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Baker C, Bruderer R, Abbott J, Arthur JSC, Brenes AJ. Optimizing Spectronaut Search Parameters to Improve Data Quality with Minimal Proteome Coverage Reductions in DIA Analyses of Heterogeneous Samples. J Proteome Res 2024; 23:1926-1936. [PMID: 38691771 PMCID: PMC11165578 DOI: 10.1021/acs.jproteome.3c00671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/18/2024] [Accepted: 04/19/2024] [Indexed: 05/03/2024]
Abstract
Data-independent acquisition has seen breakthroughs that enable comprehensive proteome profiling using short gradients. As the proteome coverage continues to increase, the quality of the data generated becomes much more relevant. Using Spectronaut, we show that the default search parameters can be easily optimized to minimize the occurrence of false positives across different samples. Using an immunological infection model system to demonstrate the impact of adjusting search settings, we analyzed Mus musculus macrophages and compared their proteome to macrophages spiked withCandida albicans. This experimental system enabled the identification of "false positives" as Candida albicans peptides and proteins should not be present in the Mus musculus-only samples. We show that adjusting the search parameters reduced "false positive" identifications by 89% at the peptide and protein level, thereby considerably increasing the quality of the data. We also show that these optimized parameters incurred a moderate cost, only reducing the overall number of "true positive" identifications across each biological replicate by <6.7% at both the peptide and protein level. We believe the value of our updated search parameters extends beyond a two-organism analysis and would be of great value to any DIA experiment analyzing heterogeneous populations of cell types or tissues.
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Affiliation(s)
- Christa
P. Baker
- Division
of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | | | - James Abbott
- Data
Analysis Group, Division of Computational Biology, School of Life
Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - J. Simon C. Arthur
- Division
of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Alejandro J. Brenes
- Division
of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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2
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Klingelhuber F, Frendo-Cumbo S, Omar-Hmeadi M, Massier L, Kakimoto P, Taylor AJ, Couchet M, Ribicic S, Wabitsch M, Messias AC, Iuso A, Müller TD, Rydén M, Mejhert N, Krahmer N. A spatiotemporal proteomic map of human adipogenesis. Nat Metab 2024; 6:861-879. [PMID: 38565923 PMCID: PMC11132986 DOI: 10.1038/s42255-024-01025-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
White adipocytes function as major energy reservoirs in humans by storing substantial amounts of triglycerides, and their dysfunction is associated with metabolic disorders; however, the mechanisms underlying cellular specialization during adipogenesis remain unknown. Here, we generate a spatiotemporal proteomic atlas of human adipogenesis, which elucidates cellular remodelling as well as the spatial reorganization of metabolic pathways to optimize cells for lipid accumulation and highlights the coordinated regulation of protein localization and abundance during adipocyte formation. We identify compartment-specific regulation of protein levels and localization changes of metabolic enzymes to reprogramme branched-chain amino acids and one-carbon metabolism to provide building blocks and reduction equivalents. Additionally, we identify C19orf12 as a differentiation-induced adipocyte lipid droplet protein that interacts with the translocase of the outer membrane complex of lipid droplet-associated mitochondria and regulates adipocyte lipid storage by determining the capacity of mitochondria to metabolize fatty acids. Overall, our study provides a comprehensive resource for understanding human adipogenesis and for future discoveries in the field.
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Affiliation(s)
- Felix Klingelhuber
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Scott Frendo-Cumbo
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Muhmmad Omar-Hmeadi
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Lucas Massier
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Pamela Kakimoto
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Austin J Taylor
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Morgane Couchet
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Sara Ribicic
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Martin Wabitsch
- Center for Rare Endocrine Diseases, Division of Paediatric Endocrinology and Diabetes, Department of Paediatrics and Adolescent Medicine, Ulm University Medical Centre, Ulm, Germany
| | - Ana C Messias
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Centre, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Arcangela Iuso
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Timo D Müller
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Walther-Straub Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University Munich (LMU), Munich, Germany
| | - Mikael Rydén
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Stockholm, Sweden
- Endocrinology unit, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Niklas Mejhert
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Natalie Krahmer
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
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3
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Sollberger G, Brenes AJ, Warner J, Arthur JSC, Howden AJM. Quantitative proteomics reveals tissue-specific, infection-induced and species-specific neutrophil protein signatures. Sci Rep 2024; 14:5966. [PMID: 38472281 PMCID: PMC10933280 DOI: 10.1038/s41598-024-56163-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/02/2024] [Indexed: 03/14/2024] Open
Abstract
Neutrophils are one of the first responders to infection and are a key component of the innate immune system through their ability to phagocytose and kill invading pathogens, secrete antimicrobial molecules and produce extracellular traps. Neutrophils are produced in the bone marrow, circulate within the blood and upon immune challenge migrate to the site of infection. We wanted to understand whether this transition shapes the mouse neutrophil protein landscape, how the mouse neutrophil proteome is impacted by systemic infection and perform a comparative analysis of human and mouse neutrophils. Using quantitative mass spectrometry we reveal tissue-specific, infection-induced and species-specific neutrophil protein signatures. We show a high degree of proteomic conservation between mouse bone marrow, blood and peritoneal neutrophils, but also identify key differences in the molecules that these cells express for sensing and responding to their environment. Systemic infection triggers a change in the bone marrow neutrophil population with considerable impact on the core machinery for protein synthesis and DNA replication along with environmental sensors. We also reveal profound differences in mouse and human blood neutrophils, particularly their granule contents. Our proteomics data provides a valuable resource for understanding neutrophil function and phenotypes across species and model systems.
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Affiliation(s)
- Gabriel Sollberger
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Alejandro J Brenes
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Jordan Warner
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - J Simon C Arthur
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Andrew J M Howden
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK.
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O’Neil JD, Bolimowska OO, Clayton SA, Tang T, Daley KK, Lara-Reyna S, Warner J, Martin CS, Mahida RY, Hardy RS, Arthur JSC, Clark AR. Dexamethasone impairs the expression of antimicrobial mediators in lipopolysaccharide-activated primary macrophages by inhibiting both expression and function of interferon β. Front Immunol 2023; 14:1190261. [PMID: 37942320 PMCID: PMC10628473 DOI: 10.3389/fimmu.2023.1190261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
Glucocorticoids potently inhibit expression of many inflammatory mediators, and have been widely used to treat both acute and chronic inflammatory diseases for more than seventy years. However, they can have several unwanted effects, amongst which immunosuppression is one of the most common. Here we used microarrays and proteomic approaches to characterise the effect of dexamethasone (a synthetic glucocorticoid) on the responses of primary mouse macrophages to a potent pro-inflammatory agonist, lipopolysaccharide (LPS). Gene ontology analysis revealed that dexamethasone strongly impaired the lipopolysaccharide-induced antimicrobial response, which is thought to be driven by an autocrine feedback loop involving the type I interferon IFNβ. Indeed, dexamethasone strongly and dose-dependently inhibited the expression of IFNβ by LPS-activated macrophages. Unbiased proteomic data also revealed an inhibitory effect of dexamethasone on the IFNβ-dependent program of gene expression, with strong down-regulation of several interferon-induced antimicrobial factors. Surprisingly, dexamethasone also inhibited the expression of several antimicrobial genes in response to direct stimulation of macrophages with IFNβ. We tested a number of hypotheses based on previous publications, but found that no single mechanism could account for more than a small fraction of the broad suppressive impact of dexamethasone on macrophage type I interferon signaling, underlining the complexity of this pathway. Preliminary experiments indicated that dexamethasone exerted similar inhibitory effects on primary human monocyte-derived or alveolar macrophages.
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Affiliation(s)
- John D. O’Neil
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Oliwia O. Bolimowska
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Sally A. Clayton
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Tina Tang
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Kalbinder K. Daley
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Samuel Lara-Reyna
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Jordan Warner
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Claire S. Martin
- School of Biomedical Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Rahul Y. Mahida
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Rowan S. Hardy
- School of Biomedical Sciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Andrew R. Clark
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
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5
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Forteath C, Mordi I, Nisr R, Gutierrez-Lara EJ, Alqurashi N, Phair IR, Cameron AR, Beall C, Bahr I, Mohan M, Wong AKF, Dihoum A, Mohammad A, Palmer CNA, Lamont D, Sakamoto K, Viollet B, Foretz M, Lang CC, Rena G. Amino acid homeostasis is a target of metformin therapy. Mol Metab 2023; 74:101750. [PMID: 37302544 PMCID: PMC10328998 DOI: 10.1016/j.molmet.2023.101750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/04/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023] Open
Abstract
OBJECTIVE Unexplained changes in regulation of branched chain amino acids (BCAA) during diabetes therapy with metformin have been known for years. Here we have investigated mechanisms underlying this effect. METHODS We used cellular approaches, including single gene/protein measurements, as well as systems-level proteomics. Findings were then cross-validated with electronic health records and other data from human material. RESULTS In cell studies, we observed diminished uptake/incorporation of amino acids following metformin treatment of liver cells and cardiac myocytes. Supplementation of media with amino acids attenuated known effects of the drug, including on glucose production, providing a possible explanation for discrepancies between effective doses in vivo and in vitro observed in most studies. Data-Independent Acquisition proteomics identified that SNAT2, which mediates tertiary control of BCAA uptake, was the most strongly suppressed amino acid transporter in liver cells following metformin treatment. Other transporters were affected to a lesser extent. In humans, metformin attenuated increased risk of left ventricular hypertrophy due to the AA allele of KLF15, which is an inducer of BCAA catabolism. In plasma from a double-blind placebo-controlled trial in nondiabetic heart failure (trial registration: NCT00473876), metformin caused selective accumulation of plasma BCAA and glutamine, consistent with the effects in cells. CONCLUSIONS Metformin restricts tertiary control of BCAA cellular uptake. We conclude that modulation of amino acid homeostasis contributes to therapeutic actions of the drug.
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Affiliation(s)
- Calum Forteath
- Division of Cellular and Systems Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK
| | - Ify Mordi
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK
| | - Raid Nisr
- Division of Cellular and Systems Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK
| | - Erika J Gutierrez-Lara
- Division of Cellular and Systems Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK
| | - Noor Alqurashi
- Division of Cellular and Systems Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK
| | - Iain R Phair
- Division of Cellular and Systems Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK
| | - Amy R Cameron
- Division of Cellular and Systems Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK; Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, RILD Building, Exeter, EX2 5DW, UK
| | - Craig Beall
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, RILD Building, Exeter, EX2 5DW, UK
| | - Ibrahim Bahr
- Division of Cellular and Systems Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK
| | - Mohapradeep Mohan
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK
| | - Aaron K F Wong
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK
| | - Adel Dihoum
- Division of Cellular and Systems Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK; Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK
| | - Anwar Mohammad
- Public Health and Epidemiology Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Colin N A Palmer
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK
| | - Douglas Lamont
- Centre for Advanced Scientific Technologies, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Kei Sakamoto
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Benoit Viollet
- Université Paris Cité, CNRS, Inserm, Institut Cochin, Paris, 75014, France
| | - Marc Foretz
- Université Paris Cité, CNRS, Inserm, Institut Cochin, Paris, 75014, France
| | - Chim C Lang
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK.
| | - Graham Rena
- Division of Cellular and Systems Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, DD1 9SY, UK.
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Feng J, Read OJ, Dinkova-Kostova AT. Nrf2 in TIME: The Emerging Role of Nuclear Factor Erythroid 2-Related Factor 2 in the Tumor Immune Microenvironment. Mol Cells 2023; 46:142-152. [PMID: 36927604 PMCID: PMC10070167 DOI: 10.14348/molcells.2023.2183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/12/2022] [Indexed: 03/18/2023] Open
Abstract
Nuclear factor erythroid 2-related factor 2 (Nrf2) mediates the cellular antioxidant response, allowing adaptation and survival under conditions of oxidative, electrophilic and inflammatory stress, and has a role in metabolism, inflammation and immunity. Activation of Nrf2 provides broad and long-lasting cytoprotection, and is often hijacked by cancer cells, allowing their survival under unfavorable conditions. Moreover, Nrf2 activation in established human tumors is associated with resistance to chemo-, radio-, and immunotherapies. In addition to cancer cells, Nrf2 activation can also occur in tumor-associated macrophages (TAMs) and facilitate an anti-inflammatory, immunosuppressive tumor immune microenvironment (TIME). Several cancer cell-derived metabolites, such as itaconate, L-kynurenine, lactic acid and hyaluronic acid, play an important role in modulating the TIME and tumor-TAMs crosstalk, and have been shown to activate Nrf2. The effects of Nrf2 in TIME are context-depended, and involve multiple mechanisms, including suppression of pro-inflammatory cytokines, increased expression of programmed cell death ligand 1 (PD-L1), macrophage colony-stimulating factor (M-CSF) and kynureninase, accelerated catabolism of cytotoxic labile heme, and facilitating the metabolic adaptation of TAMs. This understanding presents both challenges and opportunities for strategic targeting of Nrf2 in cancer.
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Affiliation(s)
- Jialin Feng
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Oliver J. Read
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Albena T. Dinkova-Kostova
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
- Department of Pharmacology and Molecular Sciences and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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