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Background: Inter-alpha inhibitor proteins (IAIPs) are immunomodulatory proteins that act as anti-inflammatory agents in hypoxic-ischemic (HI) injury. We have recently shown that administering IAIP after HI improves histopathological brain injury, and behavioral outcomes in neonatal rats. Microglia are glial cells that act as macrophages in the brain and are important constituents in the neuroinflammatory response.Objective: To determine the effect of IAIP treatment on microglial expression in specific brain regions of neonatal rats after HI brain related injury.Methods: The Vannucci model was used to induce neonatal HI brain injury. Postnatal day 7 rats were assigned to a non-ischemic sham-control group (Sham, n=11), a right carotid ligation and hypoxia exposed (8% oxygen for 90 min) placebo-treated group (IschPL, n=12), or a right carotid ligation and hypoxia IAIP-treated group (Isch-IAIP, n=12). The sex of the rats was recorded. IAIP (30 mg/kg) or PL was given intraperitoneally at 0, 24 and 48 h after HI. 72 h after HI, brains were collected, sectioned, and prepared for slides. We performed immunohistochemistry by staining with Iba-1 (selective for microglia) and DAPI. Stereological analyses were then performed with the StereoInvestigator 10.0 Fractionator probe without knowledge of group assignment to quantify microglia present in the whole hemisphere, cortex, corpus callosum, and hippocampus.Results: The number of Iba-1 positive microglial cells per area of tissue was lower in Sham than in the Isch-PL animals in the cortex, hippocampus, and hemisphere of female and in the hippocampus and corpus callosum of male rats (P <0.05). IAIP treatment appears to reduce the number of Iba-1 positive cells across all brain regions compared with the PL treated HI in the male but not female neonatal rats. Post hoc analysis showed that IAIP treatment significantly reduced the number of positive Iba-1 cells in the hippocampus of the male rats (P<0.01).