Abstract
Cognitive manifestations, including impairment in language and executive functions, are seen in amyotrophic lateral sclerosis (ALS), but the mechanisms that underlie these deficits remain unclear. To address this, we mapped prefrontal cortex regions from ALS patients by integrating spatial and single-nucleus transcriptomics in a cognitively stratified patient cohort. We uncover that cognitive impairment in ALS is associated with distinct patterns of neuronal dysfunction and glial-vascular dysregulation that vary by region and cognitive subtype. Executive dysfunction is linked to reduced mitochondrial and synaptic activity in neurons localized to the deeper layers of the dorsolateral prefrontal cortex, whereas language-related deficits track with a more diffuse, pan-regional response involving both glial and vascular abnormalities. Our analyses also identify signatures in the prefrontal cortex that span both motor and cognitive phenotypes, including a multicellular gliosis response. The findings reveal that the clinical heterogeneity of ALS is driven by phenotype-specific molecular and cellular interactions in motor and non-motor regions of the brain.