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Cancer remains the second leading cause of death in the United States and the world, despite years of research and the development of different treatments. One reason for this is cancer cells are able to survive through adaptation to their environment and aberrantly activated growth signaling. As such, developing new therapies that overcome these hurdles are necessary to combat cancer. Previous work in our laboratory using RNA interference screening identified genes that regulate the survival of glioblastoma (GBM) or autophagy in chronic myelogenous leukemia (CML) cancer cells. One screen identified Phosphatidylinositol-4,5-bisophosphate 3-kinase catalytic subunit beta (PIK3CB) in the family of Phosphatidylinositol 3-kinases (PI3K) as a survival kinase gene in GBM. Work contained in this dissertation set out to study PIK3CB mediated GBM cell survival. We report that only PIK3CB, in its family of other PI3K genes, is a biomarker for GBM recurrence and is selectively important for GBM cell survival. Another screen identified the long non-coding RNA, Linc00467, as a gene that regulates autophagy in CML. Autophagy is a dynamic survival process used by all cells, benign and cancerous, where cellular components are broken down and re-assimilated to sustain survival. Work contained in this dissertation set out to characterize the role that Linc00467 serves in regulating autophagy in a myriad of cancers. Collectively our data have showed Linc00467 to actively repress levels of autophagy in cancer cells. Further, our data revealed an important role for Linc00467 in regulating the stability of the autophagy regulating protein serine-threonine kinase 11 (STK11). Because of the unique role that Linc00467 serves in regulating autophagy we renamed it as, autophagy regulating long intergenic noncoding RNA or ARLINC. Taken together the work in this dissertation unveils the inner-workings of two important cancer cell survival pathways and shows their potential for development into therapeutic targets to treat cancer. / Ph. D.

Inhibiting BCR-ABL kinase activity with tyrosine kinase inhibitors (TKIs) has been the frontline therapy for CML. Resistance to TKIs frequently occurs, but the mechanisms remain elusive. First, to uncover survival pathways involved in TKI resistance in CML, I conducted a genome-wide RNAi screen in human CML cells to identify genes governing cellular sensitivity to the first generation TKI called IM (Gleevec). I identified genes converging on and activating the MEK/ERK pathway through transcriptional up-regulation of PRKCH. Combining IM with a MEK inhibitor synergistically kills TKI-resistant CML cells and CML stem cells. Next, I performed single cell RNA-seq to compare expression profiles of CML stem cells and hematopoietic stem cells isolated from the same patient. Among the genes that are preferentially expressed in CML stem cells is PIM2, which encodes a pro-survival serine-threonine kinase that phosphorylates and inhibits the pro-apoptotic protein BAD. Inhibiting PIM2 function sensitizes CML stem cells to IM-induced apoptosis and prevents disease relapse in a CML mouse model. Last, I devised a CRISPR-Cas9 based strategy to perform insertional mutagenesis at a defined genomic location in murine hematopoietic Ba/F3 cells. As proof of principle, we showed its capability to perform unbiased, saturated point mutagenesis in a 9 amino acid region of BCR-ABL encompassing the socalled “gatekeeper” residue, an important determinant of TKI binding. We found that the ranking order of mutations from the screen correlated well with their prevalence in IM-resistant CML patients. Overall, my findings reveal novel resistance mechanisms in CML and provide alternative therapeutic strategies.

Orientador: Carmen Silvia Passos Lima / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-21T21:59:05Z (GMT). No. of bitstreams: 1 Numa_IramaiaAngelicaNeri_M.pdf: 4547636 bytes, checksum: 22548046dff40a3bb4e586230e3f13b7 (MD5) Previous issue date: 2012 / Resumo: O mesilato de imatinibe (MI) é o tratamento de escolha para pacientes com leucemia mielóide crônica (LMC) em fase crônica, mas a resposta ao medicamento é variável em indivíduos distintos. A CYP3A4 é a principal enzima responsável pelo metabolismo hepático do MI. O alelo variante G do polimorfismo CYP3A4 A-290G codifica menor quantidade de enzima do que o alelo selvagem A, mas o papel do referido polimorfismo em pacientes com LMC tratados com MI é desconhecido. Os objetivos deste trabalho foram os de avaliar a eficácia, a toxicidade a sobrevida livre de progressão (SLP) e global (SG) de pacientes com LMC durante a administração de MI e verificar se estes parâmetros são alterados pela variabilidade interindividual no metabolismo do fármaco, relacionada ao polimorfismo CYP3A4 A-290G. Foram avaliados 100 pacientes com LMC em FC precoce atendidos no Centro de Hematologia e Hemoterapia da UNICAMP. O diagnóstico da LMC, o exame hematológico, o cariótipo, a pesquisa do gene BCR-ABL e os genótipos do polimorfismo CYP3A4 A-290G foram realizados por métodos convencionais. Os pacientes receberam o MI na dose de 400mg e a resposta ao tratamento foi avaliada segundo os critérios do European Leukemia Net. Identificamos respostas hematológicas, citogenética e molecular similares às previamente descritas. A taxa de resposta hematológica foi de 95% ao longo do estudo. Aos doze meses, as respostas citogenética completa ou parcial foram de 72% e 11% respectivamente. Já as taxas de respostas moleculares completas e maiores aos 22 meses foram de 28% e 26%, respectivamente. A sobrevida global foi de 94% aos 92 meses bem como a sobrevida livre de progressão para as fases avançadas da doença. Observamos que pacientes com resposta citogenética completa ou parcial e molecular xiv completa ou maior apresentaram maior SLP e SG do que os demais. Cerca de 13% dos pacientes era portadores do genótipo AG do polimorfismo CYP3A4 A-290G, o qual esteve associado à obtenção de resposta molecular completa tardia e tendência à menor SLP e SG. Apesar da hipótese do alelo variante (G) exibir um fenótipo metabolizador lento associado a uma menor taxa de biotransformação do MI e portando maior risco de reações tóxicas, não observamos diferenças entre as toxicidades hematológicas e não hematológica (P= 0,28). Assim, concluímos que nossos pacientes respondem de forma similar ao MI do que os demais e que o polimorfismo CYP3A4 A-290G pode vir a funcionar como biomarcador de resposta ao fármaco / Abstract: Imatinib (IM) is widely recognized as the standard of care in the first-line treatment of CML but the response to the drug is variable in different subjects. CYP3A4 is the main enzyme responsible for the hepatic metabolism of Imatinib. The G variant allele of the polymorphism A-290G encoding least amount of enzyme than the wild-type allele, but the role of this polymorphism in CML patients treated with Imatinib is unknown. The aims of this study were to assess the efficacy, toxicity, progression-free survival (PFS) and overall survival (OS) of patients with CML during the administration of Imatinib and check if these parameters are affected y interindividual variability in drug metabolism, the polymorphism related to CYP3A4 A-290G. We evaluated 100 patients with CML newly diagnosed at Center of Hematology and Hemoterapy of UNICAMP. The diagnosis of CML, hematology, karyotyping, research the BCR-ABL gene polymorphism and CYP3A4 genotypes A-290G were performed by conventional methods. Patients received a dose of 400mg IM and treatment response was assessed according to the criteria of the European Leukemia Net responses identified hematologic, cytogenetic and molecular similar to those previously described. The hematologic response rate was 95% throughout the study. At 22 months the complete or partial cytogenetic responses were 72% and 11% respectively. The complete molecular response rates at 22 months were 28% and 26%, respectively. Overall survival (OS) was 94% at 92 months and the progression-free survival (PFS) for advanced stages of the disease. We observed that patients with partial or complete cytogenetic response and major molecular and complete PFS and OS showed higher than other. We observed that patients with partial or complete cytogenetic response and major molecular xvi and complete PFS and OS showed higher than others. About 13% of patients were of AG genotype polymorphism of the CYP3A4 -290A>G, which was associated with achieving complete molecular response and late tendency to lower PFS and OS. Despite the possibility of variant allele (G) display a slow metabolizer phenotype associated with a lower rate of biotransformation of IM and carrying greater risk of toxic reactions, no significant differences between hematological and non hematological toxicities (P= 0,28). Thus, we conclude that our patients respond similary to IM than others and that the polymorphism CYP3A4 -290A>G might function as a biomarker of response to the drug / Mestrado / Ciencias Basicas / Mestra em Clínica Médica

Class of 2016 Abstract / Objectives: Patient medication adherence is a basic requirement for treating chronic myelogenous leukemia (CML) with oral tyrosine kinase inhibitors (TKIs). When imatinib adherence rates are less than 80 or 90 percent, major and complete molecular responses, respectively, do not happen. The purpose of this study was to determine the effect of a real-time medication monitoring (RTMM) reminder system adherence program on the medication possession ratio (MPR). Methods: This analytic study was a retrospective cohort study and used data extracted from chart reviews for patients who received services from 2011 to 2015. It was approved by the Institutional Review Board. The study consisted of an intervention group and a control group (50 patients each). MPRs, demographic, descriptive, and categorical variables were summarized using means, standard deviations (SD), and frequencies/percentages. Results: The study population consisted of adult patients (mean age=62.2, SD=2.7, 50% male) treated by Avella Specialty Pharmacy who received imatinib or nilotinib as treatment for CML, gastrointestinal stromal tumors (GIST), or a similar positive Philadelphia chromosome cancer. Only 4% of patients in the intervention group had an < 85% MPR, compared to 46% in the control group (p < 0.001). Conclusions: In those patients who had an MPR of ≥ 85%, the difference between the groups was statistically significant. As past studies have shown, adherence rates greater than 90% have a higher likelihood of a major or complete molecular response and a greatly reduced risk of disease progression.

In chronic myelogenous leukemia (CML), activation of BCR-ABL, the product of the bcr-abl chimeric gene, leads to constitutive activation of pathways that increase genomic instability through endogenous production of reactive oxygen species (ROS) that cause oxidative DNA damage and inactivate the function of repair proteins leading to unfaithful DNA repair. If misrepaired, oxidative DNA damage, such as 8-oxoguanine (8-oxoG), may result in point mutations and/or DNA double-strand breaks (DSBs) leading to drug resistance to the BCR-ABL kinase inhibitor imatinib mesylate (IM) and accumulation of chromosomal aberrations associated with malignant CML progression from a benign chronic phase (CP) to a fatal blast phase (BP). To determine which population of CML-CP cells, leukemia stem cells (LSCs) and/or leukemia progenitor cells (LPCs), displays elevated levels of ROS and oxidative DNA damage, and whether these elevated levels of ROS and oxidative DNA damage in CML-CP subpopulations result in the accumulation of genomic instability, we employed the tetracycline-inducible SCLtTA/BCR-ABL transgenic mouse model. We showed that LSCs, including the quiescent subpopulation, but not LPCs, displayed elevated levels of ROS and oxidative DNA damage, perhaps due to deregulated expression of genes involved in ROS metabolism, resulting in genomic instability manifested by both point mutations and genetic alterations. We also examined the effect of IM on ROS, oxidative DNA damage and genomic instability displayed by CML-CP subpopulations, and determined that elevated ROS and oxidative DNA damage were not inhibited by IM in quiescent LSCs, nor was genomic instability and deregulated gene expression prevented. To explore underlying mechanisms, i.e. BCR-ABL expression levels, by which CML-CP cells accumulate genomic instability, we examined the effect of low and high BCR-ABL expression on ROS and oxidative DNA damage in BCR-ABL-transduced human CD34+ cells. We detected elevated ROS and oxidative DNA damage in high BCR-ABL-expressing CD34+ cells compared to low BCR-ABL-expressing cells. Furthermore, BCR-ABL exerted a kinase-dependent effect on ROS-dependent DNA damage. These data support the hypothesis that genomic instability may originate from LSCs, but do not exclude the potential role of LPCs, and may have important clinical implications for CML treatment since additional genetic aberrations that encode primary resistance may protect LSCs, including the quiescent subpopulation, from eradication by tyrosine kinase inhibitors (TKIs), and the continuous accumulation of genetic errors may trigger disease relapse and progression. / Microbiology and Immunology

A leucemia mielóide crônica (LMC) é uma doença mieloproliferativa e sua patogênese está associada à expressão de um neogene, bcr-abl, que codifica uma proteína tirosina quinase Bcr-Abl. Esse trabalho tem como objetivos o estudo dos mecanismos envolvidos na resistência à morte das células Bcr-Abl positivas e a identificação de alterações gênicas nessas células. Dados de expressão gênica global obtidos por \"microarray\" mostraram uma superexpressão nas células HL-60.Bcr-Abl com relação a HL-60 dos genes faim e nipa, que foi confirmada por qRT-PCR em diferentes linhagens celulares Bcr-Abl positivas. Já os genes de trail e osm, apresentaram uma diminuição significativa em HL-60.Bcr-Abl, que foi confirmada para trail, porém osm não teve seu resultado validado. A avaliação da expressão dos genes em células de pacientes portadores de LMC, em diferentes fases da doença também foi estudada. Com esses resultados, o presente estudo visa a melhor compreensão de como alterações na expressão desses genes contribuem na fisiopatologia da LMC. / Chronic myelogenous leukemia (CML) is a stem cell disease characterized by the presence of the Bcr-Abl oncoprotein, which is the cause of the malignant transformation and the extreme resistance to apoptosis displayed by CML patients. Our aim was to analyze the alteration in global gene expression in Bcr-Abl expressing cells. Data obtained from microarray analysis showed significant up-regulation of nipa and faim in HL60.Bcr-Abl and down-regulation of osm and trail. These results were further confirmed by Real-Time PCR to nipa, faim and trail, but not for osm expression in HL-60.Bcr-Abl cells. To evaluate the potential of some of the modified genes as therapeutic targets or prognostic markers for CML, we also analyzed the expression of these genes in samples from CML patients.

Chronic Myelogenous Leukemia (CML) is a blood cancer that arises when hematopoietic cells acquire an abnormal protein known as BCR-ABL. Current therapies for CML include drugs that inhibit BCR-ABL. However, these drugs only suppress the disease and do not cure it. One reason is that BCR-ABL drugs fail to kill the primitive population of CML cells, referred to as leukemia stem cells (LSCs), which are responsible for initiating and propagating CML. Since LSCs are not killed, the cancer is not cured and many affected patients eventually relapse. Recent studies suggest that LSCs are protected from current therapies by the bone marrow micro-environment where they reside. There, cytokine signaling molecules are present, which mediate processes that protect LSCs from BCR-ABL drugs. The stem cell factor (SCF) is one of these signaling molecules. It activates the receptor c-Kit located on the surface of LSCs, and this activation in turn allows proliferating LSCs to resist BCR-ABL drugs, even without prior exposure to these drugs, i.e., innate resistance is observed. In this thesis, the mechanism of this innate resistance is investigated, so that a suitable treatment strategy can be developed. To this end, a co-agent approach based on synthetic antibodies (sABs) is proposed to inhibit the receptor c-Kit, with the goal of disrupting its activation by the ligand SCF. This disruption should in turn block the SCF-mediated innate resistance, thus potentially restoring BCR-ABL drug apoptotic activity. The method for this disruption involves targeting the c-Kit structural susceptibility. Specifically, the sABs are designed via antibody phage display technology to target the D1–D2–D3 domains representing the SCF binding sites, hence preventing downstream pathway activation. The hypothesis is that, by blocking the SCF-mediated innate resistance, a suitable combination of such an sAB co-agent and a BCR-ABL drug should be conducive to suppressing LSCs, thereby providing a potential means to improve CML treatment. In addition, to assess the performance of the proposed treatment strategy, a set of in vitro tests is conducted, focusing on performance behaviors such as cell binding, cell death, and the progenitor inhibition. The experimental results support the hypothesis that the proposed combinatorial strategy is indeed a promising approach to mitigate the innate resistance, thus restoring BCR-ABL drug apoptotic activity.

A leucemia mielóide crônica (LMC) é uma doença mieloproliferativa e sua patogênese está associada à expressão de um neogene, bcr-abl, que codifica uma proteína tirosina quinase Bcr-Abl. Esse trabalho tem como objetivos o estudo dos mecanismos envolvidos na resistência à morte das células Bcr-Abl positivas e a identificação de alterações gênicas nessas células. Dados de expressão gênica global obtidos por \"microarray\" mostraram uma superexpressão nas células HL-60.Bcr-Abl com relação a HL-60 dos genes faim e nipa, que foi confirmada por qRT-PCR em diferentes linhagens celulares Bcr-Abl positivas. Já os genes de trail e osm, apresentaram uma diminuição significativa em HL-60.Bcr-Abl, que foi confirmada para trail, porém osm não teve seu resultado validado. A avaliação da expressão dos genes em células de pacientes portadores de LMC, em diferentes fases da doença também foi estudada. Com esses resultados, o presente estudo visa a melhor compreensão de como alterações na expressão desses genes contribuem na fisiopatologia da LMC. / Chronic myelogenous leukemia (CML) is a stem cell disease characterized by the presence of the Bcr-Abl oncoprotein, which is the cause of the malignant transformation and the extreme resistance to apoptosis displayed by CML patients. Our aim was to analyze the alteration in global gene expression in Bcr-Abl expressing cells. Data obtained from microarray analysis showed significant up-regulation of nipa and faim in HL60.Bcr-Abl and down-regulation of osm and trail. These results were further confirmed by Real-Time PCR to nipa, faim and trail, but not for osm expression in HL-60.Bcr-Abl cells. To evaluate the potential of some of the modified genes as therapeutic targets or prognostic markers for CML, we also analyzed the expression of these genes in samples from CML patients.

Chronic myeloid leukemia (CML) is a disease characterized by the expansion of granulocytic cells. The BCR-ABL tyrosine kinase inhibitor imatinib, the frontline treatment for Ph+ leukemias, can induce complete hematologic and cytogenetic response in most chronic phase CML patients. Despite the remarkable initial clinic effects, it is now recognized that imatinib will unlikely cure patients because a small cell population containing leukemic stem cells (LSCs) with self-renewal capacity is insensitive to tyrosine kinase inhibitors. In Chapter I, I briefly review the BCR-ABL kinase and its related signaling pathways. BCR-ABL kinase activates several signaling pathways including MAPK, STAT, and JNK/SAPK. BCR-ABL also mediates kinase-independent pathways through SRC family kinases. I will also discuss pathways involving β-catenin, hedgehog, FoxO and Alox5 are critical to the regulation of self-renewal and differentiation in LSC of CML. As detailed in Chapter II, I describe our work evaluating the effects of omacetaxine, a novel CML drug inducing cell apoptosis by inhibition of protein synthesis, on self-renewal and differentiation of LSCs and BCR-ABL-induced CML and acute lymphoblastic leukemia (B-ALL) in mice. We found that treatment with omacetaxine decreased the number of LSCs and prolonged the survival of mice with CML or B-ALL. In chapter III, I describe that Alox5 is an essential gene in the function of LSCs and CML development. We show evidence that Alox5 affects differentiation, cell division, and survival of long-term LSCs. Treatment of CML mice with a 5-LO inhibitor also impaired the function of LSCs similarly and prolonged survival. In chapter IV, I present evidence of our work showing a further dissection the Alox5 pathway by comparing the gene expression profiles of wild type and Alox5-/- LSCs. We show that Msr1 deletion causes acceleration of CML development. We also show that Msr1 affects CML development by regulating the PI3K-AKT pathway and β-catenin. Taken together, these results demonstrate that some pathways including Alox5 and Msr1 play an important role in regulating the self-renewal and differentiation of LSC. More efforts should be put into developing the novel strategies that may effectively target LSCs and thus cure CML.