Deciphering the Role of Non-Coding RNAs in Epidermal Carcinogenesis

Grantee: Andor Pivarcsi, Senior lecturer/Associate Professor, Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala Universitet, Uppsala

Amount: DKK 4,164,300

Grant category: Research grants in open competition

Year: 2020

Geography: Sweden

The goal of this project is to investigate the potential role of long non-coding RNAs (lncRNAs, RNA molecules, which do not function through coding for protein, but by regulating other genes) in the development of the most common form of skin cancer with metastatic potential – Squamous Cell Carcinoma (SCC). Such RNAs are known to be key regulators of multiple cellular functions, tissue development and homeostasis, but their role in SCC is not clear. Andor Pivarcsi and his team have identified a group of long non-coding RNAs that have altered expression in this disease. As these lncRNAs may prove to be key players both in the development of cutaneous cancers and in the maintenance of normal skin homeostasis, they now want to investigate their function.

Andor Pivarcsi and his team will do so by defining the role and mechanism of action of selected lncRNAs by a combination of methods, including inhibiting them with anti-sense oligonucleotides, that will effectively prevent their association with natural binding partners. The results will improve our understanding of long non-coding RNAs in cutaneous malignancies and may pave the way towards improved antisense oligonucleotide-based skin cancer therapy.

Andor Pivarcsi is a former LEO Foundation Silver Award Winner (2010).

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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Targeting Aberrant STAT3 Signaling in CTCL

Grantee: Sergei Koralov, Associate Professor, NYU Langone, NY

Amount: DKK 2,676,248

Grant category: Research grants in open competition

Year: 2020

Geography: USA

The goal of this project is to elucidate the mechanism behind the beneficial effects of atovaquone, a well-tolerated anti-microbial drug, on the rare type of skin cancer – the T-cell lymphoma (CTCL). It is known that atovaquone inhibits malignant cells from growing and may induce cell death, but the precise mechanism(s) is not known.

Sergei Koralov and his team have previously developed an animal model of the CTCL disease and will use this along with cells from patients to investigate the effects of atovaquone. Specifically, they will look at how the drug affects the gene regulating protein STAT3 as hyperactivation of this has shown to be critically important in the development of cancerous T-cells.

Given the outstanding tolerability of atovaquone, it is believed that if its mode of action can be deciphered it may prove a powerful tool in the future for treatment of malignant and inflammatory diseases.

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/).

Heritability of dermoscopic patterns in melanocytic naevi; a twin study

Grantee: Emmanouil Chousakos, National and Kapodistrian University of Athens

Amount: DKK 40,400

Grant category: Research grants in open competition

Year: 2019

Geography: Greece

It is of the utmost importance for diagnosing melanoma on an early stage to identify high risk population groups, which will subsequently receive special screening and follow-up for their melanocytic lesions.

Managing patients with multiple naevi, including atypical mole syndrome patients, can be challenging for the clinicians, despite the introduction of dermoscopy, digital dermoscopy mapping and full body imaging in the everyday clinical practice.

The goal of this study is to prove the heritability of the dermoscopic pattern of melanocytic naevi. Evidence of a strong relation between the genome and the dermoscopic, hence histopathological image can be the fundament of a comparative approach among members of the same family in terms of evaluating their melanocytic lesions and their malignant potential. With this approach we will be able to establish a familial profile of the lesions.

Thermal Imaging in dermatology – Creation of the first database for artificial intelligence-based diagnostics

Grantee: Professor Alexander Navarini, Department of Dermatology and Allergy, University Hospital Basel

Amount: DKK 1,180,760

Grant category: Research grants in open competition

Year: 2019

Geography: Switzerland

Thermal imaging is an investigational tool whose advantages are undisputed in engineering, i.e. for the non-destructive testing of composite materials, or in the photovoltaic industry.

The technique consists in measuring and imaging the thermal radiation and to convert this information into temperature maps, or thermograms. Medical applications of thermal imaging exhibit great potential and the field is currently experiencing a renaissance. One reason is probably the recent dramatic improvements of infrared cameras that are now affordable and compact and can even be connected to smartphones.

This project aims to produce a full body thermal imaging scanner for patients to later use as a next generation diagnostic tool, coupled with a 360° 2- and 3-dimensional digital photography device.

Our goal is to create the first open access skin thermograms database, large enough to enable artificial intelligence analysis. Such a tool could be very useful for the quantification and potentially prediction of affected areas in different skin disease such as psoriasis and eczema.

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.