Single-cell Spatial Transcriptomics Reveals Disease-specific Microenvironmental Niches in Neurodegeneration and COVID-19

Neurodegenerative diseases and infections can produce lasting effects on brain function, yet the spatial molecular mechanisms underlying these changes remain poorly understood. Here, we present high-resolution spatial transcriptomics of 40 postmortem brain samples from patients with Parkinson’s disease, frontotemporal dementia, dementia with Lewy bodies, and severe COVID-19. Analyzing over 1.5 million spatially resolved cells across dorsolateral prefrontal cortex and anterior cingulate cortex revealed disease-specific transcriptional signatures with pronounced layer-and region-specificity. In Parkinson’s disease, we identified stressed neurons creating distinctive microenvironmental gradients where metabolic and protein degradation pathways are elevated near stress epicenters, while regenerative processes increase with distance. COVID-19 brains displayed extensive peripheral immune cell infiltration, particularly in the subcortical white matter, accompanied by compromised blood-brain barrier and coordinated neuroinflammatory responses from microglia, astrocytes, and endothelial cells. Integration of miRNA sequencing with spatial transcriptomics uncovered layer-specific regulatory patterns, including neuroinflammation-associated miR-155. This atlas provides unprecedented insights into disease pathology and highlights the critical importance of spatial molecular context in understanding brain disorders.