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Introduction: Peroxisomes are highly adaptable and dynamic organelles, undergoing a formation/degradation cycle every 24-48 hours. We have previously demonstrated that increasing peroxisomal biogenesis serves a protective function in neurons experiencing ischemic injury, in part through catalase-mediated antioxidant activity. The role of autophagy in adult cerebral ischemia has been studied, yet the specific role for the targeted destruction of damaged peroxisomes (pexophagy) in ischemic stroke has not yet been explored.Hypothesis: We hypothesize that post-ischemic pexophagy is a critical step for neuronal survival. We used a combination of pharmacologic and genetic strategies to test whether perturbation of autophagy in general and pexophagy in particular exacerbates ischemic brain injury by targeting key regulators including mammalian Target Of Rapamycin (mTOR).Methods: Transient middle cerebral artery occlusion (MCAO, 60 min) was performed in male mice treated with mTOR rapamycin (1.25 mg/kg, IP) or vehicle at the beginning of reperfusion. Similarly, TSC1 knock-out and wild-type mice underwent 60-min MCAO, and brains were harvested and analyzed for infarct size at 24 hrs of reperfusion. Separate brains we analyzed for peroxisomal membrane protein co-localization with autophagic markers, and for autophagic activity based on microtubule-associated protein 1A/1B-light chain 3 (LC3) turnover.Results: Activation of autophagy using rapamycin reduced infarct size after MCAO (27.2 ± 2.8% in rapamycin-treated mice vs. 37.3 ± 1.8 % in vehicle-treated mice in cortex , n=10 and 9 per group respectively, p=0.01), whereas TSC1 knockout mice, which have reduced pexophagy, sustained larger infarcts than WT mice (48.5 ± 4.5% in TSC1 knockout mice vs. 33.0 ± 5.8 % in vehicle-treated mice in cortex , n=4 and 5 per group respectively, p=0.007). The experiments of peroxisomal co-localization and autophagic activity have been finished but no results yet. We’ll report them later.Conclusions: We conclude that organelle autophagy, including pexophagy, is an endogenous mechanism of neuroprotection after stroke, and that both biogenesis and pexophagy of peroxisomes are protective by promoting peroxisomal turnover.