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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.

Identification of recurrent mutations through next-generation sequencing (NGS) has given us a deeper understanding of the molecular mechanisms involved in chronic lymphocytic leukemia (CLL) development and progression and provided novel means for risk assessment in this clinically heterogeneous disease. In paper I, we screened a population-based cohort of CLL patients (n=364) for TP53, NOTCH1, SF3B1, BIRC3 and MYD88 mutations using Sanger sequencing, and confirmed the negative prognostic impact of TP53, SF3B1 or NOTCH1 aberrations, though at lower frequencies compared to previous studies. In paper II, we assessed the feasibility of targeted NGS using a gene panel including 9 CLL-related genes in a large patient cohort (n=188). We could validate 93% (144/155) of mutations with Sanger sequencing; the remaining were at the detection limit of the latter technique, and technical replication showed a high concordance (77/82 mutations, 94%). In paper III, we performed a longitudinal study of CLL patients (n=41) relapsing after fludarabine, cyclophosphamide and rituximab (FCR) therapy using whole-exome sequencing. In addition to known poor-prognostic mutations (NOTCH1, TP53, ATM, SF3B1, BIRC3, and NFKBIE), we detected mutations in a ribosomal gene, RPS15, in almost 20% of cases (8/41). In extended patient series, RPS15-mutant cases had a poor survival similar to patients with NOTCH1, SF3B1, or 11q aberrations. In vitro studies revealed that RPS15mut cases displayed reduced p53 stabilization compared to cases wildtype for RPS15. In paper IV, we performed RNA-sequencing in CLL patients (n=50) assigned to 3 clinically and biologically distinct subsets carrying stereotyped B-cell receptors (i.e. subsets #1, #2 and #4) and revealed unique gene expression profiles for each subset. Analysis of SF3B1-mutated versus wildtype subset #2 patients revealed a large number of splice variants (n=187) in genes involved in chromatin remodeling and ribosome biogenesis. Taken together, this thesis confirms the prognostic impact of recurrent mutations and provides data supporting implementation of targeted NGS in clinical routine practice. Moreover, we provide evidence for the involvement of novel players, such as RPS15, in disease progression and present transcriptome data highlighting the potential of global approaches for the identification of molecular mechanisms contributing to CLL development within prognostically relevant subgroups.

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

O carcinoma espinocelular de lábio (CEC) é uma patologia relativamente freqüente e acomete preferencialmente indivíduos de pele clara e com antecedentes de exposição solar. A localização labial do CEC está associada ao comportamento clínico mais agressivo. Algumas características clínicas e histológicas, como tamanho do tumor, grau de diferenciação, espessura, invasão perineural e perivascular, atuam como fatores prognósticos do CEC de lábio. A presença do infiltrado inflamatório vem sendo associada ao comportamento de diversos tumores, dentre eles o CEC. Esse infiltrado é composto por linfócitos T, B, células natural killer, macrófagos e eosinófilos. O papel do infiltrado eosinofílico no CEC é bastante controverso, mostrando associação tanto com melhor como com pior prognóstico. Neste trabalho, tentamos relacionar os infiltrado eosinofílico e linfocítico entre si e estabelecer uma possível associação com o prognóstico do tumor. Foram avaliados 29 casos de CEC de lábio atendidos no ambulatório de cirurgia dermatológica do HC-FMUSP, no período de 1980 a 1989. Foram colhidos dados clínicos provenientes dos prontuários (sexo, idade, tabagismo, duração da lesão, presença de recidiva e metástase) e dados histológicos (grau de diferenciação, espessura, invasão perineural e perivascular, comprometimento da camada muscular, contagem de eosinófilos peritumoral e intratumoral, contagem de linfócitos) em lâminas coradas pela hematoxilia-eosina. A comparação entre a quantificação dos eosinófilos na área intra e peritumoral mostrou-se semelhante. Não foi encontrada significância estatística entre a contagem de eosinófilos tumorais e fatores que funcionam como prognósticos do CEC de lábio (espessura, duração da lesão, infiltrado perivascular e perineural, comprometimento da camada muscular, grau de diferenciação, presença de recidiva e metástase). O infiltrado linfocítico desempenha fator prognóstico nos casos de melanoma, porém, no CEC, ainda é controverso. Foi realizada a classificação semiquantitativa do infiltrado linfocítico e comparada às mesmas variáveis estudadas com os eosinófilos. Foi encontrada relação estatisticamente significativa entre maior infiltrado linfocítico e menor grau de diferenciação das células tumorais, sugerindo um papel importante dos antígenos de superfície presentes no desencadeamento da resposta imune linfocitária anti-tumoral. As outras comparações não se mostraram significativas. Tentamos relacionar ainda a quantidade de eosinófilos e linfócitos no infiltrado, e observamos que as duas populações de células se comportam de maneira independente. Concluímos então que os infiltrados eosinofílicos peritumoral e intratumoral apresentam quantidades semelhantes de eosinófilos; o infiltrado eosinofílico não tem relação com prognóstico do CEC de lábio; o número de linfócitos no infiltrado tumoral é maior em tumores mais indiferenciados; o infiltrado linfocítico não influencia no restante dos fatores que funcionam como prognóstico do CEC de lábio; a quantidade de eosinófilos e linfócitos no CEC de lábio comportam-se de maneira independentes / The squamous-cell carcinoma (SCC) is a pathology quite frequent in people in general, mostly in white persons with history of excessive exposition to the sun rays. The fact of the SCC is located on the lips is associated with the most aggressive clinical behavior. Some clinical and histological characteristics, as the size of the tumor, degree of differentiation, density, perineural and perivascular invasion, act as prognostic factors of SCC of the lip. The presence of the tumor-infiltrating has being associated with the behavior of several tumors, including SCC. This infiltrating is composed by lymphocytes T, B, natural killer cells, macrophages and eosinophils. The role of the eosinophilict infiltrating in SCC is controversial enough because it shows association with both best and worst prognosis. In this study, we tried to stablish relations between the eosinophilic and the lymphocytic infiltratings, to stablish a possibility of association with the tumor prognosis. In order to achieve our objective, we have analized 29 cases of SCC os lip observed in the ambulatory of dermatologic surgery of HC-FMUSP from 1980 to 1989. We have also collected clinical data from the patient\'s promptuaries (sex, age, tobaccoism, time of lesion, presence of recurrence and metastasis) and histological data (degree of differentiation, depth, perineural and perivascular invasion, infiltration of the muscle layer, counting of peritumoral and intratumoral eosinophils, counting of lymphocytes) in microscopic features stained with hematoxylin and eosin. When comparing quantities of eosinophils in the intra and peritumoral areas we found them similar. We have not found any significant differences between the counting of tumoral eosinophils and factors that work as SCC of lips prognosis (depth, time of lesion, perivascular and perineural invasion, infiltration of the muscle layer, degree of differentiation, presence of recurrence and metastasis). The lymphocytic infiltrating acts as prognostic factor in the cases involving melanoma, however, in CEC it is still controversial. We have proceeded a classification of the lymphocytic infiltrating and compared with the same fluctuations studied with the eosinophils. We have found a significant relationship between the higher lymphocytic infiltrating and a minor degree of differentiation of tumoral cells, which suggests that the surface antigens in the lymphocytic anti-tumor immune response have an important role. Other comparisons were not significant. We tried to list the quantity of eosinophils and lyphocytes in the infiltrating and we noted that two groups of cells had differents behaviors. We conclude, therefore, that: the peritumoral and intratumoral eosinophilic infiltrating present similar quantities of eosinophils; the eosinophilic infiltrating is not related to the SCC of lips prognosis; the number of lyphocytes in the tumoral infiltrating is higher in less differentiated tumors; the lymphcytic infiltrating has no influence in the other factors that work as lips\' CEC prognosis; and the quantity of eosinophils and lymphocites in the SCC of lips have independent behaviors

Para avaliar a reserva adrenal após o uso de glicocorticóide na fase de indução de remissão em pacientes com Leucemia Linfocítica Aguda, estudo duplo-cego foi realizado em 29 crianças e adolescentes de 1,7 a 15,9 anos (média:6,8 anos], que receberam por escolha aleatória, Prednisona na dose de 40 mg/m²/dia ou Dexametasona, 6 mg/m²/dia, via oral, por um mês. Testes do ACTH em baixa dose (1,0 µg/m² EV) foram realizados antes e a cada 7 dias por 8 semanas para avaliar pico de cortisol após o estímulo. Não houve diferença significativa entre as médias dos picos de cortisol nos testes realizados em cada grupo e entre os dois grupos, mostrando reserva adrenal adequada. Não houve correlação entre os picos de cortisol nos dois grupos e a presença de infecção / In order to evaluate adrenal reserve after adminstration of glucocorticoid during induction phase in patients with Acute LymphociticLeukemia, a double-blind study was performed in 29 children and adolescents 1,7 to 15.9 years old (mean: 6.8 years old), who randomly were chosen to receive either Prednisone, 40 mg/m²/day or Dexamethasone, 6 mg/m²/day, PO, for one month. Low-dose ACTH tests (1.0 µg/m² IV), were performed before and every 7 days after glucocorticoid for 8 weeks. There were no significant differences of cortisol mean peak levels in the tests of each group and in both group, suggesting adequate adrenal reserve. There was no correlation of cortisol mean peak levels in both groups and the presence of infection