*1G, was discovered at a high allele frequency. The physiological significance of this SNP is unclear as there are limited and confounding data, however, most of the data published to date suggest that the SNP causes decreased metabolism of drugs. Clinically, this could result in a need for a decreased dose of medication. In addition, this CYP3A4 SNP was observed to be often inherited with another SNP in the related CYP3A5 gene, called CYP3A5*3, which encodes a nonfunctional enzyme. These SNPs found in the CSKT are of particular interest, because inheriting these two SNPs together could cause drastic changes in drug metabolism since the two enzymes metabolize many of the same drugs
Single nucleotide polymorphisms in the intergenic region between metformin transporter OCT2 and OCT3 coding genes are associated with short-Term response to metformin monotherapy in type 2 diabetes mellitus patients
Publisher Copyright: © 2016 The authors Published by Bioscientifica Ltd. Copyright: Copyright 2017 Elsevier B.V., All rights reserved.Objective(s): High variability in clinical response to metformin is often observed in type 2 diabetes (T2D) patients, and it highlights the need for identification of genetic components affecting the efficiency of metformin therapy. Aim of this observational study is to evaluate the role of tagSNPs (tagging single nucleotide polymorphisms) from genomic regions coding for six metformin transporter genes with respect to the short-Term efficiency. Design: 102 tagSNPs in 6 genes coding for metformin transporters were genotyped in the group of 102 T2D patients treated with metformin for 3 months. Methods: Most significant hits were analyzed in the group of 131 T2D patients from Slovakia. Pharmacokinetic study in 25 healthy nondiabetic volunteers was conducted to investigate the effects of identified polymorphisms. Results: In the discovery group of 102 patients, minor alleles of rs3119309, rs7757336 and rs2481030 were significantly nominally associated with metformin inefficiency (P = 1.9 × 106 to 8.1 × 106). Effects of rs2481030 and rs7757336 did not replicate in the group of 131 T2DM patients from Slovakia alone, whereas rs7757336 was significantly associated with a reduced metformin response in combined group. In pharmacokinetic study, group of individuals harboring risk alleles of rs7757336 and rs2481030 displayed significantly reduced AUC∞ of metformin in plasma. Conclusions: For the first time, we have identified an association between the lack of metformin response and SNPs rs3119309 and rs7757336 located in the 5 flanking region of the genes coding for Organic cation transporter 2 and rs2481030 located in the 5 flanking region of Organic cation transporter 3 that was supported by the results of a pharmacokinetic study on 25 healthy volunteers.publishersversionPeer reviewe
Genetic variants of d4T drug transporters and dNTP pool regulators, and their association with response to d4T-ART
A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Master of Science in Genetics.
Johannesburg, South Africa
2017Background: Stavudine (d4T) use is associated with the development of sensory neuropathy (SN), several mechanisms may underlie d4T-induced toxicity, including:
(1) Inter-patient genetic variability in the genes modulating the deoxynucleotide triphosphate (dNTP) pool sizes.
(2) Variation in intracellular ARV drug concentrations due to genetic variation in drug transporters.
In our study we examined the genetic variation in four stavudine transporter genes and seven genes regulating the deoxythymidine triphosphate (dTTP) synthesis and their associations with d4T-induced SN or CD4+ T cell count or mtDNA copy number.
Methods: We examined a cohort of HIV-positive South African (SA) adults exposed to d4T, including 143 cases with SN and 120 controls without SN. 26 single nucleotide polymorphisms (SNPs) from the literature were chosen, prioritised on being tagSNPs with minor allele frequency >5% in Kenyan Luhya (a proxy population for the SA Black population); SNP functional effects and suitability for multiplex analysis on the genotyping platform. Genotyping was performed using Sequenom mass spectrometry. A qPCR assay was used to measure the mtDNA copy number. Association of sensory neuropathy, CD4+ T cell count and mtDNA copy number with genetic variants was evaluated using PLINK.
Results: All 26 SNPs were in Hardy-Weinberg equilibrium (HWE) in both the cases and controls. SNP rs8187758 of the SLC28A1 transporter gene and a 3-SNP haplotype ABCG2 were significantly associated with CD4+ T cell count after correction for multiple testing (p = 0.043 and p=0.042 respectively), but were not significant in multivariate testing. No SNP remained significantly associated with SN or mtDNA copy number, after correction for multiple testing.
Conclusion: Variation in genes encoding molecular transporters of d4T may influence CD4+ T cell counts after ART. This study presents a positive step towards achieving personalized medicine in SA.MT 201
In Vitro Functional Analysis Of Novel Single Nucleotide Polymorphisms In OATP1B1 And Potential Clinical Relevance
Statin-induced myopathy is a common adverse reaction of statin therapy. Patients with elevated plasma concentration of statins are thought to be at greater risk for myopathy. Statins are transported from the blood to hepatocytes via organic anion transporting polypeptide 1B1 (OATP1B1). Although single nucleotide polymorphisms (SNPs) in OATP1B1 have been associated with increased statin concentrations, we hypothesize that there may be other SNPs in OATP1B1 that can also contribute to reduced transport activity and increased plasma statin concentrations. OATP1B1 cDNA packaged in pEF6/V5-His TOPO was used as template, and 6 SNPs — c.298G\u3eA, c.419C\u3eT, c.463C\u3eA (*4), c.1007C\u3eG, c.1463G\u3eC (*9), and c.1738C\u3eT — were introduced separately and expressed in adenovirus. 3 SNPs abolished transport activity, 1 SNP decreased transport, 1 increased transport, and 1 did not affect transport activity. Our data support the hypothesis that there are additional loss of function SNPs in OATP1B1
The pharmacologenetics of lopinavir in a cohort of black African HIV/AIDS patients
The Sub-Saharan African region remains the most severely affected by the HIV/AIDS epidemic. At the end of 2011, The Joint United Nations Programme on HIV/AIDS (UNAIDS) estimated that about 5% of adults were living with the HIV in this region, accounting for 69% of the global HIV prevalence. Efforts to curb the epidemic are focused on managing HIV through prevention strategies, such as advocating the use of condoms or pre-exposure or post-exposure prophylactic treatment, and prolonging life through the use of antiretroviral (ARV) therapy. Drugs used in ARV therapy target different major steps of the HIV reproductive cycle. These are nucleoside and non-nucleoside reverse transcriptase inhibitors (NRTIs/NNRTIs); fusion/entry inhibitors; integrase inhibitors; and protease inhibitors (PIs). In South Africa PIs, specifically lopinavir (LPV) boosted with another PI, ritonavir (RTV) are used in second-line ARV regimens along with a backbone of 2 NRTIs. The use of ARVs is not without issues - patients often experience side-effects to the drugs such as nausea, diarrhoea, and lipodystrophy with LPV use, which may influence their adherence to treatment and eventually lead to treatment failure. Inter-individual variability exists in patients' response to treatment despite the standard dose of 400 mg/100 mg (LPV/RTV) that is given and this may be due to differences in transport or metabolism of the drug in the liver. High plasma drug levels (associated with side-effects or toxicity) may be a result of poor metabolism or conversely, low plasma drug levels (associated with failure to suppress the virus) may be a result of extensive metabolism of the drug. Proteins involved in the disposition of LPV include the drug metabolising enzymes, CYP3A4 and CYP3A5; the hepatic uptake transporter, OATP1B1; and the efflux transporter, MRP2. Variation in the genes encoding these proteins may influence their functioning and hence LPV disposition. The aim of the study was to identify significant single nucleotide polymorphisms (SNPs) in each gene; to genotype a cohort of HIV-infected patients from Malawi and South Africa to identify the frequency of those variants; and to correlate genotypes with LPV plasma levels and other clinical parameters
Pharmacokinetic and Pharmacogenetic aspects of drug-drug interactions between antiretroviral and anti-tuberculosis drugs in Ethiopian patients: Implication for optimization of TB-HIV co-treatment
TB and HIV are immuno-pathologically interacting epidemic infectious diseases affecting the lives of millions
globally & sub-Saharan African region accounts the highest burden of both diseases. Although effective therapies
are available for the management of each, TB-HIV co-treatment has faced challenges mainly due to drug-drug
interactions & overlapping drug toxicities. To overcome these, efavirenz (EFV) based highly active antiretroviral
therapy (HAART) is the preferred regimen while rifampicin (RIF) based anti-TB treatment regimen is a choice to
treat TB-HIV co-infection in resource-limited settings. RIF is a known enzyme & drug transporter inducer and/or
inhibitor. The dose of EFV to be used in the presence of RIF is, however, controversial. This thesis is primarily
carried out to investigate the pharmacogenetic and pharmacokinetic aspect of drug-drug interaction between RIF &
EFV aiming to optimize the dose of EFV to be used in TB-HIV co-infected Ethiopian patients.
This study was designed to be carried out in two sub-Saharan African countries (Ethiopia and Tanzania), owning to
the heterogeneity of the region genetically and culturally. This thesis focuses on the Ethiopian population. The thesis
was conducted by prospectively recruiting cohort of HIV infected individuals without TB (Arm 1; N = 285) in
parallel to another cohort of HIV co-infected with active TB (Arm 2; N = 196). All study participants were adults
with baseline CD4 count less than 200 cells per mm3
and were followed for a year. At baseline and follow up periods,
clinical chemistry (liver and kidney function tests), hematological parameters (complete and differential blood cell
counts) and HAART outcome monitoring (CD4 counts and HIV RNA viral load) were done. In addition, genotyping
for CYP2B6*6, CYP3A5 (*3, *6, *7), UGT2B7*2, NAT2, ABCB1 (3435 C > T & 3842 A > G) & SLCO1B1 (*1b &
*5) were also done. Pharmacokinetic variables such as plasma/intracellular concentrations of EFV, 8-hydroxyefavirenz (major metabolite) & metabolic ratio were determined at weeks 4 and/or 16, 16±1h post-dose. Besides,
cholesterol, 4β-hydroxy-cholesterol (biomarker for CYP3A activity) & metabolic ratio at weeks 0, 4, 16 & 48 were
also determined to investigate time-dependent effect of EFV on CYP3A enzyme. Socio-demographic factors (Age,
sex, baseline body weight and BMI) were also recorded.
This thesis reports paradoxical increase in plasma/intracellular EFV concentrations by RIF co-therapy; coherent to
this is improved immunological outcomes among individuals co-treated for TB and HIV with comparable virologic
success to HAART than those without RIF co-treatment. The thesis also shows wide between-subject variability in
the long-term auto-induction by EFV based on CYP2B6 genotype. Between & within-subject variability in plasma
EFV concentration and immunological outcome are shown to be influenced by RIF co-therapy, CYP2B6 genotype
and baseline body weight. Besides, the thesis demonstrates the influence of CYP2B6 genotype on CYP3A autoinduction by EFV in a gene-dose dependent manner, CYP2B6 (*6/*6 > *1/*6 > *1/*1). Furthermore, the thesis
reveals the importance of differences in ethnicity & environmental factors contributing to wide between-population
variability in EFV auto-induction comparing Ethiopian & Tanzanian patients. In addition, associations of CYP2B6,
ABCB1 (3842A >G), slow NAT2 metabolizing genotypes & plasma concentration of EFV with increased incidences
of drug-induced liver injury (DILI) and correlation of plasma and intracellular concentrations of EFV are reported in
the thesis. The thesis also shows the long-term but not short-term effects of sex and UGT2B7 genotype in predicting
auto-induction as well as plasma concentration of EFV.
In conclusion, EFV dose-escalation from 600mg to 800mg is not required during TB-HIV co-treatment in Ethiopian
patients. CYP2B6*6 genotype is not only a strong predictor for EFV pharmacokinetics but also could predict EFVbased HAART outcomes, DILI & CYP3A auto-induction by EFV. In addition to pharmacogenetic variability, the
importance of differences in ethnicity & environmental factors are highlighted to optimize HIV treatment across subSaharan Africa
Pharmacogenetics of Efavirenz response in Bantu-speaking South African HIV/AIDS patients
Includes abstract.Includes bibliographical references (leaves 82-96).Efavirenz (EFV) is used in first-line antiretroviral (ARV) therapy of HIV-infected patients, and is principally metabolised by CYP1A2, CYP2A6, CYP2B6, CYP3A4/5 and the drug transporter ABCB1. Genetic variability in the above genes may contribute to differences in EFV plasma concentrations which affect the levels of viral suppression as well as development of side effects in patients. The aim of this project was to evaluate the effects of the different genetic polymorphisms on EFV plasma concentration levels in HIV/AIDS patients receiving first-line antiretroviral treatment (ART) containing EFV
Development of genotyping systems for pharmacogenomics profiling
>Magister Scientiae - MScGenetic variability in genes encoding drug metabolizing enzymes, transporters and targets are known to be the main factors of inter-individual differences in therapeutic outcome. Genetic factors are estimated to be responsible for about 15-30% of inter-individual variation in drug disposition and response. Single-nucleotide polymorphisms (SNPs) are the most prevalent class of genetic variation that could explain the variability in drug efficacy and undesired side effects for patients. The aims of this study were to develop and evaluate the performance of robust and high throughput techniques for genotyping ten polymorphisms related to anticancer drugs and ten polymorphisms related to cholesterol lowering drugs. SNaPshot minisequencing and high resolution melt analysis (HRM) genotyping panels were developed, optimized, and their performances were evaluated and compared. SNaPshot minisequencing systems were developed and successfully optimized for the genotyping of ten SNPs associated with anticancer drug therapy, and ten SNPs associated with cholesterol lowering drugs. These systems were used to genotype the selected SNPs in 130 healthy Cape Admixed participants residing in Cape Town, South Africa. Population genetics data obtained for the studied SNPs were analysed using several statistical analysis software tools. Important population genetic parameters were calculated. Among others, allelic and genotypic frequencies were determined and compared with other populations in the world. High resolution melt analysis (HRM) genotyping panels were developed, optimized and their performance were evaluated and compared to the SNaPshot assays. HRM was explored as an alternative inexpensive and rapid methodology to genotype five SNPs related to anticancer therapy and five SNPs related to cholesterol lowering therapy (statins). Unlike the SNaPshot assays, rigorous optimization was required for the detection heterozygous genotypes via HRM. Both assays were validated using direct sequencing and compared to each other. The HRM system is a closed tube, cheap and (theoretically) rapid method for identifying genetic variations. HRM was however found to be more time consuming, needed further optimization, primer redesigning and more evaluation. The developed genotyping systems could be further validated using clinical samples from patients. This could help in optimizing drug therapy for cancer and cholesterol treatment
- …