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?