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During my PhD thesis, I mainly worked on three projects involving mathematical and bioinformatics methods in immuno-oncology. 1) Project 1: development of the SmartFACS deconvolution tool. I developed a deconvolution tool called SmartFACS in collaboration with the Mechanics and Applied Mathematics Department (ULB) and the Immunobiology Laboratory (ULB). The role of this computer program is to estimate the cellular composition of a sample from RNA sequencing data. This tool has been developed in the context of immunology, where it is often of interest to identify immune cells present in the blood or in tumors. At the time this project began, no deconvolution tool for mouse data was yet available, despite the fact that much biomedical research is carried out in mouse models. During my thesis, I therefore decided to develop a tool adapted to mouse data, while trying to improve existing tools for human data by detecting a wider range of immune populations. 2) Project 2: research of clinical biomarkers for anti-PD1 immunotherapy treatment. In collaboration with the Immunobiology group (ULB), I worked on anti-PD1 therapy, which is already used clinically for certain cancers. Unfortunately, the success rate of this treatment is still relatively moderate. This is why the aim of my project was to determine predictive markers of response to anti-PD1 in order to better understand the mechanisms of resistance and find avenues of improvement for this treatment, as well as to better identify responder patients. To achieve these objectives, a mouse model was developed in the Immunobiology Laboratory. This model enabled us to reproduce the dichotomous response observed in the clinic. My work focused on analyzing pre-treatment tumor sequencing data obtained using the mouse model, in order to compare the immune infiltrate of responder and non-responder mice. My data analyses, together with experiments conducted by Jelena Gabrilo, revealed two immune populations important for treatmen, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Le mélanome est la forme la plus agressive et la plus mortelle des cancers de la peau. Une mutation activatrice dans les gènes BRAF ou NRAS est présente dans 95% des cas de mélanomes humains. L'importance de l'inflammation chronique et du microenvironnement tumoral dans le développement, la progression et le potentiel métastatique de cette maladie est bien établie. Les molécules chimioattractantes comme la chémérine jouent dans ce contexte un rôle clé via le recrutement sélectif de populations leucocytaires spécifiques exprimant le récepteur ChemR23. Lors de ma thèse, nous avons étudié le rôle de la chémérine, dans les différentes étapes de la carcinogenèse. Elle possède des propriétés antitumorales, et notamment dans le mélanome. Cependant, les mécanismes de base de son action in vivo restent à déterminer.Suite aux études sur le modèle murin, nous avons choisi d’utiliser le poisson-zèbre afin d’investiguer in vivo les fonctions de la chémérine dans la biologie du mélanome. En effet, les résultats chez le poisson-zèbre obtenus au sein de notre laboratoire, suggèrent que l'axe chémérine/ChemR23 est hautement conservé à travers le phylum des vertébrés. Pour évaluer les propriétés antitumorales de la chémérine, j’ai utilisé différentes stratégies préalablement établies et validées chez le poisson-zèbre :un modèle mosaïque utilisant le système MiniCoopR exprimant l'oncogène NRASQ61L, un modèle génétique stable de mélanome faisant intervenir l’oncogène BRAF sur fond d’absence d’une protéine p53 fonctionnelle, et un modèle de xénogreffe de tumeurs. Mes analyses comparant l’apparition et la progression tumorale entre des animaux invalidés pour le cluster b de la chémérine ou pour son récepteur cmklr1.1 et leurs contrôles WT démontrent de manière non ambigüe que les propriétés antitumorales du système chémérine/ChemR23 sont conservées chez le poisson-zèbre.En ouvrant la voie à l’utilisation du poisson-zèbre pour l’étude des mécanismes clés par lesquels la chémérine agit sur, Doctorat en Sciences biomédicales et pharmaceutiques (Médecine), info:eu-repo/semantics/nonPublished

Papillary thyroid carcinoma (PTC) is the most frequent histological subtype of thyroid cancers (TC), and BRAFV600E genetic alteration is found in 60% of this endocrine cancer. This oncogene is associated with poor prognosis, resistance to radioiodine therapy and tumor progression. Histological follow-up by anatomo-pathologists reveals that 2/3 of surgically-removed thyroids do not present malignant lesions. Continued fundamental research into the molecular mechanisms of TC downstream of BRAFV600E remains thus central to better understand the clinical behavior of these tumors. To study PTC, we used a mouse model in which expression of BRAFV600E is specifically switched on in thyrocytes by doxycycline administration. Upon daily intraperitoneal doxycycline injection, thyroid tissue rapidly acquired histological features mimicking human PTC. Transcriptomic analysis revealed major changes in immune signaling pathways upon BRAFV600E induction. Multiplex immunofluorescence confirmed the abundant recruitment of macrophages, among which a population of LYVE-1+/CD206+/STABILIN-1+ was dramatically increased. By genetically inactivating the gene coding for the scavenger receptor STABILIN-1, we showed an increase of CD8+ T cells in this in situ BRAFV600E dependent TC. Finally, we demonstrated the presence of CD206+/STABILIN-1+ macrophages in human thyroid pathologies. Altogether, we revealed the recruitment of immunosuppressive STABILIN-1 macrophages a PTC mouse model and the relevance of these observations in human thyroid tissues.

Glioblastoma is the most common and aggressive brain cancer. The low median survival of patients diagnosed with this disease makes it an unmet medical need. Nowadays, immunotherapeutic treatments have shown remarkable results in some populations of cancer patients but are rather ineffective in improving glioblastoma patients’ outcomes when used in monotherapy. The aim of this Ph.D. thesis is to contribute to the research of glioblastoma treatments by developing combination strategies of drug delivery systems to potentiate immunotherapy efficacy. The strategies used in this work include a DNA vaccine encoding glioblastoma-associated antigens, immune checkpoint blockades, and an immunogenic chemotherapeutic agent delivered locally. Our findings confirm the benefit of combination strategies to improve the immune response and increase the survival of glioblastoma., (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2022

The management of dental emergencies is a central and essential issue in the daily practice of dentists. Through two clinical studies, we were able to identify new perspectives: 1/ The strategy of emergency management based on triage with the establishment of recommendations allowed to find an effective compromise between limiting the admission of patients and ensuring the control of their pain and the relief of their symptoms. 2/ More conservative management of irreversible pulpitis. Our data tend to support pulpotomy as an acceptable and more conservative permanent treatment option for irreversible pulpitis of mature molars. Our strategies could be considered as first-line treatments, thus providing additional steps in the therapeutic gradient., (DENT - Sciences dentaires) -- UCL, 2022

The current SARS‐CoV‐2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID‐19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS‐CoV‐2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS‐CoV‐2 would offer significant relief, although vaccine developers have warned that design, testing and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (i), but the earliest vaccines were based on the live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS‐CoV‐2 will mutate and may naturally attenuate over time (ii). What makes the current pandemic unique is that, thanks to state‐of‐the‐art nucleic acid sequencing technologies, we can follow in detail how SARS‐CoV‐2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS‐CoV‐2 variants across the globe should be of key interest in our fight against the pandemic.

Malignant mesothelioma is a disease caused by inhalation of needle-like shaped particles and whose pathogenesis is not yet fully elucidated. A long-lasting general inflammation caused by persistent mesotheliomagenic particles is not sufficient to explain mesothelioma onset. Indeed, challenging data have shown that mesothelioma occurs without chronic inflammation. Our research team previously helped to discover that, beside inflammation, particles such as silica also induce a selective, rapid and sustained accumulation of immunosuppressive cells (regulatory T lymphocytes, myeloid derived suppressive cells and M2/regulatory macrophages) participating to fibrogenesis. To determine whether carcinogenic particles such as asbestos and carbon nanotubes (CNT) also elicit immunosuppressive responses, we investigated the impact of these particles on macrophage turnover, phenotype and immunosuppressive activity. With that purpose, we intraperitoneally injected mesotheliomagenic CNT-7 (needle-like, Mitsui & Co) and non-mesotheliomagenic CNT-T (tangled, Nagoya University) particles in Wistar rats and compared the effects on peritoneal macrophage subpopulations. We showed that macrophages die very rapidly in the attempt to phagocyte mesotheliomagenic CNT. They are later replenished by monocytic-derived small peritoneal macrophages (SPM-like macrophages) possessing comparable immunosuppressive functions and signatures to Tumor-Associated Macrophages (TAM), which infiltrate mesothelioma and block T cell antitumor activities. Early immunosuppressive SPM-like macrophages express and release the shed form of the immunoregulatory syndecan-1 glycoprotein, which could explain the immunosuppression that they exert on T cells. Non-mesotheliomagenic peritoneal responses induced by CNT-T are, in contrast, characterized by a recruitment of self-proliferating large peritoneal macrophages (LPM-like macrophages) that correspond to homeostatic macrophages without immunosuppressive activity. Our o, (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2021

Novel Strategies for Cancer Immunotherapy: Targeting Immune-Mediated Suppressive Mechanisms

Cancer immunotherapies, such as monoclonal antibodies (mAbs) directed against PD-1, aim at boosting immune responses against tumor cells. They have become a standard of care for several types of cancer. However, a majority of patients do not respond to current immunotherapies. Resistance to PD-1 blockade can in part be explained by the action of TGF-b1, an immunosuppressive cytokine activated notably by regulatory T cells (Tregs) via a mechanism that requires protein GARP. We developed antibodies against GARP:TGF-b1 complexes that block TGF-b1 activation by Tregs and we evaluated their anti-tumor efficacy in tumor-bearing mice. We observed that anti-GARP:TGF-b1 mAbs induce the regression of tumors otherwise resistant to anti-PD-1, and we showed that combined blockade of GARP:TGF-b1 and PD-1 can exert anti-tumor activity via multiple modes of action. This may prove important for the selection of cancer patients who could benefit from this novel form of immunotherapy in the clinics., (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2021