3rd Student Cohort

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) affecting more than two million people worldwide. The exact pathomechanisms have remained unclear and the disease is not curable to date. The histopathology of MS is characterized by inflammation, demyelination and axonal damage. Patients typically present with a wide and heterogeneous range of symptoms depending on the lesion localization, including visual, sensory, motor and cognitive deficits. Interestingly, about two thirds of patients also show gastrointestinal dysfunction, frequently even before the onset of CNS symptoms. We have previously demonstrated the degeneration of the enteric nervous system (ENS) in experimental autoimmune encephalomyelitis (EAE), which is the most common mouse model of MS. Besides the ENS the gut wall also contains several populations of immune cells, among them are the so-called muscularis macrophages that may play an important role in mediating local immune responses. It was recently shown that this population has anti-inflammatory properties and our initial data suggest that these macrophages express casein. So far, there are no studies that further elucidate the role of muscularis macrophages in the context of MS and in relation to ENS pathology. The aim of this project is to perform an in-depth immunological characterization of casein-expressing muscularis macrophages and to identify their functional role in the generation of local immune responses. To this end, a wide range of clinical-physiological, molecular and histological methods will be employed. Using established protocols of the Kürten lab in Bonn, we will induce EAE in wild-type and casein-deficient mice to analyze the function of muscularis macrophages in this particular neuroinflammatory environment compared to homeostasis. With results obtained during the first year in Bonn, we will use the expertise of the Furness lab in Melbourne to investigate ENS function both on the clinical and physiological level in casein-deficient healthy and EAE mice, which will be complemented by histological measurements performed in Bonn. 

Human pathogenic viruses present an ongoing global public health problem highlighted by continuing endemic infections and seasonal epidemics, as well as pandemics caused by newly emerging viruses. While host proteins play specific roles in normal cellular function, some of these proteins also display antiviral activity, and are termed host restriction factors. Host restriction factors can inhibit the infection and replication of different viruses at distinct stages in the viral life cycle. In general, the expression of host restriction factors during viral infection occurs following sensing of common pathogenic components via pattern recognition receptors (PRRs) and the production of type I interferons (IFNs). IFNs, in turn, activate hundreds of interferon-stimulated genes (ISGs) resulting in the inhibition of specific viruses, and some ISGs display a broad antiviral activity. SAM domain and HD domain-containing protein 1 (SAMHD1) is an intracellular dNTP triphosphohydrolase (dNTPase), while membrane-associated RING-CH-type finger protein 8 (MARCH8) is a family member of the RING-type E3 ubiquitin ligases expressed on the cell surface. This project studies molecular pathways to understand how intracellular host factors, SAMHD1 and MARCH8, restrict the infection and replication of different RNA and DNA viruses. Research in the Reading Laboratory in Melbourne focuses on the ability of these host factors to mediate direct antiviral activity against a range of human RNA and DNA viruses, including influenza A virus, respiratory syncytial virus, herpes simplex virus and vaccinia virus. Research in the Bartok Laboratory in Bonn focuses on the ability of SAMHD1 and MARCH8 to mediate indirect antiviral activity through the modulation of type I IFN signalling and ISG induction. Overall, this project aims to identify and characterise host restriction factors with novel antiviral activity against one or more human viruses, which might represent targets for the development of broad-acting antiviral therapies in the future.

Malignant melanoma is an aggressive type of skin cancer that has the ability to metastasize to surrounding organs, rendering standard therapies ineffective. The emergence of tumor escape mechanisms in response to the microenvironment allows for tumor plasticity and tumor resistance causing limitations to treatment options. One such mechanism is phenotype switching where melanoma cells could switch between a differentiated and a de-differentiated phenotype, thereby altering the expression of specific melanocytic differentiating markers and escaping immune surveillance. Using Hölzel’s expertise in molecular and tumor biology, a B16 melanoma model would be generated featuring different phenotypic characteristics to study the effect of these phenotypic differences on immune cell phenotype via in-vitro and in-vivo approaches. Once validated, the model could be studied in-vivo to track tumor development and metastasis to the lymph node via an epicutaneous model generated in Gebhardt’s lab using different complex imaging techniques. This would allow us to study the interaction between the immune cells and melanoma cells in-vivo. In addition, it would be of interest to study human primary melanoma models by analyzing lymph node sentinels containing primary tumor lesions and analyzing their phenotype in parallel with immune cells to examine the spatial interaction, heterogeneity, and frequency at a single level using a highly multiplexed imaging technique to characterize multiple markers at the same time. Thus, by deciphering the role of melanoma phenotype on immune cell surveillance and metastasis, a better understanding could be achieved in characterizing the cell dynamics, the tumor microenvironment, therapy resistance mechanisms, and biomarkers involved in the immune-mediated control of melanoma.

Metastatic disease is the major cause for cancer-related mortality. Metastatic spread and outgrowth are accompanied by dynamic changes in the interactions between cancer and immune cells with key aspects of this crosstalk likely to depend on disease stage and the type of organ affected. The Gebhardt laboratory has recently developed a preclinical melanoma model that allows to study immune control of metastatic melanoma following curative-intent surgery of primary tumours. As part of previous joined PhD projects, the Hölzel laboratory has generated and contributed numerous genetically modified melanoma lines to the model. These cell lines are now routinely used in the Gebhardt laboratory and have been integral in generating the preliminary data that the aims of the PhD project are now following up on. More specifically, the project will investigate the functional significance of melanoma cell expression of MHC II in lymphoid metastases. In addition, the project will seek to be better understand how immune pressure impacts on the route of metastatic dissemination from primary tumours, as well as on the clonal composition of metastatic deposits in different organs. Work with the in vivo model will be conducted in the Gebhardt laboratory where all required methodologies are already established (e.g. high dimensional flow cytometry, multiphoton and bioluminescence imaging, histology). Generation of new melanoma lines and high dimensional imaging of samples shipped from Melbourne will be conducted in the Hölzel where these techniques are used routinely.

Dendritic cells are critical to the initiation of an immune response. While sparse in tissues, dendritic cells possess a remarkable and unrivalled capacity to stimulate T cells upon arrival to lymphoid tissue. This ability will be exploited throughout the project, to reveal new cellular mechanisms in dendritic cells which can possibly foster new immunotherapies, driven by dendritic cells to fight cancer. The first phase of the project will take place in the Mintern Lab in Melbourne. The Mintern lab has developed a novel technique for way genetic screens utilizing CRISPR/Cas9 to identify new molecular pathways in dendritic cells. Pathways on interest includes those who is affected by the expression of Flt3, some of these being transcription factors. Hereafter, the validated gene pathways will be targeted in mouse models of vaccination and immunotherapy. This will allow us to verify the importance of these pathways in relation to other immunological and physiological functions. The final part of the project will take place within the Paeschke lab in Bonn, where the expertise lies within techniques for determining molecular mechanisms in dendritic cells. The work planned to be carried out will include, but not be limited to knock out cell models, RNA sequencing and binding assays all utilizing cell cultures to determine the modes of action for the Flt3 related transcription factors and to some extend the effect of G-quadruplex formation in dendritic cells.

The symbiotic interactions between a host and its associated microbiome are pivotal in many physiological processes, particularly in the development and maintenance of immune cells.
Evidence from the Bedoui laboratory points towards microbiome-derived signals driving at least some parts of these host-microbiome interaction. Butyrate, a metabolite derived from the gut microbiome was shown to direct CD8 “killer” T cells to a more memory like phenotype. However, the nature of these metabolites and their underlying mechanisms by which they influence CD8 T cells remain relatively uncharacterised. Additionally, other forms of microbiota-immune cell interactions are likely to influence the phenotype of CD8 T cells. In this project, these mechanisms will be investigated utilising various techniques such as the multiplex imaging expertise of Michael Hölzel, high dimensional flow cytometry, and 16S rRNA sequencing for microbiota characterisation. Furthermore, these mechanisms will be examined in various disease contexts with the aim of discovering molecular pathways that can be targeted to reduce overall disease burden.

Scientists around the world have been working intensively to elucidate potential pathophysiological mechanisms, prognostic inflammatory markers, and potential therapeutic targets in SARS-CoV-2 infections since its outbreak in late 2019. Our research is currently focused on monocytes, which migrate from the circulating blood into the infected tissues during viral or bacterial infection and differentiate into antigen-presenting cells (APCs) according to the inflammatory milieu. As central mediators of immune responses, APCs are central for the uptake of cellular debris from infected cells as well as for phagocytosis and presentation of antigens to T cells via the MHC class II molecules. Together with Zeinab Abdullah’s group, and other collaborators of the IRTG, we observed a loss of expression of MHC class II molecules (e.g. HLA-DR) on monocytes from COVID-19 patients, particularly in severe courses. The underlying mechanism leading to this suppression is not yet fully understood and is part of our current investigation.
We are using transcriptomic and epigenetic next-generation sequencing approaches to understand changes in the expression of genes involved in the antiviral immune defence mechanisms of myeloid cells. This project aims to (1) elucidate epigenetic mechanisms contributing to the decreased expression of genes participating in antigen presentation of peripheral monocytes, (2) investigate the role of chromatin remodelers in SARS-CoV-2 infection, which may (3) explain the functional dysregulation of monocytes in severe COVID-19 patients leading to disease progression.
The Bonn-based project is headed by Susanne V. Schmidt (Group leader of the Immunogenomics Group at the Institute of Innate Immunity, University Hospital Bonn). The group's preliminary work contributed to several studies focusing on novel methods to detect SARS-CoV-2 in body fluids and the role of IFNα in NK cell dysfunction in severe COVID-19 cases. Since 2018, we have collaborated extensively with Sammy Bedoui (Peter Doherty Institute, University of Melbourne), who is an expert in the interplay of innate and adaptive immunity in viral infections. Together with Sammy Bedoui’s group, we will be able to verify and investigate dysfunctional signalling pathways in COVID-19 patients with severe progression and identify potential markers in mouse models with different COVID-19 disease courses.

In the last decade, the immunology field experienced a significant paradigm shift towards a better understanding of immunologically privileged sites. Looking at the Central Nervous System (CNS) for example, scientists in the mid-twentieth century believed this tissue to be segregated from any immune cell. This believe was founded through experiments showing the absence of graft rejections in the CNS and the presence of the blood-brain barrier. Now we know, that a plethora of immune cells reside and migrate in and around the CNS. These cells perform vital functions in homeostasis as well as disease.
One of such cell types are T cells, which were shown to invade and reside in the brain meninges and parenchyma at a steady state. Furthermore, higher numbers of Tregs and CD8+ T cells were observed in various mouse models of neurodegeneration and patient data.

With Beyer’s group (Bonn, Germany) expertise in T cell biology and high throughput single cell technologies, we aim to characterize common T cell signatures in the CNS and compare them across multiple modalities, health status, and species.
The work in Beyer’s group will be the basis for downstream molecular biology and in vivo experiments with the aim to characterize single significantly altered pathways in more detail. Kallies’ group (Melbourne, Australia) long term experience and profound knowledge of T cell residency and the impact of transcriptional factors will be vital in the second part of this project.

The skin is our largest organ and protects the body’s surface from microbial and environmental threats. The outermost layer of the skin, the epidermis, mainly consists of keratinocytes in defined stages of differentiation. These cells are central to skin immunity, as they can mount cell-autonomous immune responses and shape the behavior of skin-resident immune cells. Depending on their differentiation state, keratinocytes express selected innate immune receptors, such as the NOD-like receptor family members NLRP1 and NLRP10. Upon sensing pathogens or cellular stress, these receptors initiate signaling cascades, leading to the release of potent pro- and anti-inflammatory IL-1 family cytokines.

The Latz laboratory has recently shown how NLRP10 senses mitochondrial damage and consequently forms a canonical inflammasome. Via RNAscope staining in human skin, endogenous NLRP10 expression was found selectively in terminally differentiated keratinocytes in the stratum granulosum. Analysis of immune sensors and inflammasome effector molecules from single cell data of normal human skin showed that the NLRP10-positive keratinocytes also had high expression of anti-inflammatory members of the IL-1 cytokine family, such as IL-37 and IL-38, and of a particular gasdermin (GSDMA). Moreover, loss-of-function mutations in NLRP10, or SNPs associated with low expression of NLRP10, are associated with atopic dermatitis, suggesting that NLRP10 can negatively regulate skin inflammation. Our hypothesis is thus that NLRP10 could engage a novel form of programmed anti-inflammatory cell death in keratinocytes during the physiological cell demise in the cornification process.

In this collaborative project, we want to continue the NLRP10 investigations under two aspects. On the one hand, using the inflammasome expertise of the Latz laboratory, we will carry on with the NLRP10 mechanism studies. There are still some open questions regarding the upstream mechanism, like potential endogenous triggers of NLRP10 and its specific mitochondrial ligand, as well as the downstream inflammasome effects, such as the release of pro- or anti-inflammatory cytokines. On the other hand, we will profit from the Bedoui laboratory skin expertise, to investigate the more physiological role of NLRP10 in the skin homeostasis and pathology. In conclusion, the two laboratories are a perfect fit to investigate the role of this new inflammasome in the skin.

Cancer immunotherapies have revolutionized the treatment for many cancer patients. Despite the great success, a considerable group of patients do not respond or acquire resistance to currently approved cancer immunotherapies. Therefore, there is an unmet need to discover novel targets and pathways to improve the survival of cancer patients. Immune escape via upregulation of inhibitory molecules in the tumor microenvironment (TME) gained a lot of interest over the past years. This has led to the development of immune inhibitors such as PD-1/L1. On the contrary, little is known about the regulation of immune activating receptors in the TME. The Bald lab (Bonn, Germany) showed that CD155-expressing tumor cells induced internalization and degradation of the CD226, which rendered T-cells dysfunctional and contributed to resistance to cancer immunotherapy. Thus, the loss of CD226 represents a novel immune escape mechanism in addition to the upregulation of T-cell inhibitory receptors in tumor-infiltrating T-cells. To date, little is known about the importance of CD155-CD226 interaction between T-cells and cancer cells. Our central aim is to further advance our knowledge on the role of CD155 on APCs and tumor cells for the interaction with T-cells. The Noble Prize awarded CRISPR gene editing technology is a useful tool to study intrinsic cellular mechanism. By using genome-wide CRISPR/Cas9 screens (expertise Prof. Marco Herold in Melbourne, Australia) my research project aims to better understand the regulation of CD155 and CD226 to find new therapeutic targets and improve immunotherapies.

CD8+ T cells are an important arm of the adaptive immune response that can mediate protection from viral infections and uncontrolled malignant cell growth. However, T cells persistently responding to chronic viral infections or tumor cells often undergo functional deterioration known as T cell exhaustion. The Australian partner, Dr. Daniel Utzschneider has contributed to the elucidation of mechanisms of CD8+ T cell exhaustion in chronic viral infections and identified a specialized subset of exhausted T cells, precursors of exhausted T cells (Tpex), that maintain developmental potential and as such are the primary target for any novel immunotherapies.
With the expertise of the German partner, Prof. Christian Kurts, this project now aims to clarify the role of Tpex in the B16 melanoma model and explore their potential as immunotherapy targets in the context of solid tumors. The project will focus on the identification of factors and pathways involved in Tpex differentiation using both in vitro and in vivo approaches, and will take advantage of state-of-the-art multi-omics approaches with a special emphasis on pathways associated with regulating cellular metabolism. The identified factors will then be applied in a therapeutic vaccination approach using the B16 melanoma model, aiming to improve therapy strategies for solid tumors.