Bioinformatical Analysis of Organ-Related (Heart, Brain, Liver, and Kidney) and Serum Proteomic Data to Identify Protein Regulation Patterns and Potential Sepsis Biomarkers

Influence of 30 and 60 Min of Hypobaric Hypoxia in Simulated Altitude of 15,000 ft on Human Proteome Profile

The human body reacts to hypobaric hypoxia, e.g., during a stay at high altitude, with several mechanisms of adaption. Even short-time exposition to hypobaric hypoxia leads to complex adaptions. Proteomics facilitates the possibility to detect changes in metabolism due to changes in proteins. The present study aims to identify time-dependent changes in protein expression due to hypobaric hypoxia for 30 and 60 min at a simulated altitude of 15,000 ft. N = 80 male subjects were randomized and assigned into four different groups: 40 subjects to ground control for 30 (GC30) and 60 min (GC60) and 40 subjects to 15,000 ft for 30 (HH30) and 60 min (HH60). Subjects in HH30 and HH60 were exposed to hypobaric hypoxia in a pressure chamber (total pressure: 572 hPa) equivalent to 15,000 ft for 30 vs. 60 min, respectively. Drawn blood was centrifuged and plasma frozen (−80 °C) until proteomic analysis. After separation of high abundant proteins, protein expression was analyzed by 2-DIGE and MALDI-TOF. To visualize the connected signaling cascade, a bio-informatical network analysis was performed. The present study was approved by the ethical committee of the University of Cologne, Germany. The study registry number is NCT03823677. In comparing HH30 to GC30, a total of seven protein spots had a doubled expression, and 22 spots had decreased gene expression. In a comparison of HH60 to GC60, a total of 27 protein spots were significantly higher expressed. HH60, as compared to GC30, revealed that a total of 37 spots had doubled expression. Vice versa, 12 spots were detected, which were higher expressed in GC30 vs. HH60. In comparison to GC, HH60 had distinct differences in the number of differential protein spots (noticeably more proteins due to longer exposure to hypoxia). There are indicators that changes in proteins are dependent on the length of hypobaric hypoxia. Some proteins associated with hemostasis were differentially expressed in the 60 min comparison.

Evaluation of the Molecular Mechanisms of Sepsis Using Proteomics

Sepsis is a complex syndrome promoted by pathogenic and host factors; it is characterized by dysregulated host responses and multiple organ dysfunction, which can lead to death. However, its underlying molecular mechanisms remain unknown. Proteomics, as a biotechnology research area in the post-genomic era, paves the way for large-scale protein characterization. With the rapid development of proteomics technology, various approaches can be used to monitor proteome changes and identify differentially expressed proteins in sepsis, which may help to understand the pathophysiological process of sepsis. Although previous reports have summarized proteomics-related data on the diagnosis of sepsis and sepsis-related biomarkers, the present review aims to comprehensively summarize the available literature concerning “sepsis”, “proteomics”, “cecal ligation and puncture”, “lipopolysaccharide”, and “post-translational modifications” in relation to proteomics research to provide novel insights into the molecular mechanisms of sepsis.

Proteomic Analysis of Morphologically Changed Tissues after Prolonged Dexamethasone Treatment

Prolonged dexamethasone (Dex) administration leads to serious adverse and decrease brain and heart size, muscular atrophy, hemorrhagic liver, and presence of kidney cysts. Herein, we used an untargeted proteomic approach using liquid chromatography-tandem mass spectrometry (LC-MS/MS) for simultaneous identification of changes in proteomes of the major organs in Sprague–Dawley (SD rats post Dex treatment. The comparative and quantitative proteomic analysis of the brain, heart, muscle, liver, and kidney tissues revealed differential expression of proteins (n = 190, 193, 39, 230, and 53, respectively) between Dex-treated and control rats. Functional network analysis using ingenuity pathway analysis (IPA revealed significant differences in regulation of metabolic pathways within the morphologically changed organs that related to: (i) brain—cell morphology, nervous system development, and function and neurological disease; (ii) heart—cellular development, cellular function and maintenance, connective tissue development and function; (iii) skeletal muscle—nucleic acid metabolism, and small molecule biochemical pathways; (iv) liver—lipid metabolism, small molecular biochemistry, and nucleic acid metabolism; and (v) kidney—drug metabolism, organism injury and abnormalities, and renal damage. Our study provides a comprehensive description of the organ-specific proteomic profilesand differentially altered biochemical pathways, after prolonged Dex treatement to understand the molecular basis for development of side effects.