Pilot Projects

PFAS, also known as ‘forever chemicals’, are a group of over 4,700 man-made substances that have been used since the 1940s in products such as firefighting foams, non-stick cookware, stain- and water-resistant fabrics, cosmetics, and cleaning agents, thanks to their stability and surfactant properties. However, their strong carbon-fluorine (C-F) bonds make them highly persistent, breaking down very slowly and accumulating in the environment, animals, and humans.

PFAS contamination is now widespread, with over 70,000 known impacted sites in the US and Europe. More than 99% of people in these regions have measurable levels of PFAS in their blood. Exposure to PFAS has been linked to a range of adverse health effects, including an increased risk of cancer, reduced fertility and weakened immunity. The estimated annual healthcare costs of PFAS exposure in Europe range from 50 to 80 billion euros. While some PFAS compounds are now regulated, legislation varies internationally and there are currently no effective methods to remove PFAS from the environment or the human body. This poses a significant challenge to planetary and human health.

This HALRIC pilot project, a collaboration between Cambiotics and the University of Oslo (UiO), will utilise UiO’s advanced capabilities in bacterial strain isolation, sequencing, and bioinformatics to identify and characterise strains capable of sequestering PFAS. The aim is for Cambiotics to develop precision probiotics for pollutant detoxification by isolating anaerobic bacterial strains from faecal samples using UiO’s high-throughput technologies.

For further information about this HALRIC pilot project, please contact:

 

Eric Jaques de Muinck
University of Oslo
e.j.de.muinck@ibv.uio.no

Understanding how nuclei withstand mechanical stress is essential, because both cancer invasion and viral infection exploit these forces in ways that shape disease progression.

Cells are exposed to dynamic biomechanical forces that are transduced through a host of mechanosensitive proteins. The nucleus integrates these forces into behavioral outputs that determine cell function, fitness, and fate. This relies on intrinsic force-responsive elements at the nuclear envelope (NE) (elasticity) and chromatin (viscosity) level that control the ability of nuclei to withstand and adapt to forces. Forces place tremendous strain on integrity of cell nuclei during invasion.

To cope, cancer cells adapt nuclear properties through a process called mechano-adaptation, enabling migration through dense micro-environments. At the same time, these adaptations predispose cancer cells to nuclear fragility and NE ruptures, major catalysts of cancer evolution. During herpesvirus infection, viral capsids eject pressurized DNA into nuclei, accompanied by chromatin stiffening and NE softening. This mechano-adaptation is critical to prevent NE rupture under stress imposed by viral DNA.

As such, cancer invasion and herpesvirus infection both challenge NE integrity and exploit nuclear mechano-adaptation to mitigate damage. In this project, the team combines genetics, live microscopy, and bio-atomic force microscopy (AFM) to quantify and manipulate nuclear mechano-adaptation in cancer and infection models. Correlative AFM–fluorescence and force mapping will reveal how mechanoadaptation protects NE integrity.

By comparing models, this HALRIC pilot project aim to uncover shared mechanoprotective principles and identify common targets for intervention.

For further information about this HALRIC pilot project, please contact:

 

Coen Campsteijn
University of Oslo
coen.campsteijn@medisin.uio.no

 

Alex Evilevitch
Lund University
alex.evilevitch@med.lu.se

Cholera toxin (CT) and heat-labile enterotoxin (LT) are two similar AB5 toxins that are responsible for the diarrhea caused by Vibrio cholerae and enterotoxigenic Escherichia coli (ETEC) infections, respectively. These toxins are secreted into the lumen of the small intestine, but attack targets within the host cytosol. Upon endocytosis, CT and LT travel to the endoplasmic reticulum (ER), where their catalytic component – the A1 subunit – dissociates from the rest of the toxin. Once free, the A1 subunit naturally unfolds and is retrotranslocated to the cytosol by hijacking components of the ER associated degradation pathway (ERAD). Both steps, toxin disassembly and transport to the cytosol, involve interactions with host chaperones and are crucial for intoxication.

This HALRIC project aims to investigate how these human chaperones bind to foreign substrates such as cholera toxin by using cross-linking mass spectrometry (XL-MS). The target proteins will be produced at the University of Oslo (UiO), and the protein-protein complexes will be cross-linked and analysed by mass-spectrometry at the Swedish National Infrastructure for Biological Mass Spectrometry (BioMS) and the Science for Life Laboratory (SciLifeLab) Structural Proteomics unit at Lund University (LU).

This work will provide valuable insights into toxin-chaperone interactions and could lead to the development of new drugs that prevent cholera toxin activation inside the host.

For further information about this HALRIC pilot project, please contact:

 

Ute Krengel
University of Oslo
ute.krengel@kjemi.uio.no

Immunotherapy is revolutionizing cancer treatment by offering unprecedented long-term survival. However, its effectiveness is limited by tumour heterogeneity, drug resistance, immune evasion and the tumour microenvironment’s immunosuppressive nature. Immune reprogramming strategies targeting oncogenic transcriptional networks and enhancing immune surveillance are a promising way of overcoming these challenges.

Our laboratory has demonstrated that the transcription factors PU.1, IRF8 and BATF3 (PIB) have the ability to reprogram both human and murine fibroblasts, as well as tumour cells, into cDC1-like antigen-presenting cells. This process elicits potent anti-tumour responses and renders tumours susceptible to immune checkpoint blockade in vivo. However, the efficiency of reprogramming varies across tumour types, and the structural and mechanistic basis by which PIB cooperatively engages with chromatin to drive cDC1 identity remains unknown.

This project aims to define the nucleosome-binding logic, transcriptional cooperativity, and structural mechanisms underlying PIB-mediated chromatin remodeling. Using high-resolution cryo-electron microscopy, genome-wide chromatin accessibility and transcriptional profiling, and biochemical assays, we will investigate how PIB interacts with nucleosomes to activate immunogenic programmes. These insights will inform the rational design of synthetic transcription factors to improve immune reprogramming and establish a new platform for next-generation cancer immunotherapies.

For further information about this HALRIC pilot project, please contact:

 

Sandhya Malla
Lund University
sandhya.malla@med.lu.se

Filipe Pereira
Lund University
filipe.pereira@med.lu.se

This pilot project brings together DTU-led innovation in the form of pioneering real-time electrochemical sensors for bioprocess monitoring and microdrop Technologies expertise in high-precision inkjet dispensing. The collaboration aims to demonstrate how inkjet-based fabrication workflows can be integrated into next-generation sensor chip production for measuring small molecules (e.g. glucose) in fermentation and cultivation systems.

The project team will develop and validate a modular, automated fabrication process combining DTU’s advanced micro/nano sensor expertise with microdrop’s high-throughput dispensing capabilities. Specifically, they will demonstrate the feasibility of using inkjet printing to functionalise and protect 3D-structured electrochemical sensors with nanomaterials in a reproducible and scalable way.

By integrating microdrop’s dispensing systems into real sensor fabrication use cases, the project will provide proof of concept highlighting:

1. 1. the microdrops system’s suitability for complex sensor workflows,
   2. the integration potential with high-sensitivity and antifouling sensor designs, and
   3. the practical performance of printed sensors in bioprocess conditions.

For further information about this HALRIC pilot project, please contact:

 

Pedram Ramin
DTU Chemical Engineering
pear@kt.dtu.dk

 

Marc-Manuel Hahn
microdrop Technologies
marc-manuel.hahn@microdrop.de

Serendo Therapeutics is pioneering precision therapies for autoimmune diseases by targeting endophilin A2 (EA2), a novel intracellular modulator of T- and B-cell activation. Current treatments often rely on broad immunosuppression, which can lead to an increased risk of infection and inadequate disease control. EA2 therefore represents a breakthrough opportunity for more targeted, effective and safer interventions.

This pilot project aims to identify and validate small-molecule EA2 inhibitors through high-throughput screening (HTS), in collaboration with the DK-OPENSCREEN platform at DTU. We will transfer and adapt a functional assay to HTS format and perform a pilot screening of small molecule inhibitors. This feasibility study will establish EA2’s druggability and generate a foundation for long-term collaborative research and development. Our vision is to unlock a new class of precision immunotherapies with the potential to transform the care of autoimmune patients with significant unmet medical needs.

For further information about this HALRIC pilot project, please contact:

 

Ulrika Norin
Serendo Therapeutics
ulrika.norin@serendotx.com

G-protein-coupled receptors (GPCRs) are important drug targets, accounting for 30% of approved therapeutic targets. However, the factors that influence their activation are not well understood. For example, cholesterol has been shown to affect the signalling of some chemokine receptors (a family of GPCRs responsible for cell motility), though the exact nature of this interaction remains unclear.

Nuclear magnetic resonance (NMR) is a technology that allows us to quantify the different activation states that GPCRs adopt and the transitions between them, as well as identify atomic interactions through space. As such, it is the ideal method with which to address this issue. Nevertheless, the features of GPCRs and NMR mean that we must utilise non-traditional methods to achieve this. ¹⁹F NMR has the sensitivity to enable us to investigate the direct and indirect effects of cholesterol on chemokine receptors.

This project marks the first cross-border collaboration between our groups, in which we will develop and utilise new and existing ¹⁹F NMR methods to reveal the role of cholesterol in regulating chemokine receptors at an atomic level. This project will further our understanding of this important family of GPCRs and open up new methodologies that can be applied to other GPCRs.

For further information about this HALRIC pilot project, please contact:

 

Martin Gustavsson
University of Copenhagen
martin@sund.ku.dk

The aim of this project is to develop and pilot an integrated data infrastructure that will streamline the handling, submission and retrieval of small angle scattering (SAS) data across borders. This will be achieved by leveraging leading research infrastructures and community standards. By improving user interfaces, automating data deposition and retrieval, and enhancing support for advanced data types (including X-ray and neutron data), we will reduce the barriers faced by academic and industrial users alike.

The project will deliver practical tools, tutorials and workflows, such as automated pipelines for uploading SASView data to the SASBDB database, as well as integration with emerging databases. In doing so, it will foster cross-border collaboration and knowledge exchange. These results will promote more efficient, reproducible and FAIR data practices in life science research and industry, thereby contributing to the broader objectives of HALRIC and the ÖKS-Hamburg region.

For further information about this HALRIC pilot project, please contact:

 

Wojciech Potrzebowski
Lund University
wojciech.potrzebowski@med.lu.se

Chronic obstructive pulmonary disease (COPD) is a major global health burden, characterised by the progressive destruction of lung tissue, and considerable heterogeneity in clinical presentation and treatment response. While exercise training is a key part of COPD management and can improve symptoms, responses can vary significantly, and the underlying cellular and molecular mechanisms are not well understood.

This pilot project seeks to identify and characterise regenerative pathways in the lung that are activated by exercise. We will map cellular and extracellular matrix (ECM) phenotypes across COPD stages, focusing on exercise-induced alterations and their correlation with serum protein levels. To this end, we will employ advanced spatial and multimodal omics technologies, including high-plex spatial proteomics, mass spectrometry of lung tissue and serum, and nanoscale X-ray fluorescence imaging at the MAX IV Laboratory in Lund. The data will be correlated with lung function metrics, including AiDA, a novel method for assessing the degree of emphysema. These integrated approaches will provide into spatially organised cell–ECM interactions and exercise-induced regenerative signatures with the goal of enabling personalised, mechanism based therapies.

Through a collaborative effort initially uniting Lund University, Skåne University Hospital, Rigshospitalet, and the University of Copenhagen, our aim is to establish a Nordic Centre of Excellence for Lung Regeneration and Precision Medicine in COPD.

For further information about this HALRIC pilot project, please contact:

 

Linda Elowsson
Lund University
linda.elowsson@med.lu.se

Microvascular invasion (MVI), which is defined as the presence of cancerous cells in the small blood vessels that surround a tumour, is considered to be a key factor in determining personalised treatment approaches for hepatocellular carcinoma (HCC). Currently, histopathology is the gold standard for diagnosing MVI. However, the two-dimensional (2D) projections obtained using this method limit the ability to detect MVI in deeper layers of tissue. As MVI is present in around half of HCC cases and is strongly associated with a poor prognosis, there is clearly a need to improve the accuracy of MVI detection.

This study therefore proposes standardising the detection of MVI in HCC using high-resolution 3D X-ray microcomputed tomography (μCT) in HCC samples, as μCT can produce 3D images based on 2D projection reconstructions. This could potentially enable MVI to be detected at different levels within tumour samples, increasing the likelihood of an accurate MVI diagnosis. Images will be generated at the DanMAX beamline at MAX IV and compared with images obtained using the Exiscope Polaris at the Technical University of Denmark. Additionally, tumour samples will be analysed to identify genes associated with MVI, with the aim of proposing a novel, non-invasive method for its detection.

For further information about this HALRIC pilot project, please contact:

 

Hans-Christian Pommergaard
Rigshospitalet
hans-christian.pommergaard@regionh.dk

Allergies mediated by immunoglobulin E (IgE) encompass a wide range of conditions, including allergic asthma, food allergies, urticaria, and hypersensitivity to insect venom. Symptoms occur when allergens bind to IgE that is already bound to its high-affinity receptor (FceRI) on mast cells and basophils. Cross-linking and clustering of the IgE-FceRI complexes induced by allergens leads to cell activation and the release of inflammatory mediators that drive allergic reactions.

The severity of the allergic response can range from mild discomfort to life-threatening anaphylaxis. We have identified several binders that can modulate the IgE-mediated immune response via different mechanisms, such as preventing the formation of the IgE-FceRI complex, targeting the FceRI receptor or binding and sequestering the antigen to prevent cross-linking and clustering of the IgE-FceRI complexes. These binders exhibit diverse functional properties. Understanding their specific interactions with antigens, IgE, FceRI and the IgE-FceRI complex is fundamental to improving their efficacy and selectivity.

Such insights are essential for guiding the rational design of next-generation therapeutics for treating severe IgE-mediated allergies and preventing their life-threatening symptoms. However, obtaining high-resolution structural data remains time-consuming and is a bottleneck in therapeutic development. An efficient structural biology pipeline would accelerate therapeutic optimisation.

One of the biggest challenges in cancer surgery is defining tumour margins accurately to ensure the tumour is completely removed with an adequate margin of healthy tissue. This challenge is even greater in oral cancer due to variation in the pattern of tumour invasion between patients. Determining both the tumour margin and the pattern of invasion is strongly associated with prognosis and recurrence risk.

Currently, conventional histology only provides a two-dimensional representation of the tumour, which makes it difficult to assess invasion patterns. This project explores using micro-computed tomography (micro-CT) and synchrotron X-ray phase contrast imaging to generate 3D images of tongue tumour margins.

Previous pilot work has shown that micro-CT can distinguish tumour tissue from normal tissue, though improved soft tissue contrast is still needed. The research team will use micro-CT at DTU and synchrotron X-ray phase contrast imaging at MAX IV on paraffin-embedded tongue tumour specimens to provide 3D images of tumour margins and invasion patterns. The imaging results will be correlated with histological data.

This study is the first to compare micro-CT and synchrotron imaging for three-dimensional visualisation of oral cancer tissue, improving our understanding of tumour margins and invasion patterns. These insights could lay the foundation for further research aimed at improving tumour assessment, optimising prognosis and reducing treatment complications.

For further information about this HALRIC pilot project, please contact:

 

Tobias Todsen
Copenhagen University Hospital – Rigshospitalet
tobias.todsen@regionh.dk

Chronic kidney disease (CKD) is a global health challenge, expected to affect 10% of the population. It is characterised by progressive and irreversible loss of kidney function, increased complications and a high healthcare burden. The major causes are diabetes, hypertension, autoimmune diseases and genetic disorders.

Despite its prevalence, current diagnostic methods rely on kidney function tests, invasive biopsies and two-dimensional histology, which offer limited insight into the complex three-dimensional architecture of kidney tissue.

In this pilot project, we will assess the feasibility of using synchrotron radiation microcomputed tomography (micro-CT) to image human kidney tissue in 3D. This method is non-destructive and offers high resolution. It enables the visualisation of glomeruli, tubules and intrarenal vessels without the need for slicing or staining. We will use archived, formalin-fixed and paraffin-embedded kidney samples from the existing ENBIBA cohort to evaluate the quality and reproducibility of the imaging, as well as its correlation with conventional CT, histology and kidney function (eGFR).

If successful, this pilot study will establish a new technological platform for detecting disease-specific structural changes in CKD and supporting earlier diagnosis, the discovery of novel biomarkers, and more targeted treatment strategies based on the type and extent of CKD damage.

Figure 1. FFPE kidney biopsies were used for both H&E histology and 3D SR-µCT phase-contrast imaging. X-ray µCT (3 µm resolution) was applied for quality control, ensuring sample integrity prior to synchrotron imaging. The same region was then visualized non-destructively in 3D, complementing classical histology. The emphasized area reveals detailed microstructures of the tissue at 550 nm resolution. FFPE: Formalin-Fixed Paraffin-Embedded; H&E: Hematoxylin and Eosin; SR-µCT: Synchrotron Radiation Micro-Computed Tomography.

For further information about this HALRIC pilot project, please contact:

 

Mads Hornum
Rigshospitalet
Department of Nephrology and Endocrinology
mads.hornum@regionh.dk

The photosynthesis apparatus of green plants efficiently converts solar light into chemical energy. Considerable effort has gone into replicating the photosynthesis process in nature-inspired photosystem structures in order to solve problems such as low power conversion efficiency.

Despite great interest in this area, such issues have not yet been fully resolved. The early stages of photosynthesis involve the thylakoid membrane (TM) of chloroplasts, which contains pigment-protein complexes. The light-harvesting complex of photosystem II (LHC II) is the most abundant of these complexes. A better understanding of the coupling between energy transfer processes and the local structure and dynamics of TMs and LHC II is needed to achieve more efficient power conversion in bio-inspired devices (biophotovoltaics).

This pilot project aims to shed light on the microscopic structure and dynamics of LHC II and model TMs, particularly under in situ/operando conditions. The first phase of the project will investigate the protein system alone, while the second phase will study more complex systems, namely LHC II embedded in model TMs. The project will exploit a combination of neutron scattering methods, as well as complementary techniques such as Raman spectroscopy and calorimetry. This will be achieved through collaboration primarily between the European Spallation Source (ESS) and the University of Copenhagen (UCPH).

In response to the growing global demand for sustainable and diverse food sources, the shift from animal to plant based proteins has gained significant momentum.

Among these, pea proteins stand out for their favorable nutritional profile, functional versatility, and reduced environmental impact. The major storage proteins in pea—legumin and vicilin—constitute around 50% of the total protein content in isolates, with albumins contributing 8–20%. These proteins not only serve as key food ingredients but also as model systems for other legume proteins relevant to the green transition and bioeconomy.

This HALRIC pilot project investigates how co-extracted lipid contaminants, derived from the seed, affect the structure and functionality of pea protein fractions under varying pH and temperature conditions. While often regarded as “minor” contaminants, these lipids may significantly impact protein properties, with notable consequences during formulation, processing, and digestion.

Using pea protein as a model, we will employ a cross-border, multiscale approach combining SAXS, nanoDSC, and SR CD on purified fractions. Experiments will be carried out at Malmö (MAU) and Aarhus Universities (AU), with advanced characterization at MAX IV (CoSAXS) and ASTRID2.

Our goal is to derive general principles of plant protein–lipid interactions to aid the design of healthier, more functional, and sustainable plant-based foods, with broader relevance to applied biology and food innovation.

For further information about this HALRIC pilot project, please contact:

 

Antara Pal
Malmö University
antara.pal@mau.se

Integrins are heterodimers consisting of the non-covalently associated α- and β-subunits. Each contain a large N-terminal ectodomain, a transmembrane helix and a C-terminal cytoplasmic region. The vertebrate-specific αI integrins bind ligands through an αI domain within the α-subunit. αMβ2 and αXβ2 are αI integrins and adopts three major conformational states.

In the bent-closed conformation with low ligand affinity, the αI domain is close to the plasma membrane. In the high affinity extended-open conformation, their ectodomains are fully extended and the ”legs” of the two subunits separated. In this conformation, an αI integrin is subject to a tensile force created by two opposing forces arising from:

1. 1. binding of the extracellular ligand to the αI domain;
   2. interaction with the actin cytoskeleton through the β-subunit.

In the extended-closed (EC) conformation with low/intermediate ligand affinity, the two subunits of the integrins are close together and the β-subunit is not linked to actin.

This project focuses on structural studies of the ectodomains and their complexes with modulatory antibodies with potential for treating inflammatory and neurodegenerative disease.

A recently discovered extracellular protein has been shown to relieve pain, and recent studies suggest that it can, in some cases, cure nerve damage by inducing repair. In order to understand the protein’s effects at a molecular level and develop a method to study its interactions, we will explore whether biomolecular nuclear magnetic resonance (NMR) spectroscopy would be a feasible methodology. For this, we will need to produce a large amount of stable isotope-labelled protein for NMR.

This project brings together industry experts in protein function and drug targeting with university experts in protein production and biomolecular NMR spectroscopy, with the aim of developing a structure-based understanding of the molecular mode of action of this important protein.

ZNFX1 is a highly conserved, interferon-induced RNA helicase (1,913 amino acids) implicated in antiviral defence, inflammation control, and RNA regulation. Biallelic mutations in ZNFX1 cause immunodeficiency-91, a monogenic disorder marked by recurrent infections, systemic inflammation, and organ dysfunction. ZNFX1 contains a DExH-box helicase core and a zinc finger domain, as well as a large C-terminal region of unknown function. This suggests that it has modular roles in RNA binding, unwinding and protein interactions.

Although ZNFX1 binds double-stranded RNA and activates MAVS-dependent signalling, its structural organisation and molecular interactions remain poorly defined. We propose to characterise the architecture of human ZNFX1 using cross-linking mass spectrometry (XL-MS) and complementary proteomics.

By integrating structural modelling with advanced cross-linking techniques, we aim to identify interdomain contacts and RNA-protein interaction surfaces. Based on parallels with other RNA helicases, we expect to identify autoinhibitory domains that may regulate ZNFX1 activation.

These insights could inform future strategies to harness or dampen innate immune responses. Our data will also support the interpretation of 20 patient-derived ZNFX1 variants associated with immunodeficiency-like phenotypes, shared by our clinical collaborator

Structural information is essential for understanding protein function at a molecular level. This information is invaluable for both basic and applied science. However, many targets have remained unexplored due to the challenges associated with determining protein structures.

This pilot project aims to obtain the molecular structure of a physiologically relevant membrane protein, either in isolation or in complex with potential pharmacological compounds. We will focus on ion channel target family of SK-channels, which is essential for human health and a highly attractive target for the treatment of both acute and chronic atrial fibrillation. Breakthroughs recently achieved by the Gourdon laboratory will be utilised in conjunction with the proposed infrastructure facilities.

This project aims to gain a spatial understanding of how SK channels bind to novel, promising drug targets in their soluble domain, known as the EF hand. The focus will be on using FragMAX to prepare and evaluate protein-ligand crystals to identify novel binders that manipulate the EF-motif binding of the physiological regulator calmodulin. This knowledge will guide cryo-EM experiments on full-length proteins. Positive results have the potential to assist ongoing development of current Phase-II clinical therapeutic targets conducted by Acesion Pharma A/S for the treatment of atrial fibrillation aiding in cardiovascular health.

Predicting cellular behavior before and after treatment involves various approaches, yet gaining insights into these responses remains one of science’s greatest challenges. The functionality of a living cell is controlled by the interplay of its many components. Although progress has been made in understanding individual cell parts, fragments and enzyme levels, our understanding of cells as a whole is still lacking.

Interestingly, despite being mainly composed of water, the properties of cellular water have not yet been fully explored as indicators of cellular characteristics. The crowded nature of the cellular environment means that the properties of water molecules can vary considerably based on their surroundings. For example, water that interacts minimally with other molecules exhibits bulk water behaviour, whereas water confined by folded proteins and membranes — referred to as interface water — displays distinct properties.

In this project, we will investigate how the structure and dynamics of lung cells and their surrounding water molecules change after treatment with the monoclonal antibody tocilizumab (TCZ), either in its free form or incorporated into a bio-nanoparticle. We propose employing an integral approach, combining neutron and synchrotron X-ray scattering experiments with thermal analysis and optical photothermal infrared spectroscopy, to correlate changes in cellular water with biological outcomes resulting from TCZ treatment.

By leveraging the expertise of researchers from large-scale facilities such as MAX IV and ESS, as well as groups at the University of Copenhagen and Photothermal Spectroscopy Corp., we aim to enhance our understanding of how a newly developed bio-nanoparticle functions as a potential drug delivery system for tocilizumab.

Figure “Nano Warriors: tocilizumab takes flight to fight inflammation”

For further information about this HALRIC pilot project, please contact:

 

Heloisa N. Bordallo
University of Copenhagen
bordallo@nbi.ku.dk

Developing novel therapeutics requires a detailed understanding of how a potential drug interacts with its protein target. Traditionally, identifying a lead compound has involved experimental high-throughput screening, but this is time-consuming and expensive. In contrast, rational drug design is efficient and economical. This method is also known as reverse pharmacology, since the first step is to identify promising target proteins.

To map the interactions of the drug in the binding site of the target protein exactly, structural biology, particularly X-ray crystallography, is a key tool. However, to optimise the lead compound further, it is often crucial to understand the protonation states of either the protein or the ligand, which X-ray crystallography generally cannot achieve. Neutron crystallography (NC) is therefore potentially interesting for many structure-based drug design (SBDD) projects. However, due to the weak neutron sources currently available, it has often not been practically feasible.

The development of neutron sources and instrumentation is changing this situation. Nevertheless, the lack of adapted platforms and pipelines still hinders the use of neutron crystallography in SBDD. The NMX macromolecular diffractometer instrument at the European Spallation Source (ESS) expands the possibilities for neutron-based SBDD further, and we therefore aim to exploit this potential fully for drug discovery targeting type 2 diabetes.

For further information about this HALRIC pilot project, please contact:

 

Karin Lindkvist
Lund University
karin.lindkvist@med.lu.se

The primary objective of this pilot project is to develop a drop-on-demand sample delivery method for serial crystallography experiments at EuXFEL and synchrotrons. The goal is to enhance the efficiency of these experiments by drastically reducing the amount of sample needed and at the same time adjust to high frequency data collection.

The expertise of the collaboration partners SURFACtoBioTech and European XFEL in piezo-driven droplet technology will be combined to explore droplet frequency limits, improve nozzle reproducibility and sample exchange. The project is structured in multiple phases:

• It begins with project initiation and planning, followed by the development and optimization of a droplet formation module.
• Initial protein crystallography trials will compare the new droplet-based method with conventional techniques. A high-throughput screening system will be developed to accelerate the optimization process.
• Insights from planned serial X-ray crystallography experiments will then guide the further refinement of the droplet formation modules in subsequent phases.
• The project will culminate in validation studies with challenging protein targets and comprehensive data analysis.

Key milestones include developing a novel injection nozzle, optimising fluidic systems and implementing high-throughput screening. The project emphasises continuous improvement through the iterative testing and refinement of the droplet formation modules. The ultimate goal is to demonstrate the effectiveness of the new droplet-based approach in improving serial X-ray crystallography quality and enable screening experiment as well as the study of protein samples available only in restricted amounts.

For further information about this HALRIC pilot project, please contact:

 

Katerina Dörner
European XFEL
katerina.doerner@xfel.eu

Single-cell genomics shows promise in identifying residual cancer cells and in the early stratification of cancer patients based on tumour heterogeneity, prognostic biomarkers and molecular profiles. Therefore, the implementation of single-cell genomics in clinical settings has the potential to accelerate precision therapy efforts for malignant diseases.

Our cross-border research team, consisting of leading interdisciplinary stakeholders from academia, industry and hospitals, will collaborate to conduct a proof-of-concept study on the potential of single-cell genomics as a precision medicine tool for chronic myeloid leukaemia (CML) – a model disease for several cancers.

This project builds on the applicants’ close ties as founders of advanced single-cell genomics infrastructures in Lund and Copenhagen, their access to unique patient material and their computational platforms for optimised, easily accessible analysis and curation of single-cell data. This pipeline provides a unique opportunity to address some of the most fundamental questions in cancer research. Here, we will analyse blood and bone marrow samples from CML patients, focusing specifically on the leukaemic stem cell (LSC) population from patients in remission and relapse. This will enable us to investigate how cellular and molecular heterogeneity impacts therapy response, observe the early expansion of leukaemic clones and prospectively isolate relapse-initiating residual LSCs.

For further information about this HALRIC pilot project, please contact:

 

Göran Karlsson
Lund University
goran.karlsson@med.lu.se

This project pioneers a novel 3D spatial proteomics platform for chronic diseases by integrating Lund University’s advanced bioimaging (light-sheet microscopy/MERFISH) with Aarhus University’s multiplexed imaging-powered Deep Visual Proteomics (mipDVP). Our cross-border collaboration develops an innovative workflow combining:

1. high-plex 3D tissue imaging,
2. AI-guided single-cell analysis/automated microdissection, and
3. ultra-sensitive mass spectrometry to map protein networks in chronic diseases.

Initially focused on chronic obstructive pulmonary disease (COPD), we will establish the first end-to-end pipeline preserving spatial context during tissue remodeling. In parallel, we demonstrate platform versatility by resolving controversies in human pancreas islet architecture (e.g., true 3D islet size vs. 2D estimates and α-cell deficient islets).

The project leverages Öresund-Kattegat-Skagerrak-region research infrastructures and Miltenyi Biotech’s platforms to create a transferable framework with clinical translation pathways, including immunohistochemistry diagnostic kits for COPD biomarkers and diabetes-relevant islet signatures.

Expected outcomes: validated 3D spatial proteomics protocols; novel microenvironment-specific biomarkers; and strengthened academia-industry collaboration. This project will develop advanced 3D spatial biology tools with direct patient impact across chronic diseases within the HALRIC community.

For further information about this HALRIC pilot project, please contact:

 

Xiang Zheng
Aarhus University
xiangzheng@biomed.au.dk

Antimicrobial resistance is an increasing problem, with 10 million deaths predicted per year by 2025 due to a lack of treatment options. To mitigate this situation, innovative therapies that do not contribute to the development of resistance are needed.

Swedish biotech company Inicure AB is developing small-molecule drugs that activate the innate immune system. The compounds help the body fight infections by recruiting immune cells to the infection site without inducing resistance. The drugs have demonstrated promising effects in vitro and in mice. The next step towards clinical trials is to assess the efficacy and toxicity in a large animal.

his project is an exploratory pilot study in a pig model of urinary tract infection (UTI). Efficacy will be assessed ex vivo in human, porcine and other related animal species leukocytes for efficacy translation. Inicure will be collaborating with Professor T. E. Andersen at the University of Southern Denmark. Professor Andersen is a pioneer in the field of porcine UTI modelling and has unique experience in evaluating drugs in this animal model.

The outcome will provide important cross-species data to bridge the gap between preclinical and clinical research and support regulatory development and subsequent clinical studies. The project will combine cross-border academic and industrial expertise, contributing to HALRIC’s mission of advancing innovation through shared research infrastructures and collaborative life science solutions.

For further information about this HALRIC pilot project, please contact:

 

Thomas Emil Andersen
University of Southern Denmark
thandersen@health.sdu.dk

This project aims to develop advanced lipid-based nanocarriers functionalized with a lipid-conjugated peptide tag (pTag) for targeted drug delivery and immune activation. The system enables precise delivery of therapeutic payloads to CD40-expressing antigen-presenting cells by utilising Strike Pharma’s proprietary bispecific antibody technology, which binds both CD40 and the pTag.

By incorporating pTag into liposomes, reconstituted high-density lipoproteins (rHDL) nanodiscs, and lipid nanoparticles (LNPs), we establish a modular delivery platform adaptable to various cargo types, including mRNA, peptides, and small molecules. The pTag is anchored using DSPE-PEG-maleimide lipids, ensuring stable surface presentation and high-affinity antibody binding.

The structural characterization of the advanced nanocarriers will be performed using cryogenic transmission electron microscopy (cryo-TEM) and small angle X-ray scattering (SAXS), while the functional interaction between the nanocarrier and antibody will be evaluated using quartz crystal microbalance with dissipation monitoring (QCM-D) and surface plasmon resonance (SPR).

This cross-disciplinary collaboration between Malmö University, MAX IV Laboratory, the University of Copenhagen, and Strike Pharma integrates expertise in nanomedicine, structural biology, nanoscience, and immunotherapy to create a next-generation targeted delivery system.

This project aims to develop non-invasive or minimally invasive monitoring of endogeneous biomarkers targeting inflammatory skin disorders like contact allergy and cancer.

The main goal for this specific project is to further explore and develop the potential of using semisolid to ‘solid’ bicontinuous cubic liquid crystals as matrices for topical sampling of low molecular weight biomarkers (< 500 Da) that can diffuse through skin. The large interfacial area, comprised by these specific liquid crystals, separating their interconnected polar and apolar domains allow them to accommodate various types of solutes of hydrophilic, amphiphilic, or lipophilic nature.

Neurodegenerative diseases pose an increasing health risk and represent one of the greatest therapeutic challenges of our time. There is currently no cure for most of them. GlyT1 and GlyT2 glycine transporters control the transport of the neurotransmitter glycine across neuronal membranes in the brain and are promising therapeutic targets for several neurological disorders.

Despite extensive research, inhibitors of GlyT1 and GlyT2 have failed in preclinical and clinical studies due to low efficacy or significant side effects. A successful drug that modulates these neurotransmitter systems has yet to be developed.

In this project, our aim is to overcome the limitations of classical GlyT inhibitors by exploiting an endogenous allosteric regulatory mechanism of glycine transport. Using synthetic single-domain antibodies (sybodies) selected specifically for the inhibited state of the transporters, we will be able to lock them at a surface-exposed site distinct from the glycine-binding site and prolong glycine exposure. Combining cryo electron microscopy (cryo EM) with molecular biophysics studies will enable us to uncover the molecular mechanisms and structural determinants of allosteric inhibition.

This research project will lay the groundwork for identifying new therapeutic agents and novel strategies for effectively targeting glycine transporters. The methodological innovations developed will also be applicable to other protein targets.

Figure 1. Glycine transporters-mediated regulation of glycine neurotransmission at excitatory and inhibitory synapses. Excitatory glutamatergic synapse (left) and inhibitory glycinergic synapse (right) are depicted. GlyT1 (cyan), and GlyT2 (purple), the main regulators of glycine concentrations and dynamics of glycine neurotransmission in the synapse, are depicted. Extracellular and intracellular glycine concentrations created by GlyT1 and GlyT2 in different locations of the synapse are shown.

For further information about this HALRIC pilot project, please contact:

 

Azadeh Shahsavar
University of Copenhagen
ash@sund.ku.dk

Aging and age-related diseases profoundly affect stem cell proliferation and differentiation, which has implications for tissue homeostasis. The bone marrow niche maintains and regulates stem cells and interacts with endothelial cell subtypes. It plays a key role in mediating bone homeostasis by recruiting bone cells. During ageing and under pathological conditions, detrimental changes occur in the bone marrow niche that affect the microvascular system and lower blood flow. This is exacerbated in type 2 diabetes, a disease characterised by hyperglycaemia and high levels of inflammation.

This project brings together the expertise of the University Hospital Hamburg-Eppendorf (UKE), the University of Southern Denmark (SDU) and the German Electron Synchrotron facility (DESY). The collaboration combines expertise in bone tissue quality analysis, bone histology and high-resolution imaging, and is located close to the clinics. The project will use advanced imaging and state-of-the-art tissue analysis techniques to determine changes in the vasculature of the bone marrow in patients with type 2 diabetes. The research team will conduct 3D nano-tomographic imaging of vertebral samples from individuals with type 2 diabetes and controls to visualise the microvascular network within the human bone marrow niche. Bone histology will be used to characterise vessel type and bone marrow stem cells. This study will provide new technological approaches and insights into the underlying mechanisms of diabetes and vascular changes.

The figure shows adipocyte ghosts within the intertrabecular spaces. Bone marrow sinusoids are lined by endothelial cells resting on a discontinuous basement membrane. In the bone marrow, sinusoids are often collapsed and therefore challenging to visualise.

The hepatitis C virus (HCV) is a serious health concern, causing significant morbidity and mortality and affecting 50 million people globally. The limited number of effective drugs available is concerning, especially when you consider the ability of viruses to rapidly evolve and develop drug resistance. This project focuses on the HCV polymerase, a target for sofosbuvir (SOF), a drug that transformed the treatment of HCV in 2015. SOF works by mimicking a natural nucleotide, becoming incorporated into the synthesised RNA strand and consequently inhibiting RNA synthesis. Therefore, to understand HCV resistance to SOF at a molecular level, it is essential to study drug interactions within biologically relevant polymerase structures with RNA bound. While we have obtained a polymerase-RNA structure for HCV genotype 2, there are currently no such structures available for the clinically important genotypes 1 and 3, which account for 67% of all infections.

The aims of this project are:

1. to obtain polymerase-RNA-SOF crystal structures for HCV genotypes 1 and 3; and
2. to obtain room-temperature polymerase-RNA-SOF crystal structures for HCV genotype 2.

These structures will be instrumental in studying polymerase-SOF interactions and how polymerase mutations cause resistance.

This project will draw on the expertise and cutting-edge facilities of the MAX IV Laboratory, the experience of the University of Copenhagen in crystallising HCV polymerases, and the clinical perspective on antiviral resistance from Hvidovre Hospital.

Figure 1. Crystal structure of HCV genotype 2 polymerase with RNA (yellow), Mn2+ (red) and incoming nucleotide (blue) bound.

For further information about this HALRIC pilot project, please contact:

 

Line Abildgaard Ryberg
University of Copenhagen
line.ryberg@sund.ku.dk

Galectin-3, a key inflammatory protein involved in neurodegenerative diseases, has been identified by us and others as a therapeutic target due to its detrimental role in Alzheimer’s disease. We have demonstrated that inhibiting galectin-3 reduces neuroinflammation in microglia, resulting in improved memory, reduced amyloid beta (Aβ) plaque burden, and decreased inflammation in Alzheimer’s disease mouse models. Our initial findings have contributed to the development of galectin-3-targeting antibodies, which are currently being evaluated following a promising Phase Ib/IIa clinical trial. However, these antibodies have poor blood–brain barrier (BBB) permeability, so there is a need to discover small-molecule inhibitors with better central nervous system (CNS) availability.

This project aims to perform X-ray screening of small, potentially BBB-penetrable fragments against human and mouse galectin-3 in order to discover hit structures that can be optimised for galectin-3 inhibition and CNS availability. Mouse galectin-3 is included in the study as a key model species for neurodegeneration, and to ensure that any identified fragments optimise binding for both human and mouse proteins. The discovery of CNS-available galectin-3 inhibitors for use in mouse model proof-of-concept studies is critical for translating preclinical findings to human studies. This study will enhance our understanding of galectin-3 function in mice and lay the groundwork for future clinical studies targeting galectin-3 in neurodegenerative diseases.

Figure: Galectin-3C protein bound to a drug-like molecule called TD139, also known as GB0139. The protein is displayed as a see-through surface. The most important amino acids interacting with the ligand are shown as thicker “sticks” while the other amino acids are shown as thinner lines

For further information about this HALRIC pilot project, please contact:

 

Tomas Deierborg
Lund University
tomas.deierborg@med.lu.se

Scientific abstracts are often too dense and technical for those outside specialized communities, limiting access to important research.

This project aims to develop a module powered by a Large Language Model (LLM) that adapts life science abstracts to match the user’s knowledge level, making complex biological and medical research more accessible Key to this project is optimizing prompts that guide the LLM in simplifying or detailing content accurately. Additionally, we will explore the possibility to easily provide explanations for specific terms within abstracts, tailored to the user’s expertise. It intends to serve as a valuable tool for broadening public engagement with science.

The module will be open-source, easily integrated into existing repositories, starting with the ESS repository (Publications Portal). It aligns with key European policies — such as the European Charter for Researchers, Horizon Europe’s Open Science Agenda, and Responsible Research and Innovation (RRI) — by addressing their core goals: improving research infrastructure, promoting open science and knowledge transfer, enhancing public engagement, and maximizing the societal impact of research data.

This tool addresses a critical stage in the research lifecycle: the dissemination and reuse of research data and findings. By making complex scientific research more understandable and accessible, it directly supports the publication, communication, and outreach phase, extending the lifecycle of research data beyond initial publication and maximizing its impact. The development of this tool is inherently a collaborative effort, requiring expertise from multiple fields to ensure it is scientifically accurate, technologically robust, and user-friendly.

Example of a life science abstract made more accessible.

For further information about this HALRIC pilot project, please contact:

 

Fredrik Eriksson
European Spallation Source
fredrik.eriksson@ess.eu

Protein crosslinks are a defining feature of amyloid plaques and Lewy bodies, which are associated with neurodegenerative diseases. Although most research has centred on a few well-established and easily detectable types of crosslink, mounting evidence suggests that these account for only a small proportion of the total complement. This indicates that a wide variety of other crosslinks are present in proteins associated with neuropathology. To identify novel types of crosslink, there is an urgent need to develop improved methods to characterise, quantify and map crosslinks in a holistic and unbiased manner, rather than studying them one at a time.

This project aims to develop an agnostic (i.e. mode-independen) mass spectrometry approach for the unbiased and comprehensive detection of protein crosslinks. As a proof of concept, the focus will be on α-synuclein, the main protein associated with Parkinson’s disease. However, the workflow should be widely applicable to protein crosslink analysis in a variety of scientific disciplines and industries.

For further information about this HALRIC pilot project, please contact:

 

Per Mårten Hägglund
University of Copenhagen
pmh@sund.ku.dk

The expression of aquaporins (AQPs), a family of proteins that facilitate the transport of water, glycerol and hydrogen peroxide across the cell membrane, is known to potentiate cancer invasion and metastasis. Similarly, AQP expression levels have been shown to predict survival in patients, and play a role in tumour growth, angiogenesis and tumour cell migration. Therefore, AQPs are pivotal in cancer biology and are potential targets for drug development. Although pharmacological modulators of AQPs have been identified and tested for therapeutic potential, the drug discovery process has been severely hindered by the lack of three-dimensional structures of AQPs in complex with inhibitors. The so-called ‘resolution revolution’ in single-particle cryo-electron microscopy (cryo-EM) has made it possible to determine the high-resolution structures of previously intractable biological systems, as the requirement for sample quantity and homogeneity has been reduced. These developments therefore facilitate structural studies of integral membrane proteins, such as AQPs, in complex with putative drugs, which were previously very challenging. As AQP3-mediated H₂O₂ transport has been shown to be important for breast cancer cell migration, our aim is to synthesise novel inhibitors, investigate their potency in a breast cancer model, and determine their structure in complex with AQP3 using cryo-EM.

For further information about this HALRIC pilot project, please contact:

Karin Lindkvist
Lund University
Karin.Lindvist@med.lu.se

The digitalisation of microscopy technologies, combined with automated image analysis workflows, has transformed the field by enabling scientists to replace qualitative observations with high-quality quantitative measurements. However, determining which structures, cells or areas of interest to image to obtain relevant biological information remains a key challenge — a fundamental yet complex task. For instance, identifying a ‘representative’ cell demands years of experience and subjective judgement, making the process time-consuming and prone to bias. This highlights the urgent need for innovation in microscopy workflows.

Microscopy core facilities play a pivotal role in life science research, supporting a wide range of studies, from basic biology to clinical diagnostics. Despite their critical role, these facilities face persistent challenges, including reliance on manual operation, fragmented software ecosystems (metadata and file formats) and inconsistencies across hardware platforms. These issues undermine reproducibility and slow progress in generating robust scientific insights.

To address these challenges, the project aims to implement a smart microscopy solution — data-driven microscopy (DDM) — at the Lund University Bioimaging Centre (LBIC) and the Core Facility for Integrated Microscopy (CFIM) at the University of Copenhagen. Developed by the Nordenfelt group at Lund University (André et al., 2023), DDM has resulted in the spin-off company Cytely AB, which is the project’s industry partner.

For further information about this HALRIC pilot project, please contact:

Sebastian Wasserstrom
Lund University Bioimaging Centre
sebastian.wasserstrom@med.lu.se

Neurological disorders are the third leading cause of premature mortality in Europe. They are often related to dysfunctions or imbalances in signalling and regulatory processes mediated by neurotransmitter molecules. Despite extensive research, the therapeutic potential of modulating these neurotransmitter systems by the key neuromodulator glycine has largely remained unexplored. The glycine transporter 1 (GlyT1) controls the transport of the neurotransmitter glycine across neuronal membranes in the brain and represents a promising therapeutic target for several neurological disorders, including schizophrenia. However, despite extensive research, inhibitors of GlyT1 have failed in clinical studies due to low efficacy, and a successful drug candidate targeting GlyT1 has yet to come.

This project aims to overcome the limitations of classical GlyT1 inhibitors by exploiting an extracellular site on the transporter that is distinct from the glycine binding site. Using a GlyT1 construct that favours the outward-open conformational state and selective binders, as well as serial synchrotron crystallography (SSX), we will uncover the molecular determinants of the substrate-free outward-open state of the transporter. This research project will lay the groundwork for identifying new conformationally selective inhibitors as therapeutic agents targeting GlyT1 and similar transporters.

Figure “Uncovering the structural basis of a novel extracellular site for the development of next-generation GlyT1 Inhibitors”

For further information about this HALRIC pilot project, please contact:

 

Azadeh Shahsavar
University of Copenhagen
ash@sund.ku.dk

The role of dinucleotides in bacterial physiology

Bacteria are constantly challenged by viruses called phages. In order to survive, bacteria have evolved a variety of mechanisms to combat phage infections, which are often encoded in mobile pieces of DNA known as mobile genetic elements (MGEs). MGEs often contribute to the ‘dark proteome’, which contains genes for proteins that have not yet been characterised and which have the potential to act in bacterial immunity. However, their cellular functions remain enigmatic.

We recently discovered MGE-encoded proteins that function as DNA dinucleotide-specific nucleases (diDNases) in several bacterial species. Given their location on MGEs and their genetic context, it is likely that diDNases play a role in bacterial immunity. Building on this insight, here we investigate the role of DNA dinucleotides in bacterial physiology and immunity. The aim of this HALRIC pilot project is to decipher the function and molecular mechanism of diDNases and diDNase-associated factors using biochemical, structural, and microbiological approaches. We will use the PETRA III beamline at DESY and the protein characterisation facility at the Centre for Structural Systems Biology (CSSB) in Hamburg to achieve this. In parallel, we will evaluate the impact of dinucleotides on bacterial processes using cell-based assays at Aarhus University (AU) in Denmark. For structure determination by cryo-EM, we will use facilities at the CSSB and AU.

This work will provide new insights into how bacteria survive in hostile environments and may even help to develop new tools for biotechnology or medicine.

For further information about this HALRIC pilot project, please contact:

 

Holger Sondermann
Centre for Structural Systems Biology (CSSB) at DESY
holger.sondermann@cssb-hamburg.de

Pulmonary delivery and formulation of biopharmaceuticals (i.e., biological molecules) are among the more complex and growing scientific topics in pharmaceutical formulation. This project aims to understand critical steps in the development of novel non-invasive formulations of biopharmaceuticals using lipid nanoparticles (LNP) for pulmonary delivery in the treatment of severe respiratory diseases. The cross-border collaboration between Biofilms – Research Center for Biointerfaces at Malmö University (MaU), Copenhagen University (KU), MAX IV and Truly Labs (Medicon Village, Lund) plan to understand how formulation parameters and phisico-chemical properties will impact the therapeutic efficacy using advanced in vitro 3D models.

The team consists of experts in pharmaceutical formulation design and biobarriers (MaU), an expert in lipid nanoparticles formulation and structural characterization (KU and MAX IV), and one industrial partner involved in preclinical studies (Truly labs). They plan to formulate lipid nanoparticles (LNP) for the loading of biologics Truly Labs (i.e., mRNA) and to develop simple (2D) and advanced (3D) ex-vivo models of lung to understand the interaction between LNP and the biological barrier. Thanks to small-angle X-ray Scattering (in-house SAXS and synchrotron-SAXS, Co-SAXS) we will elucidate the relationship between the structural properties of the LNP and their therapeutic efficacy observed in advanced 2D and 3D ex-vivo models.

For further information about this HALRIC pilot project, please contact:

Sabrina Valetti
Malmö University
sabrina.valetti@mau.se

Nitrogen is essential for plant life and vital for human existence. However, plants are unable take nitrogen directly from the air and rely on bacteria capable of ‘nitrogen fixation’ to obtain this key nutrient. In legumes, this occurs directly inside root nodule organs.

The aim of this project is to explore the mechanism by which these nitrogen-fixing bacteria infect plant cells to deliver nitrogen, in order to gain a deeper understanding of the processes on which legume plants depend for their contribution to sustainable agriculture. A fast, streamlined method of acquiring 3D volumes of intact plant tissue using synchrotron X-ray phase contrast tomography techniques will be established using PETRA III at DESY. Combined with light microscopy, the tomography sample volumes will be used to study the dynamic and complex process of microbial infection from the initial passage of the plant epidermis to the colonisation of solid, compact root nodule tissue.

By combining our frontier research in the molecular biology of plants and microbes at AU with the tomography core expertise of EMBL-HH and the 3D quantification expertise of QIM-DTU, we will be able to quantify and understand the colonisation of plant tissue by microbial symbionts. The overarching goal is to develop an AI-assisted, fast, high-throughput, synchrotron-based 3D tomography for the quantitative measurement of the colonisation of plant roots by beneficial microbes, such as rhizobia, mycorrhizae, and microbiota strains, across the cell layers of intact tissues and organs.

Figure: Segmented root nodule of the model legume Lotus japonicus, obtained by X-ray tomography.

For further information about this HALRIC pilot project, please contact:

Jens Stougaard
Aarhus University
stougaard@mbg.au.dk 

Understanding biological processes such as cellular communication, immune responses, developmental programs, and tumor microenvironments requires knowledge of both molecular composition and the spatial organization of cells. Traditional microscopy techniques provide high molecular sensitivity through fluorescent probes but can only detect a limited number of biomarkers simultaneously. Conversely, single-cell sequencing can reveal entire transcriptomes, making it a powerful tool for classifying cells into types and states, but it requires tissue dissociation, leading to a loss of crucial spatial information.

This HALRIC pilot project aims to bridge this gap by developing and optimizing multiplex fluorescence in situ hybridization (FISH) methods for spatial transcriptomics. By enabling the detection of multiple mRNA species—potentially up to the whole transcriptome—while preserving subcellular localization through iterative labeling and imaging, this approach provides a more comprehensive understanding of molecular interactions within tissue architecture. Such advancements are critical for the next generation of personalized medicine, where molecular diagnostics and novel biomarkers with prognostic capabilities can guide treatment decisions.

The project is a collaboration between researchers from two countries, involving two advanced imaging core facilities—Lund University Bioimaging Centre (LBIC) in Sweden and the Danish Molecular Biomedical Imaging Center (DaMBIC) at the University of Southern Denmark—along with researchers at Skåne University Hospital. Together, they aim to refine best practices, develop probe libraries, and improve data analysis workflows, ensuring that spatial transcriptomics becomes a widely accessible tool for biomedical research and clinical applications.

By integrating cutting-edge molecular imaging with spatially resolved transcriptomics, this project supports the development of advanced diagnostics and targeted therapies, directly contributing to HALRIC’s mission of fostering cross-border collaboration and accelerating innovation in biomedical imaging.

For further information about this HALRIC pilot project, please contact:

 

Nils Norlin
Lund University
nils.norlin@med.lu.se

Today there is a gap in understanding the interdependence between soft and hard tissue in for example human bone and teeth – processes that are central to fixation, repair, and biomaterial-cell interactions. Hence, understanding these processes is important from a clinical perspective and ultimately can help impact patient care.

This HALRIC pilot project addresses key challenges in imaging the structural complexities of bones, teeth, and associated soft tissues by leveraging contrast-enhanced micro-CT and synchrotron techniques. By combining state-of-the-art technologies like phase-contrast imaging and X-ray fluorescence mapping, the project seeks to improve the standardization and reliability of non-destructive imaging techniques, enabling more precise visualization of cellular structures and their interactions within hard and soft tissues.

The initiative is a cross-border collaboration between researchers and clinicians from Lund University, Malmö University, and the University of Oslo. It fosters an interdisciplinary approach, utilizing cutting-edge research infrastructures, including MAX IV in Sweden, Elettra Sincrotrone in Italy, and SOLEIL Synchrotron in France. These efforts integrate expertise in X-ray imaging, life sciences, and clinical applications to push the boundaries of biomedical imaging.

The project’s outcomes are expected to improve patient treatment by enabling more precise diagnostics and targeted therapies in dental and orthopedic care.

For further information about this HALRIC pilot project, please contact:

Håvard J. Haugen, University of Oslo

h.j.haugen@odont.uio.no

The rise of methicillin-resistant Staphylococcus aureus (MRSA) poses a significant threat to global health. The virulence and resistance of S. aureus are facilitated by the secretion of phenol-soluble modulins (PSMs), which are amyloid-forming proteins. The PSMα1 member plays a role in biofilm scaffolding and cytolysis of host cells. Our preliminary research using cryogenic electron microscopy (cryo-EM) and X-ray fibre diffraction revealed that PSMα1 forms cross-β amyloid fibrils at low pH and assembles into tubular structures with a potential cross-α architecture at neutral pH.

This HALRIC pilot project will investigate PSMα1 aggregation and secondary structure transformations in a biological context when interacting with various bacterial and human cell lines, as well as within biofilms. We will use a high-resolution approach combining micro-optical photothermal infrared spectroscopy (OPTIR) and atomic force microscopy (AFM) based on infrared nano spectroscopy, which has recently become available at MAX IV as a unique multiscale IR platform.

This combination of methods will enable us to analyse individual fibrils interacting with different cellular and matrix components. Combining in vitro high-resolution structures with secondary structures of fibrils in their biological context will enable an in-depth mechanistic description of PSMα1’s virulent functions. This project will contribute to our understanding of the mechanisms of amyloid toxicity, as well as to the development of novel anti-virulence strategies against MRSA.

High-throughput analysis of PSMα1 conformations in cellular interactions. Created in BioRender. Landau, M. (2025).

For further information about this HALRIC pilot project, please contact:

 

Sambhasan Banerjee
Centre for Structural Systems Biology at DESY
sambhasan.banerjee@cssb-hamburg.de

Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria and serves as a crucial barrier against antibiotics and environmental threats. This barrier enables bacterial survival and antimicrobial resistance, which was responsible for over 6 million deaths worldwide in 2019. Resistance in clinically relevant pathogens such as E. coli, K. pneumoniae and P. aeruginosa is of particular concern. For antibiotics to be effective, they must penetrate the LPS barrier, consisting of an O-antigen, a core oligosaccharide and a lipid A component. The composition and structure of LPS molecules play a key role in bacterial sensitivity to last-resort antimicrobials.

The project aims to understand LPS interactions with antimicrobials, which is key to overcoming resistance mechanisms and developing new drugs. Due to the natural complexity of LPS, biophysical studies require the use of purified and reconstituted materials. Neutron reflectometry can probe the structure of these membranes at the nanometre range, providing detailed insights into the interaction between antibiotics and LPS. Deuterating specific components for these experiments enables precise observation of the effect of antimicrobial agents on membranes. One of the project’s goals is to establish a platform at ESS for producing novel deuterated LPS species, which will enable comprehensive biophysical studies of LPS-antibiotic interactions. This will support the development of new antimicrobial agents that target Gram-negative bacteria and will be a critical tool in the fight against antibiotic resistance.

For further information about this HALRIC pilot project, please contact:

Nicolò Paracini
European Spallation Source
nicolo.paracini@ess.eu

The prevalence of antibiotic-resistant infections is increasing rapidly, and it is predicted that, by 2050, the annual number of deaths from bacterial infections will exceed the number of cancer-related deaths (ARC, 2022, The Lancet, PMCID: PMC8822221).

Alternative treatments are desperately needed, and personalised bacteriophage therapy, which uses bacterial viruses to combat infection, is an exciting and promising approach. However, in order to develop phage therapy, we must first understand how bacteria defend themselves from bacteriophages in their natural environment. Many bacterial immunity systems, including restriction-modification and CRISPR-Cas systems, recognise foreign, invading DNA via specific DNA-binding domains (Georjon and Bernheim, 2023, Nat Rev Microbiol, PMID: 37460672). Among these defence systems, those that include DNA-binding Cro domain proteins are less well studied. Cro-domain proteins are found in both phages and bacteria and generally participate in transcriptional regulation; some are also expected to play a role in phage recognition (Aggarwal et al., 1988, Science, PMID: 3187531).

This HALRIC pilot project aims to understand how the bacterial Cro domain recognises DNA at a molecular level. This will be achieved by using the anomalous scattering properties of phosphorus and sulphur atoms to determine the structure of protein–DNA complexes. These structures will enable us to decipher phage defence and how it is mediated through DNA recognition.

Molecular model of how we believe bacterial Cro domain interacts with DNA (July 2025)

For further information about this HALRIC pilot project, please contact:

 

Frederik Oskar Graversgaard Henriksen
DEB-Lab, Aarhus University
fogh@mbg.au.dk

This project, a collaborative effort involving researchers from Malmö University, Lund University, and Aarhus University, investigates the anti-inflammatory properties of reconstituted high-density lipoprotein (rHDL) particles in relation to their structure. These particles, central to cholesterol transport, hold significant potential for therapeutic applications in cardiovascular disease.

The focus is on rHDL particles incorporating amyloidogenic ApoA-I variants, which exhibit superior cholesterol efflux capacity compared to those with wild-type ApoA-I. By examining these variants, the project aims to uncover how their structural features enhance their ability to modulate inflammation—a critical factor in atherosclerosis progression.

The project integrates advanced structural characterization techniques—cryo-electron microscopy (cryo-EM) and small-angle X-ray scattering (SAXS)—with functional assays. The functional studies will be conducted at Malmö University and will be used to assess how the rHDL particles impact inflammatory responses in macrophages and endothelial cells. Concurrently, structural characterization will take place at Lund University and Aarhus University, leveraging cryo-EM and SAXS expertise.

By integrating structural techniques such as cryo-EM and SAXS with functional assays, this project bridges the gap between structure and function. The findings aim to pave the way for the development of HDL-based therapeutics that address both cholesterol metabolism and inflammation, offering new strategies for tackling atherosclerosis and other inflammatory diseases.

For further information about this HALRIC pilot project, please contact:

Rita Del Giudice, Malmö University
rita.del-giudice@mau.se

Atherosclerosis is the main underlying cause of cardiovascular disease. Stroke and myocardial infarction are often fatal or debilitating consequences of a thrombus resulting from the rupture of atherosclerotic plaques. The quality and quantity of plaque components can vary greatly, and its composition impacts overall vulnerability. A key factor in clinical patient assessment is the content of calcium in the plaque. Calcifications are easily visible using clinical imaging modules, and large calcifications are classically considered to indicate stable plaque.

However, plaque calcifications are not as homogeneous as previously assumed, and deeper characterisation is vital. This project will use spatial proteomics to determine extracellular matrix profiles specific to large calcifications of differing structures in human atherosclerotic plaques. These plaques will be identified using multiple imaging modalities, including synchrotron-based imaging, µCT (microCT) and photon-counting computer tomography, as well as classical histology. Furthermore, we will investigate the associations between these proteomic profiles and features of particularly vulnerable plaques and ruptures. Increased fundamental knowledge of the molecular development of plaques would provide new insights into the mechanism of atherosclerosis. The ability to distinguish between calcification profiles and their association with plaque vulnerability would have immediate clinical value in improving patient risk stratification.

For further information about this HALRIC pilot project, please contact:

 

Luke F. Gamon
University of Copenhagen
lgamon@sund.ku.dk

 

Annelie Shami
Lund University
annelie.shami@med.lu.se

Parkinson’s disease affects 10 million people worldwide. It is characterised by the accumulation of protein aggregates in nerve cells. These aggregates are composed of a protein called alpha-synuclein (α-syn). Recent evidence suggests that α-syn can undergo liquid-liquid phase separation (LLPS), forming dense protein phases. The latter may trigger aggregation.

However, due to a lack of techniques capable of examining the early stages of LLPS, the link between α-syn aggregation and LLPS remains unclear. Current strategies focus on temporal scales at which LLPS is already in place (seconds, minutes or hours), which prevents access to the early phases (sub-second range) of condensation.

This HALRIC pilot project will exploit the potential of combining a cutting-edge time-resolved small-angle X-ray scattering (TR SAXS) technique with computer simulations. The former enables the real-time investigation of LLPS formation with an unprecedented temporal resolution of up to milliseconds. The latter will complement the experimental outcomes with a molecular view of the phenomena. By integrating these methods, we aim to identify the key factors that initiate α-syn LLPS, understand their individual contributions, create comprehensive phase diagrams and ultimately reveal the molecular processes involved in LLPS formation. The outcomes of this project could provide a new screening tool for drugs against Parkinson’s disease.

Investigating alpha synuclein liquid-liquid phase separation

For further information about this HALRIC pilot project, please contact:

 

Marco Polimeni
University of Copenhagen
marco.polimeni@sund.ku.dk

Globally, hepatocellular carcinoma is a common type of cancer with a high mortality and recurrence rate (with incidence and mortality rates of approximately 1:1). Even patients with early-stage disease who are offered curative treatment have a recurrence risk of more than 50%, as well as a significant risk of major complications following surgery. Consequently, there is a need for biomarkers to identify patients with a favourable prognosis who may benefit from treatment.

Microvascular invasion in tumours is one of the most important prognostic biomarkers, strongly correlating with recurrence and survival. However, current techniques cannot reliably identify it prior to surgery. This HALRIC pilot project will use 3D X-ray microtomography (µCT) for the first time to evaluate microvascular tumour invasion density prior to surgery.

Once the project’s feasibility has been established under the project, the team will obtain additional funding to expand it by including more patients. For this, we will correlate µCT results with the serum metabolome and the prognosis (survival and recurrence) of patients, in order to identify the clinical phenotypes of microvascular invasion. We will also assess the value of the serum metabolome in identifying patients with microvascular invasion.

For further information about this HALRIC pilot project, please contact:

 

Hans-Christian Pommergaard
Rigshospitalet
hans-christian.pommergaard@regionh.dk

Acute respiratory distress syndrome (ARDS) is a life-threatening form of respiratory failure that affects approximately 750,000 patients annually in the EU, causing significant morbidity and mortality. The pathology is characterized by acute respiratory failure that requires mechanical ventilation in severe cases. While mechanical ventilation is essential in treating respiratory failure, it can also cause or worsen lung injury –  a condition known as ventilator-induced lung injury (VILI) – through excessive mechanical strain and inflammation within the lung tissues.  The excessive mechanical strain imposed on the lung structures and linked inflammation during ARDS are contributing factors to VILI. Yet, the magnitude and distribution of strain imposed on the airspaces during mechanical ventilation, and their link to inflammation, are not fully elucidated.

This HALRIC project brings together experts from the Lund University Bioimaging Centre (LBIC), the Technical University of Denmark (DTU), Skåne University Hospital and Grenoble University Hospital, combining skills in imaging, lung pathology, and clinical research to advance the understanding of VILI.

The project will use advanced imaging and tissue analysis techniques to investigate, on both an organ and microscopic level, the underlying mechanisms causing VILI. More profound knowledge about progression of VILI is needed, including studies of changes in the structure and composition of the lung extracellular matrix (ECM).

Researchers will conduct X-ray microtomographic (µCT) 4D imaging in rat models to visualize the lungs during ARDS, before and after the induction of VILI. In addition, ex vivo precision cut lung slices (PCLS) and tissue histology will be studied to gain knowledge about the ECM and potential biomarkers that could serve as specific indicators of VILI onset.

For further information about this HALRIC pilot project, please contact:

 

Irma Mahmutovic Persson
Lund University Bioimaging Centre (LBIC)
irma.mahmutovic_persson@med.lu.se

Besides considerable scientific interest, protein-protein interactions have many societal applications, including development of new drugs and vaccines; in food formulation; and in environmentally friendly washing detergents. Neutron and X-ray scattering techniques offer exciting new ways to study such interaction at molecular length scales. However, to fully exploit new infrastructures such as ESS and MAX-IV, experimental data must be combined with models and simulations to extract the full molecular insight.

This is exactly where this project sets in: we will offer scattering users a new computational tool that can simulate scattering data of interacting proteins based on their 3D structure. This has traditionally been reserved to experts in simulations with access to vast computational resources. We propose a new set of tools to speed up this process by using existing regional infrastructures. Our methodology has been tested on e.g., antibodies and enzymatic detergents and offer a significant improvement over existing models that are mainly based on simple spheres.

For further information about this HALRIC pilot project, please contact:

 

Mikael Lund
Lund University
mikael.lund@compchem.lu.se

DESY aims to build a unique PETRA IV light source to enable groundbreaking studies in a multitude of disciplines. Within this project, the intention is to expand the experimental portfolio to include even larger user communities. Beamline P11 at PETRA III is at the forefront of these developments as it is one of the beamlines that has already implemented the rolling access model and is now taking on project-based access. With this model, users can apply for beamtime(s) combined with additional experiments.

Within this project, the team will create and combine computational tools to support full project access in drug discovery. This will be achieved by further developing their existing fragment-screening pipeline and enabling the interconnectivity of results displayed for multiple techniques. In general, drug development experiments at beamlines typically involve testing hundreds or thousands of compounds at a very fast pace. This puts the logistics of sample handling, metadata management and the efficient processing and presentation of diffraction data under extreme pressure.

The Hanseatic Science Cloud (HSC) is developing a prototype cloud solution for managing, handling and analysing large and complex data sets from research infrastructures within the HALRIC community. The HSC solution will first be made available for use and testing in pilot projects. This project also aims to engage with the HSC cloud computing and explore the possibilities of sharing data, particularly with industrial partners.

Global warming has made heat stress an unavoidable challenge for food production. Nanomaterials such as silica nanoparticles (SNPs) offer a way to enhance the sustainability of food production in the face of abiotic stresses.

While protein interactions with nanoparticles forming a protein corona (PC) are well studied in nanomedicine and nanotoxicity, this has largely been overlooked in nano-enabled agriculture, despite their potential to modulate the effects of NPs on plant cells and their resistance to stress.

This HALRIC pilot project aims to investigate the uptake, localisation and biotransformation of SNPs under normal and stressful conditions. Building upon previous in vivo studies utilising wheat as a model plant for bioimaging and PC formation, the team will conduct experiments at Aarhus University to study PC formation. Each PC formed in stressed and non-stressed wheat will be characterised using mass spectrometry-based proteomics (MS) at Lund University. They will also use MAX IV in Lund to examine the localisation and biotransformation of SNPs in chloroplasts. At the Technical University of Denmark (DTU), Confocal Laser Scanning Microscopy (CLSM) and Transmission Electron Microscopy (TEM) will be employed to study SNP localisation.

For further information about this HALRIC pilot project, please contact:

 

Duncan Sutherland
Aarhus University
duncan@inano.au.dk

Understanding how chromosomes are accurately divided during cell division is crucial for maintaining genetic stability. Errors in this process, like losing or gaining chromosomes, can lead to diseases such as cancer and birth defects.

This HALRIC pilot project is a collaboration between teams from the University of Oslo in Norway and Lund University in Sweden, marking their first joint effort. By understanding how chromosomes are properly segregated, their research aims to develop better therapies for cancer and birth defects and address genetic instability issues related to aging and fertility.

Chromosome segregation is controlled at a specific chromosome region called the centromere, where sister chromatids are held together. This is where microtubules attach to pull chromosomes into new cells. The centromere attracts various enzymes that regulate the alignment and separation of chromosomes. One critical protein in this process is shugoshin (Japanese for ‘guardian spirit’), which can recruit enzyme complexes that have both kinase (CPC with Aurora B kinase) and phosphatase (PP2A) activities. However, it is unclear if these enzyme activities can be simultaneously recruited.

The Sekulic lab in Oslo will produce the necessary proteins, which will then be analyzed by the Nilsson and Wahlgren labs in Lund using specialized biophysical techniques. They will test both normal and modified proteins to gain insights into the complex’s behavior and function. More specifically, the researchers will use small infrastructures (A4F, UV-MALS-dRI) at Lund University and the large synchrotron infrastructure (SAXS) at MAXIV to characterize the complexes shugoshin makes with CPC and/or PP2A.

For further information about this HALRIC pilot project, please contact:
nikolina.sekulic@ncmm.uio.no

Lytic polysaccharide monooxygenases (LPMOs) are enzymes with a characteristic copper site (His brace) being able to degrade recalcitrant polysaccharides and with additional implications in microbial pathogenesis of humans and important crop plants.

This pilot project is a collaboration between the University of Copenhagen (UCPH) and the MAX IV facility in Sweden. It builds on UCPH’s extensive knowledge and crystallographic studies of the model LPMO and MAX IV’s cutting-edge serial crystallography capabilities. The results could enhance our understanding of LPMOs, leading to industrial applications in biofuels and new strategies for combating pathogens. Additionally, the collaboration will contribute to optimizing time-resolved crystallography techniques at MAX IV, benefiting future research endeavors.

Single crystal structure studies of microbial LPMOs at cryo-temperatures have been instrumental in elucidating their structure-function relationship, and have been the basis for mutagenesis, protein engineering and computational chemistry aimed at understanding the details of the reaction.

Serial crystallography emerges as a promising technique to capture the dynamic process of LPMOs’ action in a time-resolved manner, as it can be carried out at room temperature, potentially providing a deeper understanding of their catalytic mechanism at the molecular level. This knowledge could lead to optimized industrial applications and innovative strategies in pathogen control. In order to use serial crystallography for a time-resolved study, the reaction must be triggered in a controlled manner, and the triggering mechanism is a specific focus of this pilot project.

For further information please contact:

Leila Lo Leggio
University of Copenhagen
leila@chem.ku.dk

The rapid growth of antibacterial resistance and the glooming predictions that it will become the leading cause of mortality has created an urgent need for novel antibiotics. To this end, antimicrobial peptides (AMPs) are promising alternatives due to their high potency and broad scope activity. However, despite their great promise, AMPs have seen little clinical use, which is largely due to their cytotoxicity and susceptibility to peptide degrading enzymes, in addition to the poor understanding of how they work. While it is largely accepted that AMPs perturb the bacterial cell membrane, there is little consensus of how they do this.

This HALRIC pilot project aims to uncover the mechanisms of AMPs and contribute to overcoming one of the major hurdles towards developing AMP-based antibiotics. The cross-border research team from the University of Oslo and MAX IV Laboratory will use a combined setup of small angle X-ray scattering with in situ fluorescence spectroscopy at the coSAXS beamline at MAX IV, to map the insertion of several different AMPs into the membrane, while simultaneously tracking the membrane leakage. This will allow them to directly link the structural effects to the perturbation of the lipid membrane, which is an essential step.

So far, much of the understanding of AMPs stems from bacterial and vesicle assays that provide only indirect information of the molecular mechanisms or scattering experiments. The latter provide information on the membrane structure and AMP insertion, but do not show how this affects the membrane integrity and its ability to maintain the necessary electrochemical gradients.

Infectious diseases disproportionately affect developing countries and vulnerable populations. The development of safe and effective antibiotic alternatives that can overcome current resistant infections will also contribute to reduce such inequalities.

For further information about this HALRIC pilot project, please contact:

 

Vladimir Rosenov Koynarev
v.r.koynarev@kjemi.uio.no
University of Oslo

During the COVID-19 pandemic, mRNA vaccines, which use lipid nanoparticles (LNPs) to deliver their instructions to cells, saved millions of lives. These LNPs are made up of several components: ionizable lipids, helper lipids, cholesterol, and polyethylene glycol-conjugated lipids. However, current mRNA vaccines can cause strong immune reactions because of the ionizable lipids. Additionally, some LNPs in the vaccine formulations are empty, which can trigger immune responses and reduce the effectiveness of mRNA treatments.

The aim of this HALRIC pilot project is to improve mRNA-LNP design and formulation for therapeutic application, by understanding how the structure and function of the different particle types are related in a single formulation.

The research team believes that reducing the number of empty LNPs could help develop better mRNA treatments by lowering unwanted immune reactions and increasing the amount of protein produced by the mRNA. To test this idea, they will study the different populations of particles in the current LNP formulations.

They will use a method called Asymmetric Flow Field-Flow Fractionation combined with Small Angle X-ray Scattering to look at the structure of each type of particle. At the same time, they will measure how much mRNA each type contains and how much protein it produces. By linking these structural and biological findings, they hope to understand how the structure of the particles affects their function. This knowledge will help them design better LNPs for delivering mRNA more effectively in therapeutic applications.

For further information about this HALRIC pilot project, please contact:
Federica.Sebastiani@sund.ku.dk
University of Copenhagen

Parthenolide is a naturally occurring compound isolated from feverfew and has long been used in traditional medicine. It has anti-inflammatory, antimicrobial and anti-cancer properties. Its anti-cancer effects are based on its ability to interfere with several cellular signalling pathways. The most well-characterised of these are the inhibition of the NF-κB pathway and STAT proteins, and the induction of oxidative stress. Parthenolide also induces severe mitotic arrest; however, the exact mechanism underlying this phenomenon is not well understood. Collaborative research between the Danish Cancer Institute and the University of Copenhagen, combining cell biology and click chemistry, identified a protein involved in the spindle assembly as target for parthenolide.

In this HALRIC project, we propose using X-ray crystallography and HDX-MS at the University of Oslo to characterise the parthenolide-protein complex, as well as using click chemistry and in silico chemical engineering to produce parthenolide derivatives with improved potency, which will then be tested in cell experiments at the University of Copenhagen. This research will reveal how parthenolide works and identify promising candidates for developing more effective, targeted cancer therapies.

For further information about this HALRIC pilot project, please contact:

 

Nikolina Sekulić
University of Oslo
nikolina.sekulic@biotek.uio.no

Haptoglobin (HP) is a protein mostly made in the liver that binds to free hemoglobin (the part of red blood cells that carries oxygen). When HP binds to hemoglobin, it helps remove this potentially harmful substance from the blood, protecting the kidneys during the breakdown of red blood cells¹.

There are different forms of HP in humans, leading to three main types², which are linked to various diseases, including type 1 diabetes³ and inflammatory bowel disease (IBD)⁴. Recently, researchers discovered that the precursor to haptoglobin, called pre-haptoglobin-2 (or zonulin), is important for celiac disease⁵ – an autoimmune disease where ingestion of gluten causes an abnormal immune response. It is estimated to affect about 1% of the world population and there is currently no cure, with the only treatment being a life-long gluten-free diet.

This HALRIC pilot project is a new collaboration between researchers in Hamburg and Aarhus and it offers an opportunity for the structural characterization of targets using an integrative structural biology approach. The goal of the project is to study the structure of zonulin and understand its roles better, including:

1) Using cryogenic electron microscopy (cryo EM) to structurally characterise the oligomeric assemblies of zonulin.
2) Validate the role of zonulin in celiac disease by performing an ELISA assay on serum.
3) Continue ongoing efforts to crystallise and determine the structure of full-length zonulin.

The University Medical Center Hamburg-Eppendorf (UKE) also joins as co-proposer to assess the clinical relevance of zonulin and its potential role as biomarker in IBD.

For further information about this HALRIC pilot project, please contact:

 

Jialing Song
DESY
jialing.song@desy.de

References:

1. Biochem Mosc Suppl B Biomed Chem., 15(3): 184–198 (2021)
2. Gen. and Mol. Biol., 31, 3,602-620 (2008)
3. J Autoimmun., 122:102674 (2021)
4. J Clin Med 2021; 10: 3905
5. PNAS, 106(39):16799-804 (2009)

This HALRIC pilot project brings together a new cross-border team with expertise in virology, bioinformatics, structural biology and immunology, as well as clinical and industrial experience. Together, they will explore the diagnostic and therapeutic potential of bispecific antibodies (bsAbs), which could lead to new ways of diagnosing and combatting coronaviruses (CoVs). CoVs are a family of RNA viruses that cause a variety of diseases, and they have a well-documented potential to cause epidemics. A key feature of CoVs is their variable and immunodominant spike (S) protein, which has undergone significant genetic changes that allow it to evade antibodies.

In response to the challenge of targeting CoVs with traditional monoclonal antibodies, the concept of using bispecific antibodies (bsAbs) that can bind to two different epitopes simultaneously has been proposed as a more efficient approach than traditional monoclonal antibodies. This research project aims to determine the neutralising potential of a panel of bsAbs towards human CoVs, and to visualise their structure and interactions with the S protein at an atomic level.

To ensure that the most potent bsAbs have the potential for future clinical and/or diagnostic use, the project will bring together a new, dedicated, translational team of virologists, structural biologists, immunotechnologists and clinicians to create synergistic effects that will increase the feasibility of achieving the aims and ensure the connection between the findings of in vitro studies at the molecular virology and structural biology levels and clinical practice.

The research team anticipates that the results generated will provide new and deeper insights into the use of CoV-specific bsAbs, with potential implications for diagnostics, treatment, and preparedness for faster responses to future pandemics. Notably, this project marks the beginning of a new, highly translational collaboration in the Öresund-Kattegat-Skagerrak-Hamburg area.

For further information about this HALRIC pilot project, please contact:

Joakim Esbjörnsson
Lund University
joakim.esbjornsson@med.lu.se

Antimicrobial resistance (AMR) is a global threat that has been thoroughly documented by WHO, EPHA, OECD and the CDC. Although the response to this threat needs to be multifaceted, one important focus is the discovery and development of efficacious and safe antibacterial compounds.

This HALRIC pilot project is a new cross border collaboration between the Universities in Copenhagen and Oslo. It will use Nuclear Magnetic Resonance (NMR) to better understand how promising peptides interact with components of bacterial and mammalian membranes and components of the blood plasma (e.g., the abundant serum albumin).

Antimicrobial peptides (AMPs) constitute a rich source of potential novel antibacterial agents that often target the membranes of bacteria and act so rapidly that AMR development is severely limited. Moreover, most pathogenic bacteria appear to lack preexisting resistance to these compounds.

Through previous international collaborations the researchers have developed an extensive library of AMPs based on bacterial type I toxins. Using established empirical design rules, these peptides have been modified to increase their solubility and their capacity to interact with charged bacterial membranes. One disadvantage of AMPs is their toxicity towards human cells, in molecular terms this means that the AMPs interact with human cell membranes in a disruptive manner that may lead to breaking down the cell (lysis).

NMR spectroscopy is a powerful technique that can probe interactions as well as structural changes of biomolecules like AMPs over a wide range of affinities and timescales, respectively.

The pilot project connects experts in peptide synthesis, structural biology, AMR, and microbiology. The peptides are designed, synthesized and purified by the researchers and where applicable clinical bacterial strains from Oslo University Hospital, Rikshospitalet will also be used.

NMR investigations will be performed in the infrastructure facility cOpenNMR at the University of Copenhagen. Alongside these studies, structural changes in the peptides when they bind to the membrane will be assessed using circular dichroism spectropolarimetry (CD).

Invasive fungal infections (IFI) present a significant challenge for clinicians in a range of clinical settings, particularly in patients with a compromised immune system or following chemotherapy. They are associated with a high prevalence of illness and mortality.

Among the numerous therapeutic options, amphotericin B (AmB) is the most common drug used for the treatment of IFIs. AmB is the initial agent of choice in the clinic due to its efficacy against fungi and low resistance. However, its low solubility and permeability allows only intravenous administration, and the nephrotoxicity (kidney damage) of available AmB formulations limits its use to the most severe cases. Despite the first commercial formulation being approved in 1959, there are still only a few AmB formulations available on the market.

The cross-border research team from the Universities in Oslo and Copenhagen have highly complementary expertise within physical chemistry/soft matter and pharmacy. In this HALRIC pilot project they will focus on the development of a novel drug delivery system based on peptoids, biocompatible polymers that mimic peptides. The objective is to design and synthesize a series of sequence-defined poly(ethylene glycol) peptoid conjugates (PEG-peptoid) that will self-assemble into nanoparticles with an amorphous/crystalline dual core and optimize the process of AmB loading. The assemblies will be characterized using small-angle X-ray and neutron scattering (SAXS and SANS), UV-vis spectroscopy, and the drug release profiles will be determined in various conditions.

For further information about this HALRIC pilot project, please contact:

Szymon Mikolaj Szostak
s.m.szostak@kjemi.uio.no

Cancer cells often exhibit unusual sugar patterns on their surfaces, which play a central role in tumor development and progression. These sugar patterns, particularly sialic acids, prevent the formation of immune responses by natural killer (NK) cells and help tumors evade the immune system, allowing them to grow and spread.

This HALRIC Pilot project aims to engineer polyelectrolyte microcapsules for targeted enzyme delivery in cancer cells. The goal is to selectively remove sialic acids from tumor cells, thereby unmasking them to the immune system and enhancing NK cell-mediated killing.

The research team of this HALRIC pilot project consists of experts from Malmö, Lund, Århus, and Copenhagen. Together, they bring their expertise to engineer polyelectrolyte capsules, analyze their internal structure, study the interactions within the capsules, and test their release efficiency in different cancer cell lines, e.g. originating from breast and ovarian tumors.

Preliminary data on the internal structure of the capsules, including their pore size and polydispersity, will be obtained using small-angle X-ray scattering (SAXS) at Malmö University. This data will be further validated at the CoSAXS beamline at the MAX IV Laboratory. Time-resolved experiments, such as enzymatic release over periods ranging from minutes to hours, will also be conducted at the CoSAXS beamline.

The composition and structural characteristics of the capsules will be determined using low-frequency Raman (LFR) spectroscopy. Finally, cryogenic transmission electron microscopy (cryo-TEM) will be employed to image the capsules, providing additional data to complement and cross-validate the SAXS findings.

For further information about this HALRIC pilot project, please contact:

Yulia Sergeeva, Malmö University
yulia.sergeeva@mau.se

This HALRIC pilot project aims to identify new potential drug candidates and enzyme inhibitors using an innovative method of soaking small molecules into crystals of target proteins. The project focuses on two specific targets: SP3, an enzyme that degrades polyurethanes, and LAR, a protein involved in synapse formation and associated with psychiatric disorders.

In collaboration with the FragMAX team at the MAX IV Laboratory, the Thirup lab at Aarhus University (AU) will employ high-throughput X-ray diffraction to screen for fragments in crystals of the target molecules. This collaboration introduces a novel approach to the Thirup lab, utilizing the FragMax facility and the advanced Eiger2 CdTe detector at BioMAX for enhanced data collection. For this purpose, a researcher from AU will prepare high-purity samples of SP3 in collaboration with a group at the Technical University of Denmark (DTU).

The established protocol from the Thirup lab will be used to produce the required amounts of LAR. The project will utilize libraries containing a total of 1140 compounds for fragment soaking experiments, with data collection and processing supported by the BioMAX beamline team. Ultimately, the analysis of the screening results will be performed jointly by the research team, providing new insights into potential drug candidates and improving the functionality of plastic-degrading enzymes.

The project has two distinct goals using the Fragment-Based Drug Design approach:

1) LAR Protein: To map pockets and cavities on LAR, facilitating the design of drugs for treating psychiatric disorders.

Figure1. Virtual drug screening results on LAR FN III domain 1-2 depicts small molecules (yellow spheres) targeting two shallow cavity/pocket on LAR.

2) SP3 Enzyme: To map the active and binding sites on SP3 and its homologs, understanding enzyme-plastic interactions. This knowledge will aid in protein engineering to enhance the enzyme’s activity in degrading polyurethane plastics, which are difficult to recycle.

Figure2. Crystals structures of Polyurethane plastic degrading enzyme SP3 (green) and two thermostable homologs (gray and orange) determined by collaboration with J.P. Morth at DTU. Active site residues based on evolutionary conserved sequence is highlighted as sticks.

For further information about this HALRIC Pilot Project, please contact:

 

Deniz Bicer
Aarhus University
Deniz09@mbg.au.dk

The ability of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) in proteins to self-associate is a vital mechanism for the formation of membrane-less organelles and cell structures. The self-association of IDPs play crucial roles in several cell functions, including immune response, genome organization, transcription, and neuronal signaling. On the other hand, several proteins that self-associate are also involved in neurological diseases, where they form toxic aggregates; these diseases include Alzheimer’s disease and Parkinson’s disease. The mechanisms behind IDP-mediated self-association still need to be better understood.

This is a continuation of the HALRIC project, which has been combining scattering and imaging techniques at European XFEL in a proof-of concept study with no established routines for processing and analyzing data. The results are expected to constitute a significant step towards deciphering the structure-function relationship of IDPs, which is vital for developing the next generations of pharmaceuticals, such as antibiotics, i.e., antimicrobial peptides. The latter aligns with the European Union’s sustainability goal for Agenda 2030. An expanded project team now wants to tune in on this data management of the large amount of data obtained in the HALRIC experiments with more extensive computer simulations at both LUNARC and the National Academic Infrastructure for Supercomputing in Sweden (NAISS).

For further information about this HALRIC pilot project, please contact:

Marie Skepö, Lund University
marie.skepo@compchem.lu.se

The World Health Organization (WHO) has reported that multidrug-resistant (MDR) bacteria cause 1.27 million deaths yearly worldwide. The yearly mortality rates are estimated to increase to 10 million in 2050 if no action is taken to develop new antibiotic formulations*. Colistin, belonging to the class of antimicrobial peptides, is an effective antibiotic for many different gram-negative bacteria but is also found to be toxic to the kidneys. If colistin’s toxicity issues can be resolved, it could be an effective option to combat MDR bacteria. One of these options could be in the form of encapsulation. The research team already investigated how colistin can be combined with PEO-b-PMAA block copolymers to create nanoparticles, known as complex coacervate core micelles (C3Ms), in which colistin is effectively encapsulated and protected.**

This HALRIC pilot project aims to elucidate the detailed internal structure of the nanoparticles and its dynamics by using small-angle neutron scattering (SANS) at large-scale infrastructures in combination with small-angle X-ray scattering (SAXS) and dynamic light scatttering (DLS) at local infrastructures at  Aarhus University (AU) and the University of Oslo (UiO). The structure and exchange kinetics, i.e., the lifetime of a single component in micelles, are important characteristics for a better pharmacologic understanding. Through the collaboration of SAXS/SANS modelling expertise between AU and UiO, the pilot project team will analyze these structures in detail using an (unpublished) core-shell SAXS/SANS model that will be specially developed for this project.

In previous work at UiO, the researchers demonstrated that these micelles are well-defined and stable. In the micelles, the positively charged colistin and the negatively charged PMAA form the core, while the PEO forms an outer protective shell. Using SAXS, the researchers elucidated the general structure and composition of these C3Ms but could neither resolve the internal structure nor the distribution of the drug, which inspired the work that is now carried out in this HALRIC pilot project.

For further information about this HALRIC pilot project, please contact:

Thomas Vogelaar
t.d.vogelaar@kjemi.uio.no

References:

* Tacconelli, E.; Carrara, E.; Savoldi, A.; Harbarth, S.; Mendelson, M.; Monnet, D. L.; Pulcini, C.; Kahlmeter, G.; Kluytmans, J.; Carmeli, Y.; Ouellette, M.; Outterson, K.; Patel, J.; Cavaleri, M.; Cox, E. M.; Houchens, C. R.; Grayson, M. L.; Hansen, P.; Singh, N.; Theuretzbacher, U.; Magrini, N. et al. Discovery, Research, and Development of New Antibiotics: The WHO Priority List of Antibiotic-Resistant Bacteria and Tuberculosis. Lancet Infect. Dis. 2018, 18 (3), 318–327. https://doi.org/10.1016/S1473-3099(17)30753-3.

** Vogelaar, T.D.; Agger, A.E.; Reseland, J.E.; Linke, D.; Jenssen, H.; Lund, R. Crafting Stable Antibiotic Nanoparticles via Complex Coacervation of Colistin with Block Copolymers. Biomacromolecules. 2024. https://doi.org/10.1021/acs.biomac.4c00337.

Structural information is essential for a molecular understanding of protein function, and invaluable for basic and applied science. Nevertheless, such possibilities have remained unexploited for many targets due to the challenges associated with determination of protein structures. The overarching goal of this HALRIC pilot project is to elucidate molecular structural information of a physiologically‐relevant membrane protein in isolation or in complex with pharmacological compound candidates, as assessed in different cellular environments.

The focus will be on the ion homeostasis target ClC‐1 that is essential for human health and is a highly attractive target in the treatment of for example autoimmune and neuromuscular diseases (1). Recent structural breakthroughs by the Gourdon and Tidow laboratories at the Universities in Lund and Hamburg will be utilized synergistically with MAX IV and DESY, as well as ILL with the potential for future usage of the ESS.

The work will aim for a spatial understanding of the how the so‐called CBS domains orchestrate the ClC‐1 function via a phenomenon referred to as ‘slow‐gating’, thereby shedding light on the basic principles and determinants that govern ClC‐1. Focus will be using SAXS/SANS solution scattering to directly evaluate the conformational changes of the CBS domains, or to guide cryo‐EM experiments. Positive results have the potential to assist ongoing development of therapeutic intervention of severe disorders conducted by NMD Pharma in Aarhus, and to permit downstream similar initiatives to improve human health.

For further information about this HALRIC pilot project, please contact:

viktoria.baagenholm@sund.ku.dk
University of Copenhagen

pontus.gourdon@med.lu.se
Lund University

Reference:

1. Pedersen et al. Acta Physiologica 2021;233:e13690

This HALRIC pilot project investigates the intricate process of protein interactions in Parkinson’s disease (PD) by studying a phenomenon called the “protein corona” (PC) formed around clumps of proteins known as Amyloid fibrils (AF). These AFs are associated with the development of PD and can interact with various proteins in the brain and blood, potentially influencing disease progression. The lack of insights into interacting proteins hinders progress in diagnosis, treatment, and interventions.

To achieve this, the cross-border research team, with members from Denmark and Sweden, brings together expertise in protein biophysics, neurology, mass spectrometry analysis, and zebrafish research facilities. These diverse skills allow the team to comprehensively study the interaction between AFs and proteins found in brain tissue, cerebral spinal fluid (CSF), and blood plasma samples from both healthy individuals and PD-diagnosed patients.

The Technical University of Denmark (DTU) focuses on capturing and profiling the PC formed around AFs from samples obtained from Bispebjerg Hospital (BH). Expertise in quantitative and clinical proteomics at Lund University (LU) is further enhancing the researchers’ understanding of the protein interactions involved in PD. Additionally, the collaborative efforts extend to Aarhus University (AU), with the utilization of zebrafish embryos as a model organism to study neuroinflammation processes in real-time.

Through this interdisciplinary approach and leveraging internationally recognized infrastructure and expertise, the pilot project aims to unravel the complex interplay between polymorphic AFs, the protein corona, and neuroinflammation in PD. Ultimately, the findings hold significant potential for advancing the development of novel therapies and diagnostic strategies for neurodegenerative diseases like Parkinson’s.

For further information about this HALRIC pilot project, please contact:

Hossein Mohammad‐Beigi
DTU Bioengineering
hosmbe@dtu.dk

This HALRIC pilot project investigates the complex process of protein-rich food digestion through a multiscale approach integrating scattering and microscopy. Pea proteins, often marketed as hypoallergenic, merit a closer examination due to allergenic potentials arising from proteins with structural similarity to soy and peanut proteins.

Large-scale facilities play a pivotal role in enabling the study of the structural evolution of food during digestion, allowing sufficient kinetic resolution and high-quality data to collect information on conditions of increased or obstructed digestion.

The research team will integrate small-angle scattering and microscopy within a microfluidic device, offering unique insights into the microstructural transformations during digestion. The influence of processing on pea allergenicity, while not fully explored, presents intriguing possibilities, hinting at potential improvements in digestion.

Leveraging cross-border collaboration and diverse infrastructures, the work plan spans preliminary experiments at Malmö University, time resolved SAXS at CoSAXS (MAXIV), and SEC-SAXS experiments at EMBL P12 beamline (DESY) in Hamburg. In order to probe the soluble protein fraction released during digestion, spectroscopic experiments and biochemical assays will be performed as well. Eventually complementary imaging techniques, such as confocal laser microscopy, will be used to explore microscale aggregates behavior upon digestion. This endeavor extends beyond food science, holding potential for tailored food design and even immunotherapy.

For further information about this HALRIC pilot project, please contact:

Davide Schirone
Malmö University
davide.schirone@mau.se

Breast cancer is one of the leading causes of mortality in the female population. Despite improvement in procedures and treatment, drastic increases in survival rates are still lacking. The overall aim of this project is to use structure- based drug design to improve the inhibitors targeting specific aquaporins (AQPs), a family of proteins that facilitate the transport of water/glycerol and hydrogen peroxide across the cell membrane.

Cancer invasion and metastasis are known to be potentiated by the expression of AQPs and likewise, the expression levels of AQPs have been shown to be prognostic for survival in patients and have a role in tumor growth, angiogenesis, and tumor cell migration. Thus, AQPs are key players in cancer biology and potential targets for drug development. Pharmacological modulators of AQPs have been identified and tested for therapeutic potential, however, the drug discovery process has been severely hampered by the lack of three-dimensional structures of AQPs in complex with inhibitors.

The so called ‘resolution revolution’ in single particle cryo-electron microscopy (cryo-EM) has opened the door for determination of high-resolution structures of previously intractable biological systems based on the reduced requirement for both quantity and homogeneity of samples. Thus, these developments facilitate the possibility to execute structural studies of integral membrane proteins, like AQPs, in complex with putative drugs that was previously very challenging. As AQP3-mediated H2O2 transport has been shown to be important for breast cancer cell migration, the research team aims to investigate the potency of AQP3 inhibitors in a breast cancer model and determine the structure of these inhibitors in complex with AQP3 applying cryo-EM.

The pilot project has a unique cross-border composition to enable the possibility to use cryo-EM to execute structural analysis of aquaporin inhibitors and validate those in breast cancer models. The research team is composed of experts in the structural biology of aquaporins on the Swedish side at Lund University and of experts in cryo-EM analysis as well as in breast cancer and in vitro models of breast cancer at Aarhus University on the Danish side. Furthermore, the industry partner Apoglyx AB develops aquaporin blockers to be used as therapeutics and the company will bring a focus on translating academic results concerning AQP inhibitors into therapies for human conditions with high unmet medical needs.

For further information about this HALRIC pilot project, please contact:

Karin Lindkvist
Lund University
Karin.Lindvist@med.lu.se

Raminta Venskutonyte
Lund University
Raminta.Venskutonyte@med.lu.se

Surgery is the primary cancer treatment, aiming for complete tumor resection with adequate margins of healthy tissue. Inadequate margins are a common problem during surgery, which significantly increases the risk of local recurrence and the need for additional treatments. Another dilemma during surgery is to assess whether there has been a microscopic metastatic spread of cancer cells lymph nodes near the tumor, which cannot be seen on preoperative imaging and will require the surgery to be more expansive.

Micro-computed tomography (micro-CT) shows promise for use in oral cancer. This technique, documented in studies on breast cancer, aims to bring enhanced precision to tongue tumor resections, potentially improving surgical outcomes and patient care ^[1-3].

To enhance surgical outcomes through better margin assessment, the pilot project will use micro-CT for tumor segmentation and assessment of surgical margins. This will include research to compare the accuracy of micro-CT with 3D ultrasound and evaluate resection margins and lymph node metastasis after surgery for head and neck cancer.

The pilot project underlines the potential of hospital-university collaborations in advancing medical technology. The proposed pilot study could lay the foundation for integrating micro-CT in hospital settings, potentially revolutionizing cancer treatment methods.

The research team will perform a synchrotron X-ray tomographic microscopy at MAX IV and 3D ultrasound scan of surgical specimens ^[4,5] at DTU, which surgeons at Rigshospitalet have removed from patients with oral squamous cell carcinoma (SCC). Following the scans, the smallest margin will be measured by three experienced head and neck surgeons on the 3D ultrasound images and micro-CT data. This imaging approach aims to optimize surgical precision and potentially reduce the need for follow-up treatments in the future.

For further information about this HALRIC pilot project, please contact:

 

Tobias Todsen
Rigshospitalet
Tobias.Todsen@regionh.dk

 

Fatemeh Makouei
Rigshospitalet
fatemeh.makouei@regionh.dk

This project focuses on experiments that will serve as a basis for understanding a family of proteins that are of utmost importance for human health. Recently, it has been shown that ~30% of all proteins in eukaryotic organisms* belong to intrinsically disordered proteins (IDPs) and that these are involved in many central biological processes and diseases.

The collaboration in this pilot project, between Lund University in Sweden and the European XFEL facility in Hamburg, Germany, is new and will enable the researchers to widen their horizons beyond their specialties since it will combine SAXS, FEL-SAS/SPI**, and atomistic computer simulations across the Öresund-Kattegat-Skagerrak-Hamburg Region. With involvement by a postdoc and a PhD student the project will also contribute to educating the next generation of researchers.

The aim of the pilot project is to investigate the possibilities of using FEL-SAS and SPI EuXFEL to study IDPs with the Histatin 5 saliva protein as a model. The research group foresee that the use of FEL-SAS/SPI to analyze IDPs and its conformational ensemble can serve as a proof-of-concept study. The results are expected to constitute a significant step towards deciphering the structure-function relationship of IDPs, which is vital for developing the next generations of pharmaceuticals, such as antibiotics, i.e., antimicrobial peptides. The latter aligns with the European Union’s sustainability goal for Agenda 2030.

For further information about this HALRIC pilot project, please contact:

Marie Skepö
Lund University
marie.skepo@compchem.lu.se

References:
*The definition of eukaryote organism is one that possesses a clearly defined nucleus (www.britannica.com)
** SAXS (Small Angle X-ray Scattering) // FEL-SAS (Free Electron Laser – Small-Angle Scattering) // SPI (Single-Particle Imaging)

This project focuses on drug discovery in the context of protein aggregation mechanisms linked to Alzheimer’s disease (AD). In collaborating with Prof. Jan Skov Pedersen from Aarhus University (AU), the Klementieva group at Lund University plan to examine how dendrimers, nonlinear polymers, bind amyloid proteins. The ultimate goal is to find a formulation of dendrimers that will protect neurons against amyloid toxicity.

The methodology involves infrared spectroscopy (Klementieva group, Medical Microspectrocopy Lab, MMS), circular dichroism (synchrotron ISA, Aarhus, Denmark), small-angle X-ray scattering (MAXIV, Co-SAXS, and Jan Skov Pedersen Lab), and transmission electron microscopy (LBIC) to analyze the structures of dendrimers in the presence of amyloids.

Anticipated outcomes include the development of molecular and polymer-based models of dendrimers, which will guide efforts to enhance the specificity of dendrimers for targeting amyloids. That will help to advance the understanding of the interaction between dendrimers and amyloids, ultimately contributing to the manipulation of dendrimers’ neuroprotective properties.

For further information about this HALRIC pilot project, please contact:

Oxana Klementieva,
Lund University
oxana.klementieva@med.lu.se

Pathogenic bacteria cause life threatening infections in animals and humans. Bacterial resistance towards antibiotics, which are used for treatment of bacterial infections, is one of the top three health threats identified by the European Commission in 2022. Light microscopy is an established powerful technique used to investigate how pathogenic bacteria physically interact with human host cells, whereas little is known about their metabolic interaction i.e., how do the bacteria fuel their energy needs inside the human cell?

Combining information on host-pathogen interaction from light microscopy with and metabolic information from Nuclear Magnetic Resonance (NMR) can increase the understanding of how invading bacteria fuel their proliferation and in extension suggest new ways to treat infections. The technology which will allow combination of light microscopy and metabolic studies with NMR is currently missing. This project will therefore develop a microfluidic chamber, which is needed to bring the two technical modalities closer together.

The project will be performed as a collaboration between the Center for Hyperpolarization in Magnetic Resonance (HYPERMAG) at the Technical University of Denmark, the Center for Structural Systems Biology (CSSB) in Hamburg and a newly established start-up company (JD Coils) in Hamburg.

The interdisciplinary project brings two scientific fields together which are normally separated by technical barriers. HYPERMAG is specialized on the application of hyperpolarization to NMR and MRI, with a world class infrastructure including three NMR spectrometers and three polarizers dedicated exclusively to dDNP research. CSSB is a leading center for live cell and correlative light and electron (cryo-)microscopy, with state-of-the-art light and fluorescence microscopes.

The partners have a common interest in providing new technology to aid the search for new targets against antibiotic resistant bacteria and the project has immediate innovative potential, which is emphasized by the participation of JD Coils.

For further information about this HALRIC pilot project, please contact:

Pernille Rose Jensen
Technical University of Denmark (DTU)
peroje@dtu.dk

About 1 in 5 adults will experience an ischemic stroke in their lifetime and its incidence is increasing with the ageing population. One of the main causes of ischemic stroke, a sudden stoppage of blood flow in a brain region, is a blood clot in the arteries due to thrombosis. The current treatment modalities are based on lysing the clot with a protease called tissue plasminogen activator (tPA) or removing the clot by surgical procedures (1). In spite of these treatment possibilities, this condition is a major cause of disability and mortality.

To address this unmet need the research team has identified a blood protease called Factor VII activating protease (FSAP) as a possible treatment for ischemic stroke (2). FSAP circulates in the blood as an inactive enzyme in its zymogen form. Exactly how it is activated is not clear, but extracellular free histones released after tissue damage, NETosis or inflammation are likely to be involved. Moreover, the researchers have identified a synthetic cyclic peptide that can also activate this enzyme (3). We hypothesize that activating the zymogen form of FSAP, that is already in the blood, could also be a means of treating ischemic stroke. However, to test this hypothesis we need to understand the detailed mechanism of how the zymogen form of FSAP is converted into an active enzyme and this is the goal of the planned project.

For further information about this HALRIC pilot project, please contact:

Sandip Kanse
University of Oslo
sandip.kanse@medisin.uio.no

References:

1. Campbell et al, Nature Rev Dis Primers, PMID: 31601801
2. Kim et al, 2022, FASEB J, PMID: 36165219
3. Berge-Seidl, 2022, ACS Chem Biol, PMID: 36070465

Atherosclerosis is the major cause of cardiovascular disease (CVD) and responsible for ~40% of all deaths in developed countries, with increasing prevalence due to sedentary lifestyles, obesity and metabolic syndrome. The disease is characterized by the formation of complex plaque within the arteries which can lead to fatal complications due to plaque rupture and thrombosis.

Inflammation within the atherosclerotic plaque causes remodeling of the extracellular matrix (ECM) proteins which are responsible for maintaining the structural integrity of the plaque. Enzymes which degrade ECM proteins are associated with disease and increased expression correlates with adverse outcomes. Previous studies have relied on bulk tissue samples, where whole plaques are homogenised prior to proteomic analysis. However, plaques are highly heterogeneous, with increased expression of inflammatory mediators in the shoulder region of the plaque. It is therefore crucial that we understand the dynamics in these tissue microenvironments to identify the mechanisms and potential markers of plaque rupture.

This project will characterise proteomic changes within human atherosclerotic plaques, both at the bulk level and spatially within the tissue microenvironment. By unraveling the complex landscape of spatial protein dynamics within the plaque, this work may offer transformative insights into cellular processes and disease mechanisms of atherosclerosis.

For further information about this HALRIC pilot project, please contact:

Luke F. Gamon
University of Copenhagen
lgamon@sund.ku.dk