Single-cell ribosome profiling to monitor the translational landscape in skin wound healing

Grantee: Ataman Sendoel, Assistant Professor, University of Zurich

Amount: DKK 3,979,800

Grant category: Research Grants in open competition

Year: 2024

Geography: Switzerland

Ataman Sendoel’s project seeks to improve our understanding of how genes are translated to protein during wound healing and clarify the potential of the involved pathways as drug targets.

Impaired wound healing poses a substantial medical challenge, particularly among the elderly. Understanding the gene expression changes during wound repair is therefore essential for devising new strategies to enhance wound healing in aging and disease.

While transcriptional (i.e., going from DNA to messenger-RNA) control has been extensively studied in the skin, recent studies have indicated that cellular behavior is strongly coupled to the regulation of translation (i.e., going from messenger-RNA to protein). However, how translation is controlled during wound repair and how its deregulation mechanistically contributes to impaired wound repair in aging remains unknown.

In this project, Ataman Sendoel and his team will exploit an in vivo strategy to comprehensively map the function of the translational landscape in skin wound healing. Leveraging a single-cell ribosome (an intracellular protein complex that translates messenger-RNA to protein) profiling strategy in vivo, the team will monitor skin cells during different wound healing stages. By coupling this with single-cell RNA sequencing, they will determine cell-type-specific translational efficiencies and identify factors relevant to wound repair in aging.

Finally, Ataman Sendoel and his team aim to carry out a mini-screen to identify FDA-approved drugs that selectively increase the translational efficiency of skin wound repair factors.

Collectively, these data will provide systematic insights into the translational landscape of skin wound repair, and how deregulated translation leads to impaired wound repair. It may also clarify if protein synthesis pathways could be targeted therapeutically to restore wound healing.

Protein stability and misfolding in keratin disorders

Grantee: Rasmus Hartmann-Petersen, Professor, University of Copenhagen

Amount: DKK 2,600,678

Grant category: Research Grants in open competition

Year: 2024

Geography: Denmark

Rasmus Hartmann-Petersen’s project aims to characterize all possible missense variants (changes in genes which introduce a different amino acid in the resulting protein) in human keratins and investigate the importance of these variants in associated diseases.

Keratins are intermediate filament proteins that form a cytoskeletal network within cells. They are expressed in a tissue-specific fashion and form heterodimers, which then further oligomerize into filaments. Variants in several keratin encoding genes are linked to a range of hereditary disorders, including several epidermal skin diseases. On the molecular level, some pathogenic keratin variants appear to cause aggregation of the keratins.

In Rasmus Hartmann-Petersen’s project it is hypothesized that most keratin-disorders are protein misfolding diseases, i.e. diseases where the underlying genetic variants cause misfolding of the encoding protein. Rasmus and his team aim to explore this hypothesis by using computational tools, including large language models (a specific form of AI). They will test the validity of the computational predictions through focused cellular studies on selected keratins and identify components regulating keratin turnover.

The results will highlight the underlying molecular mechanisms for keratin-linked human disorders and provide predictions on the severity of all possible (both known and yet unobserved) coding variants in human keratin genes. The results could be of diagnostic value, but may also highlight the cellular protein folding and protein quality control machinery as potential therapeutic targets.

Architecture of the Herpes simplex replication machinery and its inhibitors

Grantee: Eva Kummer, Associate Professor, Copenhagen University

Amount: DKK 4,902,307

Grant category: Research Grants in open competition

Year: 2024

Geography: Denmark

Eva Kummer’s project targets to improve our understanding of the replication machinery of the skin-infecting herpes simplex virus (HSV) in order to improve and expand treatment opportunities.

HSV is one of the most widespread viral infections. The virus persists lifelong in the nerve system of the host and causes recurrent infections with mild to severe symptoms.

Since decades, treatment of herpes infections has exclusively targeted the viral replicative DNA polymerase (an enzyme that copies the viral DNA) using nucleoside analogs. However, resistance to current nucleoside analogs is emerging necessitating the search for alternative targets.

A major caveat in developing anti-herpetic compounds is a lack of structural information of other components of the herpes simplex replication system, which are likely strong candidates for targeted drug development. Eva Kummer and her team will use cryo-electron microscopy to visualize the architecture and working principles of the protein complexes that drive herpes simplex replication. They will also aim to clarify how novel anti-herpetic drugs block the viral replication machinery and why naturally occurring resistance mutations inhibit their action.

Overall, the project will generate structural and functional insights of the HSV replication strategy and potentially improve and accelerate anti-viral drug design.

SKINSTRUCT – Human skin structural cells instruct T cell tissue adaptation

Grantee: Georg Stary, Associate Professor, Medical University of Vienna

Amount: DKK 3,996,806

Grant category: Research Grants in open competition

Year: 2024

Geography: Austria

Georg Stary’s project aims to investigate interactions between T cells and structural cells, including keratinocytes, in the skin and how this cellular communication may affect the function of the T cells in dermatological diseases.

Human skin is protected by specialized T cells, called tissue-resident memory T cells (TRMs), which are needed to protect against infection at the site of pathogen encounter, but can also mediate inflammation in certain conditions. The exact regulation of TRMs in human skin is not well understood, hence TRM-targeted therapies are currently unavailable.

Georg Stary and his team have discovered that T cells communicate with structural cells of the skin via certain surface molecules and acquire a TRM phenotype after interaction with keratinocytes and fibroblasts. Some of the newly described molecules that instruct T cells to become TRM have not been implicated in the regulation of T cell tissue residency before.

Georg and his team aim to explore how structural cells of the skin instruct the maintenance of human TRM, and how this cellular crosstalk changes during inflammation. Based on preliminary data, they will unravel the function of certain co-receptors in TRM regulation using modern single-cell sequencing technologies on primary tissue from patients and ex-vivo co-culture systems with genetically engineered human cells. Based on this, they will subsequently test the therapeutic potential of targeting T cell-structural cell interactions in a humanized mouse model of TRM-mediated skin inflammation.

This study will not only inform about new mechanisms of human TRM instruction in health and disease and explore options for developing clinical applications targeting interactions with structural cells, but also form the basis for designing clinical studies to treat selected TRM-mediated diseases, such as graft-versus-host disease or psoriasis.

Endothelial senescence in the pathogenesis of systemic sclerosis

Grantee: Eliza Pei-Suen Tsou, Assistant Professor, University of Michigan

Amount: DKK 3,990,092

Grant category: Research Grants in open competition

Year: 2024

Geography: USA

The goal of Eliza Pei-Suen Tsou’s project is to understand the importance of aging endothelial cells (a cell type lining blood vessels) in scleroderma.

Scleroderma is an autoimmune disease characterized by inflammation, scarring of tissues and organs, including the skin, and changes in blood vessels throughout the body.

Most patients experience vascular abnormalities as one of the first symptoms, which trigger tissue stiffness and related complications later in the disease. Although these vascular changes are early critical events, the underlying cause of why they occur has not been determined.

Eliza Pei-Suen Tsou and her team found that dermal endothelial cells from scleroderma patients function differently compared to healthy controls. In particular, these cells undergo senescence, which is a process by which a cell ages but does not die off when it should. Over time, large numbers of senescent cells build up in the body. These cells remain active and release harmful substances that may cause inflammation and damage to nearby healthy cells.

In this project, Eliza and the team aim to determine the cause for vascular abnormalities in scleroderma, with a specific focus on how senescence is involved. They hypothesize that endothelial cell senescence is fundamental in causing the disease and might be targeted for therapy. Specifically, they propose that endothelial senescence accounts for the abnormality of endothelial cells in scleroderma, resulting not only in blood vessel changes but also in tissue scarring.

The goal is to determine why the endothelial cells acquire the senescent phenotype, and what this senescent phenotype does to promote the disease.

This project may form the basis for novel approaches to treating scleroderma.

Understanding structural and functional differences between JAK family JH1 and JH2 domains

Grantee: Christopher Bunick, Associate Professor, Yale University

Amount: DKK 4,165,955

Grant category: Research Grants in open competition

Year: 2024

Geography: USA

Christopher Bunick’s project aims to improve and substantiate our current knowledge of the structure and function of Janus kinases (JAKs) to improve safety and efficacy when developing new JAK inhibitors.

Janus kinase (JAK) inhibitors are small molecule drugs that treat inflammatory dermatological conditions by inhibiting cytokine signaling. Currently targeted diseases include atopic dermatitis, psoriasis, hand eczema, alopecia areata, vitiligo, and hidradenitis suppurativa.

Optimal JAK inhibitor matching to dermatologic disease remains challenging because of cross reactivity among four related JAK kinases: JAK1, JAK2, JAK3 and TYK2. Each possesses catalytic kinase (JH1) and allosteric (JH2) domains (an allosteric domain is a site where binding of a molecule indirectly modulates the function of the protein, here the catalytic activity). Both JH1 and JH2 domains have been targeted for drug development, yet a scientific knowledge gap exists as to how the allosteric JH2 domain regulates catalytic JH1 function and the subsequent downstream activation of signal transducer and activator of transcription (STAT) proteins.

A barrier for JAK inhibitor prescription is its promiscuity; it may target more than one JAK, leading to broader cytokine suppression than desired. This poor selectivity is likely rooted in suboptimal drug discovery procedures emphasizing inhibitory capacity over selectivity, resulting in unexpected real-world side effects, including malignancy, cardiovascular events, and thrombosis.

Christopher Bunick and his team will use AI-based generative modeling, molecular dynamics, computational biophysics, structural biology, and biochemistry to (i) determine how JH2 allosterically regulates JH1; (ii) define the structural basis for enhancing selectivity against specific JAK domains; (iii) elucidate downstream mechanisms regulating STAT signaling; and (iv) elucidate molecular properties of JAKs beyond JH1/JH2 domains.

This project may pave the way for better and safer treatment of skin diseases using JAK inhibitors.

Skin microbiome-metabolome modulation of skin homeostasis

Grantee: Julia Oh, Associate Professor, The Jackson Laboratory

Amount: DKK 3,953,521

Grant category: Research Grants in open competition

Year: 2024

Geography: USA

Julia Oh’s project aims to develop a novel and more physiological approach to studying how microbes interact with human skin cells and the effects of this interaction on overall skin health.

The human skin microbiome – encompassing hundreds of bacterial and fungal species – has essential roles in maintaining skin health. Skin microbiome dysfunction can contribute to diverse skin infections, inflammatory disorders, and skin cancer.

It is important to both identify the microbe–skin cell interactions that go awry in skin disease and to evaluate the therapeutic potential of new approaches for treating skin diseases. However, a detailed mechanistic understanding of how various skin microbes interact with human cells to maintain skin health or promote skin disease is currently lacking.

The goal of Julia Oh’s project is to determine how diverse skin microbes impact the essential functions of skin cells. However, there are few experimental models that allow us to investigate the diversity of skin microbes in a physiologically relevant way.

To enable a detailed investigation of microbe–skin cell interactions and their effects on skin health, Julia Oh and her team will model microbial colonization in cultured skin tissue that is genetically modified to investigate skin cell mechanisms. Then, using metabolomics and computational models, they will identify microbial metabolites to reveal microbial mechanisms.

This new approach could broadly enable biomedical researchers to determine how microbe–skin cell interactions impact skin functions, immunity, and susceptibility to diseases arising from microbial infection, and inform potential preventative and therapeutic strategies that harness the microbiome.

Targeted and localized skin inflammation as a potential immunotherapy against cancer

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

Amount: DKK 3,987,557

Grant category: Serendipity Grants

Year: 2023

Geography: Denmark

Vasileios Bekiaris will investigate how an observed adverse impact of a drug candidate in psoriasis may be converted to a potential treatment of cancer.

Vasileios Bekiaris and his team have been studying the mechanisms by which psoriasis is induced for several years, and their goal was to find ways to suppress it. They have discovered a molecule that is necessary for the generation and function of the immune cells responsible for causing psoriasis. Moreover, they have access to a drug that targets and neutralizes this molecule, and therefore they thought that it could potentially inhibit psoriasis. Contrary to what they expected, the drug induced inflammation and exacerbated psoriasis instead of treating it. It is known that for many cancers, inflammation promotes favourable protective immunity and helps the efficacy of immunotherapy. Using a mouse melanoma model, Vasileios Bekiaris and his team have managed to generate data suggesting that the pro-inflammatory drug could in fact suppress tumour growth.

Vasileios Bekiaris will therefore investigate the drug’s potential in cancer treatment and, if successful, may open possibilities for a new immunotherapy against skin cancers. Vasileios Bekiaris and his team also believe that this data will continue their contribution towards understanding how skin inflammation is mediated.

Curing Cutaneous Calcinosis (CUCUC)

Grantee: Beate Lichtenberger, Principal Investigator, Medical University of Vienna

Amount: DKK 2,757,196

Grant category: Serendipity Grants

Year: 2023

Geography: Austria

Beate Lichtenberger investigates the mechanisms behind cutaneous calcinosis caused by over-activation of Hedgehog signaling in the dermis to improve treatment options.

Cutaneous calcinosis (CUC) is a debilitating condition characterized by the abnormal deposition of calcium salts in the skin and subcutaneous tissues, leading to pain, impaired mobility, and disfigurement. Despite its significant impact on patient quality of life, effective therapeutic interventions for CUC remain lacking, and there is no model system to study the disease. Beate Lichtenberger and her team serendipitously discovered that over-activation of Hedgehog (Hh) signaling in dermal fibroblasts leads to calcium precipitates and inflammation in limb and tail skin of mice, recapitulating the human disease

Beate Lichtenberger will elucidate the underlying mechanisms driving calcium deposition, inflammation, and tissue damage in cutaneous calcinosis. Furthermore, she will perform single cell RNA sequencing (scRNA-Seq) of human CUC tissue to assess which cell types apart from fibroblasts contribute to the pathogenesis and how

By advancing the understanding of the pathogenesis of CUC and developing targeted therapeutic strategies like repurposing of existing Hh inhibitors, Beate Lichtenberger’s project has the potential to revolutionize the treatment landscape and significantly improve the lives of individuals afflicted by this condition.

Exploring the serendipitous connection between a mitochondria fission protein and melanosomes maturation

Grantee: Marta Giacomello, Associate Professor, University of Padua

Amount: DKK 3,885,368

Grant category: Serendipity Grants

Year: 2023

Geography: Italy

Marta Giacomello aims to elucidate the role of a newly discovered mitochondrial fission protein in organelle maturation by exploring its impact on melanosome development and lipid droplet formation.

Melanogenesis, the process of synthesis and storage of the pigment responsible for skin color, melanin, occurs at specialized cell organelles named melanosomes. The mechanisms underlying melanin synthesis are not fully understood, but recent data suggest that mitochondrial physiology influences melanogenesis. Marta Giacomello and her team discovered that a mitochondrial fission factor, serendipitously found at the melanosome-mitochondria interface, controls the size of early melanosomes and melanin levels independently of its role in mitochondrial morphology.

The team aims to demonstrate that the identified mitochondria fission factor is a common regulator of organelle maturation, which exerts its specific effect based on its subcellular localization and interaction partners. They will first investigate its role in melanosome maturation, and then to generalize its function by extending the analysis to lipid droplets.

By elucidating how the identified fission factor switches from its mitochondrial to its melanosomal function, Marta Giacomello may generate milestone findings in the field of melanogenesis, and proof-of-concept evidence for its general role as a master regulator of organelles’ fission and maturation. Potentially, the results of this project could lead to breakthroughs in the fundamental understanding of cell biology.