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Wuyts S, Alves R, Zimmermann‐Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Müller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P. Consistency across multi-omics layers in a drug-perturbed gut microbial community. Mol Syst Biol 2023; 19:e11525. [PMID: 37485738 PMCID: PMC10495815 DOI: 10.15252/msb.202311525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023] Open
Abstract
Multi-omics analyses are used in microbiome studies to understand molecular changes in microbial communities exposed to different conditions. However, it is not always clear how much each omics data type contributes to our understanding and whether they are concordant with each other. Here, we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics and metabolomics). We find that all the omics methods with species resolution are highly consistent in estimating relative species abundances. Furthermore, different omics methods complement each other for capturing functional changes. For example, while nearly all the omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control. Metabolomics revealed a decrease in oligosaccharide uptake, likely caused by Bacteroidota depletion. Our study highlights how multi-omics datasets can be utilized to reveal complex molecular responses to external perturbations in microbial communities.
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Affiliation(s)
- Sander Wuyts
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Renato Alves
- European Molecular Biology LaboratoryHeidelbergGermany
| | | | | | - Sonja Blasche
- European Molecular Biology LaboratoryHeidelbergGermany
- Medical Research Council Toxicology UnitCambridgeUK
| | | | - Philipp E Geyer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Rajna Hercog
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Ece Kartal
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Lisa Maier
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Johannes B Müller
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Sarela Garcia Santamarina
- European Molecular Biology LaboratoryHeidelbergGermany
- Present address:
MOSTMICRO Unit, Instituto de Tecnologia Quimica e BiologicaUniversidade Nova de LisboaOeirasPortugal
| | | | | | - Anja Telzerow
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Peter V Treit
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Tobias Wenzel
- European Molecular Biology LaboratoryHeidelbergGermany
- Present address:
Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Catolica de ChileSantiagoChile
| | | | - Kiran R Patil
- European Molecular Biology LaboratoryHeidelbergGermany
- Medical Research Council Toxicology UnitCambridgeUK
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Proteomics Program, NNF Center for Protein Research, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Michael Kuhn
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Peer Bork
- European Molecular Biology LaboratoryHeidelbergGermany
- Max Delbrück Centre for Molecular MedicineBerlinGermany
- Yonsei Frontier Lab (YFL)Yonsei UniversitySeoulSouth Korea
- Department of Bioinformatics, BiocenterUniversity of WürzburgWürzburgGermany
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2
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Shalon D, Culver RN, Grembi JA, Folz J, Treit PV, Shi H, Rosenberger FA, Dethlefsen L, Meng X, Yaffe E, Aranda-Díaz A, Geyer PE, Mueller-Reif JB, Spencer S, Patterson AD, Triadafilopoulos G, Holmes SP, Mann M, Fiehn O, Relman DA, Huang KC. Profiling the human intestinal environment under physiological conditions. Nature 2023; 617:581-591. [PMID: 37165188 PMCID: PMC10191855 DOI: 10.1038/s41586-023-05989-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/21/2023] [Indexed: 05/12/2023]
Abstract
The spatiotemporal structure of the human microbiome1,2, proteome3 and metabolome4,5 reflects and determines regional intestinal physiology and may have implications for disease6. Yet, little is known about the distribution of microorganisms, their environment and their biochemical activity in the gut because of reliance on stool samples and limited access to only some regions of the gut using endoscopy in fasting or sedated individuals7. To address these deficiencies, we developed an ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion. Collection of 240 intestinal samples from 15 healthy individuals using the device and subsequent multi-omics analyses identified significant differences between bacteria, phages, host proteins and metabolites in the intestines versus stool. Certain microbial taxa were differentially enriched and prophage induction was more prevalent in the intestines than in stool. The host proteome and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundance predicted species that altered the bile acid pool through deconjugation. Furthermore, microbially conjugated bile acid concentrations exhibited amino acid-dependent trends that were not apparent in stool. Overall, non-invasive, longitudinal profiling of microorganisms, proteins and bile acids along the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in human physiology and disease.
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Affiliation(s)
| | - Rebecca Neal Culver
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Jessica A Grembi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacob Folz
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA
| | - Peter V Treit
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Handuo Shi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Florian A Rosenberger
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Les Dethlefsen
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Eitan Yaffe
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Johannes B Mueller-Reif
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Sean Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - George Triadafilopoulos
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA
- Silicon Valley Neurogastroenterology and Motility Center, Mountain View, CA, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA.
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA.
| | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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3
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Mann SP, Treit PV, Geyer PE, Omenn GS, Mann M. Ethical Principles, Constraints and Opportunities in Clinical Proteomics. Mol Cell Proteomics 2021; 20:100046. [PMID: 33453411 PMCID: PMC7950205 DOI: 10.1016/j.mcpro.2021.100046] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 12/11/2022] Open
Abstract
Recent advances in mass spectrometry (MS)-based proteomics have vastly increased the quality and scope of biological information that can be derived from human samples. These advances have rendered current workflows increasingly applicable in biomedical and clinical contexts. As proteomics is poised to take an important role in the clinic, associated ethical responsibilities increase in tandem with impacts on the health, privacy, and wellbeing of individuals. We conducted and here report a systematic literature review of ethical issues in clinical proteomics. We add our perspectives from a background of bioethics, the results of our accompanying paper extracting individual-sensitive results from patient samples, and the literature addressing similar issues in genomics. The spectrum of potential issues ranges from patient re-identification to incidental findings of clinical significance. The latter can be divided into actionable and unactionable findings. Some of these have the potential to be employed in discriminatory or privacy-infringing ways. However, incidental findings may also have great positive potential. A plasma proteome profile, for instance, could inform on the general health or disease status of an individual regardless of the narrow diagnostic question that prompted it. We suggest that early discussion of ethical issues in clinical proteomics can ensure that eventual healthcare practices and regulations reflect the considered judgment of the community and anticipate opportunities and problems that may arise as the technology matures.
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Affiliation(s)
- Sebastian Porsdam Mann
- Department of Media, Cognition and Communication, University of Copenhagen, Copenhagen, Denmark; Uehiro Center for Practical Ethics, University of Oxford, Oxford, UK; New address: Faculty of Law, University of Oxford, Oxford, UK.
| | - Peter V Treit
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; New address: OmicEra Diagnostics GmbH, Planegg, Germany
| | - Gilbert S Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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4
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Geyer PE, Mann SP, Treit PV, Mann M. Plasma Proteomes Can Be Reidentifiable and Potentially Contain Personally Sensitive and Incidental Findings. Mol Cell Proteomics 2021; 20:100035. [PMID: 33444735 PMCID: PMC7950134 DOI: 10.1074/mcp.ra120.002359] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/02/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
The goal of clinical proteomics is to identify, quantify, and characterize proteins in body fluids or tissue to assist diagnosis, prognosis, and treatment of patients. In this way, it is similar to more mature omics technologies, such as genomics, that are increasingly applied in biomedicine. We argue that, similar to those fields, proteomics also faces ethical issues related to the kinds of information that is inherently obtained through sample measurement, although their acquisition was not the primary purpose. Specifically, we demonstrate the potential to identify individuals both by their characteristic, individual-specific protein levels and by variant peptides reporting on coding single nucleotide polymorphisms. Furthermore, it is in the nature of blood plasma proteomics profiling that it broadly reports on the health status of an individual-beyond the disease under investigation. Finally, we show that private and potentially sensitive information, such as ethnicity and pregnancy status, can increasingly be derived from proteomics data. Although this is potentially valuable not only to the individual, but also for biomedical research, it raises ethical questions similar to the incidental findings obtained through other omics technologies. We here introduce the necessity of-and argue for the desirability for-ethical and human-rights-related issues to be discussed within the proteomics community. Those thoughts are more fully developed in our accompanying manuscript. Appreciation and discussion of ethical aspects of proteomic research will allow for deeper, better-informed, more diverse, and, most importantly, wiser guidelines for clinical proteomics.
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Affiliation(s)
- Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; OmicEra Diagnostics GmbH, Planegg, Germany.
| | - Sebastian Porsdam Mann
- Department of Media, Cognition and Communication, University of Copenhagen, Copenhagen, Denmark; Uehiro Center for Practical Ethics, Oxford University, Oxford, UK
| | - Peter V Treit
- 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; Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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5
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Porsdam Mann S, Treit PV, Geyer PE, Omenn GS, Mann M. Ethical principles, opportunities and constraints in clinical proteomics. Mol Cell Proteomics 2021:mcp.RA120.002435. [PMID: 33397710 DOI: 10.1074/mcp.ra120.002435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 11/06/2022] Open
Abstract
Recent advances in MS-based proteomics have vastly increased the quality and scope of biological information that can be derived from human samples. These advances have rendered current workflows increasingly applicable in biomedical and clinical contexts. As proteomics is poised to take an important role in the clinic, associated ethical responsibilities increase in tandem with the impact on the health, privacy, and well-being of individuals. Here we conducted and report a systematic literature review of ethical issues in clinical proteomics. We add our perspectives from a background of bioethics, the results of our accompanying paper extracting individual-sensitive results from patient samples, and the literature addressing similar issues in genomics. The spectrum of potential issues ranges from patient re-identification to incidental findings of clinical significance. The latter can be divided into actionable and unactionable findings. Some of these have the potential to be employed in discriminatory or privacy-infringing ways. However, incidental findings may also have great positive potential. A plasma proteome profile, for instance, could inform on the general health or disease status of an individual regardless of the narrow diagnostic question that prompted it. We suggest that early discussion of ethical issues in clinical proteomics is important to ensure that eventual regulations reflect the considered judgment of the community as well as to anticipate opportunities and problems that may arise as the technology matures further.
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Affiliation(s)
| | | | - Philipp Emanuel Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Germany
| | - Gilbert S Omenn
- Center for Computational Med. & Bioinformatic, University of Michigan, United States
| | - Matthias Mann
- Dept. Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Germany
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6
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Geyer PE, Voytik E, Treit PV, Doll S, Kleinhempel A, Niu L, Müller JB, Buchholtz M, Bader JM, Teupser D, Holdt LM, Mann M. Plasma Proteome Profiling to detect and avoid sample-related biases in biomarker studies. EMBO Mol Med 2019; 11:e10427. [PMID: 31566909 PMCID: PMC6835559 DOI: 10.15252/emmm.201910427] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [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: 02/04/2019] [Revised: 08/26/2019] [Accepted: 09/03/2019] [Indexed: 01/04/2023] Open
Abstract
Plasma and serum are rich sources of information regarding an individual's health state, and protein tests inform medical decision making. Despite major investments, few new biomarkers have reached the clinic. Mass spectrometry (MS)-based proteomics now allows highly specific and quantitative readout of the plasma proteome. Here, we employ Plasma Proteome Profiling to define quality marker panels to assess plasma samples and the likelihood that suggested biomarkers are instead artifacts related to sample handling and processing. We acquire deep reference proteomes of erythrocytes, platelets, plasma, and whole blood of 20 individuals (> 6,000 proteins), and compare serum and plasma proteomes. Based on spike-in experiments, we determine sample quality-associated proteins, many of which have been reported as biomarker candidates as revealed by a comprehensive literature survey. We provide sample preparation guidelines and an online resource ( www.plasmaproteomeprofiling.org) to assess overall sample-related bias in clinical studies and to prevent costly miss-assignment of biomarker candidates.
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Affiliation(s)
- Philipp E Geyer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Eugenia Voytik
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Peter V Treit
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Sophia Doll
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Alisa Kleinhempel
- Institute of Laboratory MedicineUniversity HospitalLMU MunichMunichGermany
| | - Lili Niu
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Johannes B Müller
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | | | - Jakob M Bader
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Daniel Teupser
- Institute of Laboratory MedicineUniversity HospitalLMU MunichMunichGermany
| | - Lesca M Holdt
- Institute of Laboratory MedicineUniversity HospitalLMU MunichMunichGermany
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
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7
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Niu L, Geyer PE, Wewer Albrechtsen NJ, Gluud LL, Santos A, Doll S, Treit PV, Holst JJ, Knop FK, Vilsbøll T, Junker A, Sachs S, Stemmer K, Müller TD, Tschöp MH, Hofmann SM, Mann M. Plasma proteome profiling discovers novel proteins associated with non-alcoholic fatty liver disease. Mol Syst Biol 2019; 15:e8793. [PMID: 30824564 PMCID: PMC6396370 DOI: 10.15252/msb.20188793] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/27/2019] [Accepted: 01/28/2019] [Indexed: 12/15/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) affects 25% of the population and can progress to cirrhosis with limited treatment options. As the liver secretes most of the blood plasma proteins, liver disease may affect the plasma proteome. Plasma proteome profiling of 48 patients with and without cirrhosis or NAFLD revealed six statistically significantly changing proteins (ALDOB, APOM, LGALS3BP, PIGR, VTN, and AFM), two of which are already linked to liver disease. Polymeric immunoglobulin receptor (PIGR) was significantly elevated in both cohorts by 170% in NAFLD and 298% in cirrhosis and was further validated in mouse models. Furthermore, a global correlation map of clinical and proteomic data strongly associated DPP4, ANPEP, TGFBI, PIGR, and APOE with NAFLD and cirrhosis. The prominent diabetic drug target DPP4 is an aminopeptidase like ANPEP, ENPEP, and LAP3, all of which are up-regulated in the human or mouse data. Furthermore, ANPEP and TGFBI have potential roles in extracellular matrix remodeling in fibrosis. Thus, plasma proteome profiling can identify potential biomarkers and drug targets in liver disease.
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Affiliation(s)
- Lili Niu
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Philipp E Geyer
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Nicolai J Wewer Albrechtsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lise L Gluud
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Gastrounit, Medical Division, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | - Alberto Santos
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sophia Doll
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Peter V Treit
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jens J Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Filip K Knop
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Clinical Metabolic Physiology, Steno Diabetes Center Copenhagen, Gentofte Hospital, Hellerup, Denmark
| | - Tina Vilsbøll
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Clinical Metabolic Physiology, Steno Diabetes Center Copenhagen, Gentofte Hospital, Hellerup, Denmark
| | - Anders Junker
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Clinical Metabolic Physiology, Steno Diabetes Center Copenhagen, Gentofte Hospital, Hellerup, Denmark
| | - Stephan Sachs
- Helmholtz Diabetes Center at Helmholtz Centre Munich & Division of Metabolic Diseases, Institute for Diabetes and Obesity, Technische Universität München, Munich, Germany
| | - Kerstin Stemmer
- Helmholtz Diabetes Center at Helmholtz Centre Munich & Division of Metabolic Diseases, Institute for Diabetes and Obesity, Technische Universität München, Munich, Germany
| | - Timo D Müller
- Helmholtz Diabetes Center at Helmholtz Centre Munich & Division of Metabolic Diseases, Institute for Diabetes and Obesity, Technische Universität München, Munich, Germany
| | - Matthias H Tschöp
- Helmholtz Diabetes Center at Helmholtz Centre Munich & Division of Metabolic Diseases, Institute for Diabetes and Obesity, Technische Universität München, Munich, Germany
| | - Susanna M Hofmann
- Institute for Diabetes and Regeneration, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Medizinische Klinik und Poliklinik IV, Klinikum der LMU, München, Germany
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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8
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Wewer Albrechtsen NJ, Geyer PE, Doll S, Treit PV, Bojsen-Møller KN, Martinussen C, Jørgensen NB, Torekov SS, Meier F, Niu L, Santos A, Keilhauer EC, Holst JJ, Madsbad S, Mann M. Plasma Proteome Profiling Reveals Dynamics of Inflammatory and Lipid Homeostasis Markers after Roux-En-Y Gastric Bypass Surgery. Cell Syst 2018; 7:601-612.e3. [DOI: 10.1016/j.cels.2018.10.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 09/10/2018] [Accepted: 10/25/2018] [Indexed: 12/16/2022]
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9
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Bache N, Geyer PE, Bekker-Jensen DB, Hoerning O, Falkenby L, Treit PV, Doll S, Paron I, Müller JB, Meier F, Olsen JV, Vorm O, Mann M. A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-robust Proteomics. Mol Cell Proteomics 2018; 17:2284-2296. [PMID: 30104208 PMCID: PMC6210218 DOI: 10.1074/mcp.tir118.000853] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [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: 05/11/2018] [Revised: 07/13/2018] [Indexed: 12/03/2022] Open
Abstract
Because of low throughput and limited robustness, nano-scale liquid chromatography has been a bottleneck for advancing proteomics in biomedical research. Here, we developed and evaluated two new LC concepts—“pre-formed gradients” and “offset gradients for peptide re-focusing”—that are both implemented in the Evosep One instrument. We evaluated robustness with more than 2000 HeLa runs, demonstrated absence of cross-contamination with crude plasma samples, high proteome coverage by fractionated HeLa and routinely measuring more than 5000 proteins/sample in just 21 minutes. To further integrate mass spectrometry (MS)-based proteomics into biomedical research and especially into clinical settings, high throughput and robustness are essential requirements. They are largely met in high-flow rate chromatographic systems for small molecules but these are not sufficiently sensitive for proteomics applications. Here we describe a new concept that delivers on these requirements while maintaining the sensitivity of current nano-flow LC systems. Low-pressure pumps elute the sample from a disposable trap column, simultaneously forming a chromatographic gradient that is stored in a long storage loop. An auxiliary gradient creates an offset, ensuring the re-focusing of the peptides before the separation on the analytical column by a single high-pressure pump. This simplified design enables robust operation over thousands of sample injections. Furthermore, the steps between injections are performed in parallel, reducing overhead time to a few minutes and allowing analysis of more than 200 samples per day. From fractionated HeLa cell lysates, deep proteomes covering more than 130,000 sequence unique peptides and close to 10,000 proteins were rapidly acquired. Using this data as a library, we demonstrate quantitation of 5200 proteins in only 21 min. Thus, the new system - termed Evosep One - analyzes samples in an extremely robust and high throughput manner, without sacrificing in depth proteomics coverage.
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Affiliation(s)
| | - Philipp E Geyer
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,¶Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorte B Bekker-Jensen
- ¶Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Peter V Treit
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sophia Doll
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Igor Paron
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Johannes B Müller
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Meier
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jesper V Olsen
- ¶Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Vorm
- From the ‡Evosep Biosystems, Odense, Denmark
| | - Matthias Mann
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; .,¶Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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