Le réarrangement FIP1L1-PDGFRA (F/P), identifié de manière récurrente dans les leucémies chroniques à éosinophiles, est à l’origine d’une activation constitutive de l’activité tyrosine kinase de la chaîne α du récepteur au PDGFR. Les mécanismes concourant à la prolifération éosinophile exclusive et au profil de cytotoxicité spécifique à cette leucémie sont encore mal élucidés. Ce récepteur PDGFRα;, principalement exprimé dans les cellules mésenchymateuses, y exerce des effets prolifératifs et chimiotactiques, en partie induits par la production intracellulaire de dérivés réactifs de l’oxygène (ROS). Ces constatations nous ont amené à étudier les perturbations du métabolisme oxydatif dans la leucémie F/P+, en utilisant une approche d’étude globale du protéome d’éosinophiles de sujets F/P+, comparé à des éosinophiles de sujets contrôles. Dans ce travail, nous avons démontré qu’il existe, dans les éosinophiles F/P+, une dérégulation de nombreuses protéines impliquées dans la signalisation redox intracellulaire. De plus, les modifications d’expression de certaines d’entre elles (peroxiredoxine-2, src-homology-2 domain containing tyrosine phosphatase-1 ou SHP-1), non retrouvées dans les éosinophiles de patients ayant un syndrome hyperéosinophilique idiopathique, et identifiées dans une lignée cellulaire exprimant F/P, semblent spécifiquement induites par F/P. L’activation du PDGFRα; dans les éosinophiles F/P+ est donc à l’origine d’un déséquilibre du métabolisme oxydatif dont les conséquences sur la différenciation vers le lignage éosinophile ou sur la cytotoxicité seront discutées. / The FIP1L1-PDGFRA (F/P) fusion gene, identified as a recurrent molecular finding in chronic eosinophilic leukemia, induces a constitutive activation of the kinase domain of PDGFRα. However, the molecular events contributing to the predominant eosinophil lineage expansion and to the singular cytotoxicity profile of eosinophils in this leukemia remain unclear. PDGFRα;, mainly expressed in mesenchymal cells, possesses proliferative and chemotactic properties, which are, in part, mediated by the intracellular production of reactive oxygen species (ROS). These observations prompted us to investigate the disturbances of the redox signaling in the F/P-associated leukemia, using a comparative study of the proteome of F/P+-eosinophils and eosinophils of healthy controls. Here, we report, in F/P+-eosinophils, the abnormal expression of numerous proteins implicated in oxidative metabolism. Furthermore, changes in expression of particular proteins (peroxiredoxine-2 and src-homology-2 domain containing tyrosine phosphatase-1) appears specific to F/P-Eos compared to patients with idiopathic hypereosinophilic syndrome, and could be demonstrated in F/P-expressing cell line EOL-1. Thus, the activation of PDGFRα; in F/P+-eosinophils leads to a global disturbance of the redox signaling, whose consequences on the differentiation toward eosinophil lineage and cytotoxicity will be discussed.

L'hématopoïèse est le processus développemental qui permet la formation des cellules qui composent le sang. Au niveau moléculaire, de nombreux facteurs de transcription permettent une régulation fine de ce processus et la dérégulation de leur activité, en affectant la différenciation ou la prolifération des cellules sanguines, peut conduire à l'apparition d'hémopathies telles que les leucémies. De manière intéressante, de nombreux gènes contrôlant l'hématopoïèse sont conservés entre la Drosophile et l'homme. Ces dernières années, cet insecte a donc émergé en tant que modèle pour l'étude du développement normal et pathologique des cellules hématopoïétiques. En tirant profit de cette conservation, mon travail de thèse a visé à caractériser, chez la Drosophile, le rôle et le mode d'action des protéines de la famille " Myeloid Leukemia Factor " (MLF). En effet, bien que le membre fondateur de cette famille soit impliqué dans le développement de Leucémies Aigües Myéloïdes chez l'homme, ces protéines restent très peu caractérisés. Les travaux réalisés dans l'équipe montrent que MLF contrôle l'homéostasie du système sanguin de la Drosophile, et qu'un aspect conservé de la fonction des protéines MLF est de réguler l'activité de facteurs de transcription de type RUNX dont Lozenge (LZ). Dans ce contexte, j'ai cherché à déterminer plus précisément la fonction de MLF dans l'hématopoïèse et à comprendre comment MLF régule les facteurs RUNX. In vivo, j'ai montré que MLF contrôle non seulement le nombre de cellules sanguines RUNX+/LZ+ mais aussi leur différenciation en "cellules à cristaux". L'établissement par RNAseq du transcriptome de ces cellules en contexte sauvage ou mutant pour mlf m'a permis d'identifier de nouveaux marqueurs de ce lignage et de montrer que mlf régule l'expression de nombre d'entre eux. De plus j'ai mis en évidence que ces deux aspects de la fonction de mlf passent par la régulation de LZ. Ainsi, bien que lz soit nécessaire au développement des cellules à cristaux, une diminution de son expression s'accompagne d'une augmentation du nombre de ces cellules qui présentent alors des caractéristiques " hyper-différenciées " et une sur-activation de la voie de signalisation Notch. Ces données mettent en exergue l'importance de la régulation du niveau du facteur RUNX LZ par MLF au cours de l'hématopoïèse. D'autre part, en utilisant une lignée de cellules sanguines de Drosophile en culture (cellules Kc167), j'ai pu montrer que MLF régule post-traductionnellement le niveau de LZ et que MLF et LZ interagissent physiquement. Pour ouvrir de nouvelles pistes quant aux mécanismes moléculaires d'action de MLF, j'ai également cherché ses partenaires par spectrométrie de masse. J'ai ainsi identifié la protéine chaperonne DNAJ1/HSP40 et j'ai pu mettre en évidence que ce partenaire de MLF est aussi impliqué dans la régulation de l'activité et du niveau d'expression de LZ en culture cellulaire. J'ai ensuite généré un mutant de ce gène chez la Drosophile par CRISPR et j'ai pu montrer qu'il contrôle lui aussi le développement des cellules sanguines LZ+, probablement en interaction avec MLF. Mes résultats suggèrent donc que MLF pourrait faire partie d'un complexe chaperon impliqué dans le contrôle de l'activité de LZ et dans l'hématopoïèse. / Haematopoiesis is the developmental process responsible for the formation of all blood cell types. At the molecular level, many transcription factors allow tight regulation of this process and deregulation of their activity, by affecting blood cell proliferation or differentiation, can lead to the appearance of various diseases including leukaemia. Interestingly, many genes implicated in haematopoiesis are conserved between Drosophila and human. Consequently, this insect has emerged as a potent model to study normal and pathological blood cell development. Taking advantage of this conservation, my thesis aimed at characterizing the role and mode of action of the "Myeloid Leukemia Factor" (MLF) family in Drosophila. Indeed, although the founding member of this family is involved in the development of Acute Myeloid Leukaemia in humans, this family remains poorly characterised. Previous work showed that MLF controls Drosophila blood cell homeostasis and that one conserved aspect of MLF function is to regulate the activity of RUNX transcription factor activity, including that of the Drosophila hematopoietic factor LOZENGE (LZ). Further to these results, I sought to determine more precisely MLF function in haematopoiesis and its molecular mechanism of action on RUNX factors. In vivo, I showed that mlf controls not only the number of LZ + blood cells but also their differentiation into "crystal cells. Notably, the establishment of wild type or mlf-/- LZ+ cells transcriptome by RNAseq allowed me to identify new markers for this lineage and revealed that mlf regulates the expression of a large number of them. Interestingly, I found that mlf controls both LZ+ cell number and their differentiation by regulating LZ level. Indeed, although lz is required for crystal cell development, a decrease in lz level is associated with increased LZ+ cell number and these cells exhibit "hyper-differentiated" phenotypes as well as Notch signalling pathway over-activation. These data underline the crucial role of RUNX level regulation by MLF for normal blood cell development. In parallel, using a Drosophila blood cell line (Kc167 cells), I showed that MLF physically interacts with LZ and post-translationally regulates its level. To open new leads concerning the molecular mode of action of MLF, I undertook a proteomic approach to identify its partners. Thereby, I found that the chaperon protein DNAJ1/HSP40 binds to MLF and I demonstrated that DNAJ1 is also implicated in the regulation of LZ level and activity in Kc cells. Using a CRISPR approach, I then generated a null dnaj1 allele in Drosophila and its phenotypic characterisation allowed me to show that DNAJ1 also controls the development of LZ+ blood cells, probably in interaction with MLF. All together, my results suggest that MLF could be part of a " chaperon " complex involved in controlling RUNX activity and haematopoiesis.

Class of 2004 Abstract / Objective: To develop and populate a decision-analytic model comparing the cost and efficacy of imatinib versus allogenic bone marrow transplantation (BMT) with a matched unrelated donor in the treatment of newly-diagnosed, Philadelphia positive (Ph (+)), chronic phase, chronic myelogenous leukemia (CML). Design: Markov cohort analysis and Monte Carlo microsimulation. Measurements and Main Results: Direct medical costs were measured from the perspective of a third-party payer. Efficacy data and probabilities were obtained from survivability findings emanating primarily from randomized controlled trials (RCTs). A two-year time horizon was employed with three month treatment cycles. BMT was established as the baseline comparator and the base case was defined as a 35 year old, Ph(+) male patient with newly-diagnosed CML. Results from the Monte Carlo trial found that the incremental cost-efficacy ratio was −$5,000 for imatinib (95th % Confidence Interval: −$70,000, $84,000). Analysis of the cost-efficacy plane indicated that imatinib dominated BMT in 84.69 percent of cases, while BMT was dominant in 0.76 percent of cases. Sensitivity analyses of costs and discount rates found results to be robust. Conclusion: Imatinib was observed in a majority of cases to be both less costly and more efficacious relative to BMT in the treatment of CML, suggesting that this pharmaceutical agent is a dominant therapeutic strategy. When available, the incorporation of long-term clinical data are required to assess cost-efficacy beyond the two-year time horizon of this study.

Transcription factors (TFs) are key regulators of gene expression whose failure has been implicated in many diseases, including cancer. They bind at various sites at different specificity depending on the prevailing cellular conditions, disease, development stage or environmental conditions of the cell. TF binding specificity is how well a TF distinguishes functional sites from potential non-functional sites to form a useful regulatory network. Owing to its role in diseases, various techniques have been used to determine TF binding specificity in vitro and in vivo, including chromatin immuno-precipitation followed by massively parallel sequencing (ChIP-seq). ChIP-seq is an in vivo technique that considers how the chromatin landscape affects TF binding. Motif enrichment analysis (MEA) tools are used to identify motifs that are over-represented in ChIP-seq peak regions. One such tool, CentriMo, finds over-represented motifs at the center since peak calling software are biased to declaring binding regions centered at the TF binding site. In this study, we investigate the use of CentriMo and other MEA tools to determine the difference in motif enrichment attributed presence of Chronic Myeloid leukemia (CML)), treatment with Interferon (IFN) and Dexamethasone (DEX) compared to control based on Fisher’s exact test; using uniform peaks ChIP-seq data generated by the ENCODE consortium. CentriMo proved to be capable. We observed differential motif enrichment of TFs with tumor promoter activity: YY1, CEBPA, Egr1, Cmyc family, Gata1 and JunD in K562 while Stat1, Irf1, and Runx1 in Gm12878. Enrichment of CTCF in Gm12878 with YY1 as the immuno-precipitated (ChIP-ed) factor and the presence of significant spacing (SpaMo analysis) of CTCF and YY1 in Gm12878 but not in K562 could show that CTCF, as a repressor, helps in maintaining the required YY1 level in a normal cell line. IFN might reduce Cmyc and the Jun family of TFs binding via the repressive action of CTCF and E2f2. We also show that the concentration of DEX treatment affects motif enrichment with 50nm being an optimum concentration for Gr binding by maintaining open chromatin via AP1 TF. This study has demonstrated the usefulness of CentriMo for TF binding specificity analysis.

A significant body of literature has reported strategies and techniques to assess the mechanical properties of biological samples such as proteins, cellular and tissue systems. Atomic force microscopy has been used to detect elasticity changes of cancer cells. However, only a few studies have provided a detailed and complete protocol of the experimental procedures and data analysis methods for non-adherent blood cancer cells. In this work, the elasticity of NB4 cells derived from acute promyelocytic leukemia (APL) was probed by AFM indentation measurements to investigate the effects of the disease on cellular biomechanics. Understanding how leukemia influences the nanomechanical properties of cells is expected to provide a better understanding of the cellular mechanisms associated to cancer, and promises to become a valuable new tool for cancer detection and staging. In this context, the quantification of the mechanical properties of APL cells requires a systematic and optimized approach for data collection and analysis, in order to generate reproducible and comparative data. This Thesis elucidates the automated data analysis process that integrates programming, force curve collection and analysis optimization to assess variations of cell elasticity in response to processing criteria. A processing algorithm was developed by using the IGOR Pro software to automatically analyze large numbers of AFM data sets in an efficient and accurate manner. In fact, since the analysis involves multiple steps that must be repeated for many individual cells, an automated and un-biased processing approach is essential to precisely determine cell elasticity. Different fitting models for extracting the Young’s modulus have been systematically applied to validate the process, and the best fitting criteria, such as the contact point location and indentation length, have been determined in order to obtain consistent results. The designed automated processing code described in this Thesis was used to correlate alterations in cellular biomechanics of cancer cells as they undergo drug treatments. In order to fully assess drug effects on NB4 cells, viability assays were first performed using Trypan Blue staining for primary insights before initiating thorough microplate fluorescence intensity readings using a LIVE/DEAD viability kit involving ethidium and calcein AM labelling components. From 0 to 24 h after treatment using 30 µM arsenic trioxide, relative live cell populations increased until 36 h. From 0 to 12 h post-treatment, relative populations of dead cells increased until 24 h post-treatment. Furthermore, a drastic drop in dead cell count has been observed between 12 and 24 h. Additionally, arsenic trioxide drug induced alterations in elasticity of NB4 cells can be correlated to the cell viability tests. With respect to cell mechanics, trapping of the non-adherent NB4 cells within fabricated SU8-10 microwell arrays, allowed consistent AFM indentation measurements up to 48 h after treatment. Results revealed an increase in cell elasticity up to 12 h post-treatment and a drastic decrease between 12 and 24 h. Furthermore, arsenic trioxide drug induced alterations in elasticity of NB4 cells can be correlated to the cell viability tests. In addition to these indentation and viability testing approaches, morphological appearances were monitored, in order to track the apoptosis process of the affected cells. Relationships found between viability and elasticity assays in conjunction with morphology alterations revealed distinguish stages of apoptosis throughout treatment. 24 h after initial treatment, most cells were observed to have burst or displayed obvious blebbing. These relations between different measurement methods may reveal a potential drug screening approach, for understanding specific physical and biological of drug effects on the cancer cells.

Cytogenetic evaluation of human bone marrow cells is one of the principal sources of diagnostic and prognostic information in the evaluation of the myeloid leukemias. In the majority of cases, these diseases are characterized by non-random chromosomal changes in the cells of the malignant clone. The chromosomal abnormalities are present only in the leukemic cells, which are distributed along with normal cells in the bone marrow and throughout the circulation. The objective of this thesis was to test the hypothesis that suitable criteria could be established for automated metaphase detection using human bone marrow preparations. This involved computerized, low resolution scanning of a specimen slide, and the measurement of object features which allowed metaphases to be adequately distinguished from nuclei and debris. Two approaches were investigated. The first used a line-scanning system, in which microscope slides were scanned line by line with a linear CCD detector, and focussing was performed automatically. Eighteen signal features were measured for each detected object. Three group discriminant function analysis was performed on objects from a large number of slides from both types of preparations, in order to distinguish metaphases from nuclei and debris. The second method evaluated the use of a frame scanning system. Objects were detected in a frame-by-frame scan of microscope slides, using a two dimensional CD camera. Feature measurements were performed for all objects within a specified area range, and three group discriminant function analysis was performed on data from a large number of slides. In both approaches, the performance of the discriminant functions was evaluated on independent samples collected from a number of patients, in order to determine the operational error rates of the systems. The sensitivity of the line scan system for metaphase detection was 86%, compared to 92% fror the frame scannning system, while the specificity was 84% for the line scan system, and 86% for the frame scanning system. The frame scan system was shown to be useful for determining the mitotic index of cells cultured for varying periods of time prior to fixation. Four patients with AML were examined, and the results of the analysis show that the mitotic indices could be determined in this way to an accuracy of approximately 5%. The mitotic indices differed as a function of time for different patients. / Science, Faculty of / Physics and Astronomy, Department of / Graduate

Acute myeloid leukemia (AML) often remains refractory to current chemotherapy and transplantation approaches despite many advances in our understanding of mechanisms in leukemogenesis. The bone marrow “niche” or microenvironment, however, may be permissive to leukemia development and studying interactions between the microenvironment and leukemia cells may provide new insight for therapeutic advances. Mesenchymal stem cells (MSCs) are central to the development and maintenance of the bone marrow niche and have been shown to have important functional alterations derived from patients with different hematological disorders. The extent to which MSCs derived from AML patients are altered remains unclear. The aim of this study was to detect changes occurring in MSCs obtained from human bone marrow in patients with AML by comparing their function and gene expression pattern with normal age-matched controls. MSCs expanded from patients diagnosed with acute leukemia were observed to have heterogeneous morphological characteristics compared to the healthy controls. Immunohistochemistry and flow data confirmed the typical cell surface immunophenotype of CD90+ CD105+ CD73+ CD34- CD45-, although MSCs from two patients with AML revealed reduced surface expression of CD105 and CD90 antigens respectively. Differentiation assays demonstrated the potential of MSCs from AML patients and healthy donors to differentiate into bone, fat and cartilage. However, the ability of MSCs from AML samples to support hematopoietic function of CD34+ progenitors was found to be impaired while the key hematopoietic genes were found to be differentially expressed on AML-MSCs compared to nMSCs. These studies indicate that there exist differences in the biologic profile of MSCs from AML patients compared to MSCs derived from healthy donors. The results described in the thesis provide a formulation for additional studies that may allow us to identify new targets for improved treatment of AML.

Background: Leukemia is the most common form of cancer in children, with eight out of ten children surviving the disease. Children who develop leukemia are usually between two and six years old. Fatigue is one of the most common side effects in children undergoing treatment for leukemia. Fatigues can reduce the mental, physical and social well-being of the patient. Aim: The purpose of this study was to investigate how fatigue affects children with leukaemia during care and changes in fatigue over time.  Method: A literature review that includes ten scientific articles that have been quality reviewed according to the Swedish Agency for Medical and Social Evaluation (SBU) review template and according to Willman, Stoltz och Bahtsevani (2011) template. Result: The results from 10 articles are reported in two different categories. These were; impact on quality of life during care and sleep. The results show that children with leukaemia rated their quality of life low during the care period. Fatigue also had negative effects on children's sleep. Conclusion: Sleep and quality of life in children with leukemia are negatively affected by fatigue. Changes in the degree of fatigue could be demonstrated in several articles. / SAMMANFATTNING Bakgrund: Leukemi är den vanligaste cancerformen hos barn där åtta av tio barn överlever sjukdomen. Barn som insjuknar i leukemi är oftast mellan två och sex år gamla. Fatigue är en av de vanligaste biverkningarna som förekommer hos barn som genomgår behandling av leukemi. Fatigues kan minska det psykiska, fysiska och social välbefinnandet hos patienten. Syfte: Syftet med denna studie var att undersöka hur fatigue påverkar barn med leukemi under vårdtiden samt förändringar av fatigue över tid.  Metod: En litteraturöversikt som har en deskriptiv design och de vetenskapliga artiklarna har kvalitetsgranskats efter Statens beredning för medicinsk och social utvärderings (SBU) granskningsmall samt Willman, Stoltz och Bahtsevani (2011) granskningsmall.  Resultat: Resultatet från tio artiklar redovisas i två olika kategorier. Dessa var; påverkan på livskvalitén under vårdtiden och sömn. Det framkom i resultatet att fatigue hade en negativ inverkan på livskvalitén hos barn med leukemi där barnen skattade sin livskvalité som låg under vårdtiden. Fatigue hade även negativa effekter på barns sömn.  Slutsats: Livskvalitén och sömnen hos barn med leukemi påverkades negativt av fatigue. Förändringar av graden fatigue kunde påvisas i ett flertal artiklar.

Adoptive T cell immunotherapy is emerging as a powerful approach to treat diseases ranging from cancer to autoimmunity. T cell therapy involves isolation, modification, and reintroduction of T cells as “living drugs” to induce a durable response. A key capability to fully realize the potential of T cell therapies is effective manipulation of ex vivo T cell activation, with the aim of increasing T cell production and promoting specific phenotypes. While initial efforts to modulate T cell activation have heavily focused on mimicking biochemical signaling and ligand-receptor interactions between T cells and antigen presenting cells (APCs), there is increasing appreciation for understanding the role of mechanics at this interface and utilizing these insights to improve T cell activation systems. The aims of this dissertation is to contribute to this understanding by elucidating how mechanical properties of an activating surface regulate T cell activation, and apply these insights to generate biomaterial based systems to enhance activation from leukemia patient derived T cells. We first use a hydrogel system to investigate patterns T cell activation to substrate stiffness, discovering a biphasic response of T cell activation to stiffness that is synergist with ligand density. We then generate electrospun fiber scaffolds as an alternative platform to improve T cell expansion; we discover that 3D geometry in the form of fiber diameter and span lengths affects T cell activation. Lastly, we characterize the starting makeup of T cell populations from leukemia patients to study patterns of T cell exhaustion, utilizing the developed electrospun fiber scaffold system to enhance expansion of exhausted T cells from leukemia patients, and demonstrate patient-specific responses to different scaffold formulations. This approach allows for engineering of biomaterial designs that can leverage T cell mechanobiology to enhance T cell activation, with potential to be tailored to patient-specific expansion conditions and increasing the availability of T cell therapy to a wider range of patients.

Childhood acute leukaemias are a heterogeneous group of malignant diseases. Based on cell origin, clinical manifestations, and molecular/chromosomal changes, we distinguish two main subtypes: acute myeloid leukaemia and acute lymphoblastic leukaemia. Acute lymphoblastic leukaemia (ALL) is the most frequent form of childhood leukaemia. Acute myeloid leukaemia (AML) is predominantly found in adults, being rarer in childhood. In the Czech Republic, the ALL is in childhood diagnosed approximately five times more often compared to AML. Despite the intensive research, aetiology of leukaemia has not been entirely clarified. So far, we only have knowledge of certain risk factors (ionising radiation, some chemicals and viruses) but in the vast majority of cases the aetiopathogenesis has not yet been made clear. Some of the answers may be provided by studies dealing with the presence of (pre)-leukaemic cells in a material archived prior to the clinical onset of the disease. Such are for example the so-called Guthrie cards, the dried blood samples collected immediately after birth and used in screening of the newborns for metabolic disorders. The better availability of material collected before the diagnosis of a secondary leukaemia (originally meant for the follow-up of the primary malignancy) might help us in better...