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tandem mass tag-based proteomics analysis reveals the vital role of inflammation in traumatic brain injury in a mouse model

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Neural Regeneration Research 2023年第1期18卷 155-161页

作者： Jin-Qian Dong Qian-Qian Ge Sheng-Hua Lu Meng-Shi Yang Yuan Zhuang Bin Zhang Fei Niu Xiao-Jian Xu Bai-Yun Liu Department of Neurosurgery Beijing Tiantan HospitalCapital Medical UniversityBeijingChina Beijing Key Laboratory of Central Nervous System Injury Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina Center for Nerve Injury and Repair Beijing Institute of Brain DisordersBeijingChina China National Clinical Research Center for Neurological Diseases BeijingChina

Proteomics is a powerful tool that can be used to elucidate the underlying mechanisms of diseases and identify new biomarkers.Therefore,it may also be helpful for understanding the detailed pathological mechanism of traumatic brain injury(TBI).In this study,we performed tandem mass tag-based quantitative analysis of cortical proteome profiles in a mouse model of TBI.Our results showed that there were 302 differentially expressed proteins in TBI mice compared with normal mice 7 days after injury.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that these differentially expressed proteins were predominantly involved in inflammatory responses,including complement and coagulation cascades,as well as chemokine signaling pathways.Subsequent transcription factor analysis revealed that the inflammation-related transcription factors NF-κB1,RelA,IRF1,STAT1,and Spi1 play pivotal roles in the secondary injury that occurs after TBI,which further corroborates the functional enrichment for inflammatory factors.Our results suggest that inflammation-related proteins and inflammatory responses are promising targets for the treatment of TBI.

关键词： bioinformatics complement cascade mass spectrometry neuroinflammation proteomics secondary injury subacute phase tandem mass tag transcription factor traumatic brain injury

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Proteomics of serum exosomes identified fibulin-1 as a novel biomarker for mild cognitive impairment

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Neural Regeneration Research 2023年第3期18卷 587-593页

作者： Bo Chen Li Song Juan Yang Wei-Ying Zhou Yuan-Yuan Cheng Yu-Jie Lai College of Pharmacy Chongqing Medical UniversityChongqingChina Department of Neurology the First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory of Major Neurological and Mental DisordersChongqing Key Laboratory of NeurologyChongqingChina Department of Neurology The Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina

Mild cognitive impairment(MCI)is a prodrome of Alzheimer’s disease pathology.Cognitive impairment patients often have a delayed diagnosis because there are no early symptoms or conventional diagnostic methods.Exosomes play a vital role in cell-to-cell communications and can act as promising biomarkers in diagnosing diseases.This study was designed to identify serum exosomal candidate proteins that may play roles in diagnosing MCI.mass spectrometry coupled with tandem mass tag approach-based non-targeted proteomics was used to show the differentially expressed proteins in exosomes between MCI patients and healthy controls,and these differential proteins were validated using immunoblot and enzyme-linked immunosorbent assays.Correlation of cognitive performance with the serum exosomal protein level was determined.Nanoparticle tracking analysis suggested that there was a higher serum exosome concentration and smaller exosome diameter in individuals with MCI compared with healthy controls.We identified 69 exosomal proteins that were differentially expressed between MCI patients and healthy controls using mass spectrometry analysis.Thirty-nine exosomal proteins were upregulated in MCI patients compared with those in control patients.Exosomal fibulin-1,with an area under the curve value of 0.81,may be a biomarker for an MCI diagnosis.The exosomal protein signature from MCI patients reflected the cell adhesion molecule category.In particular,higher exosomal fibulin-1 levels correlated with lower cognitive performance.Thus,this study revealed that exosomal fibulin-1 is a promising biomarker for diagnosing MCI.

关键词： Alzheimer’s disease biomarker diagnosis exosomes fibulin mass spectrometry mild cognitive impairment tandem mass tag cell adhesion molecule nanoparticle tracking analysis

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Recent advances in proteomics and metabolomics in plants

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Molecular Horticulture 2022年第1期2卷 225-262页

作者： Shijuan Yan Ruchika Bhawal Zhibin Yin Theodore W.Thannhauser Sheng Zhang Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization Agro-biological Gene Research CenterGuangdong Academy of Agricultural SciencesGuangzhouChina Proteomics and Metabolomics Facility Institute of BiotechnologyCornell University139 Biotechnology Building526 Campus RoadIthacaNY 14853USA R.W.Holley Center for Agriculture&Health USDA/ARSIthacaNYUSA

Over the past decade,systems biology and plant-omics have increasingly become the main stream in plant biology research.New developments in mass spectrometry and bioinformatics tools,and methodological schema to inte-grate multi-omics data have leveraged recent advances in proteomics and metabolomics.These progresses are driv-ing a rapid evolution in the field of plant research,greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment.Here,we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response,gene/protein function characterization,metabolic and signaling pathways exploration,and natural product discovery.We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology.This review is intended to provide readers with an overview of how advanced MS technology,and integrated application of proteomics and metabolomics can be used to advance plant system biology research.

关键词： LC-MS GC-MS Single cell proteomics Phosphoproteomics tandem mass tag Fluxomics Spatially resolved metabolomics mass spectrometry imaging

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mass Spectrometry-based Quantitative Proteomic Profiling of Human Pancreatic and Hepatic Stellate Cell Lines

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Genomics, Proteomics & Bioinformatics 2013年第2期11卷 105-113页

作者： Joao A.Paulo Vivek Kadiyala Peter A.Banks Darwin L.Conwell Hanno Steen Department of Pathology Boston Children's Hospital Proteomics Center at Boston Children's Hospital Center for Pancreatic Disease Division of GastroenterologyHepatology and EndoscopyBrigham and Women's Hospital and Department of MedicineHarvard Medical School

The functions of the liver and the pancreas differ; however, chronic inflammation in both organs is associated with fibrosis. Evidence suggests that fibrosis in both organs is partially regu- lated by organ-specific stellate cells. We explore the proteome of human hepatic stellate cells （hHSC） and human pancreatic stellate cells （hPaSC） using mass spectrometry （MS）-based quanti- tative proteomics to investigate pathophysiologic mechanisms. Proteins were isolated from whole cell lysates of immortalized hHSC and hPaSC. These proteins were tryptically digested, labeled with tandem mass tags （TMT）, fractionated by OFFGEL, and subjected to MS. Proteins significantly different in abundance （P 〈 0.05） were classified via gene ontology （GO） analysis. We identified 1223 proteins and among them, 1222 proteins were quantifiable. Statistical analysis determined that 177 proteins were of higher abundance in hHSC, while 157 were of higher abundance in hPaSC. GO classification revealed that proteins of relatively higher abundance in hHSC were associated with protein production, while those of relatively higher abundance in hPaSC were involved in cell structure. Future studies using the methodologies established herein, but with further upstream fractionation and/or use of enhanced MS instrumentation will allow greater proteome coverage, achieving a comprehensive proteomic analysis of hHSC and hPaSC.

关键词： Fibrosis Proteomics Pancreas tandem mass tag

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Global Analysis of Phosphorylation Pattern of Silkworm Cells after BmNPV Infection and the Functional Investigation of BmNPV 39K

Global Analysis of Phosphorylation Pattern of Silkworm Cells...

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作者： Jauharotus Shobahah 浙江理工大学

学位级别：硕士

Bombyx mori has become an important model organism for many fundamental studies.Bombyx mori nucleopolyhedrovirus（BmNPV）is a significant pathogen to Bombyx mori,yet also an efficient vector for recombinant protein production.A previous study indicated that acetylation plays many vital roles in several cellular processes of Bombyx mori while global phosphorylation pattern upon BmNPV infection remains elusive.Employing tandem mass tag（TMT）labeling and phosphorylation affinity enrichment followed by high-resolution LC-MS/MS analysis and intensive bioinformatics analysis,the quantitative phosphoproteome in Bombyx mori cells infected by BmNPV at 24 hpi with an MOI of 10 was extensively examined.Totally,6480 phosphorylation sites in 2112 protein groups were identified,among which 4764sites in 1717 proteins were quantified.Among the quantified proteins,81 up-regulated and 25down-regulated sites were identified with significant criteria（the quantitative ratio above 1.3 was considered as up-regulation and below 0.77 was considered as down-regulation）and with significant p-value（p＜0.05）.Some proteins of BmNPV were also hyperphosphorylated during infection,such as P6.9,39K,LEF-6,Ac58-like protein,Ac82-like protein and BRO-D.The phosphorylated proteins were primary involved in several specific functions,out of which,we focused on the binding activity,protein synthesis,viral replication and apoptosis through kinase activity.During infection,BmNPV 39K has 4 phosphorylated sites which one of them has a great phosphorylation ratio（16.683）.Interestingly,the homolog of 39k,AcMNPV orf 36 also called pp31 has been reported to be phosphorylated as well.On this basis,we then aimed to further investigate the function of phosphorylation on BmNPV 39K in the viral replication and transcription.In order to investigate the biological function of phosphorylation in BmNPV 39K,we constructed the mutant of the highest phosphorylated site of 39K(136

关键词： Bombyx ori BmNPV 39K Phosphorylation Proteomic tandem mass tag Regulation

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