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Torun F, Virreira Winter S, Doll S, Riese FM, Vorobyev A, Mueller-Reif JB, Geyer PE, Strauss MT. Transparent Exploration of Machine Learning for Biomarker Discovery from Proteomics and Omics Data. J Proteome Res 2022; 22:359-367. [PMID: 36426751 PMCID: PMC9903317 DOI: 10.1021/acs.jproteome.2c00473] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Biomarkers are of central importance for assessing the health state and to guide medical interventions and their efficacy; still, they are lacking for most diseases. Mass spectrometry (MS)-based proteomics is a powerful technology for biomarker discovery but requires sophisticated bioinformatics to identify robust patterns. Machine learning (ML) has become a promising tool for this purpose. However, it is sometimes applied in an opaque manner and generally requires specialized knowledge. To enable easy access to ML for biomarker discovery without any programming or bioinformatics skills, we developed "OmicLearn" (http://OmicLearn.org), an open-source browser-based ML tool using the latest advances in the Python ML ecosystem. Data matrices from omics experiments are easily uploaded to an online or a locally installed web server. OmicLearn enables rapid exploration of the suitability of various ML algorithms for the experimental data sets. It fosters open science via transparent assessment of state-of-the-art algorithms in a standardized format for proteomics and other omics sciences.
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Affiliation(s)
| | | | - Sophia Doll
- OmicEra
Diagnostics GmbH, 82152 Planegg, Germany
| | | | | | | | | | - Maximilian T. Strauss
- Novo
Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark,
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2
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Karayel O, Virreira Winter S, Padmanabhan S, Kuras YI, Vu DT, Tuncali I, Merchant K, Wills AM, Scherzer CR, Mann M. Proteome profiling of cerebrospinal fluid reveals biomarker candidates for Parkinson's disease. Cell Rep Med 2022; 3:100661. [PMID: 35732154 PMCID: PMC9245058 DOI: 10.1016/j.xcrm.2022.100661] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/29/2021] [Accepted: 05/23/2022] [Indexed: 11/16/2022]
Abstract
Parkinson’s disease (PD) is a growing burden worldwide, and there is no reliable biomarker used in clinical routines to date. Cerebrospinal fluid (CSF) is routinely collected in patients with neurological symptoms and should closely reflect alterations in PD patients’ brains. Here, we describe a scalable and sensitive mass spectrometry (MS)-based proteomics workflow for CSF proteome profiling. From two independent cohorts with over 200 individuals, our workflow reproducibly quantifies over 1,700 proteins from minimal CSF amounts. Machine learning determines OMD, CD44, VGF, PRL, and MAN2B1 to be altered in PD patients or to significantly correlate with clinical scores. We also uncover signatures of enhanced neuroinflammation in LRRK2 G2019S carriers, as indicated by increased levels of CTSS, PLD4, and HLA proteins. A comparison with our previously acquired urinary proteomes reveals a large overlap in PD-associated changes, including lysosomal proteins, opening up new avenues to improve our understanding of PD pathogenesis. Reproducible and scalable MS-based proteomics workflow for proteome profiling of CSF Quantification of over 1,700 proteins collected from more than 200 individuals Lysosomal and immune-related biomarker signatures specific to LRRK2 G2019S carriers Overlapping PD- and LRRK2-associated alterations in CSF and urine proteomes
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Affiliation(s)
- Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sebastian Virreira Winter
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | | | - Yuliya I Kuras
- APDA Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA; Precision Neurology Program, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Duc Tung Vu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Idil Tuncali
- APDA Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA; Precision Neurology Program, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Kalpana Merchant
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Anne-Marie Wills
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Clemens R Scherzer
- APDA Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA; Precision Neurology Program, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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Geyer PE, Arend FM, Doll S, Louiset M, Virreira Winter S, Müller‐Reif JB, Torun FM, Weigand M, Eichhorn P, Bruegel M, Strauss MT, Holdt LM, Mann M, Teupser D. High-resolution serum proteome trajectories in COVID-19 reveal patient-specific seroconversion. EMBO Mol Med 2021; 13:e14167. [PMID: 34232570 PMCID: PMC8687121 DOI: 10.15252/emmm.202114167] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/16/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
A deeper understanding of COVID-19 on human molecular pathophysiology is urgently needed as a foundation for the discovery of new biomarkers and therapeutic targets. Here we applied mass spectrometry (MS)-based proteomics to measure serum proteomes of COVID-19 patients and symptomatic, but PCR-negative controls, in a time-resolved manner. In 262 controls and 458 longitudinal samples of 31 patients, hospitalized for COVID-19, a remarkable 26% of proteins changed significantly. Bioinformatics analyses revealed co-regulated groups and shared biological functions. Proteins of the innate immune system such as CRP, SAA1, CD14, LBP, and LGALS3BP decreased early in the time course. Regulators of coagulation (APOH, FN1, HRG, KNG1, PLG) and lipid homeostasis (APOA1, APOC1, APOC2, APOC3, PON1) increased over the course of the disease. A global correlation map provides a system-wide functional association between proteins, biological processes, and clinical chemistry parameters. Importantly, five SARS-CoV-2 immunoassays against antibodies revealed excellent correlations with an extensive range of immunoglobulin regions, which were quantified by MS-based proteomics. The high-resolution profile of all immunoglobulin regions showed individual-specific differences and commonalities of potential pathophysiological relevance.
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Affiliation(s)
| | - Florian M Arend
- Institute of Laboratory MedicineUniversity HospitalLMU MunichMunichGermany
| | | | | | | | | | | | - Michael Weigand
- Institute of Laboratory MedicineUniversity HospitalLMU MunichMunichGermany
| | - Peter Eichhorn
- Institute of Laboratory MedicineUniversity HospitalLMU MunichMunichGermany
| | - Mathias Bruegel
- Institute of Laboratory MedicineUniversity HospitalLMU MunichMunichGermany
| | | | - Lesca M Holdt
- Institute of Laboratory MedicineUniversity HospitalLMU MunichMunichGermany
| | - Matthias Mann
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Daniel Teupser
- Institute of Laboratory MedicineUniversity HospitalLMU MunichMunichGermany
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Virreira Winter S, Karayel O, Strauss MT, Padmanabhan S, Surface M, Merchant K, Alcalay RN, Mann M. Urinary proteome profiling for stratifying patients with familial Parkinson's disease. EMBO Mol Med 2021; 13:e13257. [PMID: 33481347 PMCID: PMC7933820 DOI: 10.15252/emmm.202013257] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/30/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022] Open
Abstract
The prevalence of Parkinson's disease (PD) is increasing but the development of novel treatment strategies and therapeutics altering the course of the disease would benefit from specific, sensitive, and non‐invasive biomarkers to detect PD early. Here, we describe a scalable and sensitive mass spectrometry (MS)‐based proteomic workflow for urinary proteome profiling. Our workflow enabled the reproducible quantification of more than 2,000 proteins in more than 200 urine samples using minimal volumes from two independent patient cohorts. The urinary proteome was significantly different between PD patients and healthy controls, as well as between LRRK2 G2019S carriers and non‐carriers in both cohorts. Interestingly, our data revealed lysosomal dysregulation in individuals with the LRRK2 G2019S mutation. When combined with machine learning, the urinary proteome data alone were sufficient to classify mutation status and disease manifestation in mutation carriers remarkably well, identifying VGF, ENPEP, and other PD‐associated proteins as the most discriminating features. Taken together, our results validate urinary proteomics as a valuable strategy for biomarker discovery and patient stratification in PD.
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Affiliation(s)
- Sebastian Virreira Winter
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maximilian T Strauss
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Matthew Surface
- Department of Neurology, Columbia University, New York, NY, USA
| | - Kalpana Merchant
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Roy N Alcalay
- Department of Neurology, Columbia University, New York, NY, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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Karayel Ö, Tonelli F, Virreira Winter S, Geyer PE, Fan Y, Sammler EM, Alessi DR, Steger M, Mann M. Accurate MS-based Rab10 Phosphorylation Stoichiometry Determination as Readout for LRRK2 Activity in Parkinson's Disease. Mol Cell Proteomics 2020; 19:1546-1560. [PMID: 32601174 PMCID: PMC8143643 DOI: 10.1074/mcp.ra120.002055] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/17/2020] [Indexed: 12/11/2022] Open
Abstract
Pathogenic mutations in the Leucine-rich repeat kinase 2 (LRRK2) are the predominant genetic cause of Parkinson's disease (PD). They increase its activity, resulting in augmented Rab10-Thr73 phosphorylation and conversely, LRRK2 inhibition decreases pRab10 levels. Currently, there is no assay to quantify pRab10 levels for drug target engagement or patient stratification. To meet this challenge, we developed an high accuracy and sensitivity targeted mass spectrometry (MS)-based assay for determining Rab10-Thr73 phosphorylation stoichiometry in human samples. It uses synthetic stable isotope-labeled (SIL) analogues for both phosphorylated and nonphosphorylated tryptic peptides surrounding Rab10-Thr73 to directly derive the percentage of Rab10 phosphorylation from attomole amounts of the endogenous phosphopeptide. The SIL and the endogenous phosphopeptides are separately admitted into an Orbitrap analyzer with the appropriate injection times. We test the reproducibility of our assay by determining Rab10-Thr73 phosphorylation stoichiometry in neutrophils of LRRK2 mutation carriers before and after LRRK2 inhibition. Compared with healthy controls, the PD predisposing mutation carriers LRRK2 G2019S and VPS35 D620N display 1.9-fold and 3.7-fold increased pRab10 levels, respectively. Our generic MS-based assay further establishes the relevance of pRab10 as a prognostic PD marker and is a powerful tool for determining LRRK2 inhibitor efficacy and for stratifying PD patients for LRRK2 inhibitor treatment.
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Affiliation(s)
- Özge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Francesca Tonelli
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
| | - Sebastian Virreira Winter
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Phillip E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ying Fan
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
| | - Esther M Sammler
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom; Department of Neurology, School of Medicine, Ninewells Hospital, Ninewells Drive, Dundee, United Kingdom
| | - Dario R Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
| | - Martin Steger
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
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Wichmann C, Meier F, Virreira Winter S, Brunner AD, Cox J, Mann M. MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides. Mol Cell Proteomics 2019; 18:982-994. [PMID: 30755466 PMCID: PMC6495250 DOI: 10.1074/mcp.tir118.001131] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 11/06/2022] Open
Abstract
Mass spectrometry (MS)-based proteomics is often performed in a shotgun format, in which as many peptide precursors as possible are selected from full or MS1 scans so that their fragment spectra can be recorded in MS2 scans. Although achieving great proteome depths, shotgun proteomics cannot guarantee that each precursor will be fragmented in each run. In contrast, targeted proteomics aims to reproducibly and sensitively record a restricted number of precursor/fragment combinations in each run, based on prescheduled mass-to-charge and retention time windows. Here we set out to unify these two concepts by a global targeting approach in which an arbitrary number of precursors of interest are detected in real-time, followed by standard fragmentation or advanced peptide-specific analyses. We made use of a fast application programming interface to a quadrupole Orbitrap instrument and real-time recalibration in mass, retention time and intensity dimensions to predict precursor identity. MaxQuant.Live is freely available (www.maxquant.live) and has a graphical user interface to specify many predefined data acquisition strategies. Acquisition speed is as fast as with the vendor software and the power of our approach is demonstrated with the acquisition of breakdown curves for hundreds of precursors of interest. We also uncover precursors that are not even visible in MS1 scans, using elution time prediction based on the auto-adjusted retention time alone. Finally, we successfully recognized and targeted more than 25,000 peptides in single LC-MS runs. Global targeting combines the advantages of two classical approaches in MS-based proteomics, whereas greatly expanding the analytical toolbox.
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Affiliation(s)
- Christoph Wichmann
- From the ‡Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Florian Meier
- §Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.,¶NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Sebastian Virreira Winter
- §Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Andreas-David Brunner
- §Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Jürgen Cox
- From the ‡Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany;
| | - Matthias Mann
- §Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; .,¶NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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Virreira Winter S, Zychlinsky A. The bacterial pigment pyocyanin inhibits the NLRP3 inflammasome through intracellular reactive oxygen and nitrogen species. J Biol Chem 2018; 293:4893-4900. [PMID: 29414783 PMCID: PMC5880120 DOI: 10.1074/jbc.ra117.001105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/05/2018] [Indexed: 01/10/2023] Open
Abstract
Inflammasomes are cytosolic complexes that mature and secrete the inflammatory cytokines interleukin 1β (IL-1β) and IL-18 and induce pyroptosis. The NLRP3 (NACHT, LRR, and PYD domains–containing protein 3) inflammasome detects many pathogen- and danger-associated molecular patterns, and reactive oxygen species (ROS)/reactive nitrogen species (RNS) have been implicated in its activation. The phenazine pyocyanin (PCN) is a virulence factor of Pseudomonas aeruginosa and generates superoxide in cells. Here we report that PCN inhibits IL-1β and IL-18 release and pyroptosis upon NLRP3 inflammasome activation in macrophages by preventing speck formation and Caspase-1 maturation. Of note, PCN did not regulate the AIM2 (absent in melanoma 2) or NLRC4 inflammasomes or tumor necrosis factor (TNF) secretion. Imaging of the fluorescent glutathione redox potential sensor Grx1-roGFP2 indicated that PCN provokes cytosolic and nuclear but not mitochondrial redox changes. PCN-induced intracellular ROS/RNS inhibited the NLRP3 inflammasome posttranslationally, and hydrogen peroxide or peroxynitrite alone were sufficient to block its activation. We propose that cytosolic ROS/RNS inhibit the NLRP3 inflammasome and that PCN's anti-inflammatory activity may help P. aeruginosa evade immune recognition.
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Affiliation(s)
| | - Arturo Zychlinsky
- Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany.
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Johnston AC, Piro A, Clough B, Siew M, Virreira Winter S, Coers J, Frickel EM. Human GBP1 does not localize to pathogen vacuoles but restricts Toxoplasma gondii. Cell Microbiol 2016; 18:1056-64. [PMID: 26874079 PMCID: PMC4961618 DOI: 10.1111/cmi.12579] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/15/2016] [Accepted: 02/09/2016] [Indexed: 12/30/2022]
Abstract
Guanylate binding proteins (GBPs) are a family of large interferon-inducible GTPases that are transcriptionally upregulated upon infection with intracellular pathogens. Murine GBPs (mGBPs) including mGBP1 and 2 localize to and disrupt pathogen-containing vacuoles (PVs) resulting in the cell-autonomous clearing or innate immune detection of PV-resident pathogens. Human GBPs (hGBPs) are known to exert antiviral host defense and activate the NLRP3 inflammasome, but it is unclear whether hGBPs can directly recognize and control intravacuolar pathogens. Here, we report that endogenous or ectopically expressed hGBP1 fails to associate with PVs formed in human cells by the bacterial pathogens Chlamydia trachomatis or Salmonella typhimurium or the protozoan pathogen Toxoplasma gondii. While we find that hGBP1 expression has no discernible effect on intracellular replication of C. trachomatis and S. typhimurium, we observed enhanced early Toxoplasma replication in CRISPR hGBP1-deleted human epithelial cells. We thus identified a novel role for hGBP1 in cell-autonomous immunity that is independent of PV translocation, as observed for mGBPs. This study highlights fundamental differences between human and murine GBPs and underlines the need to study the functions of GBPs at cellular locations away from PVs.
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Affiliation(s)
- Ashleigh C Johnston
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, NW7 1AA, United Kingdom
| | - Anthony Piro
- Departments of Molecular Genetics and Microbiology and Immunology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Barbara Clough
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, NW7 1AA, United Kingdom
| | - Malvin Siew
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, NW7 1AA, United Kingdom
| | | | - Jörn Coers
- Departments of Molecular Genetics and Microbiology and Immunology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Eva-Maria Frickel
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, NW7 1AA, United Kingdom
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Schmid-Burgk JL, Xie Z, Frank S, Virreira Winter S, Mitschka S, Kolanus W, Murray A, Benenson Y. Rapid hierarchical assembly of medium-size DNA cassettes. Nucleic Acids Res 2012; 40:e92. [PMID: 22422837 PMCID: PMC3384347 DOI: 10.1093/nar/gks236] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Synthetic biology applications call for efficient methods to generate large gene cassettes that encode complex gene circuits in order to avoid simultaneous delivery of multiple plasmids encoding individual genes. Multiple methods have been proposed to achieve this goal. Here, we describe a novel protocol that allows one-step cloning of up to four gene-size DNA fragments, followed by a second assembly of these concatenated sequences into large circular DNA. The protocols described here comprise a simple, cheap and fast solution for routine construction of cassettes with up to 10 gene-size components.
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Virreira Winter S, Niedelman W, Jensen KD, Rosowski EE, Julien L, Spooner E, Caradonna K, Burleigh BA, Saeij JPJ, Ploegh HL, Frickel EM. Determinants of GBP recruitment to Toxoplasma gondii vacuoles and the parasitic factors that control it. PLoS One 2011; 6:e24434. [PMID: 21931713 PMCID: PMC3169597 DOI: 10.1371/journal.pone.0024434] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 08/09/2011] [Indexed: 01/20/2023] Open
Abstract
IFN-γ is a major cytokine that mediates resistance against the intracellular parasite Toxoplasma gondii. The p65 guanylate-binding proteins (GBPs) are strongly induced by IFN-γ. We studied the behavior of murine GBP1 (mGBP1) upon infection with T. gondii in vitro and confirmed that IFN-γ-dependent re-localization of mGBP1 to the parasitophorous vacuole (PV) correlates with the virulence type of the parasite. We identified three parasitic factors, ROP16, ROP18, and GRA15 that determine strain-specific accumulation of mGBP1 on the PV. These highly polymorphic proteins are held responsible for a large part of the strain-specific differences in virulence. Therefore, our data suggest that virulence of T. gondii in animals may rely in part on recognition by GBPs. However, phagosomes or vacuoles containing Trypanosoma cruzi did not recruit mGBP1. Co-immunoprecipitation revealed mGBP2, mGBP4, and mGBP5 as binding partners of mGBP1. Indeed, mGBP2 and mGBP5 co-localize with mGBP1 in T. gondii-infected cells. T. gondii thus elicits a cell-autonomous immune response in mice with GBPs involved. Three parasitic virulence factors and unknown IFN-γ-dependent host factors regulate this complex process. Depending on the virulence of the strains involved, numerous GBPs are brought to the PV as part of a large, multimeric structure to combat T. gondii.
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Affiliation(s)
| | - Wendy Niedelman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Kirk D. Jensen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Emily E. Rosowski
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Lindsay Julien
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Eric Spooner
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Kacey Caradonna
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Barbara A. Burleigh
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Jeroen P. J. Saeij
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Hidde L. Ploegh
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (HLP); (E-MF)
| | - Eva-Maria Frickel
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- * E-mail: (HLP); (E-MF)
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Hu CCA, Dougan SK, Winter SV, Paton AW, Paton JC, Ploegh HL. Subtilase cytotoxin cleaves newly synthesized BiP and blocks antibody secretion in B lymphocytes. ACTA ACUST UNITED AC 2009; 206:2429-40. [PMID: 19808260 PMCID: PMC2768844 DOI: 10.1084/jem.20090782] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Shiga-toxigenic Escherichia coli (STEC) use subtilase cytotoxin (SubAB) to interfere with adaptive immunity. Its inhibition of immunoglobulin secretion is both rapid and profound. SubAB favors cleavage of the newly synthesized immunoglobulin heavy chain–binding protein (BiP) to yield a C-terminal fragment that contains BiP’s substrate-binding domain. In the absence of its regulatory nucleotide-binding domain, the SubAB-cleaved C-terminal BiP fragment remains tightly bound to newly synthesized immunoglobulin light chains, resulting in retention of light chains in the endoplasmic reticulum (ER). Immunoglobulins are thus detained in the ER, making impossible the secretion of antibodies by SubAB-treated B cells. The inhibitory effect of SubAB is highly specific for antibody secretion, because other secretory proteins such as IL-6 are released normally from SubAB-treated B cells. Although SubAB also causes BiP cleavage in HepG2 hepatoma cells, (glyco)protein secretion continues unabated in SubAB-exposed HepG2 cells. This specific block in antibody secretion is a novel means of immune evasion for STEC. The differential cleavage of newly synthesized versus “aged” BiP by SubAB in the ER provides insight into the architecture of the ER compartments involved.
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