Le cancer épithélial de l’ovaire (EOC) est le plus mortel des cancers gynécologiques. Cette maladie complexe progresse rapidement de façon difficilement décelable aux stades précoces. De plus, malgré une chirurgie cytoréductive et des traitements de chimiothérapie le taux de survie des patientes diagnostiquées aux stades avancées demeurt faible. Dans le but d’étudier l’EOC dans un contexte ex vivo, l’utilisation de modèles cellulaires est indispensable. Les lignées cellulaires d’EOC sont un outil pratique pour la recherche cependant, la façon dont l'expression des gènes est affectée en culture par comparaison à la tumeur d'origine n'est pas encore bien élucidée. Notre objectif était donc de développer et de caractériser de nouveaux modèles de culture in vitro qui réflèteront plus fidèlement la maladie in vivo. Nous avons tout d’abord utiliser des lignées cellulaires disponibles au laboratoire afin de mettre au point un modèle 3D de culture in vitro d’EOC. Des sphéroïdes ont été générés à l’aide de la méthode des gouttelettes inversées, une méthode pionnière pour la culture des cellules tumorales. Nous avons ensuite procédé à une analyse des profils d’expression afin de comparer le modèle sphéroïde au modèle de culture en monocouche et le modèle xénogreffe in vivo. Ainsi, nous avons identifié des gènes stratifiant les modèles tridimensionnels, tant in vivo qu’in vitro, du modèle 2D monocouche. Parmi les meilleurs candidats, nous avons sélectionné S100A6 pour une caractérisation ultérieure. L’expression de ce gène fût modulée afin d’étudier l’impact de son inhibition sur les paramètres de croissance des sphéroïdes. L’inhibition de ce gène a comme effet de réduire la motilité cellulaire mais seulement au niveau du modèle sphéroïde. Finalement, toujours dans l’optique de développer des modèles d’EOC les plus représentatifs de la maladie in vivo, nous avons réussi à développer des lignées cellulaires uniques dérivées de patientes atteintes d’EOC du type séreux, soit le plus commun des EOC. Jusque là, très peu de lignées cellulaires provenant de ce type de cancer et de patientes n’ayant pas reçu de chimiothérapie ont été produites. De plus, nous avons pour la première fois caractérise des lignées d’EOC de type séreux provenant à la fois de l’ascite et de la tumeur solide de la même patiente. / The epithelial ovarian cancer (EOC) is the most lethal of gynecological cancers. This complexe and heterogenous disease progresses rapidly and is almost asymptomatic in early stages. The survival rate of patients with late stage diagnosis remains low albeit cytoreductive surgery and chemotherapy. In order to study the EOC disease in an ex vivo context, the use of different cellular models is necessary. EOC cell lines derived from long-term passages of malignant ovarian cancers are useful tools for molecular and cellular research but it is not clear how culture conditions affect overall gene expression and oncogenic potential as compared to the original tumor. The main goal of this research was to develo and characterize new in vitro model systems that will recapitulate more closely some of the growth conditions encountered by tumor cells in vivo. In order to develop an in vitro tridimensional EOC spheroid model, we have used cell lines previously established in our laboratory. Spheroids were generated using the hanging droplet method, which was innovative for the culture of cancer cells. Comparative gene expression profile analysis of monolayer cultures, 3D spheroids and in vivo xenografts were performed and we have shown that the spheroid transcriptome more closely reflects expression patterns of the in vivo model compared to that of monolayer cultures. Among the best candidates, S100A6 gene over-expressed in the 3D models versus monolayer cultures was chosen for further analysis. To begin to address how S100A6 might affect EOC growth parameters, we have inhibited its expression in our in vitro models. The loss of S100A6 in the spheroid model results in an reduction of cellular migration, which seems to be in line with previous in vivo results published by other researchers. Always with the objective of developing the most relevant to the in vivo disease model systems, we have also succeeded in developing a unique EOC cell lines derived from patients with the most frequently diagnosed serous type of cancer. Very few cell lines derived from this type of cancers and from chemotherapy naïve patients are available. Moreover, we characterize for the first time EOC serous type cell lines derived from the ascites and the solid tumor of the same patient.

Regulatory T cells (Treg) play a key role in maintaining the immune tolerance. They suppress development of autoimmune diseases and contribute to maintaining the homeostasis of the immune system. Expansion and excessive ability of regulatory T cells to suppress the immune response is increasingly observed also at many types of cancer. Due to the active inhibition of the antitumor immune response Treg contribute to tumor progression. Specific phenotype based detection and analysis of Treg functional properties may contribute to the successful monitoring of Treg accounts and to the effective cancer immunotherapy itself. Tumor cells express high amounts of so-called tumor antigens, which may play a key role in the antitumor immune response. Expression level of the tumor antigens gives the evidence about relevancy of each antigen in the specific immune response and efficiency of cancer immunotherapy. These data are obviously important to be obtained from the tumor cell lines as well as primary tumor cells. In the first part of the thesis I was focusing on the quantitative analysis of regulatory T cells in tumor tissue and peripheral blood of patients with ovarian cancer. For this purpose I used the newly introduced methyl-sensitive quantitative PCR (MS-qPCR) method and compare the data with the widely...

La chimiothérapie systémique par voie intraveineuse, essentiellement réservée aux cancers avancés, n'est pas ciblée sur la tumeur, il est très difficile d’atteindre des niveaux thérapeutiques en intra tumoral, et ses effets secondaires et sa toxicité sont doses-limitantes.La chimiothérapie localisée pourrait permettre :1) la stabilisation des molécules médicamenteuses incorporées une seule administration médicamenteuse,2) une libération prolongée et contrôlée du médicament pour assurer une diffusion adéquate et l'absorption par les cellules cancéreuses sur plusieurs cycles de division cellulaire 3) le chargement de molécules de chimiothérapie insolubles dans l’eau, 4) l’apport direct au site de la maladie, 6) des effets secondaires diminués en évitant la circulation systémique,7) des résections chirurgicales moindres en traitant les marges de la tumeur. Nous nous sommes plus particulièrement intéressés aux cancers gynécologiques. Nous avons étudié les effets pharmacologiques et cliniques de microsphères chargées en doxorubicine (Doxo) sur un modèle de carcinose péritonéale et de tumeur de glande mammaire, et étudié le profil de diffusion ganglionnaire de divers implants non chargés. 12 jours après injection laparoscopique de tumeurs VX2 sur les ligaments larges droits et gauches de lapines WNZ 12 une injection laparoscopique de 0,5 ml de microsphères chargées ou non de Doxo (respectivement DM, groupe 1 et BM, groupe 2) a été réalisée de façon aléatoire d’un côté ou de l’autre, en sous péritonéal, au site tumoral. 7 jours après les ligaments larges, l’utérus, les ovaires, les orifices de trocarts, les intestins, la vessie, le foie et les poumons ont été examinés en macroscopie et microscopie. Le volume tumoral était plus faible dans le groupe 1 (3,6 ± 3,2 cm) par rapport au groupe 2 (8,9 ± 5,4 cm) (MW, p = 0,0179). La nécrose a été observée autour de toutes les DM, sans nécrose autour des BM. La concentration de Doxo était de 2,1 ± 2,7 uM aux limites tumorales, au-dessus du niveau thérapeutique de 1,0 uM. Sur un autre modèle, 19 jours après injection locale de suspensions tumorales de VX2 sur la deuxième glande mammaire de lapines WNZ chaque glande a été aléatoirement traitée par injection locale de 0,5 ml de microsphères chargées ou non de Doxo (HSDOXO, Groupe1, et HS, groupe 2).Pour les tumeurs de moins de 5 cm3 ou 2 cm de diamètre avant traitement, le volume final était plus faible dans le groupe 1 par rapport à groupe2 (respectivement p<0.008 et p<0.3, MW)et la croissance tumorale a été diminuée après injection de HSDOXO par rapport à HS. En microscopie une nécrose tissulaire a été observée autour des HSDOXO en extratumoral, sans nécrose autour des HS.Nous avons enfin étudié la diffusion de particules de diverses tailles, non chargées, au ganglion sentinelle d’une tumeur de glande mammaire . Les animaux ont été répartis en trois groupes de trois, chacun d'eux recevant des particules de 100 nM, 1 uM ou 10 uM. Cinq jours après traitement, l'intensité de fluorescence a été évaluée par lampe UV. Le ganglion sentinelle a été disséqué selon la technique du bleu, avant curage complet. Les premiers résultats montrent la capture de particules de 1 et 100µm par les ganglions tumoraux mais aussi dans les ganglions sains, ce qui permettrait d’envisager un traitement ganglionnaire préventif et curatif.De plus en plus de tumeurs seront décelées au stade local. Par ailleurs l'identification des phénotypes génomiques permettra un traitement personnalisé « à la carte ». On pourrait envisager un dispositif de délivrance programmable traitant tous les aspects de la maladie, de l'inhibition de la croissance tumorale et de l'angiogenèse à la promotion de la cicatrisation des tissus normaux. / Systemic chemotherapy is mainly reserved for advanced cancers, is not targeted to the tumor, it is very difficult to achieve intratumoral therapeutic levels and its side effects and toxicity are dose-limiting.Local chemotherapy may have several advantages:1) stabilization of embedded drug molecules and preservation of anticancer activity,2) controlled and prolonged drug release to ensure adequate diffusion and uptake into cancer cells over many cycles of tumor cell division, 3) loading and release of water-insoluble chemotherapeutics, 4) direct delivery to the site of disease, 5) one-time administration of the drug, 6) diminished side effects due to the avoidance of systemic circulation of chemotherapeutic drugs.We were particularly interested in gynecological cancers. We studied the pharmacological and clinical effects of doxorubicin-loaded microspheres (Doxo) in a model of peritoneal carcinomatosis,a model of mammary gland tumor, and studied the diffusion profile of various micro and nanoparticles in tumoral and non tumoral lymph nodes.12 days after laparoscopic injection of VX2 tumors on the right and left broad ligament of WNZ rabbits laparoscopic injection of 0.5 ml of microspheres loaded or not with Doxo (DM or Group 1, BM Group 2 respectively) was conducted randomly to one side or another, at the sub peritoneal tumor site. 7 days after the broad ligaments, uterus, ovaries, trocars, bowels, bladder, liver and lungs were examined macroscopically and microscopically. The tumor volume was lower in group 1 (3.6 ± 3.2 cm) compared with group 2 (8.9 ± 5.4 cm) (MW, p = 0.0179). Necrosis was observed around all DM without necrosis around the BM. Doxo concentration was 2.1 ± 2.7 µM at the tumor margins, above the therapeutic level of 1.0 uM.On another model, 19 days after local injection of VX2 tumor suspensions in the second mammary gland of WNZ rabbits each gland was randomly treated by local injection of 0.5 ml of microspheres loaded or not with Doxo (HSDOXO, Group1, and HS Group 2).For tumors less than 5 cm3 or 2 cm in diameter before treatment, the final volume was lower in group 1 compared to Group 2 (p <0.008 and p <0.3, MW) and tumor growth was reduced after HSDOXO injection compared to HS. Microscopic tissue necrosis was observed around extratumoral HSDOXO without necrosis around the HS.We finally studied the diffusion of unloaded particles of various sizes on the lymph nodes of a mammary gland tumor. The animals were divided into three groups of three, each receiving particles of 100 nm, 1 µm or 10 µm. Five days after treatment, the fluorescence intensity was measured by UV lamp. The sentinel lymph node was dissected according to the technique of blue dye.The first results show the capture of 1 μm and 100μm particles by the tumoral and non tumoral lymph nodes, which would consider a preventive and curative treatment of the nodes.Since more and more tumors are detected at the local stage and with the identification of genomic phenotypes, a personalized local chemotherapy could be the next step of cancer therapy. One could imagine a programmable controlled drug delivery device dealing with all aspects of the disease, inhibition of tumor growth and angiogenesis, while promoting the healing of normal tissues.

O câncer de ovário é uma importante causa de mortalidade. O subtipo seroso de alto grau é o mais frequente e caracteriza-se por comportamento agressivo, com crescimento rápido e metástase precoce. A falta de ferramentas para diagnóstico em estádios iniciais e a insuficiência de resposta à quimioterapia convencional são dois principais obstáculos para o manejo do câncer seroso de ovário. A detecção precoce neste tumor é complicada por sintomas inespecíficos e ausência de biomarcadores confiáveis. Além disso, o desenvolvimento de resistência à quimioterapia é um desafio para o tratamento, que é geralmente baseado na combinação de platina e paclitaxel. A influência do microambiente tumoral na resposta terapêutica ainda é pouco conhecida. No entanto, há evidências crescentes de que a resposta imunológica pré-existente pode estar relacionada com a variação da sensibilidade à quimioterapia. O microambiente imunorreativo foi associado à melhor prognóstico no câncer do ovário seroso de alto grau em recente estudo canadense. Proteínas da família de Transdutores de Sinal e Ativadores da Transcrição (STATs) participam da regulação de citocinas e são determinantes nas respostas imunes no microambiente tumoral, podendo promover ou inibir o crescimento tumoral. Dados recentes mostram que a expressão elevada de um dos reguladores de STAT, STAT1 atua na tumorigênese do câncer de ovário, facilitando a resposta imune e, potencialmente, alterando a resposta à quimioterapia. Para avaliar o papel da expressão de STAT1 como biomarcador preditivo em 65 pacientes brasileiras com câncer seroso de ovário, examinamos os níveis de STAT1 por imunoistoquímica, e analisamos se houve correlação entre expressão dessa proteína e resposta clínica. Alta expressão de STAT1 foi significativamente associada maior intervalo livre de doença (P=0,0256) e maior sobrevida global (P=0,0193). Estes achados da coorte brasileira, com tempo de seguimento maior que cinco anos, confirmam a associação entre alta expressão de STAT1 e melhor resposta à quimioterapia, e fornecem validação adicional desta proteína como um biomarcador preditivo. Além disso, estes resultados chamam atenção para a possibilidade de utilizar a via de STAT1 para o desenvolvimento de novos medicamentos imunomoduladores, que poderiam melhorar a resposta ao tratamento / Ovarian cancer is a major cause of mortality worldwide. The most frequent subtype is high grade serous, which is characterized by aggressive behavior with rapid growth and early metastasis. Lack of early diagnostic tools and failure of response to conventional chemotherapies are two major impediments to serous ovarian cancer management. Early detection in initial stages is complicated by non-specific symptoms and lack of reliable biomarkers. In addition, development of chemotherapy resistance is a challenge for treatment, which is generally based on combination of platinum and paclitaxel. The influence of the microenvironment of the tumor on therapeutic response is still unknown. However, there is increasing evidence that a pre-existing immunological response may be related to variation in chemotherapy sensitivity. The immunoreactive microenvironment has been shown to be associated with better prognosis in high grade serous ovarian cancer in a recent Canadian study. The Signal Transducer and Activator of Transcription (STAT) proteins regulate cytokines and are central in determining whether immune responses in the tumor microenvironment promote or inhibit cancer. Recent data show that high expression of one of the STAT regulators, STAT1, operates in ovarian cancer tumorigenesis, facilitating immune response and potentially altering response to chemotherapy. To evaluate the role of STAT1 expression as a predictive biomarker in 65 Brazilian serous ovarian cancer patients, we examined STAT1 levels by immunohistochemistry to determine if there was correlation between expression of this protein and clinical response. High expression of STAT1 was significantly associated with both improved disease-free survival (P=0,0256) and overall survival (P=0,0193). These findings from a Brazilian cohort after more than five years of follow up confirm the association of high STAT1 expression with better response to chemotherapy, and provide additional validation of this protein as a predictive biomarker. Moreover these results draw attention to the possibility of utilizing the STAT1 pathway for the development new immunomodulator drugs, that could enhance response to treatment

Le récepteur de haute affinité 1 (NTSR1) et son agoniste, la neurotensine (NTS), sont corrélés avec l’agressivité tumorale dans la plupart des tumeurs solides, y compris les cancers hormono-dépendants. Comme l’endomètre et l’ovaire sont également soumis à une régulation hormonale, nous avons évalué la contribution de NTS/NTSR1 à la carcinogenèse de l’endomètre et de l’ovaire. L’expression du récepteur de la neurotensine 1 (NTSR1) et la méthylation du promoteur NTSR1 (HM450) ont été analysées dans 385 cas de carcinome de l’endomètre du Cancer Genome Atlas (TCGA). De plus, à partir d’une série de 100 carcinomes de l’endomètre et de 66 échantillons d’endomètre bénin, l’expression de NTS et NTSR1 a été évalué par immunohistochimie. La série TCGA d’adénocarcinomes ovariens séreux de haut grade et une série de 46 tissus ovariens ont également été analysés. Dans la série TCGA de carcinomes de l’endomètre, le taux d’ARN messager de NTSR1 (ARNm) était négativement corrélé avec la survie globale (SG) et la survie sans progression (SSP) (p = 0,0012 et p = 0,0116, respectivement), et positivement corrélé avec le grade (p = 0,0008). En incluant seulement les carcinomes endométrioïdes, le niveau d’ARNm de NTSR1 était également négativement corrélé avec la SG (log-rank:p < 0.0001) et la SSP (log-rank: p = 0.002). Une forte expression d’ARNm de NTSR1 était significativement associée à une perte de méthylation du promoteur NTSR1. L’expression immunohistochimique de NTS et NTSR1 était significativement augmentée dans l’adénocarcinome (n = 100), par rapport à l’endomètre bénin (p <0,001). L’expression de NTSR1 était positivement corrélée avec le grade (p = 0,004). Une forte expression du NTSR1 cytoplasmique était significativement corrélée avec une SG et une SSP plus courtes (p < 0,001 et p = 0,001, respectivement). Cette corrélation restait significative en excluant les sous-types non-endométrioïdes (p = 0,04 et p = 0,02, respectivement). En analyse multivariée, l’expression de NTSR1 était un facteur de mauvais pronostic indépendant (p = 0,004). Nos résultats indiquent également la présence d’une corrélation positive entre l’expression du marqueur de prolifération MCM6 et le grade histologique dans le sous-type endométrioïde (grade I, 66,7 %, grade II, 75,3 %, grade III, 81,4 %, p <0,001) et une corrélation inverse à la SG et à la SSP (p = 0,02 pour les deux). Dans la cohorte TCGA, les analyses de Cox univariées et multivariées (p = 0,003 et p = 0,03, respectivement) ont révélé que les z-scores élevés de l’ARNm de MCM6 étaient associés à une SG réduite. Ces associations étaient absentes pour Ki-67. Il n’y avait pas de corrélation significative entre NTSR1 et MCM6 ou Ki-67. Dans l’adénocarcinome de l’ovaire, la NTS et NTSR1 ont été détectés dans 72 % et 74 % des cancers de l’ovaire, respectivement. En outre, dans la grande série d’adénocarcinomes ovariens séreux de haut grade, l’ARNm de NTSR1 s’est avéré être en corrélation avec des stades plus élevés et la résistance au platine (p = 0.02). Ceci est concordant avec les résultats expérimentaux montrant que l’antagoniste très spécifique de NTSR1, le SR48692, a augmenté la réponse au carboplatine dans les cellules cancéreuses de l’ovaire et les tumeurs expérimentales induites. Lorsque le SR48692 est combiné avec du carboplatine, une augmentation majeure des dommages à l’ADN induits par le platine et de la mort cellulaire, ainsi qu’une diminution de la croissance tumorale, a été notée. La surexpression de NTSR1 est un facteur de mauvais pronostic dans les cancers de l’endomètre et de l’ovaire, mettant en évidence la contribution de NTS dans la progression du cancer et ses utilisations en tant que marqueur pronostique, et en tant que cible thérapeutique potentielle. L’ajout d’un inhibiteur de NTSR1 en association avec une thérapie à base de sel de platine pourrait améliorer la réponse au traitement / The high affinity receptor 1 (NTSR1) and its agonist, neurotensin (NTS), are correlated with tumor cell aggressiveness in most solid tumors, including hormone-dependent cancers. As the endometrium and ovary are also subjected to hormonal regulation, we evaluated the contribution of NTS to endometrial and ovarian carcinogenesis. Neurotensin receptor 1 (NTSR1) expression and NTSR1 promoter methylation (HM450) were analyzed in 385 cases of endometrial carcinoma from The Cancer Genome Atlas (TCGA). Additionally, from a series of 100 endometrial carcinomas, and 66 benign endometrium samples, NTS and NTSR1 labeling was evaluated by immunohistochemistry. The TCGA series for ovarian high-grade serous adenocarcinoma and a series of 46 ovarian tissues were also analyzed. Using TCGA series, NTSR1 messenger RNA (mRNA) level was negatively correlated with overall survival (OS) and progression-free survival (PFS) (p = 0.0012 and p = 0.0116, respectively), and positively correlated with the grade (p = 0.0008). When including only endometrioid carcinomas, NTSR1 mRNA level continued to be negatively correlated with OS (log-rank: p < 0.0001) and PFS (log-rank: p = 0.002). A higher NTSR1 mRNA level was significantly associated with a loss of NTSR1 promoter methylation. Immunohistochemical expression of NTS and NTSR1 was significantly increased in adenocarcinoma (n = 100), as compared to benign endometrium (p < 0.001). NTSR1 expression was positively correlated with grade (p = 0.004). High immunohistochemical expression of cytoplasmic NTSR1 was significantly correlated with a shorter OS and PFS (p < 0.001 and p = 0.001, respectively). This correlation remained significant when excluding non-endometrioid subtypes (p = 0.04 and p = 0.02, respectively). In multivariate analysis, the expression of NTSR1 was an independent prognostic factor (p = 0.004). Our evidence indicated also the presence of a positive correlation between expression of proliferation marker, MCM6 and the histological grade of endometrioid endometrial adenocarcinoma (grade I, 66.7 %; grade II, 75.3 %; grade III, 81.4 %; p < 0.001) and an inverse correlation with OS ans PFS (p = 0.02 for both). For in silico analyses of the TCGA cohort, both univariate and multivariate Cox analyses (p = 0.003 and p = 0.03, respectively) revealed high MCM6 mRNA Z-scores associated with reduced OS. These associations were absent for Ki-67. No significant correlation between NTSR1 and MCM6 or Ki-67 was found. In ovarian adenocarcinoma, NTS and NTSR1 were detected in 72 % and 74 % of ovarian cancer, respectively. Furthermore, in a large series of high-grade ovarian cancer, NTSR1 mRNA was shown to correlate with higher stages and platinum resistance (p = 0.02). This correlates with experimental results showing the very specific NTSR1 antagonist, SR48692, enhanced the response to carboplatin in ovarian cancer cells and experimental tumors. When SR48692 is combined with carboplatin, a major improvement of platinum-induced DNA damage and cell death, as well as a decrease in tumor growth, was noted. NTSR1 overexpression is a poor prognostic factor in endometrial and ovarian cancer, highlighting the contribution of NTS in cancer progression and its uses as a prognostic marker, and as a potential therapeutic target. The addition of NTSR1 inhibitor in combination with platinum salt-based therapy could improve the response to the drug

The tumour microenvironment comprises the non-cancerous cells present in the tumour mass (fibroblasts, endothelial, and immune cells), as well as signalling molecules and extracellular matrix. Tumour growth, invasion, metastasis, and response to therapy are influenced by the tumour microenvironment. Therefore, characterising the cellular and molecular components of the tumour microenvironment, and understanding how they influence tumour progression, represent a crucial aim for the success of cancer therapies. High-grade serous ovarian cancer provides an excellent opportunity to systematically study the tumour microenvironment due to its clinical presentation of advanced disseminated disease and debulking surgery being standard of care. This thesis first presents a case report of a long-term survivor (>10 years) of metastatic high-grade serous ovarian cancer who exhibited concomitant regression/progression of the metastatic lesions (5 samples). We found that progressing metastases were characterized by immune cell exclusion, whereas regressing metastases were infiltrated by CD8+ and CD4+ T cells. Through a T cell - neoepitope challenge assay we demonstrated that pre- dicted neoepitopes were recognised by the CD8+ T cells obtained from blood drawn from the patient, suggesting that regressing tumours were subjected to immune attack. Immune excluded tumours presented a higher expression of immunosuppressive Wnt signalling, while infiltrated tumours showed a higher expression of the T cell chemoattractant CXCL9 and evidence of immunoediting. These findings suggest that multiple distinct tumour immune microenvironments can co-exist within a single individual and may explain in part the hetero- geneous fates of metastatic lesions often observed in the clinic post-therapy. Second, this thesis explores the prevalence of intra-patient tumour microenvironment het- erogeneity in high-grade serous ovarian cancer at diagnosis (38 samples from 8 patients), as well as the effect of chemotherapy on the tumour microenvironment (80 paired samples from 40 patients). Whole transcriptome analysis and image-based quantification of T cells from treatment-naive tumours revealed highly prevalent variability in immune signalling and distinct immune microenvironments co-existing within the same individuals at diagnosis. ConsensusTME, a method that generates consensus immune and stromal cell gene signatures by intersecting state-of-the-art deconvolution methods that predict immune cell populations using bulk RNA data was developed. ConsensusTME improved accuracy and sensitivity of T cell and leukocyte deconvolutions in ovarian cancer samples. As previously observed in the case report, Wnt signalling expression positively correlated with immune cell exclusion. To evaluate the effect of chemotherapy on the tumour microenvironment, we compared site-matched and site-unmatched tumours before and after neoadjuvant chemotherapy. Site- matched samples showed increased cytotoxic immune activation and oligoclonal expansion of T cells after chemotherapy, unlike site-unmatched samples where heterogeneity could not be accounted for. In addition, low levels of immune activation pre-chemotherapy were found to be correlated with immune activation upon chemotherapy treatment. These results cor- roborate that the tumour-immune interface in advanced high-grade serous ovarian cancer is intrinsically heterogeneous, and that chemotherapy induces an immunogenic effect mediated by cytotoxic cells. Finally, the different deconvolution methods were benchmarked along with ConsensusTME in a pan-cancer setting by comparing deconvolution scores to DNA-based purity scores, leukocyte methylation data, and tumour infiltrating lymphocyte counts from image analysis. In so far as it has been benchmarked, unlike the other methods, ConsensusTME performs consistently among the top three methods across cancer-related benchmarks. Additionally, ConsensusTME provides a dynamic and evolvable framework that can integrate newer de- convolution tools and benchmark their performance against itself, thus generating an ever updated version. Overall, this thesis presents a systematic characterisation of the tumour microenvironment of high grade serous ovarian cancer in treatment-naive and chemotherapy treated samples, and puts forward the development of an integrative computational method for the systematic analysis of the tumour microenvironment of different tumour types using bulk RNA data.

Ovarian cancer is the fifth leading cause of cancer death in women between the ages of 35 and 74. With 22 thousand new cases and 15 thousand deaths annually ovarian cancer is among the most deadly cancers with a death to incidence ratio of 68%. With 70% of cases High Grade Serous Ovarian Carcinoma (HGSOC) is the most common type of ovarian cancer and causes 90% of ovarian cancer deaths. 80% of patients have reoccurrence within five years and only 15-30% of patients with recurrent metastatic ovarian cancer respond to current therapies, chemotherapy and surgery. One reason for the high reoccurrence rate is thought to be linked to the heterogeneity of tumors: there is evidence that, among tumor cells, a subpopulation is cancer stem cells (CSCs). Since CSCs are frequently drug resistant, when the patient undergoes chemotherapy many of the cells may die but the CSCs are left behind and the tumors can therefore regrow. CSCs are also more likely to undergo epithelial-mesenchymal transition which gives these cells the ability to more readily migrate and invade through the extracellular matrix, leaving the primary tumor to form metastases. One key inducer of EMT and therefore possibly of metastasis of particular interest in this project is SNAI1 (Snail). It is therefore the goal of this project to understand the growth, makeup and metastatic ability of HGSOC cell lines to test possible strategies to decrease growth of cancer and prevent metastasis. In this thesis project the phenotype, CSC population make up, and functionality of various HGSOC cell lines was examined. The cell lines assessed were A2780, Kuramochi, OVSAHO, COV318, SKOV3 and OVCAR8. A Snail knockdown OVCAR8 cell line was also assessed as described above and in a xenograft model. It was determined that the cell lines show varying phenotype from epithelial like to mesenchymal like morphology and the cell lines have varying concentrations of cancer stem cells. It was also determined that the CSC population of the HGSOC cell lines were positive for both epithelial and mesenchymal markers in the same cells. OVCAR8 stood out as a hybrid line with both epithelial and mesenchymal characteristics and was therefore chosen for the Snail knockdown model. In the Snail knockdown we observed that CSC markers were reduced, however no change between control and knockdown was seen in the in vitro functional experiments. There was a difference seen between Snail knockdown and control in the in vivo mouse xenograft model. Snail knockdown showed a trend for decreasing tumor burden in both primary and metastatic tumors and showed a significant decrease in growth of metastatic tumor at day 43. Based on these results Snail may be an important target for cancer therapy.

Le cancer épithélial de l’ovaire (CEO) est une cause majeure de mortalité parcancer gynécologique. Il est associé à un mauvais pronostic car il est souventdécouvert à un stade tardif. Mieux comprendre les causes et les mécanismesmoléculaires et cellulaires associés à la progression de ce cancer représente unenjeu majeur.Les deux chimiokines CXCL12/SDF-1 et fractalkine (FKN)/CX3CL1 ont étéimpliquées dans diverses tumeurs. La chimiokine SDF-1, a un effetimmunosuppresseur dans le CEO. Elle est aussi impliquée dans l’angiogenèsetumorale. L’effet de SDF-1 médié par CXCR4 est également impliqué dans larégulation de la prolifération, la survie, la migration et l'invasion des cellulescancéreuses. La FKN, a largement été mise en évidence dans les tissusépithéliaux et dans divers cancers où elle peut avoir soit un rôle anti-tumoral soitun rôle pro-tumoral. Jusqu’à présent la FKN n’a pas été étudié dans le CEO.Dans notre étude, nous avons démontré l’expression de SDF-1 et de la FKNdans l’épithélium de surface de l’ovaire sain et dans les tumeurs bénignes etmalignes. Ces résultats montrent que l’expression de SDF-1 et de la FKNpréexiste à la tumorigenèse. Nous avons démontré une expression hétérogènedes deux chimiokines dans les cellules du CEO. Les niveaux d’expression deSDF-1 dans les cellules tumorales sur une cohorte de 183 patientes n’ont aucunevaleur pronostique sur la survie globale et sur la survie sans progressiontumorale des patientes atteintes par le CEO. L’étude de la corrélation del’expression de la FKN avec les deux marqueurs de prolifération, Ki-67 etGILZ, sur une autre cohorte de 54 patientes, complétée par des expériences invitro, a montré que GILZ augmente l’expression de la FKN et d’autre part que laFKN elle-même augmente la prolifération. Cette étude contribue à élucider lerôle de SDF-1 et de la FKN dans le CEO. / Little is known about the molecules that contribute to tumor growth ofepithelial ovarian carcinomas (EOC) that remains the most lethal gynecologicalneoplasm in women.The two chemokines CXCL12/SDF-1 and fractalkine (FKN)/CX3CL1 havebeen widely studied in tumorigenesis. In epithelial ovarian cancer (EOC), SDF-1enhances tumor angiogenesis and contributes to the immunosuppressivenetwork. SDF-1 also acts on tumor cell proliferation and survival and, throughits main receptor CXCR4, governs the migration of malignant cells and theirinvasion of the peritoneum. The chemokine FKN has been documented inepithelial tissues and in various cancers. FKN have paradoxical effects intumors: anti-tumoral effect in some tumor entities and pro-tumoral effect inother tumor entities.In our study, we demonstrated the expression of SDF-1 and FKN on thesurface epithelium of normal ovaries and benign and malignant tumors,suggesting that the expression of these chemokines preexists to tumorigenesis.We also demonstrated an heterogeneous expression of both chemokines in EOC.In our large and homogeneous cohort (183 specimens of EOC), SDF-1expression levels had no effect on overall survival or progression-free survival.Thus, SDF-1 expression by tumor epithelial cells is not in itself a valuableprognostic factor in patients with advanced EOC. FKN immunostaining scores(in 54 specimens of EOC) correlated positively with the two proliferationmarkers : Ki-67 and GILZ. In vitro, we demonstrated that GILZ increases theexpression of FKN and that FKN itself increased proliferation. This studycontributes in elucidating the role of the two chemokines SDF-1 and FKN inEOC.

Contexte: La grande majorité des mutations délétères identifiées sur le gène BRCA1 sont des mutations « privées ». Cependant, certaines d’entre elles proviennent d’un ancêtre commun, à l’origine d’un effet fondateur. Ainsi, la mutation BRCA1-3600del11 (c.3481_3491del11, p.Glu1161Phefs*3) est localisée en France pour 82% des familles porteuses et 85% d’entre elles sont originaires du quart Nord-Est. En 2006, cette mutation représentait respectivement 51,5% et 42,0% de toutes les mutations du gène BRCA1 identifiées dans les familles lorraines et alsaciennes atteintes d’un cancer du sein et/ou de l’ovaire. En 2004, parmi les 27 cas-index ayant consulté en Alsace et présentant une mutation de BRCA1, 37% sont porteurs de cette mutation, tous issus de familles originaires des Vosges, suggérant l’existence d’un effet fondateur. L’identification d’un haplotype commun est venue confirmer l’existence de cette hypothèse. Une équipe alsacienne a mentionné dans deux publications en 2000 et 2004 sur la mise en évidence de la mutation 3600del11 que les caractéristiques des cancers associés à cette mutation, ne plaidaient pas en faveur d’une relation génotype-phénotype. Or, les caractéristiques anatomo-pathologiques des cancers associés à cette mutation n’ont pas été abordées par ces deux publications. Nous nous sommes alors posés la question de caractéristiques anatomo-pathologiques particulières des cancers du sein et des cancers de l’ovaire diagnostiqués chez les femmes porteuses de cette mutation dans notre région. Nous nous sommes également posés la question de l’existence d’un phénomène d’anticipation génétique dans ces familles. L’anticipation génétique est la survenue plus précoce d’une pathologie et/ou l’aggravation de ses signes cliniques lors de la transmission d’une mutation d’une génération à la suivante au sein d’une même famille. Très peu d’études ont cherché à mettre en évidence ce phénomène d’anticipation dans des cohortes issues de familles de syndrome sein-ovaire associées à une mutation de BRCA1 ou BRCA2. Les études publiées présentaient des biais de sélection du fait de l’inclusion de patients non testés dans leur analyse. Les études publiées sur des cohortes issues de familles présentant une mutation sur le gène BRCA1/2 suggéraient que le dépistage ciblé et l’excès de surveillance pourraient avoir une influence sur l’âge au diagnostic d’un cancer du sein chez les jeunes femmes incluses.Les améliorations majeures au niveau de la mammographie et du traitement du cancer du sein, de même que le programme de dépistage organisé pour les femmes de 50 ans et plus sont apparues en France, après 1980. A notre connaissance, à ce jour, aucune étude n’a été réalisée en France visant à identifier un phénomène d’anticipation génétique dans les familles associées à une mutation sur BRCA1ou BRCA2 et à analyser ce phénomène.Objectif: Notre premier objectif est de constituer une première cohorte lorraine de patientes porteuses de la mutation 3600del11 et d’analyser les caractéristiques anatomo-pathologiques des cancers du sein et de l’ovaire liés à cette mutation. Notre deuxième objectif rechercher l’existence d’une anticipation génétique dans des familles présentant la mutation fondatrice BRCA1-3600del11.Patientes: Quatre cent quatre patientes sont porteuses d’une mutation BRCA1 à l’Institut de Cancérologie de Lorraine (ICL) sur la période s’étendant de 1994 à 2012, parmi elles, nous avons identifié les patientes porteuses de la mutation BRCA1-3600del11. Nous avons identifié à l’Institut de Cancérologie de Lorraine, 38 paires mères-filles atteintes d’un cancer du sein ou de l’ovaire issues de 37 familles présentant le syndrome sein-ovaire associé à cette mutation dont 25 paires mères-filles atteintes d’un cancer du sein et 13 paires mères-filles atteintes d’un cancer de l’ovaire [...] / Introduction: Over 1000 alterations in the BRCA1 gene have been documented. Most of these are frameshifts and ~10% are missense mutations that generate stop codons leading to a truncated and therefore inactive BRCA1 protein. In the French population, prevalence of BRCA1 mutations has been reported in few studies; In a preliminary study of 14 breast and/or ovarian cancer families, a frequent BRCA1 mutation was detected in five unrelated families; the c.3481_3491del11 mutation (BIC: 3600del11), an 11 base-pair deletion in exon 11 leading to a premature stop codon at 1165. In a second study carried out in 2004 involving 27 index cases, the c.3481_3491del11 mutation accounted for 37%. The haplotype analysis of the families carrying the mutation c.3481_3491del11, all originating from Alsace-Lorraine (North-East of France), revealed the presence of a common allele, indicating a founder effect. Purpose: To an attempt to better define the clinical and pathologic characteristics of breast and ovarian cancer related with the 3600del11 BRCA1 mutation, we report our experience with breast and ovarian cancer patients carrying the 3600del11 mutation at the Lorraine Oncology Institute in France. The aim of the current analysis is also to evaluate any differences of breast or ovarian cancer age at diagnosis between mothers and daughters carrying the c.3481_3491del11 mutation in the BRCA1 gene.Patients: Within the population who were referred between 1994 and 2012 to our oncogenetic clinic at the Lorraine oncology institute and who underwent genetic testing for BRCA1 and BRCA2, we identified 404 women carrying a BRCA1 mutation. Interestingly, 45% (180 of 404) of women with detected BRCA1 mutation had the germline 3600del11 mutation. These women were members of 89 different families with breast and or ovarian cancer cases. A study cohort of 38 women carrying the c.3481_3491del11 mutation and affected by first breast or ovarian cancer who reported a first breast or ovarian cancer in their mother carrying the c.3481_3491del11 mutation, was identified in 37 different families including members with breast and/or ovarian cancer at the Oncology Institute of Lorraine. Twelve mothers underwent genetic testing. Twenty five pairs of the 38 mothers-daughters pairs with c.3481_3491del11 mutation were affected by breast cancer and 13 pairs by ovarian cancer.Methods: Clinical and genetic data were collected from medical files and family pedigrees. Analyses were conducted for each cancer type. We investigated an early breast cancer detection effect due to early screening programs and also an increased breast tumor aggression. Since major improvements in breast cancer clinical management and imaging techniques appeared after 1980, we compared the age at breast cancer diagnosis and the age at death in mothers and daughters before and after 1980, first, in the group of women including mothers and daughters taken together and then in mothers and daughters separately. Genetic data were retrieved from familial files and clinical and pathological data from medical files. Descriptive statistics for the study population were calculated using the SPSS software (version 20.0). Results: Ninety one patients (71, 7%) were affected by first breast cancer and 31 (24,4%) by ovarian cancer. Breast tumors were identified in 37.4% of cases aged <40 years. Estrogen receptor status and progesterone receptor status were reported to 67 patients. Hormonal receptors status was positive in 31.4% of breast tumors. A triple-negative subtype was found in 21 cases, which accounts for 65.6% of the 32 patients with 3600del11 mutation for whom HER2 status was available. Ovarian tumors of the serous type, which constitute about 71 percent of all epithelial ovarian carcinomas, predominate among patients with 3600del11 mutation. Eighty six per cent of carriers were diagnosed at advanced stages III/IV [...]

Human endogenous retroviruses (HERVs) constitute about 8% of the human genome. There are around 4000 pol-containing retroviral integrations in the human genome, which makes it impractical to measure each of them separately. Therefore we developed a set of degenerate real time PCRs to detect major groups bearing sequence similarities to gammaretroviruses, one of the largest groups of human endogenous retrovirus, and betaretroviruses, some of which have integrated into the human genome most recently and which remain the most intact. It was found that, although both gammaretroviral and betaretroviral RNAs were broadly expressed in various healthy tissues including reproductive tissues and brain, a differential expression pattern was observed. My work further revealed that HERVE and HERVW, two gammaretroviral sequences, were ubiquitously and highly expressed in pathologic and normal female reproductive tissues with tissue specific patterns. Expression of HERVE was higher in endometriotic tissue than in normal endometrium. HERVE and HERVW RNAs were higher in normal ovarian tissue than in ovarian cancer. Besides these tissue- and neoplasia-related differences, there were wide differences in HERV expression among individuals. Next, a selective pattern of HERVW upregulation was demonstrated in SK-N-DZ, a neuroblastoma cell line, upon re-oxygenation after a period of hypoxia or with 5-azacytidine, a demethylating agent. Furthermore, broad and high expressions of gammaretrovirus-like transcripts in different brain areas analyzed were identified. The expression levels were variable among different donors. In conclusion a ubiquitous HERV expression was observed in tissues and cell lines, with various patterns. At this stage the data are not sufficient to conclude whether HERV has any physiological or pathological roles in humans. However, their differential expression patterns are compatible with functional roles of HERV in humans.