{"id":{"repo_id":"cape-town","oai_identifier":"oai:open.uct.ac.za:11427/23722"},"canonical_url":"https://search.dev.ndltd.org/etd/cape-town/oai:open.uct.ac.za:11427/23722","repository":{"repo_id":"cape-town","name":"University of Cape Town","base_url":"https://open.uct.ac.za/oai/request"},"display":{"title":"Investigating the functionality of African-specific variants in the TGFB1 regulatory region and their potential role in HIV-associated kidney complications","abstract":"Transforming growth factor beta-1 (TGF-β1) is a cytokine involved in immune modulation and tissue regeneration and has a polymorphic TGFB1 promoter. African-specific single nucleotide polymorphisms (SNPs) have been identified in the TGFB1 promoter and they occur at higher frequencies in South Africans with African-genetic ancestry (≈17%) compared with West and East African genomes (<5%). However, the functional significance of these SNPs has only been partially explored. In this study it was hypothesized that higher frequencies of immunemediated disease complications in South Africans, such as HIV-associated nephropathy (HIVAN), may be influenced by functional genetic variations in TGFB1. To address this, the African-specific TGFB1 haplotypes containing singular, or combinations of, -1287 G>A (rs11466314), -1154 C>T (rs35318502), -387 C>T (rs11466316) and -14 G>A (rs9282871) were investigated for their effect on TGFB1 promoter activity. Briefly, an extended TGFB1 regulatory region driving a luciferase reporter was used as a template to generate six TGFB1 promoter haplotypes (referred to as H-1 through H-6 in this thesis) by site-directed mutagenesis and luciferase activity was used to measure promoter activity. The functional TGFB1 -1347 C>T variant was also investigated (H-5 and H-6 containing -1347 C and T alleles, respectively) because all four of the African variants more frequently co-occurred with the previously reported \"lower expressing\" TGFB1 -1347 C variant (H-1 through H- 4). Transient transfection of the TGFB1 promoter reporter constructs in two renal cell lines (RCC4+VHL and Caki- 2) showed no difference between -1347 C (H-5) and T (H-6) basal promoter activity. Having at least one African variant resulted in ~5-fold loss of basal TGFB1 promoter activity in renal cells when compared to the most common haplotype (H-5) (p<0.05). The repressive effect is mainly attributed to the -387 T variant (H-1) as the addition of other African variants on this haplotype showed no additional TGFB1 promoter repression. The repressive effect of the TGFB1 -387 T variant was maintained even after in-vitro treatment of transfected renal cells with recombinant human TGF-β1 (rhTGF-β1). To determine whether the African-specific TGFB1 promoter haplotypes (H-AFR), containing TGFB1 -387 T and tested in luciferase assays, also impact on endogenous TGF-β1 protein levels, western blot analysis was performed on human dermal fibroblasts from patients who had been genotyped. Similar to the promoter studies, basal TGF- β1 protein levels in cells with the H-AFR were ~47% lower compared to cells without (p=0.04) and no difference was seen in response to hrTGF-β1. Interestingly, when western blots were screened for phosphorylated Smad3 (pSmad3) protein levels, as an indicator of the activated TGF-β1 canonical pathway, similar pSmad3 levels were observed under basal and hrTGF-β1 stimulated conditions for all haplotypes (p>0.05). The possible interaction of HIV tat on the African TGFB1 promoter variants was also assessed. Luciferase activity was measured after co-transfecting renal RCC4+VHL and HT1080 fibroblast cells with a HIV Tat expression vector and the H-6, H-5 and H-AFR promoter luciferase constructs. Results showed that the promoter activity for all TGFB1 haplotypes was upregulated in the renal cells (≥1.6-fold; p<0.001). The same result was, however, only observed for TGFB1 haplotypes H-5 and H-AFR in the fibroblast cells (≥1.4-fold; p<0.01). This is interesting because no difference was seen between TGFB1 H-5 and H-6 basal promoter activity. To investigate whether histopathological severity of HIVAN correlated with TGF-β1 staining patterns, immunohistochemistry was performed on 20 renal biopsies from patients with HIVAN. A semi-quantitative \"histo\" score (H-score) was calculated by multiplying the percentage of positive cells with the intensity of the stain before comparing the scores with control biopsies (HIV-negative, n=3 and HIV-positive without HIVAN, n=3). Compared to the HIV-positive controls the kidney tubules of HIVAN biopsies had higher H-scores. Strikingly, the interstitium of HIVAN samples stained much more prominently (17/18) than both control groups suggesting that TGF-β1 staining in the renal interstitium appear to be specific for HIVAN. In conclusion this study shows that the African-specific haplotypes effect basal TGFB1 promoter activity and TGF-β1 protein levels. However, they do not seem to affect the cytoplasmic TGF-β1/pSmad3 protein levels in response to rhTGF-β1 autocrine stimulation. Immunohistochemistry results suggest that TGF-β1 pathway may be prominently dysregulated in the renal interstitium of HIVAN cases.","abstract_html":"Transforming growth factor beta-1 (TGF-β1) is a cytokine involved in immune modulation and tissue regeneration and has a polymorphic TGFB1 promoter. African-specific single nucleotide polymorphisms (SNPs) have been identified in the TGFB1 promoter and they occur at higher frequencies in South Africans with African-genetic ancestry (≈17%) compared with West and East African genomes (&lt;5%). However, the functional significance of these SNPs has only been partially explored. In this study it was hypothesized that higher frequencies of immunemediated disease complications in South Africans, such as HIV-associated nephropathy (HIVAN), may be influenced by functional genetic variations in TGFB1. To address this, the African-specific TGFB1 haplotypes containing singular, or combinations of, -1287 G&gt;A (rs11466314), -1154 C&gt;T (rs35318502), -387 C&gt;T (rs11466316) and -14 G&gt;A (rs9282871) were investigated for their effect on TGFB1 promoter activity. Briefly, an extended TGFB1 regulatory region driving a luciferase reporter was used as a template to generate six TGFB1 promoter haplotypes (referred to as H-1 through H-6 in this thesis) by site-directed mutagenesis and luciferase activity was used to measure promoter activity. The functional TGFB1 -1347 C&gt;T variant was also investigated (H-5 and H-6 containing -1347 C and T alleles, respectively) because all four of the African variants more frequently co-occurred with the previously reported &quot;lower expressing&quot; TGFB1 -1347 C variant (H-1 through H- 4). Transient transfection of the TGFB1 promoter reporter constructs in two renal cell lines (RCC4+VHL and Caki- 2) showed no difference between -1347 C (H-5) and T (H-6) basal promoter activity. Having at least one African variant resulted in ~5-fold loss of basal TGFB1 promoter activity in renal cells when compared to the most common haplotype (H-5) (p&lt;0.05). The repressive effect is mainly attributed to the -387 T variant (H-1) as the addition of other African variants on this haplotype showed no additional TGFB1 promoter repression. The repressive effect of the TGFB1 -387 T variant was maintained even after in-vitro treatment of transfected renal cells with recombinant human TGF-β1 (rhTGF-β1). To determine whether the African-specific TGFB1 promoter haplotypes (H-AFR), containing TGFB1 -387 T and tested in luciferase assays, also impact on endogenous TGF-β1 protein levels, western blot analysis was performed on human dermal fibroblasts from patients who had been genotyped. Similar to the promoter studies, basal TGF- β1 protein levels in cells with the H-AFR were ~47% lower compared to cells without (p=0.04) and no difference was seen in response to hrTGF-β1. Interestingly, when western blots were screened for phosphorylated Smad3 (pSmad3) protein levels, as an indicator of the activated TGF-β1 canonical pathway, similar pSmad3 levels were observed under basal and hrTGF-β1 stimulated conditions for all haplotypes (p&gt;0.05). The possible interaction of HIV tat on the African TGFB1 promoter variants was also assessed. Luciferase activity was measured after co-transfecting renal RCC4+VHL and HT1080 fibroblast cells with a HIV Tat expression vector and the H-6, H-5 and H-AFR promoter luciferase constructs. Results showed that the promoter activity for all TGFB1 haplotypes was upregulated in the renal cells (≥1.6-fold; p&lt;0.001). The same result was, however, only observed for TGFB1 haplotypes H-5 and H-AFR in the fibroblast cells (≥1.4-fold; p&lt;0.01). This is interesting because no difference was seen between TGFB1 H-5 and H-6 basal promoter activity. To investigate whether histopathological severity of HIVAN correlated with TGF-β1 staining patterns, immunohistochemistry was performed on 20 renal biopsies from patients with HIVAN. A semi-quantitative &quot;histo&quot; score (H-score) was calculated by multiplying the percentage of positive cells with the intensity of the stain before comparing the scores with control biopsies (HIV-negative, n=3 and HIV-positive without HIVAN, n=3). Compared to the HIV-positive controls the kidney tubules of HIVAN biopsies had higher H-scores. Strikingly, the interstitium of HIVAN samples stained much more prominently (17/18) than both control groups suggesting that TGF-β1 staining in the renal interstitium appear to be specific for HIVAN. In conclusion this study shows that the African-specific haplotypes effect basal TGFB1 promoter activity and TGF-β1 protein levels. However, they do not seem to affect the cytoplasmic TGF-β1/pSmad3 protein levels in response to rhTGF-β1 autocrine stimulation. Immunohistochemistry results suggest that TGF-β1 pathway may be prominently dysregulated in the renal interstitium of HIVAN cases.","abstract_has_math":false,"creators":["Buys, Joy-Mari"],"institution":"Department of Human Biology","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Heckmann, Jeannine M","Prince, Sharon","Nel, Melissa"],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016","date_published":"2016","updated_at":"2026-07-22T22:22:38Z","subjects":[],"languages":["eng"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/11427/23722","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Heckmann, Jeannine M","Prince, Sharon","Nel, Melissa"]},{"key":"dc:creator","label":"Author","values":["Buys, Joy-Mari"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2017-01-30T10:52:19Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2017-01-30T10:52:19Z"]},{"key":"dc:date.issued","label":"Date","values":["2016"]},{"key":"dc:publisher.department","label":"Dc Publisher Department","values":["Department of Human Biology"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Cape Town"]},{"key":"dc:type","label":"Dc Type","values":["Master Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Masters"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["MSc (Med)"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["eng"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/11427/23722"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Transforming growth factor beta-1 (TGF-β1) is a cytokine involved in immune modulation and tissue regeneration and has a polymorphic TGFB1 promoter. African-specific single nucleotide polymorphisms (SNPs) have been identified in the TGFB1 promoter and they occur at higher frequencies in South Africans with African-genetic ancestry (≈17%) compared with West and East African genomes (<5%). However, the functional significance of these SNPs has only been partially explored. In this study it was hypothesized that higher frequencies of immunemediated disease complications in South Africans, such as HIV-associated nephropathy (HIVAN), may be influenced by functional genetic variations in TGFB1. To address this, the African-specific TGFB1 haplotypes containing singular, or combinations of, -1287 G>A (rs11466314), -1154 C>T (rs35318502), -387 C>T (rs11466316) and -14 G>A (rs9282871) were investigated for their effect on TGFB1 promoter activity. Briefly, an extended TGFB1 regulatory region driving a luciferase reporter was used as a template to generate six TGFB1 promoter haplotypes (referred to as H-1 through H-6 in this thesis) by site-directed mutagenesis and luciferase activity was used to measure promoter activity. The functional TGFB1 -1347 C>T variant was also investigated (H-5 and H-6 containing -1347 C and T alleles, respectively) because all four of the African variants more frequently co-occurred with the previously reported \"lower expressing\" TGFB1 -1347 C variant (H-1 through H- 4). Transient transfection of the TGFB1 promoter reporter constructs in two renal cell lines (RCC4+VHL and Caki- 2) showed no difference between -1347 C (H-5) and T (H-6) basal promoter activity. Having at least one African variant resulted in ~5-fold loss of basal TGFB1 promoter activity in renal cells when compared to the most common haplotype (H-5) (p<0.05). The repressive effect is mainly attributed to the -387 T variant (H-1) as the addition of other African variants on this haplotype showed no additional TGFB1 promoter repression. The repressive effect of the TGFB1 -387 T variant was maintained even after in-vitro treatment of transfected renal cells with recombinant human TGF-β1 (rhTGF-β1). To determine whether the African-specific TGFB1 promoter haplotypes (H-AFR), containing TGFB1 -387 T and tested in luciferase assays, also impact on endogenous TGF-β1 protein levels, western blot analysis was performed on human dermal fibroblasts from patients who had been genotyped. Similar to the promoter studies, basal TGF- β1 protein levels in cells with the H-AFR were ~47% lower compared to cells without (p=0.04) and no difference was seen in response to hrTGF-β1. Interestingly, when western blots were screened for phosphorylated Smad3 (pSmad3) protein levels, as an indicator of the activated TGF-β1 canonical pathway, similar pSmad3 levels were observed under basal and hrTGF-β1 stimulated conditions for all haplotypes (p>0.05). The possible interaction of HIV tat on the African TGFB1 promoter variants was also assessed. Luciferase activity was measured after co-transfecting renal RCC4+VHL and HT1080 fibroblast cells with a HIV Tat expression vector and the H-6, H-5 and H-AFR promoter luciferase constructs. Results showed that the promoter activity for all TGFB1 haplotypes was upregulated in the renal cells (≥1.6-fold; p<0.001). The same result was, however, only observed for TGFB1 haplotypes H-5 and H-AFR in the fibroblast cells (≥1.4-fold; p<0.01). This is interesting because no difference was seen between TGFB1 H-5 and H-6 basal promoter activity. To investigate whether histopathological severity of HIVAN correlated with TGF-β1 staining patterns, immunohistochemistry was performed on 20 renal biopsies from patients with HIVAN. A semi-quantitative \"histo\" score (H-score) was calculated by multiplying the percentage of positive cells with the intensity of the stain before comparing the scores with control biopsies (HIV-negative, n=3 and HIV-positive without HIVAN, n=3). Compared to the HIV-positive controls the kidney tubules of HIVAN biopsies had higher H-scores. Strikingly, the interstitium of HIVAN samples stained much more prominently (17/18) than both control groups suggesting that TGF-β1 staining in the renal interstitium appear to be specific for HIVAN. In conclusion this study shows that the African-specific haplotypes effect basal TGFB1 promoter activity and TGF-β1 protein levels. However, they do not seem to affect the cytoplasmic TGF-β1/pSmad3 protein levels in response to rhTGF-β1 autocrine stimulation. Immunohistochemistry results suggest that TGF-β1 pathway may be prominently dysregulated in the renal interstitium of HIVAN cases."]},{"key":"dc:title","label":"Title","values":["Investigating the functionality of African-specific variants in the TGFB1 regulatory region and their potential role in HIV-associated kidney complications"]}]}],"canonical_facts":{"dc:contributor.advisor":["Heckmann, Jeannine M","Prince, Sharon","Nel, Melissa"],"dc:creator":["Buys, Joy-Mari"],"dc:date.accessioned":["2017-01-30T10:52:19Z"],"dc:date.available":["2017-01-30T10:52:19Z"],"dc:date.issued":["2016"],"dc:description.abstract":["Transforming growth factor beta-1 (TGF-β1) is a cytokine involved in immune modulation and tissue regeneration and has a polymorphic TGFB1 promoter. African-specific single nucleotide polymorphisms (SNPs) have been identified in the TGFB1 promoter and they occur at higher frequencies in South Africans with African-genetic ancestry (≈17%) compared with West and East African genomes (<5%). However, the functional significance of these SNPs has only been partially explored. In this study it was hypothesized that higher frequencies of immunemediated disease complications in South Africans, such as HIV-associated nephropathy (HIVAN), may be influenced by functional genetic variations in TGFB1. To address this, the African-specific TGFB1 haplotypes containing singular, or combinations of, -1287 G>A (rs11466314), -1154 C>T (rs35318502), -387 C>T (rs11466316) and -14 G>A (rs9282871) were investigated for their effect on TGFB1 promoter activity. Briefly, an extended TGFB1 regulatory region driving a luciferase reporter was used as a template to generate six TGFB1 promoter haplotypes (referred to as H-1 through H-6 in this thesis) by site-directed mutagenesis and luciferase activity was used to measure promoter activity. The functional TGFB1 -1347 C>T variant was also investigated (H-5 and H-6 containing -1347 C and T alleles, respectively) because all four of the African variants more frequently co-occurred with the previously reported \"lower expressing\" TGFB1 -1347 C variant (H-1 through H- 4). Transient transfection of the TGFB1 promoter reporter constructs in two renal cell lines (RCC4+VHL and Caki- 2) showed no difference between -1347 C (H-5) and T (H-6) basal promoter activity. Having at least one African variant resulted in ~5-fold loss of basal TGFB1 promoter activity in renal cells when compared to the most common haplotype (H-5) (p<0.05). The repressive effect is mainly attributed to the -387 T variant (H-1) as the addition of other African variants on this haplotype showed no additional TGFB1 promoter repression. The repressive effect of the TGFB1 -387 T variant was maintained even after in-vitro treatment of transfected renal cells with recombinant human TGF-β1 (rhTGF-β1). To determine whether the African-specific TGFB1 promoter haplotypes (H-AFR), containing TGFB1 -387 T and tested in luciferase assays, also impact on endogenous TGF-β1 protein levels, western blot analysis was performed on human dermal fibroblasts from patients who had been genotyped. Similar to the promoter studies, basal TGF- β1 protein levels in cells with the H-AFR were ~47% lower compared to cells without (p=0.04) and no difference was seen in response to hrTGF-β1. Interestingly, when western blots were screened for phosphorylated Smad3 (pSmad3) protein levels, as an indicator of the activated TGF-β1 canonical pathway, similar pSmad3 levels were observed under basal and hrTGF-β1 stimulated conditions for all haplotypes (p>0.05). The possible interaction of HIV tat on the African TGFB1 promoter variants was also assessed. Luciferase activity was measured after co-transfecting renal RCC4+VHL and HT1080 fibroblast cells with a HIV Tat expression vector and the H-6, H-5 and H-AFR promoter luciferase constructs. Results showed that the promoter activity for all TGFB1 haplotypes was upregulated in the renal cells (≥1.6-fold; p<0.001). The same result was, however, only observed for TGFB1 haplotypes H-5 and H-AFR in the fibroblast cells (≥1.4-fold; p<0.01). This is interesting because no difference was seen between TGFB1 H-5 and H-6 basal promoter activity. To investigate whether histopathological severity of HIVAN correlated with TGF-β1 staining patterns, immunohistochemistry was performed on 20 renal biopsies from patients with HIVAN. A semi-quantitative \"histo\" score (H-score) was calculated by multiplying the percentage of positive cells with the intensity of the stain before comparing the scores with control biopsies (HIV-negative, n=3 and HIV-positive without HIVAN, n=3). Compared to the HIV-positive controls the kidney tubules of HIVAN biopsies had higher H-scores. Strikingly, the interstitium of HIVAN samples stained much more prominently (17/18) than both control groups suggesting that TGF-β1 staining in the renal interstitium appear to be specific for HIVAN. In conclusion this study shows that the African-specific haplotypes effect basal TGFB1 promoter activity and TGF-β1 protein levels. However, they do not seem to affect the cytoplasmic TGF-β1/pSmad3 protein levels in response to rhTGF-β1 autocrine stimulation. Immunohistochemistry results suggest that TGF-β1 pathway may be prominently dysregulated in the renal interstitium of HIVAN cases."],"dc:identifier.uri":["http://hdl.handle.net/11427/23722"],"dc:language.iso":["eng"],"dc:publisher.department":["Department of Human Biology"],"dc:publisher.institution":["University of Cape Town"],"dc:title":["Investigating the functionality of African-specific variants in the TGFB1 regulatory region and their potential role in HIV-associated kidney complications"],"dc:type":["Master Thesis"],"dc:type.qualificationlevel":["Masters"],"dc:type.qualificationname":["MSc (Med)"]},"updated_at":"2026-07-22T22:22:38Z"}