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Fractionation-free negative enriching for in-depth C-terminome analysis

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Chinese Chemical Letters 2022年第3期33卷 1343-1345页

作者： Jingtian Lu Ting Wang Huimin Bao Haojie Lu department of chemistry and Shanghai Cancer Center Fudan UniversityShanghai 200438China Institutes of Biomedical Sciences and nhc key laboratory of glycoconjugates research Fudan UniversityShanghai 200032China

Herein, we developed a fractionation-free negative enriching method incorporating methylamidation, siteselective dimethylation and aldehyde resin coupling(MADMAR) for in-depth C-terminome analysis. The methylamidation blocked the free carboxyl group on proteins first, followed by Lys C digestion of methylamidated proteins. Then, the site-selective dimethylation blocked the N-terminal amino group of the digested peptides without affecting the amino groups of lysine. Finally, the aldehyde resin was used to capture non-C-terminal peptides containing amino groups from lysine, while leaving the C-terminal peptides without free amino group in the supernatant for its analysis. We identified 1359 database-annotated protein C-termini from 50 μg He La proteins, which was 74% more than our previous method based on aldehyde resin. Moreover, 279 protein neo-C-termini were identified.

关键词： C-terminome In-depth analysis Negative enrichment Neo-C-termini Methylamidation HeLa

Discover the Post-Translational Modification Proteome Using Mass Spectrometry

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Chinese Journal of chemistry 2021年第3期39卷 550-558页

作者： Ying Zhang Caiyun Fang Huimin Bao Wenjuan Yuan Haojie Lu Shanghai Cancer Center and Institutes of Biomedical Sciences Fudon UniversityShanghai 200032China Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research Fudan UniversityShanghai 200032China

Protein post-translational modifications(PTMs)are chemical modifications on proteins.PTMs play a key role in many cellular processes by influencing the structure of proteins and dynamically regulating their functions.Therefore,characterizing PTMs at proteome level is critical to provide invaluable insight into the functions of proteins underlying different biological processes.Advances in modern proteomics technologies including sample preparation,chromatography separation as well as mass spectrometry have propelled the PTMs proteome to further depths.During the past decade,to better examine the PTMs with high sensitivity and selectivity,our group have developed a series of MS-based novel analytical approaches to study the protein PTMs.Herein,we mainly introduce these approaches developed by our group and discuss how to overcome the technical obstacles of studying various protein PTMs with mass spectrometry.

关键词： Proteome Mass spectrometry Post translational modification Qualitative analysis Quantitative analysis

OGP: A Repository of Experimentally Characterized O-glycoproteins to Facilitate Studies on O-glycosylation

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Genomics, Proteomics & Bioinformatics 2021年第4期19卷 611-618页

作者： Jiangming Huang Mengxi Wu Yang Zhang Siyuan Kong Mingqi Liu Biyun Jiang Pengyuan Yang Weiqian Cao department of chemistry and Institutes of Biomedical Sciences Fudan UniversityShanghai 200032China The Fifth People’s Hospital Fudan Universityand the Shanghai Key Laboratory of Medical Epigeneticsthe International Co-laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyFudan UniversityShanghai 200032China nhc key laboratory of glycoconjugates research(Fudan University) Shanghai 200032China

Numerous studies on cancers, biopharmaceuticals, and clinical trials have necessitated comprehensive and precise analysis of protein O-glycosylation. However, the lack of updated and convenient databases deters the storage of and reference to emerging O-glycoprotein data. To resolve this issue, an O-glycoprotein repository named OGP was established in this work.It was constructed with a collection of O-glycoprotein data from different sources. OGP contains 9354 O-glycosylation sites and 11,633 site-specific O-glycans mapping to 2133 O-glycoproteins, and it is the largest O-glycoprotein repository thus far.Based on the recorded O-glycosylation sites, an O-glycosylation site prediction tool was developed. Moreover, an OGP-based website is already available(http://***/). The website comprises four specially designed and user-friendly modules:statistical analysis, database search, site prediction, and data submission. The first version of OGP repository and the website allow users to obtain various O-glycoprotein-related information, such as protein accession Nos., O-glycosylation sites,O-glycopeptide sequences, site-specific O-glycan structures, experimental methods, and potential O-glycosylation sites.O-glycosylation data mining can be performed efficiently on this website, which will greatly facilitate related studies. In addition, the database is accessible from OGP website(http://***/download.php).

关键词： O-glycosylation O-glycoprotein repository Site prediction O-glycoprotein related website Data mining

Nascent Proteome and Glycoproteome Reveal the Inhibition Role of ALG1 in Hepatocellular Carcinoma Cell Migration

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Phenomics 2022年第4期2卷 230-241页

作者： Xinyi Cao Yuyin Shao Peiyi Meng Zhao Cao Guoquan Yan Jun Yao Xinwen Zhou Chao Liu Lei Zhang Hong Shu Haojie Lu Institutes of Biomedical Sciences and Shanghai Cancer Center Fudan UniversityShanghai 200032China Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research Fudan UniversityShanghai 200433China department of Clinical laboratory First Affiliated Hospital of Guangxi Medical UniversityNanning 530021China Beijing Advanced Innovation Center for Precision Medicine Beihang UniversityBeijing 100083China department of Clinical laboratory Guangxi Medical University Cancer HospitalNanning 530021China

Asparagine-linked glycosylation protein 1 homolog(ALG1)participates in the initial stage of protein N-glycosylation and N-glycosylation has been implicated in the process of hepatocellular carcinoma(HCC)progression.However,whether ALG1 plays a role in human HCC remains unknown.In this study,the expression profile of ALG1 in tumorous and corresponding adjacent non-tumor tissues was analyzed.The relationship of ALG1 expression with clinical features and prognosis of HCC patients was also evaluated using immuno-histochemical method.Here we found ALG1 decreased in HCC tissues compared with adjacent normal liver tissues,which predicted an unfavorable prognosis.Combined with RNA interference,nascent proteome and glycoproteome were determined systematically in Huh7 cell line.Bioinformatics analysis indicated that the differentially expressed proteins participating in the response of ALG1 knockdown were most significantly associated with cell-cell adhesion.Functional studies confirmed that knockdown of ALG1 reduced cell adhesion capacity,and promoted cell migration.Furthermore,down-regulation of H8N2(on N-glycosite N651)and H5N4S2F1(on N-glycosite N692)from N-cadherin was identified as a feature of ALG1 knockdown.Our findings revealed that ALG1 controlled the expression of glycosylated N-cadherin and played a role in HCC migration,with implications for prognosis.

关键词： Nascent proteome ALG1 Glycosylation N-cadherin Hepatocellular carcinoma

Identification and semisynthesis of(-)-anisomelic acid as oral agent against SARS-CoV-2 in mice

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National Science Review 2022年第11期9卷 29-36页

作者： Hai-Xin Yu Nan Zheng Chi-Tai Yeh Chien-Ming Lee Qi Zhang Wen-Lv Zheng Qing Chang Yuan-He Li Yu-Jun Li Gui-Zhen Wu Jun-Min Quan Lin-Qi Zhang Yew-Min Tzeng Zhen Yang laboratory of Chemical Genomics School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School department of Medicinal research and Education Taipei Medical University-Shuang Ho Hospital department of Applied Science Taitung University Center for Global Health and Infectious Diseases Comprehensive AIDS Research Center and Beijing Advanced Innovation Center for Structural Biology School of Medicine Tsinghua University Lanzhou Institute of Separation Science State key laboratory of Bioorganic chemistry and Molecular Engineering of Ministry of Education and Beijing National laboratory for Molecular Science(BNLMS) College of Chemistry and Molecular EngineeringPeking University Shenzhen Bay laboratory nhc key laboratory of Biosafety National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention department of Applied chemistry Chaoyang University of Technology

(-)-Anisomelic acid, isolated from Anisomeles indica(L.) Kuntze(Labiatae) leaves, is a macrocyclic cembranolide with a trans-fused α-methylene-γ-lactone motif. Anisomelic acid effectively inhibits SARS-Co V-2 replication and viral-induced cytopathic effects with an EC50 of 1.1 and 4.3 μM, respectively.Challenge studies of SARS-CoV-2-infected K18-hACE2 mice showed that oral administration of anisomelic acid and subcutaneous dosing of remdesivir can both reduce the viral titers in the lung tissue at the same level. To facilitate drug discovery, we used a semisynthetic approach to shorten the project timelines. The enantioselective semisynthesis of anisomelic acid from the naturally enriched and commercially available starting material(+)-costunolide was achieved in five steps with a 27% overall yield.The developed chemistry provides opportunities for developing anisomelic-acid-based novel ligands for selectively targeting proteins involved in viral infections.

关键词： identification enantioselective semisynthesis (−)-anisomelic acid oral agent anti-SARS-CoV-2

Recent advances in the synthesis and application of N-heterocyclic carbene-based molecular cages

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Science China chemistry 2024年第5期67卷 1510-1523页

作者： Qiongjie Chai Lixin Duan Yanzhe Ma Tianheng Hou Tao Tu Shanghai key laboratory of Molecular Catalysis and Innovative Materials Department of ChemistryFudan UniversityShanghai 200438China State key laboratory of Organometallic chemistry Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai 200032China

N-Heterocyclic carbene(nhc)-based cages have emerged as a prominent and dynamic research area within the research field of chemistry. Leveraging the distinctive electronic and steric properties of nhc ligands, the design, synthesis, and application of these corresponding cages have garnered substantial scholarly interest. In recent years, we have witnessed the successful fabrication of diverse nhc-based cages through a range of synthetic methodologies, which hold significant potential for applications in molecular recognition and catalysis. In this review, we delve into the foundational synthetic strategies that underlie the creation of nhc-based cages, employing approaches encompassing metal–nhc chelation, coordination assembly,and covalent bonding. Additionally, we compile the diverse applications of these cages within catalytic processes and molecular recognition. Lastly, we shed light on the current limitations of synthesis and outline future trends in the development of nhcbased cages.

关键词： N-heterocyclic carbene molecular cages supramolecular chemistry synthetic strategies applications

α2,3-Sialylation with Fucosylation Associated with More Severe Anti-MDA5 Positive Dermatomyositis Induced by Rapidly Progressive Interstitial Lung Disease

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Phenomics

Phenomics 2023年第5期3卷 457-468页

作者： Rongrong Zhang Li Guo Jichen Sha Shuwai Chang Jiangfeng Zhao Kaiwen Wang Jiucun Wang Jianxin Gu Jing Liu Shifang Ren nhc key laboratory of glycoconjugates research Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesFudan UniversityShanghai 200032China Zhangjiang Fudan International Innovation Center Human Phenome InstituteFudan UniversityShanghai 200032China department of Rheumatology Renji HospitalShanghai Jiao Tong University School of MedicineShanghai 200032China State key laboratory of Genetic Engineering School of Life ScienceFudan UniversityShanghai 200032China

Dermatomyositis(DM)is a heterogeneous autoimmune disease associated with numerous myositis specific antibodies(MSAs)in which DM with anti-melanoma differentiation-associated gene 5-positive(MDA5+DM)is a unique subtype of DM with higher risk of developing varying degrees of Interstitial lung disease(ILD).Glycosylation is a complex posttranslational modification of proteins associated with many autoimmune diseases.However,the association of total plasma N-glycome(TPNG)and DM,especially MDA5+DM,is still unknown.TPNG of 94 DM patients and 168 controls were analyzed by mass spectrometry with in-house reliable quantitative method called Bionic Glycome method.Logistic regression with age and sex adjusted was used to reveal the aberrant glycosylation of DM and the association of TPNG and MDA5+DM with or without rapidly progressive ILD(RPILD).The elastic net model was used to evaluate performance of glycans in distinguishing RPLID from non-RPILD,and survival analysis was analyzed with N-glycoslyation score by Kaplan-Meier survival analysis.It was found that the plasma protein N-glycome in DM showed higher fucosylation and bisection,lower sialylation(α2,3-notα2,6-linked)and galactosylation than controls.In MDA5+DM,more severe disease condition was associated with decreased sialylation(specificallyα2,3-sialylation with fucosylation)while accompanying elevated H6N5S3 and H5N4FSx,decreased galactosylation and increased fucosylation and the complexity of N-glycans.Moreover,glycosylation traits have better discrimination ability to distinguish RPILD from non-RPILD with AUC 0.922 than clinical features and is MDA5-independent.Survival advantage accrued to MDA5+DM with lower N-glycosylation score(p=3e-04).Our study reveals the aberrant glycosylation of DM for the first time and indicated that glycosylation is associated with disease severity caused by ILD in MDA5+DM,which might be considered as the potential biomarker for early diagnosis of RPILD and survival evaluation of MDA5+DM.

关键词： Dermatomyositis Anti-melanoma differentiation-associated gene 5-positive Interstitial lung disease Glycosylation Matrix assisted laser desorption/ionization time of flight mass spectrometry

Tellurium-driven maple leaf-shaped manganese nanotherapeutics reshape tumor microenvironment via chemical transition in situ to achieve highly efficient radioimmunotherapy of triple negative breast cancer

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Bioactive Materials 2023年第9期27卷 560-573页

作者： Wei Huang Sujiang Shi Haoran Lv Zhenyu Ju Qinghua Liu Tianfeng Chen Jieyang Medical research Center Jieyang People’s HospitalTianfu Road 107Rongcheng DistrictJieyangGuangdong522000China department of Nephrology The First Affiliated HospitalNHC Key Laboratory of Clinical Nephrology(Sun Yat-Sen University)and Guangdong Provincial Key Laboratory of NephrologySun Yat-sen UniversityGuangzhouChina key laboratory of Regenerative Medicine of Ministry of Education Institute of Aging and Regenerative MedicineJinan UniversityGuangzhou510632China department of chemistry Jinan UniversityGuangzhou510632China

The therapeutic efficacy of radioimmunotherapy against triple negative breast cancer(TNBC)is largely limited by the complicated tumor microenvironment(TME)and its immunosuppressive state.Thus developing a strategy to reshape TME is expected to achieve highly efficient radioimmunotherapy.Therefore,we designed and synthesized a tellurium(Te)-driven maple leaf manganese carbonate nanotherapeutics(MnCO3@Te)by gas diffusion method,but also provided a chemical catalytic strategy in situ to augment ROS level and activate immune cells for improving cancer radioimmunotherapy.As expected,with the help of H2O2 in TEM,MnCO3@Te heterostructure with reversible Mn3+/Mn2+transition could catalyze the intracellular ROS overproduction to amplify radiotherapy.In addition,by virtue of the ability to scavenge H+in TME by carbonate group,MnCO3@Te directly promote the maturation of dendritic cells and macrophage M1 repolarization by stimulator of interferon genes(STING)pathway activation,resulting in remodeling immuno-microenvironment.As a result,MnCO3@Te synergized with radiotherapy and immune checkpoint blockade therapy effectively inhibited the breast cancer growth and lung metastasis in vivo.Collectively,these findings indicate that MnCO3@Te as an agonist,successfully overcome radioresistance and awaken immune systems,showing promising potential for solid tumor radioimmunotherapy.

关键词： Radioimmunotherapy Triple negative breast cancer Tellurium Manganese carbonate Tumor microenvironment

Pan-Specific Antibodies as Novel Tools to Detect Valyllysine

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Reproductive and Developmental Medicine 2020年第2期4卷 78-83页

作者： Ya-Ling Wang Min-Yan Liu Yu-Hua Li Yi-TingYang Wei-Wei Wang He-GuoYu Zhi-Yu Shao Hua Diao department of Reproductive Biology NHC Key Laboratory of Reproduction Regulation(Shanghai Institute of Planned Parenthood Research)School of Basic Medical SciencesFudan UniversityShanghai 200032China College of chemistry Chemical Engineering and BiotechnologyDonghua UniversityShanghai 201620China

Objective:Amino acyl modification of lysine residues is an essential mechanism of nutrient sensing that regulates various biological functions including reproduction.At present,the lack of pan-specific antibodies for a recently identified lysine valylation hinders the characterization and detection of this modification.The objective of this study is to raise pan-specific antibodies that may facilitate the identification of novel expression patterns of lysine valylation.Methods:Chicken ovalbumin was valylated as an immunogen to raise polyclonal antibodies(PcAbs)in rabbits.The population of the pan-specific antibodies recognizing valylated lysine was purified using the chemically synthesized valylated peptides consisting of random amino acids.The specificity of the antibodies was evaluated using ELISA,dot blots,Western blots,and immunohistochemistry(IHC)staining in human epididymis as well.Results:A preliminary and simple strategy to make an anti-valylated lysine PcAb was developed.The recognition of the antibodies to valyllysine was evaluated as pan specific.This was useful for the detection of the newly identified valyl modification using ELISA,dot blots,and Western blots.The antibodies were also successfully utilized in IHC assays,which revealed novel valyllysine modification patterns in epididymis tissues of human.Conclusions:A new antibody tool was provided for the study of lysine valylation.The novel expression patterns of valyllysine in the epididymis suggest that this modification may be involved in sperm maturation.

关键词： Anti-Valyllysine Antibody Epididymis Posttranslational Modifications Valyllysine