Proteomics analysis of N-methyl-d-aspartate-induced cell death in retinal and optic nerves

Application of Proteomics Analysis and Animal Models in Optic Nerve Injury Diseases

“…The study also found that when the optic nerve was deficient after blood injury, there was inhibition of the mTOR signaling pathway and synapse-related proteins were significantly downregulated, which again confirmed that optic neuron function gradually weakened after optic nerve injury and optic neuron function was aggravated by visual nerve injury. Proteomic analysis of the retina and optic nerve in N-methyl-d-aspartic acid-induced [ 92 ] excitotoxic ophthalmopathy in rats revealed 3532 proteins in the retina and 2593 in the optic nerve. Differential protein analysis found that these proteins were associated with ferroptosis and autophagy.…”

“… Role of proteomic studies in Optic nerve injuries and its outcomes [ 82 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 ]. …”

Mass spectrometry‐based retina proteomics

“…After rigorous optimization of sample preparation and instrumental parameters, a single‐dimension shotgun strategy with prolonged gradient elution from long nanobore (50 cm × 75 µm i.d., packed with 2‐µm particles) reversed‐phase liquid chromatography (RPLC) columns covered 5354 protein groups and 56,390 peptides in triplicate analysis, which represented approximately 50% coverage of the expressed proteome with the A375 human melanoma cell line used upon benchmarking the method (Pirmoradian et al, 2013). However, several researchers optimized their shotgun approach applied to increased‐throughput retina proteomics by relying on simple sample work‐up (Otake et al, 2020; Prokai et al, 2020; Prokai‐Tatrai et al, 2013, 2021), shorter or microbore columns packed with 3‐µm particles (Anders et al, 2017; Funke et al, 2019; Otake et al, 2020; Prokai et al, 2020; Prokai‐Tatrai et al, 2013, 2021), and faster gradients (Anders et al, 2017; Suo et al, 2022). On the other hand, the application of filter‐aided sample preparation (FASP) has been an example for the importance of enhanced work‐up methods to enable in‐depth retina proteomics (Ly et al, 2016).…”

“…Programs that utilize peak alignment algorithms, ascertain measurements for a given peptide in runs where the peptide is not identified at the MS/MS level by leveraging information from other runs, and the development of novel intensity determination and normalization procedures (Cox et al, 2014; May et al, 2008) collectively raised the confidence of researchers in label‐free quantifications based on MS peak area measurements. The availability of the method in commercial (e.g., Progenesis LC‐MS and QI, Proteome Discoverer and Mascot), and in open‐source (MaxQant, https://www.maxquant.org; Tyanova et al, 2016) software packages also has contributed to the widespread application of the technique to retina proteomics (Cehofski et al, 2015; Eastlake et al, 2018; Gharbi et al, 2021; Grotegut et al, 2020; Hauck et al, 2010; B. Liu et al, 2020; Ly et al, 2014; Perumal et al, 2020; Ruzafa et al, 2018; Suo et al, 2022; Tu et al, 2015; Zhu et al, 2017—just to mention a few of these studies).…”

Pharmacological Inhibition of Spermine Oxidase Suppresses Excitotoxicity Induced Neuroinflammation in Mouse Retina

“…Activation of microglia, which is the primary resident immune cell in the brain and retina, results in the release of inflammatory mediators such as cytokines, reactive oxygen species (ROS), and nitric oxide (NO) [8]. Retinal excitotoxicity is suggested as a major mechanism of neurodegeneration, and experimental models of excitotoxicity are extensively used for studying retinal ganglion cells (RGCs) damage and dysfunction in ocular diseases, including optic neuropathy [9,10], glaucoma [11,12], and diabetic retinopathy [13,14].…”