Magister Scientiae (Medical Bioscience) - MSc(MBS) / Breast cancer (BC) is one of the most common malignancies in women. Death results from treatment failure and metastatic disease. Thousands of lives might be saved if it was possible to detect and eliminate occult metastatic cells before they become clinically evident. Therefore, there is a critical need to identify new markers to improve treatment options for these patients. Genomic instability is the earliest indication of breast cancer and the use of genomic methodologies is a progress towards early detection and treatment, through the identification of biomarkers that can be translated into novel therapy targets. The interferon regulatory factor-1(IRF-1) gene, localized on chromosome 5q31.1, is believed to act as a tumor suppressor gene in breast cancer. The IRF-1 was found to be inactivated by single nucleotide polymorphism (SNP) in breast cancer suggesting that the loss of its function might be critical to the development of the disease. The phosphatidylinositol 3-kinase (PIK3) signaling pathway mediates key cellular functions and alterations of genes in this pathway, including PIK3CA, serine-threonine protein kinases (AKT1and AKT2), phosphatase and tensin homolog (PTEN), fibroblast growth factor receptor 2 (FGFR2) and ERBB2, whose expression have been demonstrated to be altered in breast cancer patients. In addition, these genes are linked to treatment resistance. vi In this study, we have investigated allelic loss of IRF-1 gene in primary tumors obtained from patients undergoing mastectomy at Groote Schuur hospital (Cape Town, South Africa). These samples were then further analyzed for the DNA copy number changes of specific genes involved in the PIK3/AKT signaling pathway. Statistical analysis has been performed in order to correlate genomic findings with clinical-histopathological and follow up information from the patients and to establish whether these genes can predict prognosis. Our data analysis has indicated that 46 cases (45.5%) out of 101 cases were informative for the IRF-1 dinucleotide marker used for LOH analysis (Figure 3.1). LOH was detected in 23 of these informative cases (23/46; 50%). No statistical significance was found between LOH at the IRF-1 locus and age (≤50 years or >50 years) (P value = 1.0000) and earlier stage (Stages I and II) (P value= 0.4982) based on Fisher’s exact test. Patients presented a high level of DNA copy number changes in genes involved in the PIK3/AKT pathway. The most frequent changes were observed in the PIK3CA and PTEN genes. PIK3CA presented high copy number in 36.8% of the cases. PTEN was observed with low copy number in 47.5% of the cases. This dissertation shows the effectiveness of genomic methodologies as means for the detection of early breast cancer progression in South African women. The PIK 3/AKT genes can validate the usefulness of breast cancer therapies.

TET2 et P53, deux suppresseurs de tumeurs, jouent un rôle important dans l’homéostasie des cellules souches hématopoïétiques et sont trouvés mutés dans les hémopathies malignes. Ils sont aussi impliqués dans le contrôle du cycle cellulaire et les mécanismes de réparation des dommages de l’ADN, notamment la voie de réparation par excision de base (BER). Dans la première partie de ce travail, nous avons montré que la surexpression de TET2 et l’augmentation consécutive des 5hmC, ralentit la progression du cycle cellulaire et la transition G1/S et induit une instabilité centrosomique associée à une instabilité chromosomique dans un modèle cellulaire Ba/F3. De plus, la surexpression de TET2 induit l’augmentation de la mutagenèse particulièrement des transitions C->T dans les sites CpG dans un contexte déficient en thymidine DNA glycosylase (TDG), une protéine initiatrice du BER. Dans la seconde partie de ce travail, nous avons montré que l’activation de P53, par des antagonistes de MDM2, a un effet délétère sur tous les progéniteurs hématopoïétiques. Ces antagonistes induisent aussi une cytotoxicité non seulement dans les stades précoces de la mégacaryopoïèse mais surtout dans les stades tardifs. Cette cytotoxicité n’est pas réversible, contrairement à ce qui est observé en clinique, et ne peut pas être restaurée par des doses croissantes de thrombopoïétine. Au total, TET2 et P53 doivent être strictement régulés pour assurer l’homéostasie et la stabilité génétique des cellules hématopoïétiques. / Two tumor suppresors, TET2 and P53, play an important role in the homeostasis of hematopoietic stem cells and have been found mutated in hematological malignancies. They are also involved in cell cycle control and DNA repair mechanisms, including the base excision repair pathway (BER). In the first part of this work, we showed that TET2 overexpression and the consequent increase of 5hmC, inhibit cell cycle progression particularly G1/S transition and induces centrosome instability associated with chromosomal instability in Ba/F3 cellular model. In addition, overexpression of TET2 induces increased mutagenesis particularly transitions C->T at CpG sites in a context deficient in thymidine DNA glycosylase (TDG), a protein initiating BER. In the second part of this work, we have shown that p53 activation by MDM2 antagonists has deleterious effect on all haematopoietic progenitors. These antagonists also induce cytotoxicity not only in the early stages of megakaryopoiesis but also mainly in the late stages. This cytotoxicity is not reversible, in contrast to what is observed in clinic, and can not be restored by increasing doses thrombopoietin. To conclude, TET2 and P53 must be strictly controlled to ensure homeostasis and genetic stability of the hematopoietic cells.

Le cannibalisme d’une cellule vivante par une autre cellule vivante représente une nouvelle modalité de mort cellulaire non autonome. Mes travaux de thèse ont permis d’identifier et de caractériser les acteurs impliqués et d’apprécier l’influence de ce processus sur le devenir de la cellule cannibale. Nous avons ainsi révélé que l’activation d’une signalisation cellulaire impliquée dans la régulation du cycle cellulaire va causer une libération d’ATP qui stimulera les récepteurs purinergiques P2Y2 de la cellule de manière autocrine. Cette étape sera suivie d’une augmentation de l’exposition de la protéine d’adhérence E-cadhérine à la membrane plasmique et de réarrangements du cytosquelettes médiés par la kinase ROCK, et permettra ainsi à une cellule vivante de cannibaliser une autre cellule vivante. Ce phénomène aussi connu sous le nom de « cellule dans une cellule » est fréquemment observé dans les biopsies tumorales. De plus, nous révélons au cours de ces travaux la capacité des cellules internalisées à être éliminées par un processus qui implique la protéine de l’autophagie ATG5 et les protéines pro-apoptotiques BAK et BAX. Ce processus est associé au déclenchement d’une instabilité génétique et d’un stress oxydatif au niveau des cellules cannibales et va déclencher la sénescence de ces cellules que nous avons appelé « entescence ». Cette nouvelle modalité d’induction de la sénescence participe à la suppression des tumeurs in vivo et semble prédire la réponse des patients aux traitements néoadjuvants anticancéreux. À l’opposé, l’échappement à l’entescence favorise la progression tumorale et est associé à une mauvaise réponse des patients aux traitements. L’ensemble de ces travaux met en lumière l’existence d’une nouvelle modalité d’induction de la sénescence cellulaire qui survient à la suite du cannibalisme cellulaire. Une meilleure compréhension des mécanismes impliqués dans son déclenchement et son exécution pourrait selon nous participer au développement de nouvelles approches thérapeutiques afin de lutter contre le cancer. / Cannibalism of live cells by other live cells is a new modality of non-autonomous cell death. This investigation led to the characterization of the molecular mechanisms implicated as well as the identification of the consequences of this process on the fate of the cannibal cell.We revealed that the activation of a signaling pathway involved in the regulation of the cell cycle can trigger a release of ATP that will stimulate the activity of the P2Y2 purinergic receptor in an autocrine manner. These events will lead to the increase of E-cadherin membrane exposition and change the organisation of the cytoskeleton in a ROCK-dependent manner, allowing this live cell to eat another live cell. This process called "cell in cell structure" is frequently observed in tumoral biopsies. Then, we revealed that the internalized cell will be eliminated by a process dependent on the autophagy protein ATG5 and the pro-apoptotic proteins BAX and BAK. These events are associated to the triggering of genomic instability and an oxidative stress in the cannibal cell leading these cells to a new senescence program that we called "entescence".This new senescence program seems to be a tumor suppressor mechanisms in vivo and is correlated to a better response of patient to neoadjuvant anticancer treatments. Moreover, escaping entescence seems to favor tumor growth and is associated to a bad response to anticancer treatments.Taken together, these results highlight the existence of a new senescence program that is initiated by cellular cannibalism. A better understanding of the molecular mechanisms regulating its initiation and its execution may lead to develop new innovative anticancer therapeutical approaches.

Embryonic stem (ES) cells have the ability to maintain pluripotency and self-renewal during in vitro maintenance, which is a key to their clinical applications. ES cells are a model in developmental biology studies due to their potential to differentiate in vitro. Understanding critical pathways of pluripotency, self-renewal, and differentiation during early embryonic development is important for the evaluation of the therapeutic potential of ES cells because of their ability for tumor transformation due to genetic and epigenetic instability acquired during in vitro culture maintenance. Single tandem repeats are sequences of DNA that have been implicated in the deregulation of gene expression in different human conditions. Understanding the origin of repetitive sequence instability and functions in the genome allow characterization of early genomic instability signals in ES cell pluripotency, differentiation, and tumor transformation pathways. The hypothesis of this study was that genetic stability, in repetitive sequences, located near embryonic developmental genes is responsible for pluripotency, self-renewal, differentiation, and chromatin assembly and could be a signal for adaptation, differentiation, or transformation of ES cells in vitro. Our result showed instability in specific repetitive sequences which increased during ES cell passages and embryoid body differentiation in vitro. ES cells displayed significant mean frequencies of genomic instability in repetitive regions that lead to ES cells pluripotency, self-renewal maintenance, or cell lineage specialization. The present study reports potentially biomarkers for identifying accumulation of genomic instability in specific genes that may contributes to adaptation of ES cells and could be the switch that initiates early ES cell lineage commitment in vitro. Determining genetic and epigenetic modifications, including single tandem repeat instability, gene expression changes, and chromatin modifications, is essential for elucidating possible molecular mechanisms of genomic instability and determining novel molecular characterization for diagnostic purposes to ensure ES cell stability and integrity that could potentially lead to use of ES cell derivatives that could then be a safe source needed for regenerative medicine applications

The historical narrative and our understanding about the low dose effects of radiation on the immune system has changed drastically from the beginning of the 20th century to now. A paradigm shift from the DNA target hit model to the one that also considers non-targeted effects (NTE) has attracted a lot of interest recently. Investigations to delineate mechanisms of NTE in the biological tissue have been carried out by various research groups where radiation induced genomic instability (RIGI), bystander effect (RIBE) and abscopal effect (AE) are the effects with most evidence available. This thesis addresses the question of whether low dose ionizing radiation (LDIR) stimulates or suppresses the immune system and how NTEs contribute to this immune modulation by adopting a two-pronged approach where first a narrative review constituting the introduction and literature review was performed followed by a systematic review using PRISMA guidelines to synthesize existing LDIR literature. This was prompted by our recent discovery that UVA photons are emitted by the irradiated cells and that these photons can trigger bystander effects in unirradiated recipients of these photons. Given the well-known association between UV radiation and the immune response, where these biphotons may pose as bystander signals potentiating processes in deep tissues as a consequence of ionising radiation, it is timely to revisit the field with a fresh lens. After reviewing various pathways and immune components that contribute to the beneficial and adverse effects induced by LDIR, it was found that these modulations can occur by way of NTE. However, the exact mechanistic underpinnings are still unclear and the literature examining low to medium dose effects of ionising radiation on the immune system is complex and controversial. Early work was compromised by lack of good dosimetry while later work mainly focuses on the involvement of immune responses in radiotherapy which typically uses high dose radiation. There is a lack of research in the LDIR/NTE field focussing on immune responses although bone marrow stem cells and lineages were critical in the identification and characterisation of NTE. This may be in part, a result of the difficulty of isolating NTE in whole organisms which are essential for good immune response studies. Models involving inter organism transmission of NTE are a promising route to overcome these issues. It is concluded that the simple question of whether LDIR stimulates or suppress the immune system is not as simple as initially hypothesized. An attempt was made to analyze if LDIR shifts the balance to immune suppression or enhancement via systematic review but, due to too many differences in the experimental methods in the current radiation and immune studies, a cookie-cutter answer was not possible. However, this thesis did point out the areas of concern such as lack of standardised tools in the field of radiobiological experimental research and quality of methods used which requires urgent attention. / Thesis / Master of Science (MSc)

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Background: Prostate cancer (PCa) is one of the most prevalent cancers worldwide. The clinical manifestations and molecular characteristics of PCa are highly variable. Aggressive types require radical treatment, whereas indolent ones may be suitable for active surveillance or organ-preserving focal therapies. Patient stratification by clinical or pathological risk categories still lacks sufficient precision. Incorporating molecular biomarkers, such as transcriptome-wide expression signatures, improves patient stratification but so far excludes chromosomal rearrangements. In this study, we investigated gene fusions in PCa, characterized potential novel candidates, and explored their role as prognostic markers for PCa progression. Methods: We analyzed 630 patients in four cohorts with varying traits regarding sequencing protocols, sample conservation, and PCa risk group. The datasets included transcriptome-wide expression and matched clinical follow-up data to detect and characterize gene fusions in PCa. With the fusion calling software Arriba, we computationally predicted gene fusions. Following detection, we annotated the gene fusions using published databases for gene fusions in cancer. To relate the occurrence of gene fusions to Gleason Grading Groups and disease prognosis, we performed survival analyses using the Kaplan–Meier estimator, log-rank test, and Cox regression. Results: Our analyses identified two potential novel gene fusions, MBTTPS2,L0XNC01::SMS and AMACR::AMACR . These fusions were detected in all four studied cohorts, providing compelling evidence for the validity of these fusions and their relevance in PCa. We also found that the number of gene fusions detected in a patient sample was significantly associated with the time to biochemical recurrence in two of the four cohorts (log-rank test, p-value < 0.05 for both cohorts). This was also confirmed after adjusting the prognostic model for Gleason Grading Groups (Cox regression, p-values < 0.05). Conclusions: Our gene fusion characterization workflow revealed two potential novel fusions specific for PCa. We found evidence that the number of gene fusions was associated with the prognosis of PCa. However, as the quantitative correlations were only moderately strong, further validation and assessment of clinical value is required before potential application.

Les cellules souches pluripotentes humaines (hPSC) sont des cellules capables à la fois d'autorenouvellement et de se différencier en tous les types cellulaires. Elles peuvent être issues de l'embryon (pour cellules souches embryonnaires humaines, hESC) ou être obtenues par reprogrammation d'une cellule différenciée (pour cellules souches pluripotentes induites humaines, hiPSC). Les hPSC sont au centre d'enjeux scientifiques, médicaux et économiques majeurs, en particulier dans le cadre des maladies génétiques et orphelines. En effet, elles ouvrent la porte à de nouvelles stratégies de modélisation de maladies génétiques humaines in vitro et sont une source potentiellement illimitée de cellules pour une thérapie cellulaire des maladies dégénératives. Cependant, la culture in vitro de hPSC est une étape essentielle avant toute application clinique ou recherche fondamentale. En effet, la culture cellulaire est nécessaire pour l'amplification du nombre des cellules, et est nécessaire pour toute étape de différenciation in vitro. Or c'est une étape délicate pour le succès des applications visées. Mon travail de doctorat s'est focalisé sur deux aspects de la culture des hPSC. Dans un premier temps, j'ai modélisé in vitro une voie de différenciation, le développement trophoblastique humain, en modulant les paramètres de la condition de culture, notamment en jouant sur la concentration du facteur de croissance BMP4. Ce travail m'a permis d'élucider la toute première bifurcation de différenciation cellulaire au cours du développement embryonnaire humain précoce. Dans un second temps, mon travail s'est focalisé sur le changement phénotypique et génomique des hPSC au cours de la culture in vitro. J'ai montré que l'utilisation de certains protocoles de passage cellulaire – en particulier le passage par dissociation cellulaire complète par utilisation de trypsine - se traduit par des acquisitions très précoces d'anomalies génétiques chromosomiques et sub-chromosomiques, et que des anomalies sub-chromosomiques pouvaient précéder l'apparition d'anomalies chromosomiques. Les conséquences de ces observations sont importante pour la recherche de la culture de hPSC : (1) il faut définitivement renoncer à l'utilisation des passages par dissociation cellulaire complète, y compris pour les méthodes de culture en suspension, et (2) il faut, pour valider une technique de culture, compléter systématiquement le caryotype par un examen d'analyse génétique avec une meilleure résolution. / Human pluripotent stem cells (hPSC) are the stem cells capable to self-renew and also to differentiate into all the cell types. These cells can be derived from embryos (for human embryonic stem cells, hESC) but also be obtained by reprogramming the differentiated somatic cells (for human induced pluripotent cells, hiPSC). The hPSC become central stakes of science, medicine and economy, particularly for genetic and rare diseases. In fact, they open up the new perspectives to the novel treatment strategies by remodeling human genetic diseases in vitro and at the same time they are a potentially unlimited cell source for cell therapy for especially degenerative diseases. Meanwhile, the hPSC in vitro culture is one of the most important steps before passing to the clinic applications and in fundamental research, as the proliferation and pluripotency can only be maintained in culture condition as well as many differentiation methods. My PhD work was concentrated on the hPSC in vitro culture. At first, I modeled human trophoblastic development and its differentiation pathway in vitro by modulating the parameters of culture, especially the concentration of BMP4. This work permitted clarifying the first cell lineage bifurcation in early human embryonic development. Secondly, my word was focalized on the phenotypic and genomic changes of hPSC during the in vitro culture. I demonstrated that the use of some passaging protocols in culture, particularly complete cell dissociation by trypsin, was translated by very early acquisitions of chromosomal and sub-chromosomal abnormalities, and that the appearance of sub-chromosomal abnormalities could precede chromosomal abnormalities. The consequences of these observations are important for the hPSC culture research: (1) the use of complete cell-dissociation passaging should be definitively abandoned, including the suspension culture, and (2) the genetic analyses with higher resolution should be added to validate a culture technic.

Le gène hybride BCR-ABL1, responsable de la leucémie myéloïde chronique (LMC), code une protéine à activité tyrosine kinase constitutive. Lors d’une étude transcriptomique menée au laboratoire sur des patients résistants secondaires à l’imatinib, les deux gènes codant les protéines des rétrotransposons LINE-1 ont été trouvés sous exprimés d’environ 20 fois lorsque les patients rechutent. Le rôle des transposons n’a jamais été clairement défini, ils assurent certainement une fonction importante puisqu’ils sont conservés au cours de l’évolution et présents chez tous les organismes. Le but de ce travail a été d’étudier l’implication de LINE-1 dans la LMC. La sous-expression de LINE-1 est-elle une conséquence de la présence de BCR-ABL1 ou une cause de son apparition ? Différents groupes ont montré que les rétrotransposons LINE-1 possédent la capacité de réparation des cassures double-brin de l’ADN. Nous avons fait l’hypothèse qu’une diminution de l’expression des gènes codés par les rétrotransposons LINE-1 entraînerait l’instabilité génétique observée dans la LMC. Une étude réalisée chez des patients atteints de LMC et des sujets contrôles a montré une correlation inverse entre l’expression de LINE-1 et celle de l’oncogène BCR-ABL1. Parallèlement, une étude sur des lignées cellulaires leucémiques humaines BCR-ABL positives et négatives a été réalisée. Nous avons recherché le lien qui existe entre l’expression de LINE 1, de BCR-ABL1 et la réparation des cassures double-brin de l’ADN. Nous avons montré d’une part qu’une inhibition de l’expression de BCR-ABL1 induit une augmentation de l’expression des transposons LINE-1 D’autre part, une diminution de l’expression de LINE-1 entraîne une apparition du transcrit BCR-ABL1 dans les cellules BCR-ABL negatives. / BCR-ABL1 fusion gene, responsible of the chronic myeloid leukemia (CML) encodes a constitutively activated tyrosine kinase protein. Expression of both LINE-1 retrotransposon ORFs were found decreased at the time of imatinib resistance in a comparative transcriptional study focused on secondary resistant patients. The role of retrotransposons is unclear. They are conserved through evolution. This project focuses on the involvement of LINE-1 in CML. Is LINE-1 under expression a result of BCR-ABL1 expression or is it at the origin of BCR ABL1? Different groups have shown that LINE-1 retrotransposons were able to repair DNA double strands breaks. We suggest that LINE-1 under expression could be responsible of genetic instability observed in CML. We show in a study on CML patients and healthy subjects that LINE-1 expression is inverse correlated to BCR-ABL1 expression. Moreover, study on BCR-ABL+ and BCR-ABL- human leukemic cell lines was carried on. First, we show that decrease of BCR-ABL1 expression induces increase of LINE-1 expression. Then that decrease of LINE-1 expression generates BCR-ABL1 transcript in BCR-ABL negatives cell lines.