JAK2/STAT5 Pathway Mutation Frequencies in South African BCR/ABL Negative MPN Patients.

BACKGROUND: Mutations in JAK2/STAT5 proliferation pathway genes are key in the diagnosis of myeloproliferative neoplasms (MPNBCR/ABLneg), with JAK2V617F being found in 50-97% of MPNBCR/ABLneg subtypes. Low JAK2V617F positivity at our facility suggested that our South African MPNBCR/ABLneg population may have a different mutational landscape. OBJECTIVES: We aimed to determine the JAK2/STAT5 mutation frequencies associated with our local MPNBCR/ABLneg population, thus determining the relevance of these molecular tests in this group. We also investigated the haematopathological relevance of each test request, to assess testing practises. METHOD: This study involved the retrospective audit of 886 patients for whom JAK2V617F mutation testing had been requested for a suspected MPN diagnosis. FBC indices, erythropoietin levels and bone marrow biopsy results were used to classify the patients. JAK2V617F negative patient DNA was tested for calreticulin (CALR) exon9, myeloproliferative leukaemia protein (MPL) codon515 and JAK2 exon12 mutations. RESULTS: Only 23% of the patients demonstrated JAK2V617F positivity, with an additional 29 cases of CALR/MPL mutations being detected. Mutations were only detected in patients with abnormal FBC indices, as expected, yet 37% of the test requests were not associated with abnormal parameters at the time of testing. Mutation frequencies were as follows: Polycythaemia Vera: 97% JAK2V617F/3% (JAK2, CALR, MPL) triple negative; Essential thrombocythemia: 72% JAK2V617F/23%CALR/5%triple negative; Primary Myelofibrosis: 78%JAK2V617F/16%CALR/6%triple negative. CONCLUSION: Our study demonstrated that our MPNBCR/ABLneg patients have a similar genetic landscape to other MPN populations, with >93% being able to be diagnosed by testing for the JAK2V617F and CALR exon9 mutations alone. Adoption of the WHO 2016 guidelines is recommended to guide testing practices.

Cytogenetically Normal Acute Myeloid Leukaemia at a Single Centre in South Africa.

BACKGROUND AND OBJECTIVES: The heterogeneous molecular landscape of cytogenetically normal acute myeloid leukemia (CN-AML) renders it an ongoing therapeutic challenge. The European LeukemiaNet (ELN) 2017 guidelines attempted to address this by guiding post-remission therapy according to six prognostically informative mutations. However, its applicability in a South African setting remains unclear due to limited local data. This retrospective study aimed to describe a South African CN-AML cohort according to clinicopathological and molecular features as well as treatment outcomes and, consequently, to investigate the local applicability of a triple-mutation testing approach for risk stratification in accordance with the ELN 2017 guidelines, using nucleophosmin 1 (NPM1), fms-related receptor tyrosine kinase 3 internal tandem duplication (FLT3-ITD), and CCAAT enhancer-binding protein alpha (CEBPA) mutation status. MATERIALS AND METHODS: A review of cytogenetic results for adult de novo AML cases diagnosed at Groote Schuur Hospital between 2005 and 2018 was performed. CN-AML cases were further characterized via a review of clinical and laboratory data and additional molecular testing on stored DNA samples to allow for mutation-based risk stratification and outcome analysis. RESULTS: In total, 218 patients with AML were identified, of which 33% were cytogenetically normal. NPM1, FLT3-ITD, and CEBPA mutations were found in 39%, 34%, and 9% of CN-AML cases, respectively. Retrospective risk stratification according to mutations in these three genes accurately identified both patients at a high risk of induction-resistant disease and those who required an allogeneic stem cell transplant in their first complete remission. CONCLUSION: Local rates of CN-AML and associated NPM1 and FLT3-ITD mutations were comparable to those of European cohorts. Limited mutation analysis in the form of triple-mutation testing proved to be an economical and therapeutically informative prognostication approach for CN-AML in a resource-limited setting.

The expression of multiple cancer/testis antigens can potentially be used to detect circulating disease and clonal evolution in the peripheral blood of multiple myeloma patients.

BACKGROUND: It is thought that cancer/testis antigens (CTAs) are expressed in a cascade-like manner in multiple myeloma as the disease progresses. In this pilot study, we investigated the co-expression of several CTAs in the peripheral blood (PB) during patient therapy to establish whether monitoring multiple CTAs allows for the prediction of relapse and clonal evolution. METHODS: We examined the co-expression of MAGEC1, MAGEA3, PRAME, and BAGE2 via quantitative reverse transcription-polymerase chain reaction (qRT-PCR) duplex assays in the PB mononuclear cells of 10 patients on chemotherapy at 3-month intervals, and correlated the levels to those of two basic clinical monitoring markers, serum -2-microglobulin and serum M protein. Clonal evolution was investigated using flow cytometry to label the circulating malignant stem cell components with MAGEC1, PRAME, and MAGEA3 antibodies. RESULTS: Simultaneous monitoring of MAGEC1/PRAME provided sensitive detection of circulating malignant cells in easily accessible PB samples; transcript levels increased prior to changes in indicators of clinical relapse. While MAGEA3/BAGE2 expression levels did not offer earlier prediction of relapse, they provided insight into significant changes occurring within the malignant cell population; the addition of either CTA to a MAGEC1-monitoring panel allowed for better classification of the relapse event (clonal evolution), which in turn could potentially guide treatment strategies in the future. CONCLUSION: This pilot study supports the novel idea of determining the levels and CTA expression patterns of the total circulating malignant cell population (pro-B/pre-B stem cell progenitors and proliferating plasma cells) as an alternate disease monitoring methodology.

The role of Cancer/Testis Antigens in Multiple Myeloma pathogenesis and their application in disease monitoring and therapy.

A unique group of genes, encoding tumour associated antigens, known as the Cancer/Testis Antigens (CTAs), have been explored as novel markers of disease progression and as targets of immunotherapy in several cancers, including the haematological malignancy Multiple Myeloma (MM). This review aims to update the knowledge of CTA involvement in MM pathogenesis and how their potential as biomarkers for disease monitoring and targets of immunotherapy has been explored in the MM disease arena. Despite the initial promise of these antigens, their use as immunotherapy targets has not been successful, yet with a greater understanding of their role in disease pathogenesis they may still have a significant role to play as biomarkers of disease and therapeutic targets.

Cancer testis antigen MAGE C1 can be used to monitor levels of circulating malignant stem cells in the peripheral blood of multiple myeloma patients.

PURPOSE: Monitoring the levels of malignant disease-causing cells in multiple myeloma, as opposed to the clinical symptoms alone, is an important move forward in the management of this disease. While current methods including multiparametric flow cytometry and PCR analysis of the clonal plasma cells can be used in a patient-specific manner, their use is limited and the fundamental malignant progenitor cell is not being monitored. The expression of cancer testis antigen MAGE C1 has been linked to the malignant stem cell in this disease, and thus, we investigated the use of both flow cytometric and qRTPCR approaches to monitor its expression as an alternative monitoring methodology in this pilot study. METHODS: We compared the levels of MAGE C1 in the peripheral blood to serum M protein and serum beta 2 microglobulin levels at 3-monthly intervals over a 2-year period, for 12 patients on chemotherapy regimens and 4 patients undergoing stem cell transplantation. RESULTS AND CONCLUSIONS: The analysis indicated that the novel flow cytometric analysis of MAGE C1 expression in the peripheral blood was extremely relevant as a potential minimal residual disease-monitoring tool. Expression of this cancer testis antigen was detectable in all patients throughout treatment, with comparable increases and decreases to serum M protein and/or serum beta 2 microglobulin, but with the advantage of being able to detect disease at a more sensitive level. Furthermore, due to the increased sensitivity, the ability to pre-empt disease relapse before clinical changes were evident, was preliminarily indicated. The qRTPCR approach showed potential as a monitoring tool in the chemotherapy patient cohort, with the mRNA MAGE C1 levels following a similar pattern of expression observed in the flow cytometry analysis.

The use of MAGE C1 and flow cytometry to determine the malignant cell type in multiple myeloma.

The malignant cell phenotype of Multiple Myeloma (MM) remains unclear with studies proposing it to be either clonotypic B or proliferating plasma cells. Cancer/testis antigen MAGE C1 is being extensively studied in MM and it has been suggested that it is involved in the pathogenesis of the cancer. Therefore, we report on the use of MAGE C1 to determine the malignant cell phenotype in MM using flow cytometry. Bone marrow aspirate (BM) and peripheral blood (PB) was collected from twelve MM patients at diagnosis, as well as three MM disease-free controls. Mononuclear cells were isolated using density-gradient centrifugation, and stabilized in 80% ethanol, before analysis via flow cytometry using relevant antibodies against B cell development cell-surface markers and nuclear MAGE C1. MAGE C1 expression was observed consistently in the early stem cells (CD34+) and early pro-B to pre-B cells (CD34+/-/CD19+), as well as the proliferating plasma cells in both the MM PB and BM, while no expression was observed in the corresponding control samples. Monoclonality indicated a common origin of these cell types suggesting that the CD34+/MAGE C1+ are the primary malignant cell phenotype that sustains the downstream B cell maturation processes. Furthermore, this malignant cell phenotype was not restricted to the BM but also found in the circulating PB cells.

The validation of forensic DNA extraction systems to utilize soil contaminated biological evidence.

The production of full DNA profiles from biological evidence found in soil has a high failure rate due largely to the inhibitory substance humic acid (HA). Abundant in various natural soils, HA co-extracts with DNA during extraction and inhibits DNA profiling by binding to the molecular components of the genotyping assay. To successfully utilize traces of soil contaminated evidence, such as that found at many murder and rape crime scenes in South Africa, a reliable HA removal extraction system would often be selected based on previous validation studies. However, for many standard forensic DNA extraction systems, peer-reviewed publications detailing the efficacy on soil evidence is either lacking or is incomplete. Consequently, these sample types are often not collected or fail to yield suitable DNA material due to the use of unsuitable methodology. The aim of this study was to validate the common forensic DNA collection and extraction systems used in South Africa, namely DNA IQ, FTA elute and Nucleosave for processing blood and saliva contaminated with HA. A forensic appropriate volume of biological evidence was spiked with HA (0, 0.5, 1.5 and 2.5 mg/ml) and processed through each extraction protocol for the evaluation of HA removal using QPCR and STR-genotyping. The DNA IQ magnetic bead system effectively removed HA from highly contaminated blood and saliva, and generated consistently acceptable STR profiles from both artificially spiked samples and crude soil samples. This system is highly recommended for use on soil-contaminated evidence over the cellulose card-based systems currently being preferentially used for DNA sample collection.

Development of a flow cytometric method to detect the presence of mutated nucleophosmin 1 in acute myeloid leukemia.

OBJECTIVE/BACKGROUND: Nucleophosmin 1 (NPM1) plays multiple roles in cell growth and proliferation. Deletion/insertion mutations in exon 12 of NPM1 (NPM1-DIM), commonly found in patients with acute myeloid leukemia (AML), alter the C-terminal amino acids and disrupt the normal nucleocytoplasmic shuttling function of the protein, which in turn leads to disease pathogenesis. However, this altered function as a result of NPM1-DIM positivity is actually associated with a significantly better response to therapy and overall survival, and thus it is of clinical relevance to investigate the mutation status at diagnosis. Our objective was to design a reliable flow cytometry assay to detect mutated NPM1 in peripheral blood (PB) samples from AML patients, using a polyclonal mutation-specific antibody. METHODS: A commercially available NPM1 mutation-specific polyclonal antibody in combination with a secondary goat antirabbit antibody was used to detect the C-terminal-mutated NPM1 by flow cytometry. OCI/AML3 (+) cell line and clinical PB controls were used to optimize the assay and determine sensitivity, reliability, and reproducibility parameters. The assay was then tested on a small cohort of 12 AML patients at diagnosis and compared with NPM1-DIM testing on a standard polymerase chain reaction (PCR) platform. RESULTS: Flow cytometry using the polyclonal antibody was able to reliably detect mutated NPM1 populations of at least 10%. Using an objective analysis of the mean fluorescent intensity, clear positive and negative mutated cell populations could be distinguished using the clinical AML samples. From the analysis of 12 patients, 2 were found to be positive using this assay, which corresponded with conventional PCR methodology. CONCLUSIONS: Flow cytometry may be used to detect NPM1 C-terminal mutations in AML patients using a polyclonal anti-NPM1 antibody, allowing rapid mutation status determination at diagnosis.

Serine and proline-rich ligands enriched via phage-display technology show preferential binding to BCR/ABL expressing cells.

BACKGROUND AND OBJECTIVES: Despite the use of targeted therapy, chronic myelogenous leukemia (CML) currently remains incurable with drug therapy, with patients requiring life-long treatment. Developing either a vaccine to prevent the disease or another novel drug to specifically target and eradicate the CML cell will require the identification of CML-associated cell-surface markers and molecules that can bind specifically to the cell surface. In an attempt to discover peptides that bind specifically to cells in the early chronic phase of the disease, we used phage-display technology to identify heptapeptides that bind specifically to the surface of BCR/ABL-expressing fibroblasts. METHODS: An in vitro system using NIH3T3 stably transfected with pGD210 (BCR/ABL) was used as a model for the chronic phase of the disease. The cells were panned using a linear heptapeptide phage library (Ph.D 7.0) in a negative/positive panning strategy with NIH3T3 containing only the plasmid vector as the wild type control. RESULTS: We identified four novel peptides that were enriched through this technique. These peptides contained either multiple proline residues or serine/threonine-proline pairs and showed a confirmed binding preference for BCR/ABL+ fibroblasts. The peptide Y-R-A-P-W-P-P also showed a binding affinity for granulocytes from untreated CML patients. CONCLUSION: We have identified several novel peptides that can be used in future studies to identify specific CML cell-surface antigens or provide a novel drug-delivery mechanism.