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Dragoi D, Benesic A, Pichler G, Kulak NA, Bartsch HS, Gerbes AL. Proteomics Analysis of Monocyte-Derived Hepatocyte-Like Cells Identifies Integrin Beta 3 as a Specific Biomarker for Drug-Induced Liver Injury by Diclofenac. Front Pharmacol 2018; 9:699. [PMID: 30022949 PMCID: PMC6039575 DOI: 10.3389/fphar.2018.00699] [Citation(s) in RCA: 21] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/08/2018] [Indexed: 12/12/2022] Open
Abstract
Idiosyncratic drug-induced liver injury (iDILI) is a major cause of acute liver failure resulting in liver transplantation or death. Prediction and diagnosis of iDILI remain a great challenge, as current models provide unsatisfying results in terms of sensitivity, specificity, and prognostic value. The absence of appropriate tools for iDILI detection also impairs the development of reliable biomarkers. Here, we report on a new method for identification of drug-specific biomarkers. We combined the advantages of monocyte-derived hepatocyte-like (MH) cells, able to mimic individual characteristics, with those of a novel mass spectrometry-based proteomics technology to assess potential biomarkers for Diclofenac-induced DILI. We found over 2,700 proteins differentially regulated in MH cells derived from individual patients. Herefrom, we identified integrin beta 3 (ITGB3) to be specifically upregulated in Diclofenac-treated MH cells from Diclofenac-DILI patients compared to control groups. Finally, we validated ITGB3 by flow cytometry analysis of whole blood and histological staining of liver biopsies derived from patients diagnosed with Diclofenac-DILI. In summary, our results show that biomarker candidates can be identified by proteomics analysis of MH cells. Application of this method to a broader range of drugs in the future will exploit its full potential for the development of drug-specific biomarkers. Data are available via ProteomeXchange with identifier PXD008918.
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Affiliation(s)
- Diana Dragoi
- Department of Medicine 2, Liver Centre Munich, University Hospital Munich, Munich, Germany.,MetaHeps GmbH, Martinsried, Germany
| | - Andreas Benesic
- Department of Medicine 2, Liver Centre Munich, University Hospital Munich, Munich, Germany.,MetaHeps GmbH, Martinsried, Germany
| | - Garwin Pichler
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,PreOmics GmbH, Martinsried, Germany
| | - Nils A Kulak
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,PreOmics GmbH, Martinsried, Germany
| | - Harald S Bartsch
- Institute of Pathology, Medical School, Ludwig Maximilian University, Munich, Germany
| | - Alexander L Gerbes
- Department of Medicine 2, Liver Centre Munich, University Hospital Munich, Munich, Germany
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Kulak NA, Geyer PE, Mann M. Loss-less Nano-fractionator for High Sensitivity, High Coverage Proteomics. Mol Cell Proteomics 2017; 16:694-705. [PMID: 28126900 PMCID: PMC5383787 DOI: 10.1074/mcp.o116.065136] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [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: 10/30/2016] [Revised: 01/25/2017] [Indexed: 01/22/2023] Open
Abstract
Recent advances in mass spectrometry (MS)-based proteomics now allow very deep coverage of cellular proteomes. To achieve near-comprehensive identification and quantification, the combination of a first HPLC-based peptide fractionation orthogonal to the on-line LC-MS/MS step has proven to be particularly powerful. This first dimension is typically performed with milliliter/min flow and relatively large column inner diameters, which allow efficient pre-fractionation but typically require peptide amounts in the milligram range. Here, we describe a novel approach termed "spider fractionator" in which the post-column flow of a nanobore chromatography system enters an eight-port flow-selector rotor valve. The valve switches the flow into different flow channels at constant time intervals, such as every 90 s. Each flow channel collects the fractions into autosampler vials of the LC-MS/MS system. Employing a freely configurable collection mechanism, samples are concatenated in a loss-less manner into 2-96 fractions, with efficient peak separation. The combination of eight fractions with 100 min gradients yields very deep coverage at reasonable measurement time, and other parameters can be chosen for even more rapid or for extremely deep measurements. We demonstrate excellent sensitivity by decreasing sample amounts from 100 μg into the sub-microgram range, without losses attributable to the spider fractionator and while quantifying close to 10,000 proteins. Finally, we apply the system to the rapid automated and in-depth characterization of 12 different human cell lines to a median depth of 11,472 different proteins, which revealed differences recapitulating their developmental origin and differentiation status. The fractionation technology described here is flexible, easy to use, and facilitates comprehensive proteome characterization with minimal sample requirements.
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Affiliation(s)
- Nils A Kulak
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,§PreOmics GmbH, Martinsried, Germany; and
| | - Philipp E Geyer
- From the ‡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
| | - Matthias Mann
- From the ‡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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3
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Holdt LM, Stahringer A, Sass K, Pichler G, Kulak NA, Wilfert W, Kohlmaier A, Herbst A, Northoff BH, Nicolaou A, Gäbel G, Beutner F, Scholz M, Thiery J, Musunuru K, Krohn K, Mann M, Teupser D. Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans. Nat Commun 2016; 7:12429. [PMID: 27539542 PMCID: PMC4992165 DOI: 10.1038/ncomms12429] [Citation(s) in RCA: 791] [Impact Index Per Article: 98.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 07/01/2016] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) are broadly expressed in eukaryotic cells, but their molecular mechanism in human disease remains obscure. Here we show that circular antisense non-coding RNA in the INK4 locus (circANRIL), which is transcribed at a locus of atherosclerotic cardiovascular disease on chromosome 9p21, confers atheroprotection by controlling ribosomal RNA (rRNA) maturation and modulating pathways of atherogenesis. CircANRIL binds to pescadillo homologue 1 (PES1), an essential 60S-preribosomal assembly factor, thereby impairing exonuclease-mediated pre-rRNA processing and ribosome biogenesis in vascular smooth muscle cells and macrophages. As a consequence, circANRIL induces nucleolar stress and p53 activation, resulting in the induction of apoptosis and inhibition of proliferation, which are key cell functions in atherosclerosis. Collectively, these findings identify circANRIL as a prototype of a circRNA regulating ribosome biogenesis and conferring atheroprotection, thereby showing that circularization of long non-coding RNAs may alter RNA function and protect from human disease.
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Affiliation(s)
- Lesca M. Holdt
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, 81337 Munich, Germany
- LIFE—Leipzig Research Center for Civilization Diseases, Universität Leipzig, 04103 Leipzig, Germany
- or to
| | - Anika Stahringer
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, 81337 Munich, Germany
| | - Kristina Sass
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, 81337 Munich, Germany
| | - Garwin Pichler
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Nils A. Kulak
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Wilfert
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, 81337 Munich, Germany
| | - Alexander Kohlmaier
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, 81337 Munich, Germany
| | - Andreas Herbst
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, 81337 Munich, Germany
| | - Bernd H. Northoff
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, 81337 Munich, Germany
| | - Alexandros Nicolaou
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, 81337 Munich, Germany
| | - Gabor Gäbel
- Department of Vascular and Endovascular Surgery, Ludwig-Maximilians-University Munich, 81337 Munich, Germany
| | - Frank Beutner
- LIFE—Leipzig Research Center for Civilization Diseases, Universität Leipzig, 04103 Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Markus Scholz
- LIFE—Leipzig Research Center for Civilization Diseases, Universität Leipzig, 04103 Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University Leipzig, 04107 Leipzig, Germany
| | - Joachim Thiery
- LIFE—Leipzig Research Center for Civilization Diseases, Universität Leipzig, 04103 Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Kiran Musunuru
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Knut Krohn
- LIFE—Leipzig Research Center for Civilization Diseases, Universität Leipzig, 04103 Leipzig, Germany
- Interdisciplinary Center for Clinical Research, University Leipzig, 04103 Leipzig, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, 81337 Munich, Germany
- LIFE—Leipzig Research Center for Civilization Diseases, Universität Leipzig, 04103 Leipzig, Germany
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Beck S, Michalski A, Raether O, Lubeck M, Kaspar S, Goedecke N, Baessmann C, Hornburg D, Meier F, Paron I, Kulak NA, Cox J, Mann M. The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics. Mol Cell Proteomics 2015; 14:2014-29. [PMID: 25991688 PMCID: PMC4587313 DOI: 10.1074/mcp.m114.047407] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [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: 12/12/2014] [Indexed: 11/06/2022] Open
Abstract
Hybrid quadrupole time-of-flight (QTOF) mass spectrometry is one of the two major principles used in proteomics. Although based on simple fundamentals, it has over the last decades greatly evolved in terms of achievable resolution, mass accuracy, and dynamic range. The Bruker impact platform of QTOF instruments takes advantage of these developments and here we develop and evaluate the impact II for shotgun proteomics applications. Adaption of our heated liquid chromatography system achieved very narrow peptide elution peaks. The impact II is equipped with a new collision cell with both axial and radial ion ejection, more than doubling ion extraction at high tandem MS frequencies. The new reflectron and detector improve resolving power compared with the previous model up to 80%, i.e. to 40,000 at m/z 1222. We analyzed the ion current from the inlet capillary and found very high transmission (>80%) up to the collision cell. Simulation and measurement indicated 60% transfer into the flight tube. We adapted MaxQuant for QTOF data, improving absolute average mass deviations to better than 1.45 ppm. More than 4800 proteins can be identified in a single run of HeLa digest in a 90 min gradient. The workflow achieved high technical reproducibility (R2 > 0.99) and accurate fold change determination in spike-in experiments in complex mixtures. Using label-free quantification we rapidly quantified haploid against diploid yeast and characterized overall proteome differences in mouse cell lines originating from different tissues. Finally, after high pH reversed-phase fractionation we identified 9515 proteins in a triplicate measurement of HeLa peptide mixture and 11,257 proteins in single measurements of cerebellum—the highest proteome coverage reported with a QTOF instrument so far.
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Affiliation(s)
- Scarlet Beck
- From the ‡Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | | | - Oliver Raether
- §Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Markus Lubeck
- §Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | | | - Niels Goedecke
- §Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | | | - Daniel Hornburg
- From the ‡Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Florian Meier
- From the ‡Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Igor Paron
- From the ‡Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Nils A Kulak
- From the ‡Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Juergen Cox
- ¶Computational Systems Biochemistry, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Mann
- From the ‡Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany;
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Hosp F, Scheltema RA, Eberl HC, Kulak NA, Keilhauer EC, Mayr K, Mann M. A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day. Mol Cell Proteomics 2015; 14:2030-41. [PMID: 25887394 PMCID: PMC4587330 DOI: 10.1074/mcp.o115.049460] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [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: 02/27/2015] [Indexed: 12/12/2022] Open
Abstract
The field of proteomics has evolved hand-in-hand with technological advances in LC-MS/MS systems, now enabling the analysis of very deep proteomes in a reasonable time. However, most applications do not deal with full cell or tissue proteomes but rather with restricted subproteomes relevant for the research context at hand or resulting from extensive fractionation. At the same time, investigation of many conditions or perturbations puts a strain on measurement capacity. Here, we develop a high-throughput workflow capable of dealing with large numbers of low or medium complexity samples and specifically aim at the analysis of 96-well plates in a single day (15 min per sample). We combine parallel sample processing with a modified liquid chromatography platform driving two analytical columns in tandem, which are coupled to a quadrupole Orbitrap mass spectrometer (Q Exactive HF). The modified LC platform eliminates idle time between measurements, and the high sequencing speed of the Q Exactive HF reduces required measurement time. We apply the pipeline to the yeast chromatin remodeling landscape and demonstrate quantification of 96 pull-downs of chromatin complexes in about 1 day. This is achieved with only 500 μg input material, enabling yeast cultivation in a 96-well format. Our system retrieved known complex-members and the high throughput allowed probing with many bait proteins. Even alternative complex compositions were detectable in these very short gradients. Thus, sample throughput, sensitivity and LC/MS-MS duty cycle are improved severalfold compared with established workflows. The pipeline can be extended to different types of interaction studies and to other medium complexity proteomes.
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Affiliation(s)
- Fabian Hosp
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Richard A Scheltema
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - H Christian Eberl
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Nils A Kulak
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Eva C Keilhauer
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Korbinian Mayr
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Matthias Mann
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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