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Identification of heptapeptides targeting a lethal bacterial strain in septic mice through an integrative approach

Signal Transduction and Targeted Therapy 2022年第8期7卷 3054-3068页

作者： Xiaoyan Zhang Shan Li Haihua Luo Shuyue He Huangda Yang Lei Li Tian Tian Qizheng Han Jiacong Ye Chenyang Huang Aihua Liu Yong Jiang Guangdong Provincial Key laboratory of proteomics State Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China Department of Respiratory and Critical Care Medicine Nanfang HospitalSouthern Medical UniversityGuangzhouChina

Effectively killing pathogenic bacteria is key for the treatment of *** various anti-infective drugs have been used for the treatment of sepsis,the therapeutic effect is largely limited by the lack of a specific bacterium-targeting delivery *** study aimed to develop antibacterial peptides that specifically target pathogenic bacteria for the treatment of *** lethal bacterial strain Escherichia coli MSI001 was isolated from mice of a cecal ligation and puncture(CLP)model and was used as a target to screen bacterial binding heptapeptides through an integrative bioinformatics approach based on phage display technology and high-throughput sequencing(HTS).Heptapeptides binding to *** MSI001 with high affinity were acquired after normalization by the heptapeptide frequency of the library.A representative heptapeptide VTKLGSL(VTK)was selected for fusion with the antibacterial peptide LL-37 to construct the specific-targeting antibacterial peptide *** found that,in comparison with LL37,VTK-LL37 showed prominent bacteriostatic activity and an inhibitive effect on biofilm formation in *** vivo experiments demonstrated that VTK-LL37 significantly inhibited bacterial growth,reduced HMGB1 expression,alleviated lesions of vital organs and improved the survival of mice subjected to CLP ***,membrane DEGP and DEGQ were identified as VTKbinding proteins by proteomic *** study provides a novel strategy for targeted pathogen killing,which is helpful for the treatment of sepsis in the era of precise medicine.

关键词： inhibited organs strain

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;unctional metabolomics： from biomarker ：liscovery to metabolome reprogramming

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Protein & Cell 2015年第9期6卷 628-637页

作者： Bo Peng Hui Li Xuan-Xian Peng Center for proteomics and Metabolomics State Key Laboratory of Biocontrol School of Life Sciences MOE Key Lab Aquat Food Safety School of Life Sciences Sun Yat-sen University Guangzhou 510275 China Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA 94720 USA

Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics. The crucial biomarkers can be used to reprogram a metabolome, leading to an aimed metabolic strategy to cope with alteration of internal and external environments, naming reprogramming metabo- Iomics here. The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins. The reprogramming metabolomics approach can be used to clarify metabolic mechanisms of responding to changed internal and external environmental factors and to estab- lish a framework to develop targeted tools for dealing with the changes such as controlling and/or preventing infec- tion with pathogens and enhancing host immunity against pathogens. This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of repro- gramming metabolomics.

关键词： reprogrammingregulationmetabolomics discovery metabolomicsmetabolomics metabolic strategy metabolic

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Therapeutic effect of hydrogen peroxide via altered expression of glutathione S-transferase and peroxiredoxin-2 in hepatocellular carcinoma

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Hepatobiliary & Pancreatic Diseases International 2020年第3期19卷 258-265页

作者： Zehra Hashim Amber Ilyas Shamshad Zarina Dr.Zafar H.Zaidi Center for proteomics University of KarachiKarachi 75270Pakistan

Background:Hepatocellular carcinoma(HCC)has a high incidence and mortality that epitomizes one of the prominent causes of cancer-related death *** therapeutic approaches are therefore *** oxygen species(ROS)are necessary for maintaining cell *** ROS is involved in HCC progression,hydrogen peroxide(H2O2)has anti-proliferative effect on ***:HCC Huh-7 cells were cultured and incubated with various concentrations of *** activity,levels of malondialdehyde,glutathione and protein oxidation were measured in treated and untreated Huh-7 ***,untreated and treated Huh-7 cells were subjected to two dimensional gel electrophoresis and identified protein spots which were differentially expressed by LC-MS/MS analysis.q RT-PCR was performed to validate the identified ***:H2O2 depleted glutathione(GSH)with the concomitant up-regulation of GSTP1 and Prx2.H2O2 also increased malondialdehyde and protein oxidation,decreased the activity of paraoxonase in Huh-7 ***:H2O2 could be used as a novel therapeutic agent that might be beneficial in inducing cell cytotoxicity and hence suppress HCC proliferation.

关键词： Oxidative stress Hydrogen peroxide GSTP1 Prx2 Hepatocellular carcinoma

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Dry environment on the expression of lacrimal gland S100A9,Anxa1,and Clu in rats via proteomics

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International Journal of Ophthalmology(English edition) 2024年第3期17卷 435-443页

作者： Yi-Lin Sun A-Yuan Cui Li-Xin Wang Wang-Wang Zhang Hong Shi College of Traditional Chinese Medicine Xinjiang Medical UniversityUrumqi 830011Xinjiang Uygur Autonomous RegionChina Research on High Incidence of Diseases in Xinjiang Region Key Laboratory of the Ministry of Education(Xinjiang Medical University)Urumqi 830011Xinjiang Uygur Autonomous RegionChina

●AIM:To investigate the underlying mechanism of dry environment(autumn dryness)affecting the lacrimal glands in rats.●METHODS:Twenty Sprague-Dawley rats were randomly divided into two *** rats were fed in specific pathogen free environment as the control group(n=10),and the rats fed in dry environment as the dryness group(n=10).After 24d,lacrimal glands were collected from the *** tissues morphology was observed by hematoxylineosin(HE)*** mass tags(TMT)quantitative proteomics analysis technology was used to screen the differential expressed proteins of lacrimal glands between the two groups,then bioinformatics analysis was ***,the immunohistochemical(IHC)method was used to verify the target proteins.●RESULTS:In dryness group,the lacrimal glands lobule atrophied,the glandular cavities enlarged,the sparse nuclear distribution and scattered inflammatory infiltration between the acinus were *** proteomics exhibited that a total of 195 up-regulated and 236 downregulated differential expressed proteins screened from the lacrimal glands of *** was indicated that the biological processes(BP)of differential expressed proteins mainly included cell processes and single *** cellular compositions of differential expressed proteins mainly located in cells,*** molecular functions of differential expressed proteins mainly included binding,catalytic ***,the Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis showed that the differential expressed proteins mainly involved lysosome,complement and coagulation cascade,and ribosome *** IHC result verified that the up-regulated expression proteins of Protein S100A9(S100A9),Annexin A1(Anxa1),and Clusterin(Clu)in lacrimal glands of rats in dryness group were higher than control group.●CONCLUSION:The up-regulated expression proteins of S100A9,Anxa1,and Clu may be the potential mechanisms of dry eye symptoms caused by dry *** study pr

关键词： dry eye lacrimal gland S100A9 Clu Anxa1 environment rats

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iTRAQ-based proteomic profiling reveals different protein expression between normal skin and hypertrophic scar tissue

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Burns & Trauma 2015年第2期3卷 106-113页

作者： Jianglin Tan Weifeng He Gaoxing Luo Jun Wu Institute of Burn Research State Key Laboratory of TraumaBurns and Combined InjuriesChongqing Key Laboratory for Disease ProteomicsSouthwest HospitalThird Military Medical UniversityChongqing 400038China

Background:A hypertrophic scar is a unique fibrotic disease that only exists in *** advances in burn care and rehabilitation,as well as progress in the management during these decades,the hypertrophic scar remains hard to cure following surgical methods and drugs for *** this study,we are looking forward to finding the multitude of possible traumatic mechanisms and the underlying molecular signal ways in the formation of the hypertrophic ***:We used isobaric tags for relative and absolute quantitation(iTRAQ)labeling technology,followed by high-throughput 2D LC-MS/MS,to determine relative quantitative differential proteins between the hypertrophic scar and normal skin ***:A total of 3166 proteins were identified with a high confidence(≥95%confidence).And,a total of 89 proteins were identified as the differential proteins between the hypertrophic scar and normal skin,among which 41 proteins were up-regulated and 48 proteins were down-regulated in the hypertrophic ***-Analysis indicated the up-regulated proteins were involved in extracellular matrix,whereas the down-regulated proteins were involved in dynamic junction and structural molecule ***:In our study,we demonstrate 89 proteins present differently in the hypertrophic scar compared to normal skin by iTRAQ technology,which might indicate the pathologic process of hypertrophic scar formation and guide us to propose new strategies against the hypertrophic scar.

关键词： iTRAQ Hypertrophic scar proteomics

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Toward a high resolution 2-DE profile of the normal human liver proteome using ultra-zoom gels

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Science China(Life Sciences) 2011年第1期54卷 25-33页

作者： MI Wei LIU Xin JIA Wei LI Lei CAI Yun YING WanTao QIAN XiaoHong Department of Biology Energy and Environment National Institute of Metrology Beijing 100013 China State Key laboratory of proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine Beijing 102206 China

The human liver is the largest organ in the body and has many important physiological functions. A global analysis of human liver proteins is essential for a better understanding of the molecular basis of the normal functions of the liver and of its diseases. As part of the Human Liver Proteome Project (HLPP), the goal of the present study was to visualize and detect as many proteins as possible in normal human livers using two-dimensional gel electrophoresis (2-DE). We have constructed a reference map of the proteins of human normal liver that can be used for the comprehensive analysis of the human liver proteome and other related research. To improve the resolution and enhance the detection of low abundance proteins, we developed and optimized narrow pH range ultra-zoom 2-DE gels. High resolution patterns of human liver in pH gradients 4.5-5.5, 5-6, 5.5-6.7, 6-9 and 6-11 are presented. To improve the poor resolution in the alkaline pH range of 2-DE gels, we optimized the isoelectric focusing protocol by including sample application using cup loading at the anode and incorporating 1.2% hydroxyethyl disulfide, 15% 2-propanol and 5% glycerol in the rehydration buffer. Using the optimized protocol, we obtained reproducibly better resolution in both analytical and preparative 2-DE gels. Compared with the 2386 and 1878 protein spots resolved in the wide range 3-10 and 4-7 pH gradients respectively, we obtained 5481 protein spots from the multiple (overlapping) narrow pH range ultra-zoom gels in the range of pH 4.5-9. The visualized reference map of normal human liver proteins presented in this paper will be valuable for comparative proteomic research of the liver proteome.

关键词： human liver proteome two-dimensional gel electrophoresis ultra-zoom gel mass spectrometry

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Quantitative proteomics Using Isobaric Labeling:A Practical Guide

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Genomics, proteomics & Bioinformatics 2021年第5期19卷 689-706页

作者： Xiulan Chen Yaping Sun Tingting Zhang Lian Shu Peter Roepstorff Fuquan Yang Key laboratory of Protein and Peptide Pharmaceuticals&laboratory of proteomics Institute of BiophysicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100149China Department of Biochemistry and Molecular Biology University of Southern DenmarkCampusvej 55DK-5230 Odense MDenmark

In the past decade,relative proteomic quantification using isobaric labeling technology has developed into a key tool for comparing the expression of proteins in biological *** its multiplexing capacity and flexibility make this a valuable technology for addressing various biological questions,its quantitative accuracy and precision still pose significant challenges to the reliability of its quantification ***,we give a detailed overview of the different kinds of isobaric mass tags and the advantages and disadvantages of the isobaric labeling *** also discuss which precautions should be taken at each step of the isobaric labeling workflow,to obtain reliable quantification results in large-scale quantitative proteomics *** the last section,we discuss the broad applications of the isobaric labeling technology in biological and clinical studies,with an emphasis on thermal proteome profiling and proteogenomics.

关键词： Quantitative proteomics Isobaric labeling iTRAQ TMT Mass spectrometry

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An in-depth analysis of proteomics expression profiling in rat glomeruli utilizing LC-MS

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Chinese Science Bulletin 2010年第20期55卷 2142-2151页

作者： HONG Quan XUE Peng LU Yang CHEN XiangMei QI Ka WU Di Kidney Department & Institute of Nephrology Division of Clinical Internal Medicine Chinese PLA General Hospital Beijing 100853 China laboratory of proteomics Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China

Glomeruli are an essential functional element of renal *** majority of renal diseases caused by glomerular sclerosis or fibrosis may result in renal dysfunction.A fomulate protein profile,a comprehensive analysis of glomeruli of normal rats was conducted in this study via protein *** annotation and classification of these proteins were performed and it was found that 26 had the same glomerule(endothelial cells,podocytes and mesangial cells)markers with proteins.

关键词：蛋白质组学肾小球大鼠 MS法 LC 作者内皮细胞肾功能不全

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Dynamic landscape mapping of humoral immunity to SARS-CoY-2 identifies non-structural protein antibodies associated with the survival of critical COVID-19 patients

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Signal Transduction and Targeted Therapy 2021年第9期6卷 2843-2856页

作者： Linlin Cheng Xiaomei Zhang Yu Chen Dan Wang Dong Zhang Songxin Yan Hongye Wang Meng Xiao Te Liang Haolong Li Meng Xu Xin Hou jiayu Dai Xian Wu Mingyuan Li Minya Lu Dong Wu Ran Tian Jing Zhao Yan Zhang Wei Cao Jinglan Wang Xiaowei Yan Xiang Zhou Zhengyin Liu Yingchun Xu Fuchu He Yongzhe Li Xiaobo Yu Shuyang Zhang Department of Clinical laboratory State Key Laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Science and Peking Union Medical CollegeBeijingChina State Key laboratory of proteomics Beijing Proteome Research CenterNational Center for Protein Sciences-Beijing(PHOENIX Center)Beijing Institute of LifeomicsBeijingChina

A comprehensive analysis of the humoral immune response to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)is essential in understanding COVID-19 pathogenesis and developing antibody-based diagnostics and *** this work,we performed a longitudinal analysis of antibody responses to SARS-CoV-2 proteins in 104 serum samples from 49 critical COVID-19 patients using a peptide-based SARS-CoV-2 proteome *** data show that the binding epitopes of IgM and IgG antibodies differ across SARS-CoV-2 proteins and even within the same protein.

关键词： immunity antibodies patients

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约4900年前东亚和东南亚枢纽地区狩猎采集向农业的转变

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Science Bulletin 2024年第1期69卷 103-113页

作者：马敏敏卢敏霞孙瑞朱忠华 Dorian Q.Fuller 郭健新何光林杨晓敏谭玲玲芦永秀董佳佳刘睿良杨继帅李波郭天南李小瑞赵东月张颖王传超董广辉 Key laboratory of Western China’s Environmental Systems(Ministry of Education) College of Earth and Environmental SciencesLanzhou UniversityLanzhou 730000China Zhaotong University Zhaotong 657000China Westlake laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China Yunnan Provincial Institute of Cultural Relics and Archaeology Kunming 650118China Institute of Archaeology University College LondonLondon WC1H 0PYUK School of Cultural Heritage Northwest UniversityXi’an 710069China State Key laboratory of Cellular Stress Biology School of Life SciencesXiamen UniversityXiamen 361102China Department of Anthropology and Ethnology Institute of AnthropologySchool of Sociology and AnthropologyXiamen UniversityXiamen 361005China State Key laboratory of Marine Environmental Science Xiamen UniversityXiamen 361102China Westlake Omics(Hangzhou)Biotechnology Co. Ltd.Hangzhou 310024China The Department of Asia British MuseumLondon WC1E 7JWUK Tonghai Cultural Relics Management Yuxi 652700China Group of Alpine Paleoecology and Human Adaptation Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China State Key laboratory of Tibetan Plateau Earth System Resources and EnvironmentBeijing 100101China Ministry of Education Key laboratory of Contemporary Anthropology Department of Anthropology and Human GeneticsSchool of Life SciencesFudan UniversityShanghai 200433China

The southward expansion of East Asian farmers profoundly influenced the social evolution of Southeast Asia by introducing cereal ***,the timing and routes of cereal expansion in key regions are unclear due to limited empirical *** we report macrofossil,microfossil,multiple isotopic(C/N/Sr/O)and paleoproteomic data directly from radiocarbon-dated human samples,which were unearthed from a site in Xingyi in central Yunnan and which date between 7000 and 3300 a *** isotopes reveal the earliest arrival of millet ca.4900 a BP,and greater reliance on plant and animal agriculture was indicated between 3800 and 3300 a *** dietary differences between hunter-gatherer and agricultural groups are also evident in the metabolic and immune system proteins analysed from their skeletal *** results of paleoproteomic analysis indicate that humans had divergent biological adaptations,with and without *** combined application of isotopes,archaeobotanical data and proteomics provides a new approach to documenting dietary and health changes across major subsistence transitions.

关键词： Isotopes proteomics Yunnan Millet Agricultural origins Human health

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