Effect of genetic variants in genes encoding two nuclear receptors (PXR and CAR) on efavirenz levels and treatment outcome in South African HIV-infected females

Nieuwoudt, Enid (2014-12)

Thesis (MSc)--Stellenbosch University, 2014.

Thesis

ENGLISH ABSTRACT: Efavirenz is an antiretroviral drug used in the treatment of HIV-positive patients as part of first line triple-highly active antiretroviral therapy. Treatment response varies among individuals and adverse drug reactions tend to occur, as a result of the variation in the rate of efavirenz metabolism among individuals. This is partly caused by genetic variation; therefore the study of genes involved in the metabolism of efavirenz, such as CYP2B6, could potentially enhance treatment success. The effect of CYP2B6 SNP 516G>T (part of the CYP2B6*6 allele) is particularly important, as individuals homozygous for the minor allele of this SNP have significantly increased efavirenz levels. Furthermore, nuclear receptors, specifically constitutive androstane receptor, encoded by NR1I3, and pregnane X receptor, encoded by NR1I2, are involved in the regulation of the genes responsible for efavirenz metabolism and could therefore indirectly influence the pharmacokinetics of efavirenz. The current study identified variants in the NR1I3 and NR1I2 genes through in silico analysis, bi-directional sequencing and literature searches. A total of nine NR1I3 and ten NR1I2 target variants were subsequently genotyped in 132 HIV-positive female patients from the Xhosa and Cape Mixed Ancestry populations. The resulting genotype and allele frequencies were statistically analysed to search for correlations between genetic variations and available efavirenz levels in hair samples, treatment outcome as measured by viral load, and the occurrence of adverse drug reactions. The minor allele of a NR1I2 5’-upstream SNP, rs1523128 (6334A>G), was significantly associated with decreased efavirenz levels. From analysis of the effect of composite SNPs, NR1I3 5’-upstream SNP rs55802895 (258G>A) in conjunction with CYP2B6*6, was significantly associated with efavirenz-levels. It was found that the minor allele of rs55802895 inhibited the effect of CYP2B6*6, resulting in normal efavirenz levels for individuals homozygous for the minor allele of both SNPs. Additionally, when the target NR1I3 and NR1I2 variants were analysed in conjunction with six SNPs from CYP1A2, CYP2A6, CYP3A4 and CYP3A5, 11 compound genotypes were shown to be statistically associated with mean EFV plasma levels. The study emphasises the complexity of efavirenz metabolism, and the importance of transcriptional regulation in xenobiotic metabolism.

AFRIKAANSE OPSOMMING: Efavirenz is ‘n antiretrovirale middel wat gebruik word in die behandeling van HIV-positiewe pasiënte as deel van drievoudige hoogs-aktiewe antiretrovirale terapie. Reaksie op behandeling verskil tussen individue en nadelige newe-effekte, wat veroorsaak word deur die verskil in tempo waarteen efavirenz gemetaboliseer word, neig om voor te kom. Hierdie verskille word gedeeltelik veroorsaak deur genetiese variasie; dus kan die studie van gene betrokke by die metabolisme van efavirenz, soos CYP2B6, moontlik die sukses van behandeling verhoog. Die effek van CYP2B6 SNP 516G>T (deel van die CYP2B6*6-alleel) is veral belangrik, want individue wat homosigoties is vir die minderheids-alleel het betekenisvol hoë efavirenz-vlakke. Nukleêre reseptore, spesifiek konstitutiewe androstane reseptor, deur NR1I3 gekodeer, en pregnane X reseptor, deur NR1I2 gekodeer, is betrokke by die regulering van die gene verantwoordelik vir efavirenz-metabolisme en kan dus die farmakokinetika van efavirenz beïnvloed. Die huidige studie het variante in NR1I3 en NR1I2 identifiseer deur in silico-analise, bi-direksionele volgordebepaling en ’n literatuurstudie. Nege NR1I3 en tien NR1I2-variante in totaal is vervolglik gegenotipeer in 132 HIV-positiewe vroulike pasiënte van Xhosa en Kaapse Gemengde Afkoms populasies. Die gevolglike genotipe- en alleelfrekwensies is statisties geanaliseer om vir korrelasies tussen genetiese variasies en beskikbare efavirenz-vlakke in haarmonsters, uitkoms van behandeling gemeet in virale lading en die voorkoms van nadelige newe-effekte te soek. Daar is gevind dat die minderheids-alleel van ’n NR1I2 5’-stroomop SNP, rs1523128 (6334A>G), betekenisvol geassosieer is met ’n daling in efavirenz-vlakke. Vanuit die saamgestelde SNPs, is die NR1I3 5’-stroomop SNP rs55802895 (258G>A), tesame met CYP2B6*6, betekenisvol geassosieer met efavirenz-vlakke. Daar is gevind dat die minderheids-alleel van rs55802895 die effek van CYP2B6*6 demp, en gevolglik normale efavirenz-vlakke in individue homosigoties vir die minderheids-allele van albei SNPs veroorsaak. Addisioneel is die teiken NR1I3 en NR1I2 variante gemeenskaplik met ses SNPs van CYP1A2, CYP2A6, CYP3A4 en CYP3A5 geanaliseer en 11 gekombineerde genotipes is statisties geassosieer met gemiddelde EFV plasma vlakke. Hierdie studie beklemtoon die kompleksiteit van efavirenz-metabolisme en die belangrikheid van transkripsionele regulering in xenobiotiese metabolisme.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/95893
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