Research Ilke De Boeck

Abstract

Cystic fibrosis (CF) is the most common hereditary life-threatening condition in Belgium and is included since 2019 in the newborn screening program in Flanders to promote early diagnosis and treatment and consequently outcome. Antibiotics and the more recent modulator therapies are crucial in the treatment of persons with CF, but they both have limitations. For instance, even with modulator therapy, structural lung damage persist, pathogens remain present in high numbers, and exacerbations still occur. Complementary and/or alternative treatments for persons with CF remain thus of high interest, especially preventive therapies that can be used in early stages. The use of beneficial bacteria from the airway microbiome is an appealing option as such early-stage prevention, since several studies highlight the importance of the entire microbial communities. Especially the beneficial members are known to be important for airway health and in preventing potential pathogens from causing excessive inflammation. In order to study these complex bacterial interactions in the CF host, more sophisticated models that better represent the in vivo conditions are needed. In this project, I aim to develop a CF interaction model to study these complex interactions by making use of a CF bronchoalveolar epithelial cell line and immune cell line. The interaction of both beneficial microbiome members and CF pathogens will be studied within the model, in terms of epithelial barrier stability, inflammatory cytokine and mucin expression, and cytotoxicity. This model can aid the development of microbiome therapies for the airways.

Researcher(s)

• Promoter: De Boeck Ilke

Research team(s)

• Environmental Ecology & Applied Microbiology (ENdEMIC)

Project type(s)

• Research Project

Abstract

Introduction: Most children are diagnosed with cystic fibrosis (CF) at a young age, nowadays often through neonatal screening. CF is associated with frequent respiratory tract infections. These exacerbations are often viral induced at a young age. Frequent airway infections lead to early colonization of the airways with pathogenic bacteria. Moreover, infection leads to inflammation and dysregulation of the mucus production via mucin upregulation. The result is disease progression with destruction of the normal airway structure and lung tissue. Objectives: To gain insights into the mechanisms by which viral infections leading to respiratory exacerbations induce a more pathogenic airway microbiome in young children with CF, from birth to preschool age, through airway inflammation and mucin regulation. This will help formulate informed treatment strategies both at the level of pathogenic as well as potentially beneficial microbiota members in the CF airways. Methods: Young children with CF from birth to the age of 5 years will be included at CF clinic in UZA. Oropharyngeal swabs will be collected at set time points in a longitudinal way to study the dynamics of the airway microbiome and inflammatory markers and mucins. At the moment of exacerbations extra swabs will be collected to investigate the interactions of viruses and bacteria and their influence on increased inflammation and mucin production. These data will be linked to clinical outcome measures such as lung clearance index and questionnaires on quality of life. The final part of the project exists of an in vitro study investigating the effects of specific CF respiratory microbiota members as such or in combination with viruses on TLR induction, transcriptional factor activation, cytokine and interferon signalling stimulation, and ultimately on the virus-associated infection and cytopathic effects.

Researcher(s)

• Promoter: Van Hoorenbeeck Kim
• Co-promoter: De Boeck Ilke
• Co-promoter: Spacova Irina

Research team(s)

• Laboratory Experimental Medicine and Pediatrics (LEMP)

Project type(s)

• Research Project

Abstract

The upper respiratory tract (URT) is a key habitat of the human microbiome, but it is currently underexplored compared to other body sites, especially at the functional level. URT diseases such as chronic rhinosinusitis (CRS) form leading causes for antibiotic prescription, while the functional role of bacteria in the disease pathology is still not clear. As such, CRS is a microbial disease needing new insights in functional biology and microbial ecology to design novel therapeutic strategies. Based on microbiome sequencing of the URT, the underexplored lactic acid bacterium Dolosigranulum pigrum is associated with URT health, highlighting its potential as URT probiotic. Nevertheless, fundamental and molecular research is lacking on its beneficial mechanisms of action, and on its ecological and adaptation mechanisms in the human nasal cavity. This project will therefore focus on exploring the biology and metabolic properties of D. pigrum strains isolated from healthy URT samples, using comparative genomics, phenotypic screening assays and fluorescent microscopy techniques. In addition, the barrier-enhancing and anti-inflammatory properties of D. pigrum isolates will be evaluated in complex in vitro cell culture systems. In parallel, molecular biology tools will be used for further molecular characterization of the isolated strains' mechanisms of action. Finally, the most promising D. pigrum strains will be evaluated in murine models relevant for CRS.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Vanderveken Olivier
• Fellow: De Boeck Ilke

Research team(s)

• Environmental Ecology & Applied Microbiology (ENdEMIC)

Project type(s)

• Research Project

Abstract

Chronic rhinosinusitis (CRS) is a common upper respiratory tract (URT) disease with a major socioeconomical impact linked to URT microbiota perturbations. Current treatment options often fail so the need for alternative treatment options based on better insights into the URT microbiota is high. This is reflected by the widespread interest in this topic, not only by the scientific and medical world, but also by the patients themselves. During my PhD project and in the final of "De Vlaamse PhD Cup 2020", I have been very committed to actively engage CRS patients in my research and got to know the needs of many patients. Their willingness to test alternative microbiota-based treatment options convinced me of the urgency for generating insights leading to such novel treatments. In this project, I propose to implement novel state-of-the-art techniques that will enable in depth insights into the URT microbiota and its relation with the human host. In order to do this, I propose the optimization of shotgun metagenomic sequencing for low biomass URT samples to allow better taxonomic resolution and functional characterization of the microbial communities. In addition, I will use fluorescent in situ hybridization in combination with immunohistochemistry to gain insights into the human host-bacteria behavior, as well as bacterial interspecies interactions. These insights can contribute to overcome some of the limitations in the URT microbiome field. One important research gap is for instance that it remains very difficult to determine what defines a balanced microbiota and we still do not know whether a microbial imbalance is a cause or a consequence in CRS and associated inflammation. This is mainly because most 16S amplicon sequencing techniques remain descriptive. They don't allow functional characterization and identification up to microbial species or strain level, while pathogenicity and probiotic potential are expressed at strain level. Hence, in this project, the goal is to obtain new insights in the possible driving force of the microbiome in CRS. The implementation of these techniques can help to develop better treatment strategies based on beneficial microbiota members and can help to determine which patients might benefit the most from such therapy. In addition, the shotgun sequencing and microscopy pipelines developed in this project are an important stepping stone for my upcoming FWO junior postdoc proposal, and can also be implemented in the Centre of Excellence Microbial Systems Technology of the University of Antwerp.

Researcher(s)

• Promoter: De Boeck Ilke

Research team(s)

• Environmental Ecology & Applied Microbiology (ENdEMIC)

Project type(s)

• Research Project

Abstract

Upper respiratory tract (URT) infections have a major impact on public and animal health with a high incidence in Flanders. Moreover, these infections predispose to lower respiratory tract and lung infections, which have a higher impact on health worldwide than all other infectious diseases combined. The study of the microbiome and the investigation of new possible bacterio- and probiotic therapies can deliver additional first in line solutions, which will eventually lead to lower antibiotics usage.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Vanderveken Olivier
• Fellow: De Boeck Ilke

Research team(s)

• Environmental Ecology & Applied Microbiology (ENdEMIC)

Project type(s)

• Research Project