Browsing by Author "Duarte, Raquel"

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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, Tanya
African 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 TNBC
Influence of vitamin D receptor polymorphisms on biochemical markers of mineral bone disorders in South African patients with chronic kidney disease
(2018-02) Waziri, Bala; Dix-Peek, Therese; Dickens, Caroline; Duarte, Raquel; Naicker, Saraladevi
Background: It remains unclear whether genetic factors may explain the reported variation in the levels of biochemical markers of chronic kidney disease mineral and bone disorders (CKD- MBD) across ethnic groups. Therefore, the aim of this study was to examine the influence of vitamin D receptor (VDR) polymorphisms on secondary hyperparathyroidism and its association with vitamin D levels in black and white South African study participants. Methods: This was a cross sectional study involving 272 CKD stage 3- 5D patients and 90 healthy controls. The four major VDR polymorphisms (Bsm 1, Fok 1, Taq 1, and Apa1) were genotyped using the polymerase chain reaction- restriction fragment length polymorphism (PCR –RFLP) method. In addition, biochemical markers of CKD-MBD were measured to determine their associations with the four VDR polymorphisms. Results: With the exception of Taq I polymorphism, the distribution of the VDR polymorphisms differed significantly between blacks and whites. In hemodialysis patients, the Bb genotype was significantly associated with moderate secondary hyperparathyroidism (OR, 3.88; 95 CI 1.13–13.25, p = 0.03) and severe hyperparathyroidism (OR, 2.54; 95 CI 1.08–5.96, p = 0.03). This was consistent with the observed higher levels of median parathyroid hormone, fibroblast growth factor 23 and mean phosphate in patients with Bb genotype. This candidate risk genotype (Bb) was over represented in blacks compared to whites (71.0% versus 55.6%, p < 0.0001). In an unadjusted regression model, FokFf genotype was found to be significantly associated with the risk of developing severe vitamin D deficiency < 15 ng/ml (OR, 1.89; 95 CI 1.17–3.07, p = 0.01). Conclusion: The VDR Bb genotype is an independent predictor of developing secondary hyperparathyroidism in patients with end stage kidney disease. In addition, study participants with FokFf genotype are at increased of developing severe 25 -hydroxyvitamin D [25(OH)D] deficiency.
Osteogenic competence and potency of the bone induction principle inductive substrates that initiate bone formation by autoinduction
Ripamonti, Ugo; Duarte, Raquel ; Ferretti, Carlo ; Reddi, H.
The de novo induction of bone has always been a fascinating phenomenon, keeping skeletal reconstructionists and cellular developmental biologists continuously engaged to finally provide a molecular and cellular approach to the induction of bone formation. A significant advancement was made by the purification and cloning of the human recombinant bone morphogenetic proteins, members of the transforming growth factor-b supergene family. Human bone morphogenetic proteins are powerful inducers of bone in animal models including nonhuman primates. Translation in clinical contexts has however, proven to be surprisingly difficult. This review also describes the significant induction of bone formation by the human transforming growth factor-b3 when implanted in heterotopic intramuscular sites of the Chacma baboon Papio ursinus. Large mandibular defects implanted with 250mg human transforming growth factor-b3 in human patients showed significant osteoinduction; however, the induction of bone was comparatively less than the induction of bone in P ursinus once again highlighting the conundrum of human osteoinduction: is the bone induction principle failing clinical translation?
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, Caroline
Background: 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.