A Single-cell Spatiotemporal Atlas Encoding Age-dependent Evolution of the Ischemic Penumbra

Abstract

Aging is the predominant risk factor for stroke and a major driver of poor neurological recovery. Although the ischemic penumbra represents a key therapeutic target, its age-dependent molecular landscape remains poorly understood. Here, we generated a spatiotemporal transcriptomic atlas of the post-stroke penumbra in young (3-4 months) and aged (19-20 months) mice at acute (day 3) and chronic (day 14) stages following transient focal cerebral ischemia. Integrating spatial transcriptomics with dissociated single-cell RNA sequencing revealed a persistent transcriptomic penumbra (TP) that remains detectable for at least 14 days after stroke in both age groups, far beyond the window suggested by conventional imaging modalities. Aging profoundly altered TP organization, resulting in dysregulated energy metabolism, impaired neurovascular repair, diminished pro-reparative cell-cell communication, and extensive remodeling of transcriptional regulatory networks. Using this atlas, we further identified regulatory hub genes whose predicted perturbation could simultaneously counteract multiple age-associated pathological pathways. These data define the molecular architecture of the aging post-stroke penumbra and provide a publicly accessible framework for mechanistic discovery and therapeutic target prioritization aimed at improving recovery after stroke.