Research projects

Within Organovir, 15 research projects will be carried out by motivated and talented PhD students. Find information about each research project below.

ESR 1: Coronavirus with HAE model (Poland)

Host institution: Jagiellonian University, Poland

 

 

Project description

 

This project focuses on novel 3D complex model system to study infection with respiratory viruses. During this project, you will be focussing on the following research objectives:

 

  • To create a model for human airway epithelium allowing to study the interplay between the virus and our immune system.
  • To test what happens during coronaviral infection in such a model.
  • To understand what happens on a single cell level.

 

 

With this project, we aim to achieve the following results:

 

  • Develop complex HAE tissue, combining different cell types to reflect the interaction between the pathogen and the immune system.
  • On tissue level: map coronaviral infection, cell-to-cell spread, potential of immune cells as carriers, pathogenesis.
  • On single cell level: analyse the microenvironment of the cell, innate immunity, virus-cell interaction, virus specificity.

 

 

This project includes two secondments, which are as follows:

 

  • A two-month secondment with Danmarks Tekniske Universitet (location: Lyngby, Denmark) focused on novel biomaterials / solutions for advanced 3D cultures.
  • A three-month secondment with the Universiteit van Amsterdam (location: Amsterdam, the Netherlands) focused on bringing gut organoids to JU and bringing complex HAE cultures to UvA.

 

 

The research will be carried out in a young and dynamic team lead by Krzysztof Pyrc (Virogenetics Laboratory of Virology).

ESR 2: Hydrogels, HAE gut (Denmark)

Host institution: Department of Healthcare technology, Technical University of Denmark, Denmark

 

 

Project description

 

This project focuses on make scalable hydrogel system for high throughput screening and increased cell functionalities. During this project, you will be focussing on the following research objectives:

 

  • To build stackable co-culture systems with flexible hydrogels
  • To scale the stackable system into 96-well plate format
  • To place organoids behind epithelial layer and/or endothelial layer to simulate coupled organ system

 

 

With this project, we aim to achieve the following results:

 

  • A scalable system for studying infections via e.g. the gut and ability of viruses to pass into the blood stream
  • A 3D printed 96-well plate format of stackable hydrogels for HTS applications
  • Propagation of relevant viruses in co-culture system

 

 

This project includes two secondments, which are as follows:

 

  • A three-month secondment Academisch Medisch Centrum bij de Universiteit van Amsterdam (location: Amsterdam, the Netherlands) focused on transfer of stackable hydrogel technology
  • A three-month secondment with the University of Jagiellonski (location: Krakow, Poland) focused on learning about cocultures of fibroblasts and immune cells.

 

 

Martin Dufva, Department of Healthcare Engineering, Technical University of Denmark, will guide the research project.

ESR 3: Enterovirus, blood brain barrier (France)

Host institution: University Clermont Auvergne (France) – Research Unit LMGE CNRS 6023 – EPIE team “Epidemiology and pathogeny of enterovirus infections”

 

 

Project description

 

The EPIE team works in close relationships with the department of medical virology and the National Reference Center (NRC) of enteroviruses and parechoviruses at the University hospital of Clermont-Ferrand. The activities of the NRC comprise the epidemiological and clinical surveillance of enterovirus infections.

 

 

The objectives of this project are:

 

  • Develop a 3D physiologically relevant model of the BBB that mirrors cell organization of the brain
  • Investigate the benefit of including mini-brains in the development
  • Standardisation of mini-brain infection with EVs
  • Investigate the mechanism (axonal transport or passage through BBB) of brain infection with EVs

 

 

During this project, we aim to achieve the following results:

 

  • Development of a novel 3D model of the human BBB with co-culture of neurons, astrocytes, and endothelial cells
  • Elucidation of molecular and cellular mechanism that underlie pathogenic processes of different neurotropic EVs

 

 

This project also includes a four-month secondment at the Technical University of Denmark (location: Lyngby Campus, Martin Dufva’s Lab). The secondment will focus on learning how to use advanced compartmentalized microfluidic platforms.

 

 

Jean-Luc Bailly (LMGE CNRS 6023, EPIE team) will guide the research project.

ESR 4: Skin model, enterovirus (France)

Host institution: University of Clermont Auvergne (France) – Research Unit EPIE “Epidemiology and pathogeny of enterovirus infections” (LMGE CNRS 6023)

 

 

Project description

 

This project aimed at developing a skin-like model to study the pathogenesis of hand, foot and mouth disease (HFMD) which can be caused by several types of enteroviruses. Hand, foot and mouth disease is a very common childhood disease characterised by vesicular eruption of the soles and the palms and by oral ulcerations. It is usually a benign illness, but some children can develop more severe symptoms (body-wide skin rashes, large skin blisters …). A national sentinel surveillance network composed of primary care pediatricians is currently in place in France.

 

 

During this project, you will be focusing on the following research objectives:

 

  • Develop a culture model system for human keratinocytes (human epidermis like culture)
  • Grow the epidermis-like culture on a basal layer including dermal fibroblast and dermal microvascular endothelial cells)
  • Compare different EV types for their ability to infect the cell types in the skin-like tissue.

 

 

With this project, we aim to achieve the following results:

 

  • Establishment of a skin-like model to study pathogenesis of HFMD
  • Elucidation of host immune effectors or viral genetic factors involved in the dermotropism of enteroviruses

 

 

This project also includes two secondments, which are as follows:

 

  • A three-month secondment at the National Institute for Public Health and the Environment (location: Amsterdam, the Netherlands) focused on clinical network formation for HFMD outbreaks.
  • A three-month secondment at the Technical University of Denmark (location: Lyngby, Denmark) focused on linking epidermis to connective tissue harbouring dermal fibroblasts and microvascular endothelial cells.

 

 

Dr. Audrey Mirand (LMGE CNRS 6023, EPIE team and Department of Medical Virology) will guide the research project.

ESR 5: Medium, HAE (United Kingdom)

Host institution: STEMCELL Technologies UK Ltd. Cambridge, UK

 

 

Project description

 

This project focuses on lung organoid culture and its application to respiratory virus study. During this project, you will be focusing on the following research objectives:

 

  • Develop medium for human distal lung organoid culture
  • Functional validation of the distal lung organoids (e.g., characterization of effects of virus infection on these lung organoids
  • Upscaling the production of lung organoid medium

 

 

This project includes one six-month secondment with Department of Medical Microbiology, Amsterdam University Medical Centers (Amsterdam UMC) focusing on virus study.

 

 

Juan Hou (Pulmonary research specialist at STEMCELL Technologies Vancouver) and Wing Chang (Pluripotent Stem cell specialist at STEMCELL Technologies UK) will guide the research project.

ESR 6: Influenza A virus, mucosa (Netherlands)

Host institution: Virology Division, Department of Infectious Diseases & Immunology, Utrecht University, the Netherlands

 

 

Project description

 

This project is aimed at better understanding the interaction of respiratory viruses with their glycan receptors and how they navigate through the heavily sialylated mucus barrier overlaying the epithelial cells of the respiratory tract, focussing on influenza A viruses and enterovirus-D68 (EV-D68).

 

 

Influenza A viruses infect birds and mammals such as swine and humans. They have sialic acid receptor-binding hemagglutinin (HA) and receptor-cleavage neuraminidase (NA) proteins. The functional balance between these proteins is thought to be important for host tropism and pathogenesis. This balance is poorly characterized and molecular details are largely lacking. In this project, we will focus on the HA-NA balance of human and swine influenza A viruses and the importance thereof for host tropism, with particular focus on the interaction of these viruses with the heavily sialylated mucus barrier overlaying the epithelial cells of the respiratory tract. The HA-NA balance of human and swine viruses will be studied for different functional and decoy receptors including mucus by using innovative biolayer interferometry assays (Guo et al., PLoS Pathog. 2018. 14(8):e1007233).

 

 

EV-D68 is an emerging respiratory virus that is also associated with paralysis. It also relies on sialic acid to infect cells, but this non-enveloped virus lacks a receptor-destroying enzyme. Whether mucus enhances or inhibits infection of epithelial cells is unknown. The role of sialic acid receptors as well as protein receptors for infection will be studied as well as the identity of the cell types that are infected with different EV-D68 strains.

 

 

For this project, we will establish airway epithelial cell cultures, of human and swine origin, which will be used for infection studies and for harvesting of mucus. Mucus samples will also be characterized in detail for their protein and glycan content and for their ability to inhibit virus infection.

 

 

This project also includes two secondments, which are as follows:

 

  • A two-month secondment with Epithelix Sarl (location: Genève, Switzerland) to learn more about setting up human airway epithelial cell cultures and collection of mucus.
  • A two-month secondment with the University of Genève (location: Genève, Switzerland) focused on the handling of these cultures for infection studies.

 

 

Dr. C.A.M. (Xander) de Haan and Prof. F.J.M. (Frank) van Kuppeveld (both from the Virology Division of the Utrecht University) will guide the research project.

ESR 7: Coronavirus & cross-species infectivity (Poland)

Host institution: Jagiellonian University, Poland

 

 

Project description

 

This project focuses on the potential of coronaviruses to cross tissue and species borders using 3D ex vivo cultures. During this project, you will be focussing on the following research objectives:

 

  • To create a model for coronaviral infection of the human gut, human and animal HAE cultures.
  • To test infection of different tissues with human and animal coronaviruses.
  • To understand determinants of the infection: receptor usage, cellular proteases, internalization pathways, other factors restricting viral replication.

 

 

With this project, we aim to achieve the following results:

 

  • Develop human and animal 3D gut and airway models to complement the existing ones.
  • On tissue level: identify factors limiting cross-tissue and cross-species transfer.
  • On single cell level: to understand what the virus needs to start the infection and to produce viable progeny.

 

 

This project also includes three secondments, which are as follows:

 

  • A three-month secondment with the Universiteit van Amsterdam (location: Amsterdam, the Netherlands) focused on bringing gut organoids to JU.
  • A six-month secondment with Universiteit Utrecht (location: Utrecht, the Netherlands) focused on viral infections of different tissues / species.
  • A one-month secondment with Stemcell Technologies UK LTD (location: Cambridge, United Kingdom) focused on commercial aspects of the research.

 

 

The research will be carried out in a young and dynamic team lead by Krzysztof Pyrc (Virogenetics Laboratory of Virology), who will guide the research project.

ESR 8: Respiratory microbiota & respiratory viruses (Switzerland)

Host institution: Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland

 

 

Project description

 

This project focuses on viral and bacterial interactions in the respiratory tract, more specifically, on how commensal bacteria present in the airways impact on the virulence of respiratory viruses.

 

 

During this project, you will be focussing on the following research objectives:

 

  • Assess the effect of commensal bacteria on the replication of respiratory viruses both in vitro and ex vivo in respiratory tissues.
  • Investigate the mechanism of action underlying the dynamics between commensal bacteria and viral pathogens.

 

 

With this project, we aim to better understand the nature and the mechanism of viral-bacterial interactions in the respiratory tract. This knowledge will help to improve patient management and drug/vaccine design.

 

 

The project includes two secondments in the Epithelix Company in order to learn how to reconstitute respiratory epithelia from patient biopsies and in order to set up co-cultures of airway tissues and macrophages or dendritic cells.

 

 

The research project will be guided by Prof. Caroline Tapparel Vu and Dr. Chiara Medaglia.

ESR 9: PEV3 HAE, co-culture (Netherlands)

Host institution: Department of Medical Microbiology, Amsterdam University Medical Centers (Amsterdam UMC), the Netherlands

 

 

Project description

 

This project focuses on researching the determinants of susceptibility regarding the PEV3 infection. During this project, you will be focussing on the following research objectives:

 

  • Identify the role of viral genotype and donor age in determining susceptibility of human gut to infection with PEV3
  • Identify which cells are infected by PEV3 in human gut & respiratory tissue
  • Establish the known role of PEV3 receptors in infecting human gut & respiratory tissues

 

 

With this project, we aim to achieve the following results:

 

  • Establishment of the HAE PEV3 infection
  • Establishment of human infection models to study pathogenesis of PEV3
  • Identification of viral factors (mutations) and host factors (age, tissue, receptor expression) that affect susceptibility of host cells to infection with PEV3

 

 

This project also includes two secondments, which are as follows:

 

  • A two-month secondment with Charles River (location: Leiden, the Netherlands) focused on bringing gut organoids from the Amsterdam UMC to Charles River.
  • A three-month secondment with the University of Jagielloński (location: Krakow, Poland) focused on learning about advanced cell staining and receptor identification.

 

 

Katja Wolthers (Department of Medical Microbiology) and Dasja Pajkrt(Paediatric Infectious Disease Specialist) will guide the research project.

ESR 10: Uncultivable EV/HPeV infections (Netherlands)

Host institution: Department of Medical Microbiology, Amsterdam University Medical Centers (Amsterdam UMC), the Netherlands

 

 

Project description

 

This project focuses on researching the propagation of uncultivable EV/HPeV infection in human 3D models. During this project, you will be focussing on the following research objectives:

 

  • To culture EV-C types 104, 105, 109 and 116-118 positive samples on 3D models
  • To culture HPeV8-16 positive samples on 3D models
  • To study virus replication kinetics, viral entry, and effects on gut, lung/HAE or brain organoids

 

 

With this project, we aim to achieve the following results:

 

  • The successful propagation of one or more EV/HPeV for further characterization of viral replication, tropism and virus-host interaction.

 

 

This project also includes two secondments, which are as follows:

 

  • A seven-month secondment with The National Institute for Public Health and the Environment (RIVM) focused on bringing HAE to the RIVM and to collect samples for cultivation (location: Bilthoven, the Netherlands)
  • A three-month secondment with the University of Clermont Auvergne focused on learning about the mini-brain model (location: Clermont-Ferrand, France)

 

 

Katja Wolthers (Department of Medical Microbiology) and Dasja Pajkrt(Paediatric Infectious Disease Specialist) will guide the research project.

ESR 11: HAE, respiratory viruses, antiviral testing (Belgium)

Host institution: Department of Microbiology and Immunology, Rega Institute, KULeuven, Leuven, Belgium (www.antivirals.be)

 

 

Project description

 

This project focuses on exploring the use of HAE cultures to study the treatment of viral respiratory infections. HAE cultures will be used to evaluate novel antiviral strategies to combat Respiratory Syncytial Virus (RSV) infection and explore the kinetics of replication of different RSV virus strains. This will result in an optimized culture system to be used to characterize viral strains in a relevant ex vivo system and link viral factors with pathogenesis. Using HAE derived from healthy volunteers and COPD patients (provided by P12(ES), the role of RSV in exacerbations of COPD will be studied. Novel antiviral strategies will be evaluated in the RSV/HAE infection model. This will generate important information on the therapeutic potential of the different antiviral strategies, the risk of resistance development and the use of combination strategies. These results will be compared with results from existing animal studies with the aim to reduce the use of these animal models in the future. The role of inflammation in RSV pathology and the effect of antiviral strategies to recover the inflammation will be explored in collaboration with B3(JU). A co-culture of HAE with immune cells obtained from healthy donors will be implemented and infected with several RSV strains. The cytokine profile of the co-cultures will be determined.

 

 

During this project, you will be focussing on the following research objectives:

 

  • Optimize HAE culture system to study Respiratory Syncytial Virus (RSV) infections.
  • Proof-of-principle that the RSV/HAE can be used to characterize the potency of novel antiviral strategies including the characterization of resistance associated mutations.
  • Proof-of-principle that the co-culture of immune cells and HAE can be used to characterize the potency of novel antiviral strategies against RSV. This would mainly focus on the role of alveolar macrophages in pathology and replication of RSV.
  • Demonstrate that the HAE system can bring important contributions to the drug discovery/development pipeline for respiratory pathogens.

 

 

This project also includes two secondments, which are as follows:

 

  • A two-month secondment with Epithelix (location: Geneva, Switzerland) focused on learning how to work with HAE cell cultures.
  • A three-month secondment with the University of Jagiellonski (location: Krakow, Poland) focused on learning about co-culture of HAE and immune cells.

 

 

Prof. Johan Neyts and Dr. Dirk Jochmans will guide the research project.

ESR 12: Gut, noro- and rotavirus, antiviral testing (Belgium)

Host institution: Department of Microbiology and Immunology, Rega Institute, KULeuven, Leuven, Belgium

 

 

Project description

 

The ESR will investigate viral replication assays in gut organoids towards their use in exploring novel antiviral strategies to combat noro- and rotavirus infections. The major limitation to develop novel small molecule inhibitors for human noro- (HuNoV) and rotaviruses (HRV) is the lack of a robust in vitro or in vivo culture model. Gut organoids will be implemented to study infection and replication of multiple HuNoV and HRV strains. The effect of (i) previously described antivirals with in vitro and/ or in vivo activity; (ii) novel inhibitors identified in a high throughput screening campaign (surrogate virus) of 150 000 molecules; (iii) other biologicals will be studied using this virus/gut organoid system. This will provide a unique opportunity to understand the interactions between these enteric pathogens and the gut epithelia and get further insight into details of their replication, such as viral entry and pathogenesis. Moreover, it will constitute a unique platform to assess the efficacy of inhibitors currently under development against previously uncultivable strains.

 

 

During this project, you will be focussing on the following research objectives:

 

  • Operational gut organoids for HuNoV- and RV replication and proof-of-principle that these virus- gut organoid infection models can be used to evaluate antiviral strategies including the characterization of resistance associated mutations.
  • Optimize miniaturized organoid cultures that can be used successful for medium-throughput drug screening of gastro-intestinal (GI) viruses.
  • Demonstrate that the gut organoid system can bring important contributions to the drug discovery/development pipeline for GI viruses.

 

 

This project also includes three secondments, which are as follows:

 

  • A two-week secondment with Hubrecht Institute (location: Utrecht, The Netherlands) focused on learning the basics of gut organoid cultures.
  • A three-month secondment with Charles River (location: Leiden, The Netherlands) to learn how to set up organoids in high throughput.
  • A one-month secondment with STEMCELL Technologies (location: Cambridge, UK) to learn about commercialization processes.

 

 

Prof. Johan Neyts and Dr. Joana Rocha-Pereira will guide the research project.

ESR 13: Standardizing organoid cultures, high through put (Netherlands)

Host institution: Charles River, Leiden, The Netherlands

 

 

Project description

 

During this project, you will be focussing on the following research objectives:

 

  • Develop a high throughput system with a human 3D cell infectious disease in vitro model, including relevant readouts
  • Screen a small molecule compound library to identify novel chemical hit matter
  • Apply compound capture mass spectroscopy to identify the molecular targets of hit molecules

 

 

With this project, we aim to achieve the following results:

 

  • A validated 3D phenotypic assay for evaluating effects of antiviral drugs and/or RNAi/CRISPR-mediated genome modulations on host factors influencing viral infections
  • A hit list and associated compound structures of up to ~1% of the total number of compounds tested
  • Identification of putative novel targets for antiviral therapy

 

 

This project also includes three secondments, which are as follows:

 

  • A two-week secondment at the Hubrecht Institute (location: Utrecht, The Netherlands) to learn basic gut organoid culturing skills.
  • A three-month secondment with Amsterdam UMC (location: Amsterdam, the Netherlands) focused on learning application of organoid technology for viral infection research.
  • A three-month secondment with KU Leuven (location: Leuven, Belgium) to introduce HTS screening for antiviral drug testing.

 

 

Jeroen de Groot (Senior Director Biology) and Marijn Vlaming (Director Biology) will guide the research project.

ESR 14: Ethics & organoids (Belgium)

Host institution: Centre for biomedical ethics and law, Faculty of Medicine, University of Leuven (Belgium)

 

 

Project desciption

 

This project focuses on the ethical and social challenges of organoids, with due attention to implications for policy.

 

 

During this project, you will be focussing 1) on the ethical status of organoids (in which way are organoids related to the human donor? Can we use all kinds of stem cells for making organoids?), and 2) on the implications of the use of organoids regarding the replacement and reduction of animals in experimental medical research.  This will be done by investigating the existing literature and setting up empirical tools to explore the attitudes and opinions of different stakeholders (such as donors, researchers, biobank managers, policy makers, experts involved in the use of animals for research, etc.) on the development of adaptive structures.  A cooperative analysis on ethical policies will be conducted in different European countries.

 

 

With this project, we aim to achieve the following results:

 

  • Establishment of the state of the art of the ethical aspects of the use of organoids.
  • Establishment of the views of key stakeholders on the use of organoids.
  • Development of an ethical framework for the use of organoids in medical research.

 

 

This project also includes two secondments, which are as follows:

 

  • A five-months secondment with the National (Dutch) Institute for Public Health and the Environment (location: the Netherlands) focused on the policy implications of the use of organoids
  • A two-month secondment with the Dutch Society for the Replacement of Animal Testing (location: the Netherlands) to develop tools to communicate with various stakeholders and the general public.

 

 

Kris Dierickx, professor of biomedical ethics at KU Leuven, will guide the research project.

ESR 15: Entrepreneurship & organoids (Netherlands)

Host institution: Amsterdam Business School (ABS), University of Amsterdam, the Netherlands

 

 

Project description

 

The main aim of this project is to study early investment in biotech entrepreneurial ventures, focusing on the signals of quality the entrepreneur and the venture can send and especially on the effects of how the entrepreneur or venture are categorized, in terms of industry, technology, goal of the product etc. – or categorize themselves.

 

 

The research will combine insights from management science, especially entrepreneurship and innovation, with those from categorisation theory, both in management science and in sociology, and apply a broad range of quantitative techniques, from network analysis to machine learning (esp. to analyse texts and images).

 

 

This project also includes a secondment, which is a ten-month visit at Charles River (location: Leiden, the Netherlands) focused on gathering empirical data on the decision making in new investments in organoid technology by commercial partners.

 

 

Prof.dr. Nachoem Wijnberg and Dr. Balazs Szatmari will guide the research project.