Cancer development and progression vary depending on tumor type, localization, invasion, immunogenicity and the ability of immune system to become activated. There are frequent interactions between tumor cells and immune cells, occuring locally at the site of primary tumor or distally through paracrine signalling of various mediators and cytokines. The main subject of this PhD thesis is to study key factors and aspects of immune response in cancer patients. In the first part, we analyzed immune cells infiltrating tumor tissues of ovarian cancer patients at different stages of disease. We focused on the dynamics of immune response, primarily on frequency of individual T lymphocyte populations in peripheral blood and tumor infiltrating T lymphocytes in tumors of early and advanced stages of ovarian cancer. We found that during disease progression there is a gradual decrease of proinflammatory Th17 and Th1 immune responses and a specific recruitment of regulatory T cells to the tumor site, which results in a significant immune suppression in the tumor microenvironment. In the second part, we demonstrated that the character of immune response in HPV-positive head and neck cancer patients is very different from the patients with tumors not associated with HPV infection. In HPV-positive patients, significantly...

Metabolic alterations in hepatocellular carcinoma (HCC) are fundamental for the development of diagnostic screening and therapeutic intervention since energy metabolism plays a central role in differentiated hepatocytes. In HCC research, hepatoma cell lines (HCLs) like HepG2 and Huh7 cells are still the gold standard. In this study, we characterized the metabolic profiles of primary human hepatoma cells (PHCs), HCLs and primary human hepatocytes (PHHs) to determine their differentiation states. PHCs and PHHs (HCC-PHHs) were isolated from surgical specimens of HCC patients and their energy metabolism was compared to PHHs from non-HCC patients and the HepG2 and Huh7 cells at different levels (transcript, protein, function). Our analyses showed successful isolation of PHCs with a purity of 50–73% (CK18+). The transcript data revealed that changes in mRNA expression levels had already occurred in HCC-PHHs. While many genes were overexpressed in PHCs and HCC-PHHs, the changes were mostly not translated to the protein level. Downregulated metabolic key players of PHCs revealed a correlation with malign transformation and were predominantly pronounced in multilocular HCC. Therefore, HCLs failed to reflect these expression patterns of PHCs at the transcript and protein levels. The metabolic characteristics of PHCs are closer to those of HCC-PHHs than to HCLs. This should be taken into account for future optimized tumor metabolism research.

Epigenetic modifications, such as DNA methylation and histone modifications, play important roles in gene expression and regulation, and are highly involved in cellular processes such as stem cell pluripotency/differentiation and tumorigenesis. Chromatin immunoprecipitation (ChIP) is the technique of choice for examining in vivo DNA-protein interactions and has been a great tool for studying epigenetic mechanisms. However, conventional ChIP assays require millions of cells for tests and are not practical for examination of samples from lab animals and patients. Automated microfluidic chips offer the advantage to handle small sample sizes and facilitate rapid reaction. They also eliminate cumbersome manual handling. In this report, I will talk about three different projects that utilized microfluidic immunoprecipitation followed by next genereation sequencing technologies to enable low input and high through epigenomics profiling. First, I examined RNA polymerase II transcriptional regulation with microfluidic chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) assays. Second, I probed the temporal dynamics in the DNA methylome during cancer development using a transgenic mouse model with microfluidic methylated DNA immunoprecipitation followed by next generation sequencing (MeDIP-seq) assays. Third, I explored negative enrichment of circulating tumor cells (CTCs) followed by microfluidic ChIP-seq technology for studying temporal dynamic histone modification (H3K4me3) of patient-derived tumor xenograft on an immunodeficient mouse model during the course of cancer metastasis. In the first study, I adapted microfluidic ChIP-seq devices to achieve ultrahigh sensitivity to study Pol2 transcriptional regulation from scarce cell samples. I dramatically increased the assay sensitivity to an unprecedented level (~50 K cells for pol2 ChIP-seq). Importantly, this is three orders of magnitude more sensitive than the prevailing pol2 ChIP-seq assays. I showed that MNase digestion provided better ChIP-seq signal than sonication, and two-steps fixation with MNase digestion provided the best ChIP-seq quality followed by one-step fixation with MNase digestion, and lastly, no fixation with MNase digestion. In the second study, I probed dynamic epigenomic changes during tumorigenesis using mice often require profiling epigenomes using a tiny quantity of tissue samples. Conventional epigenomic tests do not support such analysis due to the large amount of materials required by these assays. In this study, I developed an ultrasensitive microfluidics-based methylated DNA immunoprecipitation followed by next-generation sequencing (MeDIP-seq) technology for profiling methylomes using as little as 0.5 ng DNA (or ~100 cells) with 1.5 h on-chip process for immunoprecipitation. This technology enabled me to examine genome-wide DNA methylation in a C3(1)/SV40 T-antigen transgenic mouse model during different stages of mammary cancer development. Using this data, I identified differentially methylated regions and their associated genes in different periods of cancer development. Interestingly, the results showed that methylomic features are dynamic and change with tumor developmental stage. In the last study, I developed a negative enrichment of CTCs followed by ultrasensitive microfluidic ChIP-seq technology for profiling histone modification (H3K4Me3) of CTCs to resolve the technical challenges associated with CTC isolation and difficulties related with tools for profiling whole genome histone modification on tiny cell samples. / Ph. D. / The human genome has been sequenced and completed over a decade ago. The information provided by the genomic map inspired numerous studies on genetic variations and their roles in diseases. However, genomic information alone is not always sufficient to explain important biological processes. Gene activation and expression are not only associated with alteration in the DNA sequence, but also affected by other changes to DNA and histones. Epigenetics refers to the molecular mechanisms that affect gene expression and phenotypes without involving changes in the DNA sequence. For example, the DNA can get methylated, the histone protein that is wrapped around by DNA can also get methylated or acetylatied, and transcription factors can bind to different part of DNA. All of these can affect gene expression without alter the DNA sequences. Epigenetic changes occur throughout all stages of cell development or in response to environmental cues. They change transcription patterns in a tissue/cell-specific fashion. For example, transcriptional silencing of tumor-suppressor genes by DNA methylation plays an important role in cancer development. Therefore, understanding of epigenetic regulations will help to improve various aspects of biomedicine. For instance, personalized medicine can be vi tailored based on epigenetic profile of certain patient to specifically control gene expression in the disease treatment. However, the technology for profiling epigenetic modifications, i.e. Chromatin Immunoprecipitation (ChIP), suffers from serious limitations. The key limitation is the sensitivity of the assay. Conventional assay requires a large number of cells (>10⁶ cells per ChIP). This is feasible when using cell lines. However, such requirement has become a major challenge when primary cells are used because very limited amounts of samples can be generated from lab animals or patients. Population heterogeneity information may also be lost when a large cell number is used. In this project, we developed an automated ultrasensitive microfluidic chromatin/DNA immunoprecipitation followed by next-generation sequencing (ChIP/MeDIP-Seq) technology for profiling epigenetic modifications (e.g., histone modifications, transcriptional regulations, and DNA methylation). We extensively optimized design parameters for each and every step of ChIP/MeDIP (e.g. sonication/crosslinking time, antibody concentration, washing conditions) in order to reach highest sensitivity of 0.1 ng DNA (or ~50-100 cells) as starting material for IP, which is roughly 4-5 orders of magnitude higher than the prevailing protocol and 2-3 orders of magnitude higher than the-state-of-the-art(~50 ng). With such sensitivity, we were able to study temporal dynamics in the DNA methylomes during the various stages of mammary cancer development from a transgenic mouse mode. We were able to investigate transcriptional regulation of RNA polymerase II from scarce cell samples. We were also able to study histone modification (H3K4Me3) of circulating tumor cells during cancer metastasis.

Hypoxia is a common feature of solid tumors and one of the hallmarks of tumor microenvironment. Tumor hypoxia plays an important role in angiogenesis, malignant progression, metastatic development, chemo-radio resistance and favours immune evasion by the emergence of tumor variants with increased survival and anti-apoptotic potential. There is very little work done on the impact of tumor hypoxia on the regulation of tumor susceptibility to the lysis induced by cytotoxic antitumor response. Therefore, we asked whether hypoxia confers tumor resistance to cytotoxic T lymphocyte (CTL)-mediated killing. We demonstrated that exposure of target cells to hypoxia has an inhibitory effect on the CTL-mediated autologous target cell lysis. Such inhibition was not associated with an alteration of CTL reactivity and tumor target recognition. We also showed that the concomitant hypoxic induction of Signal transducer and activator of transcription 3 (STAT3) phosphorylation on tyrosine 705 residue (pSTAT3) and hypoxia inducible factor 1 alpha (HIF-1α) is functionally linked to the alteration of Non small cell lung carcinoma (NSCLC) target susceptibility to CTL-mediated killing. We also showed that hypoxia-induced resistance of lung tumor to CTL-mediated lysis was associated with autophagy induction in target cells. Inhibition of autophagy resulted in impairment of pSTAT3 (via inhibition Src kinase) and restoration of hypoxic tumor cell susceptibility to CTL-mediated lysis. Moreover, in vivo inhibition of autophagy by hydroxychloroquine (HCQ) in B16F10 tumor bearing mice and mice vaccinated with TRP2 peptide dramatically increased tumor growth inhibition. Collectively, the current study establishes a novel functional link between hypoxia-induced autophagy and the regulation of antigen specific T cell lysis and points to a major role of autophagy in the control of in vivo tumor growth.Finally, as resistance of tumor targets to killer cells is likely to be regulated by multiple factors, we further aimed to identify the microRNA's regulated by hypoxia in NSCLC and melanoma and their putative involvement in the regulation of tumor susceptibility to antigen-specific CTL-mediated killing. MicroRNA-210 (miR-210) was significantly induced in a HIF-1α dependent manner in NSCLC and melanoma cells and miR-210 was expressed in hypoxic zones of human NSCLC tissues. Moreover, we demonstrated that hypoxia-induced miR-210 regulates tumor cell susceptibility to CTL-mediated lysis in part by suppressing PTPN, HOXA1 and TP53I11 expression indicating that miR-210 plays a potential role in the regulation of anti-tumor immune response.

Nous proposons, dans cette thèse, d'utiliser les techniques de modélisation en pharmacométrie selon l'approche de population afin de décrire les cinétiques de plusieurs marqueurs tumoraux sériques, et d'analyser leurs potentielles applications. Dans un premier temps, nous avons construit un modèle reliant les cinétiques de taille tumorale et de CA-125 dans le cancer de l'ovaire. Nous avons ensuite évalué son application pour : i) la prévision de la réponse tumorale au niveau individuel ; ii) la prédiction précoce de la survie au niveau d'une population dans le développement du médicament. Dans un second temps, nous avons réalisé un travail plus méthodologique sur la modélisation des cinétiques conjointes de PSA et d'un nouveau marqueur, le nombre de cellules tumorales circulantes (CTCs), dans le cancer de la prostate. Un modèle atypique combinant plusieurs innovations en pharmacométrie a été développé. En perspective, un lien va être établi avec la survie. En conclusion, la modélisation mathématique est un outil efficace pour l'évaluation précoce de l'efficacité des traitements / Our thesis project aimed at building mathematical models, using population approach, for different serum tumor markers, in order to describe their kinetics and to assess their potential applications. In a first intent, we built a semi-mechanistic model linking tumor size changes and CA-125 kinetics induced by chemotherapy in ovarian cancer patients. This model allowed assessment of CA-125 as: i) a biomarker for tumor size dynamics and treatment efficacy for clinical purposes; ii) an early predictor of clinical benefit during drug development. Then, we realized a more fundamental work by developing a semi-mechanistic model for characterizing the relationships between PSA kinetics and circulating tumor cell count dynamics during treatment in metastatic prostate cancer patients. This is an atypical model combining several advanced features in pharmacometrics. We have planned to assess a link with survival. In conclusion, mathematical modeling could be an efficient tool for the early prediction of treatment efficacy

L'émergence des thérapies ciblées dans le traitement des cancers a rendu indispensable la mise au point de marqueurs plus spécifiques et sensibles pour la surveillance des patients. Dès le stade invasif, des cellules tumorales peuvent passer dans le sang où elles constituent les Cellules Tumorales Circulantes (CTC). Les CTC sont accessibles par une simple prise de sang, évitant les biopsies invasives. De plus, elles représentent le seul matériel tumoral résiduel après traitement. C'est la raison pour laquelle les CTC constituent un axe de recherche très actif avec plus de 400 essais cliniques incluant ces cellules comme biomarqueurs. Ces essais apportent des renseignements importants sur le risque de récidive ou de progression métastatique, et ont pour objectif de pouvoir gérer en temps réel la conduite thérapeutique. Cependant, les CTC potentiellement métastatiques ne représentent qu'une fraction très minoritaire de ces cellules circulantes. Les technologies existantes, essentiellement basées sur une simple numération, ne suffisent pas pour guider efficacement la stratégie thérapeutique. Ce projet a évalué un ensemble de critères pouvant être utile pour la prise de décisions thérapeutiques pertinentes, adaptées à chaque patient, et la mesure de l'efficacité des traitements. Ce projet sera centre sur le mélanome. Les stades d'évolution de ce cancer sont bien définis, et dans les stades avances, le risque de développer des métastases est très élevé et la détection précoce de celles-ci est un enjeu important. Par ailleurs, ce cancer bénéficie de rapides progrès thérapeutiques, les CTC constituent donc un outil intéressant pour tester l'efficacité de ces nouveaux traitements. / The emergence of targeted therapies in cancer treatment has made essential the development of more specific and sensitive markers for monitoring patients. At the invasive stage, tumor cells can pass to blood. These cells are called Circulating Tumor Cells (CTC). CTCs are accessible through a simple blood test, avoiding invasive biopsies. Moreover, they represent the only residual tumor after treatment. It is why CTCs are a very active center of research with more than 400 clinical trials involving these cells as biomarkers. These tests provide important information on the risk of recurrence or metastatic progression and aim to manage in real time the therapeutic conduct. But the CTC potentially metastatic represents only a fraction very minority of these circulating cells. Existing technologies, mainly based on simple enumeration, are not enough to effectively guide therapeutic strategy. This project has evaluated a set of criteria to make appropriate therapeutic decisions, adapted to each patient, and able to measure the effectiveness of treatments. This project will focus on melanoma. Evolution stages of this cancer are well defined, and in advanced stages, the risk of developing metastases is very high and the early detection is an important issue. Moreover, CTC could be is an interesting tool to test the effectiveness of these new treatments.

Melanomas are one of the most aggressive types of tumours, with increasing incidence, high mortality and high potential to metastasize to a variety of diverse locations. The aim of this thesis was to study the tumour as a complex structure consisting not only of tumour cells but also of tumour stroma. Stromal cells play a major role in cancer biology. This is well documented for example in squamous cell epithelium tumours of the head and neck. Similar mechanisms can be expected to occur in melanomas. In the first experiment, we simulated the conditions in vivo during the metastatic process and studied the influence of non-adhesive environment both with and without the influence of stromal fibroblasts. The presented data demonstrates a change of tumour cells' phenotype leading to increased plasticity of the melanoma cells in these conditions. It also indicates the crucial role of stromal fibroblasts in interactions with melanoma cells. Cancer cell lines show variability in their behaviour, which is in accordance with well-known melanoma heterogeneity in clinical practice. The previous experiments in our laboratory indicate that cancer associated fibroblasts are able to influence the phenotype of a tumour cell line and this effect is based on a tumour type-unspecific mechanism. In the second part of...

L’hypoxie est une caractéristique commune des tumeurs solides et l’une des spécificités du micro environnement tumoral. L’hypoxie tumorale joue un rôle important dans l’angio génèse, la progression maligne, le développement de métastases, la chimio/radio-résistance et favorise l’échappement au système immunitaire du fait de l’émergence de variant tumoraux avec un potentiel de survie et de résistance à l’apoptose augmenté. Cependant, très peu de travaux ont étudié l’impact de l’hypoxie tumorale sur la régulation de la susceptibilité des tumeurs à la lyse induite par la réponse immune cytotoxique. Nous nous sommes donc demandé si l’hypoxie pouvait conférer aux tumeurs une résistance à la lyse induite par les lymphocytes T cytotoxiques (CTL). Nous avons démontré que l’exposition de cellules cibles tumorales à l’hypoxie possédait un effet inhibiteur sur la lyse de ces cellules tumorales par des CTL autologues. Cette inhibition n’est pas associée à des altérations de la réactivité de CTL ou de la reconnaissance des cellules cibles. Cependant, nous avons montré que l’induction hypoxique concomitante de la phosphorylation de STAT3 (pSTAT3) au niveau de la tyrosine 705 et du facteur HIF-1α (Hypoxia Inducible Factor-1 alpha) est liée fonctionnellement à l’altération de la susceptibilité de cellules tumorales bronchiques non à petites cellules (NSCLC) à la mort induite par les CTL. Nous avons aussi montré que la résistance de cellules tumorales bronchiques à la lyse CTL induite par l’hypoxie était associée à une induction d’autophagie dans les cellules cibles. En effet, l’inhibition de l’autophagie empêche la phosphorylation de STAT3 (via l’inhibition de la kinase Src) et restaure la susceptibilité des cellules tumorales hypoxiques à la lyse induite par les CTL. De plus, l’inhibition in vivo de l’autophagie par l’hydroxychloroquine (HCQ) dans le modèle murin portant la tumeur B16F10 and chez les souris vaccinée avec le peptide TRP2 augmente de façon drastique l’inhibition de la croissance tumorale. Collectivement, cette étude établit un nouveau lien fonctionnel entre l’autophagie induite par l’hypoxie et la régulation de la lyse induite par les cellules T spécifique d’antigènes et souligne le rôle majeur de l’autophagie dans le contrôle de la croissance tumorale in vivo.Finalement, étant donné que le la résistance tumorale à la lyse induite par les cellules tueuses est très probablement régulée par de multiples facteurs, nous avons aussi eu pour but d’identifier les micro-ARNs (miRs) régulés par l’hypoxie dans des modèles de NSCLC et de mélanome et leur implication putative dans la régulation de la susceptibilité tumorale à la lyse induite par les cellules T spécifique d’antigènes. Le micro-ARN 210 (miR-210) est ainsi significativement induit de manière dépendante de HIF-1α dans des cellules de NSCLC et de mélanome, et miR-210 est exprimé dans les zones hypoxiques de tissus issus de NSCLC. De plus, nous avons démontré que l’induction de miR-210 par l’hypoxie régule la susceptibilité tumorale à la lyse induite par les CTL en partie grâce à l’inhibition de l’expression de PTPN, HOXA1 et TP53I11, indiquant que miR-210 joue un rôle potentiel dans la régulation de la réponse immune antitumorale. / Hypoxia is a common feature of solid tumors and one of the hallmarks of tumor microenvironment. Tumor hypoxia plays an important role in angiogenesis, malignant progression, metastatic development, chemo-radio resistance and favours immune evasion by the emergence of tumor variants with increased survival and anti-apoptotic potential. There is very little work done on the impact of tumor hypoxia on the regulation of tumor susceptibility to the lysis induced by cytotoxic antitumor response. Therefore, we asked whether hypoxia confers tumor resistance to cytotoxic T lymphocyte (CTL)-mediated killing. We demonstrated that exposure of target cells to hypoxia has an inhibitory effect on the CTL-mediated autologous target cell lysis. Such inhibition was not associated with an alteration of CTL reactivity and tumor target recognition. We also showed that the concomitant hypoxic induction of Signal transducer and activator of transcription 3 (STAT3) phosphorylation on tyrosine 705 residue (pSTAT3) and hypoxia inducible factor 1 alpha (HIF-1α) is functionally linked to the alteration of Non small cell lung carcinoma (NSCLC) target susceptibility to CTL-mediated killing. We also showed that hypoxia-induced resistance of lung tumor to CTL-mediated lysis was associated with autophagy induction in target cells. Inhibition of autophagy resulted in impairment of pSTAT3 (via inhibition Src kinase) and restoration of hypoxic tumor cell susceptibility to CTL-mediated lysis. Moreover, in vivo inhibition of autophagy by hydroxychloroquine (HCQ) in B16F10 tumor bearing mice and mice vaccinated with TRP2 peptide dramatically increased tumor growth inhibition. Collectively, the current study establishes a novel functional link between hypoxia-induced autophagy and the regulation of antigen specific T cell lysis and points to a major role of autophagy in the control of in vivo tumor growth.Finally, as resistance of tumor targets to killer cells is likely to be regulated by multiple factors, we further aimed to identify the microRNA’s regulated by hypoxia in NSCLC and melanoma and their putative involvement in the regulation of tumor susceptibility to antigen-specific CTL-mediated killing. MicroRNA-210 (miR-210) was significantly induced in a HIF-1α dependent manner in NSCLC and melanoma cells and miR-210 was expressed in hypoxic zones of human NSCLC tissues. Moreover, we demonstrated that hypoxia-induced miR-210 regulates tumor cell susceptibility to CTL-mediated lysis in part by suppressing PTPN, HOXA1 and TP53I11 expression indicating that miR-210 plays a potential role in the regulation of anti-tumor immune response.

Nous avons étudié les relations entre les différentes voies du métabolisme énergétique lors de la mise en place des effets Crabtree et Warburg. L’effet du glucose sur le métabolisme énergétique de S. cerevisiae se traduit dans un premier temps par une inhibition cinétique du métabolisme oxydatif (effet Crabtree). Après l’ajout de glucose aux cellules, nous avons mis en évidence l’accumulation d’un intermédiaire de la glycolyse, le F1,6bP. Ceci induit une diminution drastique du rapport G6P/F1,6bP. Or, il a été montré que le G6P stimule et le F1,6bP inhibe l’activité de la chaine respiratoire mitochondriale « in-situ ». L’utilisation de mutants et la modulation de ce rapport nous a permis de montrer que l’induction de l’effet Crabtree chez la levure Saccharomyces cerevisiae est dû à une diminution du rapport G6P/F1,6bP. Parallèlement, le glucose induit un réarrangement génétique qui à terme conduit à un effet Warburg. Nous avons mis en évidence une diminution, au cours du temps du contenu mitochondrial par effet de dilution, suite à un arrêt de la biogenèse mitochondriale (répression de HAP4). Nous avons pu montrer que cette diminution quantitative des OXPHOS est sans effet sur la synthèse d’ATP cellulaire. Ceci est dû à une augmentation du flux de synthèse d’ATP glycolytique. L’utilisation de mutants HAP4", nous a permis de montrer qu’il n’y a pas de lien simple entre prolifération et répression des OXPHOS. Bien que le flux glycolytique diminue dans les conditions de maintien des OXPHOS, ceci est sans effet notoire sur la vitesse de prolifération. Ceci est un rare exemple d’une situation biologique ou l’on observe un découplage entre métabolisme énergétique et prolifération. / We used the yeast Crabtree (+) model to study the relationships between the energy metabolism pathways during the implementation of the Warburg effect. The effect of glucose on S. cerevisiae energetic metabolism results initially in a kinetic inhibition of the oxidative metabolism (Crabtree effect). Rapidly after the addition of glucose, we found an accumulation of F1, 6bP. This induces a drastic reduction in the ratio G6P / F1,6bP. Moreover, it has been shown that G6P stimulates and F1,6bP inhibits the activity of the respiratory chain "in-vitro". Mutants and the modulation of this ratio allowed us to show that the induction of the Crabtree effect is due to a decrease in the G6P / F1,6bP ratio. In parallel with the implementation of the Crabtree effect, glucose induces a genetic rearrangement that leads to a Warburg effect. We showed a decrease over time of mitochondrial enzymatic equipment by dilution effect, due to a halt of mitochondrial biogenesis (transcriptional repression of HAP4). We have been able to show that this decrease in respiratory capacity has no effect on the cellular capacity for ATP synthesis. This is due to the increase in glycolytic ATP synthesis flux. Furthermore, the use of mutants where there is no repression of mitochondrial metabolism upon glucose addition allowed us to show that there is no simple link between OXPHOS activity and cell proliferation. i.e. Mitochondrial metabolism repression/high glycolytic flux is not mandatory to allow a rapid cell proliferation. This is a rare example where energetic metabolism and cell proliferation are uncoupled.

Dissertation (Ph.D.)--University of South Florida, 2008. / Title from PDF of title page. Document formatted into pages; contains 181 pages. Includes bibliographical references.