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Pauwels E, Rutz C, Provinciael B, Stroobants J, Schols D, Hartmann E, Krause E, Stephanowitz H, Schülein R, Vermeire K. A Proteomic Study on the Membrane Protein Fraction of T Cells Confirms High Substrate Selectivity for the ER Translocation Inhibitor Cyclotriazadisulfonamide. Mol Cell Proteomics 2021; 20:100144. [PMID: 34481949 PMCID: PMC8477212 DOI: 10.1016/j.mcpro.2021.100144] [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: 04/16/2021] [Revised: 08/09/2021] [Accepted: 08/30/2021] [Indexed: 11/15/2022] Open
Abstract
Cyclotriazadisulfonamide (CADA) inhibits the cotranslational translocation of type I integral membrane protein human CD4 (huCD4) across the endoplasmic reticulum in a signal peptide (SP)–dependent way. Previously, sortilin was identified as a secondary substrate for CADA but showed reduced CADA sensitivity as compared with huCD4. Here, we performed a quantitative proteomic study on the crude membrane fraction of human T-cells to analyze how many proteins are sensitive to CADA. To screen for these proteins, we employed stable isotope labeling by amino acids in cell culture technique in combination with quantitative MS on CADA-treated human T-lymphoid SUP-T1 cells expressing high levels of huCD4. In line with our previous reports, our current proteomic analysis (data available via ProteomeXchange with identifier PXD027712) demonstrated that only a very small subset of proteins is depleted by CADA. Our data also confirmed that cellular expression of both huCD4 and sortilin are affected by CADA treatment of SUP-T1 cells. Furthermore, three additional targets for CADA are identified, namely, endoplasmic reticulum lectin 1 (ERLEC1), inactive tyrosine-protein kinase 7 (PTK7), and DnaJ homolog subfamily C member 3 (DNAJC3). Western blot and flow cytometry analysis of ERLEC1, PTK7, and DNAJC3 protein expression validated susceptibility of these substrates to CADA, although with varying degrees of sensitivity. Additional cell-free in vitro translation/translocation data demonstrated that the new substrates for CADA carry cleavable SPs that are targets for the cotranslational translocation inhibition exerted by CADA. Thus, our quantitative proteomic analysis demonstrates that ERLEC1, PTK7, and DNAJC3 are validated additional substrates of CADA; however, huCD4 remains the most sensitive integral membrane protein for the endoplasmic reticulum translocation inhibitor CADA. Furthermore, to our knowledge, CADA is the first compound that specifically interferes with only a very small subset of SPs and does not affect signal anchor sequences. About 3007 proteins quantified in SILAC/MS study on CD4+ T-cells treated with CADA. Three new targets for CADA were identified: ERLEC1, PTK7, and DNAJC3. All CADA substrates carry cleavable signal peptides for translocation into ER. huCD4 remains the most sensitive substrate for the ER translocation inhibitor CADA.
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Affiliation(s)
- Eva Pauwels
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Claudia Rutz
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Becky Provinciael
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Joren Stroobants
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Enno Hartmann
- Centre for Structural and Cell Biology in Medicine, Institute of Biology, University of Lübeck, Lübeck, Germany
| | - Eberhard Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Heike Stephanowitz
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Ralf Schülein
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Kurt Vermeire
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium.
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Proteome profile of telencephalon associates attenuated neurogenesis with chronic stress induced mood disorder phenotypes in zebrafish model. Pharmacol Biochem Behav 2021; 204:173170. [DOI: 10.1016/j.pbb.2021.173170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/28/2021] [Accepted: 02/28/2021] [Indexed: 02/07/2023]
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Te Brake LHM, de Knegt GJ, de Steenwinkel JE, van Dam TJP, Burger DM, Russel FGM, van Crevel R, Koenderink JB, Aarnoutse RE. The Role of Efflux Pumps in Tuberculosis Treatment and Their Promise as a Target in Drug Development: Unraveling the Black Box. Annu Rev Pharmacol Toxicol 2017; 58:271-291. [PMID: 28715978 DOI: 10.1146/annurev-pharmtox-010617-052438] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Insight into drug transport mechanisms is highly relevant to the efficacious treatment of tuberculosis (TB). Major problems in TB treatment are related to the transport of antituberculosis (anti-TB) drugs across human and mycobacterial membranes, affecting the concentrations of these drugs systemically and locally. Firstly, transporters located in the intestines, liver, and kidneys all determine the pharmacokinetics and pharmacodynamics of anti-TB drugs, with a high risk of drug-drug interactions in the setting of concurrent use of antimycobacterial, antiretroviral, and antidiabetic agents. Secondly, human efflux transporters limit the penetration of anti-TB drugs into the brain and cerebrospinal fluid, which is especially important in the treatment of TB meningitis. Finally, efflux transporters located in the macrophage and Mycobacterium tuberculosis cell membranes play a pivotal role in the emergence of phenotypic tolerance and drug resistance, respectively. We review the role of efflux transporters in TB drug disposition and evaluate the promise of efflux pump inhibition from a novel holistic perspective.
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Affiliation(s)
- Lindsey H M Te Brake
- Department of Pharmacy, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; .,Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Gerjo J de Knegt
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Jurriaan E de Steenwinkel
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Teunis J P van Dam
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - David M Burger
- Department of Pharmacy, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Frans G M Russel
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Reinout van Crevel
- Department of Internal Medicine, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Jan B Koenderink
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rob E Aarnoutse
- Department of Pharmacy, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
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Quantitative proteomic analysis and comparison of two bone marrow stromal cell lines using the SILAC method. Exp Hematol 2016; 44:1059-1071. [PMID: 27539861 DOI: 10.1016/j.exphem.2016.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/11/2016] [Accepted: 08/04/2016] [Indexed: 01/10/2023]
Abstract
Two human bone marrow stromal cell lines, HS5 and HS27a, co-cultured with myeloid cells, have frequently been used in studies of cross talk between cells in the bone marrow microenvironment and hematopoietic cells. Altered expression of proteins is typically associated with cell-cell signal transduction and regulation of cellular functions. Many studies have focused on key proteins that contribute to functional differences in cell co-culture models, but global quantitative proteome analysis of HS5 and HS27a has not been performed. We employed the stable isotope labeling by amino acids in cell culture (SILAC) method using two stable isotopes each of arginine and lysine to label proteins in the two cell lines. Labeled proteins were analyzed by 2-D ultrahigh-resolution liquid chromatography- LTQ/Orbitrap mass spectrometry. Among 4,213 unique identified and annotated proteins in the cell lines, 1,462 were detected in two independent experiments. Of these, 69 exhibited significant upregulation and 48 significant downregulation (>95% confidence) in HS27a relative to HS5 cells. Gene ontology term and pathway analysis indicated that the differentially regulated proteins were involved in cellular movement, cell-to-cell signaling and interaction, and hematologic system development and function. A total of 55 items were identified in both genomic and proteomic databases. Quantitative reverse transcription polymerase chain reaction and Western blotting were performed on 7 proteins randomly selected from 28 differentially expressed proteins that were identified in both databases and were involved in the top networks/pathways. We observed a decrease in apoptosis in co-cultured KG1a cells when integrin αV was inhibited in HS27a cells, which suggested the functional role of integrin αV in the co-culture system. The integrated genomic/proteomic approach described here, and the identified proteins, will provide a useful basis for further elucidation of molecular mechanisms in the bone marrow microenvironment and for ongoing studies of cross talk among stromal cells and myeloma cells in co-culture systems.
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Quantitative Analysis of Differential Proteome Expression in Epithelial-to-Mesenchymal Transition of Bladder Epithelial Cells Using SILAC Method. Molecules 2016; 21:84. [PMID: 26784156 PMCID: PMC6273313 DOI: 10.3390/molecules21010084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 12/11/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is an essential biological process involved in embryonic development, cancer progression, and metastatic diseases. EMT has often been used as a model for elucidating the mechanisms that underlie bladder cancer progression. However, no study to date has addressed the quantitative global variation of proteins in EMT using normal and non-malignant bladder cells. We treated normal bladder epithelial HCV29 cells and low grade nonmuscle invasive bladder cancer KK47 cells with transforming growth factor-beta (TGF-β) to establish an EMT model, and studied non-treated and treated HCV29 and KK47 cells by the stable isotope labeling amino acids in cell culture (SILAC) method. Labeled proteins were analyzed by 2D ultrahigh-resolution liquid chromatography/LTQ Orbitrap mass spectrometry. Among a total of 2994 unique identified and annotated proteins in HCV29 and KK47 cells undergoing EMT, 48 and 56 proteins, respectively, were significantly upregulated, and 106 and 24 proteins were significantly downregulated. Gene ontology (GO) term analysis and pathways analysis indicated that the differentially regulated proteins were involved mainly in enhancement of DNA maintenance and inhibition of cell-cell adhesion. Proteomes were compared for bladder cell EMT vs. bladder cancer cells, revealing 16 proteins that displayed similar changes in the two situations. Studies are in progress to further characterize these 16 proteins and their biological functions in EMT.
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Yang G, Xu Z, Lu W, Li X, Sun C, Guo J, Xue P, Guan F. Quantitative Analysis of Differential Proteome Expression in Bladder Cancer vs. Normal Bladder Cells Using SILAC Method. PLoS One 2015; 10:e0134727. [PMID: 26230496 PMCID: PMC4521931 DOI: 10.1371/journal.pone.0134727] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 07/13/2015] [Indexed: 12/26/2022] Open
Abstract
The best way to increase patient survival rate is to identify patients who are likely to progress to muscle-invasive or metastatic disease upfront and treat them more aggressively. The human cell lines HCV29 (normal bladder epithelia), KK47 (low grade nonmuscle invasive bladder cancer, NMIBC), and YTS1 (metastatic bladder cancer) have been widely used in studies of molecular mechanisms and cell signaling during bladder cancer (BC) progression. However, little attention has been paid to global quantitative proteome analysis of these three cell lines. We labeled HCV29, KK47, and YTS1 cells by the SILAC method using three stable isotopes each of arginine and lysine. Labeled proteins were analyzed by 2D ultrahigh-resolution liquid chromatography LTQ Orbitrap mass spectrometry. Among 3721 unique identified and annotated proteins in KK47 and YTS1 cells, 36 were significantly upregulated and 74 were significantly downregulated with >95% confidence. Differential expression of these proteins was confirmed by western blotting, quantitative RT-PCR, and cell staining with specific antibodies. Gene ontology (GO) term and pathway analysis indicated that the differentially regulated proteins were involved in DNA replication and molecular transport, cell growth and proliferation, cellular movement, immune cell trafficking, and cell death and survival. These proteins and the advanced proteome techniques described here will be useful for further elucidation of molecular mechanisms in BC and other types of cancer.
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Affiliation(s)
- Ganglong Yang
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhipeng Xu
- Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Wei Lu
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiang Li
- Wuxi Medical School, Jiangnan University, Wuxi, China
| | - Chengwen Sun
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Jia Guo
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Peng Xue
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (PX); (FG)
| | - Feng Guan
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- * E-mail: (PX); (FG)
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Olšinová M, Jurkiewicz P, Pozník M, Šachl R, Prausová T, Hof M, Kozmík V, Teplý F, Svoboda J, Cebecauer M. Di- and tri-oxalkyl derivatives of a boron dipyrromethene (BODIPY) rotor dye in lipid bilayers. Phys Chem Chem Phys 2014; 16:10688-97. [DOI: 10.1039/c4cp00888j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Di- and tri-alkylated variants of a BODIPY rotor: carefully characterised probes sensing the liquid or gel state of lipid membranes.
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Affiliation(s)
- Marie Olšinová
- Department of Biophysical Chemistry
- J. Heyrovsky Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague, Czech Republic
| | - Piotr Jurkiewicz
- Department of Biophysical Chemistry
- J. Heyrovsky Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague, Czech Republic
| | - Michal Pozník
- Department of Organic Chemistry
- Institute of Chemical Technology
- Prague, Czech Republic
| | - Radek Šachl
- Department of Biophysical Chemistry
- J. Heyrovsky Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague, Czech Republic
| | - Tereza Prausová
- Department of Organic Chemistry
- Institute of Chemical Technology
- Prague, Czech Republic
| | - Martin Hof
- Department of Biophysical Chemistry
- J. Heyrovsky Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague, Czech Republic
| | - Václav Kozmík
- Department of Organic Chemistry
- Institute of Chemical Technology
- Prague, Czech Republic
| | - Filip Teplý
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague, Czech Republic
| | - Jiří Svoboda
- Department of Organic Chemistry
- Institute of Chemical Technology
- Prague, Czech Republic
| | - Marek Cebecauer
- Department of Biophysical Chemistry
- J. Heyrovsky Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague, Czech Republic
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