Epilepsy can severely affect the quality of life of patients, who are often at higher risk of mortality. However, the molecular mechanisms and pathogenesis underlying epileptogenesis are poorly understood. In this study, we performed a proteomic analysis of the hippocampus in pentylenetetrazole (PTZ)-kindled epileptic rats to explore the molecular mechanisms of epileptogenesis. We established an epileptic model in Sprague Dawley rats by injecting PTZ intraperitoneally and applied isobaric tags for relative and absolute quantification (iTRAQ) technology integrated with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify differentially expressed proteins (DEPs) in the hippocampus. A total of 99 proteins, comprising 93 upregulated and 6 downregulated proteins, were identified based on a fold change >1.2 (or <0.83) and a p-value < .05. A further bioinformatics analysis suggested that the candidate proteins were mainly involved in the ubiquitin ligase complex or metabolite homeostasis or acted as intrinsic components of the membrane. A Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway enrichment analysis identified a series of representative pathological pathways, including the calcium signaling pathway, neuroactive ligand-receptor interaction pathway, and the NF-kappa B pathway. The mass spectrometry results were further confirmed by assessing five representative proteins (Akt1, Syvn1, Amfr, Lamb1, and Cox17) using western blotting and immunohistochemistry. These results may help to reveal the molecular mechanisms underlying epileptogenesis and provide new directions or targets for epilepsy research.
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http://dx.doi.org/10.1002/jdn.10082 | DOI Listing |
Methods Mol Biol
January 2025
Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy.
Trapped ion mobility spectrometry (TIMS) using parallel accumulation serial fragmentation (PASEF) is an advanced analytical technique that offers several advantages in mass spectrometry (MS)-based lipidomics. TIMS provides an additional dimension of separation to mass spectrometry and accurate collision cross-section (CCS) measurements for ions, aiding in the structural characterization of molecules. This is especially valuable in lipidomics for identifying and distinguishing isomeric or structurally similar compounds.
View Article and Find Full Text PDFMethods Mol Biol
January 2025
Institute for Biomedicine, Eurac Research, Bolzano, Italy.
Metabolomics data analysis includes, next to the preprocessing, several additional repetitive tasks that can however be heavily dataset dependent or experiment setup specific due to the vast heterogeneity in instrumentation, protocols, or also compounds/samples that are being measured. To address this, various toolboxes and software packages in Python or R have been and are being developed providing researchers and analysts with bioinformatic/chemoinformatic tools to create their own workflows tailored toward their specific needs. This chapter presents tools and example workflows for common tasks focusing on the functionality provided by R packages developed as part of the RforMassSpectrometry initiative.
View Article and Find Full Text PDFAmino Acids
January 2025
College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
In recent years, it was found that lysine malonylation modification can affect biological metabolism and play an important role in plant life activities. Platycodon grandiflorus, an economic crop and medicinal plant, had no reports on malonylation in the related literature. This study qualitatively introduces lysine malonylation in P.
View Article and Find Full Text PDFFunct Integr Genomics
January 2025
Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL, USA.
Large-scale, pan-cancer analysis is enabled by data driven knowledge bases that link tumor molecular profiles with phenotypes. A debilitating cancer-related phenotype is skeletal muscle loss, or cachexia, which occurs partly from tumor products secreted into circulation. Using the LinkedOmicsKB knowledge base assembled from the Clinical Proteomics Tumor Analysis Consortium proteogenomic analysis, along with catalogs of human secretome proteins, ligand-receptor pairs and molecular signatures, we sought to identify candidate pan-cancer proteins secreted to blood that could regulate skeletal muscle phenotypes in multiple solid cancers.
View Article and Find Full Text PDFClin Transl Med
January 2025
Department of Dermatology and Allergy, University Hospital of Munich, Ludwig-Maximilian-University, Munich, Germany.
Background: Cancer immunotherapy has transformed metastatic cancer treatment, yet challenges persist regarding therapeutic efficacy. RECQL4, a RecQ-like helicase, plays a central role in DNA replication and repair as part of the DNA damage response, a pathway implicated in enhancing efficacy of immune checkpoint inhibitor (ICI) therapies. However, its role in patient response to ICI remains unclear.
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