Projects

Charité Corona Cross

Initial vaccination strategies focused on inducing a high amount of (neutralizing) antibodies which can prevent the virus from entering the host cells or rapidly clear the virus from the body liquids. The limited antibody persistence and the evolution of escape variants shifted the focus to efficiently induce long-living memory T-cell responses. These T-cell responses have a broader epitope coverage and can efficiently protect against severe disease even upon infection with highly mutated variants. However, the characteristics of protection, especially in vulnerable cohorts such as the elderly and immunosuppressed, remain yet to be defined. Within Charité Corona Protect (CCP), we analyze whether homo- or heterologous vaccination strategies (Henze et al., submitted), quality and longevity of immunity induced by infection or vaccination-mediated boosters (Meyer-Arndt et al., in preparation) provide better immunity. Furthermore, we investigate the quality of (cross)-reactive immune responses in young versus old individuals in the light of existing and potential arising variants of concern (Loyal et al., in preparation).

The CATCH assay – a simple and rapid method to identify T cells with high avidity

High TCR avidity enables more efficient activation through low epitope densities and is therefore a crucial factor in T cell-mediated immune responses. T cells with too low avidity for antigenic tumor or pathogenic targets may not achieve sufficient efficiency, while T cells with high avidity for self-antigens may promote autoimmune inflammation. Accordingly, knowledge of T cell avidity is essential for clinical applications, especially for cellular therapies of malignant or infectious diseases or for diagnostic procedures. The current gold standard for assessing T cell avidity involves measuring the dissociation rates of specific multimers (MHC:peptide complexes) of T cells. This method requires prior knowledge of the MHC:peptide complex and prolonged production of functional multimers. Alternatively, specific T cells can be stimulated and expanded in vitro, followed by peptide titrations. The complexity and time-consuming nature of both methods preclude their regular use in therapeutic regimens or diagnostic procedures. We have identified and patented (Loyal et al., Science, 2021) a rapid and simple method to identify individual T cells or a T cell populations TCR avidity by measuring CD3 downregulation in flow cytometry. We are currently evaluating the scope and limitations of this novel assay and validating the value of the technique in analyzing and treating malignancies and autoimmunity.

The 3D Thymus (1° MACSima project)

Initial vaccination strategies focused on inducing a high amount of (neutralizing) antibodies which can prevent the virus from entering the host cells or rapidly clear the virus from the body liquids. The limited antibody persistence and the evolution of escape variants shifted the focus to efficiently induce long-living memory T-cell responses. These T-cell responses have a broader epitope coverage and can efficiently protect against severe disease even upon infection with highly mutated variants. However, the characteristics of protection, especially in vulnerable cohorts such as the elderly and immunosuppressed, remain yet to be defined. Within Charité Corona Protect (CCP), we analyze whether homo- or heterologous vaccination strategies (Henze et al., submitted), quality and longevity of immunity induced by infection or vaccination-mediated boosters (Meyer-Arndt et al., in preparation) provide better immunity. Furthermore, we investigate the quality of (cross)-reactive immune responses in young versus old individuals in the light of existing and potential arising variants of concern (Loyal et al., in preparation).

LINE-1 Immunity

This project will investigate cellular immunity against human long interspersed element 1 (LINE-1): a prototype transposable element (TE) and its role in human malignancies. Numerous studies have consistently highlighted the high expression profile of LINE-1 in different types of cancer, emphasizing its potential significance as a tumour-specific antigen. Although some studies have identified LINE-1 reactive T-cells in the past, the throughout detailed characterization of LINE-reactive cellular immunity remains incomplete. Additionally, the question of whether LINE-1 reactive T-cells undergo negative selection in the thymus has not been addressed. Throughout the course of this project we will comprehensively characterize LINE-1 reactive T-cells in healthy donors and malignancy patients. Additionally we will investigate human thymus samples to elucidate the role of LINE-1 in negative selection of the human T cell repertoire. Therefore, we aim to determinine the frequency and functional phenotypes of specific T-cells with state-of-the-art flow cytometry and to characterize thymus and tumour samples with mass spectrometry, next-generation sequencing, and spatial imaging.

Skin – Vasculature – T cells

Over the last decade, immune-checkpoint inhibitors (ICI) immunotherapy has shown promise as a treatment for melanoma skin cancer. Immune-checkpoint therapy offers different strategies to target and block immune-checkpoint receptors, thus enabling anti-tumour immune response. However, ICI treatment has been limited to a 40-60% response rate in patients and is associated with several immune-related adverse events such as colitis, hypophysitis, hepatitis, pneumonitis, hyperthyroidism, hypothyroidism and type 1 diabetes. This calls for the development of a prediction tool that can identify patients with a greater chance of benefiting from this immunotherapy. Human-relevant platforms for drug testing can potentially better predict human response in clinical studies and present an attractive alternative for an animal testing platform in research. In this project, we aim to achieve an immune-competent human skin-on-a-chip testing platform, that can be used as a personalized prediction tool for ICI effect on patients before treatment. This platform will include a skin-on-a-chip model with circulating T cells composed of autologous cells isolated from the patient’s skin biopsies and blood samples. Establishing such a platform can potentially prevent unnecessary ICI immunotherapy in non-responsive melanoma patients and will allow further investigation of T cell activation and function in human skin.

CD8+ helper T cells

Activated CD4+ T cells transiently express CD40L and provide “help” in terms of APC licensing and/or the necessary stimuli for B cell maturation, somatic hypermutation, and class switching. In contrast, CD8+ T cells are characterized as cytotoxic T cells, that can directly kill infected target cells. However, we previously identified a CD40L expressing CD8+ T cell population, which inherits the ability of DC licensing (Frentsch et al., Blood, 2013). In-depth analysis revealed that CD8+ memory T cells have a CD4+ T cell alike diversity and can differentiate into Tc1, Tc2, Tc17, Tc17+1, and Tc22 subsets. Among them, the Tc2, Tc17, and Tc22 cell subsets lack cytotoxic features, but express high levels of CD40L, and resemble helper CD4+ T cells in their gene expression signature (Loyal et al., Nat. Comms., 2020). We could demonstrate that helper CD8+ T cells do not express the CD8 lineage transcription factor Runx3 which is in contrast present in cytotoxic CD4+ T cells and all cytotoxic cells can be distinguished from helper cells irrespective of their cell type by the expression of SLAMF7 (Loyal et al., Nat. Comms., 2020). In our current projects, we are addressing the questions of how these helper CD8+ T cells are induced and what is their role in human health and disease.

KFO 399

Although the prevalence of IgE-mediated food allergies is on the rise in most industrialized countries, it currently has no known cure. Instead, allergic patients are usually instructed to avoid food containing the allergens they are sensitized to. Our research group is part of the food@ Clinical Research Unit (KFO 339), aiming to desensitize allergic donors using a liberated diet approach: the patients are instructed to regularly consume low doses of allergens below their reaction threshold for one year (as opposed to strict avoidance of the allergens), whilst various bio-samples are collected before and after the clinical intervention. In our group, we are focusing on the identification of immune mechanisms involved in food allergy sensitization and desensitization by monitoring the response to allergens of different immune cell subsets (T cells, B cells, antigen-presenting cells, basophils). Our findings contribute to a better understanding of the immune circuits of food allergy and refine laboratory diagnostic assays.

Efficacy of immune checkpoint inhibitor treatment in melanoma

Over the past decade, immunotherapy with immune checkpoint inhibitors (ICI) has shown promise in the treatment of melanoma skin cancer. However, ICI treatment is limited to 40-60% response rate in patients and is associated with various immune-related side effects. Therefore, there is a need to develop a prognostic tool to identify patients who have a greater chance of benefiting from this immunotherapy. By combining phenotyping and quantitative analysis with quality analyses using our CATCH assay, we aim to identify biomarker signatures for therapeutic success. In combination with single-cell RNA sequencing, we aim to identify melanoma-specific TCRs with optimal TCR avidity for customized treatments.