1
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Jindra M, McKinstry WJ, Nebl T, Bittova L, Ren B, Shaw J, Phan T, Lu L, Low JKK, Mackay JP, Sparrow LG, Lovrecz GO, Hill RJ. Purification of an insect juvenile hormone receptor complex enables insights into its post-translational phosphorylation. J Biol Chem 2021; 297:101387. [PMID: 34758356 PMCID: PMC8683598 DOI: 10.1016/j.jbc.2021.101387] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022] Open
Abstract
Juvenile hormone (JH) plays vital roles in insect reproduction, development, and in many aspects of physiology. JH primarily acts at the gene-regulatory level through interaction with an intracellular receptor (JH receptor [JHR]), a ligand-activated complex of transcription factors consisting of the JH-binding protein methoprene-tolerant (MET) and its partner taiman (TAI). Initial studies indicated significance of post-transcriptional phosphorylation, subunit assembly, and nucleocytoplasmic transport of JHR in JH signaling. However, our knowledge of JHR regulation at the protein level remains rudimentary, partly because of the difficulty of obtaining purified and functional JHR proteins. Here, we present a method for high-yield expression and purification of JHR complexes from two insect species, the beetle T. castaneum and the mosquito Aedes aegypti. Recombinant JHR subunits from each species were coexpressed in an insect cell line using a baculovirus system. MET–TAI complexes were purified through affinity chromatography and anion exchange columns to yield proteins capable of binding both the hormonal ligand (JH III) and DNA bearing cognate JH-response elements. We further examined the beetle JHR complex in greater detail. Biochemical analyses and MS confirmed that T. castaneum JHR was a 1:1 heterodimer consisting of MET and Taiman proteins, stabilized by the JHR agonist ligand methoprene. Phosphoproteomics uncovered multiple phosphorylation sites in the MET protein, some of which were induced by methoprene treatment. Finally, we report a functional bipartite nuclear localization signal, straddled by phosphorylated residues, within the disordered C-terminal region of MET. Our present characterization of the recombinant JHR is an initial step toward understanding JHR structure and function.
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Affiliation(s)
- Marek Jindra
- Biology Center, Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic.
| | | | - Thomas Nebl
- CSIRO Manufacturing, CSIRO, Parkville, Victoria, Australia
| | - Lenka Bittova
- Biology Center, Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Bin Ren
- CSIRO Manufacturing, CSIRO, Parkville, Victoria, Australia
| | - Jan Shaw
- CSIRO Health and Biosecurity, CSIRO, North Ryde, New South Wales, Australia
| | - Tram Phan
- CSIRO Manufacturing, CSIRO, Parkville, Victoria, Australia
| | - Louis Lu
- CSIRO Manufacturing, CSIRO, Parkville, Victoria, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | | | | | - Ronald J Hill
- CSIRO Health and Biosecurity, CSIRO, North Ryde, New South Wales, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.
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2
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Durdevic Z, Ephrussi A. Germ Cell Lineage Homeostasis in Drosophila Requires the Vasa RNA Helicase. Genetics 2019; 213:911-922. [PMID: 31484689 PMCID: PMC6827371 DOI: 10.1534/genetics.119.302558] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/29/2019] [Indexed: 11/18/2022] Open
Abstract
The conserved RNA helicase Vasa is required for germ cell development in many organisms. In Drosophila melanogaster loss of PIWI-interacting RNA pathway components, including Vasa, causes Chk2-dependent oogenesis arrest. However, whether the arrest is due to Chk2 signaling at a specific stage and whether continuous Chk2 signaling is required for the arrest is unknown. Here, we show that absence of Vasa during the germarial stages causes Chk2-dependent oogenesis arrest. Additionally, we report the age-dependent decline of the ovariole number both in flies lacking Vasa expression only in the germarium and in loss-of-function vasa mutant flies. We show that Chk2 activation exclusively in the germarium is sufficient to interrupt oogenesis and to reduce ovariole number in aging flies. Once induced in the germarium, Chk2-mediated arrest of germ cell development cannot be overcome by restoration of Vasa or by downregulation of Chk2 in the arrested egg chambers. These findings, together with the identity of Vasa-associated proteins identified in this study, demonstrate an essential role of the helicase in the germ cell lineage maintenance and indicate a function of Vasa in germline stem cell homeostasis.
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Affiliation(s)
- Zeljko Durdevic
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany
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3
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Sulfur- 34S and 36S Stable Isotope Labeling of Amino Acids for Quantification (SULAQ34/36) of Proteome Analyses. Methods Mol Biol 2018. [PMID: 30259486 DOI: 10.1007/978-1-4939-8695-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Quantitative proteome profiling of microorganisms by isotopic labeling of amino acids is still a challenge, because only microorganisms with auxotrophic character are able to embed amino acids into their biomass in a quantitatively correct manner. Here, we describe an isotopic labeling technique (sulfur stable isotope labeling of amino acids for quantification, SULAQ) for the sulfur-containing amino acids cysteine and methionine in a broad range of organisms. The metabolic labeling approach is suitable for gel-based and gel-free protein analysis.
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4
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The receptor protein tyrosine phosphatase PTPRJ negatively modulates the CD98hc oncoprotein in lung cancer cells. Oncotarget 2018; 9:23334-23348. [PMID: 29805737 PMCID: PMC5955124 DOI: 10.18632/oncotarget.25101] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/24/2018] [Indexed: 01/16/2023] Open
Abstract
PTPRJ, a receptor protein tyrosine phosphatase strongly downregulated in human cancer, displays tumor suppressor activity by negatively modulating several proteins involved in proliferating signals. Here, through a proteomic-based approach, we identified a list of potential PTPRJ-interacting proteins and among them we focused on CD98hc, a type II glycosylated integral membrane protein encoded by SLC3A2, corresponding to the heavy chain of a heterodimeric transmembrane amino-acid transporter, including LAT1. CD98hc is widely overexpressed in several types of cancers and contributes to the process of tumorigenesis by interfering with cell proliferation, adhesion, and migration. We first validated PTPRJ-CD98hc interaction, then demonstrated that PTPRJ overexpression dramatically reduces CD98hc protein levels in A549 lung cancer cells. In addition, following to the treatment of PTPRJ-transduced cells with MG132, a proteasome inhibitor, CD98hc levels did not decrease compared to controls, indicating that PTPRJ is involved in the regulation of CD98hc proteasomal degradation. Moreover, PTPRJ overexpression combined with CD98hc silencing consistently reduced cell proliferation and triggered apoptosis of lung cancer cells. Interestingly, by interrogating the can Evolve database, we observed an inverse correlation between PTPRJ and SLC3A2 gene expression. Indeed, the non-small cell lung cancers (NSCLCs) of patients showing a short survival rate express the lowest and the highest levels of PTPRJ and SLC3A2, respectively. Therefore, the results reported here contribute to shed lights on PTPRJ signaling in cancer cells: moreover, our findings also support the development of a novel anticancer therapeutic approach by targeting the pathway of PTPRJ that is usually downregulated in highly malignant human neoplasias.
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5
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Britton L, Bridle K, Jaskowski LA, He J, Ng C, Ruelcke JE, Mohamed A, Reiling J, Santrampurwala N, Hill MM, Whitehead JP, Subramaniam VN, Crawford DH. Iron Inhibits the Secretion of Apolipoprotein E in Cultured Human Adipocytes. Cell Mol Gastroenterol Hepatol 2018; 6:215-217.e8. [PMID: 30105281 PMCID: PMC6085534 DOI: 10.1016/j.jcmgh.2018.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/02/2018] [Indexed: 12/11/2022]
Affiliation(s)
- L.J. Britton
- Gallipoli Medical Research Institute, Greenslopes Private Hospital, Greenslopes, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
- Department of Gastroenterology, Princess Alexandra Hospital, Queensland, Australia
- Mater Research, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Kim Bridle
- Gallipoli Medical Research Institute, Greenslopes Private Hospital, Greenslopes, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Lesley-Anne Jaskowski
- Gallipoli Medical Research Institute, Greenslopes Private Hospital, Greenslopes, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Jingjing He
- Mater Research, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Choaping Ng
- Mater Research, Translational Research Institute, Woolloongabba, Queensland, Australia
- School of Life Sciences, University of Lincoln, Lincoln, United Kingdom
| | - Jayde E. Ruelcke
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Queensland, Australia
| | - Ahmed Mohamed
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Janske Reiling
- Gallipoli Medical Research Institute, Greenslopes Private Hospital, Greenslopes, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Nishreen Santrampurwala
- Gallipoli Medical Research Institute, Greenslopes Private Hospital, Greenslopes, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Michelle M. Hill
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jonathan P. Whitehead
- Mater Research, Translational Research Institute, Woolloongabba, Queensland, Australia
- School of Life Sciences, University of Lincoln, Lincoln, United Kingdom
| | - V. Nathan Subramaniam
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland, Australia
| | - Darrell H.G. Crawford
- Gallipoli Medical Research Institute, Greenslopes Private Hospital, Greenslopes, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
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6
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Nguyen HD, McLachlan GJ, Hill MM. Statistical Evaluation of Labeled Comparative Profiling Proteomics Experiments Using Permutation Test. Methods Mol Biol 2018; 1549:109-117. [PMID: 27975287 DOI: 10.1007/978-1-4939-6740-7_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Comparative profiling proteomics experiments are important tools in biological research. In such experiments, tens to hundreds of thousands of peptides are measured simultaneously, with the goal of inferring protein abundance levels. Statistical evaluation of these datasets are required to determine proteins that are differentially abundant between the test samples. Previously we have reported the non-normal distribution of SILAC datasets, and demonstrated the permutation test to be a superior method for the statistical evaluation of non-normal peptide ratios. This chapter outlines the steps and the R scripts that can be used for performing permutation analysis with false discovery rate control via the Benjamini-Yekutieli method.
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Affiliation(s)
- Hien D Nguyen
- School of Mathematics and Physics,, The University of Queensland, St. Lucia, 4072, QLD, Australia
- The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Geoffrey J McLachlan
- School of Mathematics and Physics,, The University of Queensland, St. Lucia, 4072, QLD, Australia
| | - Michelle M Hill
- The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia.
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7
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Torres S, García-Palmero I, Marín-Vicente C, Bartolomé RA, Calviño E, Fernández-Aceñero MJ, Casal JI. Proteomic Characterization of Transcription and Splicing Factors Associated with a Metastatic Phenotype in Colorectal Cancer. J Proteome Res 2017; 17:252-264. [PMID: 29131639 DOI: 10.1021/acs.jproteome.7b00548] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We investigated new transcription and splicing factors associated with the metastatic phenotype in colorectal cancer. A concatenated tandem array of consensus transcription factor (TF)-response elements was used to pull down nuclear extracts in two different pairs of colorectal cancer cells, KM12SM/KM12C and SW620/480, genetically related but differing in metastatic ability. Proteins were analyzed by label-free LC-MS and quantified with MaxLFQ. We found 240 proteins showing a significant dysregulation in highly metastatic KM12SM cells relative to nonmetastatic KM12C cells and 257 proteins in metastatic SW620 versus SW480. In both cell lines there were similar alterations in genuine TFs and components of the splicing machinery like UPF1, TCF7L2/TCF-4, YBX1, or SRSF3. However, a significant number of alterations were cell-line specific. Functional silencing of MAFG, TFE3, TCF7L2/TCF-4, and SRSF3 in KM12 cells caused alterations in adhesion, survival, proliferation, migration, and liver homing, supporting their role in metastasis. Finally, we investigated the prognostic value of the altered TFs and splicing factors in cancer patients. SRSF3 and SFPQ showed significant prognostic value. We observed that SRSF3 displayed a gradual loss of expression associated with cancer progression. Loss of SRSF3 expression was significantly associated with poor survival and shorter disease-free survival, particularly in early stages, in colorectal cancer.
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Affiliation(s)
- Sofía Torres
- Functional Proteomics, Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Irene García-Palmero
- Functional Proteomics, Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Consuelo Marín-Vicente
- Functional Proteomics, Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, Madrid 28040, Spain.,Proteomic Facilities, CIB-CSIC , Madrid 28040, Spain
| | - Rubén A Bartolomé
- Functional Proteomics, Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Eva Calviño
- Functional Proteomics, Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, Madrid 28040, Spain
| | | | - J Ignacio Casal
- Functional Proteomics, Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, Madrid 28040, Spain
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8
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Mendes M, Peláez-García A, López-Lucendo M, Bartolomé RA, Calviño E, Barderas R, Casal JI. Mapping the Spatial Proteome of Metastatic Cells in Colorectal Cancer. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700094] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 07/28/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Marta Mendes
- Department of Cellular and Molecular Medicine; Centro de Investigaciones Biológicas (CIB-CSIC); Madrid Spain
| | - Alberto Peláez-García
- Department of Cellular and Molecular Medicine; Centro de Investigaciones Biológicas (CIB-CSIC); Madrid Spain
| | - María López-Lucendo
- Department of Cellular and Molecular Medicine; Centro de Investigaciones Biológicas (CIB-CSIC); Madrid Spain
| | - Rubén A. Bartolomé
- Department of Cellular and Molecular Medicine; Centro de Investigaciones Biológicas (CIB-CSIC); Madrid Spain
| | - Eva Calviño
- Department of Cellular and Molecular Medicine; Centro de Investigaciones Biológicas (CIB-CSIC); Madrid Spain
| | - Rodrigo Barderas
- Department of Cellular and Molecular Medicine; Centro de Investigaciones Biológicas (CIB-CSIC); Madrid Spain
- Instituto de Salud Carlos III.; Majadahonda Spain
| | - J. Ignacio Casal
- Department of Cellular and Molecular Medicine; Centro de Investigaciones Biológicas (CIB-CSIC); Madrid Spain
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9
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Foshag D, Henrich E, Hiller E, Schäfer M, Kerger C, Burger-Kentischer A, Diaz-Moreno I, García-Mauriño SM, Dötsch V, Rupp S, Bernhard F. The E. coli S30 lysate proteome: A prototype for cell-free protein production. N Biotechnol 2017; 40:245-260. [PMID: 28943390 DOI: 10.1016/j.nbt.2017.09.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/28/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
Protein production using processed cell lysates is a core technology in synthetic biology and these systems are excellent to produce difficult toxins or membrane proteins. However, the composition of the central lysate of cell-free systems is still a "black box". Escherichia coli lysates are most productive for cell-free expression, yielding several mgs of protein per ml of reaction. Their preparation implies proteome fractionation, resulting in strongly biased and yet unknown lysate compositions. Many metabolic pathways are expected to be truncated or completely removed. The lack of knowledge of basic cell-free lysate proteomes is a major bottleneck for directed lysate engineering approaches as well as for assay design using non-purified reaction mixtures. This study is starting to close this gap by providing a blueprint of the S30 lysate proteome derived from the commonly used E. coli strain A19. S30 lysates are frequently used for cell-free protein production and represent the basis of most commercial E. coli cell-free expression systems. A fraction of 821 proteins was identified as the core proteome in S30 lysates, representing approximately a quarter of the known E. coli proteome. Its classification into functional groups relevant for transcription/translation, folding, stability and metabolic processes will build the framework for tailored cell-free reactions. As an example, we show that SOS response induction during cultivation results in tuned S30 lysate with better folding capacity, and improved solubility and activity of synthesized proteins. The presented data and protocols can serve as a platform for the generation of customized cell-free systems and product analysis.
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Affiliation(s)
- Daniel Foshag
- Institute for Interfacial Process Engineering and Plasma Technology, University of Stuttgart, Stuttgart, Germany
| | - Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Ekkehard Hiller
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Miriam Schäfer
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Christian Kerger
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | | | - Irene Diaz-Moreno
- Instituto de Investigaciones Químicas (IIQ) - Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Sofía M García-Mauriño
- Instituto de Investigaciones Químicas (IIQ) - Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Steffen Rupp
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany.
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10
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Varano M, Gaspari M, Quirino A, Cuda G, Liberto MC, Focà A. Temperature-dependent regulation of the Ochrobactrum anthropi proteome. Proteomics 2017; 16:3019-3024. [PMID: 27753207 DOI: 10.1002/pmic.201600048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 09/13/2016] [Accepted: 10/12/2016] [Indexed: 02/05/2023]
Abstract
Ochrobactrum anthropi is a Gram-negative rod belonging to the Brucellaceae family, able to colonize a variety of environments, and actually reported as a human opportunistic pathogen. Despite its low virulence, the bacterium causes a growing number of hospital-acquired infections mainly, but not exclusively, in immunocompromised patients. The aim of this study was to obtain an overview of the global proteome changes occurring in O. anthropi in response to different growth temperatures, in order to achieve a major understanding of the mechanisms by which the bacterium adapts to different habitats and to identify some potential virulence factors. Combined quantitative mass spectrometry-based proteomics and bioinformatics approaches were carried out on two O. anthropi strains grown at temperatures miming soil/plants habitat (25°C) and human host environment (37°C), respectively. Proteomic analysis led to the identification of over 150 differentially expressed proteins in both strains, out of over 1200 total protein identifications. Among them, proteins responsible for heat shock response (DnaK, GrpE), motility (FliC, FlgG, FlgE), and putative virulence factors (TolB) were identified. The study represents the first quantitative proteomic analysis of O. anthropi performed by high-resolution quantitative mass spectrometry.
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Affiliation(s)
- Mariaconcetta Varano
- Institute of Microbiology, Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy.,Laboratory Proteomics@UMG, Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Marco Gaspari
- Laboratory Proteomics@UMG, Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Angela Quirino
- Institute of Microbiology, Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Giovanni Cuda
- Laboratory Proteomics@UMG, Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Maria Carla Liberto
- Institute of Microbiology, Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Alfredo Focà
- Institute of Microbiology, Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
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11
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Meng F, Saxena S, Liu Y, Joshi B, Wong TH, Shankar J, Foster LJ, Bernatchez P, Nabi IR. The phospho-caveolin-1 scaffolding domain dampens force fluctuations in focal adhesions and promotes cancer cell migration. Mol Biol Cell 2017; 28:2190-2201. [PMID: 28592633 PMCID: PMC5531735 DOI: 10.1091/mbc.e17-05-0278] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/02/2017] [Indexed: 12/15/2022] Open
Abstract
Caveolin-1 (Cav1), a major Src kinase substrate phosphorylated on tyrosine-14 (Y14), contains the highly conserved membrane-proximal caveolin scaffolding domain (CSD; amino acids 82-101). Here we show, using CSD mutants (F92A/V94A) and membrane-permeable CSD-competing peptides, that Src kinase-dependent pY14Cav1 regulation of focal adhesion protein stabilization, focal adhesion tension, and cancer cell migration is CSD dependent. Quantitative proteomic analysis of Cav1-GST (amino acids 1-101) pull downs showed sixfold-increased binding of vinculin and, to a lesser extent, α-actinin, talin, and filamin, to phosphomimetic Cav1Y14D relative to nonphosphorylatable Cav1Y14F. Consistently, pY14Cav1 enhanced CSD-dependent vinculin tension in focal adhesions, dampening force fluctuation and synchronously stabilizing cellular focal adhesions in a high-tension mode, paralleling effects of actin stabilization. This identifies pY14Cav1 as a molecular regulator of focal adhesion tension and suggests that functional interaction between Cav1 Y14 phosphorylation and the CSD promotes focal adhesion traction and, thereby, cancer cell motility.
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Affiliation(s)
- Fanrui Meng
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sandeep Saxena
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Youtao Liu
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Bharat Joshi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Timothy H Wong
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jay Shankar
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology and Michael Smith Labs, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Pascal Bernatchez
- James Hogg Research Centre, Institute for Heart + Lung Health, St Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada.,Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ivan R Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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12
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Biotin-transfer from a trifunctional crosslinker for identification of cell surface receptors of soluble protein ligands. Sci Rep 2017; 7:46574. [PMID: 28422167 PMCID: PMC5396193 DOI: 10.1038/srep46574] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/17/2017] [Indexed: 11/09/2022] Open
Abstract
Here we describe a novel crosslinker and its application as a biotin-transfer reagent to identify cell surface receptors of soluble protein ligands on live cells. This crosslinker contains three functional groups: an aldehyde-reactive aminooxy group, a sulfhydryl, and a biotin (ASB). It is readily synthesized via a 3-step addition reaction using standard solid-phase peptide synthesis methods and commercially available intermediates, allowing access to laboratories without specialized synthetic chemistry capabilities. For the biotin-transfer method, ASB is linked to a protein ligand through the sulfhydryl group in a two-step process that allows the introduction of a disulfide bond between the ligand and the crosslinker. Incubation of the labelled ligand with oxidized live cells leads to the formation of crosslinks with aldehyde-containing glycans on the cell surface receptor. Subsequent reduction of the disulfide bond results in biotin transfer from the ligand to the cell surface receptor. Protein biotinylation that is mediated by ligand binding to its receptor is differentiated from background biotinylation events by comparison with a similarly labelled control protein using comparative proteomic mass spectrometry to quantify streptavidin-bound proteins. Using this method, we successfully identified the cell surface receptors of a peptide hormone, a monoclonal antibody, and a single-domain antibody-Fc fusion construct.
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13
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Roperto S, Varano M, Russo V, Lucà R, Cagiola M, Gaspari M, Ceccarelli DM, Cuda G, Roperto F. Proteomic analysis of protein purified derivative of Mycobacterium bovis. J Transl Med 2017; 15:68. [PMID: 28372590 PMCID: PMC5376687 DOI: 10.1186/s12967-017-1172-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/23/2017] [Indexed: 11/29/2022] Open
Abstract
Background Tuberculin skin test based on in vivo intradermal inoculation of purified protein derivative from Mycobacterium bovis (bPPD) is the diagnostic test for the control and surveillance of bovine tuberculosis (bTB). Methods Proteomic analysis was performed on different bPPD preparations from M. bovis, strain AN5. Proteins were precipitated from bPPD solutions by TCA precipitation. The proteome of bPPD preparations was investigated by bottom-up proteomics, which consisted in protein digestion and nano-LC–MS/MS analysis. Mass spectrometry analysis was performed on a Q-exactive hybrid quadrupole-Orbitrap mass spectrometer coupled online to an Easy nano-LC1000 system. Results Three hundred and fifty-six proteins were identified and quantified by at least 2 peptides (99% confidence per peptide). One hundred and ninety-eight proteins, which had not been previously described, were detected; furthermore, the proteomic profile shared 80 proteins with previous proteomes from bPPDs from the United Kingdom and Brazil and 139 protein components from bPPD from Korea. Locus name of M. bovis (Mb) with orthologs from M. tuberculosis H37Rv, comparative gene and protein length, molecular mass, functional categories, gene name and function of each protein were reported. Ninety-two T cell mycobacterial antigens responsible for delayed-type hypersensitivity were detected, fifty-two of which were not previously reported in any bPPD proteome. Data are available via ProteomeXchange with identifier PXD005920. Conclusions This study represents the highest proteome coverage of bPPD preparations to date. Since proteins perform cellular functions essential to health and/or disease, obtaining knowledge of their presence and variance is of great importance in understanding disease states and for advancing translational studies. Therefore, to better understand Mycobacterium tuberculosis complex biology during infection, survival, and persistence, the reproducible evaluation of the proteins that catalyze and control these processes is critically important. More active and more specific tuberculins would be desirable. Indeed, many antigens contained within bPPD are currently responsible for the cross-reactivity resulting in false-positive results as they are shared between non-tuberculous and tuberculous mycobacteria. Electronic supplementary material The online version of this article (doi:10.1186/s12967-017-1172-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sante Roperto
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università di Napoli Federico II, Naples, Italy.
| | - Mariaconcetta Varano
- Dipartimento di Medicina Sperimentale e Clinica, Università di Catanzaro "Magna Græcia" Campus "S. Venuta", Catanzaro, Italy
| | - Valeria Russo
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università di Napoli Federico II, Naples, Italy
| | - Roberta Lucà
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università di Napoli Federico II, Naples, Italy
| | - Monica Cagiola
- Istituto Zooprofilattico dell'Umbria e delle Marche, Perugia, Italy
| | - Marco Gaspari
- Dipartimento di Medicina Sperimentale e Clinica, Università di Catanzaro "Magna Græcia" Campus "S. Venuta", Catanzaro, Italy
| | - Dora Maria Ceccarelli
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università di Napoli Federico II, Naples, Italy
| | - Giovanni Cuda
- Dipartimento di Medicina Sperimentale e Clinica, Università di Catanzaro "Magna Græcia" Campus "S. Venuta", Catanzaro, Italy
| | - Franco Roperto
- Dipartimento di Biologia, Università di Napoli Federico II, Naples, Italy
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14
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Kim S, Carruthers N, Lee J, Chinni S, Stemmer P. Classification-based quantitative analysis of stable isotope labeling by amino acids in cell culture (SILAC) data. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2016; 137:137-148. [PMID: 28110720 PMCID: PMC5260509 DOI: 10.1016/j.cmpb.2016.09.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 07/02/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Stable isotope labeling by amino acids in cell culture (SILAC) is a practical and powerful approach for quantitative proteomic analysis. A key advantage of SILAC is the ability to simultaneously detect the isotopically labeled peptides in a single instrument run and so guarantee relative quantitation for a large number of peptides without introducing any variation caused by separate experiment. However, there are a few approaches available to assessing protein ratios and none of the existing algorithms pays considerable attention to the proteins having only one peptide hit. METHODS We introduce new quantitative approaches to dealing with SILAC protein-level summary using classification-based methodologies, such as Gaussian mixture models with EM algorithms and its Bayesian approach as well as K-means clustering. In addition, a new approach is developed using Gaussian mixture model and a stochastic, metaheuristic global optimization algorithm, particle swarm optimization (PSO), to avoid either a premature convergence or being stuck in a local optimum. RESULTS Our simulation studies show that the newly developed PSO-based method performs the best among others in terms of F1 score and the proposed methods further demonstrate the ability of detecting potential markers through real SILAC experimental data. CONCLUSIONS No matter how many peptide hits the protein has, the developed approach can be applicable, rescuing many proteins doomed to removal. Furthermore, no additional correction for multiple comparisons is necessary for the developed methods, enabling direct interpretation of the analysis outcomes.
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Affiliation(s)
- Seongho Kim
- Biostatistics Core, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA; Department of Oncology, Wayne State University, Detroit, MI 48201, USA.
| | - Nicholas Carruthers
- Proteomics Core, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA; Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Joohyoung Lee
- Biostatistics Core, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA; Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Sreenivasa Chinni
- Department of Urology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Paul Stemmer
- Proteomics Core, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA; Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA
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15
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Shah AD, Inder KL, Shah AK, Cristino AS, McKie AB, Gabra H, Davis MJ, Hill MM. Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer. J Proteome Res 2016; 15:3451-3462. [PMID: 27384440 DOI: 10.1021/acs.jproteome.5b01035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and renal cell carcinoma. This analysis revealed that cancer development is associated with increased membrane raft-cytoskeleton interactions, with ∼40% of elevated lipid raft proteins being cytoskeletal components. Previous studies suggest a potential functional role for the raft-cytoskeleton in the action of the putative tumor suppressors PTRF/Cavin-1 and Merlin. To extend the observation, we examined lipid raft proteome modulation by an unrelated tumor suppressor opioid binding protein cell-adhesion molecule (OPCML) in ovarian cancer SKOV3 cells. In agreement with the other model systems, quantitative proteomics revealed that 39% of OPCML-depleted lipid raft proteins are cytoskeletal components, with microfilaments and intermediate filaments specifically down-regulated. Furthermore, protein-protein interaction network and simulation analysis showed significantly higher interactions among cancer raft proteins compared with general human raft proteins. Collectively, these results suggest increased cytoskeleton-mediated stabilization of lipid raft domains with greater molecular interactions as a common, functional, and reversible feature of cancer cells.
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Affiliation(s)
- Anup D Shah
- The University of Queensland Diamantina Institute, The University of Queensland , Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Kerry L Inder
- The University of Queensland Diamantina Institute, The University of Queensland , Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Alok K Shah
- The University of Queensland Diamantina Institute, The University of Queensland , Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Alexandre S Cristino
- The University of Queensland Diamantina Institute, The University of Queensland , Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Arthur B McKie
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London Hammersmith Campus , London W12 0NN, United Kingdom
| | - Hani Gabra
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London Hammersmith Campus , London W12 0NN, United Kingdom
| | - Melissa J Davis
- Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research , 1G Royal Parade, Parkville Victoria 3052, Australia
| | - Michelle M Hill
- The University of Queensland Diamantina Institute, The University of Queensland , Translational Research Institute, Brisbane, Queensland 4102, Australia
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16
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Gu L, Robinson RAS. High-throughput endogenous measurement of S-nitrosylation in Alzheimer's disease using oxidized cysteine-selective cPILOT. Analyst 2016; 141:3904-15. [PMID: 27152368 PMCID: PMC4904844 DOI: 10.1039/c6an00417b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reversible cysteine modifications play important physiological roles such as modulating enzymatic catalysis, maintaining redox homeostasis and conducting cellular signaling. These roles can be critical in the context of disease. Oxidative modifications such as S-nitrosylation (SNO) are signatures of neurodestruction in conditions of oxidative stress however are also indicators of neuroprotection and normal signaling in cellular environments with low concentrations of reactive oxygen and nitrogen species. SNO is a dynamic and low abundance modification and requires sensitive and selective analytical methods for its detection in biological tissues. Here we present an enhanced multiplexing strategy to study SNO in complex mixtures arising from tissues. This method, termed oxidized cysteine-selective cPILOT (OxcyscPILOT), allows simultaneous analysis of SNO-modified peptides in 12 samples. OxcyscPILOT has three primary steps: (1) blocking of free thiols by a cysteine-reactive reagent, (2) enrichment of peptides containing SNO on a solid phase resin, and (3) isotopic labeling and isobaric tagging of enriched peptides on the solid phase resin. This approach offers the advantage of allowing total protein abundance levels to be measured simultaneously with endogenous SNO levels and measurement of SNO levels across four biological replicates in a single analysis. Furthermore, the relative amount of SNO on a specific cysteine site can also be determined. A well-known model of Alzheimer's disease, the APP/PS-1 transgenic mouse model, was selected for demonstration of the method as several SNO-modified proteins have previously been reported in brain and synaptosomes from AD subjects. OxcyscPILOT analysis resulted in identification of 138 SNO-modified cysteines in brain homogenates that correspond to 135 proteins. Many of these SNO-modified proteins were only present in wild-type or AD mice, whereas 93 proteins had SNO signals in both WT and AD. Pathway analysis links SNO-modified proteins to various biological pathways especially metabolism and signal transduction, consistent with previous reports in the literature. The OxcyscPILOT strategy provides enhanced multiplexing capability to current redox proteomics methods to study oxidative modifications of cysteine.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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17
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Diet-induced hypercholesterolemia promotes androgen-independent prostate cancer metastasis via IQGAP1 and caveolin-1. Oncotarget 2016; 6:7438-53. [PMID: 25924234 PMCID: PMC4480691 DOI: 10.18632/oncotarget.3476] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/02/2015] [Indexed: 11/25/2022] Open
Abstract
Obesity and metabolic syndrome are associated with several cancers, however, the molecular mechanisms remain to be fully elucidated. Recent studies suggest that hypercholesterolemia increases intratumoral androgen signaling in prostate cancer, but it is unclear whether androgen-independent mechanisms also exist. Since hypercholesterolemia is associated with advanced, castrate-resistant prostate cancer, in this study, we aimed to determine whether and how hypercholesterolemia affects prostate cancer progression in the absence of androgen signaling. We demonstrate that diet-induced hypercholesterolemia promotes orthotopic xenograft PC-3 cell metastasis, concomitant with elevated expression of caveolin-1 and IQGAP1 in xenograft tumor tissues. In vitro cholesterol treatment of PC-3 cells stimulated migration and increased IQGAP1 and caveolin-1 protein level and localization to a detergent-resistant fraction. Down-regulation of caveolin-1 or IQGAP1 in PC-3 cells reduced migration and invasion in vitro, and hypercholesterolemia-induced metastasis in vivo. Double knock-down of caveolin-1 and IQGAP1 showed no additive effect, suggesting that caveolin-1 and IQGAP1 act via the same pathway. Taken together, our data show that hypercholesterolemia promotes prostate cancer metastasis independent of the androgen pathway, in part by increasing IQGAP1 and caveolin-1. These results have broader implications for managing metastasis of cancers in general as IQGAP1 and hypercholesterolemia are implicated in the progression of several cancers.
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18
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Impact of high-fat diet on the proteome of mouse liver. J Nutr Biochem 2016; 31:10-9. [DOI: 10.1016/j.jnutbio.2015.12.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 10/06/2015] [Accepted: 12/22/2015] [Indexed: 11/22/2022]
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19
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Gu L, Robinson RAS. A simple isotopic labeling method to study cysteine oxidation in Alzheimer's disease: oxidized cysteine-selective dimethylation (OxcysDML). Anal Bioanal Chem 2016; 408:2993-3004. [PMID: 26800981 DOI: 10.1007/s00216-016-9307-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/14/2015] [Accepted: 01/04/2016] [Indexed: 02/01/2023]
Abstract
Cysteine is widely involved in redox signaling pathways through a number of reversible and irreversible modifications. Reversible modifications (e.g., S-glutathionylation, S-nitrosylation, disulfide bonds, and sulfenic acid) are used to protect proteins from oxidative attack and maintain cellular homeostasis, while irreversible oxidations (e.g., sulfinic acid and sulfonic acid) serve as hallmarks of oxidative stress. Proteomic analysis of cysteine-enriched peptides coupled with reduction of oxidized thiols can be used to measure the oxidation states of cysteine, which is helpful for elucidating the role that oxidative stress plays in biology and disease. As an extension of our previously reported cysDML method, we have developed oxidized cysteine-selective dimethylation (OxcysDML), to investigate the site-specific total oxidation of cysteine residues in biologically relevant samples. OxcysDML employs (1) blocking of free thiols by a cysteine-reactive reagent, (2) enrichment of peptides containing reversibly oxidized cysteine by a solid phase resin, and (3) isotopic labeling of peptide amino groups to quantify cysteine modifications arising from different biological conditions. On-resin enrichment and labeling minimizes sample handing time and improves efficiency in comparison with other redox proteomic methods. OxcysDML is also inexpensive and flexible, as it can accommodate the exploration of various cysteine modifications. Here, we applied the method to liver tissues from a late-stage Alzheimer's disease (AD) mouse model and wild-type (WT) controls. Because we have previously characterized this proteome using the cysDML approach, we are able here to probe deeper into the redox status of cysteine in AD. OxcysDML identified 1129 cysteine sites (from 527 proteins), among which 828 cysteine sites underwent oxidative modifications. Nineteen oxidized cysteine sites had significant alteration levels in AD and represent proteins involved in metabolic processes. Overall, we have demonstrated OxcysDML as a simple, rapid, robust, and inexpensive redox proteomic approach that is useful for gaining deeper insight into the proteome of AD.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, 111 Eberly Hall, 200 University Drive, Pittsburgh, PA, 15260, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, 111 Eberly Hall, 200 University Drive, Pittsburgh, PA, 15260, USA.
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20
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Peláez-García A, Barderas R, Mendes M, Lopez-Lucendo M, Sanchez JC, García de Herreros A, Casal JI. Data from proteomic characterization of the role of Snail1 in murine mesenchymal stem cells and 3T3-L1 fibroblasts differentiation. Data Brief 2015; 4:606-13. [PMID: 26322327 PMCID: PMC4543208 DOI: 10.1016/j.dib.2015.07.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/13/2015] [Accepted: 07/20/2015] [Indexed: 02/02/2023] Open
Abstract
The transcription factor (TF) Snail1 is a major inducer of the epithelial–mesenchymal transition (EMT) during embryonic development and cancer progression. Ectopic expression of Snail in murine mesenchymal stem cells (mMSC) abrogated their differentiation to osteoblasts or adipocytes. We used either stable isotopic metabolic labeling (SILAC) for 3T3-L1 cells or isobaric labeling with tandem mass tags (TMT) for mMSC stably transfected cells with Snail1 or control. We carried out a proteomic analysis on the nuclear fraction since Snail is a nuclear TF that mediates its effects mainly through the regulation of other TFs. Proteomics data have been deposited in ProteomeXchange via the PRIDE partner repository with the dataset identifiers PXD001529 and PXD002157 (Vizcaino et al., 2014) [1]. Data are associated with a research article published in Molecular and Cellular Proteomics (Pelaez-Garcia et al., 2015) [2].
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Affiliation(s)
- A Peláez-García
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | - R Barderas
- Biochemistry and Molecular Biology I Department, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | - M Mendes
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | - M Lopez-Lucendo
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | - J C Sanchez
- Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - J I Casal
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
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21
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Sharma R, Gowda H, Chavan S, Advani J, Kelkar D, Kumar GSS, Bhattacharjee M, Chaerkady R, Prasad TSK, Pandey A, Nagaraja D, Christopher R. Proteomic Signature of Endothelial Dysfunction Identified in the Serum of Acute Ischemic Stroke Patients by the iTRAQ-Based LC–MS Approach. J Proteome Res 2015; 14:2466-79. [DOI: 10.1021/pr501324n] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rakesh Sharma
- Department
of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore 560029, India
- Department of Biochemistry, Faculty of Medicine, The University of Hong Kong, Hong Kong
- Department of Biology and Chemistry, City University of Hong Kong, Hong Kong
| | - Harsha Gowda
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Sandip Chavan
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
- Manipal University, Manipal 576 104, India
| | - Jayshree Advani
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
- Manipal University, Manipal 576 104, India
| | - Dhanashree Kelkar
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - G. S. Sameer Kumar
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Mitali Bhattacharjee
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Raghothama Chaerkady
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
- Manipal University, Manipal 576 104, India
| | - T. S. Keshava Prasad
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
- Manipal University, Manipal 576 104, India
| | - Akhilesh Pandey
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Dindagur Nagaraja
- Department
of Neurology, Dharwad Institute of Mental Health and Neuro Sciences, Dharwad 580001, India
| | - Rita Christopher
- Department
of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore 560029, India
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22
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Gu L, Evans AR, Robinson RAS. Sample multiplexing with cysteine-selective approaches: cysDML and cPILOT. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:615-630. [PMID: 25588721 DOI: 10.1007/s13361-014-1059-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/22/2014] [Accepted: 11/22/2014] [Indexed: 06/04/2023]
Abstract
Cysteine-selective proteomics approaches simplify complex protein mixtures and improve the chance of detecting low abundant proteins. It is possible that cysteinyl-peptide/protein enrichment methods could be coupled to isotopic labeling and isobaric tagging methods for quantitative proteomics analyses in as few as two or up to 10 samples, respectively. Here we present two novel cysteine-selective proteomics approaches: cysteine-selective dimethyl labeling (cysDML) and cysteine-selective combined precursor isotopic labeling and isobaric tagging (cPILOT). CysDML is a duplex precursor quantification technique that couples cysteinyl-peptide enrichment with on-resin stable-isotope dimethyl labeling. Cysteine-selective cPILOT is a novel 12-plex workflow based on cysteinyl-peptide enrichment, on-resin stable-isotope dimethyl labeling, and iodoTMT tagging on cysteine residues. To demonstrate the broad applicability of the approaches, we applied cysDML and cPILOT methods to liver tissues from an Alzheimer's disease (AD) mouse model and wild-type (WT) controls. From the cysDML experiments, an average of 850 proteins were identified and 594 were quantified, whereas from the cPILOT experiment, 330 and 151 proteins were identified and quantified, respectively. Overall, 2259 unique total proteins were detected from both cysDML and cPILOT experiments. There is tremendous overlap in the proteins identified and quantified between both experiments, and many proteins have AD/WT fold-change values that are within ~20% error. A total of 65 statistically significant proteins are differentially expressed in the liver proteome of AD mice relative to WT. The performance of cysDML and cPILOT are demonstrated and advantages and limitations of using multiple duplex experiments versus a single 12-plex experiment are highlighted.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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