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Identification of hedgehog signaling as a potential oncogenic driver in an aggressive subclass of human hepatocellular carcinoma: A reanalysis of the TCGA cohort

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Science China(Life Sciences) 2019年第11期62卷 1481-1491页

作者： Yang Zhao Li Zhang Yong Zhang Bo Meng Wantao Ying xiaohong qian College of Life Science and Bioengineering Beijing University of TechnologyBeijing 100124China State Key Laboratory of Proteomics Beijing Proteome Research CenterNational Center for Protein Sciences(Beijing)Beijing Institute of LifeomicsBeijing 102206China Center for Bioinformatics and Computational Biology Institute of Biomedical SciencesSchool of Life SciencesEast China Normal UniversityShanghai 200241China School of Statistics Faculty of Economics and ManagementEast China Normal UniversityShanghai 200241China Key Lab of Transplant Engineering and Immunology West China-Washington Mitochondria and Metabolism Research CenterWest China HospitalSichuan UniversityChengdu 610041China

Hepatocellular carcinoma(HCC)is a heterogeneous disease and the second most common cause of cancer-related death *** developments in genomic technologies helped scientists to understand the heterogeneity of HCC and identified multiple HCC-related molecular *** integrative analysis of genomic datasets including 196 patients from The Cancer Genome Atlas(TCGA)group has recently reported a new HCC subclass,which contains three subgroups(iCluster1,iCluster2,and iCluster3).However,the transcriptional molecular characteristics underlying the iClusters have not been thoroughly ***,we identified a more aggressive subset of HCC patients in the iCluster1,and re-clustered the TCGA samples into novel HCC subclasses referred to as aggressive(Ag),moderate-aggressive(M-Ag),and less-aggressive(L-Ag)*** Ag subclass had a greater predictive power than the TCGA iCluster1,and a higher level of alpha fetoprotein,microscopic vascular invasion,immune infiltration,isocitrate dehydrogenase 1/2 mutation status,and a worse survival than MAg and L-Ag *** transcriptomic analysis showed that activation of hedgehog signaling in the Ag subclass may play key roles in tumor development of aggressive ***1,a key transcriptional regulator of hedgehog signaling upregulated in the Ag subclass,was correlated with poor prognosis of HCC,and may be a potential prognostic biomarker and therapeutic target for Ag subclass HCC patients.

关键词： hepatocellular carcinoma The Cancer Genome Atlas molecular subclass Wnt hedgehog

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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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Global characterization of modifications to the charge isomers of IgG antibody

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Journal of Pharmaceutical Analysis 2022年第1期12卷 156-163页

作者： Xinling Cui Wei Mi Zhishang Hu Xiaoyu Li Bo Meng Xinyuan Zhao xiaohong qian Tao Zhu Wantao Ying State Key Laboratory of Proteomics Beijing Proteome Research CenterNational Center for Protein Sciences(Beijing)Beijing Institute of LifeomicsBeijingChina National Institute of Metrology Center for Advanced Measurement ScienceBeijingChina National Institute of Metrology Chemical Metrology&Analytical Science DivisionBeijingChina CanSino Bio Corporation Tianjin Key Laboratory of Recombinant Bacterial Recombination and Bacterial Vaccines TianjinChina

Posttranslational modifications of antibody products affect their stability,charge distribution,and drug activity and are thus a critical quality *** comprehensive mapping of antibody modifications and different charge isomers(CIs)is of utmost importance,but is *** intended to quantitatively characterize the posttranslational modification status of CIs of antibody drugs and explore the impact of posttranslational modifications on charge *** CIs of antibodies were fractionated by strong cation exchange chromatography and verified by capillary isoelectric focusing-whole column imaging detection,followed by stepwise structural characterization at three ***,the differences between CIs were explored at the intact protein level using a top-down mass spectrometry approach;this showed differences in glycoforms and deamidation ***,at the peptide level,common modifications of oxidation,deamidation,and glycosylation were *** mapping showed nonuniform deamidation and glycoform distribution among *** total,10 N-glycoforms were detected by peptide ***,an in-depth analysis of glycan variants of CIs was performed through the detection of enriched *** and quantitative analyses demonstrated the dynamics of 24 *** results revealed that sialic acid modification is a critical factor accounting for charge heterogeneity,which is otherwise missed in peptide mapping and intact molecular weight *** study demonstrated the importance of the comprehensive analyses of antibody CIs and provides a reference method for the quality control of biopharmaceutical analysis.

关键词： Antibody Charge isomers Mass spectrometry Posttranslational modification Glycopeptide

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A Tentative Study on English Euphemism

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Journal of Contemporary Educational Research 2020年第2期4卷 9-12页

作者： xiaohong qian School of Foreign Languages Qujing Teachers CollegeQujing 655001Yunnan ProvincesChina

The word“euphemism”comes from the Greek,eu--means“good”,and–pheme-,“speech”or“saying”,and together it means literally“to speak with good words or in a pleasant manner”.Euphemism,as a cultural phenomenon as well as a linguistic concept,has attracted people’s attention for a long *** has long been a topic of much *** every society there are certain things that are supposed to be *** words make someone embarrassed,unhappy,dislike or fear when used in *** we express the meaning directly,we will make such impression which is vulgar,frivolous,and *** order to avoid the embarrassment or ease the sting of harsh words,man has created euphemisms.

关键词： English euphemism Features Origin Functions

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Plasma biomarker screening for liver fibrosis with the N-terminal isotope tagging strategy

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Science China(Life Sciences) 2011年第5期54卷 393-402页

作者： LI ShuLong LIU Xin WEI Lai WANG HuiFen ZHANG JiYang WEI HanDong qian xiaohong JIANG Ying HE FuChu State Key Laboratory of Proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine Beijing 102206 China Beijing Institute of Biotechnology Beijing 100071 China People 's Hospital of Peking University Beijing 100044 China 302 Military Hospital of China Beijing 100039 China Institutes of Biomedical Sciences Fudan University Shanghai 200032 China Central Laboratory Yantai Yu-Huang-Ding Hospital Yantai 264000 China

A non-invasive diagnostic approach is crucial for the evaluation of severity of liver disease,treatment decisions,and assessing drug *** study evaluated plasma proteomic profiling via an N-terminal isotope tagging strategy coupled with liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry measurement to detect liver fibrosis *** plasma from different liver fibrosis stages,which were assessed in advance by the current gold-standard of liver biopsy,was quantitatively analyzed.A total of 72 plasma proteins were found to be dysregulated during the fibrogenesis process,and this finding constituted a valuable candidate plasma biomarker bank for follow-up *** results of fibronectin by Western blotting reconfirmed the mass-based *** Pathways Analysis showed four types of metabolic networks for the functional effect of liver fibrosis disease in chronic hepatitis B ***,quantitative proteomics via the N-terminal acetyl isotope labeling technique provides an effective and useful tool for screening plasma candidate biomarkers for liver *** quantitatively monitored the fibrogenesis process in CHB *** discovered many new valuable candidate biomarkers for the diagnosis of liver fibrosis and also partly identified the mechanism involved in liver fibrosis *** results provide a clearer understanding of liver fibrosis pathophysiology and will also hopefully lead to improvement of clinical diagnosis and treatment.

关键词： quantitative proteomics fiver fibrosis biomarker plasma hepatitis B virus

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World Governments Focus

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Women of China 1995年第4期 20-21页

作者： LIU qian xiaohong LIU

HEALTH was once a matter only doctors were concerned about. But in recent years, women’s health issues have been a part of the women’s movement. A woman’s right to health and health care is now the concern of society. In the 1990s, it is becoming apparent that quality of life is of foremost importance. At the World Summit for Children held in September 1990 in New York, government leaders from over 140 countries gathered for the first time

关键词： World Governments Focus

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A novel method for identification and relative quantification of N-terminal peptides using metal-element-chelated tags coupled with mass spectrometry

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Science China Chemistry 2014年第5期57卷 708-717页

作者： YAN Hui HAO FeiRan CAO QiChen LI JiaBin LI NanNan TIAN Fang BAI HaiHong REN XiaoJun LI XianYu ZHANG YangJun qian xiaohong Anhui Medical University State Key Laboratory of Proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine Affiliated Hospital of Liaoning University of Traditional Chinese Medicine

By means of the reaction between a DOTA-NHS-ester bifunctional reagent and N-terminal peptides of proteins, and then che- lation of lanthanide metal ions as tags, we established a novel method for the identification of N-terminal peptides of proteins and their relative quantification using metal-element-chelated tags coupled with mass spectrometry. The experimental results indicate that metal elements are able to completely label N-terminal peptides at the protein level. The N-terminal peptides are enriched as the peptides digested with trypsin are selectively eliminated by isothiocyanate-coupled silica beads. We success- fully identified the N-terminal peptides of 158 proteins of Thermoanaerobacter tengcongensis incubated at 55 and 75 ℃, among which N-terminal peptides of 24 proteins are partially acetylated. Moreover, metal-element tags with high molecule weights make it convenient for N-terminal peptides consisting of less than 6 amino acids to be identified; these make up 55 percent of the identified proteins. Finally, we developed a general approach for the relative quantification of proteins based on N-terminal peptides. We adopted lysozyme and ribonuclease B as model proteins; the correlation coefficients （R2） of the standard curves for the quantitative method were 0.9994 and 0.9997, respectively, with each concentration ratio ranging from 0.1 to 10 and both relative standard derivations （RSD） measured at less than 5%. In T. tengcongensis at two incubation tem- peratures, 80 proteins possess quantitative information. In addition, compared with the proteins of T. tengcongensis incubated at 55 ℃, in T. tengcongensis incubated at 75 ℃, 7 proteins upregulate whereas 16 proteins downregulate, and most differential proteins are related to protein synthesis.

关键词： metal-element-chelated tags N-terminal peptides proteomics mass spectrometry

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Preparation of Sequence-controlled Triblock-copolymer GraftedSilica Microparticles by Sequential-ATRP for Highly EfficientGlycopeptides Enrichment and Identification by Mass Spectrometry

Preparation of Sequence-controlled Triblock-copolymer Grafte...

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中国生物化学与分子生物学会第十一次会员代表大会暨2014年全国学术会议

作者： Weijie Qin xiaohong qian Beijing Proteome Research Center

As one of the most important sub-proteomes in eukaryote cells, N-glycoproteins play crucialroles in various of biological processes and have long been considered closely correlatedwith the occurrence, progression and metastasis of cancer. Comprehensive characterizationof protein N-glycosylation and association of their aberrant patterns to the correspondingcancer stage may provide a unique way to discover new diagnostic biomarkersand therapeutic drug targets. However, the extremely complex nature of biologicalsamples and relatively low abundance of N-glycosylated proteins makes the enrichment ofglycoprotein/glycopeptide a prerequisite for large scale N-glycosylation identification. Inthis work, we prepared sequence controlled triblock-copolymer grafted silicamicroparticles(TGP-SMs) by sequential atom transfer radical polymerization(sequential-ATRP) of monosaccharides and zwitterionic-ion monomers for highly efficient and selectiveglycopeptides enrichment. The triblock-copolymer is composed of sequence definedpoly-zwitterionic-ion, poly-N-acetylglucosamine and poly-mannose blocks. The glycopolymerblocks carrying densely packed pending sugars are excellent mimics of the naturalcarbohydrate clusters and may induce multivalent carbohydrate-carbohydrate interaction(CCI) with the target glycopeptides. Therefore, increased retention of glycopeptides can beexpected by the combination of CCI and zwitterionic-HILIC interaction. As a result, 1244 glycopeptides were identified after TGP-SMs enrichment from mouse liver, which are 65-120% higher than that obtained by homo-glycopolymer or random-copolymer graftedsilica microparticles prepared using the conventional free radical polymerization. Theseresults demonstrate the critical role of sequence-defined block-copolymer of TGP-SMs forobtaining enhanced affinity towards glycopeptides and the potential of this sequentialATRP strategy to integrate different affinity moieties into one enrichment material toachieve deeper coverage in

关键词： Protein-PTM N-glycosylation Enrichment Identification Mass-spectrometry

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An ultra-fast and highly efficient multiple proteases digestion strategy using graphene-oxide-based immobilized protease reagents

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Science China Chemistry 2014年第5期57卷 695-702页

作者： BAI HaiHong PAN YiTing REN XiaoJun HAO FeiRan DENG ShanShan FAN Chao YAN Hui SHEN BingQuan MA Lin TIAN Fang PENG Bo DENG YuLin QIN WeiJie qian xiaohong School of Life Science and Technology Beijing Institute of Technology National Center for Protein Sciences Beijing State Key Laboratory of Proteomics Beijing Proteome Research CenterBeijing Institute of Radiation Medicine

Highly efficient and rapid proteolytic digestion of proteins into peptides is a crucial step in shotgun-based proteome-analysis strategy. Tandem digestion by two or more proteases is demonstrated to be helpful for increasing digestion efficiency and de- creasing missed cleavages, which results in more peptides that are compatible with mass-spectrometry analysis. Compared to conventional solution digestion, immobilized protease digestion has the obvious advantages of short digestion time, no self-proteolysis, and reusability. We proposed a multiple-immobilized proteases-digestion strategy that combines the ad- vantages of the two digestion strategies mentioned above. Graphene-oxide （GO）-based immobilized trypsin and endoprotein- ase Glu-C were prepared by covalently attaching them onto the GO surface. The prepared GO-trypsin and GO-Glu-C were successfully applied in standard protein digestion and multiple immobilized proteases digestion of total proteins of Thermoan- aerobacter tengcongensis. Compared to 12-hour solution digestion using trypsin or Glu-C, 14% and 7% improvement were obtained, respectively, in the sequence coverage of BSA by one-minute digestion using GO-trypsin and GO-GIu-C. Multiple immobilized-proteases digestion of the total proteins of Thermoanaerobacter tengcongensis showed 24.3% and 48.7% en- hancement in the numbers of identified proteins than was obtained using GO-trypsin or GO-Glu-C alone. The ultra-fast and highly efficient digestion can be contributed to the high loading capacity of protease on GO, which leads to fewer missed cleavages and more complete digestion. As a result, improved protein identification and sequence coverage can be expected.

关键词： graphene oxide Trypsin GIu-C immobilized protease multiple proteases digestion

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磷酸化蛋白质分析技术在蛋白质组研究中的应用

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分析化学 2005年第7期33卷 1029-1035页

作者：王京兰钱小红军事医学科学院放射医学研究所军事医学科学院放射医学研究所北京100850

磷酸化修饰蛋白质的分析是蛋白质组研究中的重要内容。对于目前磷酸化蛋白质分析所涉及的各种方法,包括放射性同位素标记,抗体免疫印记等传统方法和以串联质谱各种扫描技术为基础,结合亲和提取、液相色谱质谱联用等手段的新技术、新方法... 详细信息

磷酸化修饰蛋白质的分析是蛋白质组研究中的重要内容。对于目前磷酸化蛋白质分析所涉及的各种方法,包括放射性同位素标记,抗体免疫印记等传统方法和以串联质谱各种扫描技术为基础,结合亲和提取、液相色谱质谱联用等手段的新技术、新方法,以及这些技术在磷酸化蛋白质组学中的应用予以评述。

关键词：磷酸化修饰蛋白质组生物质谱评述

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