4801
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Construction and Optimization of a Heterologous Pathway for Protocatechuate Catabolism in Escherichia coli Enables Bioconversion of Model Aromatic Compounds. Appl Environ Microbiol 2017; 83:AEM.01313-17. [PMID: 28733280 DOI: 10.1128/aem.01313-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/10/2017] [Indexed: 11/20/2022] Open
Abstract
The production of biofuels from lignocellulose yields a substantial lignin by-product stream that currently has few applications. Biological conversion of lignin-derived compounds into chemicals and fuels has the potential to improve the economics of lignocellulose-derived biofuels, but few microbes are able both to catabolize lignin-derived aromatic compounds and to generate valuable products. While Escherichia coli has been engineered to produce a variety of fuels and chemicals, it is incapable of catabolizing most aromatic compounds. Therefore, we engineered E. coli to catabolize protocatechuate, a common intermediate in lignin degradation, as the sole source of carbon and energy via heterologous expression of a nine-gene pathway from Pseudomonas putida KT2440. We next used experimental evolution to select for mutations that increased growth with protocatechuate more than 2-fold. Increasing the strength of a single ribosome binding site in the heterologous pathway was sufficient to recapitulate the increased growth. After optimization of the core pathway, we extended the pathway to enable catabolism of a second model compound, 4-hydroxybenzoate. These engineered strains will be useful platforms to discover, characterize, and optimize pathways for conversions of lignin-derived aromatics.IMPORTANCE Lignin is a challenging substrate for microbial catabolism due to its polymeric and heterogeneous chemical structure. Therefore, engineering microbes for improved catabolism of lignin-derived aromatic compounds will require the assembly of an entire network of catabolic reactions, including pathways from genetically intractable strains. Constructing defined pathways for aromatic compound degradation in a model host would allow rapid identification, characterization, and optimization of novel pathways. We constructed and optimized one such pathway in E. coli to enable catabolism of a model aromatic compound, protocatechuate, and then extended the pathway to a related compound, 4-hydroxybenzoate. This optimized strain can now be used as the basis for the characterization of novel pathways.
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4802
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Hinkelbein J, Jansen S, Iovino I, Kruse S, Meyer M, Cirillo F, Drinhaus H, Hohn A, Klein C, Robertis ED, Beutner D. Thirty Minutes of Hypobaric Hypoxia Provokes Alterations of Immune Response, Haemostasis, and Metabolism Proteins in Human Serum. Int J Mol Sci 2017; 18:E1882. [PMID: 28858246 PMCID: PMC5618531 DOI: 10.3390/ijms18091882] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/21/2017] [Accepted: 08/29/2017] [Indexed: 12/20/2022] Open
Abstract
Hypobaric hypoxia (HH) during airline travel induces several (patho-) physiological reactions in the human body. Whereas severe hypoxia is investigated thoroughly, very little is known about effects of moderate or short-term hypoxia, e.g. during airline flights. The aim of the present study was to analyse changes in serum protein expression and activation of signalling cascades in human volunteers staying for 30 min in a simulated altitude equivalent to airline travel. After approval of the local ethics committee, 10 participants were exposed to moderate hypoxia (simulation of 2400 m or 8000 ft for 30 min) in a hypobaric pressure chamber. Before and after hypobaric hypoxia, serum was drawn, centrifuged, and analysed by two-dimensional gel electrophoresis (2-DIGE) and matrix-assisted laser desorption/ionization followed by time-of-flight mass spectrometry (MALDI-TOF). Biological functions of regulated proteins were identified using functional network analysis (GeneMania®, STRING®, and Perseus® software). In participants, oxygen saturation decreased from 98.1 ± 1.3% to 89.2 ± 1.8% during HH. Expression of 14 spots (i.e., 10 proteins: ALB, PGK1, APOE, GAPDH, C1QA, C1QB, CAT, CA1, F2, and CLU) was significantly altered. Bioinformatic analysis revealed an association of the altered proteins with the signalling cascades "regulation of haemostasis" (four proteins), "metabolism" (five proteins), and "leukocyte mediated immune response" (five proteins). Even though hypobaric hypoxia was short and moderate (comparable to an airliner flight), analysis of protein expression in human subjects revealed an association to immune response, protein metabolism, and haemostasis.
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Affiliation(s)
- Jochen Hinkelbein
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital of Cologne, 50937 Cologne, Germany.
| | - Stefanie Jansen
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, 50937 Cologne, Germany.
| | - Ivan Iovino
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples "Federico II", Via S. Pansini, 5-80131 Napoli, Italy.
| | - Silvia Kruse
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital of Cologne, 50937 Cologne, Germany.
| | - Moritz Meyer
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, 50937 Cologne, Germany.
| | - Fabrizio Cirillo
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples "Federico II", Via S. Pansini, 5-80131 Napoli, Italy.
| | - Hendrik Drinhaus
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital of Cologne, 50937 Cologne, Germany.
| | - Andreas Hohn
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital of Cologne, 50937 Cologne, Germany.
| | - Corinna Klein
- CECAD Lipidomics & Proteomics Facilities, CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
| | - Edoardo De Robertis
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples "Federico II", Via S. Pansini, 5-80131 Napoli, Italy.
| | - Dirk Beutner
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, 50937 Cologne, Germany.
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4803
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Scott NE, Giogha C, Pollock GL, Kennedy CL, Webb AI, Williamson NA, Pearson JS, Hartland EL. The bacterial arginine glycosyltransferase effector NleB preferentially modifies Fas-associated death domain protein (FADD). J Biol Chem 2017; 292:17337-17350. [PMID: 28860194 DOI: 10.1074/jbc.m117.805036] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/28/2017] [Indexed: 01/01/2023] Open
Abstract
The inhibition of host innate immunity pathways is essential for the persistence of attaching and effacing pathogens such as enteropathogenic Escherichia coli (EPEC) and Citrobacter rodentium during mammalian infections. To subvert these pathways and suppress the antimicrobial response, attaching and effacing pathogens use type III secretion systems to introduce effectors targeting key signaling pathways in host cells. One such effector is the arginine glycosyltransferase NleB1 (NleBCR in C. rodentium) that modifies conserved arginine residues in death domain-containing host proteins with N-acetylglucosamine (GlcNAc), thereby blocking extrinsic apoptosis signaling. Ectopically expressed NleB1 modifies the host proteins Fas-associated via death domain (FADD), TNFRSF1A-associated via death domain (TRADD), and receptor-interacting serine/threonine protein kinase 1 (RIPK1). However, the full repertoire of arginine GlcNAcylation induced by pathogen-delivered NleB1 is unknown. Using an affinity proteomic approach for measuring arginine-GlcNAcylated glycopeptides, we assessed the global profile of arginine GlcNAcylation during ectopic expression of NleB1, EPEC infection in vitro, or C. rodentium infection in vivo NleB overexpression resulted in arginine GlcNAcylation of multiple host proteins. However, NleB delivery during EPEC and C. rodentium infection caused rapid and preferential modification of Arg117 in FADD. This FADD modification was extremely stable and insensitive to physiological temperatures, glycosidases, or host cell degradation. Despite its stability and effect on the inhibition of apoptosis, arginine GlcNAcylation did not elicit any proteomic changes, even in response to prolonged NleB1 expression. We conclude that, at normal levels of expression during bacterial infection, NleB1/NleBCR antagonizes death receptor-induced apoptosis of infected cells by modifying FADD in an irreversible manner.
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Affiliation(s)
- Nichollas E Scott
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia,
| | - Cristina Giogha
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Georgina L Pollock
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Catherine L Kennedy
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Melbourne, Australia.,the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia, and
| | - Nicholas A Williamson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Jaclyn S Pearson
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Elizabeth L Hartland
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
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4804
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Mohl BP, Emmott E, Roy P. Phosphoproteomic Analysis Reveals the Importance of Kinase Regulation During Orbivirus Infection. Mol Cell Proteomics 2017; 16:1990-2005. [PMID: 28851738 PMCID: PMC5672004 DOI: 10.1074/mcp.m117.067355] [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: 01/27/2017] [Revised: 08/08/2017] [Indexed: 01/03/2023] Open
Abstract
Bluetongue virus (BTV) causes infections in wild and domesticated ruminants with high morbidity and mortality and is responsible for significant economic losses in both developing and developed countries. BTV serves as a model for the study of other members of the Orbivirus genus. Previously, the importance of casein kinase 2 for BTV replication was demonstrated. To identify intracellular signaling pathways and novel host-cell kinases involved during BTV infection, the phosphoproteome of BTV infected cells was analyzed. Over 1000 phosphosites were identified using mass spectrometry, which were then used to determine the corresponding kinases involved during BTV infection. This analysis yielded protein kinase A (PKA) as a novel kinase activated during BTV infection. Subsequently, the importance of PKA for BTV infection was validated using a PKA inhibitor and activator. Our data confirmed that PKA was essential for efficient viral growth. Further, we showed that PKA is also required for infection of equid cells by African horse sickness virus, another member of the Orbivirus genus. Thus, despite their preference in specific host species, orbiviruses may utilize the same host signaling pathways during their replication.
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Affiliation(s)
- Bjorn-Patrick Mohl
- From the ‡Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Edward Emmott
- §University of Cambridge, Division of Virology, Department of Pathology, Lab block level 5, Box 237, Addenbrookes Hospital, Cambridge, UK
| | - Polly Roy
- From the ‡Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK;
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4805
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Vyse S, McCarthy F, Broncel M, Paul A, Wong JP, Bhamra A, Huang PH. Quantitative phosphoproteomic analysis of acquired cancer drug resistance to pazopanib and dasatinib. J Proteomics 2017; 170:130-140. [PMID: 28842319 PMCID: PMC5673060 DOI: 10.1016/j.jprot.2017.08.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 07/19/2017] [Accepted: 08/17/2017] [Indexed: 12/14/2022]
Abstract
Acquired drug resistance impacts the majority of patients being treated with tyrosine kinase inhibitors (TKIs) and remains a key challenge in modern anti-cancer therapy. The lack of clinically effective therapies to overcome resistance represents an unmet need. Understanding the signalling that drives drug resistance will facilitate the development of new salvage therapies to treat patients with secondary TKI resistance. In this study, we utilise mass spectrometry to characterise the global phosphoproteomic alterations that accompany the acquisition of resistance to two FDA-approved TKIs, pazopanib and dasatinib, in the A204 rhabdoid tumour cell line. Our analysis finds that only 6% and 9.7% of the quantified phosphoproteome is altered upon the acquisition of pazopanib and dasatinib resistance, respectively. Pazopanib resistant cells display elevated phosphorylation in cytoskeletal regulatory pathways while dasatinib resistant cells show an upregulation of the insulin receptor/IGF-1R signalling pathway. Drug response profiling rediscovers several previously reported vulnerabilities associated with pazopanib and dasatinib resistance and identifies a new dependency to the second generation HSP90 inhibitor NVP-AUY-922. This study provides a useful resource detailing the candidate signalling determinants of acquired TKI resistance; and reveals a therapeutic approach of inhibiting HSP90 function as a means of salvage therapy to overcome pazopanib and dasatinib resistance. Significance Pazopanib and dasatinib are tyrosine kinase inhibitors (TKIs) approved for the treatment of multiple cancer types. Patients who are treated with these drugs are prone to the development of drug resistance and consequently tumour relapse. Here we use quantitative phosphoproteomics to characterise the signalling pathways which are enriched in cells that have acquired resistance to these two drugs. Furthermore, targeted drug screens were used to identify salvage therapies capable of overcoming pazopanib and dasatinib resistance. This data advances our understanding of the mechanisms of TKI resistance and highlights candidate targets for cancer therapy. Pazopanib resistant cells display elevated phosphorylation in cytoskeletal regulatory pathways. Phosphoproteins in the insulin and IGF-1R pathways are upregulated in dasatinib resistant cells. Less than 10% of the phosphoproteome is altered in acquired drug-resistant A204 cells. Both dasatinib and pazopanib resistant A204 cells are vulnerable to HSP90 inhibition.
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Affiliation(s)
- Simon Vyse
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Frank McCarthy
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Malgorzata Broncel
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Angela Paul
- Proteomics Core Facility, The Institute of Cancer Research, London SW3 6JB, UK
| | - Jocelyn P Wong
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Amandeep Bhamra
- Proteomics Core Facility, The Institute of Cancer Research, London SW3 6JB, UK
| | - Paul H Huang
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK.
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4806
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Jagadeesan KK, Ekström S. MALDIViz: A Comprehensive Informatics Tool for MALDI-MS Data Visualization and Analysis. SLAS DISCOVERY 2017; 22:1246-1252. [PMID: 28825969 DOI: 10.1177/2472555217727517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Recently, mass spectrometry (MS) has emerged as an important tool for high-throughput screening (HTS) providing a direct and label-free detection method, complementing traditional fluorescent and colorimetric methodologies. Among the various MS techniques used for HTS, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) provides many of the characteristics required for high-throughput analyses, such as low cost, speed, and automation. However, visualization and analysis of the large datasets generated by HTS MALDI-MS can pose significant challenges, especially for multiparametric experiments. The datasets can be generated fast, and the complexity of the experimental data (e.g., screening many different sorbent phases, the sorbent mass, and the load, wash, and elution conditions) makes manual data analysis difficult. To address these challenges, a comprehensive informatics tool called MALDIViz was developed. This tool is an R-Shiny-based web application, accessible independently of the operating system and without the need to install any program locally. It has been designed to facilitate easy analysis and visualization of MALDI-MS datasets, comparison of multiplex experiments, and export of the analysis results to high-quality images.
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Affiliation(s)
| | - Simon Ekström
- 1 Department of Biomedical Engineering, Lund University, Lund, Sweden
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4807
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Emdal KB, Dittmann A, Reddy RJ, Lescarbeau RS, Moores SL, Laquerre S, White FM. Characterization of In Vivo Resistance to Osimertinib and JNJ-61186372, an EGFR/Met Bispecific Antibody, Reveals Unique and Consensus Mechanisms of Resistance. Mol Cancer Ther 2017; 16:2572-2585. [PMID: 28830985 DOI: 10.1158/1535-7163.mct-17-0413] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/21/2017] [Accepted: 08/10/2017] [Indexed: 12/28/2022]
Abstract
Approximately 10% of non-small cell lung cancer (NSCLC) patients in the United States and 40% of NSCLC patients in Asia have activating epidermal growth factor receptor (EGFR) mutations and are eligible to receive targeted anti-EGFR therapy. Despite an extension of life expectancy associated with this treatment, resistance to EGFR tyrosine kinase inhibitors and anti-EGFR antibodies is almost inevitable. To identify additional signaling routes that can be cotargeted to overcome resistance, we quantified tumor-specific molecular changes that govern resistant cancer cell growth and survival. Mass spectrometry-based quantitative proteomics was used to profile in vivo signaling changes in 41 therapy-resistant tumors from four xenograft NSCLC models. We identified unique and tumor-specific tyrosine phosphorylation rewiring in tumors resistant to treatment with the irreversible third-generation EGFR-inhibitor, osimertinib, or the novel dual-targeting EGFR/Met antibody, JNJ-61186372. Tumor-specific increases in tyrosine-phosphorylated peptides from EGFR family members, Shc1 and Gab1 or Src family kinase (SFK) substrates were observed, underscoring a differential ability of tumors to uniquely escape EGFR inhibition. Although most resistant tumors within each treatment group displayed a marked inhibition of EGFR as well as SFK signaling, the combination of EGFR inhibition (osimertinib) and SFK inhibition (saracatinib or dasatinib) led to further decrease in cell growth in vitro This result suggests that residual SFK signaling mediates therapeutic resistance and that elimination of this signal through combination therapy may delay onset of resistance. Overall, analysis of individual resistant tumors captured unique in vivo signaling rewiring that would have been masked by analysis of in vitro cell population averages. Mol Cancer Ther; 16(11); 2572-85. ©2017 AACR.
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Affiliation(s)
- Kristina B Emdal
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Antje Dittmann
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Raven J Reddy
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Rebecca S Lescarbeau
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Sheri L Moores
- Oncology, Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Sylvie Laquerre
- Oncology, Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Forest M White
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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4808
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Mellows B, Mitchell R, Antonioli M, Kretz O, Chambers D, Zeuner MT, Denecke B, Musante L, Ramachandra DL, Debacq-Chainiaux F, Holthofer H, Joch B, Ray S, Widera D, David AL, Huber TB, Dengjel J, De Coppi P, Patel K. Protein and Molecular Characterization of a Clinically Compliant Amniotic Fluid Stem Cell-Derived Extracellular Vesicle Fraction Capable of Accelerating Muscle Regeneration Through Enhancement of Angiogenesis. Stem Cells Dev 2017; 26:1316-1333. [PMID: 28679310 DOI: 10.1089/scd.2017.0089] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The secretome of human amniotic fluid stem cells (AFSCs) has great potential as a therapeutic agent in regenerative medicine. However, it must be produced in a clinically compliant manner before it can be used in humans. In this study, we developed a means of producing a biologically active secretome from AFSCs that is free of all exogenous molecules. We demonstrate that the full secretome is capable of promoting stem cell proliferation, migration, and protection of cells against senescence. Furthermore, it has significant anti-inflammatory properties. Most importantly, we show that it promotes tissue regeneration in a model of muscle damage. We then demonstrate that the secretome contains extracellular vesicles (EVs) that harbor much, but not all, of the biological activity of the whole secretome. Proteomic characterization of the EV and free secretome fraction shows the presence of numerous molecules specific to each fraction that could be key regulators of tissue regeneration. Intriguingly, we show that the EVs only contain miRNA and not mRNA. This suggests that tissue regeneration in the host is mediated by the action of EVs modifying existing, rather than imposing new, signaling pathways. The EVs harbor significant anti-inflammatory activity as well as promote angiogenesis, the latter may be the mechanistic explanation for their ability to promote muscle regeneration after cardiotoxin injury.
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Affiliation(s)
- Ben Mellows
- 1 School of Biological Sciences, University of Reading , Reading, United Kingdom
| | - Robert Mitchell
- 1 School of Biological Sciences, University of Reading , Reading, United Kingdom
| | - Manuela Antonioli
- 2 Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases IRCCS 'Lazzaro Spallanzani' , Rome, Italy
| | - Oliver Kretz
- 3 Department of Medicine III, Faculty of Medicine, University Medical Center Hamburg-Eppendorf , Hamburg, Germany .,4 Renal Division, Faculty of Medicine, Medical Centre, University of Freiburg , Freiburg, Germany .,5 Department of Medicine IV, Faculty of Medicine, University of Freiburg , Freiburg, Germany
| | - David Chambers
- 6 Wolfson Centre for Age-Related Diseases, King's College , London, United Kingdom
| | | | - Bernd Denecke
- 8 Interdisciplinary Centre for Clinical Research Aachen, RWTH Aachen University , Aachen, Germany
| | - Luca Musante
- 9 Centre for Bioanalytical Sciences (CBAS), Dublin City University , Dublin, Ireland
| | - Durrgah L Ramachandra
- 10 Stem Cells and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health , London, United Kingdom
| | | | - Harry Holthofer
- 9 Centre for Bioanalytical Sciences (CBAS), Dublin City University , Dublin, Ireland .,12 FRIAS Freiburg Institute for Advanced Studies, University of Freiburg , Freiburg, Germany
| | - Barbara Joch
- 5 Department of Medicine IV, Faculty of Medicine, University of Freiburg , Freiburg, Germany
| | - Steve Ray
- 13 Micregen, Biohub, Cheshire, United Kingdom
| | - Darius Widera
- 7 School of Pharmacy, University of Reading , Reading, United Kingdom
| | - Anna L David
- 14 Institute for Women's Health, University College London , London, United Kingdom .,15 NIHR University College London Hospitals Biomedical Research Centre , London, United Kingdom
| | - Tobias B Huber
- 3 Department of Medicine III, Faculty of Medicine, University Medical Center Hamburg-Eppendorf , Hamburg, Germany .,4 Renal Division, Faculty of Medicine, Medical Centre, University of Freiburg , Freiburg, Germany .,12 FRIAS Freiburg Institute for Advanced Studies, University of Freiburg , Freiburg, Germany .,16 BIOSS Centre for Biological Signalling Studies and Centre for Systems Biology (ZBSA), Albert-Ludwigs University , Freiburg, Germany
| | - Joern Dengjel
- 12 FRIAS Freiburg Institute for Advanced Studies, University of Freiburg , Freiburg, Germany .,17 Department of Biology, University of Fribourg , Fribourg, Switzerland
| | - Paolo De Coppi
- 10 Stem Cells and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health , London, United Kingdom
| | - Ketan Patel
- 1 School of Biological Sciences, University of Reading , Reading, United Kingdom .,12 FRIAS Freiburg Institute for Advanced Studies, University of Freiburg , Freiburg, Germany
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4809
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Korbakis D, Soosaipillai A, Diamandis EP. Study of kallikrein-related peptidase 6 (KLK6) and its complex with α1-antitrypsin in biological fluids. Clin Chem Lab Med 2017; 55:1385-1396. [PMID: 28672746 DOI: 10.1515/cclm-2017-0017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/27/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Human kallikrein-related peptidase 6 (KLK6) is a member of the kallikrein family of serine proteases. KLK6 is synthesized as a preproenzyme, mainly in tissues of the central nervous system (CNS), and secreted as an inactive precursor. Serum KLK6 is a biomarker of unfavorable prognosis for ovarian cancer, but its sensitivity for early detection is relatively low. Differential glycosylation of KLK6 has been identified in ascites fluid obtained from ovarian cancer patients, suggesting the presence of unique KLK6 isoforms in biological samples. METHODS In the present study, we applied a two-step enrichment approach for KLK6 in ovarian cancer ascites, followed by mice immunization and production of monoclonal antibodies. Immunoaffinity techniques coupled to mass spectrometric methods were employed for hybridoma screening and target antigen identification. RESULTS We found that the main target of the newly-generated monoclonal antibodies target was the serine protease inhibitor α1-antitrypsin (A1AT). Additional experiments confirmed that A1AT is the main inhibitor of KLK6 in biological fluids. One new antibody (24ED138) was chosen to build a hybrid assay for the accurate quantification of the A1AT-KLK6 complex in biological samples. The aforementioned assay was evaluated with serum samples collected from patients with ovarian cancer (n=24) and normal donors (n=16) and showed slight improvement in sensitivity (~12%) compared to the standard in-house KLK6 assay. CONCLUSIONS We conclude that KLK6 is present in biological fluids either as free form, or bound to A1AT, and the bound form performs better than total KLK6 as a biomarker of ovarian carcinoma.
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4810
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Dietrich L, Rathmer B, Ewan K, Bange T, Heinrichs S, Dale TC, Schade D, Grossmann TN. Cell Permeable Stapled Peptide Inhibitor of Wnt Signaling that Targets β-Catenin Protein-Protein Interactions. Cell Chem Biol 2017; 24:958-968.e5. [PMID: 28757184 DOI: 10.1016/j.chembiol.2017.06.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/31/2017] [Accepted: 06/27/2017] [Indexed: 12/30/2022]
Abstract
The Wnt signaling pathway plays a critical role in cell proliferation and differentiation, thus it is often associated with diseases such as cancers. Unfortunately, although attractive, developing anti-cancer strategy targeting Wnt signaling has been challenging given that the most attractive targets are involved in protein-protein interactions (PPIs). Here, we develop a stapled peptide inhibitor that targets the interaction between β-catenin and T cell factor/lymphoid enhancer-binding factor transcription factors, which are crucially involved in Wnt signaling. Our integrative approach combines peptide stapling to optimize proteolytic stability, with lessons learned from cell-penetrating peptide (CPP) design to maximize cellular uptake resulting in NLS-StAx-h, a selective, cell permeable, stapled peptide inhibitor of oncogenic Wnt signaling that efficiently inhibits β-catenin-transcription factor interactions. We expect that this type of integrative strategy that endows stapled peptides with CPP features will be generally useful for developing inhibitors of intracellular PPIs.
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Affiliation(s)
- Laura Dietrich
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany; Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Bernd Rathmer
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Kenneth Ewan
- School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK
| | - Tanja Bange
- Department of Mechanistic Cell Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Stefan Heinrichs
- Institute for Transfusion Medicine, University Hospital Essen, 45147 Essen, Germany
| | - Trevor C Dale
- School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK
| | - Dennis Schade
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany; Institute of Pharmacy, Department of Pharmaceutical & Medicinal Chemistry, University of Greifswald, 17489 Greifswald, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany; Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, the Netherlands.
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4811
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Chan PHW, Lee L, Kim E, Hui T, Stoynov N, Nassar R, Moksa M, Cameron DM, Hirst M, Gsponer J, Mayor T. The [PSI +] yeast prion does not wildly affect proteome composition whereas selective pressure exerted on [PSI +] cells can promote aneuploidy. Sci Rep 2017; 7:8442. [PMID: 28814753 PMCID: PMC5559586 DOI: 10.1038/s41598-017-07999-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 07/07/2017] [Indexed: 11/09/2022] Open
Abstract
The yeast Sup35 protein is a subunit of the translation termination factor, and its conversion to the [PSI +] prion state leads to more translational read-through. Although extensive studies have been done on [PSI +], changes at the proteomic level have not been performed exhaustively. We therefore used a SILAC-based quantitative mass spectrometry approach and identified 4187 proteins from both [psi -] and [PSI +] strains. Surprisingly, there was very little difference between the two proteomes under standard growth conditions. We found however that several [PSI +] strains harbored an additional chromosome, such as chromosome I. Albeit, we found no evidence to support that [PSI +] induces chromosomal instability (CIN). Instead we hypothesized that the selective pressure applied during the establishment of [PSI +]-containing strains could lead to a supernumerary chromosome due to the presence of the ade1-14 selective marker for translational read-through. We therefore verified that there was no prevalence of disomy among newly generated [PSI +] strains in absence of strong selection pressure. We also noticed that low amounts of adenine in media could lead to higher levels of mitochondrial DNA in [PSI +] in ade1-14 cells. Our study has important significance for the establishment and manipulation of yeast strains with the Sup35 prion.
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Affiliation(s)
- Patrick H W Chan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Lisa Lee
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Erin Kim
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Tony Hui
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Nikolay Stoynov
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Roy Nassar
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Michelle Moksa
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Dale M Cameron
- Department of Biology, Ursinus College, Pennsylvania, USA
| | - Martin Hirst
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Joerg Gsponer
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada. .,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
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4812
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Reid SE, Kay EJ, Neilson LJ, Henze AT, Serneels J, McGhee EJ, Dhayade S, Nixon C, Mackey JB, Santi A, Swaminathan K, Athineos D, Papalazarou V, Patella F, Román-Fernández Á, ElMaghloob Y, Hernandez-Fernaud JR, Adams RH, Ismail S, Bryant DM, Salmeron-Sanchez M, Machesky LM, Carlin LM, Blyth K, Mazzone M, Zanivan S. Tumor matrix stiffness promotes metastatic cancer cell interaction with the endothelium. EMBO J 2017; 36:2373-2389. [PMID: 28694244 PMCID: PMC5556271 DOI: 10.15252/embj.201694912] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/08/2017] [Accepted: 06/09/2017] [Indexed: 12/15/2022] Open
Abstract
Tumor progression alters the composition and physical properties of the extracellular matrix. Particularly, increased matrix stiffness has profound effects on tumor growth and metastasis. While endothelial cells are key players in cancer progression, the influence of tumor stiffness on the endothelium and the impact on metastasis is unknown. Through quantitative mass spectrometry, we find that the matricellular protein CCN1/CYR61 is highly regulated by stiffness in endothelial cells. We show that stiffness-induced CCN1 activates β-catenin nuclear translocation and signaling and that this contributes to upregulate N-cadherin levels on the surface of the endothelium, in vitro This facilitates N-cadherin-dependent cancer cell-endothelium interaction. Using intravital imaging, we show that knockout of Ccn1 in endothelial cells inhibits melanoma cancer cell binding to the blood vessels, a critical step in cancer cell transit through the vasculature to metastasize. Targeting stiffness-induced changes in the vasculature, such as CCN1, is therefore a potential yet unappreciated mechanism to impair metastasis.
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Affiliation(s)
| | - Emily J Kay
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Anne-Theres Henze
- Lab of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Jens Serneels
- Lab of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven, Belgium
| | | | | | - Colin Nixon
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - John Bg Mackey
- Cancer Research UK Beatson Institute, Glasgow, UK
- Inflammation, Repair and Development, Imperial College London, London, UK
| | - Alice Santi
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | | | - Vasileios Papalazarou
- Cancer Research UK Beatson Institute, Glasgow, UK
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, UK
| | | | | | | | | | - Ralf H Adams
- Department of Tissue Morphogenesis, Faculty of Medicine, Max-Planck-Institute for Molecular Biomedicine, University of Münster, Münster, Germany
| | | | - David M Bryant
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Manuel Salmeron-Sanchez
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, UK
| | | | - Leo M Carlin
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Massimiliano Mazzone
- Lab of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven, Belgium
- Lab of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sara Zanivan
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
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4813
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Braun DA, Rao J, Mollet G, Schapiro D, Daugeron MC, Tan W, Gribouval O, Boyer O, Revy P, Jobst-Schwan T, Schmidt JM, Lawson JA, Schanze D, Ashraf S, Ullmann JFP, Hoogstraten CA, Boddaert N, Collinet B, Martin G, Liger D, Lovric S, Furlano M, Guerrera IC, Sanchez-Ferras O, Hu JF, Boschat AC, Sanquer S, Menten B, Vergult S, De Rocker N, Airik M, Hermle T, Shril S, Widmeier E, Gee HY, Choi WI, Sadowski CE, Pabst WL, Warejko JK, Daga A, Basta T, Matejas V, Scharmann K, Kienast SD, Behnam B, Beeson B, Begtrup A, Bruce M, Ch'ng GS, Lin SP, Chang JH, Chen CH, Cho MT, Gaffney PM, Gipson PE, Hsu CH, Kari JA, Ke YY, Kiraly-Borri C, Lai WM, Lemyre E, Littlejohn RO, Masri A, Moghtaderi M, Nakamura K, Ozaltin F, Praet M, Prasad C, Prytula A, Roeder ER, Rump P, Schnur RE, Shiihara T, Sinha MD, Soliman NA, Soulami K, Sweetser DA, Tsai WH, Tsai JD, Topaloglu R, Vester U, Viskochil DH, Vatanavicharn N, Waxler JL, Wierenga KJ, Wolf MTF, Wong SN, Leidel SA, Truglio G, Dedon PC, Poduri A, Mane S, Lifton RP, Bouchard M, Kannu P, Chitayat D, Magen D, Callewaert B, van Tilbeurgh H, Zenker M, Antignac C, Hildebrandt F. Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly. Nat Genet 2017; 49:1529-1538. [PMID: 28805828 DOI: 10.1038/ng.3933] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 07/20/2017] [Indexed: 12/19/2022]
Abstract
Galloway-Mowat syndrome (GAMOS) is an autosomal-recessive disease characterized by the combination of early-onset nephrotic syndrome (SRNS) and microcephaly with brain anomalies. Here we identified recessive mutations in OSGEP, TP53RK, TPRKB, and LAGE3, genes encoding the four subunits of the KEOPS complex, in 37 individuals from 32 families with GAMOS. CRISPR-Cas9 knockout in zebrafish and mice recapitulated the human phenotype of primary microcephaly and resulted in early lethality. Knockdown of OSGEP, TP53RK, or TPRKB inhibited cell proliferation, which human mutations did not rescue. Furthermore, knockdown of these genes impaired protein translation, caused endoplasmic reticulum stress, activated DNA-damage-response signaling, and ultimately induced apoptosis. Knockdown of OSGEP or TP53RK induced defects in the actin cytoskeleton and decreased the migration rate of human podocytes, an established intermediate phenotype of SRNS. We thus identified four new monogenic causes of GAMOS, describe a link between KEOPS function and human disease, and delineate potential pathogenic mechanisms.
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Affiliation(s)
- Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jia Rao
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Geraldine Mollet
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - David Schapiro
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marie-Claire Daugeron
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Weizhen Tan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Olivier Gribouval
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Olivia Boyer
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Department of Pediatric Nephrology, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Patrick Revy
- Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,INSERM, U1163, Imagine Institute, Laboratory of Genome Dynamics in the Immune system, Paris, France
| | - Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Johanna Magdalena Schmidt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer A Lawson
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Shazia Ashraf
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeremy F P Ullmann
- Epilepsy Genetics Program and F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte A Hoogstraten
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nathalie Boddaert
- Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,INSERM, U1163, Imagine Institute, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, and INSERM U1000, Paris, France.,Department of Pediatric Radiology, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,Sorbonne Universités UPMC, UFR 927, Sciences de la Vie, Paris, France.,Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie UMR 7590, Sorbonne Universités, UPMC, Université Paris 06, Paris, France
| | - Gaëlle Martin
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Svjetlana Lovric
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Monica Furlano
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Nephrology Department, Fundació Puigvert, IIB Sant Pau, Universitat Autònoma de Barcelona and REDINREN, Barcelona, Spain
| | - I Chiara Guerrera
- Proteomics platform 3P5-Necker, Université Paris Descartes-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Oraly Sanchez-Ferras
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jennifer F Hu
- Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Sylvia Sanquer
- Department of Metabolomic and Proteomic Biochemistry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM UMR-S1124, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Nina De Rocker
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Merlin Airik
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tobias Hermle
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eugen Widmeier
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heon Yung Gee
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Won-Il Choi
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Carolin E Sadowski
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Werner L Pabst
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jillian K Warejko
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ankana Daga
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tamara Basta
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Verena Matejas
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Karin Scharmann
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Sandra D Kienast
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Babak Behnam
- Department of Medical Genetics and Molecular Biology, Iran University of Medical Sciences (IUMS), Tehran, Iran.,Medical Genetics Branch, National Human Genome Research Institute (NHGRI), Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Brendan Beeson
- Department of Diagnostic Imaging, Princess Margaret and King Edward Memorial Hospitals, Perth, Western Australia, Australia
| | | | - Malcolm Bruce
- Department of Diagnostic Imaging, Princess Margaret and King Edward Memorial Hospitals, Perth, Western Australia, Australia
| | - Gaik-Siew Ch'ng
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Shuan-Pei Lin
- Department of Pediatric Genetics, MacKay Children's Hospital, Taipei, Taiwan.,Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
| | - Jui-Hsing Chang
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Chao-Huei Chen
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, Taiwan
| | | | - Patrick M Gaffney
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Patrick E Gipson
- Internal Medicine and Pediatrics Divisions of Adult and Pediatric Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Chyong-Hsin Hsu
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Jameela A Kari
- Pediatric Nephrology Center of Excellence and Pediatric Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yu-Yuan Ke
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Cathy Kiraly-Borri
- Genetic Services of Western Australia, Princess Margaret Hospital for Children and King Edward Memorial Hospital for Women, Subiaco, Western Australia, Australia
| | - Wai-Ming Lai
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Emmanuelle Lemyre
- Service de Génétique Médicale, Département de Pédiatrie, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Rebecca Okashah Littlejohn
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Amira Masri
- Department of Pediatrics, Division of Child Neurology, Faculty of Medicine, University of Jordan, Amman, Jordan
| | - Mastaneh Moghtaderi
- Chronic Kidney Disease Research Center, Tehran University of Medical Science, Tehran, Iran
| | - Kazuyuki Nakamura
- Department of Pediatrics, Yamagata University School of Medicine, Yamagata, Japan
| | - Fatih Ozaltin
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Hacettepe University, Ankara, Turkey.,Nephrogenetics Laboratory, Hacettepe University Faculty of Medicine, Hacettepe University, Ankara, Turkey.,Hacettepe University Center for Biobanking and Genomics, Hacettepe University, Ankara, Turkey
| | - Marleen Praet
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Chitra Prasad
- Department of Genetics, Metabolism and Pediatrics, Western University, London Health Sciences Centre, London, Ontario, Canada
| | | | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Patrick Rump
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Takashi Shiihara
- Department of Pediatrics, Yamagata University School of Medicine, Yamagata, Japan
| | - Manish D Sinha
- Department of Paediatric Nephrology, Kings College London, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology &Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt.,Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Kenza Soulami
- Department of Nephrology, Ibn Rochd University Hospital, Casablanca, Morocco
| | - David A Sweetser
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Wen-Hui Tsai
- Division of Genetics and Metabolism, Department of Pediatrics, Chi Mei Medical Center, Tainan, Taiwan
| | - Jeng-Daw Tsai
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan.,Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan.,Department of Pediatrics, Taipei Medical University Hospital, Taipei, Taiwan.,Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Rezan Topaloglu
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Udo Vester
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - David H Viskochil
- Department of Pediatrics, Division of Medical Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Nithiwat Vatanavicharn
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jessica L Waxler
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Klaas J Wierenga
- Department of Pediatrics, Oklahoma University Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, USA
| | - Matthias T F Wolf
- Division of Pediatric Nephrology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sik-Nin Wong
- Department of Pediatrics and Adolescent Medicine, Tuen Mun Hospital, Tuen Mun, Hong Kong, China
| | - Sebastian A Leidel
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany.,Medical Faculty, University of Muenster, Muenster, Germany
| | - Gessica Truglio
- Epilepsy Genetics Program and F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Singapore-MIT Alliance for Research and Technology, Infectious Disease IRG, Singapore
| | - Annapurna Poduri
- Epilepsy Genetics Program and F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Maxime Bouchard
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Peter Kannu
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Daniella Magen
- Pediatric Nephrology Institute, Rambam Health Care Campus, Haifa, Israel
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Corinne Antignac
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Department of Genetics, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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4814
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Kuljanin M, Brown CFC, Raleigh MJ, Lajoie GA, Flynn LE. Collagenase treatment enhances proteomic coverage of low-abundance proteins in decellularized matrix bioscaffolds. Biomaterials 2017; 144:130-143. [PMID: 28829951 DOI: 10.1016/j.biomaterials.2017.08.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/03/2017] [Accepted: 08/12/2017] [Indexed: 12/12/2022]
Abstract
There is great interest in the application of advanced proteomic techniques to characterize decellularized tissues in order to develop a deeper understanding of the effects of the complex extracellular matrix (ECM) composition on the cellular response to these pro-regenerative bioscaffolds. However, the identification of proteins in ECM-derived bioscaffolds is hindered by the high abundance of collagen in the samples, which can interfere with the detection of lower-abundance constituents that may be important regulators of cell function. To address this limitation, we developed a novel multi-enzyme digestion approach using treatment with a highly-purified collagenase derived from Clostridium Histolyticum to selectively deplete collagen from ECM-derived protein extracts, reducing its relative abundance from up to 90% to below 10%. Moreover, we applied this new method to characterize the proteome of human decellularized adipose tissue (DAT), human decellularized cancellous bone (DCB), and commercially-available bovine tendon collagen (BTC). We successfully demonstrated with all three sources that collagenase treatment increased the depth of detection and enabled the identification of a variety of signaling proteins that were masked by collagen in standard digestion protocols with trypsin/LysC, increasing the number of proteins identified in the DAT by ∼2.2 fold, the DCB by ∼1.3 fold, and the BTC by ∼1.6 fold. In addition, quantitative proteomics using label-free quantification demonstrated that the DAT and DCB extracts were compositionally distinct, and identified a number of adipogenic and osteogenic proteins that were consistently more highly expressed in the DAT and DCB respectively. Overall, we have developed a new processing method that may be applied in advanced mass spectrometry studies to improve the high-throughput proteomic characterization of bioscaffolds derived from mammalian tissues. Further, our study provides new insight into the complex ECM composition of two human decellularized tissues of interest as cell-instructive platforms for regenerative medicine.
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Affiliation(s)
- Miljan Kuljanin
- Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Cody F C Brown
- Department of Anatomy and Cell Biology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Matthew J Raleigh
- Undergraduate Medical Education, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Gilles A Lajoie
- Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada.
| | - Lauren E Flynn
- Department of Anatomy and Cell Biology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada; Department of Chemical and Biochemical Engineering, Thompson Engineering Building, The University of Western Ontario, London, Ontario, N6A 5B9, Canada.
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4815
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Maroto R, Zhao Y, Jamaluddin M, Popov VL, Wang H, Kalubowilage M, Zhang Y, Luisi J, Sun H, Culbertson CT, Bossmann SH, Motamedi M, Brasier AR. Effects of storage temperature on airway exosome integrity for diagnostic and functional analyses. J Extracell Vesicles 2017; 6:1359478. [PMID: 28819550 PMCID: PMC5556670 DOI: 10.1080/20013078.2017.1359478] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 07/16/2017] [Indexed: 11/23/2022] Open
Abstract
Background: Extracellular vesicles contain biological molecules specified by cell-type of origin and modified by microenvironmental changes. To conduct reproducible studies on exosome content and function, storage conditions need to have minimal impact on airway exosome integrity. Aim: We compared surface properties and protein content of airway exosomes that had been freshly isolated vs. those that had been treated with cold storage or freezing. Methods: Mouse bronchoalveolar lavage fluid (BALF) exosomes purified by differential ultracentrifugation were analysed immediately or stored at +4°C or -80°C. Exosomal structure was assessed by dynamic light scattering (DLS), transmission electron microscopy (TEM) and charge density (zeta potential, ζ). Exosomal protein content, including leaking/dissociating proteins, were identified by label-free LC-MS/MS. Results: Freshly isolated BALF exosomes exhibited a mean diameter of 95 nm and characteristic morphology. Storage had significant impact on BALF exosome size and content. Compared to fresh, exosomes stored at +4°C had a 10% increase in diameter, redistribution to polydisperse aggregates and reduced ζ. Storage at -80°C produced an even greater effect, resulting in a 25% increase in diameter, significantly reducing the ζ, resulting in multilamellar structure formation. In fresh exosomes, we identified 1140 high-confidence proteins enriched in 19 genome ontology biological processes. After storage at room temperature, 848 proteins were identified. In preparations stored at +4°C, 224 proteins appeared in the supernatant fraction compared to the wash fractions from freshly prepared exosomes; these proteins represent exosome leakage or dissociation of loosely bound "peri-exosomal" proteins. In preparations stored at -80°C, 194 proteins appeared in the supernatant fraction, suggesting that distinct protein groups leak from exosomes at different storage temperatures. Conclusions: Storage destabilizes the surface characteristics, morphological features and protein content of BALF exosomes. For preservation of the exosome protein content and representative functional analysis, airway exosomes should be analysed immediately after isolation.
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Affiliation(s)
- Rosario Maroto
- Sealy Center for Molecular Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA
- Institute for Translational Sciences, UTMB, Galveston, TX, USA
| | - Yingxin Zhao
- Sealy Center for Molecular Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA
- Institute for Translational Sciences, UTMB, Galveston, TX, USA
- Department of Internal Medicine, UTMB, Galveston, TX, USA
| | - Mohammad Jamaluddin
- Institute for Translational Sciences, UTMB, Galveston, TX, USA
- Department of Internal Medicine, UTMB, Galveston, TX, USA
| | | | - Hongwang Wang
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | | | - Yueqing Zhang
- Department of Internal Medicine, UTMB, Galveston, TX, USA
| | - Jonathan Luisi
- Center for Biomedical Engineering, UTMB, Galveston, TX, USA
| | - Hong Sun
- Department of Internal Medicine, UTMB, Galveston, TX, USA
| | | | | | | | - Allan R. Brasier
- Sealy Center for Molecular Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA
- Institute for Translational Sciences, UTMB, Galveston, TX, USA
- Department of Internal Medicine, UTMB, Galveston, TX, USA
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4816
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Anselm V, Novikova S, Zgoda V. Re-adaption on Earth after Spaceflights Affects the Mouse Liver Proteome. Int J Mol Sci 2017; 18:E1763. [PMID: 28805685 PMCID: PMC5578152 DOI: 10.3390/ijms18081763] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/02/2017] [Accepted: 08/09/2017] [Indexed: 01/26/2023] Open
Abstract
Harsh environmental conditions including microgravity and radiation during prolonged spaceflights are known to alter hepatic metabolism. Our studies have focused on the analysis of possible changes in metabolic pathways in the livers of mice from spaceflight project "Bion-M 1". Mice experienced 30 days of spaceflight with and without an additional re-adaption period of seven days compared to control mice on Earth. To investigate mice livers we have performed proteomic profiling utilizing shotgun mass spectrometry followed by label-free quantification. Proteomic data analysis provided 12,206 unique peptides and 1,086 identified proteins. Label-free quantification using MaxQuant software followed by multiple sample statistical testing (ANOVA) revealed 218 up-regulated and 224 down-regulated proteins in the post-flight compared to the other groups. Proteins related to amino acid metabolism showed higher levels after re-adaption, which may indicate higher rates of gluconeogenesis. Members of the peroxisome proliferator-activated receptor pathway reconstitute their level after seven days based on a decreased level in comparison with the flight group, which indicates diminished liver lipotoxicity. Moreover, bile acid secretion may regenerate on Earth due to reconstitution of related transmembrane proteins and CYP superfamily proteins elevated levels seven days after the spaceflight. Thus, our study demonstrates reconstitution of pharmacological response and decreased liver lipotoxicity within seven days, whereas glucose uptake should be monitored due to alterations in gluconeogenesis.
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Affiliation(s)
- Viktoria Anselm
- Interfaculty Institute of Biochemistry (IFIB), Hoppe-Seyler-Straße 4, Tuebingen 72076.
| | - Svetlana Novikova
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow 119121.
| | - Victor Zgoda
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow 119121.
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4817
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Gedik N, Krüger M, Thielmann M, Kottenberg E, Skyschally A, Frey UH, Cario E, Peters J, Jakob H, Heusch G, Kleinbongard P. Proteomics/phosphoproteomics of left ventricular biopsies from patients with surgical coronary revascularization and pigs with coronary occlusion/reperfusion: remote ischemic preconditioning. Sci Rep 2017; 7:7629. [PMID: 28794502 PMCID: PMC5550488 DOI: 10.1038/s41598-017-07883-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/22/2017] [Indexed: 12/18/2022] Open
Abstract
Remote ischemic preconditioning (RIPC) by repeated brief cycles of limb ischemia/reperfusion reduces myocardial ischemia/reperfusion injury. In left ventricular (LV) biopsies from patients undergoing coronary artery bypass grafting (CABG), only the activation of signal transducer and activator of transcription 5 was associated with RIPC’s cardioprotection. We have now used an unbiased, non-hypothesis-driven proteomics and phosphoproteomics approach to analyze LV biopsies from patients undergoing CABG and from pigs undergoing coronary occlusion/reperfusion without (sham) and with RIPC. False discovery rate-based statistics identified a higher prostaglandin reductase 2 expression at early reperfusion with RIPC than with sham in patients. In pigs, the phosphorylation of 116 proteins was different between baseline and early reperfusion with RIPC and/or with sham. The identified proteins were not identical for patients and pigs, but in-silico pathway analysis of proteins with ≥2-fold higher expression/phosphorylation at early reperfusion with RIPC in comparison to sham revealed a relation to mitochondria and cytoskeleton in both species. Apart from limitations of the proteomics analysis per se, the small cohorts, the sampling/sample processing and the number of uncharacterized/unverifiable porcine proteins may have contributed to this largely unsatisfactory result.
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Affiliation(s)
- Nilgün Gedik
- Institute for Pathophysiology, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Marcus Krüger
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Matthias Thielmann
- Department of Thoracic and Cardiovascular Surgery, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg- Essen, Essen, Germany
| | - Eva Kottenberg
- Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Andreas Skyschally
- Institute for Pathophysiology, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Ulrich H Frey
- Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Elke Cario
- Experimental Gastroenterology, Department of Gastroenterology and Hepatology, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Jürgen Peters
- Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Heinz Jakob
- Department of Thoracic and Cardiovascular Surgery, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg- Essen, Essen, Germany
| | - Gerd Heusch
- Institute for Pathophysiology, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Petra Kleinbongard
- Institute for Pathophysiology, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.
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4818
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Singhal RK, Kruse C, Heidler J, Strecker V, Zwicker K, Düsterwald L, Westermann B, Herrmann JM, Wittig I, Rapaport D. Coi1 is a novel assembly factor of the yeast complex III-complex IV supercomplex. Mol Biol Cell 2017; 28:mbc.E17-02-0093. [PMID: 28794267 PMCID: PMC5620370 DOI: 10.1091/mbc.e17-02-0093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 01/30/2023] Open
Abstract
The yeast bc1 complex (complex III) and cytochrome oxidase (complex IV) are mosaics of core subunits encoded by the mitochondrial genome and additional nuclear-encoded proteins imported from the cytosol. Both complexes build in the mitochondrial inner membrane various supramolecular assemblies. The formation of the individual complexes and their supercomplexes depends on the activity of dedicated assembly factors. We identified a so far uncharacterized mitochondrial protein (open reading frame YDR381C-A) as an important assembly factor for complex III, complex IV, and their supercomplexes. Therefore, we named this protein Cox interacting (Coi) 1. Deletion of COI1 results in decreased respiratory growth, reduced membrane potential, and hampered respiration, as well as slow fermentative growth at low temperature. In addition, coi1Δ cells harbour reduced steady-state levels of subunits of complexes III and IV as well as of the assembled complexes and supercomplexes. Interaction of Coi1 with respiratory chain subunits seems transient, as it appears to be a stoichiometric subunit neither of complex III nor of complex IV. Collectively, this work identifies a novel protein that plays a role in the assembly of the mitochondrial respiratory chain.
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Affiliation(s)
- Ravi K Singhal
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Christine Kruse
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Juliana Heidler
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
| | - Valentina Strecker
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
| | - Klaus Zwicker
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Lea Düsterwald
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | | | | | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
- Cluster of Excellence "Macromolecular Complexes", Goethe University, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
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4819
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Buxton KE, Kennedy-Darling J, Shortreed MR, Zaidan NZ, Olivier M, Scalf M, Sridharan R, Smith LM. Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. J Proteome Res 2017; 16:3433-3442. [PMID: 28704058 DOI: 10.1021/acs.jproteome.7b00448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The centromere is the chromosomal locus where the kinetochore forms and is critical for ensuring proper segregation of sister chromatids during cell division. A substantial amount of effort has been devoted to understanding the characteristic features and roles of the centromere, yet some fundamental aspects of the centromere, such as the complete list of elements that define it, remain obscure. It is well-known that human centromeres include a highly repetitive class of DNA known as alpha satellite, or alphoid, DNA. We present here the first DNA-centric examination of human protein-alpha satellite interactions, employing an approach known as HyCCAPP (hybridization capture of chromatin-associated proteins for proteomics) to identify the protein components of alphoid chromatin in a human cell line. Using HyCCAPP, cross-linked alpha satellite chromatin was isolated from cell lysate, and captured proteins were analyzed via mass spectrometry. After being compared to proteins identified in control pulldown experiments, 90 proteins were identified as enriched at alphoid DNA. This list included many known centromere-binding proteins in addition to multiple novel alpha satellite-binding proteins, such as LRIF1, a heterochromatin-associated protein. The ability of HyCCAPP to reveal both known as well as novel alphoid DNA-interacting proteins highlights the validity and utility of this approach.
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Affiliation(s)
| | | | | | | | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute , San Antonio, Texas 78227, United States
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4820
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Nguyen AT, Prado MA, Schmidt PJ, Sendamarai AK, Wilson-Grady JT, Min M, Campagna DR, Tian G, Shi Y, Dederer V, Kawan M, Kuehnle N, Paulo JA, Yao Y, Weiss MJ, Justice MJ, Gygi SP, Fleming MD, Finley D. UBE2O remodels the proteome during terminal erythroid differentiation. Science 2017; 357:eaan0218. [PMID: 28774900 PMCID: PMC5812729 DOI: 10.1126/science.aan0218] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/08/2017] [Indexed: 12/13/2022]
Abstract
During terminal differentiation, the global protein complement is remodeled, as epitomized by erythrocytes, whose cytosol is ~98% globin. The erythroid proteome undergoes a rapid transition at the reticulocyte stage; however, the mechanisms driving programmed elimination of preexisting cytosolic proteins are unclear. We found that a mutation in the murine Ube2o gene, which encodes a ubiquitin-conjugating enzyme induced during erythropoiesis, results in anemia. Proteomic analysis suggested that UBE2O is a broad-spectrum ubiquitinating enzyme that remodels the erythroid proteome. In particular, ribosome elimination, a hallmark of reticulocyte differentiation, was defective in Ube2o-/- mutants. UBE2O recognized ribosomal proteins and other substrates directly, targeting them to proteasomes for degradation. Thus, in reticulocytes, the induction of ubiquitinating factors may drive the transition from a complex to a simple proteome.
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Affiliation(s)
- Anthony T Nguyen
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Paul J Schmidt
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Anoop K Sendamarai
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | - Mingwei Min
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Dean R Campagna
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Geng Tian
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yuan Shi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Verena Dederer
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mona Kawan
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nathalie Kuehnle
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yu Yao
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Monica J Justice
- Genetics and Genome Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario M5G 0A4, Canada
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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4821
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Pestell TG, Jiao X, Kumar M, Peck AR, Prisco M, Deng S, Li Z, Ertel A, Casimiro MC, Ju X, Di Rocco A, Di Sante G, Katiyar S, Shupp A, Lisanti MP, Jain P, Wu K, Rui H, Hooper DC, Yu Z, Goldman AR, Speicher DW, Laury-Kleintop L, Pestell RG. Stromal cyclin D1 promotes heterotypic immune signaling and breast cancer growth. Oncotarget 2017; 8:81754-81775. [PMID: 29137220 PMCID: PMC5669846 DOI: 10.18632/oncotarget.19953] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/09/2017] [Indexed: 12/28/2022] Open
Abstract
The cyclin D1 gene encodes the regulatory subunit of a holoenzyme that drives cell autonomous cell cycle progression and proliferation. Herein we show cyclin D1 abundance is increased >30-fold in the stromal fibroblasts of patients with invasive breast cancer, associated with poor outcome. Cyclin D1 transformed hTERT human fibroblast to a cancer-associated fibroblast phenotype. Stromal fibroblast expression of cyclin D1 (cyclin D1Stroma) in vivo, enhanced breast epithelial cancer tumor growth, restrained apoptosis, and increased autophagy. Cyclin D1Stroma had profound effects on the breast tumor microenvironment increasing the recruitment of F4/80+ and CD11b+ macrophages and increasing angiogenesis. Cyclin D1Stroma induced secretion of factors that promoted expansion of stem cells (breast stem-like cells, embryonic stem cells and bone marrow derived stem cells). Cyclin D1Stroma resulted in increased secretion of proinflammatory cytokines (CCL2, CCL7, CCL11, CXCL1, CXCL5, CXCL9, CXCL12), CSF (CSF1, GM-CSF1) and osteopontin (OPN) (30-fold). OPN was induced by cyclin D1 in fibroblasts, breast epithelial cells and in the murine transgenic mammary gland and OPN was sufficient to induce stem cell expansion. These results demonstrate that cyclin D1Stroma drives tumor microenvironment heterocellular signaling, promoting several key hallmarks of cancer.
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Affiliation(s)
- Timothy G Pestell
- Departments of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA, USA
| | - Xuanmao Jiao
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, Wynnewood, PA, USA
| | - Mukesh Kumar
- Departments of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA, USA
| | - Amy R Peck
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marco Prisco
- Departments of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA, USA
| | - Shengqiong Deng
- Departments of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA, USA.,Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhiping Li
- Departments of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA, USA
| | - Adam Ertel
- Departments of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA, USA
| | - Mathew C Casimiro
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, Wynnewood, PA, USA
| | - Xiaoming Ju
- Departments of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA, USA
| | - Agnese Di Rocco
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, Wynnewood, PA, USA
| | - Gabriele Di Sante
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, Wynnewood, PA, USA
| | - Sanjay Katiyar
- Departments of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA, USA
| | - Alison Shupp
- Departments of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA, USA
| | - Michael P Lisanti
- Translational Medicine, School of Environment and Life Sciences, Biomedical Research Centre, University of Salford, Salford, Greater Manchester, England, UK
| | - Pooja Jain
- Department of Microbiology and Immunology, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Kongming Wu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Douglas C Hooper
- Department of Microbiology, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA, USA
| | - Zuoren Yu
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, Wynnewood, PA, USA.,Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Aaron R Goldman
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - David W Speicher
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | | | - Richard G Pestell
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, Wynnewood, PA, USA.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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4822
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Tischner D, Grimm M, Kaur H, Staudenraus D, Carvalho J, Looso M, Günther S, Wanke F, Moos S, Siller N, Breuer J, Schwab N, Zipp F, Waisman A, Kurschus FC, Offermanns S, Wettschureck N. Single-cell profiling reveals GPCR heterogeneity and functional patterning during neuroinflammation. JCI Insight 2017; 2:95063. [PMID: 28768912 DOI: 10.1172/jci.insight.95063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/20/2017] [Indexed: 12/31/2022] Open
Abstract
GPCR expression was intensively studied in bulk cDNA of leukocyte populations, but limited data are available with respect to expression in individual cells. Here, we show a microfluidic-based single-cell GPCR expression analysis in primary T cells, myeloid cells, and endothelial cells under naive conditions and during experimental autoimmune encephalomyelitis, the mouse model of multiple sclerosis. We found that neuroinflammation induces characteristic changes in GPCR heterogeneity and patterning, and we identify various functionally relevant subgroups with specific GPCR profiles among spinal cord-infiltrating CD4 T cells, macrophages, microglia, or endothelial cells. Using GPCRs CXCR4, S1P1, and LPHN2 as examples, we show how this information can be used to develop new strategies for the functional modulation of Th17 cells and activated endothelial cells. Taken together, single-cell GPCR expression analysis identifies functionally relevant subpopulations with specific GPCR repertoires and provides a basis for the development of new therapeutic strategies in immune disorders.
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Affiliation(s)
| | | | | | | | | | | | - Stefan Günther
- ECCPS Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | | | | | - Nelly Siller
- Department of Neurology, Focus Program Translational Neuroscience (FTN) and Immunotherapy (FZI), Rhine-Main Neuroscience Network (rmn2, ), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | | | | | - Frauke Zipp
- Department of Neurology, Focus Program Translational Neuroscience (FTN) and Immunotherapy (FZI), Rhine-Main Neuroscience Network (rmn2, ), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | | | | | - Stefan Offermanns
- Department of Pharmacology.,Medical Faculty, J.W. Goethe University Frankfurt, Frankfurt, Germany
| | - Nina Wettschureck
- Department of Pharmacology.,Medical Faculty, J.W. Goethe University Frankfurt, Frankfurt, Germany
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4823
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Lake NJ, Webb BD, Stroud DA, Richman TR, Ruzzenente B, Compton AG, Mountford HS, Pulman J, Zangarelli C, Rio M, Boddaert N, Assouline Z, Sherpa MD, Schadt EE, Houten SM, Byrnes J, McCormick EM, Zolkipli-Cunningham Z, Haude K, Zhang Z, Retterer K, Bai R, Calvo SE, Mootha VK, Christodoulou J, Rötig A, Filipovska A, Cristian I, Falk MJ, Metodiev MD, Thorburn DR. Biallelic Mutations in MRPS34 Lead to Instability of the Small Mitoribosomal Subunit and Leigh Syndrome. Am J Hum Genet 2017; 101:239-254. [PMID: 28777931 DOI: 10.1016/j.ajhg.2017.07.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/09/2017] [Indexed: 12/30/2022] Open
Abstract
The synthesis of all 13 mitochondrial DNA (mtDNA)-encoded protein subunits of the human oxidative phosphorylation (OXPHOS) system is carried out by mitochondrial ribosomes (mitoribosomes). Defects in the stability of mitoribosomal proteins or mitoribosome assembly impair mitochondrial protein translation, causing combined OXPHOS enzyme deficiency and clinical disease. Here we report four autosomal-recessive pathogenic mutations in the gene encoding the small mitoribosomal subunit protein, MRPS34, in six subjects from four unrelated families with Leigh syndrome and combined OXPHOS defects. Whole-exome sequencing was used to independently identify all variants. Two splice-site mutations were identified, including homozygous c.321+1G>T in a subject of Italian ancestry and homozygous c.322-10G>A in affected sibling pairs from two unrelated families of Puerto Rican descent. In addition, compound heterozygous MRPS34 mutations were identified in a proband of French ancestry; a missense (c.37G>A [p.Glu13Lys]) and a nonsense (c.94C>T [p.Gln32∗]) variant. We demonstrated that these mutations reduce MRPS34 protein levels and the synthesis of OXPHOS subunits encoded by mtDNA. Examination of the mitoribosome profile and quantitative proteomics showed that the mitochondrial translation defect was caused by destabilization of the small mitoribosomal subunit and impaired monosome assembly. Lentiviral-mediated expression of wild-type MRPS34 rescued the defect in mitochondrial translation observed in skin fibroblasts from affected subjects, confirming the pathogenicity of MRPS34 mutations. Our data establish that MRPS34 is required for normal function of the mitoribosome in humans and furthermore demonstrate the power of quantitative proteomic analysis to identify signatures of defects in specific cellular pathways in fibroblasts from subjects with inherited disease.
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4824
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Maffioli E, Nonnis S, Angioni R, Santagata F, Calì B, Zanotti L, Negri A, Viola A, Tedeschi G. Proteomic analysis of the secretome of human bone marrow-derived mesenchymal stem cells primed by pro-inflammatory cytokines. J Proteomics 2017; 166:115-126. [DOI: 10.1016/j.jprot.2017.07.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/07/2017] [Accepted: 07/17/2017] [Indexed: 02/07/2023]
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4825
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Despic V, Dejung M, Butter F, Neugebauer KM. Analysis of RNA-protein interactions in vertebrate embryos using UV crosslinking approaches. Methods 2017; 126:44-53. [DOI: 10.1016/j.ymeth.2017.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/15/2017] [Accepted: 07/15/2017] [Indexed: 02/06/2023] Open
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4826
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Cutler AA, Dammer EB, Doung DM, Seyfried NT, Corbett AH, Pavlath GK. Biochemical isolation of myonuclei employed to define changes to the myonuclear proteome that occur with aging. Aging Cell 2017; 16:738-749. [PMID: 28544616 PMCID: PMC5506426 DOI: 10.1111/acel.12604] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
Skeletal muscle aging is accompanied by loss of muscle mass and strength. Examining changes in myonuclear proteins with age would provide insight into molecular processes which regulate these profound changes in muscle physiology. However, muscle tissue is highly adapted for contraction and thus comprised largely of contractile proteins making the nuclear proteins difficult to identify from whole muscle samples. By developing a method to purify myonuclei from whole skeletal muscle, we were able to collect myonuclei for analysis by flow cytometry, biochemistry, and mass spectrometry. Nuclear purification dramatically increased the number and intensity of nuclear proteins detected by mass spectrometry compared to whole tissue. We exploited this increased proteomic depth to investigate age-related changes to the myonuclear proteome. Nuclear levels of 54 of 779 identified proteins (7%) changed significantly with age; these proteins were primarily involved in chromatin maintenance and RNA processing. To determine whether the changes we detected were specific to myonuclei or were common to nuclei of excitatory tissues, we compared aging in myonuclei to aging in brain nuclei. Although several of the same processes were affected by aging in both brain and muscle nuclei, the specific proteins involved in these alterations differed between the two tissues. Isolating myonuclei allowed a deeper view into the myonuclear proteome than previously possible facilitating identification of novel age-related changes in skeletal muscle. Our technique will enable future studies into a heretofore underrepresented compartment of skeletal muscle.
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Affiliation(s)
- Alicia A. Cutler
- Department of Pharmacology; Emory University; Atlanta GA 30322 USA
- Graduate Program in Biochemistry, Cell and Developmental Biology; Emory University; Atlanta GA 30322 USA
| | - Eric B. Dammer
- Department of Biochemistry; Emory University; Atlanta GA 30322 USA
| | - Duc M. Doung
- Department of Biochemistry; Emory University; Atlanta GA 30322 USA
| | | | | | - Grace K. Pavlath
- Department of Pharmacology; Emory University; Atlanta GA 30322 USA
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4827
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Jensen SR, Schoof EM, Wheeler SE, Hvid H, Ahnfelt-Rønne J, Hansen BF, Nishimura E, Olsen GS, Kislinger T, Brubaker PL. Quantitative Proteomics of Intestinal Mucosa From Male Mice Lacking Intestinal Epithelial Insulin Receptors. Endocrinology 2017; 158:2470-2485. [PMID: 28591806 DOI: 10.1210/en.2017-00194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/31/2017] [Indexed: 12/16/2022]
Abstract
The goal of the present study was to determine whether loss of the insulin receptor alters the molecular landscape of the intestinal mucosa, using intestinal-epithelial insulin receptor knockout (IE-irKO) mice and both genetic (IRfl/fl and Villin-cre) controls. Quantitative proteomic analysis by liquid chromatography mass spectrometry was applied to jejunal and colonic mucosa from mice fed a normal chow diet and mice fed a Western diet (WD). Jejunal mucosa from IE-irKO mice demonstrated alterations in all intestinal cell lineages: Paneth, goblet, absorptive, and enteroendocrine cells. Only goblet and absorptive cells were affected in the colon. Also, a marked effect of WD consumption was found on the gut proteome. A substantial reduction was detected in Paneth cell proteins with antimicrobial activity, including lysozyme C-1, angiogenin-4, cryptdin-related sequence 1C-3 and -2, α-defensin 17, and intelectin-1a. The key protein expressed by goblet cells, mucin-2, was also reduced in the IE-irKO mice. Proteins involved in lipid metabolism, including aldose reductase-related protein 1, 15-hydroxyprostaglandin dehydrogenase, apolipoprotein A-II, and pyruvate dehydrogenase kinase isozyme 4, were increased in the mucosa of WD-fed IE-irKO mice compared with controls. In contrast, expression of the nutrient-responsive gut hormones, glucose-dependent insulinotropic polypeptide and neurotensin, was reduced in the jejunal mucosa of IE-irKO mice, and the expression of proteins of the P-type adenosine triphosphatases and the solute carrier-transporter family was reduced in the colon of WD-fed IE-irKO mice. In conclusion, IE-irKO mice display a distinct molecular phenotype, suggesting a biological role of insulin and its receptor in determining differentiated cell specificity in the intestinal epithelium.
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Affiliation(s)
- Stina Rikke Jensen
- Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Metabolic Disease Research, Novo Nordisk A/S, Måløv DK-2760, Denmark
| | - Erwin M Schoof
- Princess Margaret Hospital Cancer Centre, University Health Network, Ontario M5G 2M9, Canada
| | - Sarah E Wheeler
- Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Henning Hvid
- Metabolic Disease Research, Novo Nordisk A/S, Måløv DK-2760, Denmark
| | | | - Bo Falck Hansen
- Metabolic Disease Research, Novo Nordisk A/S, Måløv DK-2760, Denmark
| | - Erica Nishimura
- Metabolic Disease Research, Novo Nordisk A/S, Måløv DK-2760, Denmark
| | | | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Patricia L Brubaker
- Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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4828
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Sampaziotis F, Justin AW, Tysoe OC, Sawiak S, Godfrey EM, Upponi SS, Gieseck RL, de Brito MC, Berntsen NL, Gómez-Vázquez MJ, Ortmann D, Yiangou L, Ross A, Bargehr J, Bertero A, Zonneveld MCF, Pedersen MT, Pawlowski M, Valestrand L, Madrigal P, Georgakopoulos N, Pirmadjid N, Skeldon GM, Casey J, Shu W, Materek PM, Snijders KE, Brown SE, Rimland CA, Simonic I, Davies SE, Jensen KB, Zilbauer M, Gelson WTH, Alexander GJ, Sinha S, Hannan NRF, Wynn TA, Karlsen TH, Melum E, Markaki AE, Saeb-Parsy K, Vallier L. Reconstruction of the mouse extrahepatic biliary tree using primary human extrahepatic cholangiocyte organoids. Nat Med 2017; 23:954-963. [PMID: 28671689 DOI: 10.1038/nm.4360] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 05/24/2017] [Indexed: 02/02/2023]
Abstract
The treatment of common bile duct (CBD) disorders, such as biliary atresia or ischemic strictures, is restricted by the lack of biliary tissue from healthy donors suitable for surgical reconstruction. Here we report a new method for the isolation and propagation of human cholangiocytes from the extrahepatic biliary tree in the form of extrahepatic cholangiocyte organoids (ECOs) for regenerative medicine applications. The resulting ECOs closely resemble primary cholangiocytes in terms of their transcriptomic profile and functional properties. We explore the regenerative potential of these organoids in vivo and demonstrate that ECOs self-organize into bile duct-like tubes expressing biliary markers following transplantation under the kidney capsule of immunocompromised mice. In addition, when seeded on biodegradable scaffolds, ECOs form tissue-like structures retaining biliary characteristics. The resulting bioengineered tissue can reconstruct the gallbladder wall and repair the biliary epithelium following transplantation into a mouse model of injury. Furthermore, bioengineered artificial ducts can replace the native CBD, with no evidence of cholestasis or occlusion of the lumen. In conclusion, ECOs can successfully reconstruct the biliary tree, providing proof of principle for organ regeneration using human primary cholangiocytes expanded in vitro.
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Affiliation(s)
- Fotios Sampaziotis
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.,Department of Hepatology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Olivia C Tysoe
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Stephen Sawiak
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Edmund M Godfrey
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sara S Upponi
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Richard L Gieseck
- Immunopathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Miguel Cardoso de Brito
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Natalie Lie Berntsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - María J Gómez-Vázquez
- Cambridge Genomic Services, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Daniel Ortmann
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Loukia Yiangou
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK.,Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Alexander Ross
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,University Department of Paediatrics, University of Cambridge, Cambridge, UK.,Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Johannes Bargehr
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK.,Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK.,Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Alessandro Bertero
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Mariëlle C F Zonneveld
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK
| | - Marianne T Pedersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Matthias Pawlowski
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK
| | - Laura Valestrand
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Pedro Madrigal
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | - Nikitas Georgakopoulos
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Negar Pirmadjid
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Gregor M Skeldon
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, UK.,Department of Biomedical Engineering, University of Strathclyde, Glasgow, UK
| | - John Casey
- Department of Surgery, University of Edinburgh, Edinburgh Royal Infirmary, Edinburgh, UK
| | - Wenmiao Shu
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, UK.,Department of Biomedical Engineering, University of Strathclyde, Glasgow, UK
| | - Paulina M Materek
- NIHR Cambridge Biomedical Centre (BRC) hIPSCs Core Facility, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Kirsten E Snijders
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK
| | - Stephanie E Brown
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Casey A Rimland
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.,Immunopathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA.,University of North Carolina, Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | - Ingrid Simonic
- Medical Genetics Laboratories, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Susan E Davies
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Kim B Jensen
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthias Zilbauer
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - William T H Gelson
- Department of Hepatology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Graeme J Alexander
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK.,Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Sanjay Sinha
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,University Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Nicholas R F Hannan
- Center for Biomolecular Sciences, University of Nottingham, Nottingham, UK.,Nottingham Digestive Diseases Centre, NIHR Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Thomas A Wynn
- Immunopathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Espen Melum
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Athina E Markaki
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Ludovic Vallier
- Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
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4829
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Khan MM, Tran BQ, Jang YJ, Park SH, Fondrie WE, Chowdhury K, Yoon SH, Goodlett DR, Chae SW, Chae HJ, Seo SY, Goo YA. Assessment of the Therapeutic Potential of Persimmon Leaf Extract on Prediabetic Subjects. Mol Cells 2017; 40:466-475. [PMID: 28681595 PMCID: PMC5547216 DOI: 10.14348/molcells.2017.2298] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 12/12/2022] Open
Abstract
Dietary supplements have exhibited myriads of positive health effects on human health conditions and with the advent of new technological advances, including in the fields of proteomics, genomics, and metabolomics, biological and pharmacological activities of dietary supplements are being evaluated for their ameliorative effects in human ailments. Recent interests in understanding and discovering the molecular targets of phytochemical-gene-protein-metabolite dynamics resulted in discovery of a few protein signature candidates that could potentially be used to assess the effects of dietary supplements on human health. Persimmon (Diospyros kaki) is a folk medicine, commonly used as dietary supplement in China, Japan, and South Korea, owing to its different beneficial health effects including anti-diabetic implications. However, neither mechanism of action nor molecular biomarkers have been discovered that could either validate or be used to evaluate effects of persimmon on human health. In present study, Mass Spectrometry (MS)-based proteomic studies were accomplished to discover proteomic molecular signatures that could be used to understand therapeutic potentials of persimmon leaf extract (PLE) in diabetes amelioration. Saliva, serum, and urine samples were analyzed and we propose that salivary proteins can be used for evaluating treatment effectiveness and in improving patient compliance. The present discovery proteomics study demonstrates that salivary proteomic profile changes were found as a result of PLE treatment in prediabetic subjects that could specifically be used as potential protein signature candidates.
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Affiliation(s)
- Mohd M. Khan
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201,
USA
- Present address: University of Maryland School of Medicine, Baltimore, MD 21201,
USA
| | - Bao Quoc Tran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201,
USA
| | - Yoon-Jin Jang
- Department of Pharmacology, Chonbuk National University Medical School, Jeonju 54907,
Korea
| | - Soo-Hyun Park
- Clinical Trial Center for Functional Foods, Chonbuk National University Hospital, Jeonju 54907,
Korea
| | | | | | - Sung Hwan Yoon
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201,
USA
| | - David R. Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201,
USA
| | - Soo-Wan Chae
- Department of Pharmacology, Chonbuk National University Medical School, Jeonju 54907,
Korea
- Clinical Trial Center for Functional Foods, Chonbuk National University Hospital, Jeonju 54907,
Korea
| | - Han-Jung Chae
- Department of Pharmacology, Chonbuk National University Medical School, Jeonju 54907,
Korea
| | - Seung-Young Seo
- Department of Internal Medicine, Research Institute of Clinical Medicine, Chonbuk National University Medical School and Hospital, Jeonju 54907,
Korea
| | - Young Ah Goo
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201,
USA
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4830
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Strehmel N, Hoehenwarter W, Mönchgesang S, Majovsky P, Krüger S, Scheel D, Lee J. Stress-Related Mitogen-Activated Protein Kinases Stimulate the Accumulation of Small Molecules and Proteins in Arabidopsis thaliana Root Exudates. FRONTIERS IN PLANT SCIENCE 2017; 8:1292. [PMID: 28785276 PMCID: PMC5520323 DOI: 10.3389/fpls.2017.01292] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/07/2017] [Indexed: 05/18/2023]
Abstract
A delicate balance in cellular signaling is required for plants to respond to microorganisms or to changes in their environment. Mitogen-activated protein kinase (MAPK) cascades are one of the signaling modules that mediate transduction of extracellular microbial signals into appropriate cellular responses. Here, we employ a transgenic system that simulates activation of two pathogen/stress-responsive MAPKs to study release of metabolites and proteins into root exudates. The premise is based on our previous proteomics study that suggests upregulation of secretory processes in this transgenic system. An advantage of this experimental set-up is the direct focus on MAPK-regulated processes without the confounding complications of other signaling pathways activated by exposure to microbes or microbial molecules. Using non-targeted metabolomics and proteomics studies, we show that MAPK activation can indeed drive the appearance of dipeptides, defense-related metabolites and proteins in root apoplastic fluid. However, the relative levels of other compounds in the exudates were decreased. This points to a bidirectional control of metabolite and protein release into the apoplast. The putative roles for some of the identified apoplastic metabolites and proteins are discussed with respect to possible antimicrobial/defense or allelopathic properties. Overall, our findings demonstrate that sustained activation of MAPKs alters the composition of apoplastic root metabolites and proteins, presumably to influence the plant-microbe interactions in the rhizosphere. The reported metabolomics and proteomics data are available via Metabolights (Identifier: MTBLS441) and ProteomeXchange (Identifier: PXD006328), respectively.
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Affiliation(s)
- Nadine Strehmel
- Department of Stress and Developmental Biology, Leibniz Institute of Plant BiochemistryHalle, Germany
| | - Wolfgang Hoehenwarter
- Research Group Proteome Analytics, Leibniz Institute of Plant BiochemistryHalle, Germany
| | - Susann Mönchgesang
- Department of Stress and Developmental Biology, Leibniz Institute of Plant BiochemistryHalle, Germany
| | - Petra Majovsky
- Research Group Proteome Analytics, Leibniz Institute of Plant BiochemistryHalle, Germany
| | - Sylvia Krüger
- Department of Stress and Developmental Biology, Leibniz Institute of Plant BiochemistryHalle, Germany
| | - Dierk Scheel
- Department of Stress and Developmental Biology, Leibniz Institute of Plant BiochemistryHalle, Germany
| | - Justin Lee
- Department of Stress and Developmental Biology, Leibniz Institute of Plant BiochemistryHalle, Germany
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4831
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Zhang Y, Sun H, Zhang J, Brasier AR, Zhao Y. Quantitative Assessment of the Effects of Trypsin Digestion Methods on Affinity Purification-Mass Spectrometry-based Protein-Protein Interaction Analysis. J Proteome Res 2017; 16:3068-3082. [PMID: 28726418 DOI: 10.1021/acs.jproteome.7b00432] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Affinity purification-mass spectrometry (AP-MS) has become the method of choice for discovering protein-protein interactions (PPIs) under native conditions. The success of AP-MS depends on the efficiency of trypsin digestion and the recovery of the tryptic peptides for MS analysis. Several different protocols have been used for trypsin digestion of protein complexes in AP-MS studies, but no systematic studies have been conducted on the impact of trypsin digestion conditions on the identification of PPIs. Here, we used NFκB/RelA and Bromodomain-containing protein 4 (BRD4) as baits and test five distinct trypsin digestion methods (two using "on-beads," three using "elution-digestion" protocols). Although the performance of the trypsin digestion protocols change slightly depending on the different baits, antibodies and cell lines used, we found that elution-digestion methods consistently outperformed on-beads digestion methods. The high-abundance interactors can be identified universally by all five methods, but the identification of low-abundance RelA interactors is significantly affected by the choice of trypsin digestion method. We also found that different digestion protocols influence the selected reaction monitoring (SRM)-MS quantification of PPIs, suggesting that optimization of trypsin digestion conditions may be required for robust targeted analysis of PPIs.
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Affiliation(s)
- Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Hong Sun
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Jing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States.,Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States.,Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
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4832
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Rinschen MM, Hoppe AK, Grahammer F, Kann M, Völker LA, Schurek EM, Binz J, Höhne M, Demir F, Malisic M, Huber TB, Kurschat C, Kizhakkedathu JN, Schermer B, Huesgen PF, Benzing T. N-Degradomic Analysis Reveals a Proteolytic Network Processing the Podocyte Cytoskeleton. J Am Soc Nephrol 2017; 28:2867-2878. [PMID: 28724775 DOI: 10.1681/asn.2016101119] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 05/08/2017] [Indexed: 11/03/2022] Open
Abstract
Regulated intracellular proteostasis, controlled in part by proteolysis, is essential in maintaining the integrity of podocytes and the glomerular filtration barrier of the kidney. We applied a novel proteomics technology that enables proteome-wide identification, mapping, and quantification of protein N-termini to comprehensively characterize cleaved podocyte proteins in the glomerulus in vivo We found evidence that defined proteolytic cleavage results in various proteoforms of important podocyte proteins, including those of podocin, nephrin, neph1, α-actinin-4, and vimentin. Quantitative mapping of N-termini demonstrated perturbation of protease action during podocyte injury in vitro, including diminished proteolysis of α-actinin-4. Differentially regulated protease substrates comprised cytoskeletal proteins as well as intermediate filaments. Determination of preferential protease motifs during podocyte damage indicated activation of caspase proteases and inhibition of arginine-specific proteases. Several proteolytic processes were clearly site-specific, were conserved across species, and could be confirmed by differential migration behavior of protein fragments in gel electrophoresis. Some of the proteolytic changes discovered in vitro also occurred in two in vivo models of podocyte damage (WT1 heterozygous knockout mice and puromycin aminonucleoside-treated rats). Thus, we provide direct and systems-level evidence that the slit diaphragm and podocyte cytoskeleton are regulated targets of proteolytic modification, which is altered upon podocyte damage.
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC).,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Ann-Kathrin Hoppe
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Florian Grahammer
- Department of Medicine III, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Medicine IV, Medical Center and Faculty of Medicine - University of Freiburg, Freiburg, Germany
| | - Martin Kann
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Linus A Völker
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Eva-Maria Schurek
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Julie Binz
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Martin Höhne
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC).,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Milena Malisic
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Tobias B Huber
- Department of Medicine III, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Medicine IV, Medical Center and Faculty of Medicine - University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies and Center for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University, Freiburg, Germany; and
| | - Christine Kurschat
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, Department of Pathology and Laboratory Medicine, Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Bernhard Schermer
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC).,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany;
| | - Thomas Benzing
- Department II of Internal Medicine, .,Center for Molecular Medicine Cologne (CMMC).,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
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4833
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Zhao Y, Zhang Y, Sun H, Maroto R, Brasier AR. Selective Affinity Enrichment of Nitrotyrosine-Containing Peptides for Quantitative Analysis in Complex Samples. J Proteome Res 2017; 16:2983-2992. [PMID: 28714690 DOI: 10.1021/acs.jproteome.7b00275] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein tyrosine nitration by oxidative and nitrate stress is important in the pathogenesis of many inflammatory or aging-related diseases. Mass spectrometry analysis of protein nitrotyrosine is very challenging because the non-nitrated peptides suppress the signals of the low-abundance nitrotyrosine (NT) peptides. No validated methods for enrichment of NT-peptides are currently available. Here we report an immunoaffinity enrichment of NT-peptides for proteomics analysis. The effectiveness of this approach was evaluated using nitrated protein standards and whole-cell lysates in vitro. A total of 1881 NT sites were identified from a nitrated whole-cell extract, indicating that this immunoaffinity-MS method is a valid approach for the enrichment of NT-peptides, and provides a significant advance for characterizing the nitrotyrosine proteome. We noted that this method had higher affinity to peptides with N-terminal nitrotyrosine relative to peptides with other nitrotyrosine locations, which raises the need for future study to develop a pan-specific nitrotyrosine antibody for unbiased, proteome-wide analysis of tyrosine nitration. We applied this method to quantify the changes in protein tyrosine nitration in mouse lungs after intranasal poly(I:C) treatment and quantified 237 NT sites. This result indicates that the immunoaffinity-MS method can be used for quantitative analysis of protein nitrotyrosines in complex samples.
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Affiliation(s)
- Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States.,Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
| | - Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Hong Sun
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Rosario Maroto
- Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States.,Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
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4834
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Kohli P, Höhne M, Jüngst C, Bertsch S, Ebert LK, Schauss AC, Benzing T, Rinschen MM, Schermer B. The ciliary membrane-associated proteome reveals actin-binding proteins as key components of cilia. EMBO Rep 2017; 18:1521-1535. [PMID: 28710093 DOI: 10.15252/embr.201643846] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 06/06/2017] [Accepted: 06/13/2017] [Indexed: 01/01/2023] Open
Abstract
Primary cilia are sensory, antennae-like organelles present on the surface of many cell types. They have been involved in a variety of diseases collectively termed ciliopathies. As cilia are essential regulators of cell signaling, the composition of the ciliary membrane needs to be strictly regulated. To understand regulatory processes at the ciliary membrane, we report the targeting of a genetically engineered enzyme specifically to the ciliary membrane to allow biotinylation and identification of the membrane-associated proteome. Bioinformatic analysis of the comprehensive dataset reveals high-stoichiometric presence of actin-binding proteins inside the cilium. Immunofluorescence stainings and complementary interaction proteomic analyses confirm these findings. Depolymerization of branched F-actin causes further enrichment of the actin-binding and actin-related proteins in cilia, including Myosin 5a (Myo5a). Interestingly, Myo5a knockout decreases ciliation while enhanced levels of Myo5a are observed in cilia upon induction of ciliary disassembly. In summary, we present a novel approach to investigate dynamics of the ciliary membrane proteome in mammalian cells and identify actin-binding proteins as mechanosensitive components of cilia that might have important functions in cilia membrane dynamics.
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Affiliation(s)
- Priyanka Kohli
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Christian Jüngst
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sabine Bertsch
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Lena K Ebert
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Astrid C Schauss
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Markus M Rinschen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany .,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
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4835
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Sap KA, Bezstarosti K, Dekkers DHW, Voets O, Demmers JAA. Quantitative Proteomics Reveals Extensive Changes in the Ubiquitinome after Perturbation of the Proteasome by Targeted dsRNA-Mediated Subunit Knockdown in Drosophila. J Proteome Res 2017; 16:2848-2862. [DOI: 10.1021/acs.jproteome.7b00156] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Karen A. Sap
- Proteomics
Center, ‡Netherlands Proteomics Center, and §Department of Biochemistry, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics
Center, ‡Netherlands Proteomics Center, and §Department of Biochemistry, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Dick H. W. Dekkers
- Proteomics
Center, ‡Netherlands Proteomics Center, and §Department of Biochemistry, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Olaf Voets
- Proteomics
Center, ‡Netherlands Proteomics Center, and §Department of Biochemistry, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Jeroen A. A. Demmers
- Proteomics
Center, ‡Netherlands Proteomics Center, and §Department of Biochemistry, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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4836
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Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith LM. Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins. Anal Chem 2017; 89:7841-7846. [PMID: 28654248 DOI: 10.1021/acs.analchem.7b01784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Comprehensive understanding of a gene's expression and regulation at the molecular level requires identification of all proteins interacting with the gene. HyCCAPP (Hybridization Capture of Chromatin Associated Proteins for Proteomics) is an approach that uses single-stranded DNA oligonucleotides to capture specific genomic sequences in cross-linked chromatin fragments and identify associated proteins by mass spectrometry. Previous studies have shown HyCCAPP to provide useful information on protein-DNA interactions, revealing the proteins associated with the GAL1-10 region in yeast. We present here a multiplexed version of HyCCAPP. Utilizing a toehold-mediated capture/release strategy, HyCCAPP is targeted to multiple genomic loci in parallel, and the protein binders at each locus are eluted in a programmable and selective fashion. Multiplexed HyCCAPP was applied to four genes (25S rDNA, ARX1, CTT1, and RPL30) in S. cerevisiae under normal and stressed conditions. Capture and release efficiencies and specificities were comparable to those obtained without multiplexing. Using mass spectrometry-based bottom-up proteomics, hundreds of proteins were discovered at each locus in each condition. Statistical analysis revealed 34-88 enriched proteins in each gene capture. Many of these proteins had expected functions, including DNA-related and ribosome biogenesis-associated activities. Multiplexed HyCCAPP provides a useful strategy for the identification of proteins interacting with specific chromatin regions.
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Affiliation(s)
- Yunxiang Dai
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Julia Kennedy-Darling
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin , 425 Henry Mall, Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States.,Genome Center of Wisconsin, University of Wisconsin , 425G Henry Mall, Room 3420, Madison, Wisconsin 53706, United States
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4837
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Noberini R, Longuespée R, Richichi C, Pruneri G, Kriegsmann M, Pelicci G, Bonaldi T. PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples. Clin Epigenetics 2017; 9:69. [PMID: 28702092 PMCID: PMC5504751 DOI: 10.1186/s13148-017-0369-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/28/2017] [Indexed: 12/22/2022] Open
Abstract
Background Aberrations in histone post-translational modifications (hPTMs) have been linked with various pathologies, including cancer, and could not only represent useful biomarkers but also suggest possible targetable epigenetic mechanisms. We have recently developed an approach, termed pathology tissue analysis of histones by mass spectrometry (PAT-H-MS), that allows performing a comprehensive and quantitative analysis of histone PTMs from formalin-fixed paraffin-embedded pathology samples. Despite its great potential, the application of this technique is limited by tissue heterogeneity. Methods In this study, we further implemented the PAT-H-MS approach by coupling it with techniques aimed at reducing sample heterogeneity and selecting specific portions or cell populations within the samples, such as manual macrodissection and laser microdissection (LMD). Results When applied to the analysis of a small set of breast cancer samples, LMD-PAT-H-MS allowed detecting more marked changes between luminal A-like and triple negative patients as compared with the classical approach. These changes included not only the already known H3 K27me3 and K9me3 marks, but also H3 K36me1, which was found increased in triple negative samples and validated on a larger cohort of patients, and could represent a potential novel marker distinguishing breast cancer subtypes. Conclusions These results show the feasibility of applying techniques to reduce sample heterogeneity, including laser microdissection, to the PAT-H-MS protocol, providing new tools in clinical epigenetics and opening new avenues for the comprehensive analysis of histone post-translational modifications in selected cell populations. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0369-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@ SEMM, Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Rémi Longuespée
- Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 224, 69620 Heidelberg, Germany
| | - Cristina Richichi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Giancarlo Pruneri
- Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy.,School of Medicine, University of Milan, 20122 Milan, Italy
| | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 224, 69620 Heidelberg, Germany
| | - Giuliana Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Department of Translational Medicine, Piemonte Orientale University "Amedeo Avogadro", 28100 Novara, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
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4838
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Assessing the impact of protein extraction methods for human gut metaproteomics. J Proteomics 2017; 180:120-127. [PMID: 28705725 DOI: 10.1016/j.jprot.2017.07.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/28/2017] [Accepted: 07/02/2017] [Indexed: 12/26/2022]
Abstract
Metaproteomics is a promising methodology for the functional characterizations of the gut microbiome. However, the performance of metaproteomic analysis is affected by protein extraction protocols in terms of the amount of protein recovered and the relative abundance of different bacteria observed in microbiome. Currently, there is a lack of consistency on protein extraction methods in published metaproteomics studies. Here we evaluated the effects of different protein extraction methods on human fecal metaproteome characterizations. We found that sodium dodecyl sulfate (SDS)-based lysis buffer obtained higher protein yields and peptide/protein group identifications compared to urea and the non-ionic detergent-based B-Per buffer. The addition of bead beating to any of the extraction buffers increased both protein yields and protein identifications. As well, bead beating led to a significant increase of the relative abundances of Firmicutes and Actinobacteria. We also demonstrated that ultrasonication, another commonly used mechanical disruption approach, performed even better than bead beating for gut microbial protein extractions. Importantly, proteins of the basic metabolic pathways showed significantly higher relative abundances when using ultrasonication. Overall, these results demonstrate that protein extraction protocols markedly impact the metaproteomic results and recommend a protein extraction protocol with both SDS and ultrasonication for metaproteomic studies. BIOLOGICAL SIGNIFICANCE The gut microbiome is emerging as an important factor influencing human health. Metaproteomics is promising for advancing the understanding of the functional roles of the microbiome in disease. However, metaproteomics suffers from a lack of consistent sample preparation procedures. In the present study, protein extraction protocols for fecal microbiome samples were evaluated for their effects on protein yields, peptide identifications, protein group identifications, taxonomic compositions and functional category distributions. While different protocols favor different microbial taxa and protein functions, our results suggest that a protein extraction protocol using sodium dodecyl sulfate (SDS) and ultrasonication provides the best performance for general shotgun metaproteomics studies.
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4839
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Garzia A, Jafarnejad SM, Meyer C, Chapat C, Gogakos T, Morozov P, Amiri M, Shapiro M, Molina H, Tuschl T, Sonenberg N. The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs. Nat Commun 2017; 8:16056. [PMID: 28685749 PMCID: PMC5504347 DOI: 10.1038/ncomms16056] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/16/2017] [Indexed: 12/20/2022] Open
Abstract
Cryptic polyadenylation within coding sequences (CDS) triggers ribosome-associated quality control (RQC), followed by degradation of the aberrant mRNA and polypeptide, ribosome disassembly and recycling. Although ribosomal subunit dissociation and nascent peptide degradation are well-understood, the molecular sensors of aberrant mRNAs and their mechanism of action remain unknown. We studied the Zinc Finger Protein 598 (ZNF598) using PAR-CLIP and revealed that it cross-links to tRNAs, mRNAs and rRNAs, thereby placing the protein on translating ribosomes. Cross-linked reads originating from AAA-decoding tRNALys(UUU) were 10-fold enriched over its cellular abundance, and poly-lysine encoded by poly(AAA) induced RQC in a ZNF598-dependent manner. Encounter with translated polyA segments by ZNF598 triggered ubiquitination of several ribosomal proteins, requiring the E2 ubiquitin ligase UBE2D3 to initiate RQC. Considering that human CDS are devoid of >4 consecutive AAA codons, sensing of prematurely placed polyA tails by a specialized RNA-binding protein is a novel nucleic-acid-based surveillance mechanism of RQC. Translation of aberrant mRNAs causes ribosome stalling and translation arrest, followed by recycling of the stalled ribosome complex. Here the authors show that the Zinc Finger Protein 598 (ZNF598/Hel2) is implicated in sensing faulty translation of prematurely polyadenylated mRNAs through the recognition of AAA codons.
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Affiliation(s)
- Aitor Garzia
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, New York 10065, USA
| | - Seyed Mehdi Jafarnejad
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Cindy Meyer
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, New York 10065, USA
| | - Clément Chapat
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Tasos Gogakos
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, New York 10065, USA
| | - Pavel Morozov
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, New York 10065, USA
| | - Mehdi Amiri
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Maayan Shapiro
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, New York 10065, USA
| | - Thomas Tuschl
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, New York 10065, USA
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
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4840
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Bottani E, Cerutti R, Harbour ME, Ravaglia S, Dogan SA, Giordano C, Fearnley IM, D'Amati G, Viscomi C, Fernandez-Vizarra E, Zeviani M. TTC19 Plays a Husbandry Role on UQCRFS1 Turnover in the Biogenesis of Mitochondrial Respiratory Complex III. Mol Cell 2017; 67:96-105.e4. [PMID: 28673544 DOI: 10.1016/j.molcel.2017.06.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/03/2017] [Accepted: 06/01/2017] [Indexed: 12/29/2022]
Abstract
Loss-of-function mutations in TTC19 (tetra-tricopeptide repeat domain 19) have been associated with severe neurological phenotypes and mitochondrial respiratory chain complex III deficiency. We previously demonstrated the mitochondrial localization of TTC19 and its link with complex III biogenesis. Here we provide detailed insight into the mechanistic role of TTC19, by investigating a Ttc19?/? mouse model that shows progressive neurological and metabolic decline, decreased complex III activity, and increased production of reactive oxygen species. By using both the Ttc19?/? mouse model and a range of human cell lines, we demonstrate that TTC19 binds to the fully assembled complex III dimer, i.e., after the incorporation of the iron-sulfur Rieske protein (UQCRFS1). The in situ maturation of UQCRFS1 produces N-terminal polypeptides, which remain bound to holocomplex III. We show that, in normal conditions, these UQCRFS1 fragments are rapidly removed, but when TTC19 is absent they accumulate within complex III, causing its structural and functional impairment.
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Affiliation(s)
- Emanuela Bottani
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK
| | - Raffaele Cerutti
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK
| | - Michael E Harbour
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK
| | - Sabrina Ravaglia
- Istituto Neurologico "Casimiro Mondino," via Mondino 2, Pavia 27100, Italy
| | - Sukru Anil Dogan
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK
| | - Carla Giordano
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, 00161 Rome, Italy
| | - Ian M Fearnley
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK
| | - Giulia D'Amati
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, 00161 Rome, Italy
| | - Carlo Viscomi
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK
| | - Erika Fernandez-Vizarra
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK.
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK.
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4841
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Howden AJM, Stam R, Martinez Heredia V, Motion GB, ten Have S, Hodge K, Marques Monteiro Amaro TM, Huitema E. Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity. THE NEW PHYTOLOGIST 2017; 215:309-322. [PMID: 28394025 PMCID: PMC5637918 DOI: 10.1111/nph.14540] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/22/2017] [Indexed: 05/20/2023]
Abstract
Plant-pathogen interactions are complex associations driven by the interplay of host and microbe-encoded factors. With secreted pathogen proteins (effectors) and immune signalling components found in the plant nucleus, this compartment is a battleground where susceptibility is specified. We hypothesized that, by defining changes in the nuclear proteome during infection, we can pinpoint vital components required for immunity or susceptibility. We tested this hypothesis by documenting dynamic changes in the tomato (Solanum lycopersicum) nuclear proteome during infection by the oomycete pathogen Phytophthora capsici. We enriched nuclei from infected and noninfected tissues and quantitatively assessed changes in the nuclear proteome. We then tested the role of candidate regulators in immunity through functional assays. We demonstrated that the host nuclear proteome dynamically changes during P. capsici infection. We observed that known nuclear immunity factors were differentially expressed and, based on this observation, selected a set of candidate regulators that we successfully implicated in immunity to P. capsici. Our work exemplifies a powerful strategy to gain rapid insight into important nuclear processes that underpin complex crop traits such as resistance. We have identified a large set of candidate nuclear factors that may underpin immunity to pathogens in crops.
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Affiliation(s)
- Andrew J. M. Howden
- Division of Plant ScienceSchool of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI)InvergowrieDundeeDD2 5DAUK
- Dundee Effector ConsortiumJHIInvergowrieDundeeDD2 5DAUK
| | - Remco Stam
- Division of Plant ScienceSchool of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI)InvergowrieDundeeDD2 5DAUK
- Dundee Effector ConsortiumJHIInvergowrieDundeeDD2 5DAUK
- Section of Population GeneticsTechnische Universität München85354FreisingGermany
| | - Victor Martinez Heredia
- Division of Plant ScienceSchool of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI)InvergowrieDundeeDD2 5DAUK
- Dundee Effector ConsortiumJHIInvergowrieDundeeDD2 5DAUK
| | - Graham B. Motion
- Division of Plant ScienceSchool of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI)InvergowrieDundeeDD2 5DAUK
- Dundee Effector ConsortiumJHIInvergowrieDundeeDD2 5DAUK
- Cell and Molecular SciencesJHIInvergowrieDundeeDD2 5DAUK
| | - Sara ten Have
- Wellcome Trust Centre for Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
| | - Kelly Hodge
- Wellcome Trust Centre for Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
| | - Tiago M. Marques Monteiro Amaro
- Division of Plant ScienceSchool of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI)InvergowrieDundeeDD2 5DAUK
- Dundee Effector ConsortiumJHIInvergowrieDundeeDD2 5DAUK
| | - Edgar Huitema
- Division of Plant ScienceSchool of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI)InvergowrieDundeeDD2 5DAUK
- Dundee Effector ConsortiumJHIInvergowrieDundeeDD2 5DAUK
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4842
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Ray S, Patel SK, Venkatesh A, Chatterjee G, Ansari NN, Gogtay NJ, Thatte UM, Gandhe P, Varma SG, Patankar S, Srivastava S. Quantitative Proteomics Analysis of Plasmodium vivax Induced Alterations in Human Serum during the Acute and Convalescent Phases of Infection. Sci Rep 2017; 7:4400. [PMID: 28667326 PMCID: PMC5493610 DOI: 10.1038/s41598-017-04447-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 05/15/2017] [Indexed: 12/23/2022] Open
Abstract
The radial distribution of Plasmodium vivax malaria burden has evoked enormous concern among the global research community. In this study, we have investigated the serum proteome alterations in non-severe vivax malaria patients before and during patient recuperation starting from the early febrile to the defervescence and convalescent stages of the infection. We have also performed an extensive quantitative proteomics analysis to compare the serum proteome profiles of vivax malaria patients with low (LPVM) and moderately-high (MPVM) parasitemia with healthy community controls. Interestingly, some of the serum proteins such as Serum amyloid A, Apolipoprotein A1, C-reactive protein, Titin and Haptoglobin, were found to be sequentially altered with respect to increased parasite counts. Analysis of a longitudinal cohort of malaria patients indicated reversible alterations in serum levels of some proteins such as Haptoglobin, Apolipoprotein E, Apolipoprotein A1, Carbonic anhydrase 1, and Hemoglobin subunit alpha upon treatment; however, the levels of a few other proteins did not return to the baseline even during the convalescent phase of the infection. Here we present the first comprehensive serum proteomics analysis of vivax malaria patients with different levels of parasitemia and during the acute and convalescent phases of the infection.
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Affiliation(s)
- Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,Department of Clinical Biochemistry, Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, United Kingdom
| | - Sandip K Patel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Apoorva Venkatesh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Gangadhar Chatterjee
- Dept of Biochemistry, Grant Govt Medical College and Sir JJ Group of Hospitals, Byculla, Mumbai, 400008, India
| | - Naziya N Ansari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Nithya J Gogtay
- Departments of Clinical Pharmacology, Seth GS Medical College & KEM Hospital, Parel, Mumbai, 400012, India
| | - Urmila M Thatte
- Departments of Clinical Pharmacology, Seth GS Medical College & KEM Hospital, Parel, Mumbai, 400012, India
| | - Prajakta Gandhe
- Departments of Clinical Pharmacology, Seth GS Medical College & KEM Hospital, Parel, Mumbai, 400012, India
| | - Santosh G Varma
- Dept of Biochemistry, Grant Govt Medical College and Sir JJ Group of Hospitals, Byculla, Mumbai, 400008, India
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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4843
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Poppleton DI, Duchateau M, Hourdel V, Matondo M, Flechsler J, Klingl A, Beloin C, Gribaldo S. Outer Membrane Proteome of Veillonella parvula: A Diderm Firmicute of the Human Microbiome. Front Microbiol 2017; 8:1215. [PMID: 28713344 PMCID: PMC5491611 DOI: 10.3389/fmicb.2017.01215] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/14/2017] [Indexed: 12/24/2022] Open
Abstract
Veillonella parvula is a biofilm-forming commensal found in the lungs, vagina, mouth, and gastro-intestinal tract of humans, yet it may develop into an opportunistic pathogen. Furthermore, the presence of Veillonella has been associated with the development of a healthy immune system in infants. Veillonella belongs to the Negativicutes, a diverse clade of bacteria that represent an evolutionary enigma: they phylogenetically belong to Gram-positive (monoderm) Firmicutes yet maintain an outer membrane (OM) with lipopolysaccharide similar to classic Gram-negative (diderm) bacteria. The OMs of Negativicutes have unique characteristics including the replacement of Braun's lipoprotein by OmpM for tethering the OM to the peptidoglycan. Through phylogenomic analysis, we have recently provided bioinformatic annotation of the Negativicutes diderm cell envelope. We showed that it is a unique type of envelope that was present in the ancestor of present-day Firmicutes and lost multiple times independently in this phylum, giving rise to the monoderm architecture; however, little experimental data is presently available for any Negativicutes cell envelope. Here, we performed the first experimental proteomic characterization of the cell envelope of a diderm Firmicute, producing an OM proteome of V. parvula. We initially conducted a thorough bioinformatics analysis of all 1,844 predicted proteins from V. parvula DSM 2008's genome using 12 different localization prediction programs. These results were complemented by protein extraction with surface exposed (SE) protein tags and by subcellular fractionation, both of which were analyzed by liquid chromatography tandem mass spectrometry. The merging of proteomics and bioinformatics results allowed identification of 78 OM proteins. These include a number of receptors for TonB-dependent transport, the main component of the BAM system for OM protein biogenesis (BamA), the Lpt system component LptD, which is responsible for insertion of LPS into the OM, and several copies of the major OmpM protein. The annotation of V. parvula's OM proteome markedly extends previous inferences on the nature of the cell envelope of Negativicutes, including the experimental evidence of a BAM/TAM system for OM protein biogenesis and of a complete Lpt system for LPS transport to the OM. It also provides important information on the role of OM components in the lifestyle of Veillonella, such as a possible gene cluster for O-antigen synthesis and a large number of adhesins. Finally, many OM hypothetical proteins were identified, which are priority targets for further characterization.
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Affiliation(s)
- Daniel I. Poppleton
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut PasteurParis, France
| | - Magalie Duchateau
- Unité de Spectrométrie de Masse Structurale et Protéomique, Plateforme Protéomique, Départment de Biologie Structurale et Chime, Institut Pasteur, USR 2000 Centre National de la Recherche ScientifiqueParis, France
| | - Véronique Hourdel
- Unité de Spectrométrie de Masse Structurale et Protéomique, Plateforme Protéomique, Départment de Biologie Structurale et Chime, Institut Pasteur, USR 2000 Centre National de la Recherche ScientifiqueParis, France
| | - Mariette Matondo
- Unité de Spectrométrie de Masse Structurale et Protéomique, Plateforme Protéomique, Départment de Biologie Structurale et Chime, Institut Pasteur, USR 2000 Centre National de la Recherche ScientifiqueParis, France
| | - Jennifer Flechsler
- Pflanzliche Entwicklungsbiologie und Elektronenmikroskopie, Department I. Botanik, Biozentrum der LMU MünchenPlanegg-Martinsried, Germany
| | - Andreas Klingl
- Pflanzliche Entwicklungsbiologie und Elektronenmikroskopie, Department I. Botanik, Biozentrum der LMU MünchenPlanegg-Martinsried, Germany
| | - Christophe Beloin
- Unité de Génétique des Biofilms, Département de Microbiologie, Institut PasteurParis, France
| | - Simonetta Gribaldo
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut PasteurParis, France
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4844
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Hamey JJ, Wienert B, Quinlan KGR, Wilkins MR. METTL21B Is a Novel Human Lysine Methyltransferase of Translation Elongation Factor 1A: Discovery by CRISPR/Cas9 Knockout. Mol Cell Proteomics 2017; 16:2229-2242. [PMID: 28663172 DOI: 10.1074/mcp.m116.066308] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/28/2017] [Indexed: 02/03/2023] Open
Abstract
Lysine methylation is widespread on human proteins, however the enzymes that catalyze its addition remain largely unknown. This limits our capacity to study the function and regulation of this modification. Here we used the CRISPR/Cas9 system to knockout putative protein methyltransferases METTL21B and METTL23 in K562 cells, to determine if they methylate elongation factor eEF1A. The known eEF1A methyltransferase EEF1AKMT1 was also knocked out as a control. Targeted mass spectrometry revealed the loss of lysine 165 methylation upon knockout of METTL21B, and the expected loss of lysine 79 methylation on knockout of EEF1AKMT1 No loss of eEF1A methylation was seen in the METTL23 knockout. Recombinant METTL21B was shown in vitro to catalyze methylation on lysine 165 in eEF1A1 and eEF1A2, confirming it as the methyltransferase responsible for this methylation site. Proteomic analysis by SILAC revealed specific upregulation of large ribosomal subunit proteins in the METTL21B knockout, and changes to further processes related to eEF1A function in knockouts of both METTL21B and EEF1AKMT1 This indicates that the methylation of lysine 165 in human eEF1A has a very specific role. METTL21B exists only in vertebrates, with its target lysine showing similar evolutionary conservation. We suggest METTL21B be renamed eEF1A-KMT3. This is the first study to specifically generate CRISPR/Cas9 knockouts of putative protein methyltransferase genes, for substrate discovery and site mapping. Our approach should prove useful for the discovery of further novel methyltransferases, and more generally for the discovery of sites for other protein-modifying enzymes.
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Affiliation(s)
- Joshua J Hamey
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Beeke Wienert
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Kate G R Quinlan
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Marc R Wilkins
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
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4845
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Offenburger SL, Bensaddek D, Murillo AB, Lamond AI, Gartner A. Comparative genetic, proteomic and phosphoproteomic analysis of C. elegans embryos with a focus on ham-1/STOX and pig-1/MELK in dopaminergic neuron development. Sci Rep 2017; 7:4314. [PMID: 28659600 PMCID: PMC5489525 DOI: 10.1038/s41598-017-04375-4] [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: 02/08/2017] [Accepted: 05/12/2017] [Indexed: 11/09/2022] Open
Abstract
Asymmetric cell divisions are required for cellular diversity and defects can lead to altered daughter cell fates and numbers. In a genetic screen for C. elegans mutants with defects in dopaminergic head neuron specification or differentiation, we isolated a new allele of the transcription factor HAM-1 [HSN (Hermaphrodite-Specific Neurons) Abnormal Migration]. Loss of both HAM-1 and its target, the kinase PIG-1 [PAR-1(I)-like Gene], leads to abnormal dopaminergic head neuron numbers. We identified discrete genetic relationships between ham-1, pig-1 and apoptosis pathway genes in dopaminergic head neurons. We used an unbiased, quantitative mass spectrometry-based proteomics approach to characterise direct and indirect protein targets and pathways that mediate the effects of PIG-1 kinase loss in C. elegans embryos. Proteins showing changes in either abundance, or phosphorylation levels, between wild-type and pig-1 mutant embryos are predominantly connected with processes including cell cycle, asymmetric cell division, apoptosis and actomyosin-regulation. Several of these proteins play important roles in C. elegans development. Our data provide an in-depth characterisation of the C. elegans wild-type embryo proteome and phosphoproteome and can be explored via the Encyclopedia of Proteome Dynamics (EPD) - an open access, searchable online database.
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Affiliation(s)
- Sarah-Lena Offenburger
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Dalila Bensaddek
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Alejandro Brenes Murillo
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Anton Gartner
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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4846
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Cui Y, Liu X, Li X, Yang H. In-Depth Proteomic Analysis of the Hippocampus in a Rat Model after Cerebral Ischaemic Injury and Repair by Danhong Injection (DHI). Int J Mol Sci 2017; 18:ijms18071355. [PMID: 28672812 PMCID: PMC5535848 DOI: 10.3390/ijms18071355] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/17/2017] [Accepted: 06/20/2017] [Indexed: 02/07/2023] Open
Abstract
Stroke is the second most common cause of death worldwide. A systematic description and characterization of the strokes and the effects induced in the hippocampus have not been performed so far. Here, we analysed the protein expression in the hippocampus 24 h after cerebral ischaemic injury and repair. Drug intervention using Danhong injection (DHI), which has been reported to have good therapeutic effects in a clinical setting, was selected for our study of cerebral ischaemia repair in rat models. A larger proteome dataset and total 4091 unique proteins were confidently identified in three biological replicates by combining tissue extraction for rat hippocampus and LC-MS/MS analysis. A label-free approach was then used to quantify the differences among the four experimental groups (Naive, Sham, middle cerebral artery occlusion (MCAO) and MCAO + DHI groups) and showed that about 2500 proteins on average were quantified in each of the experiment group. Bioinformatics analysis revealed that in total 280 unique proteins identified above were differentially expressed (P < 0.05). By combining the subcellular localization, hierarchical clustering and pathway information with the results from injury and repair phase, 12 significant expressed proteins were chosen and verified with respect to their potential as candidates for cerebral ischaemic injury by Western blot. The primary three signalling pathways of the candidates related may be involved in molecular mechanisms related to cerebral ischaemic injury. In addition, a glycogen synthase kinase-3β (Gsk-3β) inhibitor of the candidates with the best corresponding expression trends between western blotting (WB) and label-free quantitative results were chosen for further validation. The results of Western blot analysis of protein expression and 2,3,5- chloride three phenyl tetrazole (TTC) staining of rat brains showed that DHI treatment and Gsk-3β inhibitor are both able to confer protection against ischaemic injury in rat MCAO model. The observations of the present study provide a novel understanding regarding the regulatory mechanism of cerebral ischaemic injury.
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Affiliation(s)
- Yiran Cui
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China.
| | - Xin Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China.
| | - Xianyu Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, 100700 Beijing, China.
| | - Hongjun Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China.
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4847
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Qi L, Hu M, Fu J, Liu Y, Wu M, Yu K, Liu X. Quantitative proteomic analysis of host epithelial cells infected by Salmonella enterica serovar Typhimurium. Proteomics 2017; 17. [PMID: 28544771 DOI: 10.1002/pmic.201700092] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/08/2017] [Accepted: 05/19/2017] [Indexed: 12/11/2022]
Abstract
Systems-level analyses have the capability to offer new insight into host-pathogen interactions on the molecular level. Using Salmonella infection of host epithelial cells as a model system, we previously analyzed intracellular bacterial proteome as a window into pathogens' adaptations to their host environment [Infect. Immun. 2015; J. Proteome Res. 2017]. Herein we extended our efforts to quantitatively examine protein expression of host cells during infection. In total, we identified more than 5000 proteins with 194 differentially regulated proteins upon bacterial infection. Notably, we found marked induction of host integrin signaling and glycolytic pathways. Intriguingly, up-regulation of host glucose metabolism concurred with increased utilization of glycolysis by intracellular Salmonella during infection. In addition to immunoblotting assays, we also verified the up-regulation of PARP1 in the host nucleus by selected reaction monitoring and immunofluorescence studies. Furthermore, we provide evidence that PARP1 elevation is likely specific to Salmonella infection and independent of one of the bacterial type III secretion systems. Our work demonstrates that unbiased high-throughput proteomics can be used as a powerful approach to provide new perspectives on host-pathogen interactions.
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Affiliation(s)
- Linlu Qi
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Mo Hu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Jiaqi Fu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Yanhua Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Mei Wu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Kaiwen Yu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Xiaoyun Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
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4848
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Abstract
Leucine-rich repeat-containing G-protein-coupled receptor 4 (LGR4) is produced in a broad spectrum of mouse embryonic and adult tissues and its deficiency results in embryonal or perinatal lethality. The LGR4 function was mainly related to its potentiation of canonical Wnt signaling; however, several recent studies associate LGR4 with additional signaling pathways. To obtain a suitable tool for studying the signaling properties of Lgr4, we generated a tagged variant of the Lgr4 receptor using gene targeting in the mouse oocyte. The modified Lgr4 allele expresses the Lgr4 protein fused with a triple hemagglutinin (3HA) tag located at the extracellular part of the protein. The allele is fully functional, enabling tracking of Lgr4 expression in the mouse tissues. We also show that via surface labeling, the 3HA tag allows direct isolation and analysis of living Lgr4-positive cells obtained from the small intestinal crypts. Finally, the HA tag-specific antibody can be employed to characterize the biochemical features of Lgr4 and to identify possible biding partners of the protein in cells derived from various mouse tissues.
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4849
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Ndika J, Airaksinen L, Suojalehto H, Karisola P, Fyhrquist N, Puustinen A, Alenius H. Epithelial proteome profiling suggests the essential role of interferon-inducible proteins in patients with allergic rhinitis. J Allergy Clin Immunol 2017. [PMID: 28633877 DOI: 10.1016/j.jaci.2017.05.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Seasonal allergic rhinitis (SAR) caused by intermittent exposure to seasonal pollen causes itching, nasal congestion, and repeated sneezing, with profound effects on quality of life, work productivity, and school performance. Although both the genotype and environmental factors can contribute to the immunologic basis of allergic reactions, the molecular underpinnings associated with the pathogenesis of allergic rhinitis are not entirely clear. METHODS To address these questions, nasal epithelial brushings were collected from 29 patients with SAR and 31 control subjects during and after the pollen season. We then implemented an orbitrap-based, bottom-up, label-free quantitative proteomics approach, followed by multivariate analyses to identify differentially abundant (DA) proteins among the 4 sample groups. RESULTS We identified a total of 133 DA proteins for which the most significantly overrepresented functional category was found to be interferon 1 signaling. Two proteins, cystatin 1 and myeloblastin, the former of which protects against protease activity of allergens and the latter with a role in epithelial barrier function, were DA in patients with SAR and control subjects, irrespective of season. Moreover, interferon-inducible protein with tetratricopeptide repeats 1, cystatin 1, and interferon-inducible protein with tetratricopeptide repeats 3 were found to be differentially regulated between patients with SAR and control subjects, with inverse abundance dynamics during the transition from fall to spring. CONCLUSION We identified type 1 interferon-regulated proteins as biomarkers in patients with SAR, potentially playing an important role in its pathogenesis. Moreover, when compared with patients with SAR, healthy subjects exhibit an antagonistic proteomic response across seasons, which might prove to be a therapeutic target for disease prevention.
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Affiliation(s)
- Joseph Ndika
- Department of Bacteriology and Immunology, Medicum, University of Helsinki, Helsinki, Finland
| | - Liisa Airaksinen
- Occupational Medicine, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Hille Suojalehto
- Occupational Medicine, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Piia Karisola
- Department of Bacteriology and Immunology, Medicum, University of Helsinki, Helsinki, Finland
| | - Nanna Fyhrquist
- Department of Bacteriology and Immunology, Medicum, University of Helsinki, Helsinki, Finland
| | - Anne Puustinen
- Department of Clinical Chemistry, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Harri Alenius
- Department of Bacteriology and Immunology, Medicum, University of Helsinki, Helsinki, Finland; Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
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4850
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LC-MS/MS proteomic analysis of starved Bacillus subtilis cells overexpressing ribonucleotide reductase (nrdEF): implications in stress-associated mutagenesis. Curr Genet 2017. [PMID: 28624879 DOI: 10.1007/s00294-017-0722-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The non-appropriate conditions faced by nutritionally stressed bacteria propitiate error-prone repair events underlying stationary-phase- or stress-associated mutagenesis (SPM). The genetic and molecular mechanisms involved in SPM have been deeply studied but the biochemical aspects of this process have so far been less explored. Previous evidence showed that under conditions of nutritional stress, non-dividing cells of strain B. subtilis YB955 overexpressing ribonucleotide reductase (RNR) exhibited a strong propensity to generate true reversions in the hisC952 (amber), metB5 (ochre) and leuC425 (missense) mutant alleles. To further advance our knowledge on the metabolic conditions underlying this hypermutagenic phenotype, a high-throughput LC-MS/MS proteomic analysis was performed in non-dividing cells of an amino acid-starved strain, deficient for NrdR, the RNR repressor. Compared with the parental strain, the level of 57 proteins was found to increase and of 80 decreases in the NrdR-deficient strain. The proteomic analysis revealed an altered content in proteins associated with the stringent response, nucleotide metabolism, DNA repair, and cell signaling in amino acid-starved cells of the ∆nrdR strain. Overall, our results revealed that amino acid-starved cells of strain B. subtilis ∆nrdR that escape from growth-limiting conditions exhibit a complex proteomic pattern reminiscent of a disturbed metabolism. Future experiments aimed to understand the consequences of disrupting the cell signaling pathways unveiled in this study, will advance our knowledge on the genetic adaptations deployed by bacteria to escape from growth-limiting environments.
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