Project description:Current spatial transcriptomics methods provide molecular and spatial information but no morphological readout. Here, we present STEM - a method that correlates multiplexed error-robust FISH with electron microscopy from neighboring tissue sections of the same sample. STEM links transcriptional and spatial organization of single cells with ultrastructural morphology of the tissue in vivo. Using STEM to characterize demyelinated white-matter lesions allowed us to link morphology of myelin-laden foamy microglia to transcriptional signature. Moreover, we revealed that interferon-response microglia have unique morphology and are enriched near CD8 T-cells.
Project description:Current spatial transcriptomics methods identify cell types and states in a spatial context but lack morphological information. Electron microscopy, in contrast, provides structural details at nanometer resolution without decoding the diverse cellular states and identity. STEM address this limitation by correlating multiplexed error-robust FISH with electron microscopy from adjacent tissue sections. Using STEM to characterize demyelinated lesions in mice, we were able to bridge spatially resolved transcriptional data with morphological information on cell identities. This approach allowed us to link the morphology of foamy microglia and interferon-response microglia with their transcriptional signatures.
Project description:We optimized a workflow combining imaging-based spatial transcriptomics (MERFISH) and immunostaining on ganglion cell layer retinal flatmounts of C57/Bl6J mice.The MERFISH data shows molecularly-defined retinal ganglion cell types types exhibited non-uniform distributions. We also analyzed local neighborhoods for each cell and registered several RGC types as enriched in the perivascular niche.
Project description:Microglia adopt various spatially resolved gene and functional profiles in amyloidosis mice, for example the relative enrichment of DAMs proximal to plaques. To spatially resolve these transcriptional changes and identify microglial populations responsive to TREM2 small molecule agonism, multiplexed error-robust fluorescence in situ hybridization (MERFISH) was conducted on sagittal brain sections from VG-3909–treated 5xFAD;hTREM2 mice, 12 hours post-oral dosing. Simultaneous immunostaining using an anti-amyloid antibody enabled spatial correlation of microglial transcriptomes with amyloid plaque localization. The custom MERFISH panel comprised 500 genes, included cell-type markers and microglia-focused genes.