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Coombs KM. Update on Proteomic approaches to uncovering virus-induced protein alterations and virus -host protein interactions during the progression of viral infection. Expert Rev Proteomics 2020; 17:513-532. [PMID: 32910682 DOI: 10.1080/14789450.2020.1821656] [Citation(s) in RCA: 11] [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] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Viruses induce profound changes in the cells they infect. Understanding these perturbations will assist in designing better therapeutics to combat viral infection. System-based proteomic assays now provide unprecedented opportunity to monitor large numbers of cellular proteins. AREAS COVERED This review will describe various quantitative and functional mass spectrometry-based methods, and complementary non-mass spectrometry-based methods, such as aptamer profiling and proximity extension assays, and examples of how each are used to delineate how viruses affect host cells, identify which viral proteins interact with which cellular proteins, and how these change during the course of a viral infection. PubMed was searched multiple times prior to manuscript submissions and revisions, using virus, viral, proteomics; in combination with each keyword. The most recent examples of published works from each search were then analyzed. EXPERT OPINION There has been exponential growth in numbers and types of proteomic analyses in recent years. Continued development of reagents that allow increased multiplexing and deeper proteomic probing of the cell, at quantitative and functional levels, enhancements that target more important protein modifications, and improved bioinformatics software tools and pathway prediction algorithms will accelerate this growth and usher in a new era of host proteome understanding.
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Affiliation(s)
- Kevin M Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba , Winnipeg, Manitoba, Canada.,Manitoba Centre for Proteomics and Systems Biology , Winnipeg, Manitoba, Canada.,Manitoba Institute of Child Health , Winnipeg, Manitoba, Canada
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2
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Huraiova B, Kanovits J, Polakova SB, Cipak L, Benko Z, Sevcovicova A, Anrather D, Ammerer G, Duncan CDS, Mata J, Gregan J. Proteomic analysis of meiosis and characterization of novel short open reading frames in the fission yeast Schizosaccharomyces pombe. Cell Cycle 2020; 19:1777-1785. [PMID: 32594847 PMCID: PMC7469465 DOI: 10.1080/15384101.2020.1779470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 03/06/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 01/10/2023] Open
Abstract
Meiosis is the process by which haploid gametes are produced from diploid precursor cells. We used stable isotope labeling by amino acids in cell culture (SILAC) to characterize the meiotic proteome in the fission yeast Schizosaccharomyces pombe. We compared relative levels of proteins extracted from cells harvested around meiosis I with those of meiosis II, and proteins from premeiotic S phase with the interval between meiotic divisions, when S phase is absent. Our proteome datasets revealed peptides corresponding to short open reading frames (sORFs) that have been previously identified by ribosome profiling as new translated regions. We verified expression of selected sORFs by Western blotting and analyzed the phenotype of deletion mutants. Our data provide a resource for studying meiosis that may help understand differences between meiosis I and meiosis II and how S phase is suppressed between the two meiotic divisions.
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Affiliation(s)
- Barbora Huraiova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Judit Kanovits
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Silvia Bagelova Polakova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
- Department of Membrane Biochemistry, Inst. Of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lubos Cipak
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zsigmond Benko
- Department of Membrane Biochemistry, Inst. Of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Andrea Sevcovicova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Dorothea Anrather
- Mass Spectrometry Facility and Department of Biochemistry, Max Perutz Labs, University of Vienna, Vienna Biocenter, Austria
| | - Gustav Ammerer
- Mass Spectrometry Facility and Department of Biochemistry, Max Perutz Labs, University of Vienna, Vienna Biocenter, Austria
| | | | - Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Juraj Gregan
- Department of Chromosome Biology, Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
- Advanced Microscopy Facility, Vienna Biocenter Core Facilities, Vienna, Austria
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Dwivedi P, Muench DE, Wagner M, Azam M, Grimes HL, Greis KD. Time resolved quantitative phospho-tyrosine analysis reveals Bruton's Tyrosine kinase mediated signaling downstream of the mutated granulocyte-colony stimulating factor receptors. Leukemia 2019; 33:75-87. [PMID: 29977015 PMCID: PMC6320735 DOI: 10.1038/s41375-018-0188-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [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: 01/19/2018] [Revised: 05/31/2018] [Accepted: 06/06/2018] [Indexed: 12/26/2022]
Abstract
Granulocyte-colony stimulating factor receptor (G-CSFR) controls myeloid progenitor proliferation and differentiation to neutrophils. Mutations in CSF3R (encoding G-CSFR) have been reported in patients with chronic neutrophilic leukemia (CNL) and acute myeloid leukemia (AML); however, despite years of research, the malignant downstream signaling of the mutated G-CSFRs is not well understood. Here, we used a quantitative phospho-tyrosine analysis to generate a comprehensive signaling map of G-CSF induced tyrosine phosphorylation in the normal versus mutated (proximal: T618I and truncated: Q741x) G-CSFRs. Unbiased clustering and kinase enrichment analysis identified rapid induction of phospho-proteins associated with endocytosis by the wild type G-CSFR only; while G-CSFR mutants showed abnormal kinetics of canonical Stat3, Stat5, and Mapk phosphorylation, and aberrant activation of Bruton's Tyrosine Kinase (Btk). Mutant-G-CSFR-expressing cells displayed enhanced sensitivity (3-5-fold lower IC50) for ibrutinib-based chemical inhibition of Btk. Primary murine progenitor cells from G-CSFR-Q741x knock-in mice validated activation of Btk by the mutant receptor and retrovirally transduced human CD34+ umbilical cord blood cells expressing mutant receptors displayed enhanced sensitivity to Ibrutinib. A significantly lower clonogenic potential was displayed by both murine and human primary cells expressing mutated receptors upon ibrutinib treatment. Finally, a dramatic synergy was observed between ibrutinib and ruxolinitib at lower dose of the individual drug. Altogether, these data demonstrate the strength of unsupervised proteomics analyses in dissecting oncogenic pathways, and suggest repositioning Ibrutinib for therapy of myeloid leukemia bearing CSF3R mutations. Phospho-tyrosine data are available via ProteomeXchange with identifier PXD009662.
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MESH Headings
- Adenine/analogs & derivatives
- Agammaglobulinaemia Tyrosine Kinase/antagonists & inhibitors
- Agammaglobulinaemia Tyrosine Kinase/genetics
- Agammaglobulinaemia Tyrosine Kinase/metabolism
- Animals
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Cells, Cultured
- Humans
- Leukemia, Myeloid, Acute
- Leukemia, Neutrophilic, Chronic
- Mice
- Mutation
- Phosphoproteins/metabolism
- Phosphorylation
- Piperidines
- Precursor Cells, B-Lymphoid/metabolism
- Precursor Cells, B-Lymphoid/pathology
- Protein-Tyrosine Kinases/analysis
- Protein-Tyrosine Kinases/metabolism
- Proteome/analysis
- Pyrazoles/pharmacology
- Pyrimidines/pharmacology
- Receptors, Granulocyte Colony-Stimulating Factor/genetics
- Receptors, Granulocyte Colony-Stimulating Factor/metabolism
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Affiliation(s)
- Pankaj Dwivedi
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - David E Muench
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Michael Wagner
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mohammad Azam
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| | - Kenneth D Greis
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA.
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Wang X, Liang Y, Liu L, Shi J, Zhu HJ. Targeted absolute quantitative proteomics with SILAC internal standards and unlabeled full-length protein calibrators (TAQSI). Rapid Commun Mass Spectrom 2016; 30:553-61. [PMID: 26842578 PMCID: PMC6301059 DOI: 10.1002/rcm.7482] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 09/15/2015] [Revised: 12/13/2015] [Accepted: 12/13/2015] [Indexed: 05/25/2023]
Abstract
RATIONALE Liquid Chromatography/Mass Spectrometry (LC/MS)-based proteomics for absolute protein quantification has been increasingly utilized in both basic and clinical research. There is a great need to overcome some major hurdles of current absolute protein quantification methods, such as significant inter-assay variability and the high cost associated with the preparation of purified stable-isotope-labeled peptide/protein standards. METHODS We developed a novel targeted absolute protein quantification method, named TAQSI, utilizing full-length isotope-labeled protein internal standards generated from SILAC (stable isotope labeling by amino acid in cell culture) and unlabeled full-length protein calibrators. This approach was applied to absolute quantification of carboxylesterase 1 (CES1), the primary human hepatic hydrolase, in a large set of human liver samples. Absolute CES1 quantities were derived from the standard calibration curves established from unlabeled CES1 protein calibrators and the isotope-labeled CES1 internal standards obtained from SILAC HepG2 cells. RESULTS The TAQSI assay was found to be accurate, precise, reproducible, and cost-effective. Importantly, protein quantification was not affected by various protein extraction and digestion protocols, and measurement errors associated with nonsynonymous variants can be readily identified and avoided. Furthermore, the TAQSI approach significantly simplifies the procedure of identifying the best performance surrogate peptides. CONCLUSIONS The TAQSI assay can be widely used for targeted absolute protein quantification in various biomedical research and clinical practice settings.
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Affiliation(s)
- Xinwen Wang
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
| | - Yan Liang
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
- The Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Li Liu
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
- The Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Jian Shi
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
| | - Hao-Jie Zhu
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
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5
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Zhang H, Angelopoulos N, Xu Y, Grothey A, Nunes J, Stebbing J, Giamas G. Proteomic profile of KSR1-regulated signalling in response to genotoxic agents in breast cancer. Breast Cancer Res Treat 2015; 151:555-68. [PMID: 26022350 PMCID: PMC4452580 DOI: 10.1007/s10549-015-3443-y] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/22/2015] [Indexed: 12/18/2022]
Abstract
Kinase suppressor of Ras 1 (KSR1) has been implicated in tumorigenesis in multiple cancers, including skin, pancreatic and lung carcinomas. However, our recent study revealed a role of KSR1 as a tumour suppressor in breast cancer, the expression of which is potentially correlated with chemotherapy response. Here, we aimed to further elucidate the KSR1-regulated signalling in response to genotoxic agents in breast cancer. Stable isotope labelling by amino acids in cell culture (SILAC) coupled to high-resolution mass spectrometry (MS) was implemented to globally characterise cellular protein levels induced by KSR1 in the presence of doxorubicin or etoposide. The acquired proteomic signature was compared and GO-STRING analysis was subsequently performed to illustrate the activated functional signalling networks. Furthermore, the clinical associations of KSR1 with identified targets and their relevance in chemotherapy response were examined in breast cancer patients. We reveal a comprehensive repertoire of thousands of proteins identified in each dataset and compare the unique proteomic profiles as well as functional connections modulated by KSR1 after doxorubicin (Doxo-KSR1) or etoposide (Etop-KSR1) stimulus. From the up-regulated top hits, several proteins, including STAT1, ISG15 and TAP1 are also found to be positively associated with KSR1 expression in patient samples. Moreover, high KSR1 expression, as well as high abundance of these proteins, is correlated with better survival in breast cancer patients who underwent chemotherapy. In aggregate, our data exemplify a broad functional network conferred by KSR1 with genotoxic agents and highlight its implication in predicting chemotherapy response in breast cancer.
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Affiliation(s)
- Hua Zhang
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, ICTEM Building, Du Cane Road, London, W12 ONN UK
| | - Nicos Angelopoulos
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, ICTEM Building, Du Cane Road, London, W12 ONN UK
| | - Yichen Xu
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, ICTEM Building, Du Cane Road, London, W12 ONN UK
| | - Arnhild Grothey
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, ICTEM Building, Du Cane Road, London, W12 ONN UK
| | - Joao Nunes
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, ICTEM Building, Du Cane Road, London, W12 ONN UK
| | - Justin Stebbing
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, ICTEM Building, Du Cane Road, London, W12 ONN UK
| | - Georgios Giamas
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, ICTEM Building, Du Cane Road, London, W12 ONN UK
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6
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Abstract
Quantitative proteomics, based on stable isotope labeling by amino acids in cell culture (SILAC), can be used to identify host proteins involved in the intracellular interplay with pathogens. This method allows identification of proteins subject to degradation or upregulation in response to intracellular infection. It can also be used to study intracellular dynamics (trafficking) of proteins in response to the infection. Here, we describe the analysis of changes in protein profiles determined in Golgi-enriched fractions isolated from cells that were either mock-infected or infected with Salmonella typhimurium. Using the SILAC approach we were able to identify 105 proteins in Golgi-enriched fractions that were significantly changed in their abundance as a result of Salmonella infection.
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Affiliation(s)
- Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri USA
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7
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Chen CY, Chung IH, Tsai MM, Tseng YH, Chi HC, Tsai CY, Lin YH, Wang YC, Chen CP, Wu TI, Yeh CT, Tai DI, Lin KH. Thyroid hormone enhanced human hepatoma cell motility involves brain-specific serine protease 4 activation via ERK signaling. Mol Cancer 2014; 13:162. [PMID: 24980078 PMCID: PMC4087245 DOI: 10.1186/1476-4598-13-162] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 06/19/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The thyroid hormone, 3, 3', 5-triiodo-L-thyronine (T3), has been shown to modulate cellular processes via interactions with thyroid hormone receptors (TRs), but the secretory proteins that are regulated to exert these effects remain to be characterized. Brain-specific serine protease 4 (BSSP4), a member of the human serine protease family, participates in extracellular matrix remodeling. However, the physiological role and underlying mechanism of T3-mediated regulation of BSSP4 in hepatocellular carcinogenesis are yet to be established. METHODS The thyroid hormone response element was identified by reporter and chromatin immunoprecipitation assays. The cell motility was analyzed via transwell and SCID mice. The BSSP4 expression in clinical specimens was examined by Western blot and quantitative reverse transcription polymerase chain reaction. RESULTS Upregulation of BSSP4 at mRNA and protein levels after T3 stimulation is a time- and dose-dependent manner in hepatoma cell lines. Additionally, the regulatory region of the BSSP4 promoter stimulated by T3 was identified at positions -609/-594. BSSP4 overexpression enhanced tumor cell migration and invasion, both in vitro and in vivo. Subsequently, BSSP4-induced migration occurs through the ERK 1/2-C/EBPβ-VEGF cascade, similar to that observed in HepG2-TRα1 and J7-TRα1 cells. BSSP4 was overexpressed in clinical hepatocellular carcinoma (HCC) patients, compared with normal subjects, and positively associated with TRα1 and VEGF to a significant extent. Importantly, a mild association between BSSP4 expression and distant metastasis was observed. CONCLUSIONS Our findings collectively support a potential role of T3 in cancer cell progression through regulation of the BSSP4 protease via the ERK 1/2-C/EBPβ-VEGF cascade. BSSP4 may thus be effectively utilized as a novel marker and anti-cancer therapeutic target in HCC.
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Affiliation(s)
- Cheng-Yi Chen
- Department of Biochemistry, School of Medicine, Chang-Gung University, 259 Wen-hwa 1 Road, Taoyuan, Taiwan
- Department of Medical Research, Mackay Memorial Hospital, 251 Taipei, Taiwan
| | - I-Hsiao Chung
- Department of Biochemistry, School of Medicine, Chang-Gung University, 259 Wen-hwa 1 Road, Taoyuan, Taiwan
| | - Ming-Ming Tsai
- Department of Nursing, Chang-Gung University of Science and Technology, 333 Taoyuan, Taiwan
| | - Yi-Hsin Tseng
- Department of Biochemistry, School of Medicine, Chang-Gung University, 259 Wen-hwa 1 Road, Taoyuan, Taiwan
| | - Hsiang-Cheng Chi
- Department of Biochemistry, School of Medicine, Chang-Gung University, 259 Wen-hwa 1 Road, Taoyuan, Taiwan
| | - Chung-Ying Tsai
- Department of Biochemistry, School of Medicine, Chang-Gung University, 259 Wen-hwa 1 Road, Taoyuan, Taiwan
| | - Yang-Hsiang Lin
- Department of Biochemistry, School of Medicine, Chang-Gung University, 259 Wen-hwa 1 Road, Taoyuan, Taiwan
| | - You-Ching Wang
- Department of Biochemistry, School of Medicine, Chang-Gung University, 259 Wen-hwa 1 Road, Taoyuan, Taiwan
| | - Chie-Pein Chen
- Department of Medical Research, Mackay Memorial Hospital, 251 Taipei, Taiwan
- Division of High Risk Pregnancy, Mackay Memorial Hospital, 104 Taipei, Taiwan
| | - Tzu-I Wu
- Department of Biochemistry, School of Medicine, Chang-Gung University, 259 Wen-hwa 1 Road, Taoyuan, Taiwan
| | - Chau-Ting Yeh
- Medical Research Central, Chang Gung Memorial Hospital, 333 Taoyuan, Taiwan
| | - Dar-In Tai
- Medical Research Central, Chang Gung Memorial Hospital, 333 Taoyuan, Taiwan
| | - Kwang-Huei Lin
- Department of Biochemistry, School of Medicine, Chang-Gung University, 259 Wen-hwa 1 Road, Taoyuan, Taiwan
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8
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Haaland I, Opsahl JA, Berven FS, Reikvam H, Fredly HK, Haugse R, Thiede B, McCormack E, Lain S, Bruserud Ø, Gjertsen BT. Molecular mechanisms of nutlin-3 involve acetylation of p53, histones and heat shock proteins in acute myeloid leukemia. Mol Cancer 2014; 13:116. [PMID: 24885082 PMCID: PMC4032636 DOI: 10.1186/1476-4598-13-116] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/29/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The small-molecule MDM2 antagonist nutlin-3 has proved to be an effective p53 activating therapeutic compound in several preclinical cancer models, including acute myeloid leukemia (AML). We and others have previously reported a vigorous acetylation of the p53 protein by nutlin-treatment. In this study we aimed to investigate the functional role of this p53 acetylation in nutlin-sensitivity, and further to explore if nutlin-induced protein acetylation in general could indicate novel targets for the enhancement of nutlin-based therapy. RESULTS Nutlin-3 was found to enhance the acetylation of p53 in the human AML cell line MOLM-13 (wild type TP53) and in TP53 null cells transfected with wild type p53 cDNA. Stable isotope labeling with amino acids in cell culture (SILAC) in combination with immunoprecipitation using an anti-acetyl-lysine antibody and mass spectrometry analysis identified increased levels of acetylated Histone H2B, Hsp27 and Hsp90 in MOLM-13 cells after nutlin-treatment, accompanied by downregulation of total levels of Hsp27 and Hsp90. Intracellular levels of heat shock proteins Hsp27, Hsp40, Hsp60, Hsp70 and Hsp90α were correlated to nutlin-sensitivity for primary AML cells (n = 40), and AML patient samples with low sensitivity to nutlin-3 tended to express higher levels of heat shock proteins than more responsive samples. Combination therapy of nutlin-3 and Hsp90 inhibitor geldanamycin demonstrated synergistic induction of apoptosis in AML cell lines and primary AML cells. Finally, TP53 null cells transfected with a p53 acetylation defective mutant demonstrated decreased heat shock protein acetylation and sensitivity to nutlin-3 compared to wild type p53 expressing cells. CONCLUSIONS Altogether, our results demonstrate that nutlin-3 induces acetylation of p53, histones and heat shock proteins, and indicate that p53 acetylation status and the levels of heat shock proteins may participate in modulation of nutlin-3 sensitivity in AML.
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MESH Headings
- Acetylation
- Antineoplastic Agents/pharmacology
- Benzoquinones/pharmacology
- Cell Line, Tumor
- Drug Synergism
- Gene Expression Regulation, Leukemic
- HSP27 Heat-Shock Proteins/genetics
- HSP27 Heat-Shock Proteins/metabolism
- HSP90 Heat-Shock Proteins/genetics
- HSP90 Heat-Shock Proteins/metabolism
- Histones/genetics
- Histones/metabolism
- Humans
- Imidazoles/pharmacology
- Lactams, Macrocyclic/pharmacology
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Piperazines/pharmacology
- Primary Cell Culture
- Signal Transduction
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
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Affiliation(s)
- Ingvild Haaland
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
| | - Jill A Opsahl
- Department of Biomedicine, Proteomics Unit at University of Bergen (PROBE), University of Bergen, Bergen N-5021, Norway
| | - Frode S Berven
- Department of Biomedicine, Proteomics Unit at University of Bergen (PROBE), University of Bergen, Bergen N-5021, Norway
| | - Håkon Reikvam
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
| | - Hanne K Fredly
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
| | - Ragnhild Haugse
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
| | - Bernd Thiede
- The Biotechnology Centre of Oslo, University of Oslo, Oslo N-0317, Norway
| | - Emmet McCormack
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
- Department of Internal Medicine, Haukeland University Hospital, Bergen N-5021, Norway
| | - Sonia Lain
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm SE-171777, Sweden
| | - Øystein Bruserud
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
- Department of Internal Medicine, Haukeland University Hospital, Bergen N-5021, Norway
| | - Bjørn Tore Gjertsen
- Department of Internal Medicine, Haukeland University Hospital, Bergen N-5021, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen N-5021, Norway
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9
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Abstract
Cultured primary neurons are a well-established model for the study of neuronal function. Conventional stable isotope labeling with amino acids in cell culture (SILAC) requires nearly complete metabolic labeling of proteins and therefore is difficult to apply to cultured primary neurons, which do not divide in culture. Here we describe a protocol that utilizes a multiplex SILAC labeling strategy for primary cultured neurons. In this strategy, two different sets of heavy amino acids are used for labeling cells for the different experimental conditions. This allows for a straightforward SILAC quantitation using partially labeled cells because the two cell populations are always equally labeled.
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Affiliation(s)
- Guoan Zhang
- Dept. of Biochemistry and Molecular Pharmacology and Kimmel Center for Molecular Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Katrin Deinhardt
- Institute for Life Sciences and Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ, UK
| | - Thomas A. Neubert
- Dept. of Biochemistry and Molecular Pharmacology and Kimmel Center for Molecular Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
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10
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Zhang H, Xu Y, Filipovic A, Lit LC, Koo CY, Stebbing J, Giamas G. SILAC-based phosphoproteomics reveals an inhibitory role of KSR1 in p53 transcriptional activity via modulation of DBC1. Br J Cancer 2013; 109:2675-84. [PMID: 24129246 PMCID: PMC3833216 DOI: 10.1038/bjc.2013.628] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [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: 06/11/2013] [Revised: 09/13/2013] [Accepted: 09/18/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND We have previously identified kinase suppressor of ras-1 (KSR1) as a potential regulatory gene in breast cancer. KSR1, originally described as a novel protein kinase, has a role in activation of mitogen-activated protein kinases. Emerging evidence has shown that KSR1 may have dual functions as an active kinase as well as a scaffold facilitating multiprotein complex assembly. Although efforts have been made to study the role of KSR1 in certain tumour types, its involvement in breast cancer remains unknown. METHODS A quantitative mass spectrometry analysis using stable isotope labelling of amino acids in cell culture (SILAC) was implemented to identify KSR1-regulated phosphoproteins in breast cancer. In vitro luciferase assays, co-immunoprecipitation as well as western blotting experiments were performed to further study the function of KSR1 in breast cancer. RESULTS Of significance, proteomic analysis reveals that KSR1 overexpression decreases deleted in breast cancer-1 (DBC1) phosphorylation. Furthermore, we show that KSR1 decreases the transcriptional activity of p53 by reducing the phosphorylation of DBC1, which leads to a reduced interaction of DBC1 with sirtuin-1 (SIRT1); this in turn enables SIRT1 to deacetylate p53. CONCLUSION Our findings integrate KSR1 into a network involving DBC1 and SIRT1, which results in the regulation of p53 acetylation and its transcriptional activity.
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Affiliation(s)
- H Zhang
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 ONN, UK
| | - Y Xu
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 ONN, UK
| | - A Filipovic
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 ONN, UK
| | - L C Lit
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 ONN, UK
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - C-Y Koo
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 ONN, UK
| | - J Stebbing
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 ONN, UK
| | - G Giamas
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 ONN, UK
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11
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Finka A, Goloubinoff P. Proteomic data from human cell cultures refine mechanisms of chaperone-mediated protein homeostasis. Cell Stress Chaperones 2013; 18:591-605. [PMID: 23430704 PMCID: PMC3745260 DOI: 10.1007/s12192-013-0413-3] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [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: 01/29/2013] [Revised: 02/06/2013] [Accepted: 02/07/2013] [Indexed: 10/27/2022] Open
Abstract
In the crowded environment of human cells, folding of nascent polypeptides and refolding of stress-unfolded proteins is error prone. Accumulation of cytotoxic misfolded and aggregated species may cause cell death, tissue loss, degenerative conformational diseases, and aging. Nevertheless, young cells effectively express a network of molecular chaperones and folding enzymes, termed here "the chaperome," which can prevent formation of potentially harmful misfolded protein conformers and use the energy of adenosine triphosphate (ATP) to rehabilitate already formed toxic aggregates into native functional proteins. In an attempt to extend knowledge of chaperome mechanisms in cellular proteostasis, we performed a meta-analysis of human chaperome using high-throughput proteomic data from 11 immortalized human cell lines. Chaperome polypeptides were about 10% of total protein mass of human cells, half of which were Hsp90s and Hsp70s. Knowledge of cellular concentrations and ratios among chaperome polypeptides provided a novel basis to understand mechanisms by which the Hsp60, Hsp70, Hsp90, and small heat shock proteins (HSPs), in collaboration with cochaperones and folding enzymes, assist de novo protein folding, import polypeptides into organelles, unfold stress-destabilized toxic conformers, and control the conformal activity of native proteins in the crowded environment of the cell. Proteomic data also provided means to distinguish between stable components of chaperone core machineries and dynamic regulatory cochaperones.
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Affiliation(s)
- Andrija Finka
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
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12
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Singleton RS, Trudgian DC, Fischer R, Kessler BM, Ratcliffe PJ, Cockman ME. Quantitative mass spectrometry reveals dynamics of factor-inhibiting hypoxia-inducible factor-catalyzed hydroxylation. J Biol Chem 2011; 286:33784-94. [PMID: 21808058 PMCID: PMC3190818 DOI: 10.1074/jbc.m111.262808] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [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: 05/19/2011] [Revised: 07/19/2011] [Indexed: 01/12/2023] Open
Abstract
The asparaginyl hydroxylase, factor-inhibiting hypoxia-inducible factor (HIF), is central to the oxygen-sensing pathway that controls the activity of HIF. Factor-inhibiting HIF (FIH) also catalyzes the hydroxylation of a large set of proteins that share a structural motif termed the ankyrin repeat domain (ARD). In vitro studies have defined kinetic properties of FIH with respect to different substrates and have suggested FIH binds more tightly to certain ARD proteins than HIF and that ARD hydroxylation may have a lower K(m) value for oxygen than HIF hydroxylation. However, regulation of asparaginyl hydroxylation on ARD substrates has not been systematically studied in cells. To address these questions, we employed isotopic labeling and mass spectrometry to monitor the accrual, inhibition, and decay of hydroxylation under defined conditions. Under the conditions examined, hydroxylation was not reversed but increased as the protein aged. The extent of hydroxylation on ARD proteins was increased by addition of ascorbate, whereas iron and 2-oxoglutarate supplementation had no significant effect. Despite preferential binding of FIH to ARD substrates in vitro, when expressed as fusion proteins in cells, hydroxylation was found to be more complete on HIF polypeptides compared with sites within the ARD. Furthermore, comparative studies of hydroxylation in graded hypoxia revealed ARD hydroxylation was suppressed in a site-specific manner and was as sensitive as HIF to hypoxic inhibition. These findings suggest that asparaginyl hydroxylation of HIF-1 and ARD proteins is regulated by oxygen over a similar range, potentially tuning the HIF transcriptional response through competition between the two types of substrate.
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Affiliation(s)
- Rachelle S. Singleton
- From the Center for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - David C. Trudgian
- From the Center for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Roman Fischer
- From the Center for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Benedikt M. Kessler
- From the Center for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Peter J. Ratcliffe
- From the Center for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Matthew E. Cockman
- From the Center for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
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13
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Hong D, Chen HX, Yu HQ, Wang C, Deng HT, Lian QQ, Ge RS. Quantitative proteomic analysis of dexamethasone-induced effects on osteoblast differentiation, proliferation, and apoptosis in MC3T3-E1 cells using SILAC. Osteoporos Int 2011; 22:2175-86. [PMID: 21060993 PMCID: PMC4507272 DOI: 10.1007/s00198-010-1434-8] [Citation(s) in RCA: 26] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 09/21/2010] [Indexed: 10/18/2022]
Abstract
SUMMARY The impairment of osteoblast differentiation is one cause of the glucocorticoid-induced osteoporosis (GCOP). The quantitative proteomic analysis of the dexamethasone (DEX)-induced effects of osteoblast differentiation, proliferation, and apoptosis using stable-isotope labeling by amino acids in cell culture (SILAC) demonstrated drastic changes of some key proteins in MC3T3-E1 cells. INTRODUCTION The impairment of osteoblast differentiation is one of the main explanations of GCOP. SILAC enables accurate quantitative proteomic analysis of protein changes in cells to explore the underlying mechanism of GCOP. METHODS Osteoprogenitor MC3T3-E1 cells were treated with or without 10(−6) M DEX for 7 days, and the differentiation ability, proliferation, and apoptosis of the cells were measured. The protein level changes were analyzed using SILAC and liquid chromatography-coupled tandem mass spectrometry. RESULTS In this study, 10(−6) M DEX inhibited both osteoblast differentiation and proliferation but induced apoptosis in osteoprogenitor MC3T3-E1 cells on day 7. We found that 10(−6) M DEX increased the levels of tubulins (TUBA1A, TUBB2B, and TUBB5), IQGAP1, S100 proteins (S100A11, S100A6, S100A4, and S100A10), myosin proteins (MYH9 and MYH11), and apoptosis and stress proteins, while inhibited the protein levels of ATP synthases (ATP5O, ATP5H, ATP5A1, and ATP5F1), G3BP-1, and Ras-related proteins (Rab-1A, Rab-2A, and Rab-7) in MC3T3-E1 cells. CONCLUSIONS Several members of the ATP synthases, myosin proteins, small GTPase superfamily, and S100 proteins may participate in functional inhibition of osteoblast progenitor cells by GCs. Such protein expression changes may be of pathological significance in coping with GCOP.
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Affiliation(s)
- D. Hong
- Population Council, 1230 York Avenue, New York, NY 10065, USA
- Orthopedic Department, Taizhou Hospital, Wenzhou Medical College, Linhai 317000, China
| | - H.-X. Chen
- Orthopedic Department, Taizhou Hospital, Wenzhou Medical College, Linhai 317000, China
| | - H.-Q. Yu
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - C. Wang
- Population Council, 1230 York Avenue, New York, NY 10065, USA
| | - H.-T. Deng
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - Q.-Q. Lian
- The Second Affiliated Hospital, Wenzhou Medical College, Wenzhou, Zhejiang 325000, China
| | - R.-S. Ge
- Population Council, 1230 York Avenue, New York, NY 10065, USA
- The Second Affiliated Hospital, Wenzhou Medical College, Wenzhou, Zhejiang 325000, China
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14
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Brockmeyer C, Paster W, Pepper D, Tan CP, Trudgian DC, McGowan S, Fu G, Gascoigne NRJ, Acuto O, Salek M. T cell receptor (TCR)-induced tyrosine phosphorylation dynamics identifies THEMIS as a new TCR signalosome component. J Biol Chem 2011; 286:7535-47. [PMID: 21189249 PMCID: PMC3045008 DOI: 10.1074/jbc.m110.201236] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [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: 11/06/2010] [Revised: 12/06/2010] [Indexed: 11/24/2022] Open
Abstract
Stimulation of the T cell antigen receptor (TCR) induces formation of a phosphorylation-dependent signaling network via multiprotein complexes, whose compositions and dynamics are incompletely understood. Using stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics, we investigated the kinetics of signal propagation after TCR-induced protein tyrosine phosphorylation. We confidently assigned 77 proteins (of 758 identified) as a direct or indirect consequence of tyrosine phosphorylation that proceeds in successive "signaling waves" revealing the temporal pace at which tyrosine kinases activate cellular functions. The first wave includes thymocyte-expressed molecule involved in selection (THEMIS), a protein recently implicated in thymocyte development but whose signaling role is unclear. We found that tyrosine phosphorylation of THEMIS depends on the presence of the scaffold proteins Linker for activation of T cells (LAT) and SH2 domain-containing lymphocyte protein of 76 kDa (SLP-76). THEMIS associates with LAT, presumably via the adapter growth factor receptor-bound protein 2 (Grb2) and with phospholipase Cγ1 (PLC-γ1). RNAi-mediated THEMIS knock-down inhibited TCR-induced IL-2 gene expression due to reduced ERK and nuclear factor of activated T cells (NFAT)/activator protein 1 (AP-1) signaling, whereas JNK, p38, or nuclear factor κB (NF-κB) activation were unaffected. Our study reveals the dynamics of TCR-dependent signaling networks and suggests a specific role for THEMIS in early TCR signalosome function.
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Affiliation(s)
| | | | | | | | - David C. Trudgian
- Proteomics Facility, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, United Kingdom
| | - Simon McGowan
- the Computational Biology Research Group, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom, and
| | - Guo Fu
- the Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037
| | - Nicholas R. J. Gascoigne
- the Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037
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ten Have S, Boulon S, Ahmad Y, Lamond AI. Mass spectrometry-based immuno-precipitation proteomics - the user's guide. Proteomics 2011; 11:1153-9. [PMID: 21365760 PMCID: PMC3708439 DOI: 10.1002/pmic.201000548] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [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: 08/31/2010] [Revised: 12/07/2010] [Accepted: 12/10/2010] [Indexed: 11/07/2022]
Abstract
Immuno-precipitation (IP) experiments using MS provide a sensitive and accurate way of characterising protein complexes and their response to regulatory mechanisms. Differences in stoichiometry can be determined as well as the reliable identification of specific binding partners. The quality control of IP and protein interaction studies has its basis in the biology that is being observed. Is that unusual protein identification a genuine novelty, or an experimental irregularity? Antibodies and the solid matrices used in these techniques isolate not only the target protein and its specific interaction partners but also many non-specific 'contaminants' requiring a structured analysis strategy. These methodological developments and the speed and accuracy of MS machines, which has been increasing consistently in the last 5 years, have expanded the number of proteins identified and complexity of analysis. The European Science Foundation's Frontiers in Functional Genomics programme 'Quality Control in Proteomics' Workshop provided a forum for disseminating knowledge and experience on this subject. Our aim in this technical brief is to outline clearly, for the scientists wanting to carry out this kind of experiment, and recommend what, in our experience, are the best potential ways to design an IP experiment, to help identify possible pitfalls, discuss important controls and outline how to manage and analyse the large amount of data generated. Detailed experimental methodologies have been referenced but not described in the form of protocols.
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Affiliation(s)
- Sara ten Have
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland, UK.
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Dilworth DJ, Saleem RA, Rogers RS, Mirzaei H, Boyle J, Aitchison JD. QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments. J Am Soc Mass Spectrom 2010; 21:1417-1422. [PMID: 20451407 PMCID: PMC2914207 DOI: 10.1016/j.jasms.2010.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [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: 12/09/2009] [Revised: 04/02/2010] [Accepted: 04/02/2010] [Indexed: 05/29/2023]
Abstract
Stable incorporation of labeled amino acids in cell culture is a simple approach to label proteins in vivo for mass spectrometric quantification. Full incorporation of isotopically heavy amino acids facilitates accurate quantification of proteins from different cultures, yet analysis methods for determination of incorporation are cumbersome and time-consuming. We present QTIPS, Quantification by Total Identified Peptides for SILAC, a straightforward, accurate method to determine the level of heavy amino acid incorporation throughout a population of peptides detected by mass spectrometry. Using QTIPS, we show that the incorporation of heavy amino acids in baker's yeast is unaffected by the use of prototrophic strains, indicating that auxotrophy is not a requirement for SILAC experiments in this organism. This method has general utility for multiple applications where isotopic labeling is used for quantification in mass spectrometry.
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17
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Greco TM, Seeholzer SH, Mak A, Spruce L, Ischiropoulos H. Quantitative mass spectrometry-based proteomics reveals the dynamic range of primary mouse astrocyte protein secretion. J Proteome Res 2010; 9:2764-74. [PMID: 20329800 PMCID: PMC2866110 DOI: 10.1021/pr100134n] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [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: 12/31/2022]
Abstract
Growing appreciation for astrocytes as active participants in nervous system development, neurovascular metabolic coupling, and neurological disease progression has stimulated recent investigation into specific astrocyte-secreted proteins that may mediate these functions. The current work utilized SILAC-generated isotope reference proteomes to quantify relative protein abundances between the astrocyte proteome and secretome. Multidimensional GeLC-MS/MS analysis of astrocyte conditioned media and cell lysates resulted in the relative quantification of 516 proteins, 92 of which were greater than 1.5-fold enriched in astrocyte-conditioned media (ACM). Eighty of the ACM-enriched proteins had N-terminal signal peptides, comprising well-known classically secreted proteins, such as apolipoprotein E and SPARC, and several cathepsins that localize to endosomal/lysosomal compartments. The remaining twelve ACM-enriched proteins, such as vimentin, ferritins, and histones, lacked N-terminal signal peptides. Also, 47 proteins contained predicted N-terminal signal peptides but were not enriched in ACM (<1.5-fold), 25 of which were localized to ER, Golgi, or mitochondria membrane-bound compartments. Overall, by combining quantitative proteomics with subcellular localization prediction, an informative description of protein distribution can be obtained, providing insights into protein secretion.
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Affiliation(s)
- Todd M. Greco
- Department of Pediatrics, The Children’s Hospital of Philadelphia Research Institute and The University of Pennsylvania Philadelphia, PA, 19104, USA
| | - Steven H. Seeholzer
- Department of Pediatrics, The Children’s Hospital of Philadelphia Research Institute and The University of Pennsylvania Philadelphia, PA, 19104, USA
| | - Adrian Mak
- Department of Pediatrics, The Children’s Hospital of Philadelphia Research Institute and The University of Pennsylvania Philadelphia, PA, 19104, USA
| | - Lynn Spruce
- Department of Pediatrics, The Children’s Hospital of Philadelphia Research Institute and The University of Pennsylvania Philadelphia, PA, 19104, USA
| | - Harry Ischiropoulos
- Department of Pediatrics, The Children’s Hospital of Philadelphia Research Institute and The University of Pennsylvania Philadelphia, PA, 19104, USA
- Department of Pharmacology, The Children’s Hospital of Philadelphia Research Institute and The University of Pennsylvania Philadelphia, PA, 19104, USA
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Rangiah K, Tippornwong M, Sangar V, Austin D, Tétreault MP, Rustgi AK, Blair IA, Yu KH. Differential secreted proteome approach in murine model for candidate biomarker discovery in colon cancer. J Proteome Res 2009; 8:5153-64. [PMID: 19769411 PMCID: PMC2783939 DOI: 10.1021/pr900518v] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [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: 01/11/2023]
Abstract
The complexity and heterogeneity of the plasma proteome have presented significant challenges in the identification of protein changes associated with tumor development. We used cell culture as a model system and identified differentially expressed, secreted proteins which may constitute serological biomarkers. A stable isotope labeling by amino acids in cell culture (SILAC) approach was used to label the entire secreted proteomes of the CT26 murine colon cancer cell line and normal young adult mouse colon (YAMC) cell line, thereby creating a stable isotope labeled proteome (SILAP) standard. This SILAP standard was added to unlabeled murine CT26 colon cancer cell or normal murine YAMC colon epithelial cell secreted proteome samples. A multidimensional approach combining isoelectric focusing (IEF), strong cation exchange (SCX) followed by reversed phase liquid chromatography was used for extensive protein and peptide separation. A total of 614 and 929 proteins were identified from the YAMC and CT26 cell lines, with 418 proteins common to both cell lines. Twenty highly abundant differentially expressed proteins from these groups were selected for liquid chromatography-multiple reaction monitoring/mass spectrometry (LC-MRM/MS) analysis in sera. Differential secretion into the serum was observed for several proteins when Apc(min) mice were compared with control mice. These findings were then confirmed by Western blot analysis.
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Affiliation(s)
- Kannan Rangiah
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - Montri Tippornwong
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - Vineet Sangar
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - David Austin
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - Marie-Pier Tétreault
- Division of Gastroenterology, Departments of Medicine & Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - Anil K. Rustgi
- Division of Gastroenterology, Departments of Medicine & Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - Ian A. Blair
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - Kenneth H. Yu
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
- Corresponding author: Center for Cancer Pharmacology, University of Pennsylvania School of Medicine, 856 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104-6160. Tel: 215-573-9885. Fax: 215-573-9889.
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Zhang G, Spellman DS, Skolnik EY, Neubert TA. Quantitative phosphotyrosine proteomics of EphB2 signaling by stable isotope labeling with amino acids in cell culture ( SILAC). J Proteome Res 2006; 5:581-8. [PMID: 16512673 PMCID: PMC2542903 DOI: 10.1021/pr050362b] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [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: 12/26/2022]
Abstract
Eph-related receptor tyrosine kinases (RTK) have been implicated in several biological functions including synaptic plasticity, axon guidance, and morphogenesis, yet the details of the signal transduction pathways that produce these specific biological functions after ligand-receptor interaction remain unclear. We used Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) in combination with LC-MS/MS to characterize cellular signaling following stimulation by ephrinB1-Fc of NG-108 cells that overexpress EphB2 receptors. Because tyrosine phosphorylation functions as a key regulatory event in RTK signaling, we used anti-phosphotyrosine immunoprecipitation (pY IP) of cell lysates to isolate potential participants in the EphB2 pathway. Our SILAC experiments identified 127 unique proteins, 40 of which demonstrated increased abundance in pY IPs from ephrinB1-Fc stimulated cells as compared with unstimulated cells. Six proteins demonstrated decreased abundance, and 81 did not change significantly in relative abundance. Western blotting analysis of five proteins after pY IP verified their SILAC results. On the basis of previously published work and use of PathwayAssist software, we proposed an interaction network downstream of EphB2 for the proteins with changed ratios.
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Affiliation(s)
- Guoan Zhang
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York 10016, USA
- Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
| | - Daniel S. Spellman
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York 10016, USA
- New York University and National Institutes of Health Graduate Partnership Program in Structural Biology
| | - Edward Y. Skolnik
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York 10016, USA
- Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
| | - Thomas A. Neubert
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York 10016, USA
- Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
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