Tumour initiation and progression occur due to oncogenic mutations that also contribute to therapeutic resistance in many human tumours. Mutations activating the "PI3K/AKT" signalling pathway and inactivating the "TP53" tumour suppressor gene are common mechanisms that cancer cells require to proliferate and escape pre-programmed cell death. p53 mutant (p53mut) tumours not only fail to respond to DNA damaging therapy, but are also described to promote therapeutic resistance by dominant negative suppression of p53 dependent promoter activity. Our work identifies the crucial interaction between the PI3K/AKT pathway and p53 mutations that regulate treatment sensitivity in tumours. Using a combination of in vitro and in vivo techniques we demonstrate that AKT inhibition promotes reduced cellular levels of p53mut via a novel Nucleophosmin 1 (NPM) mediated regulation of the tumour suppressor p14ARF and promotes re-engagement of cell cycle arrest, senescence and increased sensitivity to ionising radiation in both in vivo and in vitro systems. We show that the PI3K/AKT pathway plays an important role in the regulation of p53mut and inhibitors of this pathway can re-sensitise treatment resistant tumours. This has helped us to simultaneously highlight the cohort of patients where the greatest efficacy may be achieved in clinical practise. We further show that the AKT mediated regulation of NPM that we describe in solid tumours is relevant in Acute Myeloid Leukaemia (AML) with mutated NPM, albeit showing physiologically different effects. This further highlights the necessity for rational treatment planning with the newer targeted agents that inhibit specific signalling pathways in AML patients.

DNA provides the instructions and regulation of cell growth and survival. Mutations in DNA can cause uncontrolled and unregulated cell proliferation, resulting in cancer. Treatment of cancer involves physical removal of these cells through surgery or inducing cell death by causing irreversible damage to DNA through chemotherapy and radiotherapy. However, natural DNA repair mechanisms may interfere with therapy and may even be increased in cases of therapy resistant cancer. The use of chemotherapy and radiotherapy leads to increased recruitment of DNA repair proteins while aggressive, therapy resistant cancers show overexpression of DNA repair proteins. Rad51 is a protein involved in the homologous recombination (HR) DNA repair process. Rad51 is recruited to sites of DNA damage caused by double stranded breaks, often generated by chemotherapy and radiotherapy. It is expected that inhibition of Rad51 will impair the HR repair process while enhancing the effectiveness of chemotherapy and radiotherapy compared to conventional means. As a result, this literature review aims to identify and examine the drug inhibitors of Rad51 in order to demonstrate the potential viability of this novel treatment in a variety of cancers.

AML is a cancer of the blood and bone marrow characterized by the presence of highly proliferative and abnormally differentiated myeloblasts. Previous work from the Bhatia lab utilized the orthotopic xenograft model in order to isolate a population of leukemic regenerating cells (LRC) that exists prior to relapse. Affymatrix analysis of LRCs revealed up-regulation of 248 genes that can act as unique targets to prevent relapse. In order to screen compounds against all 248 targets, it is important to develop an in vitro model that is able to appropriately recapture the functional and molecular markers of LRCs. Primary AML samples were treated with 5-doses of 0.15 μM, 1 μM AraC, or DMSO control and several outcomes were measured. In vitro AraC treatment was not able to recapitulate the progenitor frequency curve and CD34 expression curve observed in vivo. Additionally, we were not able to see a consistent increase in select LRC targets DRD2, GLUT2, FUT3, and FASL via flow cytometry. Despite an increase in the mRNA levels of LRC genes 24h after treatment with 0.15 μM AraC, long term analysis could not be completed due to poor RNA quality and low expression of LRC-targets. Primary AML cells were co-culture with mouse MS-5 stromal cell line order to study the effects of mesenchymal stromal cells on AML response to AraC. Co-culture with MS-5 cells had different effects on select primary AML cells. AML 14939 showed an increase in CD34 and LRC targets DRD2 and FUT3 following AraC treatment when co-cultured with MS-5 cells; while A374 showed no differences between DMSO and AraC treated groups. Overall, these findings suggest the LRC signature is not induced by treatment with AraC alone. Complex interactions between AML cells and their bone marrow niche during AraC treatment plays an important role in the development of LRCs prior to AML relapse. / Thesis / Master of Science (MSc) / AML is a cancer of blood cells characterized by the presence of rapidly dividing cancer cells termed myeloblasts. AML has a high rate of disease relapse. The Bhatia lab modelled AML relapse in a mouse and discovered an unique population of cells that exist prior to relapse termed LRCs. LRCs express distinctive genes that can act as targets for the development of new therapies to prevent relapse. In order to screen potential relapse preventing compounds, we set out to recapture AML relapse using cells in a dish. AML cells from patients were treated with chemotherapy reagent AraC and the number of cancer progenitors and the expression of specific LRC proteins were measured. AraC did not increase the level of 3 out of 4 LRC proteins studied. We determined the LRCs were not caused by AraC treatment, and the physiology of the bone marrow environment plays an important role in inducing relapse.

<p>Inflammatory breast cancer (IBC) is an extremely rare but highly aggressive form of breast cancer characterized by the rapid development of therapeutic resistance leading to particularly poor survival. Our previous work focused on the elucidation of factors that mediate therapeutic resistance in IBC and identified increased expression of the anti-apoptotic protein, X-linked inhibitor of apoptosis protein (XIAP), to correlate with the development of resistance to chemotherapeutics. Although XIAP is classically thought of as an inhibitor of caspase activation, multiple studies have revealed that XIAP can also function as a signaling intermediate in numerous pathways. Based on preliminary evidence revealing high expression of XIAP in pre-treatment IBC cells rather than only subsequent to the development of resistance, we hypothesized that XIAP could play an important signaling role in IBC pathobiology outside of its heavily published apoptotic inhibition function. Further, based on our discovery of inhibition of chemotherapeutic efficacy, we postulated that XIAP overexpression might also play a role in resistance to other forms of therapy, such as immunotherapy. Finally, we posited that targeting of specific redox adaptive mechanisms, which are observed to be a significant barrier to successful treatment of IBC, could overcome therapeutic resistance and enhance the efficacy of chemo-, radio-, and immuno- therapies. To address these hypotheses our objectives were: 1. to determine a role for XIAP in IBC pathobiology and to elucidate the upstream regulators and downstream effectors of XIAP; 2. to evaluate and describe a role for XIAP in the inhibition of immunotherapy; and 3. to develop and characterize novel redox modulatory strategies that target identified mechanisms to prevent or reverse therapeutic resistance. </p><p> Using various genomic and proteomic approaches, combined with analysis of cellular viability, proliferation, and growth parameters both in vitro and in vivo, we demonstrate that XIAP plays a central role in both IBC pathobiology in a manner mostly independent of its role as a caspase-binding protein. Modulation of XIAP expression in cells derived from patients prior to any therapeutic intervention significantly altered key aspects IBC biology including, but not limited to: IBC-specific gene signatures; the tumorigenic capacity of tumor cells; and the metastatic phenotype of IBC, all of which are revealed to functionally hinge on XIAP-mediated NFκB activation, a robust molecular determinant of IBC. Identification of the mechanism of XIAP-mediated NFκB activation led to the characterization of novel peptide-based antagonist which was further used to identify that increased NFκB activation was responsible for redox adaptation previously observed in therapy-resistant IBC cells. Lastly, we describe the targeting of this XIAP-NFκB-ROS axis using a novel redox modulatory strategy both in vitro and in vivo. Together, the data presented here characterize a novel and crucial role for XIAP both in therapeutic resistance and the pathobiology of IBC; these results confirm our previous work in acquired therapeutic resistance and establish the feasibility of targeting XIAP-NFκB and the redox adaptive phenotype of IBC as a means to enhance survival of patients.</p> / Dissertation

<p>Apoptotic dysregulation is a hallmark of cancer cells. The inability of cancer cells to undergo apoptosis may lead to therapeutic resistance. Inflammatory breast cancer (IBC) is a highly aggressive subtype of breast cancer that is often characterized by ErbB2 overexpression and ErbB2 activation. ErbB-targeting is clinically relevant using trastuzumab (anti-ErbB2 antibody) and lapatinib (small molecule ErbB1/2 inhibitor). However, acquired resistance is a common outcome even in IBC patients who show an initial clinical response, which limits the efficacy of these agents. Little is known about the molecular mechanisms of therapeutic resistance in IBC cells. We hypothesized that apoptotic dysregulation leads to therapeutic resistance of IBC cells to therapeutic agents, including ErbB-targeting agents. To determine whether apoptotic dysregulation and changes in anti-apoptotic proteins leads to resistance of IBC cells to therapeutic agents, we performed a variety of in vitro-based studies using agents that are used in the clinic to treat IBC patients. The sensitivity of both ErbB2 overexpressing and ErbB1 activated IBC cells to various therapeutic agents was evaluated using various cell death and apoptosis assays, and anti-apoptotic protein expression post-treatment was determined using western blot analysis. The overarching theme observed was that x-linked inhibitor of apoptosis protein (XIAP) expression inversely correlated with sensitivity of cells to therapeutic agents with various mechanisms of action, including TNF-related apoptosis inducing ligand (TRAIL), doxorubicin, cisplatin, paclitaxel, and two ErbB-targeting agents: trastuzumab and a lapatinib-analog (GW583340). Moreover, there was a specific and marked overexpression of XIAP in cells with de novo resistance to trastuzumab and with acquired resistance to GW583340. The observed overexpression was identified to be caused by IRES-mediated XIAP translation. Stable XIAP overexpression using a lentiviral system reversed sensitivity to therapeutic agents (TRAIL and GW583340) in parental IBC cells. Moreover, XIAP downregulation in cells resistant to therapeutic agents (TRAIL, trastuzumab, and GW583340) resulted in decreased viability and increased apoptosis, demonstrating that XIAP is required for survival of cells with resistance to these agents. A novel mechanism of GW583340 oxidative stress-induced mediated apoptosis was identified, and resistant cells had increased antioxidant expression and capability. Interesting, inhibition of XIAP function overcame this increase in antioxidant potential, demonstrating a new function for XIAP in oxidative stress-induced apoptosis. These studies establish the feasibility of development of an XIAP inhibitor that potentiates apoptosis for use in IBC patients with resistance to therapeutic agents.</p> / Dissertation

<p>Inflammatory breast cancer (IBC) is a rare and highly aggressive form of breast cancer that is characterized by survival signaling through overexpression and/or activation of the epidermal growth factor receptors EGFR/ErbB1 and Her2/ErbB2 and defects in the apoptotic program. The development of therapeutic resistance is a significant barrier to successful treatment in IBC, and thus, strategies targeting the mechanisms that drive drug resistance could prevent or reverse therapeutic resistance, significantly improving patient prognosis. Based on analysis of previously developed models of therapeutic resistant IBC, we hypothesized that apoptotic dysregulation and redox adaptive mechanisms were central to the drug resistant phenotype in IBC cells, and that targeting of these mechanisms could overcome therapeutic resistance. Our objectives to address this hypothesis were: 1. to develop and characterize an isotype-matched IBC cellular model to investigate the mechanisms of acquired therapeutic resistance; 2. to characterize IAP-specific small molecule inhibitors as a means of targeting the mechanism of apoptotic dysregulation in IBC; and 3. to characterize a novel redox modulatory combination as a means of targeting redox adaptive mechanisms in IBC.</p><p>Analysis of cell viability, proliferation, and growth parameters, evaluation of protein expression and signaling via western immunoblot, and measurement of reactive oxygen species (ROS), antioxidants, and apoptosis in patient-derived IBC cell lines and isogenic derivatives revealed that resistance to the ErbB1/2 inhibitor lapatinib was protective against other targeted agents and chemotherapeutics. Additionally, reversal of resistance was associated with enhanced ability to accumulate ROS and downregulation of anti-apoptotic and antioxidant proteins. Targeting of resistance mechanisms using small molecule IAP inhibitors and a redox modulatory strategy both effectively induced apoptosis in therapy resistant IBC cells. Together, these results confirm XIAP and the redox adaptive phenotype as promising therapeutic targets for IBC and demonstrate the feasibility of targeting those mechanisms in order to reverse therapeutic resistance.</p> / Dissertation

Le lymphome à cellules du manteau (LCM) est un cancer lymphoïde agressif caractérisé par des rechutes itératives et un mauvais pronostique. Le LCM est associé à une génétique complexe et à des dérégulations de gènes tissu-spécifiques, potentiellement liées à des perturbations de la marque épigénétique H3K9me3. En criblant les niveaux d’H3K9me3 dans une cohorte de 120 cas de LCM, nous avons montré une perte de cette marque dans 30% des cas. Cette perte d’H3K9me3 a été reliée à une diminution de l’expression ou de l’activité des histones methyltransferases SUV39H1 et SETDB1, et à l’expression différentielle de programmes d’expression génique associés aux cellules souches embryonnaires ou hématopoïétiques, à la différentiation B et la réponse aux dommages à l’ADN. Un séquençage à haut-débit ciblé n’a pas permis de mettre en évidence de mutations associées à cette perturbation épigénétique.Nous avons également montré qu’une invalidation de l’expression de SUV39H1 causait une augmentation du volume tumoral dans un modèle de xénogreffe et qu’une perte de SETDB1 induisait un arrêt du cycle cellulaire en phase G1/S, associé à une reprogrammation cellulaire vers un phénotype pré-B. L’ensemble de ces données suggère une convergence des voies de signalisation associées à H3K9me3 vers des cibles essentielles à la pathogénèse du LCM. Les mécanismes épigénétiques associées à la régulation de ces cibles sont actuellement étudiés par immunoprécipitation de la chromatine associée à H3K9me3. Des analyses de survie dans le cadre d’un essai clinique prospectif permettront également d’établir l’impact pronostique des pertes d’H3K9me3 dans le LCM. / Mantle cell lymphoma (MCL) is an aggressive lymphoid cancer characterised by iterative clinical relapses and short survival. MCL displays complex genetics and hallmarks of misregulated expression of lineage specific genes. We have hypothesized that the latter might result from corruption of H3 lysine 9 trimethylation signaling. By screening for H3K9me3 levels across a cohort of 120 MCL cases, we found global reductions in H3K9me3 in 1/3 of cases. H3K9me3 depletion was linked to underexpression / attenuated activity of SUV39H1 and SETDB1 histone methylases, respectively, and to differential expression of key cancer signatures relating to embryonic/hematopoietic stem cell function, B cell differentiation, and DNA damage response. Targeted deep sequencing did not reveal association to mutations in known epigenetic modifiers, indicating a new, previously-unsuspected role for H3K9me3 in MCL pathogenesis. In keeping with this, knockdown of SUV39H1 increased tumour growth in MCL xenografts while SETDB1 depletion induced G1/S arrest coincident to reprogramming to a pre-B cell phenotype. Taken together this identifies convergence of H3K9me3 signaling pathways to essential targets for MCL disease pathogenesis. These are currently under investigation by H3K9me3 ChIP-seq. Survival analyses in the setting of a prospective clinical trial will establish the prognostic impact of H3K9me3 in MCL.

Esophageal cancer (EC) is an aggressive form of cancer, including squamous cell carcinoma (ESCC) and adenocarcinoma (EAC) as two predominant histological subtypes. Accumulating evidence supports the existence of cancer stem cells (CSCs) able to initiate and maintain EAC or ESCC. In this review, we aim to collect the current evidence on CSCs in esophageal cancer, including the biomarkers/characterization strategies of CSCs, heterogeneity of CSCs, and the key signaling pathways (Wnt/β-catenin, Notch, Hedgehog, YAP, JAK/STAT3) in modulating CSCs during esophageal cancer progression. Exploring the molecular mechanisms of therapy resistance in EC highlights DNA damage response (DDR), metabolic reprogramming, epithelial mesenchymal transition (EMT), and the role of the crosstalk of CSCs and their niche in the tumor progression. According to these molecular findings, potential therapeutic implications of targeting esophageal CSCs may provide novel strategies for the clinical management of esophageal cancer.

Application of cytotoxic chemotherapy still remains the essential treatment strategy in advanced colorectal cancer. The intrinsic and acquired drug resistance represents one of the reasons that may even lead to failure of cancer therapy. The DNA damage response pathways have been shown to play an important role in the development of chemoresistance. There is sufficient evidence showing the high-frequency deregulated expression of many DNA repair genes across multiple cancer types. An example of such gene in colorectal cancer is MRE11, which encodes protein known as a sensor of DNA double-strand breaks. In year 2016, there was a substantial study published by our group at The Department of Molecular Biology of Cancer (IEM CAS, Prague), the study analysed the association of polymorphisms in predicted microRNA target sites of double-strand breaks (DSBs) repair genes, including MRE11, and clinical outcome and efficacy of chemotherapy in colorectal cancer. Our hypothesis, based on the mentioned study, is that specifically and exactly defined microRNAs with ability to regulate certain DNA repair proteins may not only affect the survival of colorectal cancer cells, but also the sensitivity to chemotherapy. In practical part of the submitted thesis we have identified miR-140 as a potential regulator of...

La protéine p53 (« Gardien du génome ») doit être altérée pour que le cancer puisse se développer. Les nombreuses thérapies anti-cancéreuses disponibles sont très efficaces mais la réponse clinique est souvent transitoire et les cancers disséminés rechutent ou progressent du fait de l'évolution de sous-populations cancéreuses résistantes au traitement, impliquant souvent TP53 qui est le gène le plus muté dans les formes agressives de nombreux cancers. Nous l’avons étudié dans la leucémie lymphoïde chronique (LLC) et les syndromes myélodysplasiques avec délétion 5q (SMD del(5q)). Grâce à l’étude rétrospective longitudinale de 40 patients atteints de SMD del(5q), nous avons généré des données de NGS ciblé et montré que le statut mutationnel de TP53 au diagnostic ne permettait pas de prédire la progression tumorale, contrairement à ce qui avait été publié précédemment (Jädersten et al., JCO 2011). Nous avons montré que c’était l’évolution clonale du gène TP53 qui était l’élément clé de la progression des SMD del(5q). Nous avons observé de nombreuses émergences de clones mutés entre le stade diagnostique et un stade ultérieur de la maladie, toujours après initiation du traitement par lénalidomide.Le lénalidomide a été approuvé comme nouveau traitement spécifique et très efficace contre l’anémie liée aux SMD del(5q), permettant à la plupart des patients d’être indépendants des transfusions sanguines. Le lénalidomide permet souvent d’éradiquer le clone tumoral porteur de l’anomalie génétique del(5q) isolée, induisant une rémission clinique. Malheureusement, cette rémission est courte avec une durée médiane de 2 ans, puis, dans environ 1 cas sur 2, survient une transformation en leucémie aiguë secondaire de pronostic péjoratif.Nous avons étudié un possible lien entre le traitement par lénalidomide et l’évolution clonale de TP53 par annotation clinico-bio-thérapeutiques des résultats de séquençage de TP53 chez les 24 patients dont les échantillons séquentiels avaient été analysés. Dans notre étude, les patients avec progression tumorale (dont 10 évolutions clonales de TP53 et 1 évolution clonale de RUNX1) avaient reçu une dose cumulée de lénalidomide supérieure à celle reçue par les patients dont la tumeur était restée stable (p = 0.036). Nous avons observé chez plusieurs patients que l’éradication de la tumeur n’était pas utile à l’amélioration de la qualité de vie des patients. La non-éradication semblait même permettre un maintien de l’équilibre clonal et une compétition entre les différents sous-clones de la tumeur, résistants ou non au lénalidomide.Nous discutons de l’évolution de l'écologie de la tumeur au cours du traitement, i.e., l’évolution de ses interactions avec son micro-environnement qui se modifie après chaque nouvelle dose de traitement. Un modèle évolutif dit théorie de la thérapie adaptative, développée récemment remet en question les protocoles conventionnels de thérapie anti-cancéreuse qui préconisent souvent d'administrer la dose maximale tolérée par le patient (Gatenby, 2009). Elle suggère que la dose minimale efficace présenterait l’avantage de ne pas éradiquer les cellules cancéreuses sensibles au traitement pour qu'elles restent en compétition avec les cellules cancéreuses résistantes et limiter la progression ou la rechute. Nous suggérons de prendre en compte également la diminution des effets indésirables pour le patient, améliorant ainsi sa qualité de vie, et enfin la diminution des dépenses de santé pour la collectivité. A ce jour, peu d’études cliniques évaluent l’intérêt de l’adoption de tels protocoles de thérapie adaptative.Néanmoins, des modèles in vivo (xénogreffes) et in silico (modèles statistiques) ont permis d’analyser la dynamique évolutive des populations tumorales en fonction du traitement reçu. Ces modèles prédisent que la survie de l’hôte peut être maximisée par la mise en place d’une thérapie adaptative. / P53 protein is named «guardian of the genome » because it must be altered to let cancer grow.TP53 is the most mutated gene in agressive cancers.Numerous systemic therapies are successful for treatment of disseminated cancers. However, clinical response is often transient, and cancer undergo relapse or progression due to emergence of resistant populations. These latter often harbour TP53 mutations. We studied TP53 in chronic lymphoid leukemia (CLL) and lower-risk myelodysplastic syndroms with del(5q), MDS del(5q). We conducted a retrospective longitudinal study in 40 patients suffering from MDS del(5q). We obtained targeted NGS data showing that TP53 mutational status at diagnosis could not predict tumor progression, by contrast with previously published data (Jädersten et al., JCO 2011). We show that TP53 clonal evolution is the key feature of tumor progression in MDS del(5q). We observed numerous mutated sub-clones emerging between diagnosis and follow-up. In our study, this emergence always followed onset of lenalidomide treatment. Lenalidomide was recently approved as a new therapy specifically improving anemia in patients with MDS del(5q). It allows most patients to become red-blood-cells-transfusion independent. Lenalidomide often eradicates the major tumor clone harbouring the isolated genetic abnormality deletion (5q) and allows clinical remission. Unfortunately, this remission is short (median, 2 years) and is followed, in 1 case out of 2, by a secondary acute leukemic transformation with a very poor prognosis.We studied the issue of a possible link between lenalidomide therapy and TP53 clonal evolution by annotating TP53 sequencing results with acute biological, clinical and therapeutic features in the 24 patients with sequential samples analyzed. In our study, patients with tumor progression (10 TP53 clonal evolution and 1 RUNX1 clonal evolution) were given a higher cumulative dose of lenalidomide compared to patients with stable disease (p = 0.036). Similarly to « adaptive therapy theory »(Gatenby 2009), we observed that eradication of the tumor wasn’t useful for improvement of quality of life. Absence of eradication might even allow to maintain a clonal equilibrium and a clonal competition between the distinct tumor sub-clones, resistant to lenalidomide or not, and therefore maintain stable disease.This theory of adaptive therapy questions the classical protocols of treatments against cancer, in which the maximal tolerated dose is preferred to the minimal effective dose. The latter might however slow down cancer progression or cancer relapse, with decreased side effects in patients, and decreased health costs.To date, few clinical trials (if any) questions such protocols of adaptive therapy. However, in vivo experiments (xenografts) and in silico statistical models allowed to study evolutionary dynamics of tumor sub-populations with and without therapy.The models predict that host survival can be maximized if “treatment-for-cure strategy” is replaced by “treatment-for-stability.” Specifically, the models predict that an optimal treatment strategy will modulate therapy to maintain a stable population of chemosensitive cells that can, in turn, suppress the growth of resistant populations under normal tumor conditions, Dr Gatenby said.