Browsing by Author "Kormuth, Emil."

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Association of genetic polymorphisms in select HIV-1 replication cofactors with susceptibility to HIV-1 infection and disease progression.
(2011) Madlala, Paradise Zamokuhle.; Ndung'u, Peter Thumbi.; Kormuth, Emil.
Objective.Humans differ substantially with respect to susceptibility to human immunodeficiency virus type 1 (HIV-1) infection and disease progression. This heterogeneity is attributed to the interplay between the environment, viral diversity, immune response and host genetics. This study focused on host genetics. We studied the association of single nucleotide polymorphisms (SNPs) in peptidyl prolyl isomerase A (PPIA), transportin 3 (TNPO3) and PC4 or SFRS1 interacting protein 1 (PSIP1) genes with HIV-1 infection and disease progression. These genes code for Cyclophilin A (CypA), Transportin-SR2 (TRN-SR2) and Lens epithelium derived growth factor/p75 (LEDGF/p75) proteins respectively, which are all validated HIV replication cofactors in vitro. Methods. One SNP A1650G in the PPIA gene was genotyped in 168 HIV-1 negative and 47 acutely infected individuals using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). 6 intronic and 2 exonic haplotype tagging (ht) SNPs (rs13242262; rs2305325; rs11768572; rs1154330; rs35060568; rs8043; rs6957529; rs10229001) in the TNPO3 gene, 4 intronic ht SNPs (rs2277191, rs1033056, rs12339417 and rs10283923) and 1 exonic SNP (rs61744944, Q472L) in the PSIP1 gene were genotyped in 195 HIV-1 negative and 52 acutely infected individuals using TaqMan assays. The rs1154330, rs2277191, rs12339417 and rs61744944 were further genotyped in 403 chronically infected individuals. CypA and LEDGF/p75 messenger RNA (mRNA) expression levels in peripheral blood mononuclear cells (PBMCs) were quantified by real-time reverse transcriptase polymerase chain reaction (RT-PCR). The impact of the Q472L mutation on the interaction of LEDGF/p75 with HIV-1 integrase (IN) was measured by AlphaScreen. Results. The minor allele (G) of SNP A1650G (1650G) in the promoter region of PPIA was significantly associated with higher viral load (p<0.01), lower CD4+ T cell counts (p<0.01) and showed a possible association with rapid CD4+ T cell decline (p=0.05). The 1650G was further associated with higher CypA expression post HIV-1 infection. The minor allele (G) of rs1154330 in the intron region of TNPO3 was associated with faster HIV-1 acquisition (p<0.01), lower CD4+ T cell counts, higher viral load during primary infection (p<0.05) and rapid CD4+ T cells decline (p<0.01). The minor allele (A) of rs2277191 (rs2277191A) in the intron region of PSIP1 was more frequent among seropositives (p=0.06). Among individuals followed longitudinally, rs2277191A was associated with higher likelihood of HIV-1 acquisition (p=0.08) and rapid CD4+T cell decline (p=0.04) in the recently infected (primary infection) cohort. In contrast, the minor allele (C) of rs12339417 (rs12339417C) also in the intron region of PSIP1 was associated with higher CD4+ T cell counts during primary infection. The rs12339417C was also associated with slower rate of CD4+ T cell decline (p=0.02) and lower mRNA levels of LEDGF/p75 (p<0.01). Seroconverters had higher preinfection mRNA levels of LEDGF/p75 compared to nonseroconverters (p<0.01) and these levels decreased after HIV-1 infection (p=0.02). The Q472L mutation showed approximately 2-fold decrease in the association constant (Kd), suggesting stronger binding to HIV-1 integrase. Our findings demonstrate, for the first time, that genetic polymorphisms in the TNPO3 and PSIP1 genes may be associated with susceptibility to HIV-1 infection and the disease progression. These data provide in vivo evidence that TRN-SR2 and LEDGF/p75 are important host cofactors for HIV-1 replication. This is also the first study to show the association of genetic polymorphisms in the PPIA gene with disease outcome in a population (South African) with high burden of HIV-1 infection. Conclusions. Genetic variation in HIV-1 replication cofactors may be associated with disease outcome in a South African population. These data strongly support the role of these HIV replication cofactors in disease pathogenesis in vivo and suggest that these factors are possible targets for therapeutic interventions. However, these data will need to be replicated in larger cohorts to confirm the effect of these genetic variants. Further studies on how to target these factors in antiviral strategies are needed.
Genetic/epigenetic determinants in chemokines and chemokine receptor genes that influence HIV susceptibility in a cohort of high-risk women from South Africa.
(2010) Ramsuran, Veron.; Ndung'u, Peter Thumbi.; Ahuja, Sunil K.; Kormuth, Emil.
No abstract available.
Interleukin-10 Promoter Polymorphisms Influence HIV-1 Susceptibility and Primary HIV-1 Pathogenesis.
(The Infectious Diseases Society of America., 2008) Naicker, Dshanta Dyanedi.; Werner, Lise.; Kormuth, Emil.; Passmore, Jo-Ann Shelley.; Mlisana, Koleka Patience.; Abdool Karim, Salim Safurdeen.; Ndung'u, Peter Thumbi.
Interleukin (IL)–10 directly inhibits human immunodeficiency virus type 1 (HIV-1) replication, but it may also promote viral persistence by inactivation of effector immune mechanisms. Here, we show in an African cohort that individuals with genotypes associated with high IL-10 production at 2 promoter single-nucleotide polymorphisms ( 1082 and 592) were less likely to become HIV-1 infected but had significantly higher median plasma viral loads during the acute phase ( 3 months after infection). However, as the infection progressed, the association between genotype and median viral load was reversed. Thus, IL-10 may influence HIV-1 susceptibility and pathogenesis, but effects on the latter may differ according to the infection phase.
Neural network models for leukaemia.
(2009) Chetty, Manimagalay.; Carsky, Milan.; Kormuth, Emil.
Artificial neural networks (ANN) can detect complex non-linear relationships between independent and dependent variables. Properly trained ANNs have repeatedly demonstrated superior predictive accuracy to other predictive technologies when applied to non-linear systems. Currently there are no studies that have been carried out on predicting survival of leukaemia patients at all. The neural network prediction method adopted in this study aims to provide a robust and accurate method for predicting survival of leukaemia patients for both censored and uncensored patient data. The aim of this research was also to find out the effectiveness of neural networks in modelling leukaemia prognosis and to determine the factors that have the most influence. There is ongoing research into finding ways and means of extending the life span of diseased patients. There is great interest in identifying factors that will yield better predictions of survival for terminally ill leukaemia patients. Prognostic factors generally differ with the treatment of leukaemia. Clinicians face the problem of how to choose the appropriate treatment regime, therefore an analysis of prognostic factors that predict success or failure may identify patients who require an alternative approach of specialist or targeted treatment. Being able to predict an individual patient’s prognosis will enable clinicians to categorise them into the relevant high and low risk treatment groups for conventional treatment or allow for the patients to be incorporated into specialised treatment schedules and clinical trials if available. In this study there is believed to be relationship that exists between the results gained on diagnosis and the period of survival. A patient’s health status is dependent on various symptoms and the complexity of the medical condition is dependent on an individual’s biological system. This complexity allows for the application of artificial neural networks (ANN) in predicting outcomes in medical application, especially in prognosis prediction and survival rate. This thesis contains contributions to the development of neural network models for survival analysis of leukaemia patients. The feed forward back propagation algorithm (BPA) modified to the gradient descent BPA was identified for the training and building of the neural network for predicting survival of leukaemia patients. The prognostic factors that affect survival have also been determined by the neural networks. The comparisons of models were based on using combined groups of leukaemia patients and comparing them with individual groups of the sub-types of leukaemia, i.e. acute lymphoid leukaemia (ALL), acute myeloid leukaemia (AML), chronic myeloid leukaemia (CLL) and chronic myeloid leukaemia (CML). A combination of 38 variables was used in the development of the neural networks. The variables were age, race, sex, gender, and results of full blood counts, differential tests and flow cytometry. The survival period of patients was based on the diagnosis date and the date of treatment. Those patients who status of mortality was known as of October 2008 were considered to be uncensored and were used for the 2-year and 3-year case studies. The patients with unknown mortality were considered as censored patients and used for the censored case study. The patient data was processed into a coded system and used to build the neural networks for each data set. The choice of patient groups used for the model building was prompted by the availability of uncensored data for analysis. For the group of combined leukaemia patients and the sub-group CML-CLL, it is recommended that the 2-year neural network model be used. The main prognostic factors affecting leukaemia survival were found to be the patient’s age, the mean haemoglobin concentration, % neutrophils and the markers CD13, CD20 and CD56. The race group, platelet count, % monocytes and the markers CD3, CD4, CD34 and LC lambda were found to significantly affect the CML-CLL group of patients. For the ALL and AML groups the 3-year neural network models were favoured. Prognostic factors for the survival of ALL patients were their age, the mean corpuscular haemoglobin concentration, % blasts and the markers CD8 and CD22. For the AML group the important prognostic factors were the patient’s age, the mean corpuscular haemoglobin concentration, the % neutrophils, % lymphocytes, and the markers CD7 and CD34.
The study of the impact of selected mutations in FMS-like Tyrosine Kinase III (FLT3) and Nucleophosmin (NPM1) - and HIV status on patients with acute Myeloid Leukemia and their response to induction therapy.
(2012) Naidoo, Horacia.; Ebrahim, Safiya.; Naicker, Vincent Louis.; Sewpersad, Natasha.; Kormuth, Emil.
Acute Myeloid Leukemia (AML), the most common form of acute leukemia in adults, is only curable in approximately 30% of all cases. Despite prognostic risk stratification using sub-typing and cytogenetic analysis to direct therapy, the mortality and relapse rate remains high. AML patients with normal karyotypes are defined as intermediate risk and are the most challenging to treat. Somatic mutations may be the key in refining prognostic stratification and providing useful therapeutic targets. The FMS-like tyrosine kinase 3 (FLT3) and Nucleophosmin (NPM1) genes have common mutated forms that are associated with overall survival and response to therapy. We assessed mutations in the FLT3 and NPM1 genes and their levels of expression in twenty eight AML patients in the presence and absence of HIV and their response to induction therapy. Furthermore, we used a novel technique, High Resolution Melting (HRM) Analysis to detect FLT3 Internal Tandem Duplications (ITD) and NPM1 exon 12 mutations. Five of the patients in this study were HIV positive, three of whom did not survive post-induction therapy. Of the AML patients, 17.9% were positive for the NPM1 mutation and 21% had mutated FLT3. Interestingly, the presence of the FLT3 and NPM1 mutations were coupled with an increase in expression levels of FLT3 and NPM1 from presentation to post-induction respectively and the loss of these mutations were coupled with a decrease in levels of expression from presentation to post-induction. However, an increase/decrease from presentation to post-induction did not necessarily denote the presence/absence of a mutation. Therefore, while mutational status of genes may generally confer mRNA levels, our results showed that there existed no definitive trend between mRNA levels of NPM1 and FLT3 expression and mutational status. We found that the HRM method was definitive for the simpler NPM1 mutation however detection of the FLT3-ITD mutation was challenging. There isn’t a clear distinction between mutated and non-mutated FLT3 due to the formation of hetero-duplexes during analysis, making detection highly subjective and error-prone. Sequencing allowed confirmation of mutated FLT3 and non-mutated FLT3 which were not in all instances in concordance with HRM analysis. The prognostic value in terms of overall survival of NPM1 and FLT3 mutations in this study is indefinite. Furthermore, the analysis of the HIV positive AML patients revealed no clear correlation between NPM1 and FLT3 levels of mRNA expression and mutational status. Also, the small number of HIV positive AML patients did not allow for conclusions to be made regarding HIV status and survival when affected with AML.
The role of interleukin-10 promoter polymorphisms in HIV-1 susceptibility and primary HIV-1 pathogenesis.
(2007) Naicker, Dshanta Dyanedi.; Ndung'u, Peter Thumbi.; Kormuth, Emil.
Host genetic factors may partially account for the uneven distribution of HIV infection worldwide. In addition to influencing relative susceptibility to HIV, host genetic factors may also affect the rate of disease progression in persons who are already HIV infected. J.L-10 was previously identified as an AIDS restricting gene (ARG), i.e. human genes with polymorphic variants that influence the outcome of HIV-1 exposure or infection. IL-10 is a Th2 cytokine, with anti-inflammatory properties, and plays a significant role in the regulation of immune responses; this cytokine may also directly influence viral replication. This study focused on the role of genetic polymorphisms in the proximal promoter region of the IL-10 gene on HIV-:eptibility and primary HIV-1 pathogenesis in a South African comprising of women at high risk of HIV-1 infection In this study 228 black females from the CAPRISA Acute Infection cohort were genotyped for two polymorphisms that naturally occur within the proximal region of the IL-10 promoter, at positions -.1082 and -592 (tracking -819) relative to the transcription start site. DNA samples from study participants were genotyped using the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) method, which utilises specifically designed primers to detect single nucleotide polymorphisms. The allele frequencies for the mutant -1082G and -592A variants were 0.3203 and 0.333 respectively.Individuals homozygous for the mutation at the -392 position (AA genotype) were 2.78 times more likely to become HIV infected, compared to those who were homozygous wild type (CC genotype) at the same position (p-value=0.0237). Among those who became HIV infected, we found a hierarchical association between IL-10 promoter variants and HIV-1 plasma viral load or CD4+ T cell counts over the course year of HIV-1 infection. At earlier time points, i.e. 0-3 months post-te -1082GG group had significantly higher median viral loads than the -AA or -1082AG groups (pvalues= <0.0001 and 0.0003 respectively); and the -1082AA group had the highest median CD4'' T cell count compared to the -1082AG or -1082GG groups and this was significant (p-values= 0.0194 and 0.0122 respectively). At 6-12 months post-infection the median viral load of the -1082GG group was lower than -1082AA group, however this was not significant (p-value=0.6767). Analysis of the effect of the -592 polymorphism showed that the -592AA group had a lower median viral load at 0-3 months post-infection compared to the homozygous wild-type group (i.e. -592CC p~value=0.0093); and the median CD4+ T cell count for the -592AA group was significantly higher than the -592CC group (p~ value= 0.0198). At 6-12 months post-infection, the median viral load as well as the median CD4+ T cell count of the -592 A A group were both no longer significantly different to the -592CC group (p-values= 0.644land 0.6461 respectively). Plasma IL-10 expression was not significantly different between the IL-I0 genotypes for any of the polymorphic positions.Overall, these results suggest that polymorphisms within the IL-10 promoter may influence the risk of HIV infection and that they may affect primary HIV-1 pathogenesis. Interestingly, our data suggests that the effect of these polymorphic variants on viral and CD4+ T cell counts may vary according to time post-infection. To our knowledge, this is the first study to suggest that an ARG may have a differential effect on markers of disease progression depending on the phase of infection studied. The mechanisms underlying these observations require further studies and may have important implications for HIV/AIDS pathogenesis and the development of effective vaccine and immunotherapeutic strategies.