Les tumeurs rhabdoïdes (TR) constituent un rare cancer indifférencié du jeune enfant et du nourrisson, avec un âge médian au diagnostic de 20 mois. Ces tumeurs sont caractérisées par une inactivation biallélique du gène suppresseur de tumeur SMARCB1, un des membres du complexe SWI/SNF, acteur majeur du remodelage de la chromatine, sans autre altération génomique récurrente. Le pronostic des TR est péjoratif, le taux de survie globale atteignant 30% dans la plupart des séries, malgré des approches thérapeutiques conventionnelles particulièrement agressives. Les approches d’immunothérapies ont obtenu un succès certain dans certains cancers de l’adulte, et récentes analyses de l’infiltrat immun des cancers pédiatriques ne montrent pas un fort taux de tumeurs infiltrées à l’exception de rare types de cancers dont les TR intracrâniennes. Nous avons donc procédé à une analyse multimodale de l’infiltrat immun de cohortes de patients ainsi que d’un modèle de TR murines établi dans notre laboratoire. Nous avons identifié une forte proportion de tumeurs infiltrées dans certains sous-groupes de TR. Cet infiltrat était composé à la fois de cellules myéloïdes incluant des populations au phénotype immunosuppresseur, et lymphocytaires T notamment de phénotype résident mémoire caractérisées par une forte expansion clonale probablement spécifique d’un antigène tumoral. Nous avons identifié des cibles thérapeutiques communes aux tumeurs humaines et au modèle murin syngénique, et trouvé que cibler l’infiltrat lymphocytaire T ou myéloïde était susceptible d’induire une réponse tumorale complète avec induction d’une mémoire immunitaire, confirmant le caractère immunogénique des TR, et apportant de nouvelles stratégies thérapeutiques utiles en clinique. Enfin, nous avons identifié que les TR étaient le site d’une réexpression de rétrovirus endogènes, dépendante de celle de SMARCB1, avec activation des voies de l’interféron, apportant une base à une immunogénicité des TR issue du génome non codant. / Rhabdoid tumors (RT) are highly undifferentiated cancers occurring in infancy and early childhood, with a median age at diagnosis about 20 months. These tumors are characterized by the biallelic inactivation of SMARCB1 tumor suppressor gene, core member of the SWI/SNF complex, one major chromatin remodeling actor, in an otherwise highly stable genome. The prognosis of RT is dismal with overall survival hardly reaching 30% in most series, despite particularly aggressive conventional treatment. Immunotherapy approaches has gained a striking success within some adult cancer types and recent analyses of immune cell content of pediatric cancers don’t reveal a high rate of infiltrated tumors, except in few tumor types such as intracranial rhabdoid tumors. Then, we conducted a comprehensive analysis of the immune context of both human RT cohorts and a mouse RT model, including at single cell level. We identified a high recurrence of infiltrated tumors, in a RT-subgroup related manner, composed of both myeloid cells including cells with immune suppressive phenotypes, and T cells with notably a tissue resident memory phenotype demonstrating a high clonal expansion highly suggestive of immunogenicity. We identified common targetable immune populations between human and mouse RTs, and found that targeting both T and myeloid infiltrating cells was able to induce complete anti-tumor response with induced memory, confirming the immunogenic properties of RTs, and identifying new therapeutic strategies of clinical relevance. We finally identified that RTs were the site of SMARCB1-dependent endogenous retroviruses reexpression, with subsequent activation of interferon signaling, likely triggering the immune response in the context of RT, and providing a basis of non-coding genome-driven immunogenicity for these tumors.

L’objectif de ce travail était de comprendre l’état moléculaire des cellules dendritiques (CD) dans le microenvironnement tumoral. En intégrant l’analyse de tumeurs humaines par cytométrie en flux, de transcriptome, de secretome tumoral et l’analyse d’une base de données d’interaction CD-lymphocyte T générées in vitro, j’ai obtenus 2 résultats majeurs. Tout d’abord, nous proposons une nouvelle classification de CD activées humaines, qui sont soit « secrétantes », c’est-à-dire spécialisées dans la production de cytokines et chemokines, soit « aidantes » c’est-à-dire spécialisées dans l’induction de la sécrétion de nombreuses cytokines T helper après co-culture. Les CD infiltrant les tumeurs ORL inflammées correspondaient au type « sécrétantes ». Au-delà du nouveau concept biologique, cette classification est base théorique importante pour l’immunothérapie à base d’adjuvants. Deuxièmement, nous avons montré que l’inflammation tumorale n’était pas un facteur pronostic majeur des cancers ORL, mais que MMP2 et l’effraction extra-capsulaire étaient des facteurs pronostiques indépendants de la survie liée à la maladie. Nous avons pu classer les patients en 4 niveaux de risque et montré qu’ils avaient des chances équivalentes de réponse à l’immunothérapie. Nos données sont une base pour un essai clinique dirigé par biomarqueur, proposant de la chimiothérapie ou de l’immunothérapie néoadjuvantes, dans le but de diminuer le pourcentage de patients présentant des récidives sévères et précoces / The objective of the thesis was to decipher the molecular state of tumor infiltrating dendritic cell (DC) and their relation to the tumor microenvironment. By combining the analysis of human tumor samples by flow cytometry and RNA sequencing, of tumor secretome and of a large dataset of in vitro DC-Tcell interactions I obtained 2 main findings. First, we reported a novel classification of human activated DC, that are either “secretory” that is specialized in secreting cytokines and chemokines, or “helper” that is specialized at inducing the secretion of a broad range of T helper cytokines after cell co-culture. DC infiltrating inflamed human head and neck cancer matched the “secretory” phenotypic and transcriptomic signatures. Beyond this novel biological concept, this classification is of importance as a theoretical basis for adjuvant-based immunotherapy. Secondly, we showed that tumor inflammation was not the main prognostic factor for oral cavity cancer (OCC) patients, but that MMP2 and the presence of extra-nodal extension were independent predictors of reduced disease-specific survival. We could stratify OCC into 4 prognostic groups and showed that they had similar expected rates of response to immunotherapy. Our data may serve to design a biomarker-driven clinical trial proposing neoadjuvant chemotherapy or immunotherapy to high-risk patients, with the goal of reducing the percentage of OCC patients that will present with early and severe recurrences.

Fibroblasts are stromal cells ubiquitously present in the human body. They often appear in a quiescent state and can become activated in response to tissue remodeling signals. Activated fibroblasts acquire biosynthetic, pro-inflammatory and contractile properties, key functions for wound healing. In addition, the presence of permanently activated fibroblasts is one of the hallmarks of cancer. The purpose of this work is to investigate the differences between newborn and adult fibroblasts and keratinocytes in their implication in scarless wound healing, the origin of cancer associated fibroblasts (CAF)s and the influence of fibroblasts in melanoma invasion. Evidence suggests that wounds heal almost without scar in newborns. To understand the mechanisms that contribute to scarless wound healing we focused on the differences between newborn and adult fibroblasts and keratinocytes, which are cells present in human skin and participating in wound healing process. A comparison of the expression profile between newborn and adult fibroblasts showed differentially regulated genes related to the acute phase of the inflammatory response and ECM organization, traits involved in wound healing. We also found that newborn fibroblast showed higher differentiation potential, exhibited markers of pluripotency and...

Glioblastoma (GBM) is the most common primary brain tumor in adults and represents one of the most aggressive tumor types. Despite treatment GBM remains incurable and when treated the tumor recurs more aggressive and treatment resistant than before. The understanding of the underlying pathophysiology of GBM has increased in recent years, yet the high mortality with a 5-year survival rate of less than 10% remains. Previous studies from the research group, have shown that complement protein C3 is upregulated in stromal and glioma cells in lower oxygen tensions, and this indicates that C3 might play a role in certain GBM tumor microenvironment (TME) niches. For this reason, it is of great interest to investigate how glioma cells are affected when stimulated with C3. With cell proliferation-, migration assays and gene expression analysis with real time quantitative polymerase chain reaction (qPCR) it was possible to investigate how glioma cells respond to treatment with C3 and C3a-receptor antagonist. By optimizing an antibody panel for detection of macrophages/microglia, astrocytes and tumor cells we made it possible to study the modulation of immune parameters during treatment with C3A-receptor antagonist in mice. / Glioblastom (GBM) är den vanligaste primära hjärntumören hos vuxna och representerar en av de mest aggressiva tumörtyperna. Trots behandling förblir GBM obotlig och efter behandling återkommer tumören mer aggressiv och behandlingsresistent än tidigare. Förståelsen för den underliggande patofysiologin för GBM har ökat de senaste åren, trots detta kvarstår den höga dödligheten med en 5-årig överlevnadsprognos under 10%. Tidigare studier från forskningsgruppen har också visat att komplementprotein C3 är uppreglerat i gliomceller under lågt syretryck, vilket indikerar att C3 kan spela en roll i olika miljöer som finns i GBM. Av denna anledning är det av stort intresse att undersöka hur gliomceller påverkas när de stimuleras med C3. Med cellproliferation-, migrerings analyser och genuttrycksanalys med real time quantitative polymerase chain reaction (qPCR) var det möjligt att undersöka hur gliomceller, men även andra komponenter av tumor microenvironment (TME) svarar på behandling av C3 och C3A-receptor antagonist. Genom att optimera en antikroppspanel, med detektion av makrofager/ mikroglia, astrocyter och tumörceller har vi nu gjort det möjligt att studera moduleringen av immun parametrar vid behandling av C3A-receptor antagonist i möss.

The tumor microenvironment is a key modulator in cancer progression and has become a novel target in cancer therapy. An increase in hyaluronan (HA) accumulation and metabolism can be found in advancing tumor progression and are often associated with aggressive malignancy, drug resistance and poor prognosis. Wound-healing related myofibroblasts or activated cancer-associated fibroblasts (CAF) are assumed to be the major sources of HA. Both cell types are capable to synthesize new matrix components as well as reorganize the extracellular matrix. However, to which extent myofibroblasts and CAF perform these actions are still unclear. In this work, we investigated the matrix remodeling and HA production potential in normal human dermal fibroblasts (NHFB) and CAF in the absence and presence of transforming growth factor beta -1 (TGF-β1), with TGF-β1 being a major factor of regulating fibroblast differentiation. Three-dimensional (3D) collagen matrix was utilized to mimic the extracellular matrix of the tumor microenvironment. We found that CAF appeared to response insensitively towards TGF-β1 in terms of cell proliferation and matrix remodeling when compared to NHFB. In regards of HA production, we found that both cell types were capable to produce matrix bound HA, rather than a soluble counterpart, in response to TGF-β1. However, activated CAF demonstrated higher HA production when compared to myofibroblasts. The average molecular weight of produced HA was found in the range of 480 kDa for both cells. By analyzing gene expression of HA metabolizing enzymes, namely hyaluronan synthase (HAS1-3) and hyaluronidase (HYAL1-3) isoforms, we found expression of specific isoforms in dependence of TGF-β1 present in both cells. In addition, HAS2 and HYAL1 are highly expressed in CAF, which might contribute to a higher production and degradation of HA in CAF matrix. Overall, our results suggested a distinct behavior of NHFB and CAF in 3D collagen matrices in the presence of TGF-β1 in terms of matrix remodeling and HA production pointing to a specific impact on tumor modulation.

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The definition of clinical target volume (CTV) margins around gross tumor volume (GTV) for radiotherapy of esophageal cancer (EC) and many solid tumors is still a challenge hence the currently available in-vivo imaging techniques still fail to detect areas of microscopic tumor extension (MTE). Many parameters of the tumor microenvironment (TME), e.g., tumor cell proliferation, cancer stem cells, hypoxia, kinases, immune architecture and patient-specific parameters are hypothesized as inducers of MTE in esophageal cancer and other tumors. The correlation of these TME biomarkers with MTE before, during or after radiochemotherapy (RCHT) is crucial in the era of image-guided, adaptive high-precision photon or particle therapy. In this thesis, two study cohorts were used to assess some selected TME biomarkers and their predictive value on MTE for an improved CTV definition. The first study used immunohistochemistry analysis for the assessment of TME marker namely HIF-1α, Ki67, p53, CXCR4 and PD1 in a cohort of retrospectively collected formalin-fixed paraffin-embedded (FFPE) blocks of EC patients treated with either neoadjuvant radiochemotherapy plus resection (NRCHT+R) or resection alone (R). The subsequent study employing a multiplex-immunofluorescence technique assessed the expression of various markers, i.e., FAK, ILK, CD44, HIF-1α and Ki67, in a cohort of prospectively prepared FFPE resection specimens of EC patients with implantable fiducial gold markers at the proximal and distal tumor borders illustrating the GTV prior to NRCHT+R and correlated those markers to the MTE. The findings from our first study showed upregulation of HIF-1α, Ki67, p53, CXCR4 and PD1, within squamous cell carcinoma (SCC) and adenocarcinoma (AC) patients treated with R compared to those having undergone NRCHT+R. In the second study higher expression of FAK+, CD44+, HIF-1+, and Ki67+ cells in tumor-nests than in tumor-stroma of both SCC and AC patients was found, although ILK+ cells were higher in tumor stroma. In addition, MTE reaching up to 31 mm beyond the fiducial markers was found in three patients (all cT3N1) with a stronger expression of FAK+, CD44+ and ILK+ cells in tumor-nests in between the fiducial markers (former GTV) and beyond those (former CTV), even after NRCHT. In conclusion, there is thus far no evidence that the TME influences the CTV margin on an individual patient basis, hence differences in the TME between patients with residual tumor cells in the original CTV compared to those without were not detected.

Poor drug penetration through tumor tissue has emerged as a fundamental obstacle to cancer therapy. The solid tumor microenvironment presents several physiological abnormalities which reduce the uptake of intravenously administered therapeutics, including leaky, irregularly spaced blood vessels, and a pressure gradient which resists transport of therapeutics from the bloodstream into the tumor. Because of these factors, a systemically administered anti-cancer agent is unlikely to reach 100% of cancer cells at therapeutic dosages, which is the efficacy required for curative treatment. The goal of this project is to use high-intensity focused ultrasound (HIFU) to enhance drug delivery via phenomena associated with acoustic cavitation. ‘Cavitation’ is the formation, oscillation, and collapse of bubbles in a sound field, and can be broadly divided into two types: ‘inertial’ and ‘stable’. Inertial cavitation involves violent bubble collapse and is associated with phenomena such as heating, fluid jetting, and broadband noise emission. Stable cavitation occurs at lower pressure amplitudes, and can generate liquid microstreaming in the bubble vicinity. It is the combination of fluid jetting and microstreaming which it is attempted to explore, control, and apply to the drug delivery problem in solid tumors. First, the potential for cavitation to enhance the convective transport of a model therapeutic into obstructed vasculature in a cell-free in vitro tumor model is evaluated. Transport is quantified using post-treatment image analysis of the distribution of a dye-labeled macromolecule, while cavitation activity is quantified by analyzing passively recorded acoustic emissions. The introduction of exogenous cavitation nuclei into the acoustic field is found to dramatically enhance both cavitation activity and convective transport. The strong correlation between inertial cavitation activity and drug delivery in this study suggested both a mechanism of action and the clinical potential for non-invasive treatment monitoring. Next, a flexible and efficient method to simulate numerically the microstreaming fields instigated by cavitating microbubbles is developed. The technique is applied to the problem of quantifying convective transport of a scalar quantity in the vicinity of acoustically cavitating microbubbles of various initial radii subject to a range of sonication parameters, yielding insight regarding treatment parameter choice. Finally, in vitro and in vivo models are used to explore the effect of HIFU on delivery and expression of a biologically active adenovirus. The role of cavitation in improving the distribution of adenovirus in porous media is established, as well as the critical role of certain sonication parameters in sustaining cavitation activity in vivo. It is shown that following intratumoral or intravenous co-injection of ultrasound contrast agents and adenovirus, both the distribution and expression of viral transgenes are enhanced in the presence of inertial cavitation. This ultrasound-based drug delivery system has the potential to be applied in conjunction with a broad range of macromolecular therapeutics to augment their bioavailability for cancer treatment. In order to reach this objective, further developmental work is recommended, directed towards improving therapeutic transducer design, using transducer arrays for treatment monitoring and mapping, and continuing the development of functionalized monodisperse cavitation nuclei.