A utilização de Inibidores da Tirosino Quinase (ITQ) alterou drasticamente a expectativa de vida do paciente com Leucemia Mielóide Crônica (LMC) e o monitoramento da expressão do oncogene BCR-ABL1 tornou-se um fator prognóstico fundamental para avaliação da resposta ao tratamento. Atualmente, a necessidade de desenvolvimento de metodologias moleculares que facilitem a quantificação rápida, barata e sensível, associada à detecção precoce de baixos níveis de BCR-ABL1, tem proporcionado o surgimento de diversos ensaios comerciais para monitoramento molecular. Entretanto, estes kits possuem uma variabilidade na sua composição, execução e parâmetros analíticos, principalmente com relação à sensibilidade, o que torna os resultados, muitas vezes, não comparáveis. Esse trabalho teve como objetivo revisar a literatura buscando identificar as diferentes opções comerciais disponíveis para o monitoramento do BCR-ABL1, além de comparar os resultados de dois destes ensaios com a metodologia de referência. A partir da revisão realizada, identificamos cinco kits comerciais como principais opções disponíveis para monitoramento de BCR-ABL1 na LMC: GeneXpert® BCR-ABL Assay (Cepheid), Ipsogen® BCR-ABL1 Mbcr Fusion Quant Kit (QIAGEN), BCR-ABL1 Quant RUO™ Assay (Asuragen), LightCycler® t(9;22) Quantification Kit (Roche Molecular Biochemicals) e ODK-1201 (Otsuka Pharmaceutical Co. Ltd.). Posteriormente, comparamos os resultados e avaliamos o desempenho dos ensaios GeneXpert® BCR-ABL e do BCR-ABL1 Quant RUO™ com a metodologia de referência a partir de amostras de 60 pacientes com LMC em uso de ITQ. Identificamos uma concordância global ótima, com coeficientes de correlação de 0,97 (GeneXpert® BCR-ABL Assay) e 0,84 (BCR-ABL1 Quant RUO™ Assay). No entanto, na avaliação da concordância relacionada ao alcance ou não de uma Resposta Molecular Maior (RMM), o ensaio BCR-ABL1 Quant RUO™ apresentou melhores resultados, com uma menor discrepância para respostas moleculares profundas. A análise estratificada por subtipos de transcritos de BCR-ABL1 não mostrou diferença de desempenho entre os dois ensaios. A partir das análises comparativas realizadas e respectivas vantagens de cada teste, aliados aos dados obtidos a partir da revisão da literatura, sugere-se que o GeneXpert® BCR-ABL poderia ser utilizado como um teste primário, devido à rapidez do ensaio, enquanto o BCR-ABL1 Quant RUO™, por apresentar resultados associados a uma maior sensibilidade, poderia ser um teste secundário, a fim de confirmar resultados abaixo de uma RMM ou resultados não detectáveis. Fica evidente que a escolha de um ensaio comercial deve atender às necessidades de cada laboratório, mas que, fundamentalmente, esteja alinhada às recomendações internacionais de quantificação. / The use of tyrosine kinase inhibitors (TKIs) has drastically changed the life expectancy of patients with chronic myeloid leukemia (CML) and monitoring the expression of the BCR-ABL1 oncogene has become a key prognostic factor for assessing treatment response. The need to development molecular methodologies that facilitate fast, cheap and sensitive quantification associated with the early detection of low levels of BCR-ABL1 has led to the emergence of several commercial assays for molecular monitoring. However, these kits have variability in their composition, performance and analytical parameters, mainly in relation to the sensitivity, which makes the results often not comparable. This work aimed to review the literature in order to identify the different commercial options available for the monitoring of BCR-ABL1, in addition to comparing the results of two of these tests with the reference methodology. From the review, we identified five commercial kits as the main options available for monitoring BCR-ABL1 in the LMC: GeneXpert® BCR-ABL Assay (Cepheid), Ipsogen® BCR-ABL1 Mbcr Fusion Quant Kit (QIAGEN), BCR-ABL1 Quant RUO™ Assay (Asuragen), LightCycler® t (9; 22) Quantification Kit (Roche Molecular Biochemicals) and ODK-1201 (Otsuka Pharmaceutical Co. Ltd.). Subsequently, we compared the results and evaluated the performance of the GeneXpert® BCR-ABL and BCR-ABL1 Quant RUO™ with reference methodology from samples of 60 patients with CML using TKI. We identified an optimal overall agreement for the two trials, with correlation coefficients of 0.97 and 0.84, respectively. However, in the evaluation of the agreement related to the reach of a Major Molecular Response (MMR), the BCR-ABL1 Quant RUO™ assay presented better results, with a smaller discrepancy for deep molecular responses. Analysis stratified by subtypes of BCR-ABL1 transcripts showed no difference in performance between the two assays. From the comparative analyzes performed and the respective advantages of each test, allied to the data obtained from the literature review, it is suggested that GeneXpert® BCR-ABL assay could be used as a primary test, due to the rapidity of the assay, while the BCR-ABL1 Quant RUO™, for presenting results associated with increased sensitivity, could be a secondary test in order to confirm results below an MMR or undetected results. It is clear that the choice of a commercial assay should meet the needs of each laboratory, but that it is fundamentally in line with international quantification recommendations.

Childhood acute leukemias are genetically complex disorders, with recurrent or random aberrations found in most patients. Their proper functional characterization is crucial for understanding the role they play in the process of leukemogenesis. We aimed to identify and characterize the genetic background of two leukemic entities. The transient myeloproliferative disorder (TMD) is a preleukemic condition that occurs in 10% of newborns with Down syndrome. Trisomy 21 together with in-utero gained mutations in the GATA1 gene are essential in TMD and represent an ideal "multi-hit" model to study leukemogenesis. We investigated an alternative pathogenic mechanism enabling TMD development in a confirmed absence of trisomy 21. Novel deletions in the GATA1 and JAK1 genes were described as potential drivers of this TMD. The deletion D65_C228 in GATA1 results in the expression of an aberrant isoform, which is predicted to lose transactivation potential and, more importantly, to partially lose the ability of recognizing physiological DNA binding sites, possibly triggering TMD alone. Our thorough characterization of JAK1 F636del questions its role in TMD development. Analysis of JAK/STAT signaling suggested decrease of kinase activity upon F636 loss. Cells harboring the aberrant JAK1 did not obtain cytokine-...

Childhood acute leukemias are genetically complex disorders, with recurrent or random aberrations found in most patients. Their proper functional characterization is crucial for understanding the role they play in the process of leukemogenesis. We aimed to identify and characterize the genetic background of two leukemic entities. The transient myeloproliferative disorder (TMD) is a preleukemic condition that occurs in 10% of newborns with Down syndrome. Trisomy 21 together with in-utero gained mutations in the GATA1 gene are essential in TMD and represent an ideal "multi-hit" model to study leukemogenesis. We investigated an alternative pathogenic mechanism enabling TMD development in a confirmed absence of trisomy 21. Novel deletions in the GATA1 and JAK1 genes were described as potential drivers of this TMD. The deletion D65_C228 in GATA1 results in the expression of an aberrant isoform, which is predicted to lose transactivation potential and, more importantly, to partially lose the ability of recognizing physiological DNA binding sites, possibly triggering TMD alone. Our thorough characterization of JAK1 F636del questions its role in TMD development. Analysis of JAK/STAT signaling suggested decrease of kinase activity upon F636 loss. Cells harboring the aberrant JAK1 did not obtain cytokine-...

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BCR-ABL1 transforms hematopoietic stem cells into leukemia stem cells (LSCs) to induce chronic myeloid leukemia in chronic phase. Expression of BCR-ABL1 stimulates production of elevated levels of reactive oxygen species (ROS), which induce oxidative DNA damage. CML cells accumulate excessive amounts of ROS-induced DNA damage which can be converted to potentially lethal DNA double strand breaks (DSBs). BCR-ABL1 stimulates enhanced Rad51-mediated DSB repair by the homologous recombination repair (HRR) pathway. In these studies we show BCR-ABL1-transformed cells depend on Rad52-mediated HRR to promote repair of ROS-induced DSBs and that this activity is dependent on Rad52 binding to single-stranded DNA (ssDNA). Our results show in the absence of Rad52, BCR-ABL1-positive hematopoietic cells accumulated elevated numbers of DSBs as detected by enhanced γ--H2AX foci formation compared to cells with wild-type Rad52 which resulted in a decrease in proliferation and expansion of the Rad52-null LSC population. Expression of wild-type Rad52 in Rad52-null cells decreased the accumulation of DSBs and restored expansion of the LSC population. Inhibition of ROS with the antioxidants Vitamin E or N-acetyl cysteine exerted similar effects on the LSC population of Rad52-null cells as restoration of wild-type Rad52. Our studies also show Rad52's ssDNA-binding activity is required for the proliferation of CML cells as evidenced by the accumulation of DSBs and impairment of clonogenic potential in cells in which the Rad52-F79A ssDNA-binding deficient mutant was expressed. Inhibition of Rad52 DNA binding activity by a peptide aptamer targeting Rad52-F79 resulted in a synthetic lethal phenotype in BCR-ABL1-positive cells due to impairment of the Rad52-dependent HRR pathway, as demonstrated by immunofluorescence and HRR repair assays. Altogether we identify Rad52 as a novel target in the treatment of CML, and other BRCA1- and/or BRCA2-deficient cancers, by showing induction of synthetic lethality in proliferating BCR-ABL1-positive cells in which Rad52 ssDNA-binding activity is inhibited. / Biology

Traditionally, response to treatment in hematological malignancies is evaluated by light microscopy of bone marrow (BM) smears, but due to more effective therapies more sensitive methods are needed. Today, detection of minimal residual disease (MRD) using immunological and molecular techniques can be 100 times more sensitive than morphology. The main aim of this thesis was to compare and evaluate three currently available MRD methods in childhood acute lymphoblastic leukemia (ALL): (i) real-time quantitative PCR (RQ-PCR) of rearranged antigen receptor genes, (ii) multicolor flow cytometry (FCM) of leukemia-associated immunophenotypes and (iii) real-time quantitative PCR of fusion gene transcripts (RT-PCR). In paper I, we assessed the applicability of RQ-PCR in a population-based cohort of childhood ALL diagnosed in Sweden between 2002-2006. Clonal IG/TCR rearrangements were identified in the 96% of the 279 ALL cases. Using RQ-PCR, the quantitative range of 10-3 was reached in 93% of B-cell precursor (BCP) ALL and 86% of T-cell ALL (T-ALL) by at least one target gene. In paper II, we compared MRD detection using both RQ-PCR and FCM in the context of NOPHO ALL-2000 protocol. By applying the stratification threshold of ≥0.1% MRD late during induction therapy (day 29), we could demonstrate that both methods can predict the risk of BM relapse but not extramedullary relapse. However, the threshold of ≥0.2% MRD appears to be more optimal using RQ-PCR in BCP ALL, whilst in T-ALL, the results indicate that RQ-PCR is preferable for MRD assessment. The stability of RNA in vitro is a critical factor when using sensitive molecular techniques such as MRD detection. In paper III, we evaluated the influence on MRD detection when blood is collected in tubes with RNA stabilization reagents (PAX gene Vacutatiner®) compared to collection in EDTA-tubes (non-stabilized). We analyzed 68 matched samples from chronic myeloid leukemia patients and the results indicated that non-stabilized blood processed within 30 hours is preferable for MRD detection. In paper IV, follow-up samples from eight children with Philadelphia positive (Ph+) ALL were evaluated with the three available MRD methods. MRD measured by the fusion gene transcripts (BCR-ABL1) appeared to be the most sensitive method, however, precise quantification can be difficult and the other methods are thus complementary. In conclusion, all three applied MRD methods are useful and correlate to each other, although not necessary exchangeable in individual patients. We also conclude that MRD assessment by RQ-PCR, based on rearranged IG/TCR genes and multicolor FCM are predictive for identification of high risk childhood ALL patients.