Probiotics targeting Staphylococcus aureus toxin production in atopic dermatitis

Grantee: Hanne Ingmer, Professor, University of Copenhagen

Amount: DKK 2,681,665

Grant category: Research grants in open competition

Year: 2020

Geography: Denmark

Patients with atopic dermatitis (AD) are often colonized by the bacterial pathogen, Staphylococcus aureus (S. Aureus). S. aureus produces a large variety of toxins that contribute to the severity of AD and expression of these toxins is controlled by a cell-cell communication process called “quorum sensing”.  

Professor Ingmer and her team has previously demonstrated that some bacteria produce signaling molecules, which in S. aureus abolish toxin production through repression of quorum sensing and preliminary analyses indicate that probiotic bacteria also belong to this group. 

Thus, the goal of this project is to deliver results addressing the efficacy of probiotics. The project proposes that probiotic bacteria can reduce S. aureus toxin production and that some of the reported benefits of probiotics in AD may be associated with such activity. 

Professor Ingmer will address this hypothesis in collaboration with Statens Serum Institut, the LEO Foundation Skin Immunology Research Center, UCPH and Department of Drug Design and Pharmacology, UCPH. 

Understanding the importance of cIAPs as NF-κB molecular switches in psoriasis

Grantee: Vasileios Bekiaris, Associate Professor, Technical University of Denmark

Amount: DKK 2,815,499

Grant category: Research grants in open competition

Year: 2020

Geography: Denmark

Psoriasis is an inflammatory disease characterized by overproduction of tissue-damaging cytokines by immune cells and keratinocytes. Central cytokines in psoriasis are TNF (tumor necrosis factor) and IL-17 (interleukin 17), which are currently approved therapeutic drug targets. To improve current therapies targeted towards TNF and IL-17, it is important to better understand the biology of the two cytokines in relation to psoriasis.  

The goal of this project is to confirm that two enzymes known as cIAPs (cellular inhibitors of apoptosis proteins) play a central role in psoriasis.  

The two cIAPs are believed to modulate the response of the immune system and of keratinocytes to TNF in order to fine-tune IL-17 production. The project will investigate whether lack of the two cIAPs or their pharmacologic inhibition makes the immune response less pathogenic and reduces the pro-inflammatory nature of keratinocytes during psoriasis.  

Systemic effects of atopic dermatitis: Dysregulated immune responses to the intestinal microbiota

Grantee: Jeppe Madura Larsen, Senior Researcher, Technical University of Denmark

Amount: DKK 4,349,062

Grant category: Research grants in open competition

Year: 2020

Geography: Denmark

Atopic Dermatitis (AD) is a common inflammatory skin disease affecting 15% of children and 3-5% of adults. AD is associated with the risk for developing co-morbidities such as other atopic diseases (food allergy, asthma, and rhinitis) and infections. Co-morbidities are believed to occur because of functional changes in the immune system of AD patients, however, it remains unknown how these changes are established. Emerging experimental studies suggest the existence of a skin-gut immune axis, but the role for the gut remains largely unexplored in AD.

The goal of this project is to determine if AD changes the bacterial microbiota composition and function in the gut, alters the intestinal and systemic immune system, and increases the risk for food allergy co-morbidity via oral sensitization. The project hypothesizes that AD drives dysregulated immune responses to the gut microbiota, which in turn changes the immune system giving rise to atopic co-morbidities and risk for infections. In other words, it is envisaged that AD patients become “allergic” to the bacteria present in their intestine – leading to a “persistent allergic reaction” due to continuous presence of bacteria in the intestine.

The project will use a rat model of AD to investigate the hypothesis and perform a human case-control study to support the clinical relevance of the findings. Identification of bacterial drivers of persistent type-2 inflammation could open new avenues for the prevention and treatment of AD and related co-morbidities.

Deciphering the functional role of circular RNAs in psoriasis

Grantee: Lasse Sommer Kristensen, Associate Professor, Department of Biomedicine, Aarhus University

Amount: DKK 2,467,477

Grant category: Research grants in open competition

Year: 2020

Geography: Denmark

This project aims to answer key questions related to a recently discovered new class of biomolecules, called circular RNAs. These RNA molecules appear to have an important role in early immune responses and the project aims to functionally characterize them in psoriasis patients and compare the results with data from healthy controls.

To study the RNA molecules, the project uses a combination of traditional molecular biology approaches and high-throughput technologies such as RNA-sequencing and NanoString technology.

In summary, this project aims to shed light on the distribution and functional relevance of circular RNAs within psoriatic plagues as well as in normal skin and potentially open new avenues for better treatment and management of psoriasis.

Rapid Clinical Assessment of Skin Barrier Function by Corneocytes Nanotexture

Grantee: Edwin En-Te Hwu, Associate Professor, Technical University of Denmark

Amount: DKK 2,824,593

Grant category: Research grants in open competition

Year: 2020

Geography: Denmark

The goal of this project is to develop a clinically applicable imaging method for evaluation of atopic dermatitis (AD) development, progression and impact of therapeutic intervention.

It is known that AD is closely linked to the status of the skin barrier and therefore Edwin En-Te Hwu and his team will utilize a newly developed biomarker for skin barrier function, the Dermal Texture Index. This index is based on the number of circular nano-objects found on corneocytes (skin cells in the outermost part of the epidermis) of the skin by atomic force microscopy (AFM). However, the current analytical setup is both costly and has a limited throughput which makes it less suitable in a clinical setting.

The team has recently developed a new AFM technique and now aims to develop ‘Dermal AFM’, which will allow a ten times higher throughput in a clinically applicable unit. The unit may also help facilitate the understanding of the biology behind the observed corneocyte nanostructures.

The project is a collaboration between Denmark, Netherlands and Taiwan headed by DTU Health Technology.

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Unveiling AMBRA1 as a prognostic biomarker in in vivo pre-clinical models of cutaneous melanoma

Grantee: Daniela De Zio, Danish Cancer Society Research Center, Copenhagen

Amount: DKK 2,900,000

Grant category: Research grants in open competition

Year: 2019

Geography: Denmark

The survival rate of patients with advanced melanoma has improved in recent years due to the clinical application of immune checkpoint inhibitors, as well as kinase inhibitors in BRAF/RAS-mutated melanoma cases.

However, melanoma remains a fatal diagnosis as a consequence of emerging resistance mechanisms and the absence of reliable biomarkers that identify high-risk tumour subsets, therefore impacting the stratification of these subsets for novel adjuvant therapies.

In the search for novel oncosuppressors that are altered in melanoma, we have found a promising candidate in the protein called AMBRA1. AMBRA1 has a fundamental role in the positive regulation of autophagy – a process which can elicit both pro- and anti-tumorigenic roles. Additionally, AMBRA1 finely modulates other crucial oncogenic processes, such as cell proliferation, cell invasion, and cell death.

Our preliminary research in a mouse model of melanoma has proven Ambra1 to be a crucial oncosuppressor, whose expression has been found highly altered in a number of human melanoma cells. Thus, by applying melanoma cell and mouse models in combination with systems biology approaches and state-of-the-art technologies, we aim to decipher the response of Ambra1-deficient melanomas to the current therapies.

Moreover, we will investigate the role of Ambra1 in regulating lipid metabolism in melanoma, which has recently been shown to profoundly affect its progression. Additionally, our aim is to assess the prognostic relevance of AMBRA1 in human cohorts of melanoma patients and understand whether AMBRA1 expression correlates with disease progression and whether it influences treatment.

Outcomes from this project will pave the way for novel clinical insight into the prognosis and treatment of melanoma patients.

This project is co-supported by a Young Investigator award from the Melanoma Research Alliance (MRA) in the USA of 224,500 USD (https://www.curemelanoma.org/research/grants/).

Novel quorum sensing inhibitors for anti-virulence treatment of skin infections caused by pathogenic Gram-positive bacteria

Grantee: Professor Christian Adam Olsen, Department of Drug Design and Pharmacology, University of Copenhagen

Amount: DKK 2,110,500

Grant category: Research grants in open competition

Year: 2019

Geography: Denmark

Staphylococcal bacteria are the most common cause of skin and soft tissue infections (SSTI) and with the rise of methicillin-resistant Staphylococcus aureus (MRSA) minor infections can lead to severe medical conditions.

The increasing antibiotic resistance development demands the search for alternative medicines with differing profiles ranging from prophylactic treatment of small infections to combating life-threatening conditions.

In the present project, we aim to inhibit this quorum sensing through a novel concept and thereby develop pan-staphylococcal inhibitors that are capable of treating the virulence in skin infections without the use of antibiotics.

Targeting the virulence of a bacterial infection rather than the viability of the pathogen represents such an alternative, because it increases the chance of clearance through the human immune system and attenuates disease symptoms while minimizing the risk of emerging resistance.

The expression of virulence factors in Gram-positive bacteria, including staphylococci, is regulated through quorum sensing (QS), which is a mechanism that allows bacteria to change gene expression in response to cell density.

This cell-to-cell communication is mediated by the secretion and detection of molecules termed autoinducing peptides (AIPs).

Functional characterization of dermokine in epidermal differentiation

Grantee: Professor MSO Ulrich auf dem Keller, Department of Biotechnology and Biomedicine, Technical University of Denmark

Amount: DKK 2,603,579

Grant category: Research grants in open competition

Year: 2019

Geography: Denmark

Epidermal renewal and keratinocyte differentiation are pivotal for skin homeostasis and maintenance of the skin’s barrier function, which is impaired in inflammatory skin diseases.

Expression of dermokine, a member of the stratified epithelium secreted peptides complex, is highly upregulated under these conditions, but its functional contribution to epidermal stratification and differentiation remains largely elusive.

We have identified dermokine as a substrate of the wound- and tumor-related matrix metalloproteinase (MMP) 10 in vitro and in vivo, a proteolytic processing event that might play a role in maintaining the phenotype of transient amplifying keratinocytes in hyperproliferative epidermis.

In this project, we will characterize the activity of dermokine and analyze its putative function in keratinocyte differentiation. Using advanced proteomics, we will identify surface binding proteins for dermokine on keratinocytes. Newly identified dermokine-receptor interactions will be characterized and related to signaling pathways that are activated in response to dermokine binding.

To test the hypothesis that MMP10 modulates dermokine activity, we will analyze the full-length protein in comparison to a truncated mutant, resulting from MMP10 cleavage. This mutant will be characterized for altered effects on keratinocyte differentiation, binding to receptor candidates and activation of downstream signaling.

This study will provide insight into the function and mechanisms of action of dermokine in normal and hyperproliferative epithelia and add to current knowledge on MMPs as modulators of extracellular signaling ligands in the skin. Anticipated results will help to devise new strategies for therapeutic intervention with barrier defects in inflammatory skin diseases.

Exploiting the untapped potential of the dermis to provide novel insight into the function of the skin microbiome

Grantee: Assistant Professor Christopher James Barnes, PhD, Natural History Museum of Denmark, University of Copenhagen

Amount: DKK 2,388,289

Grant category: Research grants in open competition

Year: 2019

Geography: Denmark

The skin microbiome has been thought to be highly individual, a kind of ‘microbial fingerprint’.

Yet scratching beneath the surface with DNA metabarcoding different skin compartments, we have found considerably less variation in the bacterial communities of the dermal compartment compared to the outer epidermal, challenging this dogma.

Here, we will extend upon these findings by performing a more comprehensive shotgun metagenomic approach, assessing whether compositional differences in the dermal and epidermal microbiomes effect their functioning.

The invasiveness of biopsies has been a major limitation in sampling of dermal microbiomes. Tape-stripping is a minimally invasive technique that penetrates through the epidermal compartment to the barrier with the dermis, and here we assess whether tape-stripping can substitute biopsies in accessing the potentially more informative, less environmentally variable skin microbiomes.

Finally, we will compare the dermal microbiomes of healthy controls to patients suffering atopic dermatitis (AD). Sufferers of AD have been repeatedly shown to have a perturbed epidermal microbiome, but they also have perturbed immune systems. Here we perform shotgun metagenomic and metatranscriptomic approaches to test for functional differences between the microbiomes of AD patients and healthy controls.

Studying the differences between healthy and diseased dermal microbiomes may ultimately fast-track identifying influential microbes associated with diseases, and their function within them.

Towards the targeted phage-based nanodelivery of genome editing complexes to render pathogenic skin bacteria harmless

Grantee: Associate Professor Nicholas Taylor, Faculty of Health and Medical Sciences, University of Copenhagen

Amount: DKK 2,996,539

Grant category: Research grants in open competition

Year: 2019

Geography: Denmark

Bacterial skin infections are caused by bacteria that rely on several proteins to be infectious and resist antibiotic treatment. These proteins are encoded in the genome, or DNA, of the bacteria.

The specific knockout of these genes by genome editing has been shown to inhibit pathogenic bacteria, but delivery of the complexes that perform these modifications is still a major challenge.

To overcome this hurdle, we propose to use the large protein-injecting bacteriophage (a virus that can infect a bacterium) to inject a genome editing complex into bacteria. We will investigate the structure of the bacteriophage, to better understand which parts we can modify. We will exchange the recognition target of the bacteriophage, so that it can specifically bind to a bacterium of choice.

Additionally, we will modify the large protein of the bacteriophage that it normally injects, and replace it with a genome-editing complex: this will allow the targeted destruction of the DNA fragments in the bacterium that encode a protein that allows it to survive antibiotic treatment.