SPATIAL MULTIOMICS MAPPING OF NEUROINFLAMMATION IN A MOUSE MODEL OF AMYOTROPHIC LATERAL SCLEROSIS

The immune response plays an important role in the onset of Amyotrophic Lateral Sclerosis (ALS), a disorder characterized by the progressive loss of the motor neurons (PMID: 30663610). Understanding the spatial immune and structural landscape of the brain is crucial for gaining insight into the neurodegenerative brain.
We employed a multiomics assay combining multiplexed immunofluorescence and RNA in situ hybridization for detecting proteins and RNA simultaneously on the same section, to assess neuroimmune changes in an ALS mouse model. Brain sections from TAR6/6 transgenic mice overexpressing human TAR DNA-binding protein 43 (TDP-43) protein were used (PMID: 29787578). Sections were stained and imaged using the COMET™ platform, integrating RNAscope™ (PMID: 22166544) HiPlex Pro and sequential immunofluorescence (seqIF™, PMID: 37813886) into a fully-automated workflow. Multiomics images were analyzed using HORIZON™ software.
High-plex proteomic panels enabled mapping of key cell types (neurons, astrocytes, microglia, oligodendrocytes) and vasculature-associated cells. Transcriptomic targets included markers of neuronal and glial function. This multiomics assay allowed spatial profiling of cell types, detection of immune activation, and characterization of molecular changes in the ALS model. Our tissue-wide analysis revealed region-specific increases in markers of astrogliosis and microgliosis, such as Gfap, Tspo, and Cd11c; along with signs of axonal loss and synaptic disruption indicated by a reduction in the mRNA expression levels of Nf-M, Nf-L, and Dlg4.
This multiomics approach enables a single-cell-resolution view of the spatial dynamics of neurodegeneration and neuroimmunity, offering novel insights into the molecular pathology of ALS and the broader mechanisms driving neurodegenerative diseases.