Doctoral Degrees (Chemical Pathology)

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Browsing Doctoral Degrees (Chemical Pathology) by Author "Okunola, Abisola Oyedele"

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    Investigation of the role of vitamin D metabolism in South African breast cancer patients using a pathology-supported genetic testing platform
    (Stellenbosch : Stellenbosch University., 2020-03) Okunola, Abisola Oyedele; Kotze, Maritha J.; Erasmus, Rajiv T.; Zemlin, Annalise E.; Torrorey-Sawe, Rispah; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Chemical Pathology.
    ENGLISH ABSTRACT: The high global breast cancer incidence drives the development of novel genomic approaches for disease prevention and targeted treatment. Towards this goal, a pathology-supported genetic testing (PSGT) platform was established to facilitate risk management of non-communicable diseases across the continuum of care, ranging from early-stage to metastatic disease and cancer survivorship. The causes and consequences of low vitamin D levels recently reported in the majority of postmenopausal breast cancer patients treated with aromatase inhibitors at the Tygerberg Academic Hospital, in the Western Cape Province of South Africa, were addressed in this study using PSGT to translate genomic findings into clinical practice. The aim was to determine the relationship between clinical characteristics, tumour histopathology and genetic variation underlying vitamin D metabolism in postmenopausal breast cancer patients at increased risk of osteoporosis, identified as a significant co-morbidity in the study population. Clinical and lifestyle information of 116 postmenopausal women with known vitamin D status diagnosed with breast carcinoma between 2014 and 2017 was extracted from a central genomics database linked to a biobank of DNA samples extracted from blood. Whole exome sequencing (WES) was performed on the Ion Torrent platform, followed by variant calling of vitamin D-related genes, while simultaneously assessing BRCA1/2 mutation status. Allele-specific real-time polymerase chain reaction (PCR), Sanger sequencing and long-range nanopore sequencing using the pocket-size MinION device were used to verify the WES results and to screen for variants in the vitamin D receptor (VDR) and E-cadherin (CDH1) genes beyond the coding regions covered by WES. Seasonal variation (p = 0.009) and high body mass index (BMI) (p = 0.032) contributed significantly to vitamin D levels, with the lowest values recorded during winter. WES initially performed in 10 breast cancer patients selected based on vitamin D levels at extreme upper and lower ranges, identified GC rs4588 (c.1364C>A, T455K) as a potential contributing factor vitamin D deficiency in the five patients with ultra-low vitamin D levels (≤12 ng/mL). However, 2/5 patients with levels in the upper extreme of vitamin D (>30 ng/mL), also tested positive for this variant and no significant association was detected after extended genotyping in 100 South African patients using real-time PCR. Sanger sequencing subsequently performed in 14 breast cancer patients diagnosed with osteoporosis prior to initiation of aromatase inhibitor therapy, highlighted the potential significance of genetic variation in the VDR gene. WES analysis of VDR in an extended sample of 55 breast cancer patients furthermore confirmed the significant effect of genetic variation in this gene on bone health (p < 0.001). The CDH1 gene known to be activated by VDR was furthermore analysed in patients stratified by tumour type. CDH1 c.G671A (p.R224H) detected in a breast cancer patient with invasive carcinoma of no special type (ICNST) was classified as benign, since pathogenic germline CDH1 variants are associated with invasive lobular carcinoma and diffuse gastric cancer, but not ICNST. CDH1 c.A1298G (p.D433G) was detected in a patient with invasive lobular carcinoma together with a pathogenic BRCA1 variant detected by WES. Although this finding supports a likely benign classification for CDH1 p.D433G as reported in the international ClinVar database, a family history of stomach cancer raised the possibility of a CDH1 modifier gene effect on BRCA1 gene expression. New insights gained through integration of pathology and genomic findings were incorporated into a pharmaco-diagnostic algorithm applicable to hormone receptor-positive postmenopausal breast cancer patients. The PSGT platform facilitated interpretation of research results of study participants through use of WES and recommendation of genetic counselling where appropriate.