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Lee RFS, Chernobrovkin A, Rutishauser D, Allardyce CS, Hacker D, Johnsson K, Zubarev RA, Dyson PJ. Expression proteomics study to determine metallodrug targets and optimal drug combinations. Sci Rep 2017; 7:1590. [PMID: 28484215 PMCID: PMC5431558 DOI: 10.1038/s41598-017-01643-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/03/2017] [Indexed: 01/01/2023] Open
Abstract
The emerging technique termed functional identification of target by expression proteomics (FITExP) has been shown to identify the key protein targets of anti-cancer drugs. Here, we use this approach to elucidate the proteins involved in the mechanism of action of two ruthenium(II)-based anti-cancer compounds, RAPTA-T and RAPTA-EA in breast cancer cells, revealing significant differences in the proteins upregulated. RAPTA-T causes upregulation of multiple proteins suggesting a broad mechanism of action involving suppression of both metastasis and tumorigenicity. RAPTA-EA bearing a GST inhibiting ethacrynic acid moiety, causes upregulation of mainly oxidative stress related proteins. The approach used in this work could be applied to the prediction of effective drug combinations to test in cancer chemotherapy clinical trials.
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Affiliation(s)
- Ronald F S Lee
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexey Chernobrovkin
- Karolinska Institute, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Scheeles väg 2, S-171 77, Stockholm, Sweden
| | - Dorothea Rutishauser
- Karolinska Institute, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Scheeles väg 2, S-171 77, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Claire S Allardyce
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - David Hacker
- Protein Expression Core Facility, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Kai Johnsson
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Roman A Zubarev
- Karolinska Institute, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Scheeles väg 2, S-171 77, Stockholm, Sweden
| | - Paul J Dyson
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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Kistowski M, Dębski J, Karczmarski J, Paziewska A, Olędzki J, Mikula M, Ostrowski J, Dadlez M. A Strong Neutrophil Elastase Proteolytic Fingerprint Marks the Carcinoma Tumor Proteome. Mol Cell Proteomics 2016; 16:213-227. [PMID: 27927741 DOI: 10.1074/mcp.m116.058818] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 11/12/2016] [Indexed: 12/18/2022] Open
Abstract
Proteolytic cascades are deeply involved in critical stages of cancer progression. During the course of peptide-wise analysis of shotgun proteomic data sets representative of colon adenocarcinoma (AC) and ulcerative colitis (UC), we detected a cancer-specific proteolytic fingerprint composed of a set of numerous protein fragments cleaved C-terminally to V, I, A, T, or C residues, significantly overrepresented in AC. A peptide set linked by a common VIATC cleavage consensus was the only prominent cancer-specific proteolytic fingerprint detected. This sequence consensus indicated neutrophil elastase as a source of the fingerprint. We also found that a large fraction of affected proteins are RNA processing proteins associated with the nuclear fraction and mostly cleaved within their functionally important RNA-binding domains. Thus, we detected a new class of cancer-specific peptides that are possible markers of tumor-infiltrating neutrophil activity, which often correlates with the clinical outcome. Data are available via ProteomeXchange with identifiers: PXD005274 (Data set 1) and PXD004249 (Data set 2). Our results indicate the value of peptide-wise analysis of large global proteomic analysis data sets as opposed to protein-wise analysis, in which outlier differential peptides are usually neglected.
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Affiliation(s)
- Michał Kistowski
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw
| | - Janusz Dębski
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw
| | - Jakub Karczmarski
- §Department of Genetics, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wilhelma Konrada Roentgena 5, 02-781 Warsaw, Poland
| | - Agnieszka Paziewska
- §Department of Genetics, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wilhelma Konrada Roentgena 5, 02-781 Warsaw, Poland
| | - Jacek Olędzki
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw
| | - Michał Mikula
- §Department of Genetics, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wilhelma Konrada Roentgena 5, 02-781 Warsaw, Poland
| | - Jerzy Ostrowski
- ¶Department of Gastroenterology Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michał Dadlez
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw;
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Pham VC, Anania VG, Phung QT, Lill JR. Complementary methods for the identification of substrates of proteolysis. Methods Enzymol 2014; 544:359-80. [PMID: 24974297 DOI: 10.1016/b978-0-12-417158-9.00014-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Proteolysis describes the cleavage of proteins into smaller components, which in vivo occurs typically to either activate or impair the functionality of cellular proteins. Proteolysis can occur during cellular homeostasis or can be induced due to external stress stimuli such as heat, biological or chemical insult, and is mediated by the activity of cellular enzymes, namely, proteases. Proteolytic cleavage of proteins can influence protein activation by exposing an active site or disrupting inhibitor binding. Conversely, proteolytic cleavage of many proteins has also been shown to lead to protein degradation resulting in inactivation of the substrate. Thousands of proteolytic events are known to take place in regulated cellular processes such as apoptosis and pyroptosis, however, their individual contribution to these processes remains poorly understood. Additionally, many cellular homeostatic processes are regulated by proteolytic events, however, in some cases, few proteolytic substrates have been identified. To gain further insight into the mechanism of action of these cellular processes, and to characterize biomarkers of cell death and other pathological indications, it is imperative to utilize a complete arsenal of tools for studying proteolysis events in vivo and in vitro. In this chapter, we focus on alternative methodologies to N-terminomics for profiling substrates of proteolysis and describe an additional suite of tools including orthogonal biophysical separation techniques such as COFRADIC or GASSP, and affinity capture tools that can enrich for newly formed C-termini (C-terminomics) generated as a result of caspase-mediated proteolysis.
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Affiliation(s)
- Victoria C Pham
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Veronica G Anania
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Qui T Phung
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Jennie R Lill
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California, USA.
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4
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Størvold GL, Landskron J, Strozynski M, Arntzen MØ, Koehler CJ, Kalland ME, Taskén K, Thiede B. Quantitative profiling of tyrosine phosphorylation revealed changes in the activity of the T cell receptor signaling pathway upon cisplatin-induced apoptosis. J Proteomics 2013; 91:344-57. [DOI: 10.1016/j.jprot.2013.07.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 07/08/2013] [Accepted: 07/22/2013] [Indexed: 12/18/2022]
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Rainczuk A, Condina M, Pelzing M, Dolman S, Rao J, Fairweather N, Jobling T, Stephens AN. The utility of isotope-coded protein labeling for prioritization of proteins found in ovarian cancer patient urine. J Proteome Res 2013; 12:4074-88. [DOI: 10.1021/pr400618v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Mark Condina
- Bruker Biosciences Pty. Ltd., Preston,
Victoria, Australia, 3072
| | - Matthias Pelzing
- Bruker Biosciences Pty. Ltd., Preston,
Victoria, Australia, 3072
| | | | | | | | - Tom Jobling
- Obstetrics and Gynaecology, Monash
Medical Centre, Clayton VIC 3168 Australia
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Murugaiyan J, Rockstroh M, Wagner J, Baumann S, Schorsch K, Trump S, Lehmann I, Bergen MV, Tomm JM. Benzo[a]pyrene affects Jurkat T cells in the activated state via the antioxidant response element dependent Nrf2 pathway leading to decreased IL-2 secretion and redirecting glutamine metabolism. Toxicol Appl Pharmacol 2013; 269:307-16. [DOI: 10.1016/j.taap.2013.03.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 03/20/2013] [Accepted: 03/25/2013] [Indexed: 02/01/2023]
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Stoehr G, Schaab C, Graumann J, Mann M. A SILAC-based approach identifies substrates of caspase-dependent cleavage upon TRAIL-induced apoptosis. Mol Cell Proteomics 2013; 12:1436-50. [PMID: 23319142 PMCID: PMC3650350 DOI: 10.1074/mcp.m112.024679] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The extracellular ligand-induced extrinsic pathway of apoptosis is executed via caspase protease cascades that activate downstream effectors by means of site-directed proteolysis. Here we identify proteome changes upon the induction of apoptosis by the cytokine tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) in a Jurkat T cell line. We detected caspase-dependent cleavage substrates by quantifying protein intensities before and after TRAIL induction in SDS gel slices. Apoptotic protein cleavage events are identified by a characteristic stable isotope labeling with amino acids in cell culture (SILAC) ratio pattern across gel slices that results from differential migration of the cleaved and uncleaved proteins. We applied a statistical test to define apoptotic substrates in the proteome. Our approach identified more than 650 of these cleaved proteins in response to TRAIL-induced apoptosis, including many previously unknown substrates and cleavage sites. Inhibitor treatment combined with triple SILAC demonstrated that the detected cleavage events were caspase dependent. Proteins located in the lumina of organelles such as mitochondria and endoplasmic reticulum were significantly underrepresented in the substrate population. Interestingly, caspase cleavage is generally observed in not only one but several members of stable complexes, but often with lower stoichiometry. For instance, all five proteins of the condensin I complex were cleaved upon TRAIL treatment. The apoptotic substrate proteome data can be accessed and visualized in the MaxQB database and might prove useful for basic and clinical research into TRAIL-induced apoptosis. The technology described here is extensible to a wide range of other proteolytic cleavage events.
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Affiliation(s)
- Gabriele Stoehr
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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Leng J, Zhu D, Wu D, Zhu T, Zhao N, Guo Y. Analysis of the differentially expressed low molecular weight peptides in human serum via an N-terminal isotope labeling technique combining nano-liquid chromatography/matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:2555-2562. [PMID: 23008073 DOI: 10.1002/rcm.6369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE Peptidomics analysis of human serum is challenging due to the low abundance of serum peptides and interference from the complex matrix. This study analyzed the differentially expressed (DE) low molecular weight peptides in human serum integrating a DMPITC-based N-terminal isotope labeling technique with nano-liquid chromatography and matrix-assisted laser desorption/ionization mass spectrometry (nano-LC/MALDI-MS). METHODS The workflow introduced a [d(6)]-4,6-dimethoxypyrimidine-2-isothiocyanate (DMPITC)-labeled mixture of aliquots from test samples as the internal standard. The spiked [d(0)]-DMPITC-labeled samples were separated by nano-LC then spotted on the MALDI target. Both quantitative and qualitative studies for serum peptides were achieved based on the isotope-labeled peaks. RESULTS The DMPITC labeling technique combined with nano-LC/MALDI-MS not only minimized the errors in peptide quantitation, but also allowed convenient recognition of the labeled peptides due to the 6 Da mass difference. The data showed that the entire research procedure as well as the subsequent data analysis method were effective, reproducible, and sensitive for the analysis of DE serum peptides. CONCLUSIONS This study successfully established a research model for DE serum peptides using DMPITC-based N-terminal isotope labeling and nano-LC/MALDI-MS. Application of the DMPITC-based N-terminal labeling technique is expected to provide a promising tool for the investigation of peptides in vivo, especially for the analysis of DE peptides under different biological conditions.
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Affiliation(s)
- Jiapeng Leng
- Shanghai Mass Spectrometry Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
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9
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Shetty V, Nickens Z, Testa J, Hafner J, Sinnathamby G, Philip R. Quantitative immunoproteomics analysis reveals novel MHC class I presented peptides in cisplatin-resistant ovarian cancer cells. J Proteomics 2012; 75:3270-90. [PMID: 22504797 DOI: 10.1016/j.jprot.2012.03.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 03/01/2012] [Accepted: 03/25/2012] [Indexed: 10/28/2022]
Abstract
Platinum-based chemotherapy is widely used to treat various cancers including ovarian cancer. However, the mortality rate for patients with ovarian cancer is extremely high, largely due to chemo-resistant progression in patients who respond initially to platinum based chemotherapy. Immunotherapy strategies, including antigen specific vaccines, are being tested to treat drug resistant ovarian cancer with variable results. The identification of drug resistant specific tumor antigens would potentially provide significant improvement in effectiveness when combined with current and emerging therapies. In this study, using an immunoproteomics method based on iTRAQ technology and an LC-MS platform, we identified 952 MHC class I presented peptides. Quantitative analysis of the iTRAQ labeled MHC peptides revealed that cisplatin-resistant ovarian cancer cells display increased levels of MHC peptides derived from proteins that are implicated in many important cancer pathways. In addition, selected differentially presented epitope specific CTL recognize cisplatin-resistant ovarian cancer cells significantly better than the sensitive cells. These over-presented, drug resistance specific MHC class I associated peptide antigens could be potential targets for the development of immunotherapeutic strategies for the treatment of ovarian cancer including the drug resistant phenotype.
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Affiliation(s)
- Vivekananda Shetty
- Immunotope, Inc., 3805 Old Easton Road, Doylestown, PA 18902, United States.
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10
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Jehmlich N, Kopinke FD, Lenhard S, Vogt C, Herbst FA, Seifert J, Lissner U, Völker U, Schmidt F, von Bergen M. Sulfur-36
S stable isotope labeling of amino acids for quantification (SULAQ). Proteomics 2011; 12:37-42. [DOI: 10.1002/pmic.201100057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 10/12/2011] [Accepted: 10/25/2011] [Indexed: 11/10/2022]
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11
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Wei YYC, Naderi S, Meshram M, Budman H, Scharer JM, Ingalls BP, McConkey BJ. Proteomics analysis of chinese hamster ovary cells undergoing apoptosis during prolonged cultivation. Cytotechnology 2011; 63:663-77. [PMID: 21853334 DOI: 10.1007/s10616-011-9385-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 07/20/2011] [Indexed: 12/19/2022] Open
Abstract
The degradation of environmental conditions, such as nutrient depletion and accumulation of toxic waste products over time, often lead to premature apoptotic cell death in mammalian cell cultures and suboptimal protein yield. Although apoptosis has been extensively researched, the changes in the whole cell proteome during prolonged cultivation, where apoptosis is a major mode of cell death, have not been examined. To our knowledge, the work presented here is the first whole cell proteome analysis of non-induced apoptosis in mammalian cells. Flow cytometry analyses of various activated caspases demonstrated the onset of apoptosis in Chinese hamster ovary cells during prolonged cultivation was primarily through the intrinsic pathway. Differential in gel electrophoresis proteomic study comparing protein samples collected during cultivation resulted in the identification of 40 differentially expressed proteins, including four cytoskeletal proteins, ten chaperone and folding proteins, seven metabolic enzymes and seven other proteins of varied functions. The induction of seven ER chaperones and foldases is a solid indication of the onset of the unfolded protein response, which is triggered by cellular and ER stresses, many of which occur during prolonged batch cultures. In addition, the upregulation of six glycolytic enzymes and another metabolic protein emphasizes that a change in the energy metabolism likely occurred as culture conditions degraded and apoptosis advanced. By identifying the intracellular changes during cultivation, this study provides a foundation for optimizing cell line-specific cultivation processes, prolonging longevity and maximizing protein production.
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Proteomic approaches in understanding action mechanisms of metal-based anticancer drugs. Met Based Drugs 2011; 2008:716329. [PMID: 18670610 PMCID: PMC2486358 DOI: 10.1155/2008/716329] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 04/20/2008] [Accepted: 06/17/2008] [Indexed: 12/13/2022] Open
Abstract
Medicinal inorganic chemistry has been stimulating largely by the success of the anticancer drug, cisplatin. Various metal complexes are currently used as therapeutic agents (e.g., Pt, Au, and Ru) in the treatment of malignant diseases, including several types of cancers. Understanding the mechanism of action of these metal-based drugs is for the design of more effective drugs. Proteomic approaches combined with other biochemical methods can provide comprehensive understanding of responses that are involved in metal-based anticancer drugs-induced cell death, including insights into cytotoxic effects of metal-based anticancer drugs, correlation of protein alterations to drug targets, and prediction of drug resistance and toxicity. This information, when coupled with clinical data, can provide rational basses for the future design and modification of present used metal-based anticancer drugs.
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Petković M, Kamčeva T. FAB, ESI and MALDI Mass Spectrometric methods in the study of metallo-drugs and their biomolecular interactions. Metallomics 2011; 3:550-65. [DOI: 10.1039/c0mt00096e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Wu W, Yan C, Gan T, Chen Z, Lu X, Duerksen-Hughes PJ, Zhu X, Yang J. Nuclear proteome analysis of cisplatin-treated HeLa cells. Mutat Res 2010; 691:1-8. [PMID: 20540955 DOI: 10.1016/j.mrfmmm.2010.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 05/16/2010] [Accepted: 06/01/2010] [Indexed: 05/29/2023]
Abstract
Cisplatin has been widely accepted as one of the most efficient anticancer drugs for decades. However, the mechanisms for the cytotoxic effects of cisplatin are still not fully understood. Cisplatin primarily targets DNA, resulting in the formation of DNA double strand breaks and eventually causing cell death. In this study, we applied two-dimensional electrophoresis coupled with LC-MS/MS to analyze the nuclear proteome of HeLa cells treated with cisplatin, in an effort to uncover new mechanistic clues regarding the cellular response to cisplatin. A total of 19 proteins were successfully identified, and these proteins are involved in a variety of basal metabolic and biological processes in cells, including biosynthesis, cell cycle, glycolysis and apoptosis. Six were related to the regulation of mRNA splicing, and we therefore asked whether the Fas gene might undergo alternative splicing following cisplatin treatment. This proved to be the case, as the splicing forms of Fas were modified in cisplatin-treated HeLa cells. This work provides novel information, from the perspective of the nuclear response, for understanding the cytotoxicity caused by cisplatin-induced DNA damage.
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Affiliation(s)
- Wei Wu
- Department of Toxicology, Zhejiang University School of Public Health, and Department of Pharmacy, Lishui People's Hospital, Zhejiang 310058, China
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Peš O, Preisler J. Off-line coupling of microcolumn separations to desorption mass spectrometry. J Chromatogr A 2010; 1217:3966-77. [DOI: 10.1016/j.chroma.2010.02.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 01/13/2023]
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Koehler CJ, Strozynski M, Kozielski F, Treumann A, Thiede B. Isobaric peptide termini labeling for MS/MS-based quantitative proteomics. J Proteome Res 2009; 8:4333-41. [PMID: 19655813 DOI: 10.1021/pr900425n] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since its introduction, isobaric peptide labeling has played an important role in relative quantitative comparisons of proteomes. This paper describes isobaric peptide termini labeling (IPTL), a novel approach for the identification and quantification of two differentially labeled states using MS/MS spectra. After endoproteinase Lys-C digestion, peptides were labeled at C-terminal lysine residues with either 2-methoxy-4,5-dihydro-1H-imidazole (MDHI) or with tetradeuterated MDHI-d(4). Subsequently, their N-termini were derivatized either with tetradeuterated succinic anhydride (SA-d(4)) or with SA. The mixed isotopic labeling results in isobaric masses and provided several quantification data points per peptide. The suitability of this approach is demonstrated with MS and MS/MS analyses of Lys-C digests of standard proteins. A conceptually simple quantification strategy with a dynamic range of 25 is achieved through the use of Mascot score ratios. The utility of IPTL for the analysis of proteomes was verified by comparing the well-characterized effect of the antimitotic inhibitor S-Trityl-l-Cysteine (STLC) on HeLa cells that were treated for either 24 or 48 h with the inhibitor. Many apoptosis-linked proteins were identified as being differentially regulated, confirming the suitability of IPTL for the analysis of complex proteomes.
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Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini. Proc Natl Acad Sci U S A 2009; 106:19310-5. [PMID: 19892738 DOI: 10.1073/pnas.0908958106] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Proteolysis has major roles in diverse biologic processes and regulates the activity, localization, and intracellular levels of proteins. Linking signaling pathways and physiologic processes to specific proteolytic processing events is a major challenge in signal transduction research. Here, we describe N-CLAP (N-terminalomics by chemical labeling of the alpha-amine of proteins), a general approach for profiling protein N-termini and identifying protein cleavage sites during cellular signaling. In N-CLAP, simple and readily available reagents are used to selectively affinity label the alpha-amine that characterizes the protein N terminus over the more highly abundant epsilon-amine on lysine residues. Protein cleavage sites are deduced by identifying the corresponding N-CLAP peptides, which are derived from the N-termini of proteins, including the N-termini of the newly formed polypeptide products of proteolytic cleavage. Through selective affinity purification and tandem mass spectrometry analysis of 278 N-CLAP peptides, we characterized proteolytic cleavage events associated with methionine aminopeptidases and signal peptide peptidases, as well as proteins that are proteolytically cleaved after cisplatin-induced apoptosis. Many of the protein cleavage sites that are elicited during apoptotic signaling are consistent with caspase-dependent cleavage. These data demonstrate the utility of N-CLAP for proteomic profiling of protein cleavage sites that are generated during cellular signaling.
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Strohalm M, Novak P, Pompach P, Man P, Kavan D, Witt M, Dzubak P, Hajduch M, Havlicek V. Utilization of high-accuracy FTICR-MS data in protein quantitation experiments. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:1565-1570. [PMID: 19536796 DOI: 10.1002/jms.1602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Human acute T-lymphoblastic leukemia cell line (CEM) treated with cisplatin, and the stable isotope labeling by amino acids in cell culture (SILAC) strategy were used to present an improved method of data processing in high-accuracy mass spectrometry (MS). By using peptide mass fingerprinting with low mass tolerance, we were able to utilize far more data retained in MS scans which would normally be missed by a standard processing method. This new way of data interpretation results in an improvement of the relevance of quantitation experiments and enabled us to search and quantify different types of posttranslational modifications. Furthermore, we used this technique to distinguish among different protein isoforms, commonly returned by Mascot search engine.
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Affiliation(s)
- Martin Strohalm
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague, 142 20, Czech Republic
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Challenges in cancer research and multifaceted approaches for cancer biomarker quest. FEBS Lett 2009; 583:1772-84. [DOI: 10.1016/j.febslet.2009.03.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 03/18/2009] [Accepted: 03/18/2009] [Indexed: 12/15/2022]
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20
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Casado P, Prado MA, Zuazua-Villar P, Del Valle E, Artime N, Cabal-Hierro L, Rupérez P, Burlingame AL, Lazo PS, Ramos S. Microtubule interfering agents and KSP inhibitors induce the phosphorylation of the nuclear protein p54(nrb), an event linked to G2/M arrest. J Proteomics 2008; 71:592-600. [PMID: 18832053 DOI: 10.1016/j.jprot.2008.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2008] [Revised: 08/19/2008] [Accepted: 09/08/2008] [Indexed: 01/19/2023]
Abstract
Microtubule interfering agents (MIAs) are anti-tumor drugs that inhibit microtubule dynamics, while kinesin spindle protein (KSP) inhibitors are substances that block the formation of the bipolar spindle during mitosis. All these compounds cause G2/M arrest and cell death. Using 2D-PAGE followed by Nano-LC-ESI-Q-ToF analysis, we found that MIAs such as vincristine (Oncovin) or paclitaxel (Taxol) and KSP inhibitors such as S-tritil-l-cysteine induce the phosphorylation of the nuclear protein p54(nrb) in HeLa cells. Furthermore, we demonstrate that cisplatin (Platinol), an anti-tumor drug that does not cause M arrest, does not induce this modification. We show that the G2/M arrest induced by MIAs is required for p54(nrb) phosphorylation. Finally, we demonstrate that CDK activity is required for MIA-induced phosphorylation of p54(nrb).
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Affiliation(s)
- Pedro Casado
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33071, Oviedo, Spain
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Dix MM, Simon GM, Cravatt BF. Global mapping of the topography and magnitude of proteolytic events in apoptosis. Cell 2008; 134:679-91. [PMID: 18724940 DOI: 10.1016/j.cell.2008.06.038] [Citation(s) in RCA: 282] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 05/14/2008] [Accepted: 06/19/2008] [Indexed: 11/18/2022]
Abstract
Proteolysis is a key regulatory process that promotes the (in)activation, translocation, and/or degradation of proteins. As such, there is considerable interest in methods to comprehensively characterize proteolytic pathways in biological systems. Here, we describe a robust and versatile proteomic platform that enables direct visualization of the topography and magnitude of proteolytic events on a global scale. We use this method to generate a proteome-wide map of proteolytic events induced by the intrinsic apoptotic pathway. This profile contained 91 characterized caspase substrates as well as 170 additional proteins not previously known to be cleaved during apoptosis. Surprisingly, the vast majority of proteolyzed proteins, regardless of the extent of cleavage, yielded persistent fragments that correspond to discrete protein domains, suggesting that the generation of active effector proteins may be a principal function of apoptotic proteolytic cascades.
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Affiliation(s)
- Melissa M Dix
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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