Indiana University-Purdue University Indianapolis (IUPUI) / Cancer cells display increased metabolic demands to support their proliferation and biosynthetic needs. It has been extensively shown in cancers, that amino acids have functions beyond the role of mRNA translation. The breadth of functions makes amino acid restriction an effective strategy for cancer therapy; hence an important line of research involves targeting amino acid acquisition and metabolism therapeutically. Currently, asparagine depletion via L-Asparaginase in acute lymphoblastic leukemia (ALL) remains the only clinically approved therapy to date. In the first project, we showed that ALL cells are auxotrophic for asparagine and rely on exogenous sources for this non-essential amino acid. However, sensitivity to L-Asparaginase therapy is mitigated by the expression of the enzyme asparagine synthetase (ASNS), involved in de novo asparagine biosynthesis. We showed that this adaptive response requires two essential steps; demethylation of the ASNS promoter and recruitment of activating transcription factor 4 (ATF4) to the promoter to drive ASNS transcription. Our follow-up study in ALL cells showed that asparagine bioavailability (through de novo biosynthesis or exogenous sources) is essential to maintain the expression of the critical oncogene c-MYC. c-MYC is a potent transcription factor and is dysregulated in over 60% of cancers, including hematopoietic malignancies. We showed that this regulation by asparagine is primarily at the translation level and c-MYC expression is rescued only when exogenous asparagine is available or when cells can undertake de novo biosynthesis. At the biochemical level, asparagine depletion also causes an induction of ATF4 mediated stress response and suppression of global translation mediated by decreased mammalian target of rapamycin complex 1 (mTORC1) activity. However, we found that neither inhibition of the stress response or rescuing global translation rescued c-MYC protein expression. We also extended this observation to c-MYC-driven lymphomas using cell lines and orthotopic in vivo models. We showed that genetic inhibition of ASNS or pharmacological inhibition of asparagine production can significantly limit c-MYC protein and tumor growth when environmental asparagine is limiting. Overall, our work shows an essential role for asparagine in lymphoid cancers and has expanded on the usage of L-Asparaginase to resistant leukemias and lymphomas.

Acute Lymphoblastic Leukemia (ALL) is an aggressive hematologic tumor and is the most common malignancy in children (Horton and Steuber 2014). This disease is characterized by the infiltration of bone marrow by malignant immature lymphoid progenitor cells and is invariably fatal without treatment. Although multi-agent combination chemotherapy is curative in a significant fraction of ALL patients, treatment currently fails in approximately 20% of children and up to 50% of adults with ALL, making relapse and drug resistance the most substantial challenge in the treatment of this disease(Fielding, Richards et al. 2007, Aster and DeAngelo 2013). Understanding what causes treatment failure is of great medical importance as second line therapies also fail in the majority of relapse T-cell ALL (TALL) patients (Fielding, Richards et al. 2007, Aster and DeAngelo 2013). Using next-generation sequencing to compare the genomes of tumors before and after therapy, mutations in gene cytosolic 5’-nucleotidase II (NT5C2) were discovered in 19% of pediatric samples with relapsed T-ALL(Tzoneva, Carpenter et al. 2013). Preliminary structure function analysis and subsequent in vitro experimental nucleotidase activity assays confirmed that these mutations lead to hyperactive NT5C2 protein. Furthermore, NT5C2 mutant proteins conferred resistance to 6-mercaptopurine and 6-thioguanine chemotherapy drugs when expressed in ALL lymphoblasts, suggesting NT5C2 is responsible for the inactivation of nucleoside-analog chemotherapy drugs. In order to assess the ability of these mutations to lead to novel inhibitor schemes, the functional impact of each mutation was analyzed through robust structure function methods. The result of this in silico analysis, is the identification of a potential allosteric regulatory mechanism of negative feedback inhibition never before described. Most notably, the majority of NT5C2 mutations identified have characteristics that suggest they abrogate the function of this proposed mechanism, yielding a novel viable target for the development of allosteric inhibitors specific for constitutively active NT5C2 mutant proteins. Overall these findings support a prominent role for activating mutations in NT5C2 and chemotherapy resistance in ALL, and highlight new avenues for relapsed ALL therapy development in the future.

Thesis (Ph. D.)--University of North Texas, Aug., 2007. / Title from title page display. Includes bibliographical references.

[Truncated abstract] The treatment of childhood acute lymphoblastic leukaemia (ALL) is one of the great success stories of paediatric oncology, transforming a universally fatal disease into one where 75 to 90% of children are now cured. Although in the past survival for children with T-cell ALL (T-ALL) lagged behind that of children with pre-B ALL, the use of contemporary intensified treatment strategies has significantly diminished this difference, with many investigators reporting similar cure rates for both groups of patients. Despite these marked improvements, numerous challenges still face physicians treating children with T-ALL. Firstly, there have been no additional major improvements in outcome over the last decade, despite additional treatment intensification. Secondly, effective regimens remain elusive for treating children with relapsed T-ALL or patients with resistant disease. Finally, there is a need to identify patients currently potentially overtreated and thus unnecessarily subjected to acute and long term toxicities without benefit. A major challenge therefore, is the identification of novel reliable prognostic markers, in order to identify patients at high risk of relapse and conversely those least likely to relapse, to guide therapy appropriately. Children predicted with a high risk of relapse would be candidates for intensification of therapy and/or novel experimental agents. Conversely, patients predicted to be at low risk of relapse could be offered clinical trials using reduced intensity therapy, thereby minimising toxicity. '...' Crucially, the 3-gene predictor was validated in a completely independent cohort of T-ALL patients, also treated on CCG style therapy. Our 3-gene predictor appears to identify a high risk group of patients which require alternative therapeutic strategies in order to attain a cure. This study has also identified a potential novel agent for the treatment of T-ALL, which may be used as an anthracycline potentiator or anthracycline-sparing agent. We hypothesised that genes associated with a relapse signature provide promising targets for novel therapies. We tested the hypothesis that CFLAR, an inhibitor of the extrinsic apoptotic pathway and a member of the 3-gene predictor may be involved in the development of resistance to chemotherapy. To test our hypothesis we used a novel agent, 2-cyano-3, 12-dioxooleana-1,9 (11)-dien-28-oic acid (CDDO), previously shown to inhibit CFLAR protein, in two cell lines established in our laboratory from paediatric patients diagnosed with T-ALL. We found that CDDO displayed single agent activity at sub-micromolar concentrations in both cell lines tested. Importantly, minimally lethal doses of CDDO resulted in significant enhancement of doxorubicin mediated cytotoxicity in one of the cell lines assessed. The findings presented as part of this thesis have revealed the value of gene expression analysis of childhood T-ALL for identifying novel prognostic markers. This study has shown that expression profiles may provide better prognostic information than currently available clinical variables. Additionally, genes that constitute a relapse signature may provide rational targets for novel therapies, as demonstrated in this study, which assessed a potential novel agent for the treatment of T-ALL.

[Truncated abstract] Childhood acute lymphoblastic leukaemia (ALL) accounts for the largest number of cases of childhood cancer (25-35%) and is the primary cause of cancer related morbidity. Today more than 76% of children with ALL are alive and disease free at 5 years. Approximately one in 900 individuals between the ages of 16 and 44 years is a survivor of childhood cancer. In contrast, those patients who relapse with childhood ALL currently have a 6-year event free survival of 20-30%. The short arm of chromosome 9p is mutated or deleted in many cancers including leukaemia. Aberrations of the INK4A/ARF and INK4B loci at the 9p21 band are linked to the development and progression of cancer. In murine cancer models there is evidence to suggest that mutations of Ink4a/Arf and p53 gene loci promote resistance to chemotherapeutic drugs known to trigger apoptosis. The initial aim of this project was to develop an accurate, reproducible method to detect deletions at the INK4A/ARF locus in patient bone marrow specimens. This technique was then applied to detect the incidence of deletions of this locus in childhood ALL specimens. The hypothesis developed was that deletion at the INK4A/ARF locus at diagnosis in childhood ALL is an independent prognostic marker and is involved in disease progression. A secondary aim of this study was to determine which deletions at the INK4A/ARF and INK4B loci are the most relevant in leukaemogenesis in childhood ALL. ... This study has shown that deletion of the INK4A/ARF locus is an independent prognostic indicator in childhood ALL. In addition, the frequency of deletion at the INK4A/ARF and INK4B loci is increased at relapse compared to diagnosis in childhood ALL. In the relapse study group, deletion of the p16INK4A gene at diagnosis was associated with a decreased median time to relapse compared to other genes analysed. Murine studies suggest that such deletions may result in an increased resistance to chemotherapy. If the findings from this study are confirmed in a larger cohort, it is expected that therapeutic interventions based on assessment of the p16INK4A gene in diagnostic childhood ALL specimens will be implemented to prevent relapse in standard risk patients and help to improve the outcome in high risk patients.

Thesis (Ph. D.)--West Virginia University, 2010. / Title from document title page. Document formatted into pages; contains x, 102 p. : ill. (some col.). Includes abstract. Includes bibliographical references.

Acute lymphoblastic leukemia is the most common malignancy in children. The most important examination at the time of diagnosis includes karyotype of leukemic cells which divides patients into prognostic groups according to cytogenetic finding. In up to 90 % of patients the chromosomal aberrations with well known clinical significance are designated. One of cytogenetic type is high hyperdiploid ALL (51-68 chromosomes) associated with favorable prognosis. Nevertheless, relapses of the disease occur even in these children. One possible reason why this happens could be an increased genomic instability of leukemic cells that causes cryptic structural rearrangements. In a retrospective study, we examined a total of 232 children with newly diagnosed B-ALL using conventional cytogenetic analyses and interphase fluorescence in situ hybridization (I-FISH) with a panel of DNA probes (Abbott Vysis) in order to detect heteroploid cells. In patients with suspect cryptic structural chromosome aberrations, we analyzed the karyotypes in detail by multicolor FISH and multicolor banding (mFISH/mBAND; MetaSystems). The extent of aberrations was determined by comparative genomic hybridization on BAC arrays (array CGH; BlueGnome). Cell clones with high hyperdiploid karyotype were detected in a total of 102 children (44 %). In...

A mucosite bucal está entre as principais complicações decorrentes do tratamento antineoplásico em pacientes com leucemia linfóide aguda (LLA). Entre os fatores de risco para sua ocorrência destacam-se a idade, o gênero e a leucometria inicial, além das drogas quimioterápicas com comprovada ação estomatotóxicas. O objetivo deste estudo foi investigar a prevalência e os fatores de risco para a mucosite bucal em pacientes com LLA submetidos a diferentes protocolos de tratamento quimioterápicos. Um total de 169 prontuários clínicos de pacientes oncológicos pediátricos submetidos a diferentes protocolos de tratamento para LLA no Setor de Oncologia Pediátrica do Hospital Infantil Darcy Vargas, na cidade de São Paulo, no período compreendido entre 1994 a 2005 foram, retrospectivamente, avaliados. Os dados demográficos (idade e gênero) e clínicos (leucometria inicial, protocolo de tratamento a que foi submetido, evolução, ocorrência de mucosite e outras lesões bucais) foram registrados. A associação da mucosite bucal com as variáveis clínicas e demográficas foi obtida pelos testes do qui-quadrado e análise de regressão logística multivariada. Os resultados demonstraram uma freqüência de mucosite bucal em 46% dos pacientes oncológicos pediátricos com LLA sem correlação estatisticamente significativa entre sua ocorrência e o gênero (p=0,08), a idade (p=0,33) e a leucometria inicial (p=0,34). Na análise multivariada o protocolo de tratamento do grupo Berlim- Frankfurt-Munique de 1995 (ALL-BFM 95), de acordo com as variáveis avaliadas neste estudo, mostrou ser o fator mais significativo (p=0,009) para a ocorrência da mucosite bucal. Esses resultados fortemente sugerem uma maior estomatotoxicidade do protocolo ALL-BFM 95 comprovadas pela maior freqüência de mucosite bucal nos pacientes ontológicos pediátricos com LLA. Portanto, concluímos que a mucosite bucal deveria ser sistematicamente analisada nos centros especializados no tratamento da LLA que adotam diferentes protocolos de tratamento, visando não somente contribuir com a análise do grau de toxicidade das drogas quimioterápicas, mas principalmente, melhorar a qualidade de vida do paciente com base em condutas terapêuticas e profiláticas mais efetivas na prevenção de sua ocorrência. / Oral mucositis is one of the main complications secondary to antineoplastic treatment in patients with acute lymphoblastic leukemia (ALL). The risk factors for its occurrence include age, gender and initial leukocyte count, besides chemotherapeutic drugs with known stomatotoxic action. This study investigated the prevalence and risk factors to oral mucositis in patients with ALL submitted to different chemotherapeutic treatment protocols. A total of 169 clinical records of pediatric oncology patients submitted to different treatment protocols for ALL at the Pediatric Oncology Sector of the Child Hospital Darcy Vargas, in the city of São Paulo, in the period 1994 to 2005 were retrospectively evaluated. Demographic (age and gender) and clinical data (initial leukocyte count, treatment protocol adopted, evolution, occurrence of mucositis and other oral lesions) were recorded. The association of oral mucositis with the clinical and demographic variables was assessed by the chi-square test and multivariate logistic regression analysis. The results demonstrated occurrence of oral mucositis in 46% of pediatric oncology patients with ALL, without statistically significant correlation between its occurrence and gender (p=0.08), age (p=0.33) and initial leukocyte count (p=0.34). Multivariate analysis revealed that the Berlin-Frankfurt-Munich protocol of 1995 (ALL-BFM 95) was the most significant factor (p=0.009) to the occurrence of oral mucositis according to the variables evaluated in this study. These results strongly suggest the greater stomatotoxic effect of the ALL-BFM 95 protocol, as demonstrated by the higher frequency of oral mucositis in pediatric oncology patients with ALL. Thus, it may be concluded that oral mucositis should be systematically analyzed in centers specialized in the treatment of ALL adopting different treatment protocols, with a view to contribute to analysis of the degree of toxicity of chemotherapeutic drugs and mainly to improve the quality of life of patients on the basis of more effective therapeutic and prophylactic approaches for prevention of its occurrence.

A leucemia linfóide aguda (LLA) é a neoplasia hematológica mais comum na infância e representa uma doença heterogênea em relação à biologia e ao prognóstico e seu tratamento consiste principalmente em quimioterapia. Apesar dos avanços no tratamento, cerca de 20% dos pacientes apresentam recaída da doença e/ou óbito indicando a necessidade de terapias diferenciadas para esse grupo. Recentemente, drogas epigenéticas como inibidores de DNA metiltransferases (iDNMTs) tem mostrado efeitos anti-neoplásicos promissores para o tratamento de diversos tipos de neoplasias incluindo a LLA. Nos tumores, a hipermetilação gênica é encontrada em vários genes, incluindo genes de reparo do DNA, reguladores do ciclo celular e apoptose. Sendo assim, drogas desmetilantes estão sendo apontadas como promissores agentes para o tratamento do câncer. A Zebularina (ZB) é um iDNMT análogo de citidina que inibe a metilação do DNA. Esta droga tem mostrado resultados animadores para o tratamento de diversas neoplasias, incluindo glioblastoma, leucemia mielóide aguda, câncer de mama, próstata e outros. O objetivo deste trabalho foi avaliar os efeitos do tratamento com a ZB, associada ou não à quimioterápicos, em linhagens celulares pediátricas de LLA, por meio de ensaios funcionais como proliferação celular, capacidade clonogênica, apoptose e ciclo celular. Além disso, foi analisada a capacidade desmetilante da droga e a expressão dos genes DNMT1, DNMT3a e DNMT3b após o tratamento com a ZB. A ZB inibiu a proliferação celular de maneira dose e tempo-dependente e agiu sinergicamente quando combinada com o MTX em ambas as linhagens. Ela também diminuiu a capacidade clonogênica e aumentou a taxa de apoptose nas duas linhagens estudadas. Além disso, o tratamento com ZB causou uma parada na fase S do ciclo celular na linhagem ReH. A ZB foi capaz de desmetilar parcialmente o gene AhR e reduzir a expressão dos genes DNMT1, DNMT3a e DNMT3b. Todos os dados encontrados no presente trabalho sugerem que as drogas desmetilantes podem ser interessantes agentes para o tratamento da LLA pediátrica. / Acute lymphoblastic leukemia (ALL) is the most common hematologic malignancy in childhood and represents a heterogeneous disease regarding its biology and prognosis. Its treatment consists mainly of chemotherapy. Despite advances in treatment, about 20% of patients experience disease recurrence and/or death indicating the need for differentiated therapies for this group. Recently, epigenetic drugs such as DNA methyltransferases inhibitors (iDNMTs) has shown antineoplastic and promising results for several types of tumors including ALL. Gene hypermethylation is found in several genes in tumors cells, including genes responsible for DNA repair, cell cycle and apoptosis regulators. Therefore, demethylating agents may be promising agents for cancer treatment. Zebularine (ZB) an iDNMT is a cytidine analogue that inhibits DNA methylation. This drug has shown promising results for the treatment of many cancers, including glioblastoma, acute myeloid leukemia, breast and prostate cancer and others. The aim of this study was to evaluate the effects of ZB treatment, associated or not with chemotherapeutic agents, in childhood ALL cell lines through functional tests such as cell proliferation, clonogenic capacity, apoptosis and cell cycle. In addition, we examined the demethylating ability of ZB and the expression of DNMT1, DNMT3a and DNMT3b genes after treatment with this agent. ZB inhibited cell proliferation in a dose- and time-dependent manner and showed synergistic effects when combined with MTX in both cell lines. ZB treatment also reduced clonogenic capacity and increased the number of apoptotic cells in both cell lines studied. Furthermore, treatment with ZB caused an S phase cell cycle arrest in ReH cell line. ZB was able to partially demethylate AhR gene and reduce the expression of genes DNMT1, DNMT3a and DNMT3b. These results suggest that demethylating drugs may be interesting agents for the treatment of childhood ALL.

A L-asparaginase (EC 3.5.1.1) é uma enzima importante para o tratamento da leucemia linfoblástica aguda (LLA), neoplasia mais frequente em crianças e adolescentes. A L-asparaginase hidrolisa a L-asparagina resultando em ácido aspártico e amônio, impedindo que as células tumorais utilizem esse aminoácido para síntese proteica, ocasionando a morte celular apoptótica. Atualmente a enzima é obtida a partir de Escherichia coli e Erwinia chrysanthemi; no entanto, ambas as formulações estão associadas a um alto índice de efeitos adversos que comprometem a evolução e eficácia do tratamento. A levedura Saccharomyces cerevisiae tem o gene ASP1 responsável pela produção de L-asparaginase 1 (Sc_ASPase1) que tem sido pouco estudada. Para elucidar as características de Sc_ASPase1 nós expressamos a proteína em E. coli BL21(DE3) e a purificamos por cromatografia de afinidade. Sc_ASPase1 tem uma atividade especifica de 195,4 U/mg para L-asparagina e de 0,36 U/mg para L-glutamina, e um comportamento alostérico com um K0.5 de 75 µM para L-asparagina. Por meio de mutação sitio dirigida demonstramos a importância dos resíduos Thr64-Thy78-Th141-Lys215 para a catálise. As isoformas mutantes da proteína A331D, K335E, Y243S, S301N e ΔG77 não apresentaram melhoria nos parâmetros cinéticos ou atividade específica. Construímos e clonamos Sc_ASPase1 com a deleção dos primeiros 52 aminoácidos, porém nas condições testadas a proteína foi expressa na forma insolúvel. Demonstramos que Sc_ASPase1 possui potencial antineoplásico, pois com 10 U/mL de enzima foi capaz causar a 85% de mortalidade da linhagem leucêmica MOLT-4. Na mesma concentração, a enzima de E. coli é capaz de matar 95% de células dessa mesma linhagem. / L-Asparaginase (EC 3.5.1.1) is an important enzyme for the treatment of acute lymphoblastic leukemia (ALL), the most common malignancy in children and adolescents. L-asparaginase hydrolyzes L-asparagine resulting in ammonium and aspartic acid, preventing tumor cells of using such amino acid for protein synthesis, leading to apoptotic cell death. Currently, the enzyme is obtained from Escherichia coli and Erwinia chrysanthemi; however, both formulations are associated with a high incidence of side effects that compromise the progress and effectiveness of treatment. The yeast Saccharomyces cerevisiae has ASP1 gene responsible for the production of L-asparaginase 1 (Sc_ASPase1) that has been poor studied. To elucidate the characteristics of Sc_ASPase1, we expressed the protein in E. coli BL21 (DE3) cells and purified it by affinity chromatography. Sc_ASPase1 has a specific activity of 195.4 U/mg for L-asparagine and 0.36 U/mg for L-glutamine, and an allosteric behavior with a K0.5 of 75 µM for L-asparagine. Through site directed mutation, we demonstrated the importance of Thr64-Thy78-Th141-Lys215 residues for catalysis. The mutant protein isoforms A331D, K335E, Y243S, S301N and ΔG77 showed no improvement in kinetic parameters or specific activity. We build and cloned Sc_ASPase1 with the deletion of the first 52 amino acids, but under the conditions tested the protein was expressed in insoluble form. Sc_ASPase1 have demonstrated potential antineoplastic activityc, since 10 U/mL of enzyme lead to 85% of mortality in leukemia cell line MOLT-4. At the same concentration, the E. coli enzyme kills 95% of the cells of the same line.