Title Promoter Affiliations Abstract "Deciphering the dendritic cell compartment in ovarian cancer to assess their potential as tumor vaccines." "An Coosemans" "Laboratory for Tumor Immunology and Immunotherapy, Vrije Universiteit Brussel" "Advanced stage ovarian cancer (OC) patients only have an overall 5-year survival of 20%. While targeted therapies such as PARP inhibitors have improved progression free survival, immunotherapy has so far not resulted in clear patient benefit. Importantly, the role of tumor-dendritic cells (DCs) as a key player in mounting an adaptive immune response has not been investigated yet in OC. Indeed, our lab has uncovered that vaccination with tumor-cDCs can elicit a therapeutically relevant immune response.Therefore, in this project, we will evaluate the cDC heterogeneity in OC and the potential to use tumor-cDCs as vaccine to treat OC. More specifically, we will identify and characterize different cDC populations at the transcriptomic, proteomic and functional level in both a murine OC model and patient samples using state-of-the-art technologies. As in OC, BRCA1/2 mutations are present in 20% of the patients and determine patient outcome, their role in defining cDC function will also be studied. On top, we will investigate the impact of chemotherapy and PARP inhibitors on tumor-cDC function and assess the role of immunosuppressive cells thereon. As last, in the murine OC model, the effectiveness of the different cDC populations as OC vaccine will be assessed.The results of this project will provide new insights into the role of cDCs in OC and will propose a novel therapeutic approach for OC that overcomes the currently witnessed barriers to effective therapeutic responses." "Study of DDR/PARP1 signaling in the pathogenesis and treatment of soft tissue mineralization, using pseudoxanthoma elasticum as a model." "Olivier Vanakker" "Department of Biomolecular Medicine, University of Angers, University of Modena and Reggio Emilia" "DNA damage response (DDR) mechanisms - in particular PARP1 signaling - are suggested to be important in the emergence of soft tissue mineralization (STM). A hallmark STM disorder is pseudoxanthoma elasticum (PXE), caused by mutations in the liver transporter ABCC6, with a complex and incompletely understood pathogenesis. Several dysregulated mediators in PXE show remarkable resemblance with PARP1 signaling cascades; our preliminary data show activated PARP1 signaling in PXE patients, reduced mineralization in vitro and in vivo after PARP inhibition, and identify miR-204 as a regulator. Now, we will perform a more profound study of the pathophysiological role of PARP1 signaling in PXE and evaluate its use as a biomarker and therapeutic target for this intractable disease. First, we will study the mechanisms involved in activating the DDR/PARP1 cascade in PXE fibroblasts and the regulatory role of miRNAs. Second, we will evaluate possible correlations between PARP1 activity, circulating miRNAs and PARP1-related genomic variants and the clinical severity of PXE. Finally, we will evaluate several known PARP1 inhibitors as potential treatment in PXE, using in vitro and in vivo models. Taken together, this project will lead to major advances in the complex pathogenesis of PXE, will delineate non-invasive (miRNA) biomarkers for the disease and will lead to novel therapies by drug-repurposing for this disorder. As such it will significantly improve patient management and treatment." "Pharmacogenetic profiling of VEGF-inhibitors forcancer therapy and assessing the vascular effects of VEGF during neurodegeneration." "Diether Lambrechts" "Laboratory of Translational Genetics (VIB-KU Leuven)" "Mismatch repair (MMR) deficiency represents a well-established cause ofLynch syndrome, which is an autosomal dominantly inherited disorder of cancer susceptibility triggered by loss-of-function mutations in MMR genes (MLH1, MSH2, MSH6 or PMS2).(URL:#_ENREF_1) Lynch syndrome is responsible for 2-5% of endometrial (EM) or colorectal (CRC) tumors. Additionally, epigenetic silencing of MLH1 contributes to another 15-28% of these tumors.(URL:#_ENREF_2) Deficiency of the MMR machinery leads to DNA replicationerrors in the tumor tissue, but not in the normal surrounding tissue. In particular, errors often accumulate as insertion/deletion (indel) mutations in mono- and di-nucleotide repeats - a phenomenon referred to as microsatellite instability (MSI).(URL:#_ENREF_3)MMR-deficient tumors constitute a specific subtype due to their different prognosis and clinical outcome.(URL:#_ENREF_4) For instance, untreated CRC cancer patients with MMR-deficient tumors have a modestly better prognosis, but do not seem to benefit from 5-fluorouracil-based adjuvant chemotherapy, which is the first-choice chemotherapy for CRC cancer. In particular, in MMR-deficient tumors, mismatches induced by 5-fluorouracil are tolerated, leading to failure to induce cell death.(URL:#_ENREF_5) MMR-deficient tumors are also resistant to cisplatin and carboplatin, which are frequently used chemotherapies in EM cancer.(URL:#_ENREF_5) Furthermore, MMR-deficient tumors can be resistant to targeted therapies, because they acquire secondary mutations in genes that activate alternative or downstream signaling pathways (e.g. PIK3CA). Another possibility is that epigenetic silencing of MLH1 coincides with particular mutations, such as the BRAF V600E mutation(URL:#_ENREF_6), which represents an established negative predictor of response to targeted anti-EGFR therapies in advanced CRC cancer.(URL:#_ENREF_7) There have been some efforts to individualize the treatment of MMR-deficient cancers. These focused on identifying synthetic lethal interactions with the MMR pathway or targeting secondary mutations occurring as a result of MMR-deficiency. However, until now, these efforts failed to translate into clinically effective treatment options.The objectives of this thesis were to generate a more comprehensive picture of the mutation spectra arising in MMR-deficient tumors and to more rationally predict their response to therapies. Firstly, whole-exome sequencing was applied to characterize the unique somatic mutation patterns underlying MMR-deficient tumors. Each MMR-deficient tumor exhibited a clear hypermutator phenotype, containing on average 50 times more novel somatic mutations than MMR-proficient tumors. The mutations in MMR-deficient tumors were mostly occurring as indels in homopolymers. Indels were clearly less frequent in exons, suggesting that they are loss-of-function mutations undergoing negative clonal selection during tumorigenesis. On the other hand, a large set of recurrent indels affecting MMR-deficient tumors was identified implying positive clonal selection. Secondly, a novel MSI panel was designed to detect MMR-deficiency in clinical tumor samples by high-throughput profiling of the selected recurrent indels. This Sequenom-based panel was tested on more than 400 tumor samples, fromendometrial, colorectal and ovarian cancer patients, and demonstrated that it outperforms the standard diagnostic panel (i.e. the revised Bethesda panel). Thirdly, pathway analyses revealed that the recurrent indels in MMR-deficient tumors preferentiallyaffect the DNA double-strand break repair (DSBR) by homologous recombination (HR) pathway, containing on average 3.3 indels per tumor. The biological relevance of these secondary mutations was validated by performing functional studies in 11 primary tumor cultures. Double immunostaining for γH2AX and RAD51, as a measure of DSBs and ongoing HR, respectively, showed that MMR-deficient tumors mobilized less RAD51-positive foci, after DSB formation. BrdU and PI cell cycle analysis using FACS, as well as Western blots were used to exclude a reduced S/G2 phase or a reduced RAD51 expression as confounding factors for areduced DSBR by HR activity. Thereby, it is confirmed that the DSBR by HR pathway is also functionally affected in MMR-deficient tumors. Moreover, DSB inducers, such as the PARP inhibitor olaparib, triggered a dose-dependent reduction in proliferation in primary cultures of MMR-deficient tumors, identifying a synthetic lethal interaction. In addition, to more accurately measure the level of HR-deficiency in MMR-deficient tumors, the level of knock-down of BRCA1, BRCA2 and ATR needed to achieve an olaparib sensitivity similar to that observed in MMR-deficient cells was assessed. It is established that the loss of DSBR by HR activity in MMR-deficient tumors corresponds to a loss of about 70-80% BRCA1 or -2 expression, indicating that the sensitivity to olaparib that is observed in MMR-deficient tumors is intermediateto that of cells heterozygous and homozygous-deficient for BRCA1.Insummary, this thesis not only provides the first comprehensive catalogue of somatic mutations accumulating in MMR-deficient tumors, but also demonstrates the relevance of these mutations in the detection of MSI within the diagnostic setting, and potentially also the targeted treatment of these tumors." "Predictive genetic markers in gynaecological cancers: how to improve targeted therapy." "Toon Van Gorp" "Gynaecological Oncology" "The development of more targeted therapies opened up a completely new era in treatment of gynaecological malignancies. However, little is known about the ideal position and timing in the treatment strategy and which patients in particular will benefit from treatments such as poly (ADP-ribose) polymerase inhibitors (PARPi) and immune checkpoint blockade (ICB). The aim of this proposal is to find (epi-)genetic markers that predict response to these treatments. 1) PARPi proved to be a successful treatment in BRCA mutated ovarian cancer. However, other functional defects in the homologous recombination DNA repair pathway seem to cause a good  response to PARPi. The first aim of this project is to develop and validate an inhouse homologous recombination repair deficiency (HRD) test that can predict response to PARPi in BRCA mutated and non-mutated ovarian cancer. 2) The current predictive biomarkers that are being used in clinical practice do not seem to be reliable enough to predict response to ICB in both ovarian and cervical cancer. To achieve a blueprint of the tumor’s ecosystem at single cell resolution, we will perform single cell RNA-sequencing (scRNA-seq) and single cell T-cell receptor sequencing (scTCR-seq), and evaluate these in the light of clinical response of our patients. Furthermore, besides the tumor microenvironment, we aim to analyse the role of methylation in the resistance of cervical cancer cells to immune therapy. " "Deciphering the dendritic cell compartment in ovarian cancer to assess their potential as tumor vaccines." "Damya Laoui" "Department of Bio-engineering Sciences" "Advanced stage ovarian cancer (OC) patients only have an overall 5- year survival of 20%. While targeted therapies such as PARP inhibitors have improved progression free survival, immunotherapy has so far not resulted in clear patient benefit. Importantly, the role of tumor-dendritic cells (DCs) as a key player in mounting an adaptive immune response has not been investigated yet in OC. Indeed, our lab has uncovered that vaccination with tumor-cDCs can elicit a therapeutically relevant immune response. Therefore, in this project, we will evaluate the cDC heterogeneity in OC and the potential to use tumor-cDCs as vaccine to treat OC. More specifically, we will identify and characterize different cDC populations at the transcriptomic, proteomic and functional level in both a murine OC model and patient samples using state-of-the-art technologies. As in OC, BRCA1/2 mutations are present in 20% of the patients and determine patient outcome, their role in defining cDC function will also be studied. On top, we will investigate the impact of chemotherapy and PARP inhibitors on tumor-cDC function and assess the role of immunosuppressive cells thereon. As last, in the murine OC model, the effectiveness of the different cDC populations as OC vaccine will be assessed. The results of this project will provide new insights into the role of cDCs in OC and will propose a novel therapeutic approach for OC that overcomes the currently witnessed barriers to effective therapeutic responses." "Atlas of therapeutic targets in metastatic breast cancer." "Christine Desmedt" "Laboratory for Translational Breast Cancer Research, Translational Cell & Tissue Research" "Recently, we have been witnessing a strong expansion of the therapeutic arsenal that can be used to treat patients with metastatic breast cancer (MBC), with the addition of novel endocrine therapies, antibody-drug conjugates, CDK4/6, PI3K, PARP and immune checkpoint inhibitors among others. For some therapies, the presence of the target in a tumor sample is required for the patient to receive the treatment, while for other therapies it is not. Absence or molecular alterations of the targets have also been associated with resistance for some therapies. Knowledge about these targets in MBC is however limited and intra-patient inter-metastasis largely unknown, mainly because of the lack of metastatic samples to investigate these questions. Here, we will use the unique repository of MBC samples that we collect in the context of our post-mortem tissue donation program (NCT04531696) to tackle three main objectives: 1) investigate the intra-patient inter-metastasis heterogeneity of the most relevant treatment targets; 2) provide an atlas of all relevant targets for MBC, focusing on the association or mutual exclusivity of the targets; 3) investigate whether expression levels or molecular alterations of the targets are associated with resistance mechanisms.To conclude, with this study, we expect to be able to refine eligibility criteria to select patients for these novel treatments, to identify treatment resistance mechanisms and to refine treatment strategies for these patients." "Flanders BioImaging: Leading Imaging Application Integrated Service and Enablement (FBI-LIAISE)." "Winnok De Vos" "Molecular Imaging and Radiology (MIRA), Katholieke Universiteit Leuven, Hasselt University, Ghent University, Vrije Universiteit Brussel, Laboratory of cell biology and histology" "Flanders Bioimaging (FBI) is an inter-university consortium of advanced light microscopy and biomedical imaging core facilities conceived to integrate, optimize and coordinate the state-ofthe- art imaging infrastructure and expertise in Flanders. Its primary aim is to provide European research access to cutting-edge spearpoint imaging applications at each site via membership of EuroBioImaging, a landmark European Research Infrastructure Consortium. Relying on a track record of scientific collaboration and public-private partnerships, FBI will provide end-to-end solutions, supporting investigators with study design, novel modes of access (e.g., sample shipping, virtual microscopy…), development of novel imaging techniques, advanced image analysis, and training in all aspects from data collection to analysis and interpretation. Workflows developed within FBI comply with FAIR data management principles and internal quality control efforts assure standardized and reliable service. FBI will raise the efficiency of imaging infrastructure exploitation, accelerate technological development and consolidate the leading international position of Flanders in bio-imaging." "Predictive genetic markers for targeted therapy in gynaecological malignancies: bridging the gap between “one-size-fits-all” and more personalised treatment approach." "Toon Van Gorp" "Gynaecological Oncology, Laboratory of Translational Genetics (VIB-KU Leuven)" "Even with today’s ongoing progress in diagnosis and treatment options, HGSOC is still characterized by poor long-term survival and high recurrence rates. Platinum-based chemotherapy and surgery are key in the treatment but development of resistance remains a major clinical problem. Recently, more targeted therapies, such as PARPi have been developed which could help to turn around the ‘one-chemo-fits-all’ approach. This breakthrough can have a major impact for 800 women newly diagnosed with ovarian cancer in Belgium every year. Unlike classical chemotherapy, that acts on the cell division of all body cells, this targeted therapy interferes mainly with the DNA of the ovarian cancer cell. Several phase III clinical studies showed promising results with a sustained response and also improved quality of life. PARPi are expected to be one of the cornerstones of future treatment of ovarian carcinoma and to be introduced early in the disease to postpone possible relapse or even cure some patients. However, so far, little is known about the ideal timing in the treatment strategy of the individual patient and which patients will benefit in particular. The aim of this dissertation was to answer the question which therapy is the right therapy for the right patient at the right time in the treatment process. The result is the development of the Leuven HRD test. " "Exploring the potential and underlying mechanisms of therapeutic activation of p53 in combination with immunotherapy to stimulate an innate immune response against non-small cell lung cancer." "Evelien Smits" "Center for Oncological Research (CORE)" "Cancer treatment is advancing to personalized precision medicine following the continuous development of new targeted therapies and immunotherapies. Despite several recent breakthroughs, lung cancer remains the leading cause of cancer-related death worldwide. Non-small cell lung cancer is characterized by a 5-year survival rate of less than 20%, which is often the result of resistance mechanisms against current therapies. At the Center for Oncological Research we focused on targeting the tumor suppressor p53 protein to overcome resistance to conventionally used DNA-damaging agents. We showed that therapeutic reactivation of either wild type or mutant p53 greatly increased the cytotoxic response to cisplatin in a synergistic manner. Now we want to further improve these results by involving the immune system in the antitumor effect. Therefore, this study will explore the potential of p53 targeting therapies, as monotherapy or in combination with the DNA-damaging agent cisplatin, to eliminate tumor cells by recruitment and activation of natural killer (NK) cells. The outcome of this study could result in an innovate therapeutic strategy which combines a DNA-damaging agent with state-of-the-art targeted- and immunotherapy. As such, tumor cells can be targeted more directly and eliminated using the patient's own defense systems." "Exploring the potential and underlying mechanisms of therapeutic activation of p53 in combination with immunotherapy to stimulate an innate immune response against non-small cell lung cancer." "Evelien Smits" "Center for Oncological Research (CORE), Molecular Imaging, Pathology, Radiotherapy & Oncology (MIPRO)" "Cancer treatment is advancing to personalized precision medicine following the continuous development of new targeted therapies and immunotherapies. Despite several recent breakthroughs, lung cancer remains the leading cause of cancer-related death worldwide. Non-small cell lung cancer is characterized by a 5-year survival rate of less than 20%, which is often the result of resistance mechanisms against current therapies. At the Center for Oncological Research we focused on targeting the tumor suppressor p53 protein to overcome resistance to conventionally used DNA-damaging agents. We showed that therapeutic reactivation of either wild type or mutant p53 greatly increased the cytotoxic response to cisplatin in a synergistic manner. Now we want to further improve these results by involving the immune system in the antitumor effect. Therefore, this study will explore the potential of p53 targeting therapies, as monotherapy or in combination with the DNA-damaging agent cisplatin, to eliminate tumor cells by recruitment and activation of natural killer (NK) cells. The outcome of this study could result in an innovate therapeutic strategy which combines a DNA-damaging agent with state-of-the-art targeted- and immunotherapy. As such, tumor cells can be targeted more directly and eliminated using the patient's own defense systems."