Integrative Analysis of Organoids Enables Mechanistic Studies in Pharmaceutical Research: Development, Volatilomics, Single Cell Metabolite/Lipid Fingerprinting, and Function

• Subject Area: Analytical Chemistry ; Image and Language Processing, Computer Graphics and Visualisation, Human Computer Interaction, Ubiquitous and Wearable Computing ; Bioinformatics and Theoretical Biology ; Biomedical Systems Technology ; Experimental Models for the Understanding of Nervous System Diseases ; Hematology, Oncology
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 497984836

Due to their physiological relevance and the use of human cells, 3D-cell cultures and organoids have gained importance in basic pharmacological and applied drug research. In the current project, fusion and complementation of available platforms and expertise at Hochschule Mannheim (HSMA) will enable the formation of a high-content analytical platform for integrated pharmacology and toxicology, volatilomics, single cell metabolite-/lipid fingerprinting, and functional studies on 3D-cell cultures and organoids. This platform will enable studies of cell type-specific connections between cellular behavior and metabolism. Therefore, technologies for online and endpoint measurements will be combined and resulting data will be analyzed by machine learning (ML) procedures. Three exemplary 3D-cell culture models at different levels of complexity from the fields of oncology and neurosciences will be studied with respect to their development, volatilomics, single cell metabolite-/lipid fingerprinting, and function: 1) a cell-line based bone metastasis model, 2) a patient-derived tumor organoid model, 3) an hiPSC-derived model of the neuromuscular junction. Using these paradigms, molecular mechanisms of tumor-bone interaction, metabolic dependency of tumor organoids, and synapse formation will be investigated. These studies will involve analytical technologies ranging from online measurement of volatile organic compounds (volatilomics) paired with live-cell imaging, to endpoint analysis using mass spectrometry 3D-imaging, single cell metabolite-/lipid fingerprinting, as well as high-resolution 3D-fluorescence microscopy. The qualitative and quantitative exploration of the resulting multidimensional and hyperspectral datasets will necessitate ample automated and intelligent algorithms based on ML. Building upon the available equipment and staff, the work plan requires additional funding for a live-cell imaging and analysis system, a GC-IMS gas analysis module including a cold plasma ionization source, a cell dispenser, a GPU server, and 84 PM salary for scientists. Goals of the project are: establishment, integration, and application of the added technologies, in order to perform the research described above and publication of data and concepts, intensification of the interdisciplinary cooperation within HSMA, and enhancement of scientific visibility, in particular, towards Heidelberg University and KIT.

• DFG Programme: Major Instrumentation Initiatives
• Major Instrumentation: GC-IMS ; GPU-Server ; Live Cell Imaging and Analysis System ; Zelldispenser
• Instrumentation Group: 1060 Dilutoren, Pipettiergeräte, Probennehmer ; 1340 Gaschromatographen (außer GC-MS-Kopplung) ; 3100 Immunochemische Bestimmungsgeräte (außer Immunelektrphorese 141) ; 7070 Arbeitsplatzrechner, Personalcomputer
• Applicant Institution: Technische Hochschule Mannheim
• Leader: Professor Dr. Rüdiger Rudolf
• Co-Investigators: Professor Dr. Carsten Hopf; Professor Dr.-Ing. Oliver Wasenmüller; Professor Dr. Philipp Weller