Ultra-high-multiplex tissue scanner

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The large-scale device applied for here is a system for the spatially resolved detection of proteins and RNA transcripts ("Spatial Proteomics & Transcriptomics"), which has the capacity for single cell and subcellular resolution. This system is to be integrated into the "Advanced Tissue Imaging & Digital Pathology" Core Facility to be established at the Institute of Pathology at the University Hospital of Tübingen, where it will be used as a central component. In recent years, there has been a tremendous surge in the development of spatially resolved proteomics and transcriptomics. While some systems for spatial proteomics based on imaging mass spectrometry can only image approx. 40 proteins can be visualized at a time, the new optical methods based on repetitive staining/bleaching or DNA-labeled antibodies have capacities of 100+ proteins. Whereas until recently spatial transcriptomics could only display dots of approximately 50-100 micrometers in diameter, new instruments that came to the market in 2022 enable resolution in the 100-200 nanometer range, i.e., at the single cell level and even subcellular. Only this single-cell resolution allows the assignment of proteins and RNA transcripts to certain cell types in the tissue, which is essential for understanding the interactions between different cell types by means of messengers such as cytokines and chemokines, which often cannot be visualized by means of pure proteomics. In addition, until recently, only fresh-frozen tissue samples could be analyzed; however, the technologies have now been extended to paraffin-embedded tissues. This opens up the possibility of studying large clinical cohorts whose tissues are stored in the paraffin archives of pathology institutes. Most importantly, the new technologies will allow a combination of spatial proteomics and transcriptomics, which will once again fundamentally change our understanding of the tumor microenvironment, and how immune cells within it communicate with each other. These technologies will reveal new ways to improve the prediction of response to (immuno)therapies and play a crucial role in the discovery of new therapeutic targets. Numerous studies are currently being planned and will be addressed with the requested device, including cutaneous T-cell lymphoma, gastroesophageal adenocarcinoma, colorectal carcinoma, chronic myeloid leukemia, malignant melanoma, etc.