Masters Degrees (Haematological Pathology)

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    Screening and characterisation of BCR::ABL1 kinase domain mutations in chronic myeloid leukaemia participants at Tygerberg Hospital, South Africa
    (Stellenbosch : Stellenbosch University, 2023-03) Shareefa, Isaacs; Swanepoel, Carmen; Chapanduka, Zivanai; Stellenbosch University. Faculty of Medicine and Health Science. Dept. of Pathology. Haematological Pathology.
    ENGLISH SUMMARY: To date, an increased number of drug resistant cancers have been observed. The underlying mechanisms are not well understood; therefore, we use Chronic Myeloid Leukaemia (CML) as a disease model to explore the type and frequencies of potential drug resistant causing mutations and the effect on survival at Tygerberg Hospital (TBH). The underlying genetic abnormality is a t(9::22) chromosomal translocation, and consequent fusion between the Breakpoint Cluster Region and the Non-Receptor Tyrosine Kinase Abelson genes (BCR::ABL1). Although Tyrosine Kinase Inhibitors (TKD), such as Imatinib (Gleevec), effectively decrease BCR::ABL1 mRNA transcript levels whereby the drug acts on the protein and inhibits its mode of action, point mutations within the kinase domain (KD) have shown to confer resistance to treatments. A retrospective audit was conducted on a CML cohort from 2013 to 2020, and 20 of these participants were recruited for detection of KD mutations within the ABL1 oncogene. Peripheral blood from routine diagnostic screening by the NHLS Molecular Haematology diagnostic laboratory were obtained for the mutation detection assay via bi-directional Sanger Sequencing. Identified sequence variants were then subjected to various bioinformatics tools to investigate variant, protein, and consequent effect on pathways. For the audit, a total of 165 patients with confirmed CML treated at TBH was captured. Descriptive statistics showed 46.1% of CML patients were female, and 53.9% were male. The patients were from 69 different areas in the Northern part of the Cape Metropole and surrounding Boland areas in Western Cape, South Africa. Quantitative analysis showed the youngest patient to be two years old and the oldest 88 years old, x̄ = 45-46 years. We found a weak linear correlation between age and BCR::ABL1 mRNA transcript levels. A significant difference in BCR::ABL1 mRNA transcript levels (p < 0.000) was seen in CML patients on treatment after 1 year. Of interest’s sake, 104 of the initial 165 patients who were diagnosed were still undergoing treatment. Moreover, 57 out of the 165 patients presented with possible resistance; 75% were categorized as failure and 25%at warning stage according to European Leukaemia Net guidelines. In the second part of the study, 20 participants’ samples were screened for variants. The screening sample group had a mortality rate of 20% who had a relative survival rate of less than five years. Sanger sequence analysis showed potential variants of interest in Exon 4 and of the ABL1 gene, although bioinformatics analysis alludes to the fact that these variants are not likely to play a role in resistance. In conclusion, the TBH CML cohort has a younger age at diagnosis which puts a greater strain on the public sector, and a significant number of patients are lost to follow up. More so, the age relative to CML deaths, as well as relative survival greatly differs from literature. Additionally, although synonymous mutations have recently shown to be pathological, the two variants found within our cohort has not been published to do so. CML could be a poster child for personalised medicine as the survival rate of CML patients is nearing that of the general population and treatment-free remission is attainable. Unfortunately, the paucity of CML data, drug availability and monitoring limitations are some of the obstacles that hinders South Africa from achieving these goals.
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    Imatinib resistance : the role of pharmacogenetic variability in a South African chronic myeloid leukemia cohort
    (Stellenbosch : Stellenbosch University, 2023-03) De Long, Chantal; Swanepoel, Carmen; Stellenbosch University. Faculty of Medicine and Health Science. Dept. of Pathology. Haematological Pathology.
    ENGLISH SUMMARY: Drug-resistant cancers are often associated with poor patient outcomes and the underlying mechanism is poorly understood. Chronic Myeloid Leukemia (CML) serves as a disease model for studying cancer drug resistance, specifically to Imatinib, a tyrosine kinase inhibitor. Approximately 20-30% of patients become resistant to Imatinib. Variability in patient drug response could be due to single nucleotide variants (SNVs) in genes that encode for Imatinib-metabolizing enzymes and transporters. The overall aim of the present study is to determine whether selected SNVs located within genes CYP3A4/3A5, SLCO1A2, SLC22A4, and SLC22A1 that encode selected drug transporters (Cytochrome P450, OATP1A2, OCTN1, hOCT1), respectively, contribute to an alternative mechanism leading to Imatinib resistance in a South African cohort. A maximum of 45 samples from Imatinib-resistant CML patients were analysed along with 44 non-resistant CML patients (controls). The selected SNVs were analysed using PCR-based genotyping assays. Baseline allelic and genotypic frequencies within our CML cohort was determined and compared between Imatinib good responders and Imatinib resistant groups. In our study we observed that there were differences in allele frequencies for the following SNVs in genes SLC22A4, SLCO1A2, CYP3A4 and CYP3A5 when compared to the global/African frequencies. Furthermore, obtained results showed that the observed and expected genotype frequencies were comparable for genes SLC22A1, SLC22A4, and SLCO1A2, however, our observed genotype frequencies were different from the expected genotype frequencies for the following genes SLCO1A2, CYP3A4 and CYP3A5. Interesting findings include, the rs35191146 (ATG>AT: delG) that was linked poor Imatinib treatment outcome, however, the simultaneous presence of rs628031 (A>G: M408V) circumvented this effect. All patients within our cohort have both Met420 and Met408Val. Another interesting finding is the coincidental finding of variants SLC22A4 rs11568500 (c.616_617delinsCC), and SLC22A1 rs35191146 (c.1258_1260delATG and g.160139876_160139883delGTAAGTTG), which would be explored in future studies. Even though the selected SNVs do not affect Imatinib resistance in our cohort, our study to the best of our knowledge is the only study to determine baseline allelic and genotypic frequencies for CML patients treated with Imatinib in South Africa. Therefore, the data obtained from our study can serve as a useful tool to further investigate the pharmacogenetic variability in South Africa. In conclusion, our study adds to the body of knowledge out there related to SNV and its potential clinical relevance related to imatinib resistance especially within our diverse African cohort. This in turn highlights the need for future studies focusing on larger cohorts, with a larger selection of SNVs at more health care institutions across South Africa.
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    Investigating the use of standardized EuroFlow flow cytometry panels for the characterisation and diagnosis of Chronic lymphocytic leukaemia in the Tygerberg Academic Hospital, South Africa.
    (Stellenbosch : Stellenbosch University, 2017-12) Musaigwa, Fungai; Swanepoel, Carmen Catherine-Ann; Stellenbosch University. Faculty of Medicine and Health Science. Dept. of Pathology. Haematological Pathology.
    ENGLISH ABSTRACT : Background: Flow cytometry (FC) immunophenotyping is crucial in the diagnosis and classification standardisation of haematological malignancies. FC techniques require standardisation to produce reliable and reproducible results which are important in inter-laboratory studies for laboratory methodology improvement. The aim of this study is to introduce standardised multicolour FC in the diagnosis of haematological malignancies using chronic lymphocytic leukaemia (CLL) as the proof of principle. In addition, we aim to document the incidence of CLL from the year 2011 to 2016 in the Tygerberg Academic Hospital (TAH) catchment area of Cape Town, South Africa (SA). Methods: Twenty CLL patients were recruited at TAH. Bio-specimens were prepared and analysed on the Beckman Coulter Navios flow cytometer using Euroflow™ standardised FC protocols and immunophenotypic panels with two tubes for detecting B-cell chronic lymphoproliferative disorders (B-CLPD). Tube 1 included CD20, CD4, CD45, CD8, lg-Kappa, CD56, lg-Lambda, CD5, CD19, TCRyσ, CD3 and CD38. Tube 2 included CD20, CD45, CD23, CD10, CD79b, CD19, CD200 and CD43. Combined, the two tubes identified CLL from other B-CLPD. The CLL immunophenotypic profiles were stored in a database using the compass tool of the Infinicyt™ FC software. In addition, the clinical records of patients diagnosed with CLL at TAH over a 6-year period from the year 2011 to 2016 were retrieved and analysed using descriptive statistics. Results: In comparison with the SA National Health Laboratory Service (NHLS) results at TAH, the Euroflow™ standardised multicolour FC panels and protocols are suitable for immunophenotyping CLL in this SA population. An immunophenotype database for 20 CLL diagnosed at TAH was constructed using the EuroFlow™ standardised multicolour FC panels. For the epidemiology part of the study, a total of 80 CLL patients were studied. There were slightly more females (51.2%) and the mean age at diagnosis was 67 years (37 to 95). Ninety one percent of the patients were aged 50 years and above. Males presented with the disease at a younger age (mean 63 years) than females (mean 70 years). CLL concurrent with HIV was not common (4%) and these patients were younger than 50 years. Twenty-one patients were tested for chromosomal aberrations trisomy 12 and deletion 11q, 24% and 33% were positive respectively. Deletion 13q was assessed in 25 patients and 16% were positive. Twenty patients were tested for deletion 17p and all were negative. Translocations t(8;14), t(11;14) and t (14;18) were negative in 1, 8 and 4 patients respective. Discussion: Accurate and consistent laboratory techniques and strict standardisation in FC enhances the confidence in inter-laboratory studies. Establishment of haematological malignancy immunophenotype databases would allow for faster differential diagnoses of new disease cases which is needed within our setting. Furthermore, these databases permit clear identification of atypical cases. Monitoring haematological malignancy trends is a crucial step in the management of the disease.
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    African civil society initiatives to drive a biobanking, biosecurity and infrastructure development agenda in the wake of the West African Ebola outbreak
    (African Field Epidemiology Network, 2016) Abayomi, Akin; Gevao, Sahr; Conton, Brian; Deblasio, Pasquale; Katz, Rebecca
    This paper describes the formation of a civil society consortium, spurred to action by frustration over the Ebola crises, to facilitate the development of infrastructure and frameworks including policy development to support a harmonized, African approach to health crises on the continent. The Global Emerging Pathogens Treatment Consortium, or GET, is an important example of how African academics, scientists, clinicians and civil society have come together to initiate policy research, multilevel advocacy and implementation of initiatives aimed at building African capacity for timely and effective mitigations strategies against emerging infectious and neglected pathogens, with a focus on biobanking and biosecurity. The consortium has been able to establish it self as a leading voice, drawing attention to scientific infrastructure gaps, the importance of cultural sensitivities, and the power of community engagement. The GET consortium demonstrates how civil society can work together, encourage government engagement and strengthen national and regional efforts to build capacity.
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    Evaluation and validation of room temperature biospecimens transportation and storage technologies as an alternative cost effective solution to cold chain logistics and storage within biobanking and/or diagnostics
    (Stellenbosch : Stellenbosch University, 2017-03) Abulfathi, Fatima Adam; Swanepoel, Carmen Catherine-Ann; Grewal, Ravnit Kuar; Abayomi, Akin; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology: Haematological Pathology
    ENGLISH ABSTRACT : Background: Cold chain management (CCM) is an important aspect of biobanking operation. However challenges such as constant power failure, limited access to dry ice transport and storage of human samples collected at various sites all over the world or at difficult out of reach places. and liquid nitrogen, transport logistics and courier delays especially in Africa becomes a major challenge. Ensuring samples are maintained at the proper temperature throughout all processes is imperative to maximal long term viability and usability. Thus we consider room temperature storage (RTS) technologies as an innovative, cost effective and green alternative to cold chain logistics. Methods: Various room temperature storage technologies were evaluated for the stabilization and storage of whole blood DNA and RNA, buffy coat, genomic DNA and urine DNA. The stabilizers include the Biomatrica liquid gard technology and dry matrix technology as well as DNAgenotek Hemagene buffy-coat stabilizers, Paxgene RNA and Norgen urine tubes. Samples were stored with and without a stabilizer under different temperature conditions namely room temperature, 45oC,-80oC, -20oC and liquid nitrogen (- 196oC) over different time periods to determine effect on sample integrity and quality. At the end of each time point DNA/RNA was extracted and the integrity of the samples determined by assessing the concentration, purity and integrity. Further downstream analysis such as polymerase chain reaction (PCR), quantitative real time PCR and DNA sequencing was conducted. In addition, a shipping cost analysis between satellite sites in African and our biobank was done to compare frozen and room temperature shipping. Results The study results show that sample integrity/quality for biospecimens stored at room temperature with stabilizers were comparable and more cost effective than cold chain storage systems. In addition some stabilizers showed better stabilizing properties than others. Conclusion: Room temperature storage provides an innovative and cost effective method of storage and shipping to cold chain management systems (CCM). Green technologies forms a small part of biobanking operations however its results would be beneficial as low energy options for biobanking are particular critical in low resource settings which have infrastructural challenges. In turn, it would also be a more cost-effective option for the transport and storage of human samples collected at various sites all over the world or at difficult out of reach places.