Temporal dynamics of mRNA translation dysregulation and codon decoding during murine stroke evolution

Ischemic stroke is the second leading cause of mortality worldwide, yet there are limited neuroprotective therapeutics available. Ischemic stroke triggers rapid and complex molecular changes, yet the dynamics of mRNA translation during stroke remain largely unexplored. Here, we present the first temporal ribosome profiling (Ribo-seq) analysis in a murine distal middle cerebral artery occlusion (dMCAO) model, assessing translational regulation at 1-, 6-, and 24-hours post-stroke. We identified distinct stage-specific phenomena, including a hyperacute GC-ending codon bias and a transient burst of stop-codon readthrough (SCRT) at 1-hour, predominantly affecting neuronal and synaptic pathways, and an activation of pathways linked to vascular remodeling and endothelial function. From 6-hours onward, we observed progressive ribosome pausing, altered elongation dynamics, and widespread frameshifting affecting mitochondrial, synaptic, and metabolic genes, coinciding with strong immune pathway activation. These events cannot be evaluated at the level of transcript abundance, underscoring the value of translation-focused approaches. Our findings reveal that translational control in stroke follows a phased program, with multiple regulatory and maladaptive phenomena impacting the gene expression and outcome of stroke. This work uncovers hidden layers of translational regulation in stroke pathophysiology and identifies potential mechanistic targets that could be explored for potential therapeutics development.