Research Patrick Pauwels

Abstract

In the past five years, RNA therapeutics have witnessed a true revolution. Several RNA-based therapies have been approved for the treatment of genetic diseases, with unprecedented successes, as in spinal muscular atrophy. Moreover, the past year showed the world that RNA-based therapies, namely mRNA vaccines, can be the answer to a worldwide pandemic and save the lives of millions. RNA therapies are however lagging behind in clinical oncology. The overarching aim of this multi-armed project is to develop RNA-based cancer treatments. In parallel, the development of immune checkpoint inhibitors has revolutionized cancer care, but its success remains limited to a subset of patients. Altogether, for 60 percent of the eight million new cancer patients diagnosed in Europe each year, including almost all children with solid tumors, there is no EMA- or FDA-approved immunotherapy option, and they are left out of the circle of hope. In response, CANCERNA aims to build on these two breakthroughs and apply RNA-based therapeutics to overcome key barriers to unfold successful anti-cancer immune responses. Our two key objectives are: on one hand, harness the modulation of RNA processing to enhance the accessibility and immune susceptibility of the tumour and its microenvironment. While on the other hand, enhance the activity of the immune system by retargeting immune effector cells and developing personalized mRNA vaccines. The project will focus on two cancer types: acute myeloid leukemia and uveal melanoma. The collective knowledge of our consortium of RNA scientists, clinicians and biotech-pharma experts in RNA processing, RNA drug design and delivery, biocomputing and immuno-oncology provides a unique opportunity to significantly advance novel RNA technologies into successful cancer therapies.

Researcher(s)

• Promoter: Smits Evelien
• Co-promoter: De Waele Jorrit
• Co-promoter: Lion Eva
• Co-promoter: Pauwels Patrick
• Co-promoter: Van Audenaerde Jonas

Research team(s)

• Center for Oncological Research (CORE)

Project website

Project type(s)

• Research Project

Abstract

Pancreatic ductal adenocarcinoma (PDAC) is the third deadliest cancer worldwide with an increasing incidence. The 5-year survival of 7% has barely changed in 50 years and is stated as the worst of any cancer type. The immunosuppressive tumour microenvironment is believed to be the major confounding factor involved in failure of current therapies. Because of the high medical need, we will investigate the potential of a novel personalised and modified chimeric antigen receptor (CAR)-natural killer (NK) cell therapy combined with an innovative immune-priming agent. More specifically, we will first modify NK cells using the revolutionary CRISPR-Cas9 technology to make them insensitive to transforming growth factor beta-mediated immunosuppression in the tumour microenvironment. Next, these ameliorated NK cells will be modified to target both the tumour and the surrounding tumour microenvironment using different CAR constructs. Additionally, to invigorate our CAR-NK cell therapy, we will combine this with an immunostimulatory agent. This not only has the capacity to broadly activate the immune system but can also induce a greater attraction of our CAR-NK cells into the tumour to make our CAR-NK cell therapy more efficient. Hence, supported by our encouraging preliminary data, we are convinced that this project has great potential to finally overcome the crucial hurdles that block the advancement of treatment options for PDAC patients.

Researcher(s)

• Promoter: Smits Evelien
• Co-promoter: Pauwels Patrick

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Both targeted and immunotherapies are the key to precision medicine for the treatment of cancer patients. Deregulated signalling of the epidermal growth factor receptor (EGFR) plays an integral role in the tumourigenesis of multiple cancer types. Furthermore, it is well established that immune checkpoints are crucial for the tumour cell's escape from the immune system. The presence of drug resistance and/or immune evasion is a major obstacle to progress in the field. In our project, we will concentrate specifically on head and neck squamous cell carcinoma (HNSCC), a highly relevant tumour type with poor prognosis that is intensively studied at the Centre for Oncological Research (CORE) Antwerp. To date, there is still an urgent need to enhance the response to cetuximab treatment in recurrent/metastatic (R/M) HNSCC. Over the last years, cetuximab-related resistance mechanisms have been extensively studied at CORE. Based on our results and reports in literature, we hypothesize that inhibiting oncogenic bypass pathways responsible for cetuximab resistance, by a novel treatment strategy can lead to elimination of HNSCC cells that are resistant to treatment with cetuximab alone. In the proposed project, we will investigate the potency of a novel triple combination strategy in order to enhance the response to cetuximab therapy in HNSCC patients. To achieve this, cetuximab will be combined with buparlisib, a selective PI3K inhibitor, and an immune checkpoint inhibitor. Importantly, we will investigate the role of human papilloma virus (HPV) in this response, as HPV positive HNSCC patients represent a biologically distinct group. Furthermore, the nature of our project is translational, as from the beginning, we will use patient-derived HNSCC tumour organoids to validate our results from cell line experiments. These patient-derived tumour organoids are a very innovative and reliable model to identify effective treatment strategies and can actually be considered as a 'patient in the lab'. We are convinced that precision medicine using combinations of targeted therapies with immunotherapy may achieve the much-needed progress in HNSCC treatment. As reported in literature, both cetuximab and buparlisib treatment are able to promote anti-tumour immune response. Therefore, in the first work package, we will characterize the anti-tumour activity and immunomodulating effects of cetuximab in combination with buparlisib in HNSCC cell lines and patient-derived HNSCC organoids. Secondly, we will investigate the immunomodulating effects of cetuximab in combination with buparlisib on immune cells. In parallel, the effect of this combination treatment on the immune checkpoint profile will be assessed. Finally, the novel triple combination therapy consisting of cetuximab, buparlisib and an immune checkpoint inhibitor will be investigated in a humanized, PBMC engrafted HNSCC mouse model. This preclinical work will ultimately guide the start-up of a clinical trial to demonstrate feasibility of the novel triple combination therapy to treat HNSCC patients. Given the extensive preclinical (both in vitro and in vivo) and translational work packages to optimise the novel triple combination strategy, we are confident that the data generated in this project will provide insight into how therapeutic response to cetuximab treatment can be optimized, thus favouring the setup of a successful clinical trial with the newly identified triple combination therapy.

Researcher(s)

• Promoter: Lardon Filip
• Co-promoter: Pauwels Patrick
• Co-promoter: Peeters Marc
• Co-promoter: Prenen Hans
• Co-promoter: Smits Evelien
• Co-promoter: Wouters An

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

The research activities of the consortium IPPON (Integrated Personalized & Precision Oncology Network) are at the forefront of integrated personalized cancer medicine, with emphasis on 1) developing novel and more effective therapeutic strategies; 2) an improved detection and understanding of mechanisms driving therapeutic resistance; and 3) identifying and validating biomarkers for early detection and personalized therapy, in different cancers in need for improved therapeutic outcomes. In this way, we aim to deliver the right treatment to the right cancer patient at the right time. Novel and emerging anticancer strategies that we investigate include - but are not limited to - locoregional perfusion, targeted therapy, immunotherapy, cold atmospheric plasma therapy as well as novel combination therapies. We are convinced that the interdisciplinary collaboration between basic, translational and clinical researchers, catalyzed through this consortium, will enable us to tackle burning research questions and clinical unmet needs to advance the field of personalized cancer medicine. The members of our consortium bring together unrivaled access to biobank patient samples and to a dedicated clinical phase I/II oncological unit with a unique and complementary set of methods and skills covering the entire spectrum of molecular techniques, 2D and 3D cellular assays (in vitro and ex vivo), small- and large animal studies and clinical studies. IPPON gathers experts with an excellent research track record in fundamental, translational and clinical oncology; surgical techniques; targeted therapy; immunotherapy; (epi)genomics; (epi)transcriptomics; proteomics; imaging; liquid biopsies; pathology and clinical studies.

Researcher(s)

• Promoter: Peeters Marc
• Co-promoter: Dewilde Sylvia
• Co-promoter: Hendriks Jeroen
• Co-promoter: Lardon Filip
• Co-promoter: Pauwels Patrick
• Co-promoter: Smits Evelien
• Co-promoter: Van Dam Peter
• Co-promoter: Vanden Berghe Wim
• Co-promoter: Van den Wyngaert Tim

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Inspired by the mission of the EU commission, this project commits to tackle a major societal challenge, i.e. fighting cancer. A striking target for 2030 has been set by the EU: more than 3 million lives saved, living longer and better, achieve a thorough understanding of cancer, prevent what is preventable, optimize diagnosis and treatment, support the quality of life of all people exposed to cancer, and ensure equitable access to the above across Europe. This project contributes to (early) diagnosis and follow up of the disease. More and more biomarkers are discovered and validated for cancer and the highly precise determination thereof is high on the priority list, necessitating analytical devices that allow rapid and accurate analysis with high sensitivity. Electrochemical biochips are an emerging tool for point-of-care diagnostic systems due to their inherent high sensitivity and cost and time effectiveness. We propose the combined use of electrochemical detection with a light-triggered sensing technology for the specific and selective photoelectrochemical detection of low concentrations of cancer biomarkers (i.e. KRAS mutations), also allowing us to detect a panel of cancer biomarkers. Detection and quantification of the selected target sequences will be performed in liquid biopsies, to ensure the translation from a lab technology to a device for clinicians and even patients.

Researcher(s)

• Promoter: De Wael Karolien
• Co-promoter: Pauwels Patrick
• Co-promoter: Peeters Marc
• Co-promoter: Van Camp Guy

Research team(s)

Project type(s)

• Research Project

Abstract

In general, when a patient is diagnosed with invasive breast cancer the amplification status of the HER2 gene is evaluated by immunohistochemistry (IHC) and/or fluorescent in situ hybridization (FISH) on the primary tumor. International literature demonstrates that in 7-20% of cases HER2 heterogeneity takes place, especially between the primary tumor and bone metastasis. Furthermore, heterogeneity in time can occur due to treatment selection. Although reports have demonstrated that heterogeneity of the HER2 status at different sites occurs, only seldom new biopsies are analyzed to re-evaluate the HER2 status. By liquid biopsy, we can overcome this issue as liquid biopsies can (more) easily be repeated over time and contains cell-free tumor DNA (ctDNA) from the whole tumor mass. Hence this research can lead to a more detailed analysis of the presence of heterogeneity of HER2 amplification in this patient group. With this project, we plan to develop an assay that can accurately detect HER2 amplification in a liquid biopsy of breast cancer patients. Furthermore, we will investigate HER2 heterogeneity in breast cancer patients who progress upon first-line treatment (such as hormone therapy). By analysis of a liquid biopsy upon progression to first-line therapy in patients without HER2 amplification (at diagnosis on primary tissue biopsy), we expect to identify the patient group in which the HER2 amplification status has changed (significantly) and might benefit from anti-HER2 therapy. The innovative aspect of this project is that we will evaluate HER2 amplification (by ddPCR) in both the blood and urine simultaneously. Whereas blood sampling is minimally invasive, urine sampling is non-invasive and can easily be repeated over time. We will combine the HER2 amplification data with the results of a methylation assay (ddPCR) or the results of other frequent occurring gene aberrations (AVENIO ctDNA) to know whether enough tumor DNA is present in the circulation/urine for reliable analysis. Currently knowledge on the presence of ctDNA in the cfDNA fraction is lacking in many liquid biopsy studies. As long as we have no idea on the presence of ctDNA in our sample, we cannot distinguish a negative result from a non-informative result due to low ctDNA content by liquid biopsy. The overall aim of this project is to evaluate the discrepancies of HER2 amplification status between primary tumor and metastatic lesions that develop during therapy. To meet this objective we will pursue following aims: - Develop and evaluate an assay to measure HER2 amplification in the blood and urine by ddPCR. - Develop and evaluate a methylation assay to estimate the amount of cfDNA derived from tumor cells present in the blood and urine by ddPCR. - Evaluate an NGS assay detecting multiple breast-specific gene aberrations in the cfDNA from blood (AVENIO ctDNA assay). - Evaluate HER2 amplification in patients without a FISH positive HER2 status of the primary tumor who develop multiple organ metastasis during therapy.

Researcher(s)

• Promoter: Pauwels Patrick

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Today, most cancers are diagnosed through tactile lesions, imaging techniques, or clinical symptoms. This diagnosis is confirmed by a histopathological examination of a core biopsy of the primary lesion. However, a biopsy is very invasive, quite difficult to obtain and causes great discomfort to the patient. Because tissue (re) biopsy is often a problem, the use of liquid biopsies has become extremely popular in recent years. While the detection of diagnostic, prognostic and predictive biomarkers is generally performed on tissue samples, detection on liquid biopsies shows promise. Currently, liquid biopsy analysis is mainly focused on plasma testing. Compared to tissue tests, blood tests are minimally invasive. While a blood sample is considered minimally invasive, a skilled caregiver is required to draw blood from patients. In addition, the patient's health status may not allow for additional blood draws. Obtaining urine, on the other hand, is non-invasive, does not depend on the health status of the patient, is without limitation on volume or frequency of collection, and can be performed at home or at the physician's office. There is a huge variety of biomarkers in liquid biopsies, including circulating tumor cells (CTCs), cell free nucleic acids (cfNA), exosomes and proteins that show promise for non-invasive testing. Depending on the type of molecule, different "omic" technologies (i.e. genomics, transcriptomics, proteomics and metabolomics) are used to detect them. Realizing the potential of urine as a liquid biopsy requires research into optimal collection methods and storage conditions for the detection of biomarkers. Colli-Pee® was developed by Novosanis and allows to collect urine in a standardized and volumetric way. If collection methods and storage conditions can be standardized, yellow can become the new red and urine can replace or equate blood in cancer detection.

Researcher(s)

• Promoter: Pauwels Patrick
• Co-promoter: Zwaenepoel Karen
• Fellow: Jordaens Stephanie

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Lung cancer is a heterogeneous disease with high prevalence and mortality. Despite improvements in treatment, lung cancer takes over 1,000 lives each day in Europe alone. The benefit of targeted therapy is illustrated for ALK-driven non-small cell lung cancer (NSCLC), with a median survival of 7 years, compared to <20% overall 5 year survival for lung cancer in general. As targeted inhibitors do not actively kill tumor cells, aberrant cells remain dormant in the patient. To tackle inevitable resistance and disease progression, novel generation drugs are needed to target the resistance mechanism. However, for ROS1-fusions, a relatively recently described oncogene representing 1-2% of NSCLC, only a single targeted drug is currently approved. Hence, patients resort to chemotherapy, off-label use or clinical studies on disease progression. Due to the scarcity of ROS1+ NSCLC, clinical decisions are guided by sporadic case reports and in vitro experiments based on synthetic setups in non-human cell models. Here, we couple modern genome engineering and computational prediction on drug/target interactions with patient-driven efforts to generate relevant disease models. We will introduce 13 known and predicted resistance mutations into 6 patient-derived cell lines, followed by experimental and computational evaluation of available targeted drugs. Complementing experimental and computational data results in an objective model to guide clinical decision making in rare cancer types.

Researcher(s)

• Promoter: Van Camp Guy
• Co-promoter: Pauwels Patrick
• Co-promoter: Vandeweyer Geert

Research team(s)

Project type(s)

• Research Project

Abstract

Malignant pleural mesothelioma (MPM) is a fatal cancer that is in most patients causally associated with asbestos exposure. Due to its aggressive nature and despite the effectiveness of conventional anti-cancer treatment, the prognosis of patients diagnosed with MPM remains dismal with a median overall survival of only 9-12 months and a 5- year survival rate of only 5%. In the last decade, no improvement of survival has been achieved in this disease. Therefore, new therapeutic strategies are needed in order to prolong survival of MPM patients. Smart combination strategies might improve the anti-tumor response by interfering with different hallmarks of cancer and multiple immune escape mechanisms. In this research project tumor-induced immunosuppression will be tackled via two different pathways: immune checkpoint blockade will be used to reactivate silenced anti-tumor immune responses while blockade of the VEGF/VEGFR signaling pathway will be used to target the tumor vasculature in order to reduce angiogenesis thereby reducing tumor growth. In addition, we are keen to assess the positive impact that exercise may have on these combination strategies.

Researcher(s)

• Promoter: Smits Evelien
• Co-promoter: Lardon Filip
• Co-promoter: Pauwels Patrick
• Co-promoter: van Meerbeeck Jan

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

The first aim of this study is to investigate the efficiency of three circulating cell-free DNA (cfDNA) stabilizing blood collection tubes at room temperature as well as at a lower temperature. The setup of this study will be similar to that of our comparison study of the centrifugation protocols. Blood samples from KRAS-mutated cancer patients will be collected. In addition to these three collection tubes, one blood sample will be collected in a standard EDTA tube, which will be used as a gold standard. We will perform digital droplet PCR (ddPCR) analysis, which is a highly sensitive technique designed to detect low abundant genetic aberrations. This will provide us with the absolute amount of KRAS mutated ctDNA as well as the allele frequency (AF). Furthermore, we will also perform a fragment analysis by quantitative, real-time PCR (qPCR). This will allow me to assess the cfDNA quality. Based on the results of these analyses, we will be able to select the most optimal cfDNA stabilizing blood collection tube. This will complete our work in providing an optimized liquid biopsy workflow for implementation in clinical practice. The second aim is to perform simultaneous cfDNA and cfRNA analysis of plasma samples from early stage PDAC patients to identify novel biomarkers. Blood samples of 19 PDAC patients are being collected prior to surgery and at specific time point after surgery. CfDNA analysis will also be performed by KRAS ddPCR. On the other hand, the cfRNA will be sequenced by Biogazelle, a company which specializes in RNA research. They will perform differential gene expression analysis (i.e. looking at differences of individual genes) as well as gene set enrichment analysis (i.e. looking at differences in sets of related genes). We will further analyze results with regards to described gene alterations in collaboration with the department of Pathology (UZA). Thorough statistical analysis will be performed to determine the influence of these results and the KRAS mutational status on the success of the surgery and survival of these patients. These results would not only significantly boost further research in the diagnosis and follow-up of PDAC patients, but would also provide novel insights in simultaneous cfDNA and cfRNA analysis.

Researcher(s)

• Promoter: Pauwels Patrick

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Colorectal cancer (CRC) retains its position as one of the most prevalent types of cancer with around 700,000 deaths per year worldwide. Treatments focused on altering the immune system have recently paved their way into oncology with clinical achievements seen in a broad spectrum of solid tumors. However, signals of activity in CRC are largely involving microsatellite instable tumors, leaving a great need for effective immunotherapy in the majority of patients. The biologica! complexity of the tumor microenvironment seems to be an obstacle for cancer immunotherapy, suggesting that a strategy to solely targeting tumor cells is inadequate to overwhelm the aggressively growing tumor in CRC. Cancer-associated fibroblasts (CAFs) represent the dominant constituents of the tumor stroma and play a critica! role in the proliferative and invasive behavior of CRC. Additionally, CAFs provide a physical barrier for the efficient delivery of systemic therapy to the tumor making it an attractive target to combine with conventional treatment. Clinically addressing CAFs has been challenging due to its heterogeneous nature with both cancer-promoting and cancer-restraining features. We have recently identified a phenotypically distinct subset of CAFs in invasive CRC specimens, marked by the expression of CD70, and associated with poor prognosis of the patient. Moreover, CD70-positive CAFs proved to stimulate tumor invasion and to promote immune escape by the accumulation of immune suppressive regulatory T-cells. lnterestingly, CD70 is totally absent from normal epithelial tissue making it a safe target to eradicate the tumor-promoting CAFs. Based on our preliminary data, we hypothesize that targeting CD70-positive CAFs in CRC has a potential triple mode of action by enhancing anti-tumor immunity, eradicating a permissive niche for tumor invasion and increasing the efficacy of first-line chemotherapeutics. The primary objective of the proposed project is to find the ideal approach to deplete CD70-positive CAFs. The second objective is to design a combination strategy of CD70-targeted therapy with a first-line chemotherapeutic agent that elicits a potent anti-tumor immune response. The third objective is to identify potential bloodbased biomarkers for diagnosis and to monitor treatment response. Experiments will be performed in vitro under normoxic and hypoxic conditions and in vivo in an orthotopic syngeneic mouse model to identify the ideal timing and dosing of our combination strategy. This translational research project wil! lead to the launch of a phase 1/11 clinical trial in patients with advanced CRC with a grim prognosis of only 12 to 14 months. Since we have also found CD70 expression in the desmoplastic stroma of pancreatic cancer, this study will also pave the way to application in one of the most therapeutically resistant maliçinancies.

Researcher(s)

• Promoter: Pauwels Patrick
• Co-promoter: Jacobs Julie
• Co-promoter: Lardon Filip
• Co-promoter: Peeters Marc
• Co-promoter: Rolfo Christian
• Co-promoter: Smits Evelien

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Both targeted therapies and immunotherapies are now at the forefront of personalized cancer medicine. Aberrant signalling of the epidermal growth factor receptor (EGFR) plays an integral role in the tumorigenesis of multiple cancer types, making it a compelling drug target. In addition, it is well established that natural killer (NK) cells possess natural anti-tumour activity and can mediate antibody dependent cellular cytotoxicity (ADCC) upon binding with monoclonal antibodies, such as the EGFR inhibitor cetuximab. However, the presence of drug resistance and/or immune evasion is a major obstacle to progress in this field. In our project, we will concentrate specifically on head and neck squamous carcinoma (HNSCC), a highly relevant tumour type with poor prognosis that is intensively studied at the Center for Oncological Research (CORE) Antwerp. In this research project, we hypothesize that increasing the NK cell activity by cetuximab in combination with targeting NK cell immune checkpoint molecules can synergistically generate immune mediated elimination of HNSCC cells that are resistant to treatment with cetuximab alone. Importantly, we will investigate the role of human papilloma virus (HPV) in this response, as HPV positive HNSCC patients represent a biologically distinct group. By characterizing NK cell functionality and, by extension, the whole immune checkpoint profile in HNSCC, we aim to rationally design new combination strategies to overcome cetuximab resistance, with the ultimate goal to improve the prognosis and life quality of HNSCC patients. Hereby, we will focus on HPV status and the hypoxic microenvironment as important mediators of treatment response. Therefore, the nature of our project is translational, as from the beginning, the link with clinical data is considered to be imperative before moving on to further preclinical investigation of the identified combination strategies. Successful combinations will be validated in animal studies, which will ultimately guide the start-up of a clinical trial to demonstrate feasibility of the most promising combination therapy to treat HNSCC patients. Given the extensive preclinical (both in vitro and in vivo) and translational work packages to optimise the novel combination strategy, we are confident that the data generated in this project will favour the setup of a successful clinical trial with the newly identified combination regimen.

Researcher(s)

• Promoter: Lardon Filip
• Co-promoter: Pauwels Patrick
• Co-promoter: Peeters Marc
• Co-promoter: Smits Evelien
• Co-promoter: Wouters An

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Non-small cell lung cancer (NSCLC) remains the leading cause of cancer mortality worldwide and a marginally improving 5-year overall survival rate which remains below 20%. Successful therapeutic advances have emerged, but these treatment options are limited to only a small subset of NSCLC patients. Therefore, new treatment strategies are needed that will result in durable responses for the majority of NSCLC patients. In this regard, combining an immune modulatory chemotherapeutic agent with immunotherapy would be a suitable and promising approach. On the one hand, it has been shown that certain chemotherapeutics can induce immunogenic cell death, thereby releasing neoantigens and enabling tumor-specific cytotoxic T cell responses. On the other hand, CD70 has emerged as a promising target to be blocked in various hematological and solid malignancies. Its overexpression on tumor cells is associated with immune suppression in the tumor microenvironment. CD70 overexpression on NSCLC cells was detected by us in a subset of patients (16%). More importantly, preliminary findings from our group demonstrated the ability of certain chemotherapeutics to induce CD70 overexpression on NSCLC cells, which broadens the therapeutic window of anti-CD70 immunotherapy. Built on these preliminary findings, the primary aim of this study is to identify the ideal chemotherapeutic agent to combine with anti-CD70 immunotherapy by thoroughly evaluating several chemotherapeutics for their capacity to induce immunogenic cell death and stimulate CD70 overexpression on NSCLC cells. The second aim is to investigate the anti-tumor capacity of this treatment strategy together with the recently approved immune checkpoint inhibitor anti-programmed death (PD)-1, in order to develop an innovative approach that tackles the immunosuppressive factors of the tumor from different angles. Experiments will be performed in vitro in normoxic and hypoxic conditions and in vivo in a syngeneic mouse model. This project has the exciting potential to unravel a novel combination strategy for NSCLC patients that enables specific targeting of the tumor cells and realizes durable responses by stimulating the anti-tumor immune response. In addition, these study results might also pave the way for improved treatment options in other tumor types.

Researcher(s)

• Promoter: Pauwels Patrick
• Co-promoter: Jacobs Julie
• Co-promoter: Smits Evelien
• Fellow: Flieswasser Tal

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

In order to provide cancer patients with personalized treatment, molecular understanding of the tumor is indispensable. Therefore, tumor biopsies are needed. However, tissue biopsies might put the patient at risk and are encumbered by heterogeneity and suboptimal tissue acquisition. On the other hand, circulating tumor DNA (ctDNA) and RNA (ctRNA) in liquid biopsies are not only of interest during the initial work-up of a cancer patient, but also because of this approach allows monitoring of the disease during treatment, including the detection of acquired resistance, which can enable a fast switch to an alternative therapy. In this project we will evaluate the use of plasma, platelets and urine as liquid biopsy in the setting of real-time disease monitoring in a patient-friendly way. We will concentrate specifically on two tumor types with poor prognosis, i.e. non-small cell lung cancer (NSCLC) and pancreatic ductal adenocarcinoma (PDAC). Investigating urine as non-invasive sampling method and the value of liquid biopsies to monitor response to immunotherapy are two major innovative goals of this project. As the first objective, we will investigate the correlation between blood, urine and tumor tissue of NSCLC patients for the detection of targetable mutations. For the first time, real-time follow-up will be established by screening the ctDNA and ctRNA from blood and urine samples of not only EGFR mutated NSCLC patients, but also ALK- and ROS1 translocated patients during tyrosine kinase inhibitor (TKI) therapy for known and novel resistance mechanisms. Furthermore, the prognostic and predictive value of the quantification of mutated ctDNA and ctRNA in blood and urine will be examined. As the second objective, KRAS mutated NSCLC patients as a non-targetable mutation will be included in order to correlate the mutational status of blood, urine and tumor tissue. The innovative aspect is that both patients undergoing surgery with curative intent and patients undergoing chemotherapy will be included. Furthermore, a proof-of-concept study with blood and urine samples from PDAC patients before and during neoadjuvant therapy and pre- and post-surgery will be performed to assess the necessity and success of the therapy. The third objective is to develop liquid biopsy-based assays inn order to monitor the immune system and tumor load during immune therapy, which is now hampered by the concept of pseudoprogression and the lack of reliable biomarkers. At the moment there are no reliable data on the evolution of tumor necrosis during immune therapy. We will evaluate if monitoring immune makers and proliferation via liquid biopsy can predict which patients benefit of this costly therapy. To conclude, the results of this study will boost implementation of liquid biopsies (plasma and/or urine) in routine clinical care to facilitate personalized treatment of cancer patients.

Researcher(s)

• Promoter: Pauwels Patrick

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Cancer cells are embedded in stroma, the connective tissue framework of solid tumors. The mutual and interdependent interactions between the cancer cells and their microenvironment (TME) are increasingly recognized as effective targets for cancer therapy. The most abundant cells in the TME are the cancer-associated fibroblasts (CAFs). Although it has been shown that CAFs play an important role in the proliferative and invasive behavior of colorectal cancer (CRC), CAFs represent a heterogeneous population with both cancer-promoting and cancer-restraining actions, lacking specific markers to target them. Although absent from normal tissue, various tumor types have shown expression of CD70 on the malignant cells. It has been demonstrated that these CD70-positive tumor cells can suppress the immune system by inducing an accumulation of the immune suppressive regulatory T cells (Tregs). In this study, we will be the first to determine the role of CD70 in CRC, not merely focusing on the tumor cells but also taking the TME into account. Our preliminary data point towards the expression of CD70, not on the tumor cells itself but on the CAFs in CRC. Moreover, our results have shown that the presence of CD70 on the CAFs was associated with poor prognosis of the patient. In this project, we will further investigate the role of CD70-positive CAFs in CRC. Thereby, we will assess the migratory and invasive properties of CD70-positive CAFs and investigate its effect on the tumor cells. In addition, we will determine whether expression of CD70 on CAFs enhances immune suppression by the accumulation of Tregs. These experiments will lead to the completion of a PhD.

Researcher(s)

• Promoter: Pauwels Patrick
• Co-promoter: Smits Evelien
• Fellow: Jacobs Julie

Research team(s)

Project type(s)

• Research Project

Abstract

The introduction of targeted therapies is now at the forefront of personalised medicine in cancer treatment. After the initial promise of targeted therapies, drug resistance is however emerging as the major obstacle to progress in this field. In this project, we will focus on identification of new combination therapies to overcome intrinsic and acquired resistance to cetuximab, a monoclonal antibody targeting the epidermal growth factor receptor (EGFR). Hereby, we will concentrate specifically on head and neck squamous carcinoma (HNSCC), a highly relevant tumour type with poor prognosis that is intensively studied at the Center for Oncological Research (CORE) Antwerp. First, we will screen for new drug combinations by next-generation whole-exome sequencing and tumour kinome profiling of cetuximab-sensitive versus -resistant (intrinsic and acquired) HNSCC cell lines. Next, based on an integrative analysis of both the genetic profile and the kinome profile of cetuximab resistance, new combination treatments can be designed rationally to overcome cetuximab resistance. The molecular pathways underlying the cytotoxic effects of the selected compounds, in combination with chemotherapy and/or irradiation, will be investigated thoroughly, with focus on the hypoxic microenvironment as an important additional cause of therapy resistance. In conclusion, based on our screening results, new combination therapies will be designed rationally in order to thwart resistance to EGFR-targeting agents. Successful combinations will be forwarded into animal studies and ultimately into a clinical trail to demonstrate feasibility of the most promising combination therapy to treat HNSCC patients.

Researcher(s)

• Promoter: Lardon Filip
• Co-promoter: Pauwels Patrick
• Co-promoter: Peeters Marc
• Co-promoter: Wouters An

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Non-small cell lung cancer (NSCLC) retains its position as the most lethal type of cancer with around 1.3 million deaths per year worldwide and a marginally improving 5-year overall survival rate which remains below 20%, pointing to the need for new therapeutic options. Immunotherapy, in which the patient's immune system is used to selectively eliminate cancer cells, is considered a very promising candidate. Results of the recently approved immunotherapeutic agent nivolumab underscore the potential of immunotherapy in NSCLC, but also leave room for improvement. This study will focus on the CD70-CD27 signaling pathway as an interesting novel target to enhance anti-tumoral immune responses in NSCLC in combination with low doses of chemotherapy. CD70 is a member of the tumor necrosis factor family and its expression is normally restricted to activated T and B cells. Constitutive expression of CD70 by tumor cells can facilitate immune evasion by increasing the amount of suppressive regulatory T cells, inducing T cell apoptosis and skewing T cells towards T cell exhaustion. Previously, we have detected constitutive overexpression of CD70 in NSCLC tumor specimens, also in patients that lack other targeted treatment options. This CD70 expression can be exploited by CD70-targeting antibody-dependent cellular cytotoxicity (ADCC)-inducing antibodies. Our preliminary data show that the combination of anti-CD70 therapy with low doses of chemotherapy significantly increases cytotoxicity of the drug, compared to single treatment regimens. The main objective of the current project proposal is to rationally design and to preclinically evaluate a combination therapy of chemotherapy with CD70-targeted immunotherapy as a novel treatment option for patients with NSCLC.

Researcher(s)

• Promoter: Smits Evelien
• Co-promoter: Lardon Filip
• Co-promoter: Pauwels Patrick
• Co-promoter: Rolfo Christian
• Co-promoter: Van Schil Paul

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

This research project focuses on DFNA5 based upon strong indications for its role as tumour suppressor gene, its function in apoptosis and its potential role as early biomarker in cancer. DFNA5 was identified in 1998 in our lab, as a gene causing autosomal dominant non syndromic hearing loss [3]. Since then, a number of papers on DFNA5 have been published pointing towards a possible involvement in cancer [4-15].

Researcher(s)

• Promoter: Peeters Marc
• Co-promoter: Lardon Filip
• Co-promoter: Pauwels Patrick
• Co-promoter: Van Camp Guy
• Fellow: Croes Lieselot

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Lung cancer still remains one of the most deadliest cancers worldwide, with over 14 million new diagnoses and 8.2 million cancer-related deaths in 2012. Since only a minority of the patients respond to chemotherapy and targeted therapies, immunotherapy might be a valid alternative. The major goal of these therapies is to activate the tumor-deleting characteristics of the immune system. It is known however, that the immune system activity diminishes with age. Therefore, an important question remains whether elderly lung cancer patients would benefit from these immunotherapies. In this project, we will characterize which immune-related proteins and peptides are expressed within the lung tumor microenvironment of elderly patients, at places where immune cells and tumor cells co-reside. This will provide us insights to which factors are important for the maintenance of the immune-suppresive microenvironment. Further comparison of protein/peptide expression patterns of different elderly lung cancer patients might deliver a protein/peptide panel, able to predict which subgroup of patients might benefit from the immunotherapy, thereby optimizing therapy response, minimizing therapy-related toxicity and improving quality of life.

Researcher(s)

• Promoter: Baggerman Geert
• Co-promoter: Maes Evelyne
• Co-promoter: Pauwels Patrick

Research team(s)

Project type(s)

• Research Project

Abstract

With this project, we aim to monitor lung cancer patients in real time by detecting tumour DNA in serum. Two assays will be developed and validated for this purpose - A DNA integrity assay in which the quantification of apoptotic and necrotic DNA is performed using real-time PCR testing. - Mutation analysis using targeted next generation sequencing. Genetic aberrations in a panel of tumour suppressor and oncogenes will be quantified to determine the tumour load.

Researcher(s)

• Promoter: Pauwels Patrick

Research team(s)

Project type(s)

• Research Project

Abstract

The prognosis of malignant pleural mesothelioma (MPM) patients remains dismal with a median overall survival of only 9-12 months. The immune system plays a critica I role in protection against MPM with preliminary clinical evidence that immunotherapy can lead to MPM contro!. Here, we will be the first to investigate the immune checkpoint programmed-death 1 (PD-1) and its ligands as novel and potentially highly effective immunotherapeutic targets in MPM.

Researcher(s)

• Promoter: Smits Evelien
• Co-promoter: Pauwels Patrick
• Co-promoter: van Meerbeeck Jan

Research team(s)

Project type(s)

• Research Project

Abstract

This research project focuses on DFNA5 based upon strong indications for its role as tumour suppressor gene, its function in apoptosis and its potential role as early biomarker in cancer. DFNA5 was identified in 1998 in our lab, as a gene causing autosomal dominant non syndromic hearing loss [3]. Since then, a number of papers on DFNA5 have been published pointing towards a possible involvement in cancer [4-15].

Researcher(s)

• Promoter: Peeters Marc
• Co-promoter: Lardon Filip
• Co-promoter: Pauwels Patrick
• Co-promoter: Van Camp Guy
• Fellow: Croes Lieselot

Research team(s)

Project type(s)

• Research Project

Abstract

This project represents a formal research agreement between UA and on the other hand the Hercules Foundation. UA provides the Hercules Foundation research results mentioned in the title of the project under the conditions as stipulated in this contract.

Researcher(s)

• Promoter: Vanden Berghe Wim
• Co-promoter: Kooy Frank
• Co-promoter: Lardon Filip
• Co-promoter: Pauwels Patrick
• Co-promoter: Van Ostade Xaveer

Research team(s)

Project type(s)

• Research Project

Abstract

Neuroendocrine tumors (NET) form a heterogeneous group of malignancies. The phosphoinositide-3-kinase/Akt/mammalian target of rapamycin (PI3K-Akt-mTOR) signaling pathway has been demonstrated to play a major role in NET by regulating cell growth, proliferation, cell survival and protein synthesis ). Furthermore, alterations in genes regulating this pathway are reported in pancreatic NET (PNET). Furthermore, elevated mTOR expression and activity is associated with a higher proliferative capacity and worse prognosis. mTOR proves to be an interesting target for therapy of NET with mTOR-inhibiting rapamycin and analogs (rapalogs) such as everolimus. mTOR acts as the catalytic subunit of two functionally distinct complexes, named mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2). Although effectively blocking mTORC1, rapalogs only have a limited, dose-dependent action on the mTORC2. Recent phase III trials with everolimus show an improved progression-free survival in monotherapy in progressive advanced pancreatic NET and in combination with long-acting octreotide in advanced carcinoid tumors. However, adaptive resistance to mTOR inhibition with rapalogs is described. This adaptive resistance may be caused by induction of activating phosphorylation of Akt, upstream of mTOR in the PI3K-Akt-mTOR pathway. The effect of rapalogs on mTOR signaling may be circumvented through increased activity of mTORC2 and this may lead to resistance to rapalogs. The first aim (WP 1) of the project is to investigate the resistance mechanisms that play a key role in adaptation to everolimus treatment in PNET. To accomplish this, in vitro transcription and phosphorylation of the components of the PI3K-Akt-mTOR pathway will be studied in sensitive and secondary resistant PNET cell lines. For the transcription studies, gene expression microarrays will be performed on RNA extracted from the cell lines that are sensitive and the ones with induced (secondary) resistance. The role of Akt phosphorylation by reduced inhibition of S6K1-IRS-IGF axis and other possible unknown feedback loops will be evaluated with the western blotting. The second aim (WP 2) of the project is to determine whether DNA methylation of genes and promoter regions associated with the mTOR pathway play a role in adaptive resistance to everolimus. Therefore the DNA methylation status of sensitive and secondary resistant PNET cell lines will be studied using Illumina's Infinium methylation 450k beadchip microarrays. These methylation microarray data will be integrated with the transcription microarray data to identify functional methylation pattern changes. In patient material, important epigenetic changes, identified in the cell lines, will be quantified with pyrosequencing and will be correlated with gene expression, studied with real time PCR. Furthermore, this will be correlated to resistance to everolimus in a retrospective study with the goal of describing predictive biomarkers for response to therapy with everolimus. The third aim (WP 3) of the project is to evaluate if dual inhibition of mTOR and interesting therapeutic targets (such as IGF, PI3K, mTORC2, EGFR), which will be identified in the first parts of this research project, might overcome acquired resistance to everolimus. The role of the transcription and phosphorylation of the PI3K-Akt-mTOR pathway during dual inhibition will be studied in vitro in sensitive and secondary resistant PNET cell lines. An in vivo experiment using an orthotopic PNET cancer model, comparing dual inhibition to, respectively, placebo, mTOR inhibition alone and inhibition of the identified therapeutic targets alone will be conducted. Response will be evaluated using microPET/CT. Ex vivo studies using immunohistochemistry, real time PCR and western blotting will be used to the dual inhibition to activation of the PI3K-Akt-mTOR pathway.

Researcher(s)

• Promoter: Peeters Marc
• Co-promoter: Op de Beeck Ken
• Co-promoter: Pauwels Patrick

Research team(s)

Project type(s)

• Research Project

Abstract

This project represents a research agreement between the UA and on the onther hand IWT. UA provides IWT research results mentioned in the title of the project under the conditions as stipulated in this contract.

Researcher(s)

• Promoter: Pauwels Patrick
• Co-promoter: Germonpre Paul

Research team(s)

Project type(s)

• Research Project

Abstract

This project represents a research agreement between the UA and on the onther hand IWT. UA provides IWT research results mentioned in the title of the project under the conditions as stipulated in this contract.

Researcher(s)

• Promoter: Pauwels Patrick

Research team(s)

Project type(s)

• Research Project

Abstract

Pancreatic cancer is characterized by a poor prognosis and shows an almost inevitable mortality. It is shown that the tumor microenvironment, mainly the stroma around the tumor, which can constitute up to 80% of the tumor mass, would facilitate the rapid progress of pancreatic cancer. The precise role of this stroma as well as his contribution to tumor progression and therapeutic resistance is still poorly understood in pancreatic cancer and other solid tumors. This in vitro study aims at elucidating the presence and functional impact of critical components of the stroma, which can affect the behavior of pancreatic tumor cells.

Researcher(s)

• Promoter: Peeters Marc
• Co-promoter: Deschoolmeester Vanessa
• Co-promoter: Lardon Filip
• Co-promoter: Pauwels Patrick
• Fellow: Quix Céline

Research team(s)

Project type(s)

• Research Project

Abstract

The detection of minimal disease in blood of patients with cancer is hampered by a lack of sensitivity and accuracy of the currently available tests. The availability of the real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and the possibility to measure the expression of multiple genes simultaneously has initiated some change in this area. In previous research we showed a superior sensitivity of qRT-PCR for CK-19/MAM compared to immunocytochemistry for the detection of disseminated tumor cells (DTCs) in bone marrow and to the FDA approved CellSearch System (Veridex, Raritan, NJ) for the detection of circulating tumor cells (CTCs) in peripheral blood. Through the molecular characterization of CTCs in patients with metastatic breast cancer, this project aims to identify a set of markers that can be used to further enhance the sensitivity of the currently available qRT-PCR test. In addition, characterization of CTCs can improve our insight in the pathogenesis of cancer metastasis. By comparison of the gene expression profiles of blood samples enriched for CTCs and the residual CTC-depleted blood samples, a CTC-specific genome-wide gene expression profile will be generated. Crossvalidation of these discriminatory genes will be done on the primary tumor. Using discriminant analysis with the expression profile of healthy volunteers, an optimization of the amount of markers and their expression level will be determined to achieve a zero misclassification of healthy volunteers (sensitivity 100%) and an as correct as possible classification of patients with breast cancer.

Researcher(s)

• Promoter: Peeters Marc
• Co-promoter: Pauwels Patrick
• Fellow: Peeters Dieter

Research team(s)

Project type(s)

• Research Project

Abstract

This project represents a research agreement between the UA and on the onther hand IWT. UA provides IWT research results mentioned in the title of the project under the conditions as stipulated in this contract.

Researcher(s)

• Promoter: Pauwels Patrick
• Fellow: Deben Christophe

Research team(s)

Project type(s)

• Research Project

Abstract

This proposed multidisciplinary research consortium, consisting of 6 different laboratories from the University of Antwerp, aims to understand the cellular and/or functional interactions of NSC implants in healthy and injured neural tissue (cuprizone-mediated demyelinisation mouse model). With this research project, which focuses on the in vivo molecular and physiological control of NSC, we aim to contribute to the in vivo study and modulation of NSC migration, survival, differentiation and functional integration.

Researcher(s)

• Promoter: Berneman Zwi
• Co-promoter: Giugliano Michele
• Co-promoter: Jorens Philippe
• Co-promoter: Pauwels Patrick
• Co-promoter: Ponsaerts Peter
• Co-promoter: Van Der Linden Annemie
• Co-promoter: Ysebaert Dirk

Research team(s)

Project type(s)

• Research Project

Abstract

We first aim to identify and functionally describe immune-suppressive proteins and/or signalling molecules on glioma cells, which lead to inhibition of microglia. Then, we will develop strategies to modify microglia in order to prevent inhibition by glioma cells in vitro and in vivo. We specifically aim to genetically engineer microglia with 'short interfering RNAs' against receptors or signalling molecules involved in immune inhibition by GL261 cells in order to improve their cellular therapeutic potency.

Researcher(s)

• Promoter: Berneman Zwi
• Co-promoter: Pauwels Patrick
• Co-promoter: Ponsaerts Peter
• Co-promoter: Ysebaert Dirk

Research team(s)

Project type(s)

• Research Project

Abstract

In this project, we aim to further elucidate the mechanisms leading to immune-mediated rejection of allografts in the CNS. For this, we will non-invasively (by in vivo bioluminescence imaging) identify the exact timing and degree of microglia immune-reactivity in relation to immune-mediated rejection of different allogeneic adult-, embryo- and placenta-derived cell populations.

Researcher(s)

• Promoter: Berneman Zwi
• Co-promoter: Pauwels Patrick
• Co-promoter: Ponsaerts Peter
• Co-promoter: Van Der Linden Annemie
• Co-promoter: Ysebaert Dirk

Research team(s)

Project type(s)

• Research Project

Abstract

The detection of minimal disease in blood of patients with cancer is hampered by a lack of sensitivity and accuracy of the currently available tests. The availability of the real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and the possibility to measure the expression of multiple genes simultaneously has initiated some change in this area. In previous research we showed a superior sensitivity of qRT-PCR for CK-19/MAM compared to immunocytochemistry for the detection of disseminated tumor cells (DTCs) in bone marrow and to the FDA approved CellSearch System (Veridex, Raritan, NJ) for the detection of circulating tumor cells (CTCs) in peripheral blood. Through the molecular characterization of CTCs in patients with metastatic breast cancer, this project aims to identify a set of markers that can be used to further enhance the sensitivity of the currently available qRT-PCR test. In addition, characterization of CTCs can improve our insight in the pathogenesis of cancer metastasis. By comparison of the gene expression profiles of blood samples enriched for CTCs and the residual CTC-depleted blood samples, a CTC-specific genome-wide gene expression profile will be generated. Crossvalidation of these discriminatory genes will be done on the primary tumor. Using discriminant analysis with the expression profile of healthy volunteers, an optimization of the amount of markers and their expression level will be determined to achieve a zero misclassification of healthy volunteers (sensitivity 100%) and an as correct as possible classification of patients with breast cancer.

Researcher(s)

• Promoter: Pauwels Patrick
• Co-promoter: Peeters Marc
• Fellow: Peeters Dieter

Research team(s)

Project type(s)

• Research Project

Abstract

Researcher(s)

• Promoter: Pauwels Patrick
• Promoter: Van Marck Eric
• Co-promoter: Lardon Filip
• Co-promoter: Peeters Marc

Research team(s)

Project type(s)

• Research Project