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After being theorized by Veselago in 1967, recent developments in metamaterials over the last two decades have allowed scientists and researchers to physically demonstrate that artificial composite media can be engineered to exhibit exotic material properties, such as negative refractive index, by exploiting features in arrays of sub-wavelength unit inclusions. These unconventional electromagnetic properties are realized through the coupling of the microscopic unit inclusions, which govern the macroscopic properties of the structure. After demonstrating that a periodic array of capacitively-loaded loop (CLL) inclusions paired with continuous wire results in negative refraction, this study performs numerical simulations to characterize random metamaterial structures. These structures consist of CLLs that are randomized in both position and orientation. In addition, this thesis introduces an innovative antenna enhancing structure consisting of capacitively-loaded loop (CLL) metamaterial elements loaded radially around a standard dipole antenna at an electrically small distance. As a result of this innovative arrangement, the dipole antenna is easily transformed into a directive mechanically scanned antenna with high realized gain. The desired directivity and gain can be tuned based on the number of radial CLL fins placed around the dipole. Interactions between the antenna and metamaterial elements result in significant enhancement of the maximum radiated field amplitude and front-to-back ratio. This innovative CLL-loaded dipole antenna is compared to the conventional Yagi-Uda antenna. The structures presented in this thesis are modeled using full-wave simulation, and one antenna structure is experimentally verified as a proof-of-concept. / Master of Science

La leucémie lymphoïde chronique (LLC), hémopathie lymphoïde fréquente, se caractérise par une évolution clinique extrêmement variable. Bien que les marqueurs de pronostic soient nombreux dans la LLC, aucun n'est univoque. Dans ce contexte, identifier de nouveaux facteurs prédictifs et comprendre la pathophysiologie de marqueurs pronostiques déjà établis constituent deux objectifs importants pour améliorer la prise en chargethérapeutique de cette hémopathie. Nous avons tout d'abord choisi d'étudier la valeur pronostique et les mécanismes de régulation de l'expression du gène anti-apoptotique MCL1. Nous avons montré que l'expression de MCL1 est un marqueur prédictif de la survie globale parmi l'ensemble despatients et parmi les stades précoces ; ce marqueur est également prédictif de la survie sans traitement des patients en stade A. Ainsi, l'expression de MCL1 permet d'identifier précocement les formes de LLC à haut risque et faible risque d'évolution défavorable. Nous avons également démontré que l'expression de MCL1 est fortement corrélée à l'expression de VEGF, confirmant le rôle de cette voie de signalisation dans la survie des lymphocytes tumoraux et suggérant que VEGF pourrait réguler positivement l'expression de MCL1 selon un mode autocrine. Nous avons ensuite exploré la fonction télomérique en rapport avec les anomalies chromosomiques à valeur pronostique, reflets de l'instabilité génomique. Notre travail a contribué à démontrer la relation entre l'instabilité génomique et le statut télomérique, évalué par la longueur des télomères et l'expression de hTERT et des gènes du complexe shelterin. Nous avons ainsi mis en évidence trois groupes de patients présentant des profilscytogénétiques et télomériques distincts : le premier groupe combine une cytogénétique favorable, des télomères longs, une expression faible ou absente de hTERT et une expression forte des gènes du complexe shelterin ; le troisième groupe se caractérise par de multiples aberrations chromosomiques (notamment délétions 17p et 11q), une augmentation de l'expression de hTERT et une diminution de la longueur des télomères et des niveaux d'expression de TRF1, TRF2 et POT1 ; le deuxième groupe est intermédiaire. Ces résultats confirment l'existence d'un lien entre statut télomérique et instabilité génomique au cours de la LLC et soulignent le rôle de la perte de TP53 ou ATM dans cette dysfonction télomérique. L'altération du statut télomérique est par ailleurs associée à des caractéristiques de pronostic défavorable, comme l'absence de mutation des IgVH, l’expression de CD38 et le doublement rapide de la lymphocytose. Enfin, nous avons évalué l’intérêt de la technique de MLPA pour la mise en évidence des anomalies cytogénétiques récurrentes à valeur pronostique de la LLC. Nous avons montré qu'il existe une bonne concordance entre la technique de référence et la MLPA, qui constitue une approche rapide et peu coûteuse pour la recherche d'anomalies génomiques présentes dans une majorité de cellules malignes. Nous avons cependant mis en évidence des cas intéressants de faux-positifs et de faux-négatifs avec la MLPA, indiquant que cette méthode ne peut pas remplacer les techniques classiques, mais constitue une approche complémentaire permettant une évaluation simultanée de divers déséquilibres. / Chronic lymphocytic leukemia (CLL) is a frequent lymphoid hemopathy characterized by an extremely variable clinical course. Although there are numerous prognostic markers in CLL, none is univocal. In this context, identifying new predictive factors and understanding the pathophysiology of previously established prognostic markers represent two important aims to improve therapeutic management of this hemopathy. We first chose to study the prognostic value and mechanisms of regulation of antiapoptotic MCL1 gene expression. We showed that MCL1 expression is a predictive marker of overall survival within the whole patient cohort and among early stages; this marker is also a predictor of treatment free survival of stage A patients. Thus, MCL1 expression allows early identification of CLL forms with high risk and low risk of unfavourable evolution. We alsodemonstrated that MCL1 expression is strongly correlated to VEGF expression, confirming the role of this signalling pathway in tumour lymphocytes survival and suggesting that VEGF may be a positive autocrine regulator of MCL1 expression. We then explored telomeric function regarding prognosis-related chromosomal anomalies, reflecting genomic instability. Our work contributed to demonstrate the relationship between genomic instability and telomeric status, evaluated by telomere length and expression of hTERT and shelterin complex genes. We described three groups of patients with distinct cytogenetic and telomeric profile: first group combines good-prognosis cytogenetics, long telomeres, low or negative hTERT expression and high expression of the shelterin complex genes; third group displays multiple chromosome aberrations (particularly 17p and 11q deletions), increased hTERT expression and decreased telomere length and TRF1, TRF2 and POT1 expression levels; second group is intermediate. These results confirm the relationship between telomeric status and genomic instability in CLL and underline the role of TP53 or ATM loss in this telomeric dysfunction. The alteration of telomeric status is also associated with poor-prognosis features, such as unmutated IgVH, CD38 expression and rapid lymphocytosis doubling time. Finally, we evaluated the contribution of MLPA approach for detection of recurrent prognosis-related cytogenetic anomalies. We found a good concordance between the goldstandard technique and MLPA, which represent a time and cost-effective approach for the detection of genomic aberrations affecting most malignant cells. We however described interesting MLPA false-positive and false-negative cases, indicating that this method may not replace classic techniques, but may constitute a complementary approach allowingsimultaneous evaluation of various imbalances.

In recent years, the genetic landscape of B-cell derived lymphoid malignancies, including chronic lymphocytic leukemia (CLL), has been rapidly unraveled, identifying recurrent genetic mutations with potential clinical impact. Interestingly, ~30% of all CLL patients can be assigned to more homogeneous subsets based on the expression of a similar or “stereotyped” B-cell receptor (BcR). Considering that biased distribution of genetic mutations was recently indicated in specific stereotyped subsets, in paper I, we screened 565 subset cases, preferentially assigned to clinically aggressive subsets, and confirm the SF3B1 mutational bias in subset #2 (45%), but also report on similarly marked enrichment in subset #3 (46%). In contrast, NOTCH1 mutations were predominantly detected in subsets #1, #8, #59 and #99 (22-34%). This data further highlights a subset-biased acquisition of genetic mutations in the pathogenesis of at least certain subsets. Aberrant NF-κB signaling due to a deletion within the NFKBIE gene previously reported in CLL warranted extended investigation in other lymphoid malignancies. Therefore, in paper II, we screened 1460 patients with various lymphoid malignancies for NFKBIE deletions and reported enrichment in classical Hodgkin lymphoma (27%) and primary mediastinal B-cell lymphoma (PMBL) (23%). NFKBIE-deleted PMBL cases had higher rates of chemorefractoriness and inferior overall survival (OS). NFKBIE-deletion status remained an independent prognostic marker in multivariate analysis. EGR2 mutations were recently reported in advanced stage CLL patients; thus, in paper III we screened 2403 CLL patients for mutations in EGR2. An overall mutational frequency of 3.8% was reported and EGR2 mutations were associated with younger age, advanced stage and del(11q). EGR2 mutational status remained an independent marker of poor outcome in multivariate analysis, both in the screening and validation cohorts. Whole-genome sequencing (WGS) of 70 CLL cases, assigned to poor-prognostic subsets #1 and #2 and indolent subset #4, were investigated in Paper IV and revealed a similar skewing of SF3B1 mutations in subset #2 and NOTCH1 mutations in subset #1 to that reported in Paper I. Additionally, an increased frequency of the recently proposed CLL driver gene RPS15 was observed in subset #1. Finally, novel non-coding mutational biases were detected in both subset #1 and #2 that warrant further investigation.

Student Number : 9708297R - MSc (Med) dissertation - School of Medicine - Faculty of Health Sciences / B chronic lymphocytic leukaemia (B-CLL) is a monoclonal haematopoietic disorder with expansion of small lymphocytes of B-cells. B-CLL cells accumulate in blood, bone marrow, lymph nodes and spleen, resulting in enlargement of these organs and decreased bone marrow function. B-CLL is the most common leukaemia, with an annual incidence of 1.8 to 3.0 per 100 000 population in the United States. It is characterised by the accumulation of long-lived monoclonal CD5+ B lymphocytes. In vivo normal B-lymphocytes derive growth factors through interactions with T-cells and monocytes. In culture however, survival and growth of activated B-cells depends on the availability of external factors such as interleukins. B-CLL cells populations are unable to survive in culture long enough to respond to the addition of growth factors. Such factors are important for the proliferation and survival of many cell types and in the absence of cytokines, these cells die as a result of apoptosis. Chronic lymphocytic leukaemia cells are influenced in vitro by a number of exogenously added cytokines that include IFN- α, IFN-γ, IL-2, IL-4, IL-10, IL-13, IL-15, TGF- β and TNF- α. The aim of this study was to investigate the effect of cytokines e.g., IFN, IL-2, IL-6, IL7 and IL-10 on the proliferation and survival of B-CLL cells and furthermore to compare the induction and reduction of spontaneous and induced apoptosis in vitro. Patients with B-CLL were recruited from three centres. Thirty blood samples were collected, separated using Ficoll Hypaque Gradient and purified by rosetting with AET treated SRBC. The proliferation and survival of B-CLL cells were studied in vitro in response to GM-CSF, IFN, IL-2, IL-6, IL7 and IL-10,. The survival and apoptosis of B-CLL cells in cultures with or without interleukins and other growth factors were studied under microscopic examinations and DNA agarose gel electrophoresis. It was observed in B-CLL cells cultures that IFN and IL-2 enhanced proliferation significantly. IL6, IL-7 and GM-CSF also enhanced proliferation of B-CLL cells but not to the greater extent than IL2 and IFN. IL-10 inhibited proliferation of B-CLL cells when compared to controls. In a long-term (5-day) culture, survival of B-CLL cells was greatly enhanced by IFN and followed by IL-2. Therefore it appeared that IFN and IL-2 are the two most potent growth factors tested in this study to promote B-CLL cells proliferation and survival. The combination of these mitogens did not further enhanced proliferation. IL-6 and GM-CSF enhanced proliferation and survival of B-CLL cells. IL-7 promoted proliferation but had no effect on survival of B-CLL cells in-vitro. IL-10 enhanced apoptosis and did not promote survival of B-CLL cells in-vitro. IFN and IL2 are survival and promoting growth factors for B-CLL cells in culture. In contrast, IL-10 has demonstrated to induce apoptotic cell death of B-CLL cells. In conclusion B-CLL cells proliferated equally well with IFN and IL-2. IL-6, IL-7 and GM-CSF had a much lower proliferation and survival effect with noticeable antiapototic activity when compared to IFN and IL-2. IL-7 was found not to promote survival of B-CLL cells and IL-10 enhanced cell death by apoptosis.

Des lésions de l’ADN sont impliquées dans les mécanismes de l’oncogenèse. De plus, la prolifération incontrôlée des cellules tumorales induit l’accumulation d’aberrations géniques. En réponse à ce stress génotoxique, les cellules en transformation expriment les ligands NKG2D MICA et MICB, molécules du CMH de classe I non conventionnelles qui activent une réponse cytotoxique T et NK contre cette transformation. Dans les syndromes lymphoprolifératifs chroniques, les mécanismes de la leucémogenèse reposent essentiellement sur une stimulation antigénique ou une activation des voies du récepteur à l’antigène (BCR) qui induit la prolifération cellulaire. De plus, les ligands MICA/B ne sont pas retrouvés à la surface de ces cellules. Les objectifs de cette thèse sont (i) rechercher si l’activation de la prolifération lymphocytaire peut induire l’expression de MICA/B et (ii) étudier les mécanismes induisant cette expression et leurs liens avec les voies de lésions/réparations de l’ADN. Pour cela, nous avons mis en place des conditions d’activation du récepteur à l’antigène permettant d’obtenir une prolifération (objectivée après marquage par CFSE) de lymphocytes B sains et de lymphocytes issus de patients porteurs de leucémie lymphoïde chronique (LLC), la plus fréquente des leucémie de l’adulte. L’expression des ligands MICA et MICB a ensuite été évaluée par qPCR, cytométrie en flux, western blots et ELISA. L’implication des différentes voies de signalisation en aval du récepteur à l’antigène a été analysée, ainsi que la cinétique d’apparition des lésions de l’ADN durant ce processus. Mes résultats montrent que MICA/B ne sont pas exprimés à la surface des lymphocytes B issus de donneurs sains ou de patients porteurs de LLC. Cependant, l’activation de la prolifération lymphocytaire induit une activation transcriptionnnelle de MICA ainsi que son expression à la surface de ces cellules. Cette expression est induite par différentes voies du récepteur à l’antigène ainsi que par la voie JAK/STAT et est indépendante des lésions de l’ADN qui surviennent plus tardivement dans la cellule. Au total, l’activation du récepteur à l’antigène qui induit la prolifération lymphocytaire induit également l’expression du ligand MICA (et non MICB) à la surface des lymphocytes sains et cette capacité d’expression est conservée dans les cellules de LLC qui ne l’expriment pas. Ces résultats suggèrent que MICA pourrait jouer un rôle crucial aux stades précoces de l’immunité anti-proliférative, ce qui ouvre la voie à de potentielles applications thérapeutiques. / Tumor cell’s uncontrolled proliferation induces an accumulation of genetic aberrations. In response to this genotoxic stress, most cells in transformation express NKG2D ligands (not expressed on resting cells), including MICA and MICB, which are non-conventional MHC class I molecules that could induce a cytotoxic T and NK response against the transformed cell. In chronic lymphoproliferative conditions, leukemogenic mechanisms rely in part on antigenic stimulations and/or activation of the B cell antigen receptor (BCR) pathways that induce cell proliferation. My thesis aims at studying : (i) the induction of MICA/B expression during lymphocyte proliferation and (ii) the mechanisms inducing this expression and their relationship with the DNA damage/repair pathways.I did generate BCR activation conditions to obtain B cells proliferation from healthy control individuals and from patients suffreing from chronic lymphocytic leukemia (CLL), the most common leukemia in adults. MICA and MICB expression was assessed by quantitative PCR, flow cytometry, Western blotting and ELISA after activation of B-cell proliferation. The different signaling pathways downstream BCR were analyzed, as were the kinetics of the DNA damage during this process. The results show that MICA/B aren’t expressed on cell surface of B cells from healthy control individuals or CLL patients before activation. Lymphoproliferative stimulation however up-regulates both MICA mRNA and surface protein in these same cells. This expression was induced by several BCR and by JAK/STAT pathways and seems to be indpendant of DNA damage. In conclusion, antigen receptor activation that induces lymphocyte proliferation also induces MICA expression (but not MICB) on B cells surface from healthy control individuals and this expression capacity is conserved in B cells from patients suffering from CLL. These results suggest that MICA may play a crucial role in the early stages of anti-proliferative immunity, which opens the avenue for therapeutic interventions.

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.

Notre équipe a précédemment démontré que l'Interleukine (IL)-24 une cytokine de la famille de l'IL-10 a un effet cytostatique voire cytotoxique sur des cellules B normales ou leucémiques mises préalablement en cycle mais non sur des cellules quiescentes. L'IL-24 inhibe également la différenciation plasmocytaire des cellules B humaines du centre germinatif dans un modèle de différentiation in vitro. Nous avons utilisé ce modèle pour analyser pour la première fois le transcriptome de cellules B stimulées ou non par IL-24 au bout de 6 et 36 h. Plusieurs transcrits impliqués dans le métabolisme et la réplication de l'ADN sont inhibés précocement à l'exception d'IGF-1 qui est stimulé. L'IGF1 ayant été décrit comme une molécule de survie des cellules B ou pré-B, nous avons analysé son effet biologique et démontré qu'il a au contraire un rôle proapoptotique à doses physiologiques. En revanche, l'IL-24 induit l'expression plus tardive des gènes de la voie mitochondriale de la mort cellulaire programmée (MCP). Cet effet est également retrouvé dans des LLC « IgVH mutées » ou non mais avec une cinétique distincte des cellules B normales. Au total, dans des cellules activées au préalable, l'IL-24 induit séquentiellement un blocage précoce du cycle cellulaire suivi d'une apoptose. D'autres gènes potentiellement importants dans la synapse immune ainsi que dans la régulation de l'immunité innée sont décrits et suggèrent que l'IL-24 a un rôle immunologique particulier au-delà de son effet cytostatique et potentiellement anti-tumoral / We have previously shown that Interleukin(IL)-24 a class-II cytokine of the IL-10 family has cytostatic and cytotoxic properties on normal and malignant human B-cells previously engaged into the cell cycle, but not on quiescent B-cells. IL-24 also inhibits the differentiation of germinal center B-cells in plasma cells in an in vitro model; the later was used to compare for the first time the transcriptome of B-cells cultured or not with IL-24 for 6 and 36h. Several "early" transcripts involved in DNA metabolism and replication were inhibited whereas that of Igf1 a molecule described as a B-cell growth factor was induced. We show herein that IgF1 has instead a proapoptotic role on B-cells at physiological concentrations. In contrast, several genes of the intrinsic apoptotic pathway were stimulated after 36h. This expression pattern was also found in CLL cells whether they were "IgVH mutated" or "unmutated", albeit with distinct kinetics from normal B-cells. In addition several genes belonging to the immune synapse and innate immunity were regulated by IL-24. These results disclose additional, possibly immunoregulatory properties, for IL-24 than its already described cytostatic and potentially anti-tumoral effects

<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