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.

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.

<p>The telomeres are specialized structures at the end of the chromosomes composed of the repeated DNA sequence (TTAGGG)n and specific proteins bound to the DNA. The telomeres protect the chromosomes from degradation and end to end fusions. Due to the end-replication problem, the telomeric DNA shortens every cell division, forcing the cells into senescence at a critical telomere length. This process can be counteracted by activating a specialized enzyme, telomerase, which adds telomeric repeats to the chromosome ends leading to an extended or infinite cellular life span. Telomerase activity is absent in most somatic tissues but is found in germ cells, stem cells, activated lymphocytes and the vast majority of tumor cells and permanent cell lines. Hence, telomerase has been suggested as a target for cancer treatment as malignant cells almost exclusively express the enzyme and in that context telomere length measurements will be of great importance.</p><p>Telomere length is traditionally measured with a Southern blot based technique. A new method for telomere analysis of cells in suspension, called flow-FISH, was developed based on fluorescence in situ hybridization using a telomeric peptide nucleic acid (PNA) probe,</p><p>DNA staining with propidium iodide and quantification by flow cytometry. Flow-FISH had high reproducibility and the telomere length measurements showed good correlation with Southern blotting results. The flow-FISH technique also allows studies of cells in specific phases of the cell cycle and the replication timing of telomeric, centromeric and other repetitive sequences were analyzed in a number of cells. Like previous studies, centromeres were shown to replicate late in S phase while the telomere repeats were found to replicate early in S phase or concomitant with the bulk DNA, which is opposite to the patterns described in yeast.</p><p>In benign immunopurified lymphocytes from tonsils, high telomerase activity was found in germinal center (GC) B cells. This population also had high hTERT mRNA levels and displayed a telomere elongation as shown by flow-FISH and Southern blotting. Combined immunophenotyping and flow-FISH on unpurified tonsil cells confirmed the results.</p><p>Chronic lymphocytic leukemia (CLL), the most common leukemia in adults, can be divided into pre-GC CLL, characterized by unmutated immunoglobulin VH genes and worse prognosis, and post-GC CLL, with mutated VH genes and better prognosis. In 61 cases of CLL, telomere length was measured with Southern blotting and VH gene mutation status was analyzed. A new association was found between VH mutation status and telomere length, where cases with longer telomeres and mutated VH genes (post-GC CLL) had better prognosis</p><p>than CLL with short telomeres and unmutated VH genes (pre-GC CLL). A larger study of 112 CLL cases was performed using flow-FISH. The same correlation between telomere length and VH mutation status was found but gender seemed to be of importance as telomere length was a significant prognostic factor for the male CLL patients but not in the female group. Age of the patients and spread of disease seemed to affect the prognostic value of VH gene mutation status.</p>

The telomeres are specialized structures at the end of the chromosomes composed of the repeated DNA sequence (TTAGGG)n and specific proteins bound to the DNA. The telomeres protect the chromosomes from degradation and end to end fusions. Due to the end-replication problem, the telomeric DNA shortens every cell division, forcing the cells into senescence at a critical telomere length. This process can be counteracted by activating a specialized enzyme, telomerase, which adds telomeric repeats to the chromosome ends leading to an extended or infinite cellular life span. Telomerase activity is absent in most somatic tissues but is found in germ cells, stem cells, activated lymphocytes and the vast majority of tumor cells and permanent cell lines. Hence, telomerase has been suggested as a target for cancer treatment as malignant cells almost exclusively express the enzyme and in that context telomere length measurements will be of great importance. Telomere length is traditionally measured with a Southern blot based technique. A new method for telomere analysis of cells in suspension, called flow-FISH, was developed based on fluorescence in situ hybridization using a telomeric peptide nucleic acid (PNA) probe, DNA staining with propidium iodide and quantification by flow cytometry. Flow-FISH had high reproducibility and the telomere length measurements showed good correlation with Southern blotting results. The flow-FISH technique also allows studies of cells in specific phases of the cell cycle and the replication timing of telomeric, centromeric and other repetitive sequences were analyzed in a number of cells. Like previous studies, centromeres were shown to replicate late in S phase while the telomere repeats were found to replicate early in S phase or concomitant with the bulk DNA, which is opposite to the patterns described in yeast. In benign immunopurified lymphocytes from tonsils, high telomerase activity was found in germinal center (GC) B cells. This population also had high hTERT mRNA levels and displayed a telomere elongation as shown by flow-FISH and Southern blotting. Combined immunophenotyping and flow-FISH on unpurified tonsil cells confirmed the results. Chronic lymphocytic leukemia (CLL), the most common leukemia in adults, can be divided into pre-GC CLL, characterized by unmutated immunoglobulin VH genes and worse prognosis, and post-GC CLL, with mutated VH genes and better prognosis. In 61 cases of CLL, telomere length was measured with Southern blotting and VH gene mutation status was analyzed. A new association was found between VH mutation status and telomere length, where cases with longer telomeres and mutated VH genes (post-GC CLL) had better prognosis than CLL with short telomeres and unmutated VH genes (pre-GC CLL). A larger study of 112 CLL cases was performed using flow-FISH. The same correlation between telomere length and VH mutation status was found but gender seemed to be of importance as telomere length was a significant prognostic factor for the male CLL patients but not in the female group. Age of the patients and spread of disease seemed to affect the prognostic value of VH gene mutation status.

In chronic lymphocytic leukemia (CLL), the presence of multiple subsets expressing ‘stereotyped’ B-cell receptors (BCRs) has implicated antigen(s) in leukemogenesis. These stereotyped subsets display similar immunoglobulin (IG) gene usage, almost identical complementarity determining region 3’s and may share clinical features. For instance, subsets #1 (IGHV1/5/7/IGKV1-39) and #2 (IGHV3-21/IGLV3-21) have inferior outcome compared to non-subset patients, whereas subset #4 (IGHV4-34/IGKV2-30) display a favourable prognosis. The aim of this thesis was to investigate genomic aberrations, gene expression patterns and methylation profiles in stereotyped subsets and compare epigenetic profiles in CLL and mantle cell lymphoma (MCL). In paper I, we investigated genomic aberrations in subsets #2, #4 and #16 and in non-stereotyped samples (n=101) using high-density 250K SNP arrays. Subset #2 and non-subset #2 IGHV3-21 cases displayed a higher frequency of aberrations than subset #4 cases. The high incidence of del(11q) in both subset #2/non-subset #2 may reflect the adverse survival reported for IGHV3-21 patients. In contrast, the lower frequency of genetic events and lack of poor-prognostic aberrations in subset #4 may partially explain their indolent disease. In paper II, we analysed the global RNA expression in subset #4, #16 and non-subset IGHV4-34 CLL patients (n=25). Subsets #4 and 16 showed distinct gene expression profiles, where genes involved in cell regulatory pathways were significantly lower expressed in subset #4, in line with their low-proliferative disease. In paper III, a genome-wide methylation array was applied to investigate methylation profiles in subsets #1, #2 and #4 (n=39). We identified differential methylation patterns for all subsets and found affected genes to be involved in e.g. apoptosis and therapy resistance. When performing functional annotation, a clear enrichment of genes involved in adaptive immunity was observed. These genes were preferentially methylated in subset #1 when compared to either subset #2 or #4, possibly due to different antigen responses. In paper IV, the genome-wide methylation profiles for 30 CLL and 20 MCL patients were investigated. Distinct methylation profiles were observed, where MCL displayed a more homogeneous profile. Homeobox transcription factor genes showed a higher degree of methylation in MCL, while apoptosis-related genes and proliferation-associated genes were methylated in CLL. In summary, this thesis demonstrates that stereotyped CLL subsets display differences in gene expression profiles, genetic aberrations and methylation patterns, underscoring the functional relevance of subgrouping according to BCR stereotypy. The distinct methylation profiles of CLL and MCL suggests that different epigenetic mechanisms are involved in the pathogenesis of these B-cell malignancies.

<p>B-cell chronic lymphocytic leukemia (CLL) is the most common leukemia in the Western world. Although treatment of this disease has advanced considerably over the past decade, CLL remains incurable with current chemotherapeutics. In addition, available drug regimens for CLL are associated with frequent cytopenia-related complications, such as infection and fatigue. Thus, the major challenge in CLL treatment today is the need for alternative therapeutics with decreased toxicity and improved efficacy for disease refractory to currently available drugs.</p><p> </p><p>CLL is characterized by slow accumulation of malignant cells, which are supported in the microenvironment by cell-cell interactions and soluble cytokines such as tumor necrosis factor (TNF). We evaluated the effect of the small molecule TNF inhibitor LMP-420 on primary CLL cells. LMP-420 exhibited cytotoxic activity against these cells in the MTS assay, with similar potency to the front-line CLL drug fludarabine. LMP-420 induced time- and dose-dependent apoptosis in CLL cells, as demonstrated by annexin V staining, caspase activation, and DNA fragmentation. These changes were associated with decreased expression of the anti-apoptotic proteins Mcl-1, Bcl-xL, Bcl-2, and XIAP. CLL cells from patients with poor prognostic indicators exhibited LMP-420 sensitivity equal to that for cells from patients with favorable characteristics. In addition, LMP-420 potentiated the cytotoxic effect of fludarabine and inhibited in vitro proliferation of CLL cells. In contrast to other CLL therapeutics, LMP-420 exhibited minimal effects on normal peripheral blood mononuclear cell viability, mitogen-stimulated B- and T-cell proliferation, and hematopoietic colony formation. Our data suggest that LMP-420 may be a useful treatment for CLL with negligible hematologic toxicities. </p><p> </p><p>The effect profile of this compound in normal immune cells and the microarray studies in CLL cells indicate that the mechanism of action of LMP-420 likely involves modulation of the NF-kB pathway. Our initial studies demonstrate moderate but significant inhibitory activity against p65, a key member of the NF-kB transcription factor family. Research is ongoing to gain a better understanding of the specific cytotoxicity of LMP-420 for CLL cells and to elucidate other components of its mechanism of action. Regardless of the ultimate mechanistic findings with LMP-420, our studies support this molecule as a promising new CLL therapeutic that warrants further preclinical evaluation.</p> / Dissertation

A previous population-based study of survival in Chronic Lymphocytic Leukemia (CLL) patients in the province of Manitoba demonstrated a lower five-year relative survival among CLL patients compared with the age- and gender-adjusted general population. This decreased relative survival was most pronounced among elderly male CLL patients. In this study, we have demonstrated that the reduced five-year relative survival observed in CLL patients compared to the general population of Manitoba may partially be attributed to increased risk of second cancers and non-referral to specialized CLL clinics. The increased risk of second cancers in CLL patients compared to Follicular Lymphoma (FL), a similar indolent B cell malignancy, was only observed after CLL diagnosis indicating that a CLL-specific factor may be responsible for the increased risk of second cancers in these patients. The risk of second cancers is independent of treatment and surveillance bias but is further increased with chemotherapy. A superior outcome in CLL patients who have been referred to the CancerCare Manitoba (CCMB) specialized CLL clinic was observed that was independent of age, gender, treatment and history of previous cancers. This superior outcome was most pronounced in the elderly CLL patients. We propose that CLL patients should be referred to CLL-specific hematologists and, where not possible, that guidelines created by such experts be followed. Appropriate screening for second cancers should be performed during routine follow up of CLL patients.

Uncovering the chromosomal abnormalities associated with human malignancy can provide significant insights into the molecular basis of tumorigenesis, as well as identifying potential targets for therapy. The present study set out to examine the genetic characteristics of t(2;7)(p11-12;q21-22) translocations arising in conjunction with chronic B-cell neoplasia. Using long-range PCR, a t(2;7) was initially mapped in an individual presenting with the preclinical entity CD5- monoclonal B-cell lymphocytosis. This revealed a breakpoint at 2p11.2 localized to the recombination signal of the immunoglobulin kappa (IGK) variable gene IGKV3-15, and a breakpoint at 7q21.2 located 520 bp upstream of cyclin dependent kinase 6 (CDK6). The same approach was subsequently employed to elucidate near-identical t(2;7) breakpoints in 4 additional cases presenting with chronic lymphocytic leukemia or indolent non-Hodgkin lymphomas. The remarkable consistency of these translocations implicates the dysregulation of CDK6 via translocation to IGK as a recurrent pathomechanism during the emergence of B-cell lymphoproliferative disorders.