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Hu J, Zhu LP, Wang RQ, Zhu L, Chen F, Hou Y, Ni K, Deng S, Liu S, Ying W, Sun JL, Li H, Jin T. Identification, Characterization, Cloning, and Cross-Reactivity of Zan b 2, a Novel Pepper Allergen of 11S Legumin. J Agric Food Chem 2024; 72:8189-8199. [PMID: 38551197 PMCID: PMC11010233 DOI: 10.1021/acs.jafc.4c00351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
Protein from Sichuan peppers can elicit mild to severe allergic reactions. However, little is known about their allergenic proteins. We aimed to isolate, identify, clone, and characterize Sichuan pepper allergens and to determine its allergenicity and cross-reactivities. Sichuan pepper seed proteins were extracted and then analyzed by SDS-PAGE. Western blotting was performed with sera from Sichuan pepper-allergic individuals. Proteins of interest were purified using hydrophobic interaction chromatography and gel filtration and further analyzed by analytical ultracentrifugation, circular dichroism spectroscopy, and mass spectrometry (MS). Their coding region was amplified in the genome. IgE reactivity and cross-reactivity of allergens were evaluated by dot blot, enzyme-linked immunosorbent assay (ELISA), and competitive ELISA. Western blot showed IgE binding to a 55 kDa protein. This protein was homologous to the citrus proteins and has high stability and a sheet structure. Four DNA sequences were cloned. Six patients' sera (60%) showed specific IgE reactivity to this purified 11S protein, which was proved to have cross-reactivation with extracts of cashew nuts, pistachios, and citrus seeds. A novel allergen in Sichuan pepper seeds, Zan b 2, which belongs to the 11S globulin family, was isolated and identified. Its cross-reactivity with cashew nuts, pistachios, and citrus seeds was demonstrated.
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Affiliation(s)
- Jing Hu
- Hefei
National Laboratory for Physical Sciences at Microscale, the CAS Key
Laboratory of Innate Immunity and Chronic Disease, School of Basic
Medicine Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Li-Ping Zhu
- Allergy
Department, State Key Laboratory of Complex Severe and Rare Diseases,
Peking Union Medical College Hospital, Chinese
Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Rui-qi Wang
- Allergy
Department, State Key Laboratory of Complex Severe and Rare Diseases,
Peking Union Medical College Hospital, Chinese
Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Lixia Zhu
- Hefei
National Laboratory for Physical Sciences at Microscale, the CAS Key
Laboratory of Innate Immunity and Chronic Disease, School of Basic
Medicine Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Feng Chen
- Hefei
National Laboratory for Physical Sciences at Microscale, the CAS Key
Laboratory of Innate Immunity and Chronic Disease, School of Basic
Medicine Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yibo Hou
- Allergy
Department, State Key Laboratory of Complex Severe and Rare Diseases,
Peking Union Medical College Hospital, Chinese
Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Kang Ni
- Hefei
National Laboratory for Physical Sciences at Microscale, the CAS Key
Laboratory of Innate Immunity and Chronic Disease, School of Basic
Medicine Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Shasha Deng
- Hefei
National Laboratory for Physical Sciences at Microscale, the CAS Key
Laboratory of Innate Immunity and Chronic Disease, School of Basic
Medicine Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Siyu Liu
- Hefei
National Laboratory for Physical Sciences at Microscale, the CAS Key
Laboratory of Innate Immunity and Chronic Disease, School of Basic
Medicine Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Wantao Ying
- State
Key Laboratory of Medical Proteomics, Beijing Proteome Research Center,
National Center for Protein Sciences (Beijing), Beijing Institute
of Lifeomics, Beijing 102206, China
| | - Jin-Lyu Sun
- Allergy
Department, State Key Laboratory of Complex Severe and Rare Diseases,
Peking Union Medical College Hospital, Chinese
Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Hong Li
- Allergy
Department, State Key Laboratory of Complex Severe and Rare Diseases,
Peking Union Medical College Hospital, Chinese
Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Tengchuan Jin
- Hefei
National Laboratory for Physical Sciences at Microscale, the CAS Key
Laboratory of Innate Immunity and Chronic Disease, School of Basic
Medicine Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
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2
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Zhang J, Yan M, Ji A, Sun Q, Ying W. Mass spectrometry-based proteomic analysis of biological stains identifies body fluids specific markers. Forensic Sci Int 2024; 357:112008. [PMID: 38522320 DOI: 10.1016/j.forsciint.2024.112008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 03/26/2024]
Abstract
The identification of biological stains and their tissue resource is an important part of forensic research. Current methods suffer from several limitations including poor sensitivity and specificity, trace samples, and sample destruction. In this study, we profiled the proteomes of menstrual blood, peripheral blood, saliva, semen, and vaginal fluid with mass spectrometry technology. Tissue-enhanced and tissue-specific proteins of each group have been proposed as potential biomarkers. These candidate proteins were further annotated and screened through the combination with the Human Protein Atlas database. Our data not only validates the protein biomarkers reported in previous studies but also identifies novel candidate biomarkers for human body fluids. These candidates lay the foundation for the development of rapid and specific forensic examination methods.
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Affiliation(s)
- Jian Zhang
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China; State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Meng Yan
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Anquan Ji
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China
| | - Qifan Sun
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China.
| | - Wantao Ying
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
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3
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Li X, Kong R, Hou W, Cao J, Zhang L, Qian X, Zhao L, Ying W. Integrative proteomics and n-glycoproteomics reveal the synergistic anti-tumor effects of aspirin- and gemcitabine-based chemotherapy on pancreatic cancer cells. Cell Oncol (Dordr) 2024; 47:141-156. [PMID: 37639207 DOI: 10.1007/s13402-023-00856-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
OBJECTIVE AND DESIGN Pancreatic cancer is a highly malignant tumor that is well known for its poor prognosis. Based on glycosylation, we performed integrated quantitative N-glycoproteomics to investigate the synergistic anti-tumor effects of aspirin and gemcitabine on pancreatic cancer cells and explore the potential molecular mechanisms of chemotherapy in pancreatic cancer. METHODS AND RESULTS Two pancreatic cancer cell lines (PANC-1 and BxPC-3) were treated with gemcitabine, aspirin, and a combination (gemcitabine + aspirin). We found that the addition of aspirin enhanced the inhibitory effect of gemcitabine on the activity of PANC-1 and BxPC-3 cells. Quantitative N-glycoproteome, proteome, phosphorylation, and transcriptome data were obtained from integrated multi-omics analysis to evaluate the anti-tumor effects of aspirin and gemcitabine on pancreatic cancer cells. Mfuzz analysis of intact N-glycopeptide profiles revealed two consistent trends associated with the addition of aspirin, which showed a strong relationship between N-glycosylation and the synergistic effect of aspirin. Further analysis demonstrated that the dynamic regulation of sialylation and high-mannose glycoforms on ECM-related proteins (LAMP1, LAMP2, ITGA3, etc.) was a significant factor for the ability of aspirin to promote the anti-tumor activity of gemcitabine and the drug resistance of pancreatic cancer cells. CONCLUSIONS In-depth analysis of N-glycosylation-related processes and pathways in pancreatic cancer cells can provide new insight for future studies regarding pancreatic cancer therapeutic targets and drug resistance mechanisms.
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Affiliation(s)
- Xiaoyu Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38 Life Park Road, Changping District, Beijing, 102206, China
- Institute of Analysis and Testing, Beijing Center for Physical & Chemical Analysis), Beijing Academy of Science and Technology, Beijing, 100094, China
| | - Ran Kong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38 Life Park Road, Changping District, Beijing, 102206, China
- Biomedical Engineering Department, Peking University, Beijing, 100191, China
| | - Wenhao Hou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38 Life Park Road, Changping District, Beijing, 102206, China
| | - Junxia Cao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38 Life Park Road, Changping District, Beijing, 102206, China
| | - Li Zhang
- Center for Bioinformatics and Computational Biology, School of Life Sciences, Institute of Biomedical Sciences, East China Normal University, Shanghai, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38 Life Park Road, Changping District, Beijing, 102206, China
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, No. 100 Ping Le Yuan, Chaoyang District, Beijing, 100124, China.
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38 Life Park Road, Changping District, Beijing, 102206, China.
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Xing M, Wang S, Cui F, Liu H, Zhang X, Gao Z, Ying W, Shi E. Comprehensive insight on protein modification by V-type agent: A chemical proteomic approach employing bioorthogonal reaction. Proteomics 2024; 24:e2300039. [PMID: 37654063 DOI: 10.1002/pmic.202300039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 06/21/2023] [Accepted: 07/12/2023] [Indexed: 09/02/2023]
Abstract
Organophosphorus compounds (OPs) such as chemical agents and pesticides are posing critical threats to civilians due to their irreversible phosphonylation of diverse amino acids residues forming different protein adducts. However, traditional analytical approaches are quite limited in capturing the myriad of post-translational events that affect protein functions, especially in identifying the low-abundance OP adducts. Herein a systematic proteomic strategy based on a typical click-enrich-release-identify bioorthogonal operation was firstly developed by employing an alkynyl-tagged V-type agent probe (AVP) and a biotin-based azido-enrichment linker (BTP-N3 ). AVP targeting peptides from human serum albumin (HSA) or plasma were captured by BTP-N3 via CuAAC click reaction, enriched by streptavidin beads, released by selective alkaline hydrolysis of phenacyl ester bond, and subsequently sequenced by LC-MS/MS. This strategy has helped identifying 1115 unique OP adduction sites on 163 proteins in human plasma, and covers lots of OP adducts that cannot be achieved by traditional detection methods. The comprehensive coverage of novel OP substrates provided a general and sensitive approach to retrospective verification and/or dose assessment of toxic OPs.
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Affiliation(s)
- Meining Xing
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (Beijing), Beijing, China
| | - Shuo Wang
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Fangfang Cui
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (Beijing), Beijing, China
| | - Haibo Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Xiangye Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (Beijing), Beijing, China
| | - Zhenhua Gao
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (Beijing), Beijing, China
| | - Enxue Shi
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
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5
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Min Y, Zhao X, Ying W. Identification of Core-Fucosylated Glycoproteins by Single-Step Truncation of N-Glycans. Curr Protoc 2024; 4:e982. [PMID: 38270535 DOI: 10.1002/cpz1.982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Alpha-1,6 core fucosylation (CF) is a unique glycoform of N-glycans, and studies showed that CF modifications are involved in the occurrence and progression of various diseases and may provide potential disease biomarkers. Current strategies for the CF glycoproteome are often based on multistep enrichment of glycoproteins or glycopeptides and sequential cleavage with different glycosidases to truncate the N-glycans. Although the detection ability of low-abundance glycoproteins is improved, sample loss, high cost, and the time-consuming multistep operation also affect the reproducibility of results and the practicality of the method. Here we developed a single-step truncation (SST) strategy and evaluated its potential for the CF glycoproteome of human serum. The SST strategy has the advantages of fewer operational steps, lower cost, higher number of identifications, and better quantitative stability compared with previous approaches and provides an efficient solution for large-scale quantitative analysis of the CF glycoproteome. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Single-step truncation strategy for core fucosylation glycoproteome analysis in human serum Basic Protocol 2: Liquid chromatography-tandem mass spectrometry quantification of site-specific core fucosylation glycopeptides Alternate Protocol: Pretreatment of cellular samples of core fucosylation glycoproteome with single-step truncation strategy.
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Affiliation(s)
- Yao Min
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xinyuan Zhao
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Wantao Ying
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
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6
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Huang Y, Shao X, Liu Y, Yan K, Ying W, He F, Wang D. RUPE-phospho: Rapid Ultrasound-Assisted Peptide-Identification-Enhanced Phosphoproteomics Workflow for Microscale Samples. Anal Chem 2023; 95:17974-17980. [PMID: 38011496 DOI: 10.1021/acs.analchem.3c02623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Global phosphoproteome profiling can provide insights into cellular signaling and disease pathogenesis. To achieve comprehensive phosphoproteomic analyses with minute quantities of material, we developed a rapid and sensitive phosphoproteomics sample preparation strategy based on ultrasound. We found that ultrasonication-assisted digestion can significantly improve peptide identification by 20% due to the generation of longer peptides that can be detected by mass spectrometry. By integrating this rapid ultrasound-assisted peptide-identification-enhanced proteomic method (RUPE) with streamlined phosphopeptide enrichment steps, we established RUPE-phospho, a fast and efficient strategy to characterize protein phosphorylation in mass-limited samples. This approach dramatically reduces the sample loss and processing time: 24 samples can be processed in 3 h; 5325 phosphosites, 4549 phosphopeptides, and 1888 phosphoproteins were quantified from 5 μg of human embryonic kidney (HEK) 293T cell lysate. In addition, 9219 phosphosites were quantified from 1-2 mg of OCT-embedded mouse brain with 120 min streamlined RUPE-phospho workflow. RUPE-phospho facilitates phosphoproteome profiling for microscale samples and will provide a powerful tool for proteomics-driven precision medicine research.
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Affiliation(s)
- Yuanxuan Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Science-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xianfeng Shao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Science-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yuanyuan Liu
- The π-HuB Project Infrastructure, Guangzhou 510000, China
| | - Kehan Yan
- The π-HuB Project Infrastructure, Guangzhou 510000, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Science-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Science-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
- The π-HuB Project Infrastructure, Guangzhou 510000, China
- Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Dongxue Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Science-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
- The π-HuB Project Infrastructure, Guangzhou 510000, China
- Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
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Wang Y, Meng B, Wang X, Wu A, Li X, Qian X, Wu J, Ying W, Xiao T, Rong W. Noninvasive urinary protein signatures combined clinical information associated with microvascular invasion risk in HCC patients. BMC Med 2023; 21:481. [PMID: 38049860 PMCID: PMC10696877 DOI: 10.1186/s12916-023-03137-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 10/30/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Microvascular invasion (MVI) is the main factor affecting the prognosis of patients with hepatocellular carcinoma (HCC). The aim of this study was to identify accurate diagnostic biomarkers from urinary protein signatures for preoperative prediction. METHODS We conducted label-free quantitative proteomic studies on urine samples of 91 HCC patients and 22 healthy controls. We identified candidate biomarkers capable of predicting MVI status and combined them with patient clinical information to perform a preoperative nomogram for predicting MVI status in the training cohort. Then, the nomogram was validated in the testing cohort (n = 23). Expression levels of biomarkers were further confirmed by enzyme-linked immunosorbent assay (ELISA) in an independent validation HCC cohort (n = 57). RESULTS Urinary proteomic features of healthy controls are mainly characterized by active metabolic processes. Cell adhesion and cell proliferation-related pathways were highly defined in the HCC group, such as extracellular matrix organization, cell-cell adhesion, and cell-cell junction organization, which confirms the malignant phenotype of HCC patients. Based on the expression levels of four proteins: CETP, HGFL, L1CAM, and LAIR2, combined with tumor diameter, serum AFP, and GGT concentrations to establish a preoperative MVI status prediction model for HCC patients. The nomogram achieved good concordance indexes of 0.809 and 0.783 in predicting MVI in the training and testing cohorts. CONCLUSIONS The four-protein-related nomogram in urine samples is a promising preoperative prediction model for the MVI status of HCC patients. Using the model, the risk for an individual patient to harbor MVI can be determined.
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Affiliation(s)
- Yaru Wang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of Clinical Trial Research Center, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Bo Meng
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Xijun Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Anke Wu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaoyu Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Jianxiong Wu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China.
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China.
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Weiqi Rong
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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8
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Min Y, Wu J, Hou W, Li X, Zhao X, Guan X, Qian X, Hao C, Ying W. Differential analysis of core-fucosylated glycoproteomics enabled by single-step truncation of N-glycans. Glycoconj J 2023; 40:541-549. [PMID: 37542637 DOI: 10.1007/s10719-023-10130-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/14/2023] [Accepted: 07/19/2023] [Indexed: 08/07/2023]
Abstract
Alpha-1,6 fucosylation of N-glycans (core fucosylation, CF) represents a unique form of N-glycans and is widely involved in disease progression. In order to accurately identify CF glycoproteins, several approaches have been developed based on sequential cleavage with different glycosidases to truncate the N-glycans. Since multi-step sample treatments may introduce quantitation bias and affect the practicality of these approaches in large-scale applications. Here, we systematically evaluated the performance of the single-step treatment of intact glycopeptides by endoglycosidase F3 for CF glycoproteome. The single-step truncation (SST) strategy demonstrated higher quantitative stability and higher efficiency compared with previous approaches. The strategy was further practiced on both cell lines and serum samples. The dysregulation of CF glycopeptides between preoperative and postoperative serum from patients with pancreatic ductal adenocarcinoma was revealed, and the CF modifications of BCHE_N369, CDH5_N112 and SERPIND1_N49 were found to be potential prognostic markers. This study thus provides an efficient solution for large-scale quantitative analysis of the CF glycoproteome.
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Affiliation(s)
- Yao Min
- School of Basic Medical Science, Anhui Medical University, Hefei, 230032, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Jianhui Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, 102206, China
| | - Wenhao Hou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Xiaoyu Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Xinyuan Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Xiaoya Guan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Chunyi Hao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, 102206, China.
| | - Wantao Ying
- School of Basic Medical Science, Anhui Medical University, Hefei, 230032, China.
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China.
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9
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Huang D, Leng Y, Zhang X, Xing M, Ying W, Gao X. Serial and multi-level proteome analysis for microscale protein samples. J Proteomics 2023; 288:104993. [PMID: 37619946 DOI: 10.1016/j.jprot.2023.104993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023]
Abstract
Post-translational modifications (PTMs), such as phosphorylation and ubiquitination, play key roles in signal transduction and protein homeostasis. The crosstalk of PTMs greatly expands the components of proteome and protein functions. Multi-level proteome analysis, which involves proteome investigations of total lysate and PTMs in this context, provides a comprehensive approach to explore the PTM crosstalk of a biological system under diverse disturbances. However, multi-level proteome practice remains technically challenging. Here we intended to build a strategy for multi-level proteome analysis, in which we focus on the serial profiling the total proteome, ubiquitinome and phosphoproteome from the microscale of starting material. We started by evaluating five common lysis buffers and found that the sodium deoxycholate buffer provided the best overall performance. We then developed an approach for serial enrichment and profiling of the multi-level proteome. To expand the depth of identification, we customized the variable windows to perform data-independent acquisition (DIA) sequencing for each proteome. In total, we identified 6465 proteins, ∼20,000 GlyGly sites (class 1), and ∼ 19,000 phosphosites (class 1) sequentially using 1 mg of HeLa digest by three DIA measurements. We applied this strategy to analyze MG132-treated HeLa cells and observed the crosstalk between ubiquitination and phosphorylation. Our method can be referenced for other multi-level proteome studies with microscale samples. SIGNIFICANCE: Lysis buffer containing sodium deoxycholate provided the best overall performance in multi-level proteome analysis. One step of ubiquitination enrichment before phosphorylation enrichment does not reduce the reproducibility of phosphoproteome. Customized isolation windows were established for DIA analysis on each level of proteome. Combined the serial enrichment approach and the customized single-shot DIA method enabled the multi-level proteome of microscale protein samples.
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Affiliation(s)
- Dongying Huang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yeye Leng
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiangye Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Meining Xing
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wantao Ying
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.
| | - Xiaoxia Gao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China.
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10
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Yang L, Weng S, Qian X, Wang M, Ying W. Correction to "Strategy for Microscale Extraction and Proteome Profiling of Peripheral Blood Mononuclear Cells". Anal Chem 2023; 95:12192. [PMID: 37535394 DOI: 10.1021/acs.analchem.3c03282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Affiliation(s)
- Li Yang
- School of Basic Medical Science, Anhui Medical University, Hefei 230032, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Shuang Weng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Mingchao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wantao Ying
- School of Basic Medical Science, Anhui Medical University, Hefei 230032, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
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11
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Zheng R, Weng S, Xu J, Li Z, Wang Y, Aizimuaji Z, Ma S, Zheng L, Li H, Ying W, Rong W, Xiao T. Autophagy and biotransformation affect sorafenib resistance in hepatocellular carcinoma. Comput Struct Biotechnol J 2023; 21:3564-3574. [PMID: 37520282 PMCID: PMC10372478 DOI: 10.1016/j.csbj.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/22/2023] [Accepted: 07/04/2023] [Indexed: 08/01/2023] Open
Abstract
As sorafenib is a first-line drug for treating advanced hepatocellular carcinoma, sorafenib resistance has historically attracted attention. However, most of this attention has been focused on a series of mechanisms related to drug resistance arising after sorafenib treatment. In this study, we used proteomic techniques to explore the potential mechanisms by which pretreatment factors affect sorafenib resistance. The degree of redundant pathway PI3K/AKT activation, biotransformation capacity, and autophagy level in hepatocellular carcinoma patients prior to sorafenib treatment might affect their sensitivity to sorafenib, in which ADH1A and STING1 are key molecules. These three factors could interact mechanistically to promote tumor cell survival, might be malignant features of tumor cells, and are associated with hepatocellular carcinoma prognosis. Our study suggests possible avenues of therapeutic intervention for patients with sorafenib-resistance and the potential application of immunotherapy with the aim of improving the survival of such patients.
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Affiliation(s)
- Ruiqi Zheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Shuang Weng
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jianping Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing 100021, China
| | - Zhuo Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing 100021, China
| | - Yaru Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zulihumaer Aizimuaji
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Sheng Ma
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Linlin Zheng
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Haiyang Li
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
- College of Life Science and Bioengineering, Beijing University of Technology, No. 100, Pingleyuan, Chaoyang District, Beijing 100124, China
| | - Weiqi Rong
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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12
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Foley K, Dai Y, Ding Q, Du F, Li J, Lv C, Prince T, Sun Y, Wang M, Wang R, Yang X, Wang Y, Wang Z, Ma L, Long Ye L, Wei Yin W, Chenghao Ying C, Min Yu M, Zhu Y, Ying W. Tumor-selective, chaperone-mediated protein degradation (CHAMP) of the bromodomain transcription factor BRD4. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)00875-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Yin X, Li X, Mu L, Bai H, Yang Y, Chen N, Wu L, Fu S, Li J, Ying W, Ye J. Affinity-Driven Site-Specific High Mannose Modification Determines the Structural Polymerization and Function of Tetrameric IgM in a Primitive Vertebrate. J Immunol 2022; 209:593-605. [PMID: 35868636 DOI: 10.4049/jimmunol.2100921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/21/2022] [Indexed: 10/17/2023]
Abstract
Teleost tetramer IgM is the predominant Ig in the immune system and plays essential roles in host defense against microbial infection. Due to variable disulfide polymerization of the monomeric subunits, tetrameric IgM possesses considerable structural diversity. Previous work indicated that the teleost IgM H chain was fully occupied with complex-type N-glycans. However, after challenge with trinitrophenyl (TNP) Ag, the complex N-glycans in the Asn-509 site of Oreochromis niloticus IgM H chain transformed into high mannose. This study, therefore, was conducted to examine the functional roles of the affinity-related high-mannose modification in tilapia IgM. The TNP-specific IgM Ab affinity maturation was revealed in tilapia over the response. A positive correlation between TNP-specific IgM affinity and its disulfide polymerization level of isomeric structure was demonstrated. Mass spectrometric analysis indicated that the relationship between IgM affinity and disulfide polymerization was associated with the Asn-509 site-specific high-mannose modification. Furthermore, the increase of high mannose content promoted the combination of IgM and mannose receptor (MR) on the surface of phagocytes. Moreover, the increased interaction of IgM and MR amplified the phagocytic ability of phagocytes to Streptococcus agalactiae. To our knowledge, this study demonstrates that site-specific high-mannose modification associates with IgM Ab affinity and its structural disulfide polymerization and amplifies the phagocytosis of phagocytes by the combination of IgM and MR. The present study provides evidence for understanding the association of IgM structure and function during the evolution of the immune system.
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Affiliation(s)
- Xiaoxue Yin
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Xiaoyu Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Life Omics, Beijing, People's Republic of China
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, People's Republic of China
| | - Liangliang Mu
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Hao Bai
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Yanjian Yang
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Nuo Chen
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Liting Wu
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Shengli Fu
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Jun Li
- School of Science and Medicine, Lake Superior State University, Sault Ste. Marie, MI; and
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Life Omics, Beijing, People's Republic of China
| | - Jianmin Ye
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou, People's Republic of China
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14
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Yang L, Weng S, Qian X, Wang M, Ying W. Strategy for Microscale Extraction and Proteome Profiling of Peripheral Blood Mononuclear Cells. Anal Chem 2022; 94:8827-8832. [PMID: 35699231 DOI: 10.1021/acs.analchem.1c05365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peripheral blood mononuclear cells (PBMCs) play vital roles in physiological and pathological processes and represent a rich source for disease monitoring. Typical molecular profiling on PBMCs involves the sorting of cell subsets and thus requires a large volume of peripheral blood (PB), which impedes the clinical practicability of omics tools in PBMC measurements. It would be clinically invaluable to develop a convenient approach for preparing PBMCs from small volumes of PB and for deep proteome profiling of PBMCs. To this end, here, we designed an apparatus (PBMC-mCap) for microscale enrichment and proteome analysis of PBMCs, which pushed the needed PB volume from the normal 2 mL or higher to 100 μL or lower, comparable to the volume of a drop of finger blood. A PBMC-specific mass spectra library containing 8869 proteins and 121,956 peptides was further built, which, in combination with the optimized data-independent acquisition strategy, helped to identify 6000 and 6500 proteins from PBMCs with 100 μL and 1 mL of PB as initial materials, respectively. Further application of the strategy for PBMC proteomes revealed a steady difference between gender (male vs female) and upon stimulus (COVID-19 vaccination). For the latter, we observed differentially expressed genes and pathways involving the activation of immune cells, including the NF-κB pathway, inflammation response, and antiviral response. Our strategy for the proteome analysis of microscale PBMCs may provide a convenient clinical toolkit for disease diagnosis and healthy state monitoring.
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Affiliation(s)
- Li Yang
- School of Basic Medical Science, Anhui Medical University, Hefei 230032, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing 102206, China
| | - Shuang Weng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing 102206, China
| | - Mingchao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing 102206, China
| | - Wantao Ying
- School of Basic Medical Science, Anhui Medical University, Hefei 230032, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing 102206, China
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15
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Zhao T, Wang M, Zhao X, Weng S, Qian K, Shi K, Gu Y, Ying W, Qian X, Zhang Y. YTHDF2 Inhibits the Migration and Invasion of Lung Adenocarcinoma by Negatively Regulating the FAM83D-TGFβ1-SMAD2/3 Pathway. Front Oncol 2022; 12:763341. [PMID: 35186724 PMCID: PMC8847186 DOI: 10.3389/fonc.2022.763341] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/17/2022] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE YTH domain family 2 (YTHDF2) is an important N6-methyladenosine (m6A) reader, but its role in lung adenocarcinoma remains elusive. This study assessed its function in lung adenocarcinoma. METHODS YTHDF2 expression in lung adenocarcinoma was explored using public databases, such as The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumour Analysis Consortium (CPTAC). The effect of YTHDF2 on a lung adenocarcinoma cell line was explored by performing cytological and molecular experiments. Molecules downstream of YTHDF2 were identified using proteomics, and the related pathways were verified through cytological and molecular biology experiments. RESULTS YTHDF2 expression was upregulated in lung adenocarcinoma, and patients with high YTHDF2 expression experienced prolonged overall survival. In two lung cancer cell lines, YTHDF2 knockdown inhibited proliferation but promoted migration, invasion, and the epithelial-mesenchymal transition. The proteomic analysis identified 142 molecules downstream of YTHDF2, and 11 were closely related to survival. Further experiments revealed that YTHDF2 inhibited expression of the family with sequence similarity 83D (FAM83D)-TGFβ1-SMAD2/3 pathway components. This study is the first to show that YTHDF2 regulated the downstream TGFβ1-SMAD2/3 pathway through FAM83D in lung adenocarcinoma. CONCLUSION YTHDF2 inhibits the migration and invasion of lung adenocarcinoma cells by regulating the FAM83D-TGFβ1-pSMAD2/3 pathway, which may play an important role in lung cancer metastasis.
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Affiliation(s)
- Teng Zhao
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Mingchao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xin Zhao
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Shuang Weng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Kun Qian
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Kejian Shi
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yanfei Gu
- Department of Oncology, United Family New Hope Oncology Center, Beijing, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yi Zhang
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
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16
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Hu X, Shen N, Liu A, Wang W, Zhang L, Sui Z, Tang Q, Du X, Yang N, Ying W, Qin B, Li Z, Li L, Wang N, Lin H. Bone marrow mesenchymal stem cell-derived exosomal miR-34c-5p ameliorates RIF by inhibiting the core fucosylation of multiple proteins. Mol Ther 2022; 30:763-781. [PMID: 34678513 PMCID: PMC8821970 DOI: 10.1016/j.ymthe.2021.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/02/2021] [Accepted: 10/10/2021] [Indexed: 02/07/2023] Open
Abstract
Renal interstitial fibrosis (RIF) is an incurable pathological lesion in chronic kidney diseases. Pericyte activation is the major pathological characteristic of RIF. Fibroblast and macrophage activation are also involved in RIF. Studies have revealed that core fucosylation (CF), an important post-translational modification of proteins, plays a key role in pericyte activation and RIF by regulating multiple profibrotic signaling pathways as a hub-like target. Here, we reveal that mesenchymal stem cell (MSC)-derived exosomes reside specifically in the injured kidney and deliver microRNA (miR)-34c-5p to reduce cellular activation and RIF by inhibiting CF. Furthermore, we showed that the CD81-epidermal growth factor receptor (EGFR) ligand-receptor complex aids the entry of exosomal miR-34c-5p into pericytes, fibroblasts, and macrophages. Altogether, our findings reveal a novel role of MSC-derived exosomes in inhibiting multicellular activation via CF and provide a potential intervention strategy for renal fibrosis.
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Affiliation(s)
- Xuemei Hu
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian 116011, China,Graduate School of Dalian Medical University, 9 Western Section, Lvshun South Street, Lvshunkou District, Dalian 116044, China
| | - Nan Shen
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian 116011, China
| | - Anqi Liu
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian 116011, China,Graduate School of Dalian Medical University, 9 Western Section, Lvshun South Street, Lvshunkou District, Dalian 116044, China
| | - Weidong Wang
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian 116011, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Qingzhu Tang
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian 116011, China
| | - Xiangning Du
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian 116011, China
| | - Ning Yang
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian 116011, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206 China
| | - Biaojie Qin
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian 116011, China
| | - Zhitong Li
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian 116011, China,Graduate School of Dalian Medical University, 9 Western Section, Lvshun South Street, Lvshunkou District, Dalian 116044, China
| | - Lin Li
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian 116011, China,Graduate School of Dalian Medical University, 9 Western Section, Lvshun South Street, Lvshunkou District, Dalian 116044, China
| | - Nan Wang
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian 116011, China,Corresponding author: Nan Wang, Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian, 116011, China.
| | - Hongli Lin
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian 116011, China,Corresponding author: Hongli Lin, Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Key Laboratory of Kidney Disease of Liaoning Province, The Center for the Transformation Medicine of Kidney Disease of Liaoning Province, No. 222 Zhongshan Road, Dalian, 116011, China.
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17
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Abstract
Histidine phosphorylation (pHis), which plays a key role in signal transduction in bacteria and lower eukaryotes, has been shown to be involved in tumorigenesis. Due to its chemical instability, substoichiometric properties, and lack of specific enrichment reagents, there is a lack of approaches for specific and unbiased enrichment of pHis-proteins/peptides. In this study, an integrated strategy was established and evaluated as an unbiased tool for exploring the histidine phosphoproteome. First, taking advantage of the lower charge states of pHis-peptides versus the non-modified naked peptides at weak acid solution (∼pH 2.7), strong cation exchange (SCX) chromatography was used to differentiate modified and non-modified naked peptides. Furthermore, selective enrichment of the pHis-peptide was performed by applying Cu-IDA beads enrichment. Finally, stable isotope dimethyl labeling was introduced to guarantee high-confidence assignment of pHis-peptides. Using this integrated strategy, 563 different pHis-peptides (H = 1) in 385 proteins were identified from HeLa lysates. Motif analysis revealed that pHis prefers hydrophobic amino acids and has the consensus motif-HxxK, which covered the reports from different approaches. Thus, our method may provide an unbiased and effective tool to reveal histidine phosphoproteome and to study the biological process and function of histidine phosphorylation.
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Affiliation(s)
- Fangfang Cui
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
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18
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Kawahara R, Chernykh A, Alagesan K, Bern M, Cao W, Chalkley RJ, Cheng K, Choo MS, Edwards N, Goldman R, Hoffmann M, Hu Y, Huang Y, Kim JY, Kletter D, Liquet B, Liu M, Mechref Y, Meng B, Neelamegham S, Nguyen-Khuong T, Nilsson J, Pap A, Park GW, Parker BL, Pegg CL, Penninger JM, Phung TK, Pioch M, Rapp E, Sakalli E, Sanda M, Schulz BL, Scott NE, Sofronov G, Stadlmann J, Vakhrushev SY, Woo CM, Wu HY, Yang P, Ying W, Zhang H, Zhang Y, Zhao J, Zaia J, Haslam SM, Palmisano G, Yoo JS, Larson G, Khoo KH, Medzihradszky KF, Kolarich D, Packer NH, Thaysen-Andersen M. Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nat Methods 2021; 18:1304-1316. [PMID: 34725484 DOI: 10.1101/2021.03.14.435332] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/22/2021] [Indexed: 05/18/2023]
Abstract
Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved 'high-coverage' and 'high-accuracy' glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics.
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Affiliation(s)
- Rebeca Kawahara
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Anastasia Chernykh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Kathirvel Alagesan
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia
| | | | - Weiqian Cao
- Institutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Robert J Chalkley
- UCSF, School of Pharmacy, Department of Pharmaceutical Chemistry, San Francisco, CA, USA
| | - Kai Cheng
- State University of New York, Buffalo, NY, USA
| | - Matthew S Choo
- Analytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Nathan Edwards
- Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Radoslav Goldman
- Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
- Department of Oncology, Georgetown University, Washington, DC, USA
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Yingwei Hu
- Department of Pathology, The Johns Hopkins University, Baltimore, MD, USA
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Jin Young Kim
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea
| | | | - Benoit Liquet
- Department of Mathematics and Statistics, Macquarie University, Sydney, NSW, Australia
- CNRS, Laboratoire de Mathématiques et de leurs Applications de PAU, E2S-UPPA, Pau, France
| | - Mingqi Liu
- Institutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Bo Meng
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China
| | | | - Terry Nguyen-Khuong
- Analytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jonas Nilsson
- Proteomics Core Facility, Sahlgrenska academy, University of Gothenburg, Gothenburg, Sweden
| | - Adam Pap
- BRC, Laboratory of Proteomics Research, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gun Wook Park
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Benjamin L Parker
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia
| | - Josef M Penninger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Toan K Phung
- School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia
| | - Markus Pioch
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
- glyXera GmbH, Magdeburg, Germany
| | - Enes Sakalli
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Miloslav Sanda
- Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA
- Department of Oncology, Georgetown University, Washington, DC, USA
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia
| | - Nichollas E Scott
- Deparment of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Georgy Sofronov
- Department of Mathematics and Statistics, Macquarie University, Sydney, NSW, Australia
| | - Johannes Stadlmann
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hung-Yi Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Pengyuan Yang
- Institutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China
| | - Hui Zhang
- Department of Pathology, The Johns Hopkins University, Baltimore, MD, USA
| | - Yong Zhang
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Joseph Zaia
- Department of Biochemistry, Boston University Medical Campus, Boston, MA, USA
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, UK
| | - Giuseppe Palmisano
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jong Shin Yoo
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| | - Göran Larson
- Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kai-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Katalin F Medzihradszky
- UCSF, School of Pharmacy, Department of Pharmaceutical Chemistry, San Francisco, CA, USA
- BRC, Laboratory of Proteomics Research, Szeged, Hungary
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia
| | - Nicolle H Packer
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia.
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19
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Yu G, Zhang Y, Meng B, Xie X, Wang Z, Ying W, Lv J, Zhang H. O-glycoforms of polymeric IgA1 in the plasma of patients with IgA nephropathy are associated with pathological phenotypes. Nephrol Dial Transplant 2021; 37:33-41. [PMID: 34152412 DOI: 10.1093/ndt/gfab204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND IgA1 O-glycosylation plays an important role in the pathogenesis of IgA nephropathy (IgAN). However, variations in IgA1 O-glycoforms have not been explored. We aimed to investigate the IgA1 O-glycoforms in the hinge region (HR) of polymeric IgA1 and then evaluate the association between IgA1 O-glycoforms and crescent formation in IgAN. METHODS The discovery cohort (cohort 1) comprised 11 crescentic IgAN patients, 10 noncrescentic IgAN patients and 10 healthy controls, and the validation cohort (cohort 2) comprised 11 crescentic IgAN patients, 9 noncrescentic IgAN patients, and 9 healthy controls. A total of 143 IgAN patients with different crescent percentages (cohort 3) were also included. Polymeric IgA1 was purified from the plasma of the participants. The variation in O-glycoforms was evaluated by estimating the molecular weights of IgA1 hinge glycopeptides using reversed-phase liquid chromatography (LC) and tandem mass spectrometry under electron-transfer/higher-energy collision dissociation (EThcD) fragmentation mode. RESULTS In discovery cohort (cohort 1), the numbers of GalNAc bound to one HR were lower in IgAN patients. The proportions of GalNAc3 (defined as O-glycans bound to one HR at 3 sites) and GalNAc4 were highest in crescentic IgAN patients followed by noncrescentic IgAN patients and were lowest in healthy controls (GalNAc 3: 9.92%±3.37% vs 6.65%±1.53% vs 4.05%±1.24%; P < 0.001; GalNAc4: 45.91%±4.75% vs 41.13%±2.95% vs 40.98%±2.95%; P = 0.004). The proportions of GalNAc5 and GalNAc6 were lowest in crescentic IgAN patients followed by noncrescentic IgAN patients and were highest in healthy controls (GalNAc5: 50.15%±4.27% vs 47.92%±4.09% vs 45.87%±3.79%, P = 0.028; GalNAc6: 6.58%±2.53% vs 6.04%±1.35% vs 4.65%±2.27%; P = 0.034). These results were consistent in the validation cohort (cohort 2); In another cohort with 143 patients with different crescents percentage (cohort 3), the numbers of GalNAc in polymeric IgA1 decreased with increasing percentage of crescents. CONCLUSIONS The numbers of GalNAc in IgA1 HRs were lower in IgAN patients, especially in crescentic IgAN patients, and may be associated with a severe IgAN phenotype.
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Affiliation(s)
- Guizhen Yu
- Renal Division, Peking University First Hospital, China.,Peking University Institute of Nephrology, China.,Key Laboratory of Renal Disease, Ministry of Health of China.,Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, China.,Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences
| | - Yong Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.,Key Lab of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bo Meng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xinfang Xie
- Renal Division, Peking University First Hospital, China.,Peking University Institute of Nephrology, China.,Key Laboratory of Renal Disease, Ministry of Health of China.,Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, China.,Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences
| | - Zi Wang
- Renal Division, Peking University First Hospital, China.,Peking University Institute of Nephrology, China.,Key Laboratory of Renal Disease, Ministry of Health of China.,Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, China.,Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Jicheng Lv
- Renal Division, Peking University First Hospital, China.,Peking University Institute of Nephrology, China.,Key Laboratory of Renal Disease, Ministry of Health of China.,Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, China.,Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences
| | - Hong Zhang
- Renal Division, Peking University First Hospital, China.,Peking University Institute of Nephrology, China.,Key Laboratory of Renal Disease, Ministry of Health of China.,Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, China.,Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences
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20
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Pourtaheri N, Ying W, Kim J, Henriquez C. Thresholds for Transverse Stimulation: Fiber Bundles in a Uniform Field. IEEE Trans Neural Syst Rehabil Eng 2021; PP. [PMID: 34077366 DOI: 10.1109/tnsre.2009.2039600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cable theory is used to model fibers (neural or muscular) subjected to an extracellular stimulus or activating function along the fiber (longitudinal stimulation). There are cases however, in which activation from fields across a fiber (transverse stimulation) is dominant and the activating function is insufficient to predict the relative stimulus thresholds for cells in a bundle. This work proposes a general method of quantifying transverse extracellular stimulation using ideal cases of long fibers oriented perpendicular to a uniform field (circular cells in a 2-D extracellular domain). Several methods are compared against a fully coupled model to compute electrical potentials around each cell of a bundle and predict the magnitude of applied plate potential (Öp) needed to activate a given cell (Öpact). The results show that with transverse stimulation, the effect of cell presence on the external field must be considered to accurately compute Öpact. They also show that approximating cells as holes can accurately predict firing order and Öpact of cells in bundles. Potential profiles from this hole model can also be applied to single cell models to account for time-dependent transmembrane voltage responses and more accurately predict Öpact. The approaches used herein apply to other examples of transverse cell stimulation where cable theory is inapplicable and coupled model simulation is too costly to compute.
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21
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Weng S, Wang M, Zhao Y, Ying W, Qian X. Optimised data-independent acquisition strategy recaptures the classification of early-stage hepatocellular carcinoma based on data-dependent acquisition. J Proteomics 2021; 238:104152. [PMID: 33609755 DOI: 10.1016/j.jprot.2021.104152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/21/2021] [Accepted: 02/08/2021] [Indexed: 12/27/2022]
Abstract
Proteomics is increasingly used for exploring disease biomarkers and therapeutic targets. The data-independent acquisition (DIA) method collects all peptide signals in a sample, and provides a convenient way to archive disease-related molecular features for further exploration. In this study, we first established a high-coverage human hepatocellular carcinoma (HCC) spectral library containing 9393 protein groups, 119,903 peptides. Furthermore, we optimised the DIA method with respect to four key parameters: settings for mass spectrometry acquisition, gradient length, amount of sample loading, and length of analytical column. More than 6000 proteins from HepG2 cells could be stably quantified using the optimised one-shot DIA approach with a 2 h gradient time. One-shot DIA identified a similar number of proteins as did multi-fraction data-dependent acquisition (DDA) from the same group of HCC samples, but at a quarter of the total acquisition time. DIA data could recapture the classification results obtained from DDA data, thus paving the way for large-scale, multi-centre proteomics analysis of clinical samples. SIGNIFICANCE: The organ-specific spectral library for HCC and the optimised 2 h DIA approach met the urgent demands for large-scale quantitative proteomics analysis of HCC clinical samples. Compared with multi-fraction-DDA, the optimised one-shot DIA could reach a similar identification while consuming shorter acquisition time, thus making it possible to analyse thousands of clinical samples.
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Affiliation(s)
- Shuang Weng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Mingchao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yingyi Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
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22
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Liu C, Si X, Yan S, Zhao X, Qian X, Ying W, Zhao L. Development of the C12Im-Cl-assisted method for rapid sample preparation in proteomic application. Anal Methods 2021; 13:776-781. [PMID: 33492312 DOI: 10.1039/d0ay02079f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chromatography and mass spectrometry (MS) techniques have greatly improved the power of proteomic analyses. However, sample processing methods used prior to MS, including protein extraction and digestion, remain bottlenecks in the large-scale clinical application of proteomics. Ionic liquids, composed entirely of ions, have high solubility in various solvents. In this study, the effects of the cationic surfactant 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) on protein digestion were evaluated for clinical proteomic applications. C12Im-Cl was compatible with trypsin and reduced the protein digestion time from 16 h to 1 h. Residual C12Im-Cl was easily removed with a strong anion exchange membrane before MS. We evaluated the performance of C12Im-Cl extraction and rapid protein digestion using formalin-fixed paraffin-embedded liver cancer tissues. The number of proteins and peptides identified was nearly equal to that identified by the traditional filter-aided sample preparation method (2705 vs. 2739 and 16 682 vs. 17 214). In general, the C12Im-Cl-aided rapid sample preparation method is promising for proteomic applications.
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Affiliation(s)
- Chang Liu
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China.
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23
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Cui X, Mi W, Hu Z, Li X, Meng B, Zhao X, Qian X, Zhu T, Ying W. Global characterization of modifications to the charge isomers of IgG antibody. J Pharm Anal 2020; 12:156-163. [PMID: 35573890 PMCID: PMC9073142 DOI: 10.1016/j.jpha.2020.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 11/08/2020] [Accepted: 11/17/2020] [Indexed: 11/02/2022] Open
Abstract
Posttranslational modifications of antibody products affect their stability, charge distribution, and drug activity and are thus a critical quality attribute. The comprehensive mapping of antibody modifications and different charge isomers (CIs) is of utmost importance, but is challenging. We intended to quantitatively characterize the posttranslational modification status of CIs of antibody drugs and explore the impact of posttranslational modifications on charge heterogeneity. The 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 levels. First, 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 status. Second, at the peptide level, common modifications of oxidation, deamidation, and glycosylation were identified. Peptide mapping showed nonuniform deamidation and glycoform distribution among CIs. In total, 10 N-glycoforms were detected by peptide mapping. Finally, an in-depth analysis of glycan variants of CIs was performed through the detection of enriched glycopeptides. Qualitative and quantitative analyses demonstrated the dynamics of 24 N-glycoforms. The 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 analyses. This study demonstrated the importance of the comprehensive analyses of antibody CIs and provides a reference method for the quality control of biopharmaceutical analysis. A stepwise investigation on the diversity and dynamics of modifications of antibody charge isomers (CIs) was performed. The results from SCX-HPLC and cIEF-WCID supported each other. In-depth analysis on glycan variants of CIs was achieved by analyzing the enriched glycopeptides. Sialic acid and deamidation modifications were critical factors for the charge heterogeneity.
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24
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Xu JY, Zhang C, Wang X, Zhai L, Ma Y, Mao Y, Qian K, Sun C, Liu Z, Jiang S, Wang M, Feng L, Zhao L, Liu P, Wang B, Zhao X, Xie H, Yang X, Zhao L, Chang Y, Jia J, Wang X, Zhang Y, Wang Y, Yang Y, Wu Z, Yang L, Liu B, Zhao T, Ren S, Sun A, Zhao Y, Ying W, Wang F, Wang G, Zhang Y, Cheng S, Qin J, Qian X, Wang Y, Li J, He F, Xiao T, Tan M. Integrative Proteomic Characterization of Human Lung Adenocarcinoma. Cell 2020; 182:245-261.e17. [DOI: 10.1016/j.cell.2020.05.043] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/08/2020] [Accepted: 05/21/2020] [Indexed: 12/24/2022]
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25
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Yu G, Zhang Y, Xie X, Meng B, Ying W, Lv J, Zhang H. P0356QUANTITATIVE ASSESSMENT OF GALNAC NUMBER IN THE HINGE REGION OF IGA1 IN IGA NEPHROPATHY WITH CRESCENTS FORMING. Nephrol Dial Transplant 2020. [DOI: 10.1093/ndt/gfaa142.p0356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background and Aims
Aberrant IgA1 O-linked glycosylation of IgA1 hinge region (HR) has been shown playing an important role in the pathogenesis of IgA nephropathy (IgAN). Serum levels of galactose-deficient IgA1 (Gd-IgA1) was associated with the development and progression in IgAN, however variations in the composition of IgA1 HR glycoforms are unknown. In this study we aim to quantitative assessment of GalNAc number in the hinge region of IgA1 in IgAN with crescents forming using mass spectrometry.
Method
Plasma polymeric IgA1 (pIgA1) was purified from a discovery cohort including crescentic IgAN (n=11) non-crescentic IgAN (n=10) and healthy controls (HC, n=10) and a validation cohort (crescentic IgAN, n=10; non-crescentic IgAN, n=10 and healthy controls, n=11). After denaturation, reduction, alkylation and trypsin digestion, liquid chromatography-high-resolution mass spectrometry (LC-MS) was used to analyse the IgA1 HR glycans. The intensity of the identified IgA1 O-glycopeptide was calculated and expressed as the relative abundance for each glycopeptide. The molecular weight (MW) of intact O-glycopeptide was calculated as the formula following:
MW = HR + x GalNAc + y Gal + z NeuAc + H+
(x, y and z represent the number of GalNAc, galactose and NeuAc which bind to one HR in IgA1 O-linked glycopeptides respectively)
Glycopeptide content ratio = (glycopeptide peak intensity/ total glycopeptide intensity) ×100%.
Results
In the discovery cohort population, the level of Gd-IgA1 was highest in patients with crescentic IgAN, middle in patients with non-crescentic IgAN and lowest in healthy controls (347.69±57.89 U/ml vs 336.32±38.44 U/ml vs 330.14±33.22 U/ml), albeit that didn’t reach the statistical significance. There were significantly difference in GalNAc number of IgA1 HR among patients with IgAN and healthy controls. Overall the numbers of GalNAc bound to one HR was much lower in the patients than healthy controls. As shown in the Figure 1, the proportion of GalNAc 3, defined as O-glycans that were bound to one HR at 3 sites, were highest in patients with crescentic IgAN, then the non-crescentic IgAN and lowest in the healthy controls (9.92%±3.37% vs 6.65%±1.53% vs 4.05%±1.24%; p-value for the trend<0.001). Similar results were observed in GalNAc 4 (45.91%±4.75% vs 41.13%±2.95% vs 40.98%±2.95%; P=0.004. However regarding the GalNAc 5 and GalNAc 6, crescentic IgAN was lowest, then non-crescentic IgAN and highest in the healthy control (GalNAc 5: 45.17%±5.46% vs 46.90%±2.78% vs 48.05%±3.02%, P=0.001 GalNAc 6:1.62%±1.60% vs 3.95%±1.92% vs 5.39%±2.38%; P<0.001). These results were consistent in the validation cohort (Figure 1).
Conclusion
GalNAc numbers in IgA1 HR was lower in patients with IgAN especially in crescentic IgAN. These results suggest that the O-glycans of IgA1 were associated with the severe phenotype in IgA nephropathy.
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Affiliation(s)
- Guizhen Yu
- Peking University First Hospital, Renal Division, Beijing, P.R. China
| | - Yong Zhang
- Beijing Institute of Lifeomics, Beijing Institute of Lifeomics, Beijing, P.R. China
| | - Xinfang Xie
- Peking University First Hospital, Renal Division, Beijing, P.R. China
| | - Bo Meng
- Beijing Institute of Lifeomics, Beijing Institute of Lifeomics, Beijing, P.R. China
| | - Wantao Ying
- Beijing Institute of Lifeomics, Beijing Institute of Lifeomics, Beijing, P.R. China
| | - Jicheng Lv
- Peking University First Hospital, Renal Division, Beijing, P.R. China
- Peking University First Hospital
| | - Hong Zhang
- Peking University First Hospital, Renal Division, Beijing, P.R. China
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26
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Li X, He Q, Yu Z, Xie Y, Zhao X, Huang Y, Wang Y, Ke X, Qian X, Dong J, Ying W. Site-Specific and Quantitative N-Glycan Heterogeneity Analysis of the Charge Isomers of an Anti-VEGF Recombinant Fusion Protein by High-Resolution Two-Dimensional Gel Electrophoresis and Mass Spectrometry. Anal Chem 2020; 92:5695-5700. [DOI: 10.1021/acs.analchem.0c00592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaoyu Li
- College of Life Science and Bioengineering, Beijing University of Technology, No. 100, Pingleyuan, Chaoyang District, Beijing, 100124, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
| | - Qing He
- Therapeutic Proteins Key Laboratory of Sichuan Province, Chengdu Kanghong Pharmaceutical Group Co., Ltd., No. 36, Shuxi road, Jinniu District, Chengdu, Sichuan 610036, China
| | - Zixiang Yu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
| | - Yuping Xie
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
| | - Xinyuan Zhao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
| | - Yi Huang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
| | - Yongzhong Wang
- Suqiao Biologics (Suzhou) Co., Ltd, No. 188, Dongping Street, Industrial Park, Suzhou, Jiangsu 215123, China
| | - Xiao Ke
- Therapeutic Proteins Key Laboratory of Sichuan Province, Chengdu Kanghong Pharmaceutical Group Co., Ltd., No. 36, Shuxi road, Jinniu District, Chengdu, Sichuan 610036, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
| | - Junxing Dong
- College of Life Science and Bioengineering, Beijing University of Technology, No. 100, Pingleyuan, Chaoyang District, Beijing, 100124, China
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Wantao Ying
- College of Life Science and Bioengineering, Beijing University of Technology, No. 100, Pingleyuan, Chaoyang District, Beijing, 100124, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
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27
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Gong K, Xia M, Wang Y, Bai L, Ying W, Zhu F, Chen Y. Importance of glycosylation in the interaction of Tamm-Horsfall protein with collectin-11 and acute kidney injury. J Cell Mol Med 2020; 24:3572-3581. [PMID: 32045104 PMCID: PMC7131921 DOI: 10.1111/jcmm.15046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/01/2020] [Accepted: 01/17/2020] [Indexed: 12/19/2022] Open
Abstract
Both Tamm-Horsfall protein (THP) and collectin-11 (CL-11) are important molecules in acute kidney injury (AKI). In this study, we measured the change of glycosylation of THP in patients with AKI after surgery, using MALDI-TOF MS and lectin array analysis. The amount of high-mannose and core fucosylation in patients with AKI were higher than those in healthy controls. In vitro study showed that THP could bind to CL-11 with affinity at 9.41 × 10-7 mol/L and inhibited activation of complement lectin pathway. The binding affinity decreased after removal of glycans on THP. Removal of fucose completely ablated the binding between the two proteins. While removal of high-mannose or part of the N-glycan decreased the binding ability to 30% or 60%. The results indicated that increase of fucose on THP played an important role via complement lectin pathway in AKI.
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Affiliation(s)
- Kunjing Gong
- Renal DivisionDepartment of MedicinePeking University First HospitalBeijingChina
- Institute of NephrologyPeking UniversityBeijingChina
- Key Laboratory of Renal DiseaseMinistry of Health of ChinaBeijingChina
- Key Laboratory of Chronic Kidney Disease Prevention and TreatmentMinistry of EducationBeijingChina
| | - Min Xia
- Renal DivisionDepartment of MedicinePeking University First HospitalBeijingChina
- Institute of NephrologyPeking UniversityBeijingChina
- Key Laboratory of Renal DiseaseMinistry of Health of ChinaBeijingChina
- Key Laboratory of Chronic Kidney Disease Prevention and TreatmentMinistry of EducationBeijingChina
| | - Yaqin Wang
- Renal DivisionDepartment of MedicinePeking University First HospitalBeijingChina
- Institute of NephrologyPeking UniversityBeijingChina
- Key Laboratory of Renal DiseaseMinistry of Health of ChinaBeijingChina
- Key Laboratory of Chronic Kidney Disease Prevention and TreatmentMinistry of EducationBeijingChina
| | - Lufeng Bai
- Renal DivisionDepartment of MedicinePeking University First HospitalBeijingChina
- Institute of NephrologyPeking UniversityBeijingChina
- Key Laboratory of Renal DiseaseMinistry of Health of ChinaBeijingChina
- Key Laboratory of Chronic Kidney Disease Prevention and TreatmentMinistry of EducationBeijingChina
| | - Wantao Ying
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for protein science (Beijing)Beijing Institute of lifeomicsBeijingChina
| | - Fengxue Zhu
- Department of Critical Care MedicinePeking University People's HospitalBeijingChina
| | - Yuqing Chen
- Renal DivisionDepartment of MedicinePeking University First HospitalBeijingChina
- Institute of NephrologyPeking UniversityBeijingChina
- Key Laboratory of Renal DiseaseMinistry of Health of ChinaBeijingChina
- Key Laboratory of Chronic Kidney Disease Prevention and TreatmentMinistry of EducationBeijingChina
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28
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Zhao X, Yu Z, Huang Y, Liu C, Wang M, Li X, Qian X, Ying W. Integrated Strategy for Large-Scale Investigation on Protein Core Fucosylation Stoichiometry Based on Glycan-Simplification and Paired-Peaks-Extraction. Anal Chem 2020; 92:2896-2901. [PMID: 31986883 DOI: 10.1021/acs.analchem.9b05276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Core fucosylation (CF) is a special form of N-glycosylation and plays an important role in pathological and biological processes. Increasing efforts in this area are focused on the identification of CF glycosites, whereas evidence showed that the stoichiometry of CF occupancy is functionally important. Here, an integrated strategy based on "Glycan-Simplification and Paired-Peaks-extraction" (GSPPE) for detecting large-scale stoichiometries of CF was developed. After HILIC enrichment of intact glycopeptides, sequential cleavages by endoglycosidases H and endoglycosidases F3 were performed to generate simplified glycopeptide forms (SGFs), i.e., peptide-GlcNAc (pep-HN) and peptide-GlcNAc-Fucose (pep-CF). These paired SGFs were found to be eluted consecutively on a reversed-phase chromatography column, which allowed us to obtain peak areas of SGF pairs, even if only one of the peaks was captured by the mass spectrometer (MS), by introducing the Paired-Peaks-Extraction algorithm. Thus, the missing value dilemma of random data-dependent MS/MS acquisition was reduced and the stoichiometry of site-specific CF could be calculated. We systematically evaluated the feasibility of this strategy using standard glycoproteins and then explored urinary samples from healthy individuals and hepatocellular carcinoma (HCC) patients. In total, 1449 highly reliable core fucose glycosites and their corresponding CF stoichiometries were obtained. Dozens of glycosites that differed significantly in the urine of healthy individuals and HCC patients were disclosed. The developed approach and program presented here may promote studies on core fucosylation and lead to a deeper understanding of their dysregulation in physiological- or pathological processes.
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Affiliation(s)
- Xinyuan Zhao
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China
| | - Zixiang Yu
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China.,Department of Pathology, Zhongshan Hospital , Fudan University , Shanghai 200032 , P. R. China.,Anhui Medical University , No. 81, Meishan Road , Hefei , Anhui 230032 , P. R. China
| | - Yi Huang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China.,Anhui Medical University , No. 81, Meishan Road , Hefei , Anhui 230032 , P. R. China
| | - Chang Liu
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China.,College of Life Science and Bioengineering , Beijing University of Technology , No. 100, Pingleyuan, Chaoyang District , Beijing 100124 , P. R. China
| | - Mingchao Wang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China
| | - Xiaoyu Li
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China.,College of Life Science and Bioengineering , Beijing University of Technology , No. 100, Pingleyuan, Chaoyang District , Beijing 100124 , P. R. China
| | - Xiaohong Qian
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China
| | - Wantao Ying
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China
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29
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Huang J, Wang Q, Hu Y, Qi Z, Lin Z, Ying W, Zhou M. Proteomic Profiling for Serum Biomarkers in Mice Exposed to Ionizing Radiation. Dose Response 2019; 17:1559325819894794. [PMID: 31853238 PMCID: PMC6909274 DOI: 10.1177/1559325819894794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 12/11/2022] Open
Abstract
In response to large-scale radiological incidents, rapid, accurate, and early triage biodosimeters are urgently required. In this study, we investigated candidate radiation-responsive biomarkers using proteomics approaches in mouse models. A total of 452 dysregulated proteins were identified in the serum samples of mice exposed to 0, 2, 5.5, 7, and 8 Gy at 6, 24, and 72 hours postirradiation. Ninety-eight proteins, including 46 at 6 hours, 36 at 24 hours, and 36 at 72 hours, were identified as radiation-responsive proteins (RRPs). Gene Ontology analysis showed the RRPs were involved in proteolysis, extracellular space, hydrolase activity, and carbohydrate binding. Kyoto Encyclopedia of Genes and Genome enrichment showed the RRPs were regulated in "the pentose phosphate pathway," "the proteasome," and "AGE-RAGE signaling in diabetic complications." There were 3 proteins changed and overlapped at all the 3 time points, 8 proteins changed at 6 and 24 hours, 4 proteins changed at 24 and 72hours, and 2 proteins changed at both 6 and 72 hours. Of these proteins, ORM2, HP, SAA1, SAA2, MBL2, COL1A1, and APCS were identified as candidate biomarkers for biodosimeter-based diagnosis through Pearson correlation analysis.
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Affiliation(s)
- Jinfeng Huang
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, People’s Republic of China
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Qi Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Yingchun Hu
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Zhenhua Qi
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Zhongwu Lin
- Science Research Management Department of the Academy of Military Sciences, Beijing, People’s Republic of China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, People’s Republic of China
| | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, People’s Republic of China
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30
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Zhang Y, Jing H, Meng B, Qian X, Ying W. L-cysteine functionalized straticulate C 3N 4 for the selective enrichment of glycopeptides. J Chromatogr A 2019; 1610:460545. [PMID: 31551124 DOI: 10.1016/j.chroma.2019.460545] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/11/2019] [Accepted: 09/14/2019] [Indexed: 02/05/2023]
Abstract
The facile enrichment of glycopeptides or glycoproteins poses great challenges for glycoproteomic research. In this study, a novel hydrophilic material, named zwitterionic hydrophilic L-cysteine derivatized straticulate-C3N4 composites (LCAC), were synthesized and evaluated for the enrichment of N-glycopeptides. LCAC exhibited good biocompatibility, excellent hydrophilicity and selectivity, by virtue of the large surface of C3N4 and the zwitterionic property offered by cysteine. LCAC demonstrated excellent performance for N-glycopeptide enrichment with the sensitivity of 0.033 fmol/µL, selectivity of 1:100, and high recovery rate (∼85%). The performance of LCAC was demonstrated by the identification of 35 N-glycopeptides from IgG, as well as capturing 1809 human urine N-glycopeptides corresponding to 876 N-glycoproteins. Comparing the LCAC with our developed phenylboronic acid functionalized material showed a certain complementary due to the different binding mechanism. The simple production and enhanced hydrophilic properties make the material a promising choice for glycoproteomics researches.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China; Key Lab of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hongyu Jing
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Bo Meng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
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31
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Liu L, Li L, Ma C, Shi Y, Liu C, Xiao Z, Zhang Y, Tian F, Gao Y, Zhang J, Ying W, Wang PG, Zhang L. O-GlcNAcylation of Thr 12/Ser 56 in short-form O-GlcNAc transferase (sOGT) regulates its substrate selectivity. J Biol Chem 2019; 294:16620-16633. [PMID: 31527085 DOI: 10.1074/jbc.ra119.009085] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/11/2019] [Indexed: 02/05/2023] Open
Abstract
O-GlcNAcylation is a ubiquitous protein glycosylation playing different roles on variant proteins. O-GlcNAc transferase (OGT) is the unique enzyme responsible for the sugar addition to nucleocytoplasmic proteins. Recently, multiple O-GlcNAc sites have been observed on short-form OGT (sOGT) and nucleocytoplasmic OGT (ncOGT), both of which locate in the nucleus and cytoplasm in cell. Moreover, O-GlcNAcylation of Ser389 in ncOGT (1036 amino acids) affects its nuclear translocation in HeLa cells. To date, the major O-GlcNAcylation sites and their roles in sOGT remain unknown. Here, we performed LC-MS/MS and mutational analyses to seek the major O-GlcNAcylation site on sOGT. We identified six O-GlcNAc sites in the tetratricopeptide repeat domain in sOGT, with Thr12 and Ser56 being two "key" sites. Thr12 is a dominant O-GlcNAcylation site, whereas the modification of Ser56 plays a role in regulating sOGT O-GlcNAcylation, partly through Thr12 In vitro activity and pulldown assays demonstrated that O-GlcNAcylation does not affect sOGT activity but does affect sOGT-interacting proteins. In HEK293T cells, S56A bound to and hence glycosylated more proteins in contrast to T12A and WT sOGT. By proteomic and bioinformatics analyses, we found that T12A and S56A differed in substrate proteins (e.g. HNRNPU and PDCD6IP), which eventually affected cell cycle progression and/or cell proliferation. These findings demonstrate that O-GlcNAcylation modulates sOGT substrate selectivity and affects its role in the cell. The data also highlight the regulatory role of O-GlcNAcylation at Thr12 and Ser56.
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Affiliation(s)
- Li Liu
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Ling Li
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Cheng Ma
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Yangde Shi
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Congcong Liu
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Zikang Xiao
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Yong Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China.,West China-Washington Mitochondria and Metabolism Research Center, Key Laboratory of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fang Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yang Gao
- School of medicine, Nankai University, Tianjin 300071, China
| | - Jie Zhang
- School of medicine, Nankai University, Tianjin 300071, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Peng George Wang
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China.,Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Lianwen Zhang
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
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32
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Zhao Y, Zhang L, Zhang Y, Meng B, Ying W, Qian X. Identification of hedgehog signaling as a potential oncogenic driver in an aggressive subclass of human hepatocellular carcinoma: A reanalysis of the TCGA cohort. Sci China Life Sci 2019; 62:1481-1491. [PMID: 31313086 DOI: 10.1007/s11427-019-9560-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 05/06/2019] [Indexed: 02/05/2023]
Abstract
Hepatocellular carcinoma (HCC) is a heterogeneous disease and the second most common cause of cancer-related death worldwide. Marked developments in genomic technologies helped scientists to understand the heterogeneity of HCC and identified multiple HCC-related molecular subclasses. An 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 investigated. Herein, 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) subclasses. The 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 M-Ag and L-Ag subclasses. Global transcriptomic analysis showed that activation of hedgehog signaling in the Ag subclass may play key roles in tumor development of aggressive HCC. GLI1, 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.
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Affiliation(s)
- Yang Zhao
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Li Zhang
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.,School of Statistics, Faculty of Economics and Management, East China Normal University, Shanghai, 200241, China
| | - Yong Zhang
- Key Lab of Transplant Engineering and Immunology, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Bo Meng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Xiaohong Qian
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China. .,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
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33
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Zhang C, Xie F, Li L, Zhang C, Zhang Y, Ying W, Liu L, Yan X, Yin F, Zhang L. Hepatocyte nuclear factor 1 alpha (HNF1A) regulates transcription of
O
‐GlcNAc transferase in a negative feedback mechanism. FEBS Lett 2019; 593:1050-1060. [PMID: 30953348 DOI: 10.1002/1873-3468.13381] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Chuanhui Zhang
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin China
| | - Fei Xie
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin China
| | - Ling Li
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin China
| | - Cheng Zhang
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin China
| | - Yong Zhang
- State Key Laboratory of Proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine China
- Key Lab of Transplant Engineering and Immunology MOH West China‐Washington Mitochondria and Metabolism Research Center West China Hospital Sichuan University Chengdu China
| | - Wantao Ying
- State Key Laboratory of Proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine China
| | - Li Liu
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin China
| | - Xuli Yan
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin China
| | - Futao Yin
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin China
| | - Lianwen Zhang
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin China
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34
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Yan M, Zhao Y, Zhang Y, Ying W, Qian X. [Establishment of a microscale peptide prefractionation system based on ultra performance liquid chromatography and the eight-port rotor valve]. Se Pu 2019; 37:477-483. [PMID: 31070329 DOI: 10.3724/sp.j.1123.2018.11021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Liquid chromatography (LC) and mass spectrometry (MS)-based proteomics now allows very deep coverage of proteomes. Two-dimensional high performance liquid chromatography (2-D HPLC) is a useful tool for the proteome analysis of complex biosystem. However, it has drawback of a long running time, and it typically requires peptide amounts in the milligram range, and large volume of collected fractions. In this study, we introduce ultra-performance liquid chromatography (UPLC) and an eight-port rotor valve as a highly efficient and convenient method for a first-dimension separation and collection system. The combination of our UPLC-based fractionation using basic buffers with an online LC-MS/MS provided orthogonal peptide separation and demonstrated the powerful performance for protein identification. Upon applying the novel method to triplicate measurements of a human cell line, we observed excellent quantitative reproducibility between replicates (coefficient of determination R2>0.95) and more than 23.52% peptide identifications over the conventional StageTip approach. The fractionation method described here is flexible, straightforward, and robust, and it enables proteome analysis with minimal sample requirements.
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Affiliation(s)
- Meng Yan
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yang Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiaohong Qian
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
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35
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Jiang Y, Sun A, Zhao Y, Ying W, Sun H, Yang X, Xing B, Sun W, Ren L, Hu B, Li C, Zhang L, Qin G, Zhang M, Chen N, Zhang M, Huang Y, Zhou J, Zhao Y, Liu M, Zhu X, Qiu Y, Sun Y, Huang C, Yan M, Wang M, Liu W, Tian F, Xu H, Zhou J, Wu Z, Shi T, Zhu W, Qin J, Xie L, Fan J, Qian X, He F. Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma. Nature 2019; 567:257-261. [PMID: 30814741 DOI: 10.1038/s41586-019-0987-8] [Citation(s) in RCA: 480] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 02/01/2019] [Indexed: 12/28/2022]
Abstract
Hepatocellular carcinoma is the third leading cause of deaths from cancer worldwide. Infection with the hepatitis B virus is one of the leading risk factors for developing hepatocellular carcinoma, particularly in East Asia1. Although surgical treatment may be effective in the early stages, the five-year overall rate of survival after developing this cancer is only 50-70%2. Here, using proteomic and phospho-proteomic profiling, we characterize 110 paired tumour and non-tumour tissues of clinical early-stage hepatocellular carcinoma related to hepatitis B virus infection. Our quantitative proteomic data highlight heterogeneity in early-stage hepatocellular carcinoma: we used this to stratify the cohort into the subtypes S-I, S-II and S-III, each of which has a different clinical outcome. S-III, which is characterized by disrupted cholesterol homeostasis, is associated with the lowest overall rate of survival and the greatest risk of a poor prognosis after first-line surgery. The knockdown of sterol O-acyltransferase 1 (SOAT1)-high expression of which is a signature specific to the S-III subtype-alters the distribution of cellular cholesterol, and effectively suppresses the proliferation and migration of hepatocellular carcinoma. Finally, on the basis of a patient-derived tumour xenograft mouse model of hepatocellular carcinoma, we found that treatment with avasimibe, an inhibitor of SOAT1, markedly reduced the size of tumours that had high levels of SOAT1 expression. The proteomic stratification of early-stage hepatocellular carcinoma presented in this study provides insight into the tumour biology of this cancer, and suggests opportunities for personalized therapies that target it.
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Affiliation(s)
- Ying Jiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Aihua Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yang Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.,College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Huichuan Sun
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinrong Yang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Baocai Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Wei Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Liangliang Ren
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Bo Hu
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chaoying Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Li Zhang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Guangrong Qin
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China
| | - Menghuan Zhang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China
| | - Ning Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Manli Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yin Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Jinan Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yan Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xiaodong Zhu
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yang Qiu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yanjun Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Cheng Huang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Meng Yan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Mingchao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Wei Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Fang Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Huali Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Jian Zhou
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhenyu Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Weimin Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China
| | - Jia Fan
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China. .,College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China.
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
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36
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Gao F, Jiao F, Xia C, Zhao Y, Ying W, Xie Y, Guan X, Tao M, Zhang Y, Qin W, Qian X. A novel strategy for facile serum exosome isolation based on specific interactions between phospholipid bilayers and TiO 2. Chem Sci 2019; 10:1579-1588. [PMID: 30842820 PMCID: PMC6369439 DOI: 10.1039/c8sc04197k] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/30/2018] [Indexed: 01/08/2023] Open
Abstract
Exosomes are cell-derived, phospholipid bilayer-enclosed vesicles that play important roles in intercellular interactions and regulate many biological processes. Accumulating evidence suggests that serum exosomes are potential biomarkers for the early diagnosis of cancer. To aid the downstream molecular analyses of tumour-secreted exosomes, purified exosomes are highly desirable. However, current techniques for exosome isolation are time-consuming and highly instrument-dependent, with limited specificity and recovery. Thus, rapid and efficient methods are strongly needed for both basic research and clinical applications. Here, we present a novel strategy for facile exosome isolation from human serum by taking advantage of the specific interaction of TiO2 with the phosphate groups on the lipid bilayer of exosomes. Due to their simplicity and highly affinitive binding, model exosomes can be reversibly isolated with a high recovery (93.4%). Downstream characterization and proteome profiling reveal that high-quality exosomes can be obtained from human serum by this TiO2-based isolation method in 5 min, which is a fraction of the time required for the commonly used ultracentrifugation method. We identified 59 significantly up-regulated proteins by comparing the serum exosomes of pancreatic cancer patients and healthy donors. In addition to the 30 proteins that were reported to be closely related to pancreatic cancer, we found an additional 29 proteins that had not previously been shown to be related to pancreatic cancer, indicating the potential of this novel method as a powerful tool for exosome isolation for health monitoring and disease diagnosis.
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Affiliation(s)
- Fangyuan Gao
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | - Fenglong Jiao
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
- School of Life Science and Technology , Beijing Institute of Technology , China
| | - Chaoshuang Xia
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | - Yang Zhao
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | - Wantao Ying
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | - Yuping Xie
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | | | - Ming Tao
- Peking University Third Hospital , China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | - Weijie Qin
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | - Xiaohong Qian
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
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37
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Jiang B, Huang J, Yu Z, Wu M, Liu M, Yao J, Zhao H, Yan G, Ying W, Cao W, Yang P. A multi-parallel N-glycopeptide enrichment strategy for high-throughput and in-depth mapping of the N-glycoproteome in metastatic human hepatocellular carcinoma cell lines. Talanta 2019; 199:254-261. [PMID: 30952254 DOI: 10.1016/j.talanta.2019.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/25/2019] [Accepted: 02/03/2019] [Indexed: 02/06/2023]
Abstract
N-glycosylation is deeply involved in many biological processes, and approximately 50% of mammalian proteins are predicted to be glycosylated. Many large-scale studies have been carried out to reveal the glycosylation status involved in different physiological pathologies across species. However, the lack of a highly specific and high-throughput N-glycosylated enrichment method not only results in extended time requirements but also limits the depth of mapping when handling a large number of samples. In this study, we firstly optimized traditional zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) enrichment and found that using of 70% acetonitrile (ACN), 0.1% trifluoroacetic acid (TFA) as the enrichment buffer, 2800 g as the washing speed and 600 μL as the washing volume achieved the best specificity, which is higher than 75%. On this basis, we developed a multi-parallel enrichment strategy assisted by a filter-coated 96-well plate, which achieved high specificity and high throughput simultaneously. This strategy allowed us to enrich large numbers of fractionated samples from hepatocellular carcinoma (HCC) cell lines in less than 2 h. Its good specificity helped us achieve in-depth mapping of the N-glycoproteome in metastatic HCC cell lines. A total of 5466 N-glycosites from 2383 glycoproteins were identified, among which 1900 N-glycosites were unannotated in UniProt. The in-depth glycoproteome mapping provides insight into the N-glycosylation status in HCC cell lines with differences in metastatic potential and contributes to biomarker discovery.
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Affiliation(s)
- Biyun Jiang
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China; Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China
| | - Jiangming Huang
- Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China
| | - Zixiang Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeOmics, Beijing 102206, People's Republic of China
| | - Mengxi Wu
- Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China
| | - Mingqi Liu
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China; NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200433, People's Republic of China
| | - Jun Yao
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China; Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China
| | - Huanhuan Zhao
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China
| | - Guoquan Yan
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China; Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeOmics, Beijing 102206, People's Republic of China.
| | - Weiqian Cao
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China; NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200433, People's Republic of China.
| | - Pengyuan Yang
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China; Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China; NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200433, People's Republic of China.
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38
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An Z, Zhai L, Ying W, Qian X, Gong F, Tan M, Fu Y. PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome. Mol Cell Proteomics 2019; 18:391-405. [PMID: 30420486 PMCID: PMC6356076 DOI: 10.1074/mcp.ra118.000812] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 11/02/2018] [Indexed: 12/27/2022] Open
Abstract
The open (mass tolerant) search of tandem mass spectra of peptides shows great potential in the comprehensive detection of post-translational modifications (PTMs) in shotgun proteomics. However, this search strategy has not been widely used by the community, and one bottleneck of it is the lack of appropriate algorithms for automated and reliable post-processing of the coarse and error-prone search results. Here we present PTMiner, a software tool for confident filtering and localization of modifications (mass shifts) detected in an open search. After mass-shift-grouped false discovery rate (FDR) control of peptide-spectrum matches (PSMs), PTMiner uses an empirical Bayesian method to localize modifications through iterative learning of the prior probabilities of each type of modification occurring on different amino acids. The performance of PTMiner was evaluated on three data sets, including simulated data, chemically synthesized peptide library data and modified-peptide spiked-in proteome data. The results showed that PTMiner can effectively control the PSM FDR and accurately localize the modification sites. At 1% real false localization rate (FLR), PTMiner localized 93%, 84 and 83% of the modification sites in the three data sets, respectively, far higher than two open search engines we used and an extended version of the Ascore localization algorithm. We then used PTMiner to analyze a draft map of human proteome containing 25 million spectra from 30 tissues, and confidently identified over 1.7 million modified PSMs at 1% FDR and 1% FLR, which provided a system-wide view of both known and unknown PTMs in the human proteome.
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Affiliation(s)
- Zhiwu An
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China;; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wantao Ying
- State key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing 102206, China, Beijing Institute of Lifeomics, Beijing 100850, China
| | - Xiaohong Qian
- State key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing 102206, China, Beijing Institute of Lifeomics, Beijing 100850, China
| | - Fuzhou Gong
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China;; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China;.
| | - Yan Fu
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China;; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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39
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Chang C, Gao Z, Ying W, Fu Y, Zhao Y, Wu S, Li M, Wang G, Qian X, Zhu Y, He F. LFAQ: Toward Unbiased Label-Free Absolute Protein Quantification by Predicting Peptide Quantitative Factors. Anal Chem 2018; 91:1335-1343. [PMID: 30525483 DOI: 10.1021/acs.analchem.8b03267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mass spectrometry (MS) has become a predominant choice for large-scale absolute protein quantification, but its quantification accuracy still has substantial room for improvement. A crucial issue is the bias between the peptide MS intensity and the actual peptide abundance, i.e., the fact that peptides with equal abundance may have different MS intensities. This bias is mainly caused by the diverse physicochemical properties of peptides. Here, we propose an algorithm for label-free absolute protein quantification, LFAQ, which can correct the biased MS intensities by using the predicted peptide quantitative factors for all identified peptides. When validated on data sets produced by different MS instruments and data acquisition modes, LFAQ presented accuracy and precision superior to those of existing methods. In particular, it reduced the quantification error by an average of 46% for low-abundance proteins. The advantages of LFAQ were further confirmed using the data from published papers.
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Affiliation(s)
- Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Zhiqiang Gao
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science , Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190 , China.,School of Mathematical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yan Fu
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science , Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190 , China.,School of Mathematical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yan Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Songfeng Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Mengjie Li
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science , Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190 , China.,School of Mathematical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Guibin Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China.,Anhui Medical University , Hefei , 230032 China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
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40
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Li X, Jiang J, Zhao X, Zhao Y, Cao Q, Zhao Q, Han H, Wang J, Yu Z, Peng B, Ying W, Qian X. In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins. Oncotarget 2017; 7:22031-49. [PMID: 27014972 PMCID: PMC5008342 DOI: 10.18632/oncotarget.8247] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 02/05/2016] [Indexed: 12/29/2022] Open
Abstract
Cancer cell metastasis is a major cause of cancer fatality. But the underlying molecular mechanisms remain incompletely understood, which results in the lack of efficient diagnosis, therapy and prevention approaches. Here, we report a systematic study on the secretory proteins (secretome) and secretory N-glycoproteins (N-glycosecretome) of four human hepatocellular carcinoma (HCC) cell lines with different metastatic potential, to explore the molecular mechanism of metastasis and supply the clues for effective measurement of diagnosis and therapy. Totally, 6242 unique gene products (GPs) and 1637 unique N-glycosites from 635 GPs were confidently identified. About 4000 GPs on average were quantified in each of the cell lines, 1156 of which show differential expression (p<0.05). Ninety-nine percentage of the significantly altered proteins were secretory proteins and proteins correlated to cell movement were significantly activated with the increasing of metastatic potential of the cell lines. Twenty-three GPs increased both in the secretome and the N-glycosecretome were chosen as candidates and verified by western blot analysis, and 10 of them were chosen for immunohistochemistry (IHC) analysis. The cumulative survival rates of the patients with candidate (FAT1, DKK3) suggested that these proteins might be used as biomarkers for HCC diagnosis. In addition, a comparative analysis with the published core human plasma database (1754 GPs) revealed that there were 182 proteins not presented in the human plasma database but identified by our studies, some of which were selected and verified successfully by western blotting in human plasma.
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Affiliation(s)
- Xianyu Li
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China.,Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jing Jiang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xinyuan Zhao
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yan Zhao
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Qichen Cao
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Qing Zhao
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Huanhuan Han
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jifeng Wang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Zixiang Yu
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Bo Peng
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Wantao Ying
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xiaohong Qian
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
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41
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Zhang Y, Xie X, Zhao X, Tian F, Lv J, Ying W, Qian X. Systems analysis of singly and multiply O-glycosylated peptides in the human serum glycoproteome via EThcD and HCD mass spectrometry. J Proteomics 2017; 170:14-27. [PMID: 28970103 DOI: 10.1016/j.jprot.2017.09.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/26/2017] [Accepted: 09/28/2017] [Indexed: 01/20/2023]
Abstract
Human serum has been intensively studied to identify biomarkers via global proteomic analysis. The altered O-glycoproteome is associated with human pathological state including cancer, inflammatory and degenerative diseases and is an attractive source of disease biomarkers. Because of the microheterogeneity and macroheterogeneity of O-glycosylation, site-specific O-glycosylation analysis in human serum is still challenging. Here, we developed a systematic strategy that combined multiple enzyme digestion, multidimensional separation for sample preparation and high-resolution tandem MS with Byonic software for intact O-glycopeptide characterization. We demonstrated that multiple enzyme digestion or multidimensional separation can make sample preparation more efficient and that EThcD is not only suitable for the identification of singly O-glycosylated peptides (50.3%) but also doubly (21.2%) and triply (28.5%) O-glycosylated peptides. Totally, with the strict scoring criteria, 499 non-redundant intact O-glycopeptides, 173 O-glycosylation sites and 6 types of O-glycans originating from 49 O-glycoprotein groups were identified in human serum, including 121 novel O-glycosylation sites. Currently, this is the largest data set of site-specific native O-glycoproteome from human serum samples. We expect that the strategies developed by this study will facilitate in-depth analyses of native O-glycoproteomes in human serum and provide opportunities to understand the functional roles of protein O-glycosylation in human health and diseases. BIOLOGICAL SIGNIFICANCE The altered O-glycoproteome is associated with human pathological state and is an attractive source of disease biomarkers. However, site-specific O-glycosylation analysis is challenging because of the microheterogeneity (different glycoforms attached to one glycosylation site) and macroheterogeneity (site occupancy) of O-glycosylation. In this work, we developed a systematic strategy for intact O-glycopeptide characterization. This study took advantage of the inherent properties of the new fragmentation method called EThcD, which provides more complete fragmentation information about O-glycosylated peptides and a more confident site localization of O-glycans than collision-induced dissociation (HCD). We demonstrated that multiple enzyme digestion or multidimensional separation can make sample preparation more efficient and that EThcD was not only suitable for the identification of singly O-glycosylated peptides (50.3%) but also doubly (21.2%) and triply (28.5%) O-glycosylated peptides. Finally, we got a largest data set of site-specific native O-glycoproteome from human serum samples. Furthermore, quantitative analysis of intact O-glycopeptides from the serum samples of IgA nephropathy (IgAN) patients and healthy donors was performed, and the results showed the potential of the strategy to discover O-glycosylation biomarkers. We expect that the strategies developed by this study will facilitate in-depth analyses of native O-glycoproteomes in human serum and lead to exciting opportunities to understand the functional roles of protein O-glycosylation in human health and diseases.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Xinfang Xie
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
| | - Xinyuan Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Fang Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Jicheng Lv
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing 102206, China.
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing 102206, China.
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42
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Ding C, Li Y, Guo F, Jiang Y, Ying W, Li D, Yang D, Xia X, Liu W, Zhao Y, He Y, Li X, Sun W, Liu Q, Song L, Zhen B, Zhang P, Qian X, Qin J, He F. A Cell-type-resolved Liver Proteome. Mol Cell Proteomics 2016; 15:3190-3202. [PMID: 27562671 PMCID: PMC5054343 DOI: 10.1074/mcp.m116.060145] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 01/16/2023] Open
Abstract
Parenchymatous organs consist of multiple cell types, primarily defined as parenchymal cells (PCs) and nonparenchymal cells (NPCs). The cellular characteristics of these organs are not well understood. Proteomic studies facilitate the resolution of the molecular details of different cell types in organs. These studies have significantly extended our knowledge about organogenesis and organ cellular composition. Here, we present an atlas of the cell-type-resolved liver proteome. In-depth proteomics identified 6000 to 8000 gene products (GPs) for each cell type and a total of 10,075 GPs for four cell types. This data set revealed features of the cellular composition of the liver: (1) hepatocytes (PCs) express the least GPs, have a unique but highly homogenous proteome pattern, and execute fundamental liver functions; (2) the division of labor among PCs and NPCs follows a model in which PCs make the main components of pathways, but NPCs trigger the pathways; and (3) crosstalk among NPCs and PCs maintains the PC phenotype. This study presents the liver proteome at cell resolution, serving as a research model for dissecting the cell type constitution and organ features at the molecular level.
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Affiliation(s)
- Chen Ding
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; **State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Yanyan Li
- ¶School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Feifei Guo
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Ying Jiang
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Wantao Ying
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Dong Li
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Dong Yang
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Xia Xia
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Wanlin Liu
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Yan Zhao
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Yangzhige He
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; ¶School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xianyu Li
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Wei Sun
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Qiongming Liu
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Lei Song
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Bei Zhen
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Pumin Zhang
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Xiaohong Qian
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China;
| | - Jun Qin
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; ‖Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030; **State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Fuchu He
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; **State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
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Marrone KA, Ying W, Naidoo J. Immune-Related Adverse Events From Immune Checkpoint Inhibitors. Clin Pharmacol Ther 2016; 100:242-51. [PMID: 27170616 DOI: 10.1002/cpt.394] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/06/2016] [Accepted: 05/07/2016] [Indexed: 01/11/2023]
Abstract
Immunotherapy for cancer treatment has come of age, specifically with the use of immune checkpoint antibodies directed against molecules such as CTLA-4, PD-1, and PD-L1. Single-agent and combinatorial approaches utilizing these agents and other immunotherapies that may enhance antitumor effects are under investigation. With increasing clinical use of these agents, an appreciation for their toxicities comes to the fore. Adverse events that occur as a result of the immunologic effects of these therapies are termed "immune-related adverse events" (irAEs), and range in both frequency and severity in reported single-agent and combination studies. Improvements in our understanding of how and why irAEs develop and how to effectively manage them are needed. Herein we provide a state-of-the-art synopsis of the incidence, clinical features, mechanisms, and management of selected irAEs with immune checkpoint inhibitors currently in use.
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Affiliation(s)
- K A Marrone
- Department of Oncology, Sidney Kimmel Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
| | - W Ying
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - J Naidoo
- Department of Oncology, Sidney Kimmel Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
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44
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Chu T, Jiang L, Ying W, Han B. M30/M65 ratio predicts the outcome of paclitaxel chemotherapy for NSCLC. Clin Transl Oncol 2016; 19:326-331. [PMID: 27468866 DOI: 10.1007/s12094-016-1533-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/12/2016] [Indexed: 11/29/2022]
Abstract
PURPOSE Paclitaxel is an effective treatment for some of the non-small-cell lung cancer (NSCLC) patients. However, prediction of the outcome of paclitaxel treatment at the early stage of the chemotherapy is difficult. M30 and M65 are circulating fragments of cytokeratin 18 released during apoptosis or necrosis, respectively, and have been used as markers to evaluate chemotherapy in some cancers. Here, we aimed to examine M30 and M65 values for predicting the therapeutic outcome of paclitaxel treatment of NSCLC. METHODS The serum levels of M30 and M65 before and after paclitaxel treatment in advance-stage NSCLC patients were analyzed, and compared to those in healthy controls. The importance of the M30 and M65 levels to the outcome of chemotherapy was analyzed. RESULT We found that the serum M30 and M65 levels were higher in patients with NSCLC (n = 44) than in control healthy subjects (n = 56) (p < 0.001). Two days after paclitaxel treatment, the serum levels of both M30 and M65 significantly increased in NSCLC patients (p < 0.001). Neither marker alone significantly correlated with overall patient survival, but the ratio of M30 vs M65 appeared to be an important prognostic factor for the overall survival of the patients (p < 0.01). CONCLUSION Our results suggest that the serum M30/M65 ratio may be a prognostic factor for the outcome of paclitaxel treatment in NSCLC.
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Affiliation(s)
- T Chu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, 241 Huaihai Road, Shanghai, 200030, China
| | - L Jiang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, 241 Huaihai Road, Shanghai, 200030, China
| | - W Ying
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiaotong University, 1954 Huashan Road, Shanghai, 200030, China.
| | - B Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, 241 Huaihai Road, Shanghai, 200030, China.
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Sheng QK, Zhou KF, Hu HM, Zhao HB, Zhang Y, Ying W. Effect of Bacillus subtilis Natto on Meat Quality and Skatole Content in TOPIGS Pigs. Asian-Australas J Anim Sci 2016; 29:716-21. [PMID: 26954164 PMCID: PMC4852235 DOI: 10.5713/ajas.15.0478] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/19/2015] [Accepted: 09/29/2015] [Indexed: 12/05/2022]
Abstract
This study investigated the effect of Bacillus subtilis (B. subtilis) natto on meat quality and skatole in TOPIGS pigs. Sixty TOPIGS pigs were randomly assigned to 3 groups (including 5 pens per group, with 4 pigs in each pen) and fed with basic diet (control group), basic diet plus 0.1% B. subtilis natto (B group), and basic diet plus 0.1% B. subtilis natto plus 0.1% B. coagulans (BB group), respectively. All pigs were sacrificed at 100 kg. Growth performance, meat quality, serum parameters and oxidation status in the three groups were assessed and compared. Most parameters regarding growth performance and meat quality were not significantly different among the three groups. However, compared with the control group, meat pH24, fat and feces skatole and the content of Escherichia coli (E. Coli), Clostridium, NH3-N were significantly reduced in the B and BB groups, while serum total cholesterol, high density lipoprotein, the levels of liver P450, CYP2A6, and CYP2E1, total antioxidant capability (T-AOC) and glutathione peroxidase and Lactobacilli in feces were significantly increased in the B and BB groups. Further, the combined supplementation of B. subtilis natto and B. coagulans showed more significant effects on the parameters above compared with B. subtilis, and Clostridium, and NH3-N. Our results indicate that the supplementation of pig feed with B. subtilis natto significantly improves meat quality and flavor, while its combination with B. coagulans enhanced these effects.
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Affiliation(s)
- Q. K. Sheng
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100,
China
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Jinan 250100,
China
- Corresponding Author: Q. K. Sheng. Tel: +86-531-88622516, Fax: +86-531-88622516, E-mail:
| | - K. F. Zhou
- Shandong Chief Animal Husbandry and Veterinarian Station, Jinan 250002,
China
| | - H. M. Hu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100,
China
| | - H. B. Zhao
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100,
China
| | - Y. Zhang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100,
China
| | - W. Ying
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100,
China
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46
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Ding K, Wu S, Ying W, Pan Q, Li X, Zhao D, Li X, Zhao Q, Zhu Y, Ren H, Qian X. Leveraging a Multi-Omics Strategy for Prioritizing Personalized Candidate Mutation-Driver Genes: A Proof-of-Concept Study. Sci Rep 2015; 5:17564. [PMID: 26631547 PMCID: PMC4668376 DOI: 10.1038/srep17564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/02/2015] [Indexed: 02/07/2023] Open
Abstract
The expression of mutant forms of proteins (e.g., oncogenes and tumor suppressors) has implications in cancer biology and clinical practice. Initial efforts have been made to characterize the transcription of tumor-mutated alleles; however, few studies have been reported to link tumor-mutated alleles to proteomics. We aimed to characterize the transcriptional and translational patterns of tumor-mutated alleles. We performed whole-exome sequencing, RNA-seq, and proteome profiling in a hyper-mutated patient of hepatocellular carcinoma. Using the patient as a model, we show that only a small proportion of tumor-mutated alleles were expressed. In this case, 42% and 3.5% of the tumor-mutated alleles were identified to be transcribed and translated, respectively. Compared with genes with germline variations or without mutations, somatic mutations significantly reduced protein expression abundance. Using the transcriptional and translational patterns of tumor-mutated alleles, we classified the mutations into four types, and only one type may be associated with the liver cancer and lead to hepatocarcinogenesis in the patient. Our results demonstrate how tumor-mutated alleles are transcribed and translated, and how the expression enables the classification of somatic mutations that cause cancer. Leveraging multiple ‘omics’ datasets provides a new avenue for understanding patient-specific mutations that underlie carcinogenesis.
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Affiliation(s)
- Keyue Ding
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education of China; Depeartment of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P. R. China, 400010
| | - Songfeng Wu
- State Key Laboratory of Proteomics, National Protein Science Beijing Center, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China, 102206
| | - Wantao Ying
- State Key Laboratory of Proteomics, National Protein Science Beijing Center, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China, 102206
| | - Qi Pan
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education of China; Depeartment of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P. R. China, 400010
| | - Xiaoyuan Li
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China, 100730
| | - Dachun Zhao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China, 100730
| | - Xianyu Li
- State Key Laboratory of Proteomics, National Protein Science Beijing Center, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China, 102206
| | - Qing Zhao
- State Key Laboratory of Proteomics, National Protein Science Beijing Center, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China, 102206
| | - Yunping Zhu
- State Key Laboratory of Proteomics, National Protein Science Beijing Center, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China, 102206
| | - Hong Ren
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education of China; Depeartment of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P. R. China, 400010
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, National Protein Science Beijing Center, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China, 102206
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47
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Jin Z, Lü Y, Zhou S, Hao F, Fu B, Ying W, Qian X, Zhang Y. [A simple preparation method of an electric heating apparatus for heating capillary chromatographic columns and its application in liquid chromatography-mass spectrometry system]. Se Pu 2015; 33:563-70. [PMID: 26536758 DOI: 10.3724/sp.j.1123.2015.01036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
For deep coverage of proteome, especially in performing qualitative identification and quantitative analysis of low-abundance proteins, the most commonly used method is the application of a longer capillary chromatographic column or a capillary column packed with smaller particle sizes. However, this causes another problem, the very high back pressure which results in liquid leaks in some connection parts in a liquid chromatograph. To solve this problem, an electric heating apparatus was developed to raise the temperature of a capillary column for reducing its back pressure, which was further applied in a capillary high performance liquid chromatography-tandem mass spectrometry system (cHPLC-MS/MS), and evaluated in the terms of chromatographic column back pressure and chromatographic column efficiency using bovine serum albumin (BSA) tryptic digests and yeast tryptic digests, separately. The results showed that at the optimum current, our electric heating apparatus could reduce the column pressure of a capillary column packed with 3 µm packing materials by at least 50% during the separation of BSA tryptic digestion and yeast tryptic digestion, compared with that without electric heating. The column efficiency was also increased slightly. This suggested that the electric heating apparatus can significantly reduce the column pressure, which provides an efficient way to use capillary chromatographic columns packed with smaller sizes of particles at a lower pressure.
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48
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Wencui Z, Qi Z, Ying W, Di W. Preparation of solid lipid nanoparticles loaded with garlic oil and evaluation of their in vitro and in vivo characteristics. Eur Rev Med Pharmacol Sci 2015; 19:3742-3750. [PMID: 26502865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
OBJECTIVE Solid lipid nanoparticles (SLN) are colloidal drug carriers and may be suitable for delivery of garlic oil, a nutraceutical with medicinal properties, whose use has been limited by its poor solubility. We tested whether poor solubility of garlic oil would be overcome by complexing with SLN by high-pressure homogenization and ultrasound techniques. The effects of lipid phase, surfactant mixture and loading concentration of garlic oil on particle size and distribution were also investigated. MATERIALS AND METHODS High pressure homogenization technique was used to prepare SLN, using orthogonal experiment method to optimize entrapment efficiency, loading efficiency, and recovery of SLN. Pharmacokinetics of garlic oil loaded solid lipid nanoparticles after oral administration to rats was studied by using LC/MS/MS method. RESULTS Mean particle size and zeta potential of SLN were, respectively, 106.5 ± 40.3 nm and -30.2 mv. The majority of SLN had a less ordered arrangement of crystals at room temperature, which was beneficial for increasing the drug loading capacity. Drug entrapment efficiency was > 90 percent and showed a relatively long-term physical stability. It was feasible to prepare a lyophilized product with good long-term stability. When 10% trehalose and 5% sucrose were used as cryopreservants, SNL particle size increased from 106.5 nm prior to lyophilisation to 155.3 nm after reconstitution. The garlic oil content in SLN decreased to about 85% (respectively, 34.3 vs. 39.4 mg/mL prior to lyophilisation) due to volatility of garlic oil. Pharmacokinetic studies in rats demonstrated that distribution and elimination of diallyl trisulfide (DATS) and diallyl disulfide (DADS) in garlic oil were rapid. Additionally, elimination of garlic oil-SLN complex is faster than that of garlic oil alone, probably, due to phagocytosis. CONCLUSIONS An SLN complex with garlic oil exhibits characteristics similar to those of parenteral emulsions, even after lyophilization and reconstitution.
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Affiliation(s)
- Z Wencui
- The 208 Hospital of Chinese People's Liberation Army, Changchun, P.R. China.
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Jiang K, Gao Y, Hou W, Tian F, Ying W, Li L, Bai B, Hou G, Wang PG, Zhang L. Proteomic analysis of O-GlcNAcylated proteins in invasive ductal breast carcinomas with and without lymph node metastasis. Amino Acids 2015; 48:365-74. [PMID: 26374642 DOI: 10.1007/s00726-015-2089-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/26/2015] [Indexed: 02/02/2023]
Abstract
The potential role of protein O-GlcNAcylation in cancer has been studied extensively, and the spread of cancer cells to regional lymph nodes is the first step in the dissemination of breast cancer. However, the correlation between O-GlcNAcylation and lymphatic metastasis in breast cancer remains elusive. In this study, we demonstrated that the overall O-GlcNAcylation as well as O-GlcNAc transferase (OGT) tends to decrease in response to the augmentation of lymph node metastasis (LNM) in invasive ductal breast carcinomas (IDCs). Although accumulating evidence indicates that individual O-GlcNAcylation may be important in the pathogenesis of breast cancer, O-GlcNAcylated proteins in IDCs are still largely unexplored. Herein, O-GlcNAcylated proteins of IDCs were chemo-enzymatically enriched and identified via liquid chromatography combined with tandem mass spectrometry. In total, 155 O-GlcNAcylated proteins were determined, of which 41 were only observed in LNM tissues, while 40 were unique in non-LNM samples. Gene ontology analysis showed that O-GlcNAc is primarily a nucleocytoplasmic post-translational modification, and most enriched functional terms were related to cancer development in both metastatic and non-metastatic IDCs. Moreover, several O-GlcNAcylated proteins involved in glycolysis and its accessory pathway were identified from LNM and non-LNM groups, respectively. These results indicate that the O-GlcNAcylation statuses of individual proteins were independent of the overall O-GlcNAcylation levels of metastatic and non-metastatic IDCs. Aberrant O-GlcNAc modification of these proteins might be associated with LNM progression.
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Affiliation(s)
- Kuan Jiang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
| | - Yang Gao
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Weiwei Hou
- Department of Pathology, The Central Hospital of Taian, 29 Longtan Road, Taian, 271000, China
| | - Fang Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Ling Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
| | - Bingyang Bai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
| | - Gang Hou
- Department of Pathology, The Central Hospital of Taian, 29 Longtan Road, Taian, 271000, China.
| | - Peng George Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China.
| | - Lianwen Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China.
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50
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Chen M, Huang H, He H, Ying W, Liu X, Dai Z, Yin J, Mao N, Qian X, Pan L. Quantitative proteomic analysis of mitochondria from human ovarian cancer cells and their paclitaxel-resistant sublines. Cancer Sci 2015; 106:1075-83. [PMID: 26033570 PMCID: PMC4556398 DOI: 10.1111/cas.12710] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/24/2015] [Accepted: 05/26/2015] [Indexed: 01/10/2023] Open
Abstract
Paclitaxel resistance is a major obstacle for the treatment of ovarian cancer. The chemoresistance mechanisms are partly related to the mitochondria. Identification of the relevant proteins in mitochondria will help in clarifying the possible mechanisms and in selecting effective chemotherapy for patients with paclitaxel resistance. In the present study, mitochondria from two paclitaxel-sensitive human ovarian cancer cell lines (SKOV3 and A2780) and their corresponding resistant cell lines (SKOV3-TR and A2780-TR) were isolated. Guanidine-modified acetyl-stable isotope labeling and liquid chromatography-hybrid linear ion trap Fourier-transform ion cyclotron resonance mass spectrometry (LC-FTICR MS) were performed to find the expressed differential proteins. Comparative proteomic analysis revealed eight differentially expressed proteins in the ovarian cancer cells and their paclitaxel-resistant sublines. Among them, mimitin and 14-3-3 ζ/δ were selected for further research. The effects of mimitin and 14-3-3 ζ/δ were explored using specific siRNA interference in ovarian cancer cell lines and immunohistochemistry in human tissue specimens. The downregulation of mimitin and 14-3-3 ζ/δ using specific siRNA in paclitaxel-resistant ovarian cancer cells led to an increase in the resistance index to paclitaxel. Multivariate analyses demonstrated that lower expression levels of the mimitin and 14-3-3 ζ/δ proteins were positively associated with shorter progression-free survival (PFS) and overall survival (OS) in patients with primary ovarian cancer (mimitin: PFS: P = 0.041, OS: P = 0.003; 14-3-3 ζ/δ: PFS: P = 0.031, OS: P = 0.011). Mimitin and 14-3-3 protein ζ/δ are potential markers of paclitaxel resistance and prognostic factors in ovarian cancer.
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Affiliation(s)
- Ming Chen
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong Huang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Haojie He
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, China
| | - Xin Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, China.,Central Laboratory, Yantai Yuhuangding Hospital, Yantai, China
| | - Zhiqin Dai
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Gynecological Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China
| | - Jie Yin
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ning Mao
- Department of Cell Biology, Institute of Basic Medical Sciences, Beijing, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, China
| | - Lingya Pan
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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