The most common human leukemia is B-cell chronic lymphocytic leukemia (B-CLL), which is characterized by a progressive accumulation of abnormal B-lymphocytes in blood, bone marrow and secondary lymphoid organs. Typically disease progression is slow, but as the number of leukemic cells increases, they interfere with the production of other important blood cells, causing the patients to be in an immunosuppressive state. To study the basis of this immunoregulation, we used cells from the transgenic Eμ-TCL1 mouse, which spontaneously develop B-CLL due to a B-cell specific expression of the oncogene, TCL1. Previously we showed that Eμ-TCL1 CLL cells constitutively produce an anti-inflammatory cytokine, IL-10. Here we studied the role of IL-10 in CLL cell survival in vitro and the development of CLL in vivo. We found that neutralization of IL-10 using anti-IL-10 antibodies or blocking the IL-10 receptor (IL-10R) using anti-IL-10R antibodies did not affect the survival of CLL cells in vitro. On the other hand, adoptively transferred Eμ-TCL1 cells grew at a slower rate in IL-10R KO mice vs. wild type (WT) mice. There was a significant reduction in CLL cell engraftment in the spleen, bone marrow, peritoneal cavity and liver of the IL-10R KO compared to WT mice. Further studies revealed that IL-10 could be playing a role in the tumor microenvironment possibly by affecting anti-tumor immunity. This was seen by a reduction in the activation of CD8+ T cells as well as a significantly lower production of IFN-γ by CD4+ T cells purified from CLL-injected WT mice compared to those purified from CLL-injected IL-10R KO mice. Also CLL-primed IL-10R null T cells were more effective than those from similarly CLL-primed wild type mice in controlling CLL growth in immunodeficient recipient mice. These studies demonstrate that CLL cells suppress host anti-tumor immunity via IL-10 production. This led us to investigate possible mechanisms by which IL-10 is produced. We found a novel role of B-cell receptor (BCR) signaling pathway in constitutive IL-10 secretion. Inhibition of Src or Syk family kinases reduces the constitutive IL-10 production by Eμ-TCL1 cells in a dose dependent manner. We identified the transcription factor Sp1 as a novel regulator of IL-10 production by CLL cells and that it is regulated by BCR signaling via the Syk/MAPK pathway.

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Immune cell function varies tremendously between individuals, posing a major challenge to the development and success of emerging cellular immunotherapies. In the context of T cell therapy for cancer, long-term diseases such as Chronic Lymphocytic Leukemia (CLL) often induce T cell deficiencies resembling cellular exhaustion, complicating the preparation of therapeutic quantities of cells and maintaining efficacy once reintroduced to patients. The ability to rapidly estimate the responsiveness of an individual’s T cells could provide a powerful tool for tailoring treatment conditions and monitoring T cell functionality over the course of therapy. This dissertation investigates the use of short-term cellular behavior assays as a predictive indicator of long-term T cell function. Specifically, the short-term spreading of T cells on functionalized planar, elastic surfaces was quantified by 11 morphological parameters. These parameters were analyzed to discern the impact of both intrinsic factors, such as disease state, and extrinsic factors, such as substrate stiffness. This study identified morphological features that varied between T cells isolated from healthy donors and those from patients being treated for CLL. Combining multiple features through a machine learning approach such as Decision Tree or Random Forest provided an effective means for identifying whether T cells came from healthy or CLL donors. To further automate this assay and enhance the classification outcome, an image-based deep learning workflow was developed. The image-based deep learning approach notably outperformed morphometric analysis and showed great promise in classifying both intrinsic disease states and extrinsic environmental stiffness. Furthermore, we applied this imaging-based deep learning method to predict T cell proliferative capacity under different stiffness conditions, enabling rapid and efficient optimization of T cell expansion conditions to better guide cellular immunotherapy. Looking ahead, future efforts will focus on optimizing and generalizing the model to enhance its predictive accuracy and applicability across diverse patient populations. Additionally, we aim to incorporate multi-channel imaging that captures detailed T cell subset information, enabling the model to better understand the complex interactions between different cellular features and their influence on long-term proliferation. Our ultimate vision is to translate this technology into an automated device that offers a streamlined and efficient assessment of T cell functions. This device could serve as a critical tool in optimizing T cell production and monitoring T cell functions for both autologous and allogeneic cell therapies, significantly improving the effectiveness and personalization of cancer immunotherapy.

Les télomères sont les extrémités des chromosomes et sont protégés par le complexe shelterin pour ne pas être reconnus comme des cassures accidentelles d'ADN double brin. Un enjeu majeur dans la recherche sur les télomères est de comprendre comment l'intégrité des extrémités des chromosomes au cours de l'oncogenèse est modifiée. La perte de répétitions télomériques à chaque division cellulaire peut être compensée par l’activité de l’enzyme télomérase qui ajoute "de novo" des motifs télomériques. Bien que la télomérase soit surexprimée dans la majorité des cellules cancéreuses, l’impact de modifications des protéines shelterin qui coiffent les télomères dans le processus oncogénique n'est pas clair. Dans la première étude, nous avons analysé l'état des télomères de patients atteints de la Leucémie Lymphoïde Chronique (LLC) uniquement au stade précoce de la LLC, stade A de Binet. La LLC est une leucémie commune aux pays occidentaux et se développe chez les personnes âgées. Nous avons montré que la majorité des patients atteints de la maladie présente des télomères dysfonctionnels. Les dommages télomériques ne corrèlent pas avec la longueur des télomères ou le statut mutationnel des patients, mais corrèlent avec la faible expression des protéines télomériques TIN2 et TPP1. Dans la seconde étude, nous avons montré que l'expression de l'oncogène H-RasV12 confère une résistance accrue vis-à-vis des télomères dysfonctionnels et aucun défaut de croissance n’est observable lorsque TRF2, une protéine télomérique est inhibée. Cet effet dépend de l'expression de l'interleukine 6 (IL-6), révélant un rôle inattendu de cette cytokine dans la fonction des télomères. De plus, la co-inhibition de TRF2 et IL-6 dans les cellules RasV12 conduit à blocage G2 / M associé à une séparation des chromatides sœurs. Ces résultats suggèrent que l'induction de la tumorigénicité par l’oncogène Ras protège les télomères contre les dommages et que la ségrégation des chromosomes est dépendante de TRF2 et IL-6. / Telomeres protect the chromosome extremities from being repaired and recognized as accidental DNA breaks double-strand. A major issue in telomere research is to understand how systems monitoring the integrity of chromosomes ends change during oncogenesis. Although telomerase overexpression occurs in the majority of cancer cells, whether other types of telomere changes play roles in the oncogenic process is unclear. In the first study, we analyzed the status of telomeres in patients with early stage Chronic Lymphocytic Leukemia (B-CLL), which is a common leukemia in Western countries that develops in the elderly. We showed that the majority of CLL patients exhibit telomeric dysfunction. It does not correlate with telomere length or mutation status of patients, but correlates with low expression of telomeric proteins TIN2 and TPP1. In the second study, we showed that expression of the H-RasV12 oncogene confers increased resistance to telomere uncapping and protects against to growth defects when TRF2, a telomeric protein, is depleted. This effect depends upon the expression of interleukin 6 (IL-6), revealing an unexpected role for this cytokine in telomere function. Notably, the co-inhibition of TRF2 and IL-6 in RasV12 cells led to G2/M block associated with an increased incidence of premature sister chromatid separation. These findings suggest that the induction of a tumorigenic state by oncogenic Ras protects against telomere damage and chromosome segregation defects in TRF2-compromised cells through an increase of IL-6 expression

La spectroscopie vibrationnelle est une technologie permettant de générer une grande quantité de données très informatives quant à la composition moléculaire des échantillons analysés. Lorsqu'elle est couplée à des méthodes chimiométriques de traitement et de classification de données, elle devient un outil très performant pour l'identification de structures et sous-structures des échantillons. Appliqué dans le domaine du biomédical, cet outil présente alors un fort potentiel pour le diagnostic de maladie. C'est dans ce cadre qu'ont été réalisés les travaux de ce manuscrit. Dans une première étude relevant du développement algorithmique, un algorithme automatique de classification non supervisée (basé sur les Fuzzy C-Means) et récemment implémenté au sein du laboratoire pour apporter une aide au diagnostic de cancers cutanés par imagerie infrarouge, a été amélioré afin de i) considérablement réduire le temps nécessaire à son exécution ii) augmenter la qualité des résultats obtenus sur les données infrarouge et iii) étendre son champs d'application à des données réelles et simulées, habituellement employées dans la littérature. Cet outil a été testé sur des données infrarouge acquises sur 16 échantillons de cancers cutanés (BCC, SCC, maladie de Bowen et mélanomes), et sur 49 jeux de données réels et simulés. Les résultats obtenus ont montré la capacité de ce nouvel algorithme à estimer des partitions proches de la réalité quelque soit le type de données étudié. La seconde étude de ce manuscrit avait pour but de mettre au point un outil chimiométrique autonome d'aide au diagnostic de la leucémie lymphoïde chronique par spectroscopie Raman. Dans ce travail, des traitements numériques et l'algorithme de classification supervisée Support Vector Machines, ont été appliqués à des données acquises sur des cellules sanguine de 27 témoins et 49 patients présentant une leucémie lymphoïde chronique. Les résultats de classification obtenus ont montré une sensibilité de 80% et une spécificité de 100% dans la détection de la maladie. / Vibrational spectroscopy is a technology able to record a large amount of molecular information from studied samples. Coupled with chemometrics and classification methods, vibrational spectroscopy is an efficient tool to identify sample structures and substructures. When applied to the biomedical field, this tool shows a high potential for disease diagnosis. It is in this context that the works presented in this thesis have been realized. In a first study, dealing with algorithmic development, an automatic and unsupervised classification algorithm (based on the Fuzzy C-Means) and developed by our laboratory in order to help for skin cancer diagnosis using IR spectroscopy, was improved in order to i) reduce the computational time needed to realize clustering, ii) increase results quality obtained on infrared data, iii) and extend its application fields to simulated and real datasets, commonly used in the literature. This tool has been tested on 16 infrared spectral images of skin cancers (BCC, SCC, Bowen's disease and melanoma), and 49 real and simulated datasets. The obtained results showed the ability of this new algorithm to estimate realistic data partitions regardless the considered dataset. The second study of this work aimed at developing an independent chemometric tool to assist for chronic lymphocytic leukemia diagnosis by Raman spectroscopy. In this second work, different numerical preprocessing steps and a supervised classification algorithm, Support Vector Machines, have been applied on data recorded on blood cells coming from 27 healthy persons and 49 patients with chronic lymphocytic leukemia. The classification results showed a sensitivity of 80% and a specificity of 100% in the disease diagnosis.

[pt] Esta tese propõe uma metodologia, baseada em procedimentos quantitativos, para estimação do risco de evento adverso (recaída ou morte) em crianças portadoras de Leucemia Linfoblástica Aguda (LLA). A metodologia proposta foi implementada e analisada utilizando dados de grupo de crianças diagnosticadas no Setor de Hematologia do Instituto de Puericultura e Pediatria Martagão Gesteira (IPPMG) da UFRJ e no Serviço de Hematologia Hospital Universitário Pedro Ernesto (HUPE) da UERJ que constituem uma considerável parcela dos casos de LLA na infância registrados no Rio de Janeiro nos últimos anos. A estimação do risco de recaída foi realizada através de um modelo de Redes Neurais após uma seqüência de procedimentos de pré- tratamento de variáveis e de refinamentos do método no que concerne a saída alvo da rede. O tratamento das variáveis é fundamental uma vez que o número reduzido de amostras é uma característica intrínseca deste problema. Embora a LLA seja o câncer mais freqüente a infância, sua incidência é de aproximadamente 1 caso por 100 mil habitantes por ano. Os resultados encontrados foram satisfatórios obtendo-se um percentual de acerto de 93% (fora da amostra) para os pacientes que recaíram quando comparados com o método classicamente utilizado na clínica médica para a avaliação do risco de recidiva (método do grupo BFM). Espera-se que os resultados obtidos possam vir a dar subsídios às condutas médicas em relação à estimativa do risco de recidiva dos pacientes, portanto, podendo vir a ser útil na modulação da intensidade da terapêutica. / [en] In this it is proposed a methodology, based on quantitative procedure, to estimate the adverse event risk (relapse or death) in Acute Lymphoblastic Leukemia (ALL) in children. This methodology was implemented and analyzed in a dataset composed by children diagnosed and treated at the hematology service of the Instituto de Puericultura e Pediatria Martagão Gesteira (IPPMG) in the Federal University of Rio de Janeiro and of the Hospital Universitário Pedro Ernesto (HUPE) in the University of state of Rio de Janeiro. This group constitutes a considerable fraction of the ALL cases in childhood registered in the last few years in Rio de Janeiro. The relapse risk was estimated by a Neural Networks model after a sequence of variable pre-treatment procedures. This treatment has a fundamental importance due to the small number of cases (an intrinsic characteristic of this problem). Although, the ALL is the most frequent cancer in childhood, it incidence is approximately just 1 case for 100 000 inhabitants by year. The obtained results may be considered excellent when compared with the classical risk estimative method used in the medical clinics (BFM risk). A perceptual of successes of 93% (out-of-sample) in no- relapse patients was achieved. We expect that the obtained results may subsidize medical conduct concerning the risk of adverse event and so it could be useful in the treatment intensity modulation.

La LLC est caractérisée par une forte hétérogénéité de présentation clinico-biologique avec description de formes indolentes (IGVH mutes, ZAP-70-) et de formes agressives (IGVH non mutes, ZAP-70+). Le BCR et les voies de signalisation en aval ont fait l’objet d'une étude transcriptionnelle de la réponse à une forte stimulation du BCR, que nous avons poursuivi par une approche protéomique. La MW est un syndrome lymphoprolifératif chronique dont la physiopathologie reste actuellement mal comprise même si une mutation récurrente a été récemment décrite. Nous avons pu montrer que l’analyse globale de 48 profils protéomiques permettait de distinguer les cellules de LLC M et UM avant toute stimulation. Parmi les protéines différentiellement exprimées, on peut citer notamment la protéine HCLS1, dont le rôle a déjà été explore dans la LLC. De plus, la stimulation du BCR induit une réponse protéomique spécifique dans les cellules de LLC agressives, correspondant a des variations d’expression de protéines impliquées dans la signalisation cellulaire, la régulation de la réponse immunologique, le métabolisme protéique, la croissance cellulaire et l’apoptose. La diminution d’expression de 2 protéines, RAD23B et PDCD4, après stimulation du BCR de cellules de LLC agressives a été confirmée par Western-Blot chez 19 patients. Cette technologie DIGE permettant également l’étude de différents isoformes protéiques (et notamment d’isoformes de phosphorylation), nous avons observe des modifications d’état de phosphorylation de plusieurs protéines impliquées dans le cytosquelette après stimulation du BCR (lamines, vimentine….). Une étude protéomique par électrophorèse bidimensionnelle E2D DIGE sur des cellules primaires de sang et de moelle issues de patients porteurs de MW non préalablement traités, en comparaison a d’autres syndromes lymphoprolifératifs tels les lymphomes de la zone marginale (LZM) ou la LLC, a permis de mettre en évidence un profil protéomique spécifique des cellules de MW. Parmi les spots polypeptidiques différentiellement exprimés, est à souligner la sous-expression de la protéine Ku70 chez les patients porteurs de MW par rapport aux autres lymphoproliférations. La confirmation de cette sous-expression de Ku70 a été validée au niveau transcriptionnel par PCR classique et au niveau protéique par Western-Blot dans une plus grande cohorte de patients. La mise en évidence de ces protéines d'intérêt dans l'agressivité et la physiopathologie de ces néoplasies lymphoïdes ouvrent la voie à de nouvelles études portant sur la régulation de ces molécules / CLL is characterized by a strong heterogeneity of clinical and biological presentation with indolent forms (mutated IgVH, ZAP-70-) and aggressive forms (unmutated IgVH, ZAP-70 +). BCR and the downstream signaling pathways have been the subject of a study of the transcriptional response to a strong stimulation of the BCR. We continued with a proteomic approach. WM is a chronic lymphoproliferative disorder whose pathophysiology remains poorly understood, although a recurrent mutation has recently been described. We have shown that the overall 48 proteomic profiles analysis allowed to distinguish between CLL cells M and UM before stimulation. Among the differentially expressed proteins include HCLS1 including protein, whose role has already been explored in CLL. Furthermore, stimulation of the BCR induces a specific response in proteomics aggressive LLC cells, corresponding to protein expression changes involved in cellular signaling, regulation of the immune response, protein metabolism, cell growth and apoptosis. The decrease in expression of two proteins, and RAD23B PDCD4 after stimulation aggressive cells was confirmed by Western blotting in 19 patients. This DIGE technology also allows the study of different protein isoforms (especially phosphorylation isoforms), we observed phosphorylation state changes more involved in the cytoskeleton after stimulation of RCC (rolled, vimentin ....). A proteomic study by two-dimensional electrophoresis E2D DIGE on primary cells of blood and marrow from carriers MW previously untreated patients, in comparison to other lymphoproliferative disorders such as marginal zone lymphoma (MZL) or CLL, helped to highlight a specific proteomic profile of cell MW. Among the spots differentially expressed polypeptide is to highlight the under-expression of Ku70 protein in patients MW compared with other lymphoproliferative disorders. The confirmation of this under-expression of Ku70 was confirmed at the transcriptional level by conventional PCR and at the protein level by Western blotting in a larger cohort of patients. We were able to highlight specific proteomic profiles aggressive forms and identification of differently expressed proteins allowed to identify new proteins involved in aggressiveness and pathophysiology of diseases, opening the way for new studies will focus on the regulation of these molecules of interest

Une cellule reçoit en permanence des signaux de son environnement. Cette stimulation induit une cascade de signalisation activant un programme génique et protéomique dynamique aboutissant à une réponse cellulaire adaptée. Dans la leucémie lymphoïde chronique (LLC), la stimulation du récepteur à l’antigène induit un programme et une réponse anormale à l’origine de la prolifération leucémique. Notre objectif est de caractériser ce programme cellulaire pathologique. Pour cela, nous avons mis en place un modèle de stimulation afin de reproduire ex vivo cette stimulation du récepteur à l’antigène de cellules primaires issues de patients porteurs de LLC et d’activer ce programme cellulaire. Nous avons alors analysé la dynamique transcriptionnelle et protéomique activée dans ces cellules afin de caractériser les anomalies de ce programme. Cette étude nous a permis de mettre en évidence la spécificité de ce programme prolifératif et de caractériser les gènes clés de ce programme tumoral. Ces gènes constituent de potentielles cibles thérapeutiques innovantes. / A cell constantly receives signals from its environment. This stimulation induces a signalling cascade activating a dynamic genic and proteomic program, leading to an adapted cellular response. In chronic lymphocytic leukemia (CLL), an antigen receptor stimulation induces a program and an abnormal response behind leukemic proliferation. Our aim was to characterize the pathological cell program. To achieve this, we have implemented a stimulation model to reproduce ex vivo antigen receptor stimulation of primary cells from CLL patients and activate this cellular program. We then analyzed the transcriptional and proteomic dynamics activated in these cells in order to characterize the abnormalities of this program. This study allows us to highlight the specificity of this proliferative program and to identify key genes of tumor program. These genes constitute potential new therapeutic targets.