Phage therapy to treat group A Streptococcus in Necrotizing Soft Tissue Infection

Grantee: Thomas Sicheritz-Pontén, Professor, University of Copenhagen

Amount: DKK 3,988,469

Grant category: Research Grants in open competition

Year: 2023

Geography: Denmark

The project led by Thomas Sicheritz-Pontén from the Globe Institute at the University of Copenhagen, aims to carry out the fundamental work needed to develop targeted phage therapy (using bacteria-infecting viruses) to counter Necrotizing Soft Tissue Infections (NSTI).  This innovative treatment approach necessitates an in-depth understanding of the causative organisms, which will be achieved through sequencing these organisms and employing machine learning algorithms to predict their susceptibility to specific phages.

Necrotizing Soft Tissue Infections (NSTI), also known as “flesh-eating disease”, are rapidly escalating globally, posing a deadly bacterial threat that necessitates innovative therapeutic strategies due to its profound impact on human health. NSTI is characterized by aggressive skin manifestations primarily caused by Group A Streptococcus (Strep A). Although prompt surgery and antibiotics serve as the first-line treatment, infections often progress to necrosis, rendering antibiotics ineffective and often necessitating amputation and in worst case death.

Bacteriophages, or simply phages, offer a promising avenue to address this severe skin and soft tissue infection. Phages are viruses that selectively infect and eliminate bacteria, including antibiotic-resistant strains, without harming human cells.

Thomas Sicheritz-Pontén and team will do the fundamental work needed to identify prototype tailored phage therapies targeting Strep A. Along with his team, comprised of chief physicians from three different Danish hospitals, the UK Centre for Phage Research and the University of Copenhagen, Thomas Sicheritz-Pontén intends to identify phages capable of rapidly eradicating the bacteria, harness bacterial enzymes (endolysins), and employ phage satellites (mobile genetic elements that parasitize phages) for gene delivery.

By collaborating across research hubs, the team will decode Strep A’s genetic makeup, thereby facilitating the creation of precise phage cocktails and develop a novel molecular typing system to predict bacterial susceptibility, streamlining targeted phage treatments.

If successful, Thomas Sicheritz-Pontén’s project may greatly aid the battle against deadly NSTI infections through innovative development of phage therapy.

Programming dermal fibroblasts to stimulate hair follicle regeneration

Grantee: Peggy Myung, Associate Professor, Yale University

Amount: DKK 2,135,432

Grant category: Research Grants in open competition

Year: 2023

Geography: USA

Peggy Myung’s project aims to elucidate how two key molecular signals regulate the development of dermal condensate cells, a group of cells pivotal for hair formation.

The hair follicle dermal condensate (DC) is a cluster of quiescent dermal cells that can induce new hair follicle formation and holds the potential to revolutionize hair loss treatments. However, a key barrier to exploiting DCs to make new hair is that the molecular and cellular mechanisms that lead to DC formation are poorly understood.

Peggy Myung and her team recently identified two morphogen signals that are necessary and sufficient to drive DC formation. These two signals cooperate to unfold an initial stage of progenitor proliferation followed by a stage of cell cycle exit and DC maturation. Importantly, these stages of differentiation depend on levels of these two signals: Low levels induce progenitor proliferation; higher levels induce quiescence and DC maturation.

They hypothesize that different signaling levels regulate these stages of differentiation by inducing distinct signature genes that cause either DC progenitor expansion or terminal differentiation. They recently established a high-throughput dermal culture system to test this hypothesis. Using this novel platform and in vivo hair reconstitution assays, they aim to define how modulation of levels of these two signals regulates dermal gene expression profiles, cell cycle dynamics and DC function.

If successful, Peggy Myung’s project may define tunable molecular targets to develop novel treatments for hair loss and to make DC organoids for drug testing.

The ribotoxic stress response in inflammatory skin disease

Grantee: Simon Bekker-Jensen, Professor, University of Copenhagen, Center for Healthy Aging

Amount: DKK 3,823,440

Grant category: Research Grants in open competition

Year: 2023

Geography: Denmark

Simon Bekker-Jensen’s project investigates the potential role of the NLRP1 (Nucleotide-Binding Oligomerization Domain, Leucine Rich Repeat and Pyrin Domain Containing 1) inflammasome in combination with the upstream activator Ribotoxic Stress Response (RSR) in AD and psoriasis.

Inflammatory and hyperproliferative skin diseases, including atopic dermatitis (AD) and psoriasis, are associated with cascades of inflammatory events. A key player in innate skin immunity is the NLRP1 inflammasome, which mediates inflammation and cell death in response to a wide array of stress insults. In human keratinocytes, NLRP1 was recently shown by Simon Bekker-Jensen’s team and others to be activated by the Ribotoxic Stress Response (RSR) upon exposure to UV-B irradiation and a range of bacterial toxins.

Based on their preliminary data demonstrating that the RSR also mediates inflammation and keratinocyte hyperproliferation in vivo, the team hypothesize that these pathways have broader implications for the pathogenesis of inflammatory skin diseases.

In Simon Bekker-Jensen’s project, the validity of the RSR as a therapeutic target in the common inflammatory skin diseases psoriasis and AD will be explored. By genetic deletion and pharmacological inhibition of the RSR, the team will interrogate this pathway in several mouse models of inflammatory skin diseases. In addition, they will generate a humanized NLRP1 mouse model to study the RSR-NLRP1 signaling axis in vivo. Finally, by using 3D organotypic skin models and skin biopsies from patients, they aim to firmly establish the role of the RSR in psoriasis and AD.

The long-term goal is to leverage this insight to develop new therapeutic options for the management and treatment of inflammatory skin diseases.

Unravelling the diversity and function of skin-resident T cells

Grantee: Laura Mackay, Professor, University of Melbourne

Amount: DKK 3,826,119

Grant category: Research Grants in open competition

Year: 2023

Geography: Australia

Laura Mackay’s project investigates how tissue-resident T cell (TRM) populations in skin vary in development and function across body surfaces exposed to different environmental factors.

The generation of optimal immunotherapies requires effective T cell responses. Whilst some T cells patrol the blood, a unique subset called tissue-resident memory T (TRM) cells permanently exist within the tissues of the body. T cells that reside in the skin comprise distinct populations that differentially contribute to protecting the skin against disease.

The previous work of Laura Mackay and her team has demonstrated that different populations of skin-resident T cells in mice rely on separate molecular processes to function effectively. However, understanding of how human skin-resident T cells develop and control infectious insults and inflammatory disorders remains limited.

This project aims to determine skin TRM cell variation across the body, encompassing skin sites exposed to different environmental factors, such as sun exposure and hair follicle density, as well as in the context of disease. The team will seek to define the molecules that enhance skin-resident T cell function and survival, thus identifying factors that may prevent disease in healthy skin.

Overall, the aim is to generate fundamental new knowledge about the regulation of skin immunity and homeostasis. This knowledge is critical for the development of treatments and immunotherapies to harness T cell immunity for skin disorders.

Influence of dietary derived gut microbial metabolites on skin barrier and atopic dermatitis development in early life (Infant AD)

Grantee: Clarissa Schwab, Associate Professor, Aarhus University

Amount: DKK 3,910,741

Grant category: Research Grants in open competition

Year: 2023

Geography: Denmark

Clarissa Schwab’s project aims to investigate the role of switching from liquid to solid diet in the development of AD during infancy.

Atopic dermatitis (AD) is one of the first manifestations of allergic diseases that occur in early life. In industrial countries, up to 30% of children suffer from AD imposing an enormous burden to the quality of life and to health systems.

Not all factors contributing to the occurrence of AD are known, but the development of the gut microbiota in relation to a switch from liquid to solid diet during the first year of life might play an important role.

This project, ‘Infant AD’, suggests that a combination of specific food components and the appearance of certain gut bacteria is critical to producing gut metabolites that affect the immune system, and ultimately the state of the skin. To tackle such a complex system at the interface of diet, microbiome and the host, the concept of Infant AD is based on a unique combination of microbial and/or nutritional intervention studies using in vitro and in vivo models with state-of-the-art microbiome and metabolome analysis that will be supported by data collected from the Swiss birth cohort Childhood, Allergy, Nutrition and Environment (CARE).

Infant AD may shed further light on the complex interactions between diet, microbial activity and the immune system that could lead to novel measures to lower the risk of AD development in infancy.

Microbial impact on vitiligo development

Grantee: Caroline Le Poole, Professor, Northwestern University

Amount: DKK 2,979,828

Grant category: Research Grants in open competition

Year: 2023

Geography: USA

Caroline Le Poole’s project aims to investigate the potential link between the gut microbiome composition and vitiligo development.

The etiology of vitiligo involves a complex hereditary component, as well as environmental factors that precipitate disease. Caroline Le Poole and her team initially asked whether the gut microbiome impacts T cell-mediated autoimmune depigmentation. Manipulating the gut microbiome by oral antibiotics, they demonstrated a significant impact on vitiligo development in an established mouse model of the disease. Specifically, when using ampicillin to favor gut colonization by Pseudomonas species, they observed accelerated vitiligo development. Meanwhile, neomycin treatment was associated with an abundance of Bacteroides species in the gut, while mice in this group did not develop measurable depigmentation. These and other findings suggest that specific microbes can influence vitiligo development.

Here, they will test the hypothesis that the microbiome is a causative pathogenic factor fueling the autoimmune response to melanocytes causing the hallmark progressive depigmentation seen in vitiligo. The team will use mouse and human fecal transplants and manipulate the diet of vitiligo-prone mice. Moreover, individual microbial species will be introduced into germ-free mice before assessing depigmentation kinetics. Ultimately, therapeutic benefit may be derived from promoting the species that support regulatory T cell activity.

Striving to develop and implement culturally sensitive dermatologic care with the focus on eczema and psoriasis in the Cree Territory of James Bay (Eeyou Istchee)

Grantee: Ivan Litvinov, Associate Professor, McGill University Health Centre

Amount: DKK 3,074,290

Grant category: Research Grants in open competition

Year: 2023

Geography: Canada

Ivan Litvinov’s project aims to co-create with Indigenous partners and implement a culturally sensitive dermatological care system in the Cree territories in Quebec, one of Canada’s First Nations. Dermatologic care for Canadian Indigenous populations is severely lacking currently. While many safe advanced treatments are available for debilitating diseases, including atopic dermatitis that affects ~15-20% of First Nations in Quebec, these treatments are not accessible in the Northern remote regions due to a lack of established care.

Ivan Litvinov’s proposed implementation science project will be centered on meaningful engagement of patients, health care providers (HCPs) and wider communities, continuous monitoring, analysis, and feedback based on collected data to the members of the steering committee and to the Cree Health Board/Elders overseeing the effort with the goal of achieving the Quintuple Aim (improved patient experience, better outcomes, lower costs, clinician well-being and health equity) for the region.

Ivan Litvinov’s project will leverage the existing RUISSS (Réseau Universitaire Intégré de Santé et de Services Sociaux) infrastructure to establish in-person care in 3 key Cree communities and will 1) establish a Learning Healthcare System (LHS); 2) collect quantitative and qualitative data on skin diseases, barriers and treatments; 3) recruit and support healthcare professionals to the region to foster a community of practice and promote a community of concern amongst patients through Patient and Public Involvement, knowledge mobilization and educational activities.

The impact of the project will be a co-creation of a culturally sensitive sustainable dermatologic care in the region. Results of this work will be shared with other specialties working in the region, other First Nation communities in Quebec in Canada and in other countries (e.g., Greenland).

High-resolution identification of bacterial-host interactions in atopic dermatitis during flare development and treatment

Grantee: Blaine Fritz, Postdoc, University of Copenhagen

Amount: DKK 2,956,179

Grant category: Research Grants in open competition

Year: 2023

Geography: Denmark

Blaine Fritz’s project investigates the ongoing genetic changes and interactions between bacteria and patients’ skin during development of atopic dermatitis to identify novel putative treatment targets.

Atopic dermatitis (AD) is one of the most common skin diseases, affecting up to 20% of children and 10% of adults. AD presents as localized, itching patches of eczema, frequently first observed during childhood and often persisting throughout the patient’s life.

Dysregulated immune response, microbial imbalances, and skin barrier dysfunction are among several, interacting factors, which invoke and perpetuate AD. In up to 90% of patients, aggressive pathogens such as Staphylococcus aureus displace the protective microbiota of the skin resulting in reduced microbial diversity and increased lesion severity. Clinicians commonly utilize antibiotics to treat bacterial infection in AD, but the efficacy is unclear and antibiotic treatment increases the probability of resistance.

The mechanisms and specific gene targets involved in host-microbial interactions by both commensal (non-pathogenic) and infecting bacteria are not well studied. This project hypothesizes that both protective and pathogenic bacteria on the skin dynamically activate specific host-genes and pathways during progression of an AD flare. To test this hypothesis, Blaine Fritz will utilize an integrated, machine-learning-based approach to identify longitudinal (i.e., over time) changes in gene-expression associated with the presence of specific bacteria during flare and treatment to identify direct, host-microbial interactions.

The findings will aid in elucidating bacteria’s role in AD and may guide antibiotic treatment, as well as identify novel targets for antibiotic-independent treatments.

Dissecting the immunopathogenesis of Dermatitis Herpetiformis – a blistering skin disorder

Grantee: Ludvig Sollid, Professor, University of Oslo

Amount: DKK 3,996,277

Grant category: Research Grants in open competition

Year: 2023

Geography: Norway

Ludvig Sollid’s project aims to improve the understanding of the pathogenic immune responses in dermatitis herpetiformis and hereby design and investigate potential new therapeutics for the disease.

Dermatitis Herpetiformis (DH) is a chronic autoimmune bullous skin disease characterised by itchy blisters localised at specific surfaces of the body. DH can be considered a cutaneous manifestation of the gluten sensitive condition Coeliac Disease (CeD). The treatment for DH, as it is for CeD, is a life-long gluten-free diet and therefore novel treatments are sought for.

The diagnosis of DH is made by detection of granular IgA deposits in the dermis layer of the skin. These IgA deposits are immune complexes involving the autoantigen transglutaminase 3 (TG3) which is expressed in the epidermis, the outmost layer that sits above the dermis.

In this project Ludvig Sollid and his team aim to dissect the immunopathogenesis of DH, specifically addressing the mechanism for the generation of TG3 autoantibodies. Based on a model for the generation of autoantibodies to another transglutaminase (transglutaminase 2, TG2) in CeD, they will explore whether B cells carrying B-cell receptors isolated from DH patients, can bind complexes of TG3 and gluten peptides and thereby present gluten peptides to T cells so that T-cell help is provided.

Specifically, they will characterise the substrate binding site of TG3, identify the preferred gluten peptide substrates for TG3, and also characterise, in detail, the structural basis for binding of DH autoantibodies including antibodies that augment TG3 activity.

Based on these new insights, the team will design TG3 inhibitors which have potential therapeutic usage for treatment of DH along with a TG2 inhibitor which recently proved efficacious for treatment of CeD.


Non-Tuberculous Mycobacterial Skin and Soft Tissue Infections: Using a Site-of-Disease Approach to Understand Pathophysiology and Improve Outcome

Grantee: Arjan van Laarhoven, PhD, Radboud University Medical Center

Amount: DKK 3,987,136

Grant category: Research Grants in open competition

Year: 2023

Geography: Netherlands

Arjan van Laarhoven’s project aims to improve the treatment of patients infected with mycobacteria by looking at the patient’s individual immune responses to the infection and combining this with optimized treatment with antibiotics.

Non-tuberculous mycobacteria (NTM) can cause debilitating skin and soft tissue infections (SSTI). NTM SSTI incidence rises with an aged population and increased use of immunosuppression. These infections require treatment with multiple antibiotics for minimally 4-6 months. Still, non-response or worsening of skin lesions occurs frequently, because antibiotics fail or too much inflammation occurs.

Arjan van Laarhoven and his team hypothesize that differences in the patients’ immune systems, so-called ‘patient endotypes’, drive these diverging treatment courses. Currently, the involved immune processes in the skin are not identified for NTM SSTI. In addition, it is unknown what antibiotic concentrations in the skin are needed to kill the NTM.

In this study, the team will investigate the individual immune response in the skin of NTM SSTI patients by measuring the activity of genes in individual cells, and how these cells interact. They will compare this to the immune cells in the patients’ blood and will use the combined information to understand how patients differ in their immune response to the infection. These findings will be related to the clinical response to antibiotic treatment.

After eight weeks of antibiotic treatment, a second biopsy will be taken, in which measurement of the number of live mycobacteria and the local skin drug concentrations of azithromycin and clofazimine will be repeated.

By providing targets for optimizing treatment with both antibiotics and anti-inflammatory or immunostimulating drugs, this project aims to improve the outlook for NTM SSTI patients.