Decoding Neuro-Immune Interactions: Spatial Multiomics Analysis of Mouse Brain via same-section RNA and Protein Co-detection 3572

Description The rise of spatial biology has transformed our ability to investigate tissue structures and cellular interactions at a single-cell resolution. Through techniques such as multiplexed immunofluorescence (mIF) or RNA in situ hybridization (ISH), it is possible to achieve a detailed mapping of key histological and cellular components along with their activation states. Combining those two technologies on the same tissue section could allow for better profiling of complex tissues like the mouse brain. Here, using the COMET™ staining and imaging platform, RNAscope™ HiPlex Pro and sequential immunofluorescence (seqIF™) assays were integrated and fully automated for same-section RNA and protein detection on fixed-frozen mouse brain tissues. Through precise temperature control and gentle reagent distribution, fragile frozen sections can now be used to visualize up to a 12-plex RNA and 24-plex protein panel. Using this newly developed multiomics assay, we designed a panel to deepen the understanding of normal brain function and architecture through mapping of molecular networks and by studying the interactions between major brain cell types (e.g., neurons, astrocytes, oligodendrocytes) and different immune cells (e.g., microglia and macrophages). Our results highlight the compatibility of combined RNAscope™ HiPlex Pro and seqIF™ workflows on the COMET™ with frozen sections, while showing valuable insights into the interactions between the immune and nervous system. Funding Sources Supported by Innosuisse through the innovation project 104.554 IP-LS Topic Categories Neuroimmunology (NEUR)