Multiplex antibody-based imaging platform

• Subject Area: Microbiology, Virology and Immunology
• Term: Funded in 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 561487582

Single cell analyses of dissociated cells from tissues by flow cytometry, cytometry of time of flight or single cell RNA sequencing has allowed the definition and characterization of cell type subpopulations and functional cell states at unprecedented depth. However, results of these analyses critically lack spatial information. Recent advances in multi-parameter spatial analysis allow to overcome this limitation. Functional states and subpopulations of immune cells, but also tissue cells, can be distinguished by detection of specific combinations of marker proteins as identified by flow cytometry and cell sorting using well-defined antibody panels. To enable such analyses on tissue sections with cellular resolution, we apply for a fully automated multiplex antibody-based imaging platform for cyclic immunofluorescence staining and imaging. This method allows detection of over a hundred proteins on the same section so that defined cell subpopulations and target proteins can be identified. Importantly, this method also preserves sample integrity, so that the tissue section can be subjected to subsequent analyses. The platform comes with an intuitive software that enables users to perform image analysis, including marker expression, cell segmentation, cell gating, unbiased clustering, dimensionality reduction, and distance analyses. We plan to integrate this multiplex antibody-based imaging platform into the Core Facility Bioimaging at the Biomedical Center (BMC) of the Ludwig-Maximilians-Universität München (LMU) with accessibility for users from the BMC, LMU, LMU University Hospital and other institutions. Contributing researchers from the fields of Immunology, Haematology, Gastroenterology and Neuroimmunology will work together to establish antibody-panels and analysis workflows for various murine and human tissue samples. The aim is to generate maps of the spatial organisation and interactions of immune and non-immune cells and proteins in specific tissue niches and in tissue samples ranging from experimental animals, organoids and patient material. The high-dimensional and spatial information gained from these analyses is essential to address the specific research questions in the described projects. Availability of this new technology will greatly advance progress in these and other related projects and will foster collaborations.

• DFG Programme: Major Research Instrumentation
• Major Instrumentation: Multiplex Antikörper-basierte Bildgebungsplattform
• Instrumentation Group: 5090 Spezialmikroskope
• Applicant Institution: Ludwig-Maximilians-Universität München
• Leader: Professorin Dr. Anne Krug