Title Promoter Affiliations Abstract "Coevolution of epithelium and immune response in colorectal cancer: comprehensive longitudinal analysis and manipulation of crosstalk leading to exhausted responses in dedicated mouse models." "Sabine Tejpar" "Digestive Oncology" "Overall MSS colorectal cancer (CRC) is considered a cold tumor, nonresponsiveto immunotherapy, in contrast to MSI CRC. We observe all MSSare dysfunctional at the level of T cell responses, but with heterogeneousmechanisms with some having cytotoxic CD8 T cells stuck in stroma,whereas in others T cells are in tolerogenic/pro-tumorigenic states as Tregand Th17, or some are entirely cold. Our extensively mapped outdifferences in immunogenicity/immune evasive interactions in CRC arelikely caused by co-evolution of epithelial transformations with theirmicroenvironment. To understand CRC's evolutionary consequences forimmunogenicity, we will use a set of unique mouse models matching patientheterogeneity to longitudinally follow tumor establishment,immunogenicity and manipulate immune evasive interactionsobserved in human CRC. These results will provide first insight in howimmune-ignored tumors are established, possible therapeutic manipulationsand a toolkit to phenotype and manipulate immunogenicity in a large varietyof models for therapies." "CRYPTIC TRANSCRIPTS: THE MASKED HEROES WHO BREAK TUMOR IMMUNE TOLERANCE AND FREE THE RESPONSE TO IMMUNE THERAPY." "Diether Lambrechts" "Laboratory of Translational Genetics (VIB-KU Leuven), Laboratory of Tumor Inflammation and Angiogenesis (VIB-KU Leuven)" "In the last years, immunotherapy revolutionized cancer treatment in terms of quality of life and life years saved. Immune-checkpoint blockage (ICB) therapy, like anti-programmed death-1 (anti-PD-1) therapy, blocks the inhibitory interaction between immune-checkpoint ligands on the tumor and their receptors on T-cells (or vice versa). Despite the ground-breaking clinical success, ICB therapy responses are variable and unpredictable, while resistance, relapse and side-effects often occur. As societal, financial and emotional burdens are increasing, the need for a conclusive and clinically-applicable predictive biomarker becomes more and more clear. Tumor-intrinsic characteristics like tumor immunogenicity play a key role, while the influence of the tumor micro-environment (TME) cannot be ignored. Therefore, I aim to evaluate both tumor-intrinsic traits, like tumor immunogenicity, and changes in the TME to unravel the mechanism underlying immunotherapy response in (hypoxic) tumors and to combat resistance. Previously, we already showed that DNA methylation repels binding of the hypoxia-inducible factors (HIFs), the main transcription factors executing the hypoxic response. Interestingly, we observed that, upon pharmacological demethylation, many new HIF binding sites were enriched at repetitive elements like cryptic transcripts (CTs), which extend well beyond the known retrotransposons. Interestingly, these retrotransposons have been associated with tumor immunogenicity, immune activation and ICB response. As such, hypoxia-induced CTs have the potential to break tumor immunotolerance (the tolerance of the immune system towards the tumor) and improve ICB responses specifically in hypoxic tumors. In this PhD thesis, I thus studied whether and how these CTs increase tumor immunogenicity, activate the immune system and ameliorate the response to ICB therapy. I focused specifically on hypoxic tumors at first, but also verified our results as a general principle. The fine-grained resolution of single-cell technologies moreover allowed me to distinguish CT expression in cancer versus stromal cells while complementary evaluating the role of the TME, specifically dendritic cells, in this ICB response." "The microbiome in colorectal metastases: nature and impact on local immune and inflammatory response, disease evolution and response to therapy" "Jeroen Raes" "Laboratory of Molecular Bacteriology (Rega Institute)" "Despite evidence associating colorectal cancer (CRC) and microbiome, its role in metastatic CRC remainsunexplored. In this project, we aim to characterize bacterial colonization of CRC metastases matched withprimary tumors, surrounding normal tissues and evaluate its relationship with tumor characteristics, includingmolecular subtype, pattern of histological growth, local immune response and alteration in T-cell antigenpresentation, as well as its impact on disease outcome. A large series of frozen tumor samples from severalsources will be analyzed by a combination of direct identification of bacterial species by 16S rRNA profiling,RNA-seq, in situ hybridization with broad-spectrum and strain-specific probes to identify, quantify and locatebacteria, and multiplexed immunofluorescence coupled to computerized image analysis to characterize theimmune and inflammatory infiltrate. This project will provide much-needed insights in the role of the microbiomeand immune microenvironment in metastatic tumor development and maintenance, as well as disease outcomeand therapy response." "Strengthening Animal Production and Health through the Immune Response" "Hans Nauwynck" "Department of Translational Physiology, Infectiology and Public Health, University of Liverpool, INRA Transfert (France), Xeolas Pharmaceuticals (Ireland), STICHTING WAGENINGEN RESEARCH, SPOREGEN LIMITED, National Veterinary Institute, French National Institute for Agricultural Research, VACCIBODY AS, Swedish University of Agricultural Sciences, The Pirbright Institute, Wageningen University & Research, Parco Tecnologico Padano, University of Bern, University of Lausanne, Virbac (France), European Forum of Farm Animal Breeders, Cardiff University, Warsaw University of Life Sciences, Chinese Academy of Agricultural Sciences, Royal Veterinary College, Shanghai Veterinary Research Institute, University of Edinburgh, Federal Department of Home Affairs, Ingenasa (Spain)" "SAPHIR aims to develop vaccine strategies effective against endemic pathogens responsible for high economic losses in livestock in order to strengthen the profitability of food animal systems, improve animal welfare and reduce xenobiotic usage in farming with a One Health perspective. SAPHIR will bring novel vaccine strategies to the market i) at short term, with several promising vaccines brought to demonstration (RTL6), ii) at long term, with cutting edge strategies brought at proof of concept (RTL3) and iii) in line with socio-economic requirements. SAPHIR has selected two representative pathogens of pigs (Porcine Reproductive and Respiratory Syndrome Virus and Mycoplasma hyopneumoniae), chickens (Eimeria and Clostridium perfringens) and cattle (Bovine Respiratory Syncytial Virus, Mycoplasma bovis) to develop generic vaccine approaches applicable to other pathogens. SAPHIR will issue i) knowledge of immune mechanisms of protection, ii) affordable, safe and multivalent vaccines with DIVA properties, iii) efficient adjuvants targeting dendritic cells, optimal formulations, new mucosal and skin delivery systems, a new generation of DNA vectors and viral replicon platforms for fostering an earlier and longer duration of immunity including the perinatal period, and iv) basal biomarkers of individual immuno-competence for future breeding strategies. The SAPHIR dissemination and training programme includes creation of an integrated health management website, launch of a Global Alliance for Veterinary Vaccines and organization of workshops directed at food animal system stakeholders. This will ensure optimal research translation of SAPHIR outputs to market and field applications.SAPHIR brings together interdisciplinary expertise from fourteen academic institutes including a Chinese partner, five SMEs and two pharmaceutical companies." "Pandemic preparedness: developing a multiplexed mass spectrometry assay to screen for pathogens and the induced immune response." "Dieter Deforce" "Department of Pharmaceutics, Sciensano (Belgium)" "The SARS-CoV-2 pandemic has abruptly illustrated the lack of pandemic preparedness. Therefore, health organisations as the WHO have recommended the development of a robust molecular screening platform for early detection and monitoring of the spread of pathogens through the population. This implies supplementing current diagnostic tests like nucleic acid amplification tests (NAATs) with tests targeting other biomolecules, like proteins. Therefore, infectious proteomics holds great promise as orthogonal test procedure. Our previous effort on SARS-CoV-2 already demonstrated that MS-based methods could be used as an alternative for diagnostic testing. Here, I propose to extend the assay by incorporating biomarker peptides for other pathogens, monitoring innate immunity and for serology testing. For the discovery phase, I will use a state of the art data independent acquisition (DIA) method i.e. Scanning SWATH. Next, I will introduce the use of peptide immuno-enrichment technology (SISCAPA). This uncouples the assay from the matrix while increasing the sensitivity into the attomole range and combined with automated sample preparation and peak detection, would enable throughputs up to 500 samples per day per MS instrument. Large-scale validation will be done on patient samples originating from the Severe Acute Respiratory Infections (SARI) surveillance network in collaboration with Sciensano." "TArget: Immune response in acquired thrombotic thrombocytopenic purport." "Karen Vanhoorelbeke" "Chemistry, Kulak Kortrijk Campus" "Research about the immune response in acquired thrombotic thrombocytopenic purport.(TARGET)." "Unraveling the role of invariant Natural Killer T-cells in the immune response to Streptococcus pneumoniae." "Isabelle Meyts" "Inborn Errors of Immunity, Mechanical Engineering Technology, Geel Campus, Adaptive Immunology" "Streptococcus pneumoniae is a leading cause of life threatening infections like meningitis, pneumonia and septicaemia and the main pathogen involved in otitis and bronchitis. Pneumococcal capsular polysaccharides are the most important virulence factor of S. pneumoniae. Anti-polysaccharide antibodies have shown to be crucial for opsonisation and effective phagocytosis of S. pneumoniae, thereby providing protection against early phase disease. Patients with polysaccharide antibody deficiency (PsAD) suffer from recurrent upper and lower respiratory tract infections due to a deficient antibody response to capsular polysaccharides. This defect can present isolated (Specific Antibody Deficiency or SAD) or in the context of a broader immunodeficiency. Correct diagnosis is crucial to initiate appropriate treatment like immunoglobulin replacement therapy or prophylactic antibiotics, preventing irreversible organ damage (hearing loss, bronchiectasis). PsAD is diagnosed by measuring anti-polysaccharide IgG prior to and after Pneumococcal Polysaccharide Vaccine (PPV), but this method faces many challenges. The gold standard is a laborious and expensive WHO standardized ELISA. Guidelines to define a normal response remain controversial. Furthermore, standard vaccination of children with protein-conjugated pneumococcal polysaccharides (PCV) induces a T dependent antibody response, and is likely to influence the magnitude and nature of the antibody response to PPV. Finally, reports on hyporesponsiveness to subsequent vaccinations with polysaccharide vaccines raise concerns on the potential harmful effect of immunizing immunocompromised patients with PPV.Our first aim was to facilitate and improve diagnosis of PsAD. In Chapter 1, we demonstrated the need for alternatives methods to detect PsAD by showing that previous vaccination with PCV influences the response to PCV-PPV shared serotypes but also to non-PCV serotypes. Allohemagglutinins (AHA), antibodies to A and B polysaccharides on erythrocytes, are mentioned in many immunology reviews and textbooks as an alternative method to detect PsAD. Only a few dated studies described normal values of AHA and research on the diagnostic value of AHA to detect SAD was lacking. We conducted a retrospective study in 180 patients, and found low sensitivity and specificity of AHA to detect PsAD and no correlation of low AHA with low PPV response (Chapter 2). More importantly, low AHA did not associate with clinical signs of PsAD like recurrent lower respiratory tract infections and bronchiectasis. In Chapter 3, we aimed to investigate Typhim Vi vaccine as an alternative for PPV to diagnose PsAD. Typhim Vi vaccine contains Vi capsular polysaccharides from Salmonella typhi, a new or ‘neo-antigen’ for most European individuals, facilitating interpretation of the response. Hundred healthy volunteers were vaccinated with Typhim Vi and Pneumovax vaccine. We established normal values for post-vaccination IgG and fold increase of antibody titres pre- to post-vaccination after Typhim Vi vaccination. We confirmed that AAAAI criteria for PsAD cannot be applied to bead-based assay results for PPV response. Instead we propose serotype-specific 5th percentile cut-off values for post-vaccination IgG and fold increase post PPV measured by bead-based assay. Finally, we also assessed AHA in these 100 healthy subject and demonstrated a large spread of AHA, with fifth percentile cut-offs much lower than the currently used thresholds, again questioning the clinical value of low AHA. A follow-up study in 100 patients with suspected humoral immunodeficiency is currently recruiting participants to validate our findings in a patient population.Despite the importance of antibodies to capsular polysaccharides in the protection against pneumococcal disease, the mechanisms inducing a class switched IgG response to polysaccharides are still poorly understood. A number of ‘second signals’ required for an IgG response to polysaccharides have been identified and Primary Immunodeficiencies (PIDs) affecting one of the ‘second signal’ pathways are associated with PsAD (e.g. MyD88 and IRAK4 deficiency causing abnormal TLR signalling). However, in most patients with isolated PsAD (thus SAD) and in many patients with PID, a cause has not yet been found. The second aim of this thesis, was to investigate the role of invariant Natural Killer T (iNKT) cells in the pneumococcal polysaccharide antibody response in humans. iNKT cells are a specialized subset of T cells that use their restricted set of T cell receptors to recognize self and foreign lipids presented by CD1d on B cells and antigen presenting cells. Whilst the involvement of iNKT cells in the innate and adaptive response to S. pneumoniae in mice has clearly been demonstrated, the evidence in humans is scarce. We described the association of absent iNKT cells and pneumococcal infections in two siblings from consanguineous parents. Pneumococcal polysaccharide response was completely abolished. Based on the clinical presentation, a very rare calcium release activated calcium channelopathy due to STIM1 mutation was suspected and confirmed by genetic and functional testing (Chapter 4). This report was the first to describe prolonged survival in STIM1 deficiency, and auto-inflammatory manifestations other than auto-immune cytopenia namely severe colitis and psoriasis. In the last chapter (Chapter 5), we describe an unusual presentation of autosomal dominant hyper IgE syndrome with normal IgE, normal polysaccharide antibody response and normal iNKT cell numbers. Low iNKT cells in patients with PsAD and increased susceptibility of patients with low iNKT to S. pneumoniae infections hint towards a role of iNKT cells in the generation of polysaccharide antibody response. However, further studies are needed to elucidate the exact role of iNKT cells in T independent responses and to reveal the pathways involved. Multiple second signals are required for a fully functional polysaccharide response. The future identification of underlying genetic defects in patients with PsAD by next generation sequencing will hopefully shed a light on redundant and non-redundant signals for the polysaccharide antibody response. " "Exploitation of lipid metabolism in improving cancer immune checkpoint therapy response" "Johan Swinnen" "Laboratory of Lipid Metabolism and Cancer" "Immune-checkpoint inhibitor therapy (ICI), aimed at enhancing CD8+ T-cell activity against solid tumours, is revolutionising cancer management, providing unprecedented and sustained responses in several cancer types, including melanoma, clear cell renal cell carcinoma and lung cancer. Unfortunately, only a subset of patients benefits from ICI, emphasizing the need for strategies that sensitise tumours to ICI. Here, by analogy with other immune-related diseases and based on strong preliminary data, we propose that poly-unsaturated fatty acids (PUFA) and particularly their oxygenated metabolites, play a crucial role in immune responses and can be exploited to attract and activate CD8+ T-cell and to improve immune responses. Using cutting-edge technologies, including mass spectrometry imaging (MSI) of ICI-responsive versus non-responsive clinical tumors, we aim 1) to identify lipid profiles and PUFA metabolites that are associated with different ICI responses in cancer, 2) to validate the role of the identified lipid metabolites and related enzymes in immune cell infiltration and fate, and 3) to design strategies to exploit lipid metabolism in enhancing immune-cancer cell killing." "Assessment of differences in the anti-tumor immune response between lung cancer patients with and without COPD." "Diether Lambrechts" "Laboratory of Translational Genetics (VIB-KU Leuven), Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE)" "Chronic obstructive pulmonary disease (COPD) has been consistently linked to lung cancer development. However, the precise mechanisms underlying this link are still incompletely understood. Preliminary observations obtained by genome-wide methylation profiling and wholetranscriptome sequencing of lung tumors suggest a weaker anti-tumor immune response in COPD versus non-COPD patients. This project therefore aims to establish differences in the immune response to lung tumors between patients with and without COPD. Specifically, we intend to confirm that COPD tumors are less infiltrated by immune cells as a sign of the impaired anti-tumor immune response in these patients. We will validate this finding by comparing the response of innate and adaptive immune cells to tumor cells in primary co-culture experiments and by assessing the specificity of tumor-infiltrating T-cells between COPD and non-COPD patients. In an attempt to redirect the anti-tumor immune response in COPD patients, we will seek for COPD-specific tumor antigens and evaluate whether these may be used to generate tumor-reactive T-cells. By also assessing the prognostic value of COPD and of a COPD-specific immune gene signature, we anticipate that this project will provide clinically relevant insights into the link between COPD and lung cancer. Additionally, our findings may stimulate efforts into developing specific immunotherapies targeted to lung cancer patients with COPD." "The role of B-lymphocytes, T-lymphocytes and antigen-presenting cells in the human immune response to pneumococcal polysaccharides." "Xavier Bossuyt" "Clinical and Diagnostic Immunology, Inborn Errors of Immunity" "Streptococcus pneumoniae is an important pathogenic bacterium. It is the most important cause of pneumonia and an important cause of morbidity and mortality worldwide. The pneumococcal polysaccharides (caps-PS) are an important determinant of virulence and anti-caps-PS antibodies confer protection against infection. Our knowledge on the regulation of the immune response to S. Pneumoniae in general and to caps-PS in particular is limited. Current research proposal is a continuation of previous work and aims at the elucidation of the molecular and immunological mechanisms that govern the regulation of the human immune response to S. pneumoniae. The following points will be explicitly addresssed: · To unravel the role of distinct B lymphocyte subsets (naive versus IgM memory versus switched memory B lymphocytes) in the immune response to S. pneumoniae. · To unravel the mechanisms by which T lymphoycytes and antigen presenting cells affect the immune response to caps-PS [role of MHC-II, CD1, TLR]. The proposed project should enhance our understanding of the immunological mechanisms that govern the immune response to S. pneumonia."