High resolution transcriptome analysis on a mouse model of hypoxic ischemic encephalopathy using single-nucleus RNA-seq

Hypoxic-ischemic encephalopathy (HIE) encompasses brain injuries resulting from reduced or interrupted oxygen or blood flow to the brain before, during, or immediately after birth. During the acute phase, neuronal damage is driven by excitotoxicity, with permanent injury manifesting over the subsequent hours. Current treatment options have limited efficacy, underscoring the need for deeper insights into HIE pathogenesis and the development of novel therapeutic strategies. Recent advances in single-cell RNA sequencing (snRNA-seq) have enabled molecular investigations of diverse diseases. However, the large size of neurons has posed challenges in studying conditions where neuronal damage is central. To address this, we employed snRNA-seq to evaluate region-specific neuronal damage in a mouse model of HIE. Our HIE model was established in postnatal day-7 mice, with cortical and hippocampal tissues harvested from the ipsilesional side one week post-injury. Analysis revealed pronounced changes in the hippocampus, especially in the CA1 region, with a significant reduction in neuronal populations in the affected hemisphere. These alterations were specific to combined hypoxic-ischemic conditions and were not observed with hypoxia or ischemia alone. In contrast, changes in the cerebral cortex were less prominent. Transcriptomic analysis showed similar gene expression patterns in the cortex and hippocampus of the HIE group, including the identification of genes related to viral response pathways, suggesting a potential link to interferon activation. These findings provide valuable insights into the molecular and anatomical impact of HIE and highlight the hippocampus as a critical focus for understanding disease mechanisms and therapeutic development.