Electronic Theses and Dissertations (PhDs)
Permanent URI for this collectionhttps://hdl.handle.net/10539/37932
Browse
20 results
Search Results
Item Nutrition of ageing black South African women and correlates with anthropometry and cardiometabolic outcomes(University of the Witwatersrand, Johannesburg, 2023-09) Kankwende, Caroline Belinda Tsitsi; Gradidge, Philippe; Norris, Shane; Chikowore, TinasheBackground: Obesity is most prevalent among black women who reside in urban areas in South Africa yet the nutrient patterns of this cohort of women has never been investigated, nor have correlates of body composition indices such as adiposity and body mass index (BMI). These body composition indices are important to analyse as they have been shown to be positively associated with hypertension which is prevalent in this cohort of women. Aim: There were three main goals: 1) To determine the baseline nutrient patterns of middle-aged black South African women residing in Soweto and correlates to body composition indices 2) To evaluate the longitudinal association of nutrient patterns with adiposity in a cohort of middle-aged black South African women over a period of 5.5- years 3) To elucidate the longitudinal associations of nutrient patterns and blood pressure and to explore whether this is an indirect effect mediated by body mass index (BMI) using structural equation modelling Methods: A longitudinal study of children and their families, originally called the Birth to Twenty Plus (Bt20+) cohort and now referred to as the Middle-aged Soweto Cohort (MASC), was used to as the original dataset for this thesis. This study also drew on another embedded study, the Study of Women Entering and in Endocrine Transition (SWEET) study of older women transitioning through menopause. Data on (i) dietary information; (ii) body composition and anthropometry measurements; (iii) blood pressure; (iv) lifestyle behaviours (physical activity, tobacco use, and alcohol use); (v) psychosocial factors; (vi) socioeconomic status; and (vii) educational status were used. A total of 498 Women aged between 40 and 60 years old were included in the study. Principle component analysis (PCA) was applied on the dietary data both at baseline and at 5- years follow-up. This was conducted to extract nutrient patterns from 25 nutrients derived from the food frequency questionnaire (FFQ) and the resulting nutrient patterns are detailed in results chapter 3 (nutrient patterns derived from the baseline FFQ) and results chapter 4 (comparison between both baseline and follow-up nutrient patterns from the FFQ). Simple and complex body composition were recorded for each participant with complex body measurements taken using (DXA). Chapter 3 details the results of the 3 baseline nutrient patterns and correlates with body composition parameters. Using generalized estimating equations, associations between both baseline and 5- years follow-up nutrient patterns and adiposity were evaluated. The results are discussed in results chapter 4. Lastly, the results chapter 5 examined associations between both baseline and follow-up nutrient patterns and blood pressure were examined and furthermore, investigated whether BMI mediates the relationship between repeated measures of nutrient patterns and blood pressure. Results: The majority of the research participants (88%) were classified as individuals having obese status defined by their BMI. The fat mass index (FMI), lean mass index (LMI), gynoid fat, hip and waist circumference, and visceral and subcutaneous adipose tissue (VAT and SAT respectively) measurements were all substantially larger in the group with predominantly individuals having overweight and obese classification compared to woman in the lean group (p <0.001). Protein consumption was greater in the group with individuals having overweight/obese classification, while fat and carbohydrate consumption were matched. At baseline, the "Plant driven nutrient pattern," characterized by higher factor loadings of plant protein, starch, and B vitamins, explained 25% of the total nutritional variance; the "Animal protein driven nutrient pattern," characterized by animal protein and saturated fat, explained 23% of the variance; and the third pattern was the "Vitamin C, sugar and potassium driven nutrient pattern," which had higher factor loadings of vitamin C, sugar and potassium. At baseline, increased consumption of the animal protein driven nutrient pattern resulted in a 1.19 kg/m2 (p = 0.002) increase in BMI, 10.17 cm2 for VAT, 24.43 cm2 for SAT, 0.01 (p = 0.009) increase for VAT/SAT ratio, 0.69 kg/m2 (p = 0.005) increase for FMI, and 0.48 kg/m2 (p = 0.002) increase for LMI. Furthermore at baseline, statistically significant associations were found for the animal protein driven nutrient pattern with all body composition indicators. Subcutaneous adipose tissue increased in the presence of a plant-driven nutrition pattern (p = 0.045). At 5-year follow-up, although the value of the factor loadings of the individual nutrients changed between baseline and follow-up, the nutrients with the highest loadings for each principal component (PC) did not change therefore the overall nutrient patterns remained the same. Only DXA-derived measurements of fat mass, FMI, VAT, and gynoid fat mass (FM) increased with time, while lean mass considerably reduced. Repeated measures of the animal protein driven nutrient pattern was associated with significant increases in FMI, LMI and VAT and repeated measures of the vitamin C, sugar, and potassium driven nutrient pattern was significantly associated with an increase in FMI and LMI. For the purposes of this study, repeated measures of animal-driven nutrient patterns were shown to be significantly related with repeated measures of systolic blood pressure (SBP) only. When structural equation modelling (SEM) was applied, only significant relationships were observed between age and SBP. This relationship was not mediated by BMI but may involve other factors that were not included in this analysis. Conclusions: This thesis explored the nutrient patterns linked to obesity and cardiometabolic complications, namely blood pressure, in a cohort of black middle-aged African females. It has been previously demonstrated that this cohort has been has a high prevalence of obesity. According to literature reviews, programs focusing on nutritional and behavioural changes could aid African women in their fight against the obesity and hypertension epidemic that we are facing today. The animal-driven nutrient pattern was found to be substantially associated with increases in body fat in this cohort at baseline. At 5-year follow-up, the nutrient patterns remained the same and repeated measurements of the vitamin C, sugar, and potassium-driven nutrient pattern were associated with significant increases in FMI and LMI and the animal-driven nutrient pattern remained significantly associated with LMI, FMI and VAT, a measure of visceral obesity which is a major risk factor for cardiometabolic conditions. This is problematic in a population that consists predominantly of individuals that are classified as having an obese and overweight status. As a result of a higher BMI, a greater likelihood of developing cardiometabolic multimorbidity exists which is defined as the co-occurrence of two or three cardiometabolic conditions. This may result in reduced quality of life and an increased burden on the already overstretched healthcare system in South Africa. Furthermore, this study found that only the animal protein driven nutrient pattern had a significant relationship with SBP which was significant. When SEM was applied, BMI did not mediate the relationship between blood pressure and any of the nutrient patterns. No other noteworthy direct relationships between blood pressure and the other nutrient patterns were found. Researchers can apply the findings of this study to improve nutritional policies and guidelines aimed at combating not just obesity, but high blood pressure among black women in Sub-Saharan Africa. It is necessary to conduct further extensive research to verify these findings.Item Role of novel biomarkers in predicting chronic kidney disease progression among black patients attending a tertiary hospital in Johannesburg, South Africa(University of the Witwatersrand, Johannesburg, 2023) Meremo, Alfred Jackson; Naicker, Saraladevi; Duarte, Raquel; Paget, Graham; Dickens, CarolineBackground: Chronic kidney disease (CKD) is a leading health issue and its magnitude has been increasing globally; where the developing countries are the most affected and they are the least equipped to deal with its associated consequences. Chronic kidney disease can rapidly and quietly progress to late CKD stages in impoverished environments. Early recognition of patients who are likely to develop end-stage kidney disease (ESKD) is important. Methodology: A prospective longitudinal study was conducted on CKD patients of black ethnicity attending at the Charlotte Maxeke Johannesburg Academic Hospital (CMJAH) renal outpatient clinic in South Africa, as from September 2019 to March 2022. Patients provided blood and urine samples for investigations in the laboratory at study enrolment (0) and at the 24 months follow up. The concentrations of the transforming growth factor isoforms [(TGF)-β1, TGF-β2 and TGF-β3) were determined in serum and urine at baseline using the Human TGF-β duoset ELISA. Data were descriptively and inferentially processed by the REDcap and analyzed using STATA version 17 and multivariable logistic regression analysis was applied to find out the predictors of CKD progression. Results: A total of 312 patients were recruited into the study; the median age was 58 (IQR 46 -67) years and 162 (51.9 %) were male. Hypertension was present in majority (96.7 %) of the patients. Diabetes mellitus was present in 38.7 % of patients and 38.1 % of the study patients had both hypertension and diabetes mellitus. A total of 297 (95.2%) patients completed the study. Death was reported in 5 (1.6%) patients and 10 (3.2%) of patients were lost to follow up. The prevalence of CKD progression was 49.5%, 33% had CKD remission and 17.5% had CKD regression while the prevalence of CKD progression by change in uPCR > 30% was 51.9%. Almost half (47.8 %) had a sustained decline in eGFR of > 4 ml/min/1.73 m2 /year or more, 35.0% of the patients moved to a more severe stage of CKD and 19.9% had more than 30% 6 decline in eGFR in two years. For patients with CKD progression, 54.9% patients were men and at baseline, their median age was 59 (46 - 67) years, urine protein creatinine ratio (uPCR) increased at 0.039 (0.015-0.085) g/mmol, eGFR was 37 (32 -51) mL/min/1.73 m2; the median serum TGF-β1 was 21210 (15915 – 25745) ng/L and the median urine TGF-β3 was 17.5 (5.4 –76.2) ng/L. For those who had CKD progression, hypertension was present in the majority (95.2%) of the patients. Diabetes mellitus was present in 59 (40.1%) patients and 58 (39.5%) patients had both hypertension and diabetes mellitus; 48.3% had severely increased proteinuria, 45.6% patients had anaemia, 34.0% had hyperuricemia and 17.7% had hypocalcaemia at baseline. For those patients with CKD progression vs those without CKD progression, the baseline median serum TGF-β1 was 21210 (15915 – 25745) ng/L vs 24200 (17570 – 29560) ng/L, the baseline median urine TGF-β3 was 17.5 (5.4 – 76.2) ng/L vs 2.8 (1.8 – 15.3) ng/L; however, baseline serum and urine TGF-β isoforms did not predict progression of CKD on univariate and multivariable analyses. Regarding use of medications among patients with CKD progression, calcium channel blockers (amlodipine) were used by majority (85.2 %) of the patients. Diuretics were used by 63.4% of the patients and 31.7 % of the patients were using insulin. Variables associated with CKD progression after multivariable logistic regression analysis were moderately elevated proteinuria (OR 2.1, 95% CI (1.1 – 3.9), P= 0.019), severely elevated proteinuria (OR 6.1, 95 % CI (3.2 – 11.6), P = 0.001), hyponatraemia (OR 4.5, 95% CI 1.8 - 23.6, P= 0.042), hypocalcaemia (OR 3.8, 95 % CI 1.0 - 14.8, P = 0.047), anaemia (OR 2.1, 95% CI 1.0 - 4.3, P= 0.048), elevated HbA1c (OR 1.8, 95 % CI 1.2 - 2.8, P = 0.007), diabetes mellitus (OR 1.8, 95 % CI 1.9 - 3.6, P = 0.047), current smoking (OR 2.8, 95 % CI 1.9 - 8.6, P = 0.049), medications which were calcium channel blockers (OR 2.07, 95 % CI 1.04 – 4.12, P = 0.038), diuretics (OR 2.35, 95 % CI 1.37 – 4.00, P = 0.002), insulin (OR 1.96, 95 % CI 1.01 – 3.84, P = 0.048) and baseline serum calcium levels (OR 0.06, 95 % CI 0.01 -0.64, P = 0.019). An increase in uPCR > 30% at two years identified most patients with CKD progression; clinicians and nephrologists should utilize change in uPCR > 30% at two years to identify those patients with CKD who are likely to progress more rapidly, who require closer surveillance and monitoring with emphasis on slowing or stopping progression of the CKD. Conclusion: Our study has demonstrated a higher prevalence of CKD progression in a prospective longitudinal study among black patients than that reported in previous studies. CKD progression was associated with current smoking, hyponatremia, hypocalcemia, anaemia, elevated HbA1c, diabetes mellitus, and proteinuria. While patients with CKD progression had lower baseline concentrations of serum TGF-β1 and increased baseline urinary TGF-β3 concentrations, baseline serum and urine TGF-β isoforms did not predict progression of CKD. The roles of the various serum and urine TGF-β isoforms in CKD progression at baseline are still unclear and highlight the importance of further studies to determine their isoform specific effects.Item Predicting in-hospital mortality in heart failure patients using machine learning(University of the Witwatersrand, Johannesburg, 2023-05) Mpanya, Dineo; Ntsinjana, HopewellThe age of onset and causes of heart failure differ between high-income and low-and-middle-income countries (LMIC). Heart failure patients in LMIC also experience a higher mortality rate. Innovative ways that can risk stratify heart failure patients in this region are needed. The aim of this study was to demonstrate the utility of machine learning in predicting all-cause mortality in heart failure patients hospitalised in a tertiary academic centre. Six supervised machine learning algorithms were trained to predict in-hospital all-cause mortality using data from 500 consecutive heart failure patients with a left ventricular ejection fraction (LVEF) less than 50%. The mean age was 55.2 ± 16.8 years. There were 271 (54.2%) males, and the mean LVEF was 29 ± 9.2%. The median duration of hospitalisation was 7 days (interquartile range: 4–11), and it did not differ between patients discharged alive and those who died. After a prediction window of 4 years (interquartile range: 2–6), 84 (16.8%) patients died before discharge from the hospital. The area under the receiver operating characteristic curve was 0.82, 0.78, 0.77, 0.76, 0.75, and 0.62 for random forest, logistic regression, support vector machines (SVM), extreme gradient boosting, multilayer perceptron (MLP), and decision trees, and the accuracy during the test phase was 88, 87, 86, 82, 78, and 76% for random forest, MLP, SVM, extreme gradient boosting, decision trees, and logistic regression. The support vector machines were the best performing algorithm, and furosemide, beta-blockers, spironolactone, early diastolic murmur, and a parasternal heave had a positive coefficient with the target feature, whereas coronary artery disease, potassium, oedema grade, ischaemic cardiomyopathy, and right bundle branch block on electrocardiogram had negative coefficients. Despite a small sample size, supervised machine learning algorithms successfully predicted all-cause mortality with modest accuracy. The SVM model will be externally validated using data from multiple cardiology centres in South Africa before developing a uniquely African risk prediction tool that can potentially transform heart failure management through precision medicine.Item Identification of (Novel) Immune Targets with Potential Roles in the Progression of Pancreatic Ductal Adenocarcinoma (PDAC)(University of the Witwatersrand, Johannesburg, 2024) Nsingwane, Zanele; Nweke, EkeneBackground: Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer with a growing incidence and mortality despite novel therapeutic strategies. Its aggressiveness and difficulty to treat suggest the need for a better understanding of associated molecular mechanisms which could be targeted for treatment. The complement signalling pathway may play diverse roles in PDAC by eliciting an immune response, inducing inflammatory responses, and may elevate pathways linked to chemoresistance. However, their role in the progression of PDAC is not fully understood. This study aimed to identify potential immune response-related targets in a group of patients. Methods: In this study, 30 tissue samples (tumours and corresponding normal tissues) were obtained from 15 PDAC patients, 34 plasma samples were obtained from 25 PDAC patients, 6 patients with chronic pancreatitis, and 3 healthy control participants. Targeted pathway-specific PCR analysis was conducted to determine the gene expression profiles of immune-response-related genes. The circulating levels of complement proteins C3 and C5 were further investigated. Pharmacological inhibition of the complement pathway in MIA PaCa-2 pancreatic cancer cell lines was performed and the effect on cells was assessed by cell proliferation, cell migration, and cell cycle assays. Finally, SWATH-mass spectrometry was performed to identify potential molecular mechanisms during inhibition. Results: The results identified C3 to be overly expressed in early PDAC compared to later stages in plasma (p=0.047). Pharmacological inhibition of the complement pathway led to increased cell growth (p<0.0001), proliferation (p=0.001) and migration (p=0.002) in vitro. Proteomic analysis implicated several proteins such as the mitochondrial and histone proteins, that could play a role in inducing this phenotype. Conclusion: Both Complement C3 and C5 are elevated in PDAC samples compared to healthy ones. Furthermore, the inhibition of the complement pathway was shown in vitro to result in a more aggressive phenotype by stimulating cellular growth, proliferation, and migration, indicating the involvement of complement C3 and C5 in tumour progression. This study helps to further delineate the role of the complement pathway in PDAC progression.Item An in-silico analysis of the glycosylation inhibitors Brefeldin A and Tunicamycin C in colorectal cancer; characterization of novel targets(University of the Witwatersrand, Johannesburg, 2024) Naidoo, VivashColorectal cancer (CRC), a prevalent malignancy in South Africa, is significantly influenced by posttranslational modifications such as glycosylation. This study investigates the complex interactions between genes, signalling pathways, and cellular processes involved in CRC progression and glycosylation. The glycosylation inhibitors, Tunicamycin and Brefeldin A, are known to hinder colon cancer cell proliferation, migration, and invasion, making them potential therapeutic agents. We used Swiss Target Prediction Software to identify target proteins for both compounds and revealed that Protein Kinase C Alpha (PRKCA), Peroxisome Proliferator- Activated Receptor Gamma (PPARG), and Mitogen-Activated Protein Kinase 1 (MAP2K1) are specific for Brefeldin A, and TK1 and PRKCA for Tunicamycin, respectively. These proteins were selected based on their potential role in the glycosylation process and their role in CRC-related pathways. Further, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis disclosed significantly enriched pathways, including Epstein-Barr virus infection, cellular senescence, and cancer pathways. The 3D-crystallographic structures of PrKC1 (PDB ID 6ar4), TK1 (PDB ID 1w4r), PrCK1 (PDB ID: 6ar4) and MAPK (PDB ID: 3eqc) were retrieved from RCSB Protein Data Bank. The compounds BSP and EGCG were downloaded from PubChem. All non-relevant co-crystallized molecules, including ions, crystallographic water, and others, were removed. Missing residues in the proteins were filled in using the MODELLER algorithm on the UCSF Chimera Graphic User Interface. Molecular docking of Tunicamycin C and Brefeldin A was performed with UCSF Chimera, and the docked conformations were visualised in Maestro and Chimera. The complexes with the top docking scores were selected and prepared for molecular dynamics simulation studies to offer structural and dynamic perspectives on the inhibitory potential of the compounds against the target proteins. The Origin Lab software tool was used to post- analyze the docking conformations. Molecular Dynamics simulation was conducted using Graphics Processing Units version of the Particle Mesh Ewald Molecular Dynamics engine in the AMBER18 suite. Our investigation into the dynamic events leading to the proximal binding of Tunicamycin at the pockets of TK1 and PrKC1 suggested that the binding of Tunicamycin induced a conformational perturbation of the 3D structures of these proteins, resulting in a structural deviation that inhibited their activity. Tunicamycin's time-based dynamics indicated a stable pattern, leading to optimal interaction and maximal stabilization in the hydrophobic pockets of TK1 and PrKC1. Binding energy calculations showed a high-affinity interaction of Tunicamycin with these proteins. Similarly, the structural investigation revealed that the binding of Brefeldin A to Mitogen- Activated Protein Kinase (MAPK) and Protein Kinase C (PrKC1) inhibited their activity. A detailed analysis of active site residues revealed crucial residues that contributed to the binding stabilization of Brefeldin A. It was noted that the Brefeldin A/MAPK complex produced a binding energy of -22.18±4.50Kcal/mol while the Brefeldin A/PrCK1 complex produced a binding energy of -23.90±5.36Kcal/mol. These findings provide crucial insights into designing novel inhibitors of TK1 and PrKC1, potentially blocking glycosylation progression in cancer treatment. This study underscores the potential for exploiting glycosylation inhibition as a therapeutic strategy against CRC, opening avenues to mitigate cancer progressionItem Association of genetic variants with breast cancer intrinsic subtypes and splice variants of the fibroblast growth factor receptor 2 in a South African population(University of the Witwatersrand, Johannesburg, 2023) Dix-Peek, Thérèse; Duarte, Raquel; Augustine, TanyaAfrican populations are more genetically diverse than other groups, but there is a paucity of information about breast carcinomas. South Africa uses immunohistochemistry (IHC) rather than multiparameter genomic assays, such as PAM50, to classify tumors. Genome-wide association studies have shown variants in fibroblast growth factor receptor 2 (FGFR2) are associated with breast cancer, but this has not been examined in black, African women. This thesis investigated intrinsic subtypes; the effects of four FGFR2 single nucleotide polymorphisms (SNPs), and FGFR2 mRNA expression and splice variants associated with breast cancer subtypes. In a cohort of 378 breast cancer patients, we investigated the concordance between tumor samples classified by IHC and PAM50. The SNPs rs2981582, rs35054928, rs2981578 and rs11200014 were examined in 1001 patients with, and 1005 participants without, cancer. The FGFR2 mRNA expression and IIIb and IIIc isoforms were examined using cBioPortal, TCGA Splice Seq and TSVdb databases. Statistical analyses were performed using STATA v14.2. This study was approved by the Human Research Ethics Committee of the University of the Witwatersrand (clearance certificate no M161116). IHC classified patients as estrogen receptor-positive (77.45%), progesterone receptor-positive (70.56%), and epidermal growth factor receptor 2 (HER2)-positive (32.28%). These results, together with ki67, were used as surrogates for intrinsic subtyping, and showed 7% IHC-A-clinical, 73% IHC-B-clinical, 5% IHC-HER2-clinical and 15% triple negative (TNBC). PAM50 gave 19% luminal-A, 32% luminal-B, 24% HER2-enriched and 25% basal-like. Concordance was highest between basal-like and TNBC and lowest between luminal-A and IHC-A. There was no association with the SNPS, rs2981582, rs35054928, rs2981578 and rs11200014, and breast cancer in the black, South African population. However, rs2981578 was associated with invasive lobular carcinoma (ILC) and HER2-positive breast cancer was associated with rs11200014. ILC and ER-positive cancers were associated with higher FGFR2, while TNBC or HER2-positive breast cancers were associated with lower FGFR2. The IIIb isoform was prevalent in ER- positive breast cancer and IIIc prevalent in HER2-positive breast cancer. Genetic information from the black South African population can improve understanding of breast cancer in our population. We suggest that the cutoff for Ki67 be changed to 20-25% to better reflect the luminal subtype classifications. Lobular carcinoma is associated with rs2981578, and HER2-postive carcinoma is associated with rs11200014. Increased levels of FGFR2 mRNA and IIIb isoforms are associated with ER-positive breast cancer, while lower levels of FGFR2 and higher IIIc isoforms are associated with HER2 and TNBCItem Gene expression patterns of signalling pathways in PDAC: towards inhibiting metastases(University of the Witwatersrand, Johannesburg, 2024) Xelwa, Ntombikayise Hendrietta MarciaPDAC has a poor prognosis, with its prevalence varying by geographical location. In South Africa, PDAC ranked seventh among all cancer-related deaths in 2020 for both sexes. Specifically, it was the seventh leading cause of cancer death among males and the sixth among females. In 2020, an estimated 1,982 cancer deaths in South Africa were attributed to pancreatic cancer, with 1,006 occurring in males and 976 in females. However, the annual reported number of PDAC deaths in South Africa varies. This study aimed to identify potential novel therapeutic targets for PDAC in patients from the African population. Following ethical approval, tissue from fifteen patients (15 tumour and 15 corresponding normal tissues) were obtained during Whipple procedures from PDAC patients who consented to the study. Despite the development of new treatment strategies, patient outcomes have not significantly improved underscoring the necessity for extensive research to identify novel treatment options. A discovery study was conducted to determine the gene expression profile of signalling pathway-related genes using PDAC tissue samples. Top upregulated pathways included those involved in cytokine signalling, receptor kinase signalling, and PI3/Akt signalling. SPP1 was one of the most highly expressed genes identified in PDAC patients compared to normal corresponding tissues suggesting its potential role in the progression of the disease. To investigate SPP1's role in PDAC, RNA interference was employed to knockdown SPP1 in a PDAC cell line, MIA PaCa-2. Knockdown was confirmed by a significant reduction in SPP1 expression at the mRNA level. Combining SPP1 knockdown with conventional chemotherapy used for PDAC, gemcitabine, resulted in a synergistic effect, leading to an enhanced early apoptotic response. The study also examined the migratory and invasive capabilities of MIA PaCa-2 cells, revealing a noticeable decline in these abilities upon reduction in SPP1 expression with gemcitabine treatment. Furthermore, proteomic analyses uncovered the complex network of cellular processes influenced by the downregulation of SPP1 and the synergistic effects of combination therapy. Altogether, the findings from this study demonstrate the role of SPP1 in PDAC indicating that it could serve as a promising therapeutic target. The synergistic effects observed when SPP1 knockdown was combined with gemcitabine treatment suggest a potential avenue for developing more effective treatments for PDAC while exploring tumour cell adaptation for survival.Item Evaluation of the postgraduate family medicine decentralised training programme at the university of Witwatersrand, South Africa, using the logic model(University of the Witwatersrand, Johannesburg, 2024) Erumeda, Neetha Joe; George, Ann ZetaPostgraduate family medicine decentralised training programmes were implemented in South Africa about 15 years ago, but the University of the Witwatersrand’s programme has not been comprehensively evaluated. This study evaluated the programme using a complex programme evaluation logic model based on linearity theory. This theory assumes ideal inputs and processes produce good programmatic outputs and outcomes. Resources and support were evaluated as inputs, postgraduate supervision and workplace-based learning as processes, supervisory feedback as outputs and workplace-based assessments as outcomes. A parallel convergent mixed-methods instrumental case study was conducted with purposively-sampled family physicians (n=11) and trainees (n=11) from five decentralised training sites. Semi-structured interviews were audio recorded, transcribed verbatim, and analysed inductively using MAXQDA 2020 software. Descriptive statistical analysis was conducted on components of registrars’ learning portfolios (scores, supervisory feedback, and skills competence) and examination results using Stata 14.2 software. An integrative analysis involving transforming the quantitative results to qualitative findings and drawing meta-inferences was conducted. The integrated findings were used to modify the initial logic model and identify key recommendations to optimise the programme. The integrative analysis identified the need for more material and human resources, university and district management support, and standardised resources, supervision, and learning practices. Supervisors’ knowledge, skills, and behaviours varied across sites and their feedback was insufficient regarding soft skills like clinical reasoning and patient negotiation. Workplace-based assessments did not meet the required standards across training years and districts. Interpersonal interactions with patients, peers, supervisors and other professionals, engagement in district activities, promoted learning. Registrars’ professionalism and self-learning need improvement. The key recommendations include more explicit national guidelines, sufficient support from the provincial department, university, and district management, well maintained infrastructure, sufficient skilled supervisors, more professional development training for supervisors, protected time for registrar learning, and better use of self-learning and reflection. Emulating successful contextual adaptations while addressing challenges across sites contributes to thriving decentralised training programmes in district health systems. An improved understanding of the concepts and their interrelationships in training programmes could be translated to similar decentralised training platforms across medical disciplines of sub-Saharan Africa or low-middle income countriesItem Relationship of diet and physical activity with genetic susceptibility to obesity: a longitudinal analysis in adults in South Africa(University of the Witwatersrand, Johannesburg, 2024) Muti, Monica; Chikowore, Tinashe; Ware, LisaBackground Obesity-related disease conditions are a major public health concern in South Africa, exerting a healthcare cost of between ZAR 30 million and ZAR 36 million, the bulk of which is due to hypertension and type 2 diabetes. Moreover, evidence reveals that women in South Africa have higher BMI compared to men, yet men exhibit less insulin sensitivity and reduced beta cell function as well as stronger associations of adiposity with type 2 diabetes compared to women. The mechanisms underlying these sex differences are not known. BMI is highly polygenic in nature; however, genetic prediction of BMI has mostly been conducted using data from European ancestry populations that have poor predictive capacity in African ancestry populations. Moreover, the relationship of polygenic risks and proteomic profiles with regards to susceptibility to obesity and related cardiometabolic traits is yet to be explored in African populations. It has also been reported that using variants associated with the statistical variance of quantitative traits (vQTLs) like BMI aids in the depiction of components of BMI genetic susceptibility, which interacts with environmental factors such as diet and exercise. However, such studies are limited in continental Africans. Aim This thesis, sought to determine the interplay of diet and physical activity with BMI genetic susceptibility. The specific objectives were: 1. To determine the association of physical activity with BMI in middle-aged black South African men and women. 2. To develop a highly predictive genetic risk score for BMI and test its longitudinal predictive ability in middle-aged black South African men and women. 3. To determine gene x lifestyle (GXE) interactions that influence BMI in Black South African adult men and women. Methods Data from 11853 adult men and women in the African-Wits-INDEPTH partnership for Genomic studies (AWI-Gen) Cohort was used to fulfil objective 1. To fulfil objectives 2 and 3, data from 5921 AWI-Gen cohort participants in the three South African (SA) sites and a sub-study of AWI-Gen focusing on the factors influencing the risk of type 2 diabetes mellitus among middle-aged black South African men and women (GSK) was used. For objective 1, a sex-stratified meta-analysis of cross-sectional data from the study participants was used to assess the association of physical activity with BMI. The PRS-CSx method was used to develop a multi-ancestry PRS for BMI and evaluate its longitudinal prediction of severe obesity to meet objective 2. For objective 3, the Levene’s test, implemented in the OCSA Package, was used to determine candidate gene-interacting variants that exhibited trait variance heterogeneity in the study population. Detailed methods are in the relevant sections for each objective. Results Meeting the recommended weekly physical activity levels of at least 150 minutes was associated with a BMI that was 0.80kg/m2 lower in men (95% CI = -1.14; -0.47) and 0.68kg/m2 lower in women (95% Ci = -1.03; -0.33). Sex and site-specific differences were also observed in domains of physical activity with an inverse relationship between transport-related physical activity and BMI being observed among men in Agincourt (beta = -1.15 kg/m2, 95% CI = -2.26; -0.04) and Nanoro (beta = -0.79 kg/m2, 95%CI = -1.25; -0.33). Work related physical activity was associated with lower BMI in Navrongo men (beta = -0.76 kg/m2, 95% CI=-1.25; -0.27) and Nanoro women (beta = -0.90 kg/m2, 95%CI = -1.44; -0.36). The multi-ancestry PRS demonstrated superior predictive ability, explaining approximately 1.9% of variance in BMI compared to 0.7% and 1.2% explained by two scores developed using single ancestry methods. In addition, over a period of ten years, the multi-ancestry PRS was associated with repeated measures of BMI (β = 1.51 p = < 0.001) and there was significant longitudinal PRS * sex interaction (Pinteraction = 0.029), prompting subsequent sex-stratified analysis. In the combined analysis of men and women, being in the top 20% of the PRS distribution (top 20) was associated with three times greater hazard of severe obesity (hazard ratio = 2.98, 95% CI = 1.75 - 5.07, p = 5.33e-05) compared to being in the bottom 20% of the PRS distribution (bottom 20). This observation was shown to be driven by women, where being a woman in the top 20 was associated with 3.5 greater hazard of severe obesity (hazard ratio 3.48, 95% CI = 1.96 – 6.16, p = 1.94e-05) compared to being in the bottom 20 while the associations were not significant in men (hazard ratio = 1.13, 95% CI = 0.24 – 5.37, p = 0.878). Comparison of the associations of dysglycaemia with PRS, BMI and the proteomic score revealed no apparent sex differences in the association between BMI PRS and dysglycaemia for most of the glycaemic markers except for Matsuda Index though men exhibited lower insulin sensitivity compared to women. The proteomic score predicted higher insulin resistance in women than in men. Gene x lifestyle interaction analysis revealed novel interactions between three genetic variants with diet and lifestyle factors. The effect of the rs557505940 variant on BMI was accentuated by higher fruit intake (betainteraction = 0.03, Pinteraction = 0.04) in the combined analysis of men and women while higher SES, carbohydrate intake and self- reported physical activity attenuated the effect of rs527747185 (betainteraction = -0.349, Pinteraction = 0.037), rs3016751 (betainteraction = -0.056, Pinteraction = 0.035) and rs188275749 (betainteraction = -0.048, Pinteraction = 0.0001) respectively on BMI in men. Conclusions Sex and geographical differences exist in associations between domains of physical activity and BMI. In addition, genetic risk better predicts incident severe obesity in women than in men while proteomic profiles have a weak correlation with PRS and show heterogenous associations with dysglycaemia, fat distribution, nutrient patterns and physical activity between men and women. Novel GXE interactions were also observed. These results underscore the need for further inquiry into the sex differences in genetic risk and environmental factors associated with BMI. Furthermore, a precision approach to obesity prevention and control, paying attention to the sex differences and contextual factors may be more efficient.Item The effects of indigenous South African plant extracts (cotyledon c. orbiculata and tulbaghia. violacea) on triple negative breast cancer cells(University of the Witwatersrand, Johannesburg, 2024) Alaouna, Mohammed; Dlamini, ZodwaThis dissertation explored the potential therapeutic applications of water and methanol extracts of C. orbiculata and Tulbaghia violacea, indigenous to Southern Africa, targeting triple-negative breast cancer (TNBC). TNBC, a significant subset of breast cancer cases, is notably challenging because of the absence of key hormone receptors, often leading to less favourable patient outcomes and a high relapse rate within five years. The research approach was both thorough and meticulous, utilising two cell lines: one representing normal breast tissue and the other representing TNBC. Extensive cytotoxicity assays were conducted to determine the IC50 values for TNBC cells, which is critical for understanding how plant extracts affect cellular activities such as migration, invasion, adhesion, cell cycle regulation, and apoptosis induction. Additionally, the antioxidant properties of these extracts were examined, which showed significant effects, especially in the aqueous extract of Tulbaghia violacea, on TNBC cellular dynamics. This study employed a comprehensive array of analytical techniques, including Fourier transform infrared spectroscopy (FTIR), gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR) spectroscopy, to identify the specific molecular constituents of these extracts. Computational docking studies have focused on the interactions between these molecules and the anti-apoptotic protein, COX2. Whole transcriptome sequencing of RNA from both TNBC and normal breast cells treated with T. violacea extract provided valuable insights into the affected signaling pathways. An antibody array assay further elucidated protein changes in the receptor tyrosine kinase (RTK) pathway. The half-maximal inhibitory concentration (IC50) values were determined for the aqueous and methanol extracts of T. violacea at 400 μg/mL and 820 μg/mL, respectively, and for C. orbiculata at 830 μg/mL and 700 μg/mL, respectively. Exposure to the water-soluble extract of T. violacea resulted in a marked increase in apoptosis in TNBC cells, with approximately 82% undergoing programmed cell death, compared to 32% in normal breast cells. Chemical profiling identified a range of compounds, including 36 distinct compounds identified through GC-MS and 61 identified through NMR, many of which bear structural similarities to known anti-cancer agents. Notably, five compounds demonstrated a high affinity forbinding to COX2, with d-glycero-d-galacto-heptose achieving an impressive docking score, surpassing several established COX2 inhibitors. This study highlights the therapeutic potential of T. violacea compounds and lays the groundwork for further exploration of their mechanisms of action and potential applications in cancer treatment. This emphasises the importance of investigating natural plant extracts as a source for the development of new and effective treatments for TNBC, which is an area of urgent need in oncology