DNMT3A drives mitochondrial dysfunction in intracerebral hemorrhage via PGC-1α promoter hypermethylation

Mitochondrial dysfunction drives secondary injury in intracerebral hemorrhage (ICH), yet its upstream regulatory mechanisms remain elusive. This study examines whether ICH-induced DNA methyltransferase 3 A (DNMT3A) activation triggers PGC-1α promoter hypermethylation, causing mitochondrial impairment and neuronal damage through epigenetic silencing of this key metabolic regulator. Both in vitro and in vivo approaches were employed. Primary mouse cortical neurons were treated with hemin (20 µM) to mimic ICH injury. Epigenetic editing using CRISPR-dCas9-DNMT3A, dual-luciferase reporter assays, and chromatin immunoprecipitation were applied to assess locus-specific methylation and promoter activity. In vivo, a collagenase VII-induced striatal ICH model was established in C57BL/6 mice. Interventions included the DNMT3A inhibitor 5-Aza-CdR (1 mg/kg, i.p.) and AAV-shDNMT3A gene therapy. Mitochondrial function (ATP/ROS levels, TEM imaging), gene/protein expression (qPCR/Western blot), promoter methylation (MeDIP-qPCR), and neurobehavioral outcomes (mNSS, rotarod, H&E staining) were evaluated. ICH significantly upregulated DNMT3A expression and activity, leading to hypermethylation of the PGC-1α promoter and transcriptional repression of PGC-1α. This suppression impaired mitochondrial biogenesis (↓TFAM, ↓NRF1) and antioxidant capacity (↓SOD2), resulting in ATP depletion, ROS overproduction, and increased neuronal apoptosis. Both pharmacological inhibition (5-Aza-CdR) and genetic knockdown (AAV-shDNMT3A) of DNMT3A reversed PGC-1α promoter hypermethylation, restored mitochondrial homeostasis, attenuated neuronal apoptosis, and improved functional recovery post-ICH (P < 0.05 vs. ICH group). Our findings demonstrate that DNMT3A promotes PGC-1α promoter hypermethylation, exacerbating mitochondrial dysfunction and brain injury after ICH. Targeted inhibition of DNMT3A mitigates these effects, supporting the DNMT3A-PGC-1α axis as a promising therapeutic target for ICH treatment.