Browsing by Author "Dandara, Collet"

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    The 341C/T polymorphism in the GSTP1 gene is associated with increased risk of oesophageal cancer
    (BioMed Central Ltd, 2010) Li, Dongping; Dandara, Collet; Parker, M Iqbal
    BACKGROUND: The Glutathione S-transferases (GSTs) comprise a group of enzymes that are critical in the detoxification of carcinogens. In this study the effects of polymorphisms in these genes on the risk of developing oesophageal squamous cell carcinoma (OSCC) were evaluated in a hospital-based case-control study in two South African population groups. Genetic polymorphisms in GSTs were investigated in 245 patients and 288 controls samples by PCR-RFLP analysis. RESULTS: The GSTP1 341T variant was associated with significantly increased risk of developing OSCC as observed from the odds ratios for the GSTP1 341C/T and GSTP1 341T/T genotypes (OR = 4.98; 95%CI 3.05-8.11 and OR = 10.9; 95%CI 2.43-49.1, respectively) when compared to the homozygous GSTP1 341C/C genotype. The risk for OSCC in the combined GSTP1 341C/T and T/T genotypes was higher in tobacco smokers (OR = 7.51, 95% CI 3.82-14.7), alcohol consumers (OR = 15.3, 95% CI 1.81-12.9) and those using wood or charcoal for cooking and heating (OR = 12.1, 95% CI 3.26-49) when compared to those who did not smoke tobacco, or did not consume alcohol or user other forms of fuel for cooking and heating. Despite the close proximity of the two GSTP1 SNPs (313A>G and 341C>T), they were not in linkage disequilibrium in these two population groups (D':1.0, LOD: 0.52, r2: 0.225). The GSTP1 313A/G polymorphism on the other hand, did not display any association with OSSC. The homozygous GSTT1*0 genotype was associated with increased risk of OSCC (OR = 1.71, 95%CI 1.18-2.46) while the homozygous GSTM1*0 genotype was associated with significantly decreased risk of OSCC in the Mixed Ancestry subjects (OR= 0.39, 95%CI 0.25-0.62). CONCLUSIONS: This study shows that the risk of developing OSCC in the South African population can be partly explained by genetic polymorphisms in GST coding genes and their interaction with environmental factors such as tobacco smoke and alcohol consumption.
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    9β Polymorphism of the Glucocorticoid Receptor Gene Appears to Have Limited Impact in Patients with Addison’s Disease
    (Public Library of Science, 2014) Ross, Ian Louis; Dandara, Collet; Swart, Marelize; Lacerda, Miguel; Schatz, Desmond; Blom, Dirk Jacobus
    BACKGROUND: Addison’s disease (AD) has been associated with an increased risk of cardiovascular disease. Glucocorticoid receptor polymorphisms that alter glucocorticoid sensitivity may influence metabolic and cardiovascular risk factors in patients with AD. The 9β polymorphism of the glucocorticoid receptor gene is associated with relative glucocorticoid resistance and has been reported to increase the risk of myocardial infarction in the elderly. We explored the impact of this polymorphism in patients with AD. Materials and METHODS: 147 patients with AD and 147 age, gender and ethnicity matched healthy controls were recruited. Blood was taken in a non-fasted state for plasma lipid determination, measurement of cardiovascular risk factors and DNA extraction. RESULTS: Genotype data for the 9β polymorphism was available for 139 patients and 146 controls. AD patients had a more atherogenic lipid profile characterized by an increase in the prevalence of small dense LDL (p = 0.003), increased triglycerides (p = 0.002), reduced HDLC (p<0.001) an elevated highly sensitive C-reactive protein (p = 0.01), compared with controls. The 9β polymorphism (at least one G allele) was found in 28% of patients and controls respectively. After adjusting for age, gender, ethnicity, BMI and hydrocortisone dose per metre square of body surface area in patients, there were no significant metabolic associations with this polymorphism and hydrocortisone doses were not higher in patients with the polymorphism. CONCLUSIONS: This study did not identify any associations between the 9β polymorphism and cardiovascular risk factors or hydrocortisone dose and determination of this polymorphism is therefore unlikely to be of clinical benefit in the management of patients with AD.
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    A cost effective RFLP method to genotype Solute carrier organic anion 1B1 (SLCO1B1) c.1929A>C (p.Leu643Phe, rs34671512); a variant with potential effect on rosuvastatin pharmacokinetics
    (BioMed Central, 2018-06-14) Soko, Nyarai D; Masimirembwa, Collen; Dandara, Collet
    Objective: This study describes a restriction fragment polymorphism protocol for rapidly screening the polymorphism SLCO1B1 c.1929A>C in genomic DNA samples. The polymorphism SLCO1B1 c.1929A>C has been associated with increased activity resulting in increased hepatic uptake of drugs. Currently SLCO1B1 c.1929A>C is genotyped using direct sequencing techniques and 5′ nuclease based assays which can be cost prohibiting in resource limited settings. The aim of this study therefore was to design and validate a cost effective RFLP for genotyping the SLCO1B1 c.1929A>C polymorphism. This study was designed to investigate the effect of the polymorphism SLCO1B1 c.1929A>C on interindividual variability in rosuvastatin pharmacokinetics in healthy volunteers of African descent. Results We describe a restriction fragment length polymorphism method to genotype SLCO1B1 c.1929A>C polymorphism using the restriction enzyme Ase1. A student’s t test with Welch correction was used to establish association between the SLCO1B1 c.1929A>C variant and rosuvastatin exposure. The frequency of the SLCO1B1 c.1929C allele amongst Zimbabweans was 6%. The SLCO1B1 c.1929C allele was associated with a 75% reduction (P < 0.001) in rosuvastatin exposure when compared to individuals carrying the wild type SLCO1B1 c.1929A allele. Polymorphism c.1929A>C may therefore play a significant role in rosuvastatin response. The RFLP method is quick and cost effective.
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    APOE, PCSK9, and CETP genetic variants as potential biomarkers of dyslipidaemia in black South Africans with Type 2 Diabetes Mellitus
    (2018) Evans, Jonathan; Dandara, Collet
    Dyslipidaemia is a commonly encountered clinical condition and is a major risk factor for cardiovascular diseases. Although there are many factors associated with dyslipidaemia, a strong genetic component is evident. Apolipoprotein E (APOE), proprotein convertase subtilisin/kexin type 9 (PCSK9), and cholesteryl ester transfer protein (CETP) are key regulators of plasma cholesterol levels. Thus, genetic variation in the genes coding for these proteins contributes to dyslipidaemia. In this study, a cohort of black South African Type 2 Diabetes Mellitus (T2DM) patients was characterized for mutations in genes coding for APOE, PCSK9, and CETP, and the possible effects of these variants on their lipid profiles was evaluated. Participants (n=417) were recruited from the Chris Hani Baragwaneth Hospital Diabetes Clinic, Johannesburg from whom blood samples were obtained for DNA extraction. The cohort was further stratified into two groups; individuals on statin treatment (Sim+, n=291), and the second that was not on treatment (Sim-, n=87). Lipid profiles were determined by enzymatic methods. DNA was genotyped for APOE, PCSK9, and CETP variants using PCRRFLP and Sanger sequencing. Analysis of the effects of the genetic variants was carried out in two ways. Firstly, for all the participants combined, and then by separating those on statin treatment from those without (Sim+ vs. Sim-). Genotype and allele frequencies were calculated followed by genotype-phenotype correlations with lipid profiles. Univariate analysis showed a significant association between the APOE4 isoform and lower HDL-c levels in the combined cohort (p=0.034). The effects were more pronounced in the Sim- group (p=0.004) but were absent in the Sim+ group. Contrary to above, APOE2 was significantly associated with lower total cholesterol (TC) (p< 0.001) and lower LDL-c (p< 0.001) when compared to APOE3 in the combined cohort. Upon analysing treatment groups, the correlations were observed in the Sim+ group (p=0.027 and p=0.003, respectively), while there were no observed correlations in the Sim- group. The CETP rs34065661C/G and G/G genotypes were significantly associated with increased HDL-c levels (p=0.017; when applying a dominant genetic model) in the combined cohort, as well as in the Sim+ group (p=0.026). Multivariate analysis, using a generalized linear model, confirmed associations between APOE rs429358C and lower HDL-c (OR=0.881, p=1.64e04), and APOE rs7412T and decreased LDL-c (OR=0.759, p=0.012). No significant associations were observed for PCSK9 polymorphisms. We report significant associations between APOE and CETP genetic variations and altered lipid levels in this black South African T2DM population. These genetic variants could be biomarkers for dyslipidaemia among Africans. However, it is imperative that the APOE, PCSK9, and CETP genes are fully characterized for additional polymorphisms in order to come up with a better genetic profile that explains the variance in lipid levels observed in the black South African population. The impact of these genetic variants could be relevant to other black African populations as well.
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    CCR2-V64I polymorphism is associated with increased risk of cervical cancer but not with HPV infection or pre-cancerous lesions in African women
    (BioMed Central Ltd, 2010) Chatterjee, Koushik; Dandara, Collet; Hoffman, Margaret; Williamson, Anna-Lise
    BACKGROUND: Cervical cancer, caused by specific oncogenic types of human papillomavirus (HPV), is the second most common cancer in women worldwide. A large number of young sexually active women get infected by HPV but only a small fraction of them have persistent infection and develop cervical cancer pointing to co- factors including host genetics that might play a role in outcome of the HPV infection. This study investigated the role of CCR2-V64I polymorphism in cervical cancer, pre-cancers and HPV infection in South African women resident in Western Cape. CCR2-V64I polymorphism has been previously reported to influence the progression to cervical cancer in some populations and has also been associated with decreased progression from HIV infection to AIDS. METHODS: Genotyping for CCR2-V64I was done by PCR-SSP in a case-control study of 446 women (106 black African and 340 mixed-ancestry) with histologically confirmed invasive cervical cancer and 1432 controls (322 black African and 1110 mixed-ancestry) group-matched (1:3) by age, ethnicity and domicile status. In the control women HPV was detected using the Digene Hybrid Capture II test and cervical disease was detected by cervical cytology. RESULTS: The CCR2-64I variant was significantly associated with cervical cancer when cases were compared to the control group (P = 0.001). Further analysis comparing selected groups within the controls showed that individuals with abnormal cytology and high grade squamous intraepitleial neoplasia (HSIL) did not have this association when compared to women with normal cytology. HPV infection also showed no association with CCR2-64I variant. Comparing SIL positive controls with the cases showed a significant association of CCR2-64I variant (P = 0.001) with cervical cancer. CONCLUSIONS: This is the first study of the role of CCR2-V64I polymorphism in cervical cancer in an African population. Our results show that CCR2-64I variant is associated with the risk of cervical cancer but does not affect the susceptibility to HPV infection or HSIL in South African women of black and mixed-ancestry origin. This result implies that the role of CCR2 is important in invasive cancer of the cervix but not in HPV infection or in the development of pre-cancers.
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    Chemotherapeutic drugs, 5-fluorouracil and cisplatin, differentially affect exprssion of drug metabolising enzyme genes in an oesophageal cancer cell line
    (2014) Hassen, Naseeha; Dandara, Collet; Mowla, Shaheen; Parker, M I
    Cancer is a leading cause of death worldwide. Oesophageal cancer in particular is the sixth most common cause of cancer deaths globally and its incidence and mortality rates in Southern Africa are among the highest in the world. One of the major challenges with cancer treatment is the vast variability in patient response to chemotherapy, which is predominantly due to genetic variability. The most relevant genes in this context encode the CYP and GST drug metabolising enzymes (DMEs) as these enzymes metabolise up to 90% of clinically-prescribed medication. Patients are also exposed to a variety of other compounds that along with chemotherapeutic drugs may alter DME gene expression. Changes in DME gene expression influence the therapeutic outcomes for patients; thus, understanding the effects of drugs and compounds on the expression of DMEs is crucial for the advancement of personalised medicine. The aim of this study was to determine the effects of two commonly-used chemotherapeutic drugs, as well as a CYP-inducing compound, on the differential expression of four pharmacogenetically relevant DME-encoding genes, CYP1A1, 1A2, 1B1 and GSTP1, in a human oesophageal cancer cell line.
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    Chronic kidney disease in HIV populations: prevalence, risk factors and role of transforming growth factor beta (TGF-߀1) polymorphisms
    (2019) Ekrikpo, Udeme Ekpenyong; Okpechi, Ikechi; Kengne, Andre Pascal; Bello, Aminu; Dandara, Collet; Wonkam, Ambroise
    Background and purpose: With the advent of antiretroviral therapy, HIV-infected individuals now live longer and are at increased risk of chronic kidney disease (CKD). Also, recent studies indicate a genetic predisposition to CKD in the African HIV population. This work investigated the prevalence of CKD (and its correlates) in the global and local HIV population and proceeded to investigate the diagnostic utility of urinary transforming growth factor-beta-1 (TGF-β1) for CKD in the HIV population and determine the association between polymorphisms of TGF-β1 gene and prevalent CKD. Methods: A meta-analysis was performed to document the prevalence of CKD in the global HIV population. From the local HIV population in Nigeria, the prevalence of CKD and traditional risk factors for cardiovascular disease was determined. Using ELISA, TGF-β1 levels was assayed in the urine samples of HIV patients with or without CKD to investigate the ability of urinary TGF-β1 to diagnose early CKD. SNP genotyping of rs1800469, rs1800470, rs1800471, rs121918282 in TGF-β1, rs60910145 (APOL1), rs73885319 (APOL1), rs71785313 (APOL1) and rs743811 (HMOX1) was performed using predesigned TaqMan genotyping assays. Results: Using meta-analytic methods, the global pooled CKD prevalence was 6.4% (95%CI 5.2–7.7%) with MDRD, and 4.8% (2.9–7.1%) with CKD-EPI. Among the WHO regions, Africa had the highest MDRD-based prevalence, 7.9% (5.2-11.1%) with the West African subregion carrying the heaviest burden, 14.6% (9.9- 20.0%). Among the local HIV population, using the CKD-EPI equation, the prevalence of CKD was 13.4% (11.6- 15.4%). Hypertension prevalence was 26.7% (25.5-28.0%); diabetes 5.6% (4.5-6.7%); obesity 8.3% (7.6-9.1%) and dyslipidaemia 29.1% (26.1-32.1%). HIV-infected individuals with CKD had significantly higher levels of urinary TGF-β1-creatinine ratio (uTGFβ1Cr) after controlling for potential confounding factors in regression models. However, within the CKD-HIV group, uTGFβ1Cr reduced as CKD stage worsened. The presence of APOL1 genetic risk independently increased the risk of CKD (OR 2.54, 95% CI 1.44-4.51) in the HIV population while the TGF-β1 SNP, rs1800470, appeared to have a protective effect (OR 0.44 (95% CI 0.20-0.97). There was no significant association between HMOX1 SNPs and CKD occurrence. Conclusion: There is a high prevalence of CKD (and other cardiovascular risk factors) in the adult HIVpopulation. Urinary TGF-β1 may be useful in the non-invasive detection of early CKD in the HIV population. Genetic testing may be used to predict the risk of CKD in the HIV population.
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    Distal sensory polyneuropathy in HIV/TB co-infection : the role of vitamin B6 and N-acetyltransferase 2 genetic variation
    (2012) Centner, Chad; Heckmann, Jeannine; Dandara, Collet
    Both human immunodeficiency virus (HIV) infection and tuberculosis (TB) are complicated by a painful distal sensory polyneuropathy (DSP) that may be due to virus-related HIV-DSP, antiretroviral toxic neuropathy (ATN) or isoniazid-induced peripheral neuropathy (INH-PN). In co-infection with and co-treatment for HIV/TB, DSP risk is increased. Factors driving this risk may be vitamin B6 deficiency and slow metabolism of INH mediated by N-acetyltransferase 2 (NAT2) acetylation, both known risk
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    Fas and FasL gene polymorphisms are not associated with cervical cancer but differ among Black and Mixed-ancestry South Africans
    (BioMed Central Ltd, 2009) Chatterjee, Koushik; Engelmark, Malin; Gyllensten, Ulf; Dandara, Collet; Merwe, Lize; Galal, Ushma; Hoffman, Margaret; Williamson, Anna-Lise
    BACKGROUND:Cervical cancer is one of the most important cancers in African women. Polymorphisms in the Fas (FasR) and Fas ligand (FasL) genes have been reported to be associated with cervical cancer in certain populations. This study investigated whether these polymorphisms are associated with cervical cancer or human papillomavirus (HPV) infection in South African women.FINDINGS:Participants were 447 women with invasive cervical cancer (106 black African and 341 women of mixed-ancestry) and 424 healthy women controls, matched by age, (101 black African and 323 women of mixed-ancestry) and domicile (rural or urban). Two polymorphisms in Fas gene (FasR-1377G/A, FasR-670A/G) and one in FasL gene (FasL844T/C) were genotyped by TaqMan. None of the polymorphisms, or the Fas haplotypes, showed a significant association with cervical cancer. There was also no association with HPV infection in the control group. However, on analysis of the control group, highly significant allele, genotype and haplotype differences were found between the two ethnic groups. There were generally low frequencies of FasR-1377A alleles, FasR-670A alleles and FasL-844C alleles in black women compared to the women of mixed-ancestry. CONCLUSION: This is the first study on the role of Fas and FasL polymorphisms in cervical cancer in African populations. Our results suggest that these SNPs are not associated with cervical cancer in these populations. The allele frequencies of the three SNPs differed markedly between the indigenous African black and mixed-ancestry populations.
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    Fighting Cancer around the World: A Framework for Action
    (2022-10-25) Horgan, Denis; Mia, Rizwana; Erhabor, Tosan; Hamdi, Yosr; Dandara, Collet; Lal, Jonathan A.; Domgue, Joel Fokom; Ewumi, Oladimeji; Nyawira, Teresia; Meyer, Salomé; Kondji, Dominique; Francisco, Ngiambudulu M.; Ikeda, Sadakatsu; Chuah, Chai; De Guzman, Roselle; Paul, Anupriya; Reddy Nallamalla, Krishna; Park, Woong-Yang; Tripathi, Vijay; Tripathi, Ravikant; Johns, Amber; Singh, Mohan P.; Phipps, Maude E.; Dube, France; Whittaker, Kate; Mukherji, Deborah; Rasheed, Hadi Mohamad Abu; Kozaric, Marta; Pinto, Joseph A.; Doral Stefani, Stephen; Augustovski, Federico; Aponte Rueda, Maria Eugenia; Fujita Alarcon, Ricardo; Barrera-Saldana, Hugo A.
    Tackling cancer is a major challenge right on the global level. Europe is only the tip of an iceberg of cancer around the world. Prosperous developed countries share the same problems besetting Europe–and the countries and regions with fewer resources and less propitious conditions are in many cases struggling often heroically against a growing tide of disease. This paper offers a view on these geographically wider, but essentially similar, challenges, and on the prospects for and barriers to better results in this ceaseless battle. A series of panels have been organized by the European Alliance for Personalised Medicine (EAPM) to identify different aspects of cancer care around the globe. There is significant diversity in key issues such as NGS, RWE, molecular diagnostics, and reimbursement in different regions. In all, it leads to disparities in access and diagnostics, patients’ engagement, and efforts for a better understanding of cancer.
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    Functional Genome-wide Association Studies (fGWAS) and genomics landscape of signatures of polygenic adaptation in Botswana populations with HIV-1 C infection
    (2022) Choga, Wonderful Tatenda; Chimusa, Emile Rugamika; Dandara, Collet; Thami, Prisca K
    The burden of the human immunodeficiency virus subtype (HIV) is catastrophic, especially in Botswana, a nation in Southern Africa, where 20.7% of persons aged 15 to 49 years are living with HIV (PWH). Although HIV exposure rates are extremely high, individual differences in clinical outcomes point to the importance of host genetic variables. Genome-wide association studies (GWAS) are methods widely used for identifying single nucleotide polymorphisms (SNPs) linked to different phenotypes such as HIV-1 subtype C (HIV-1C) susceptibility or resistance. Even though, conventional GWAS techniques alone cannot illuminate the associated functional pathways beyond detecting association SNPs. Alternatively, functional genome-wide association studies (fGWAS), which are post-GWAS analyses, can be utilized to put GWAS summary results into functional context. We hereby, first describe the fGWAS employing whole genome sequences (WGS) of Batswana exposed to HIV-1C. Although autosomal SNPs are widely utilized for functional-GWAS research, recent studies have also linked mitochondria DNA (mtDNA) haplotypes to various HIV outcomes. We explored the possibility of using both autosomal and mtDNA SNPs to enrich fGWAS analysis. On another hand, people from Botswana (collectively called Batswana) exhibits a homogenous genetic structure and has also been identified as the closest population to the most recent common ancestor (MRCA) of human species. Concomitantly the population has extremely high HIV1C burden. It remains unclear if increased susceptibility to HIV-1C infection may be associated with its closeness to the ancestral genomes. We investigated the genomics landscape of signatures of polygenic adaptation to the HIV-1C in Botswana using genomewide scans for selection (GWSS). For the first goal, we looked at several HIV-related studies that had been done in Botswana from 1995 to 2020. We saw significant advancements in the fight against the pandemic, including the early introduction of second generation antiretrovirals like dolutegravir (DTG), the first African nation to reach the 2030 UNIAIDS targets (95-95-95), and a 0.3% decrease in mother-to-child transmission rates. However, the main limitations include the spread of HIV 1C that is resistant to treatment and the evolution of medication resistance mutations have presented a serious danger to ending the epidemic. We demonstrated that research on host genetic variables that affect HIV-1C clinical outcomes among Batswana are still understudied. Overall, Botswana has significant advancements in the widespread deployment of antiretroviral treatment (ART) and high viral load suppression rates. For the second goal, we employed WGS to carry out GWAS using autosomal SNPs (chromosomes 1-22). fGWAS was conducted using the ensuing results. There were 394 WGS of the Batswana that were analysed. The research subjects came from the earlier Botswana based Mashi and Tshedimoso studies. A total of 11,364,691 million autosomal, biallelic SNPs were collected and utilised for further studies after variant calling, strict variant filtering, quality checking; and phasing using the tools PLINK V2.00A2LM and EAGLE v2.1, respectively. A total of 226 PWH (all female) and 112 controls (those without HIV infection30 men and 82 females-) were included in the 338 samples that passed quality control. Despite the fact that the data come from a population of Botswana that speaks 25 different languages and that there are well-known linguistic and cultural differences, principal component analysis (PCA) based on autosomal SNPs failed to identify any substructures. Interestingly, we identified 12.2% of the genetic variants that were reported among Batswana but not found in publicly available. Softwares EMMAX and PLINK V2.00A2LM were used concurrently for association analysis, and 137 significant SNPs located on chromosomes 1, 3, 6, and 7 were identified. Nine of the closest genes including –LINC01266, LINC00578, SLC26A8, DNAH11, PLCB1, CRYBB2P1, AL512484.1, SMYD3, LOC105373269–, were effectively mapped to six of the seven lead SNPs at -log10Pvalue≤6. For gene set enrichment analysis, the Gene MANIA online tool was employed, and 20 additional genes with physical co-expression of 81% were identified: – CFTR, RACGAP1, PCF11, DGKQ, HAP1, PRKCA, GNA11, SLC26A10, SLC26A7, SLC26A11, SLC26A9, DCTN1, SPTBN1, DNAH2, SLC26A5, SLC26A1, SLC26A6, SLC26A3, SLC26A4, CDC20–. Both the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases had several terms related to these genes. Enriched biological pathways include enhanced antiporter activity, gastric and pancreatic secretion, solute carrier (SLC)-mediated transmembrane transport, and neurodegenerative processes. Such terms have also been linked to various clinical phenotypes including HIV-1 infection, human cytomegalovirus (CMV), and cancers suggesting possible cross phenotype associations. For the third goal, we used PRSice to calculate polygenic risk scores for individuals; Botswana population was set as target data while summary statistics of Uganda population exposed to HIV was base dataset. We then used the results to determine everyone's risk exposure level based on the best predictive threshold (PT). PT and HIV susceptibility were substantially associated. The best-fit prediction for Botswana was PT =0.129 (β=-120.02, standard error=61.14, pvalue=5.0x10-2) and 1.3% of the variance in HIV-1 susceptibility at the population level could be explained by the scores. In order to evaluate the population recombination history, we also evaluated the linkage disequilibrium (LD) degradation. According to LD decay statistics of r 2, LD decays more quickly in PWH than in those without HIV, suggesting the potential influence of selection pressure acting on HIV infection response. In addition, we evaluated the minor allele frequency (MAF) and generated allele frequency distributions. When comparing cases and controls, derived allele frequency (DAF) revealed a significant difference in the derived allele at low MAF (bin-width = 0-0.05), suggesting that uncommon variations may be involved in HIV-1 susceptibility. Consequently, the postGWAS studies also included the rare-variant analyses that were available. Thirdly, we looked at mtDNA to identify variations linked to HIV-1 susceptibility and their functional pathways. Analyses of phylogenetic relatedness and haplogroups were also conducted. The mtDNA sequences' median coverage was (1060; Q1:738.5 – Q3:1397). The total genotyping rate for mtDNA QC was 0.99, with 560 variations being eliminated because of minor allele criteria of 0.01. We then discovered a total of 351 variation sites and 64 highresolution haplogroups among the 338 people who passed QC. One mtDNA variation, m.2072A>G, was identified by association analysis using a logistic regression model with 10 PCs and gender as covariates. Based on functional predictions, it was assigned to a non-coding transcript exon of the MT-RNR2 gene's 16S ribosomal RNA (rRNA), and it was regarded as having potential pathogenicity. We were able to identify 67 high-resolution haplogroups. L0a1b1a1 was the most prevalent haplogroup (n = 39), but 27 uncommon haplotypes, such as H, R, L0f1, and L0g, were also discovered. Other common haplotypes included L0a1b1a1, L2a1b1a, and L0d1b2b1b, which had prevalence rates of 10%, 8%, and 7%, respectively, while L0d3b1 and L3e1b2 each had a 6%. L3e1b2 and L0a1bla1 (pvalue=0.02), L3d1a1a1 (pvalue=0.03), L3e1a3a, L0d2a1a3, L0d2a1, and L0d1d (pvalue <0.01), totaling 7 (11%) haplogroups, were statistically higher among PWH than HIV-negative persons. When a post-analysis was conducted to see if any of the 7 significant haplogroups were related to vulnerability to HIV infection, no significant connection was discovered. Finally, we investigated the genetic basis of HIV-1 infection susceptibility in Batswana. Integrated Haplotype Scores (iHS) revealed strong selection signals on 32 out of 332 genes putatively under strong selection, including BX664718.2, EMB, ERICH1, GGNBP1, GOSR2, KSR1P1, LINC01016, LINC01667, LINC01691, LINC02798, MAP3K14, MIR1268 2. The most enriched clusters were associated with immune pathways, including cytokine signaling pathways, cytokine regulatory pathways, and phosphorylation, when substantially overrepresented GO terms and KEGG pathways were searched for among the candidate genes. Notably, the majority of the genes were involved in the regulation and activation of NF-kappaB and I-kappaB kinase. In addition to HIV-1 infections, IKBKB has also been linked to CMV, hepatitis virus infections, and tuberculosis (TB). In conclusion, this project presented new insights into the multifaceted demographic history that shaped the existing genetic landscape of the population of Botswana. Although utilizing autosomal chromosomes failed to reveal any population sub-structuring, mtDNA diversity confirms variety and substantial sub-structure in the population of Botswana. Additionally, we identified new potential genes, pathways, and targets that are involved in the regulation of HIV-1 susceptibility Batswana, which predisposes the population to high acquisition than resistance rates seen. The gene sets identified here were also enriched for other features, including as TB, HBV, and CMV, which have been found to be very prevalent in Botswana and among PWH.
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    Genetic aetiology of autosomal recessive non-syndromic hearing loss in sub-Saharan African patients: evaluation using targeted and whole exome sequencing
    (2019) Lebeko, Kamogelo; Wonkam, Ambroise; Dandara, Collet; Mowla, Shaheen
    Hearing Loss (HL) is one of the highest contributors to disability worldwide. The highest incidence of the disease is seen in developing countries, such as those in subSaharan Africa (SSA). Patients affected with disabling HL are reported to be more than 466 million worldwide. The causes of HL can either be environmental or genetic with each contributing about 50% towards all cases, in many settings. In developing countries, the environment might contribute more due to poor health services and infrastructure available to the population. In the absence of environmental causes, there is a genetic component at play, that is largely unknown in African populations. Up to 70% of HL of genetic origin are non-syndromic (NS). The mode of inheritance is recessive in nearly 77% of non-syndromic HL. Up to date, more than 100 genes have been associated with HL harbouring more than 1000 causative variants. In many populations of European and Asian descent, pathogenic variants in GJB2 (connexin gene 26) and GJB6 (connexin gene 30) are a major contributor to autosomal recessive non-syndromic hearing loss (ARNSHL). Comprehensive hearing health care programs should cover genetic causes by providing molecular testing, and genetic counselling, specifically SSA where genes and mutations causing HL remain largely unknown. The aim of this project was thus to uncover the genetic causes of HL among patients’ cohorts from Cameroon and South Africa. This was addressed by 1) sequencing common variants in the most relevant genes in other populations (GJB2 and GJB6), 2) using a targeted gene panel to resolve HL in 10 multiplex families from Cameroon presenting with ARNSHL and negative for GJB2 and GJB6 mutations screening, 3) screening novel variants found in known genes in a cohort of 82 singleplex HL cases from Cameroon and South Africa, and lastly, 4) using Whole Exome sequencing to explore the two unresolved multiplex cases with and subsequent findings confirmed by functional studies, and also screened in 80 singleplex HL cases. The following findings are reported: GJB6, GJA1 mutations screening and literature review No GJA1 or GJB6 mutation was not found in multiplex and simplex cases of HL in both Cameroonians and South Africans. The review of the literature confirms that the prevalence of GJB2- or GJB6-related NSHL is approximating to zero in most subSaharan African populations. Targeted Exome Sequencing (OtoSCOPE) The targeted genes, panel that included 116 genes, was able to resolve 7 of 9 families (77.8%) which were successfully sequenced, with one family failing to be sequenced. The causative variants identified in the 7 resolved families were : 1) compound heterozygous c.5806_5808delCTC and c.5880_5882delCTT in MYO7A; 2) compound heterozygous c.646T>A (p.Phe216Ile) and c.38G>A (p.Arg13His) in LOXHD1; 3) homozygous c.766-2A>G in OTOF; 4) a deletion and a complex copy number variation in STRC; 5) compound heterozygous c.1678G>A (p.Asp560Asn) and c.2007C>A(p.Asp669Glu) in SLC26A4; 6) Homozygous c.1996C>T(p.Arg666Stop) in MYO7A; 7) compound heterozygous c.6399C>A(p.Asp2133Glu) and c.2000T>C (p.Met667Thr) in CDH23. Five out of 12 variants were novel. Screening of these causative variants in known genes, in 82 singleplex HL cases from Cameroon and South Africa was unable to resolve any of the cases: the variants were in either heterozygous in low frequency or absent. Bioinformatic pathways exploration of SNP data of known HL genes revealed an extensive network within the HL genes, with 10 identified as important nodes, including MYO7A. Most HL genes were found to be involved in two biological processes which were sensory perception of mechanical stimulus (GO: 0050954, p= 1.430e-8) and sound (GO: 0007605, p = 1.246e-8). The molecular functions of variants found within these genes were found to mostly fall within the binding (GO: 0005488) and/or structural molecule activity (GO: 0005198). Whole Exome sequencing Whole exome sequencing was performed on four of the nine multiplex families: the two families that were unresolved by targeted panel sequencing, and two previously resolved families that were used as positive controls for the variant annotation and filtering pipeline. The results were the resolution of 3/4 families, including the two- positive control. The previously unresolved “family 8” was found to harbour a novel variant within the GRXCR2 gene, a gene only associated with HL once before. The c.251delC variant was revealed through in silico studies to cause a premature stop codon at position 116 due to its frameshift effect. The screening of this variant in our cohort of 80 singleplex cases revealed one other unrelated HL patient harbouring this causative variant. Due to the limited literature on the gene and its protein, in silico studies were used to show the predicted secondary structure folding of the protein as well as potential protein binding regions. Analysis showed that the predicted loss of a stable region of the protein as well as that of a putative binding domain could explain the pathogenic nature of the variant. In vitro studies showed that the variant hindered the detection of the protein by way of a DDK tag downstream in the plasmid. Additionally, GFP-Tagged GRXCR2 showed altered expression pattern in the variant when compared to the wildtype. In summary, our data has revealed the efficacy of using next generation sequencing tools in resolving HL among sub-Saharan African patients as opposed to the single candidate gene approach. In our quest, we have employed two widely used strategies, targeted panel and whole exome sequencing (WES), both of which have had great successes in various populations. The targeted approach was able to resolve 77.8% of our families but did not detect variants for two of the families revealing the presence of other variants harboured in rarely associated gene not captured or included on the panel. This prompted for the use of a more comprehensive approach such as WES. These results corroborated with those of two families previously resolved by targeted exome sequencing. Additionally, one of the previously unresolved family was now resolved. This showed that WES was sensitive enough to detect variants in known HL genes but comprehensive enough to detect variants in other regions of the exome which have not been associated with HL or rarely associated with HL. The benefit of WES also extends to the contribution of exomic data from patients of African descent as there is an underrepresentation of this group in exome repositories as well as genomic or SNP databases. To the best of our knowledge, this is the first study to use WES to resolve HL in patients of African descent. The other benefit of such a venture is the use of this data not only for patients in SSA but also those in the diaspora. In conclusion, we have successfully demonstrated the feasibility of using NGS tools in identifying causative variants in HL patients in SSA. Additionally, we have shown that WES is a more suitable approach to trying to resolve HL in Africa. Therefore, the data strongly support that genetic studies on families segregating HL in SSA could be the next frontier of HL genetic research, of global importance through discovering novel variants in known genes, and potentially novel genes. These studies will improve HL genetic diagnosis, retrospective counselling and testing, prevention and care including future prediction of treatment outcomes in sub-Saharan Africans, and in people of African descent.
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    Genetic polymorphisms in the drug metabolizing genes and their roles in the development of oesophageal cancer
    (2008) Li, Dong-Ping; Parker, Iqbal; Dandara, Collet
    Although the incidence and mortality due to the oesophageal squamous cell carcinoma (OSCC) in Black South Africans is extremely high, very little is known about the aetiology and molecular biology of the disease. In order to make a contribution to the understanding to the causes of this disease we investigated the role of the polymorphisms in the genes coding for the cytochrome P450 (CYP1A1, CYP1A2, CYP1B1, CYP2E1), sulphotransferase 1A1 (SULT1A1), glutathione S-transferases (GSTT1. GSTM1 and GSTP1) alcohol dehydrogenase (ADH2 and ADH3) and aldehyde dehydrogenase (ALDH2) because the products of these genes are involved in the metabolism or biotransformation of harmful compounds.
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    Genetic variation in toll like receptors 2, 7, 9 and interleukin-6 is associated with cytomegalovirus infection in late pregnancy
    (2020-05-25) Mhandire, Doreen Z; Mhandire, Kudakwashe; Magadze, Mulalo; Wonkam, Ambroise; Kengne, Andre P; Dandara, Collet
    Background Maternal cytomegalovirus (CMV) infection and/or reactivation in pregnancy is associated with a myriad of adverse infant outcomes. However, the role of host genetic polymorphisms in modulating maternal CMV status is inconclusive. This study investigated the possible association of single nucleotide polymorphisms in toll-like receptor (TLR) and cytokine genes with maternal plasma CMV DNA status in black Zimbabweans. Methods In a cross-sectional study, 110 women in late gestation who included 36 CMV infected cases and 74 CMV uninfected, age and HIV status matched controls were enrolled. Twenty single nucleotide polymorphisms in 10 genes which code for proteins involved in immunity against CMV were genotyped using Iplex GOLD SNP genotyping protocol on the Agena MassARRAY® system. Statistical analyses were performed using Stata SE and the ‘Genetics’ and ‘SNPassoc’ packages of the statistical package R. Results The TLR7 rs179008A > T (p < 0.001) polymorphism was associated while the TLR9 rs352139T > C (p = 0.049) polymorphism was on the borderline for association with CMV positive (CMV+) status. In contrast, the interleukin (IL)-6 rs10499563T > C (p < 0.001) and TLR2 rs1816702C > T (p = 0.001) polymorphisms were associated with CMV negative (CMV-) status. Furthermore, allele frequencies of SNPs in TLR2, TLR4, TLR9, TLR7, IL-6, IL-10, IL-28B, IL-1A and interferon AR1 (IFNAR1) genes are being reported here for the first time in a Zimbabwean population. The allele frequencies in the Zimbabwean population are generally comparable to other African populations but different when compared to European and Asian populations. Conclusions Toll-like receptor and interleukin genetic polymorphisms influence CMV status in late gestation among black Zimbabweans. This is attributable to possible modulation of immune responses to CMV reactivation in a population previously exposed to CMV infection.
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    Heterozygous p.Asp50Asn mutation in the GJB2 gene in two Cameroonian patients with keratitis-ichthyosis-deafness (KID) syndrome
    (BioMed Central Ltd, 2013) Wonkam, Ambroise; Noubiap, Jean; Bosch, Jason; Dandara, Collet; Toure, Genevieve
    BACKGROUND: Keratitis-Ichthyosis-Deafness (KID) syndrome (OMIM 148210) is a congenital ectodermal defect that consists of an atypical ichthyosiform erythroderma associated with congenital sensorineural deafness. KID appears to be genetically heterogeneous and most cases are caused by GJB2 mutations. Mutations in African patients have been rarely described.CASE PRESENTATION:We report on two unrelated Cameroonian individuals affected with sporadic KID, presenting with the classic phenotypic triad. The two patients were heterozygous for the most frequent p.Asp50Asn mutation. This first report in patients from sub-Saharan African origin supports the hypothesis that the occurrence of KID due to p.Asp50Asn mutation in GJB2 seems not to be population specific. CONCLUSIONS: Our finding has implication in medical genetic practice, specifically in the molecular diagnosis of KID in Africans. These cases also reveal and emphasize the urgent need to develop appropriate policies to care for patients with rare/orphan diseases in Sub-Saharan Africa, as many of these cases become more and more recognizable.
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    HIV-associated sensory neuropathy in an African cohort a longitudinal study of risk factors predisposing to antiretroviral induced painful neuropathy
    (2013) Van der Watt, Johan J; Heckmann, Jeannine M; Dandara, Collet; Wilkinson, Robert J
    Distal sensory polyneuropathy (DSP) amongst human immunodeficiency virus (HIV)-infected patients is frequently a painful and disabling condition. HIV-associated DSP is either a consequence of HIV (HIV-DSP) or antiretroviral-induced toxic neuropathy (ATN). The purpose of this research was to investigate the characteristics of HIV-associated DSP over the first 24 weeks of starting cART in an African community-based cohort. Apart from studying the longitudinal association of candidate risk factors based on previous reports, we focused on two additional aspects. Firstly, the Nacetyltransferase 2 (NAT2) genotype, which determines an individual's acetylation status, influences the risk for isoniazid (INH)-associated neuropathy.
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    Human host and malaria parasite genome variations to susceptibility to malaria
    (2023) Hordofa, Hundaol; Dandara, Collet; Chimusa Emile
    Background: Inter-ethnic differences in response to medication can be explained through population structure as observed from genetic variants affecting drug metabolism. Antimalarial drugs are used in populations carrying different profiles of genetic variability. However, there is limited information on the distribution of genetic variants of pharmacogenomics importance in African populations. Aims: We set out to determine whether there are differences in the pharmacogenetic profiles when comparing populations residing in malaria endemic and non-endemic areas. Methodology: Genome-wide genotype datasets (n=13, 447) from four malaria endemic African populations, including Mali, Kenya, Gambia, and Malawi, which were part of the MalariaGEN consortium, were accessed. As comparator, reference datasets of global populations comprising of 20 ethnic groups (n~5,000) from African Genome Variation Project (AGVP) and 1000 Genome consortium project were accessed, considering their malaria epidemiology. Pharmacogenes that are verified from databases such as PharmVar and PharmGKB, and nomenclature sites for uridine 5'-diphospho-glucuronosyltransferases (UGT), solute carrier (SLC) transporters, ATP-binding cassette (ABC) transporters, thiopurine Smethyl transferase (TPMT), and N-acetyltransferases (NAT) were used. Pharmacogenes reported to affect antimalarial drugs were noted and their distribution analysed. Single nucleotide polymorphisms (SNPs) that map to pharmacogenes were retrieved from dbSNP databases and used in the comparison of the populations from malaria endemic and nonendemic regions, through population structure evaluation using pharmacogenes variants. As part of confirmation, genotyping for CYP2C8 SNPs was carried out in native South African population groups, which we have access to our laboratory. CYP2C8 is particularly interesting because of its central involvement in the metabolism of some of the major antimalarial drugs. Results: There were quantitative and qualitative differences in the distribution of pharmacogenes variants when comparing populations from malaria endemic regions to those from non-endemic regions. For instance, the analysis of the minor allele frequency (MAF) proportion of all pharmacogenes variants obtained from the databases revealed that a high proportion of common variants (MAF > 0.05) of pharmacogenes were higher in the four African population from malaria endemic areas (MAF proportion > 50%) compared with world populations from malaria non-endemic areas (MAF proportion < 50%). There were a disproportionately higher number of variants in cytochrome P450 enzymes such as CYP2A13 and CYP2F1 in the malaria endemic populations (> 80%) compared to non-endemic populations (< 65%). Further analysis based on antimalarial specific pharmacogenes variants showed that UGT1A9 had the highest proportion of variants (> 80%) in the malaria endemic populations. The ABC drug transporters such as ABCC4, ABCC1 and ABCC2 were found to have a higher proportion of pathogenic SNPs in populations of the four malaria endemic areas (> 50%) compared with those from non-endemic areas (< 30%). Principal component analysis (PCA) based on pharmacogenes variants also showed clear differentiation into different population. Moreover, four CYP2C8 variants (rs11572103T>A (*2), rs11572101A>G, rs11572100T>C and rs1926705C>T), characterized in South Africans, were found to have III statistically significant difference (p-value < 0.05) in allele frequency when compared with global populations. Conclusions: The findings from this study revealed the profiles of pharmacogenes variants in populations from malaria endemic and non-endemic geographical regions. The variants in CYP2A13, CYP2F1, and UGT1A9 were found in higher proportions in populations from malaria endemic areas compared to non-malaria endemic areas. This suggests that pharmacogenetic testing for patients based on antimalarial pharmacogenes having a higher proportion of variants in malaria endemic areas (e.g., UGT1A9) may be necessary. Moreover, a high frequency in the functional variant of CYP2C8, rs11572103T>A (*2), was found in the South African population. This may also have relevance for future consideration of pharmacogenetic testing for a person traveling to malaria endemic areas from non-endemic areas, such as South Africa. Future studies should be done using large scale sequencing datasets from malaria endemic areas and assess the effect of common variants of antimalarial pharmacogenes on the safety and efficacy of currently used antimalarial drugs.
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    Investigation of microRNA expression in thyroid carcinoma among South Africa patients
    (2017) Mokhesi, Neo; Naidoo, Richard; Govender, Dhiren; Ross, Ian L; Dandara, Collet
    Objective: Thyroid cancer affects approximately 298 million people worldwide and the major challenge is reliably distinguishing patients who present with poor prognosis from those who do not. There are genetic markers that have been shown to be associated with poor clinical outcome in thyroid cancer, which include mutations in the BRAF and RAS genes. In addition to genetic variation, recent studies have reported on the effects of micro-ribonucleic acids' (miRNAs) differential expression observed in tumour and normal tissue as another possible marker of thyroid cancer prognosis. Therefore, miRNA expression signatures in thyroid cancer could be used as biomarkers for prognosis and diagnosis. This study compared the expression of miRNAs in papillary thyroid cancer and follicular thyroid cancer. Methods: As part of a preliminary study, 66 differentiated thyroid cancer samples were obtained from patients attending Groote Schuur Hospital and used in the study. MiRNA miScript polymerase chain reaction (PCR) Array (Qiagen) was used to determine the differential miRNA expression profiles between follicular thyroid carcinoma (FTC) and papillary thyroid carcinoma (PTC). Real time PCR was employed to confirm the expression levels of miRNA- 21 and miRNA-122. Results: 17 miRNAs were upregulated in PTC and 14 in FTC. There were significant differences in the miRNA expression between FTC and PTC. For example, miRNA-21 was the most upregulated miRNA in PTC and miRNA-122 in FTC. We found no correlation of the expression of these miRNAs to clinicopathological features. We observed an association of BRAF mutation positivity to advanced tumour stage and advanced age of presentation however, no correlation was seen to miRNA-21 or miRNA-122 expression. Conclusion: Although we did not observe correlations between miRNAs and any of the clinicopathological features, microRNA expression profile signatures were able to differentiate between PTC and FTC and could potentially be further validated as diagnostic markers.
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    Leveraging the microbiome in host genome wide association studies
    (2021) Awany, Denis; Chimusa, Emile R; Dandara, Collet
    Genome-wide association study (GWAS) has emerged as an effective method for detecting genetic polymorphisms associated with expressed phenotypes. Over the past decade, GWAS of human traits and diseases has revolutionized the field of complex disease genetics, identifying hundreds of genetic variants associated with several different phenotypes, ranging from metabolic diseases to cardiovascular and neuropsychiatric conditions. These associations have provided fundamental insights into the genetic architecture of disease susceptibility and led to initial forays into clinical applications, particularly in creation of genetic risk scores for improved disease risk prediction and identification of new drug targets for novel drug development. Despite this gratifying success, however, for almost all complex traits, the identified genetic loci explain only a small proportion, generally less than half, of the estimated heritability. A number of alternative explanations have been offered for this, including undetected genetic effects, unaccounted-for environmental factors, and gene–gene and gene–environment interaction effects. Although there is no consensus on these explanations, it is universally acknowledged that a substantial proportion of the trait heritability is attributable to existence of a large number of undetected genetic variants distributed across the entire allele frequency spectrum, each of which has very small to modest effect on the phenotype, and non host-DNA factors that contribute to phenotypic variation. In parallel to host GWAS, the advent of next-generation sequencing technologies (NGS) that enable culture-independent profiling of microbial communities has led to the rediscovery of the microbiome - the collective genome of the microorganisms that inhabit the body - and the emergence of microbiome-wide association studies. These studies have linked the gut microbiome to a variety of human conditions, ranging from neurological conditions, such as Parkinson's disease and autism, to metabolic diseases, such as obesity, diabetes, and cardiovascular disease. Given the critical importance of the microbiome in host phenotype, it is clear that in order to more comprehensively understand the basis of host phenotypic status, both the host's genotype and microbiome information have to be examined. This thesis explores the dissection of microbial taxa and host genetic polymorphisms associated with human complex traits and diseases, and the interaction of human host genetic polymorphisms with the microbiome. Then, a Bayesian statistical framework, based on the Dirichlet process random effects model, is proposed for identifying microbial species associated with host phenotype. The proposed method uses a weighted combination of phylogenetic and radial basis function kernels to model microbial taxa effects, and a non-parametrically defined latent variable to model latent heterogeneity among samples. Philosophically, the non-parametric specification amounts to the addition of an infinite amount of prior information about all fine details of the parameters being modelled; thus represents an attractive strategy. The utility of the method is demonstrated through simulation experiments and application to real microbiome datasets for schizophrenia, HIV/AIDS, and atherosclerosis diseases, where it is shown that the method is not only robust but also has high statistical power for association inference, resulting in a framework that can contribute to our understanding of the link between the microbiome and human diseases. Understanding the human genetic predisposing factors in concert with this link will make human GWAS fulfil its translational potential, from patient stratifcation and disease risk prediction to identification of new biology and drug discovery.
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    A Monoallelic Variant in REST Is Associated with Non-Syndromic Autosomal Dominant Hearing Impairment in a South African Family
    (2021-11-06) Manyisa, Noluthando; Schrauwen, Isabelle; de Souza Rios, Leonardo Alves; Mowla, Shaheen; Tekendo-Ngongang, Cedrik; Popel, Kalinka; Esoh, Kevin; Bharadwaj, Thashi; Nouel-Saied, Liz M.; Acharya, Anushree; Nasir, Abdul; Wonkam-Tingang, Edmond; Kock, Carmen de; Dandara, Collet; Leal, Suzanne M.; Wonkam, Ambroise
    Hearing impairment (HI) is a sensory disorder with a prevalence of 0.0055 live births in South Africa. DNA samples from a South African family presenting with progressive, autosomal dominant non-syndromic HI were subjected to whole-exome sequencing, and a novel monoallelic variant in REST [c.1244GC; p.(C415S)], was identified as the putative causative variant. The co-segregation of the variant was confirmed with Sanger Sequencing. The variant is absent from databases, 103 healthy South African controls, and 52 South African probands with isolated HI. In silico analysis indicates that the p.C415S variant in REST substitutes a conserved cysteine and results in changes to the surrounding secondary structure and the disulphide bonds, culminating in alteration of the tertiary structure of REST. Localization studies using ectopically expressed GFP-tagged Wild type (WT) and mutant REST in HEK-293 cells show that WT REST localizes exclusively to the nucleus; however, the mutant protein localizes throughout the cell. Additionally, mutant REST has an impaired ability to repress its known target AF1q. The data demonstrates that the identified mutation compromises the function of REST and support its implication in HI. This study is the second report, worldwide, to implicate REST in HI and suggests that it should be included in diagnostic HI panels.